Ebook Textbook of diagnostic microbiology (5th edition): Part 2

(BQ) Part 2 book Textbook of diagnostic microbiology presents the following contents: Laboratory identification of significant isolates, aboratory diagnosis of infectious diseases an organ system approach to diagnostic microbiology.

CHAPTER 23   The Spirochetes A Christian Whelen CHAPTER OUTLINE Borrelia recurrentis and Similar Borreliae Borrelia burgdorferi ■ TREPONEMES General Characteristics Clinically Significant Species Treponema pallidum subsp pallidum Other Treponemal Diseases ■ LEPTOSPIRES General Characteristics Virulence Factors and Pathogenicity Infections Caused by Leptospires Epidemiology Laboratory Diagnosis Antimicrobial Susceptibility ■ BORRELIAE General Characteristics Clinically Significant Species OBJECTIVES After reading and studying this chapter, you should be able to: Describe the general characteristics of the genera of spirochetes List the risk factors associated with Borrelia spp endemic relapsing fever infection Describe the pathogenesis and clinical manifestations of Borrelia spp infection, including high-risk factors Compare the causative agents and arthropod vectors of relapsing fever and Lyme disease Describe the laboratory diagnosis of relapsing fever and how it differs from the diagnosis of other spirochete diseases in the United States Compare and contrast the four human pathogens of the genus Treponema Describe the primary, secondary, and tertiary clinical manifestations of syphilis Discuss the epidemiology of leptospirosis in the United States Evaluate the diagnostic tests used to identify Treponema pallidum in the clinical laboratory 10 Describe the two-tiered approach to laboratory diagnosis of Lyme disease ■ Case in Point A 29-year-old man arrived at a local medical clinic in Los Angeles complaining of diarrhea, fever, chills, muscle aches, and headaches He had returned days earlier after competing in the Eco-Challenge in Malaysian Borneo During the competition, he had completed various events, including mountain biking, caving, climbing, jungle trekking, swimming, and kayaking in fresh and salt water He was still recovering from multiple abrasions from the jungle trekking and mountain biking While kayaking the Segama River, his kayak capsized and he had inadvertently swallowed several mouthfuls of river water His two teammates were on doxycycline as malaria prophylaxis before and during the race Neither of them became ill Issues to Consider After reading the patient’s case history, consider: ■ Risk factors for acquiring infectious disease for the patient Agents that cause influenza-like illness and methods to identify or rule out those agents ■ Effective prophylaxis, if available, for influenza-like illness ■ Empiric therapy options Key Terms Chancre Endemic relapsing fever Endemic syphilis Epidemic relapsing fever Erythema migrans (EM) Gummas Jarisch-Herxheimer reaction Leptospirosis Lyme borreliosis Pinta tahir99 VRG Endemic Relapsing fever Rapid plasma reagin (RPR) test Spirochetes Syphilis Venereal Disease Research Laboratory (VDRL) test Weil disease Yaws Zoonoses 529 530 PART II  Laboratory Identification of Significant Isolates T he order Spirochaetales contains two families: Leptospiraceae and Spirochaetaceae The family Leptospiraceae contains the genus Leptospira, and the family Spirochaetaceae contains Borrelia and Treponema These three genera include the causative agents of important human diseases such as syphilis, zoonoses (transmitted from animals to humans) such as leptospirosis, and vector-borne diseases such as Lyme borreliosis or Lyme disease and relapsing fever The spirochetes are slender, flexuous, helically shaped, unicellular bacteria ranging from 0.1 to 0.5 µm wide and from to 20 µm long, with one or more complete turns in the helix They differ from other bacteria in that they have a flexible cell wall around which several fibrils are wound These fibrils, termed the periplasmic flagella (also known as axial fibrils, axial filaments, endoflagella, and periplasmic fibrils), are responsible for motility A multilayered outer sheath similar to the outer membrane of gram-negative bacteria completely surrounds the protoplasmic cylinder (the cytoplasmic and nuclear regions are enclosed by the cytoplasmic membrane–cell wall complex and periplasmic flagella) The spirochetes exhibit various types of motion in liquid media They are free-living, or survive in association with animal and human hosts as normal biota or pathogens In addition, they can use carbohydrates, amino acids, long-chain fatty acids, or long-chain fatty alcohols as carbon and energy sources Metabolism can be anaerobic, facultatively anaerobic, or aerobic, depending on the species Treponema reproduce via transverse fission, whereas Leptospira and Borrelia divide by the more common binary fission Leptospires General Characteristics Organisms of the genus Leptospira are tightly coiled, thin, flexible spirochetes, 0.1 µm wide and to 15 µm long (Figure 23-1) In contrast to both Treponema and Borrelia organisms, the spirals FIGURE 23-1  Dark field image of Leptospira interrogans serotype Sejroe Wolffi 3705 The tight coils and bent ends are characteristic of this organism (×1000) (Courtesy State Laboratories Division, Hawaii Department of Health.) are very close together, so the organism may appear to be a chain of cocci One or both ends of the organism have hooks rather than tapering off Their motion is rapid and rotational Historically, pathogenic organisms were identified as Leptospira interrogans and saprophytes were categorized as Leptospira biflexa More than 200 different serovars (serotypes) of L interrogans sensu lato have been reported Although genetic typing has established relatedness based on nucleic acid similarities and is taxonomically correct, serogroup-based nomenclature continues to be preferred by scientists and physicians Electron microscopy reveals a long axial filament covered by a very fine sheath, similar to treponemes and borreliae All species have two periplasmic flagella The organisms cannot be readily stained, but they can be impregnated with silver and visualized Unstained cells are not visible by bright field microscopy but are visible by dark field, phase contrast, and immunofluorescent microscopy Leptospires are obligately aerobic and can be grown in artificial media such as Fletcher’s semisolid, Stuart liquid, or Ellinghausen-McCullough-Johnson-Harris (EMJH) semisolid media Virulence Factors and Pathogenicity Leptospiral disease in the United States is caused by more than 20 different serovars, the most common of which are Icterohaem­ orrhagiae, Australis, and Canicola Some serovars of L interrogans sensu lato and L biflexa sensu lato are pathogenic for a wide range of wild and domestic animals and humans, but mechanisms of pathogenicity are not well understood Factors that may play a role in pathogenicity include reduced phagocytosis in the host, a soluble hemolysin produced by some virulent strains, cellmediated sensitivity to leptospiral antigen by the host, and small amounts of endotoxins produced by some strains The clinical findings in animals with leptospirosis suggest the presence of endotoxemia Infections Caused by Leptospires Leptospires present in water or mud are most likely to enter the human host through small breaks in the skin or intact mucosa The initial sites of multiplication are unknown Nonspecific host defenses not stop multiplication of leptospires, and leptospiremia occurs during the acute illness Late manifestations of the disease may be caused by the host’s immunologic response to the infection The incubation period of leptospirosis is usually 10 to 12 days but ranges from to 30 days The onset of clinical illness is usually abrupt, with nonspecific, influenza-like constitutional symptoms such as fever, chills, headache, severe myalgia, and malaise The subsequent course is protean, frequently biphasic, and often results in hepatic, renal, and central nervous system involvement The major renal lesion is an interstitial nephritis with associated glomerular swelling and hyperplasia that does not affect the glomeruli The most characteristic physical finding is conjunctival suffusion, but this is seen in less than 50% of patients Severe systemic disease (Weil disease) includes renal failure, hepatic failure, and intravascular disease and can result in death Duration of the illness varies from less than week to weeks Late manifestations can be caused by the host’s immunologic response to the infection In patients with a leptospiral bacteremia, immunoglobulin M (IgM) antibodies are detected tahir99 VRG CHAPTER 23  The Spirochetes within week after onset of disease and may persist in high titers for many months Immunoglobulin G (IgG) antibodies are usually detectable month or more after infection Convalescent serum contains protective antibodies Epidemiology Leptospirosis is a zoonoses primarily associated with occupational or recreational exposure Working with animals or in ratinfested surroundings poses hazards for veterinarians, dairy workers, swine handlers, slaughterhouse workers, miners, sewer workers, and fish and poultry processors In the United States, most cases of leptospirosis disease result from recreational exposures In California residents, 59% of leptospirosis cases were acquired during freshwater recreation from 1982 to 2001; in the last of those years, the rate was 85% Leptospirosis ceased to become a nationally notifiable disease in 1995 Leptospirosis is still reportable in Hawaii, and from 1999 to 2008, Hawaii averaged 20 confirmed cases annually Cases are likely unrecognized nationwide and also go unreported in Hawaii In the natural host, leptospires live in the lumen of renal tubules and are excreted in the urine Dogs, rats, and other rodents are the principal animal reservoirs Hosts acquire infections directly by contact with the urine of carriers or indirectly by contact with bodies of water contaminated with the urine of carriers Leptospires can survive in neutral or slightly alkaline waters for months Protective clothing (boots and gloves) should be worn in situations involving possible occupational exposure to leptospires Control measures include rodent elimination and drainage of contaminated waters Vaccination of dogs and livestock has been effective in preventing disease but not the initial infection and leptospiruria Short-term prophylaxis consisting of weekly doxycycline may be appropriate in high-risk groups with expected occupational exposure ✓ 531 Isolation and Identification Isolation of leptospires is accomplished by direct inoculation of to drops of freshly drawn blood or CSF into laboratory media such as Fletcher, Stuart, or EMJH, and incubating the media in the dark at room temperature Urine can also be cultured and is most productive after the first week of illness Several dilutions should be used (undiluted, 1 : 10, and 1 : 100) and/or filtered (0.45 µm) to minimize the effects of inhibitory substances Tubes are examined weekly for evidence of growth such as turbidity, haze, or a ring of growth A drop taken from a few millimeters below the surface is examined by dark field microscopy for tightly coiled, rapidly motile spirochetes, with hooked ends Serotypes have historically been identified by microscopic agglutination testing using sera of defined reactivity; however, other methods such as pulsed field gel electrophoresis and 16s rRNA DNA sequencing are also being investigated Serologic Tests In patients with a leptospiral bacteremia, IgM antibodies are detected within week after onset of disease and may persist in high titers for many months A month or more after the onset of illness, IgG antibodies can be detected in some patients A U.S Food and Drug Administration–approved, visually read IgM enzyme-linked immunosorbent assay (ELISA; Pan Bio INDx, Baltimore, MD) is available and has been shown to have high sensitivity (98%) and specificity (90.6%) in acute leptospirosis cases A macroscopic slide agglutination test for rapid screening as well as the gold standard microscopic agglutination testing is available for the detection of leptospiral antibodies, but both require the maintenance of defined serotypes in culture, so performance is typically limited to confirmatory laboratories Antimicrobial Susceptibility Case Check 23-1  Leptospires are present in water and mud contaminated by the urine of reservoir animals The Case in Point describes significant and repeated exposure risk that should be reported to the primary health provider on presentation Otherwise, the initial clinical impression might resemble influenza, especially if presentation occurs during periods of high influenza activity Laboratory Diagnosis Specimen Collection and Handling During the acute phase (first week) of the disease, blood or cerebrospinal fluid (CSF) should be collected Optimal recovery occurs if fresh specimens are inoculated directly into laboratory media Urine can also be collected, but yield is much higher after the first week of illness, and shedding can occur intermittently for weeks Microscopic Examination Although direct demonstration of leptospires in clinical specimens during the first week of the disease by special stains, dark field, or phase contrast microscopy is possible, it is not recommended Direct demonstration is only successful in a small percentage of cases, and false-positive results may be reported because of the presence of artifacts, especially in urine Susceptibility testing of leptospires is not normally performed in the clinical laboratory; leptospires have been shown to be susceptible in vitro to streptomycin, tetracycline, doxycycline, and the macrolide antimicrobials in vitro Although treatment data are too sparse to be definitive, penicillin is considered beneficial and alters the course of the disease if treatment is initiated before the fourth day of illness Doxycycline appears to shorten the course of the illness in adults and reduce the incidence of convalescent leptospiruria ✓ Case Check 23-2  At least two deaths occurred in 2009, when confusion with pandemic influenza delayed appropriate antimicrobial therapy in patients with severe leptospirosis The Case in Point describes two teammates who were on doxycyline for malaria prophylaxis, which is also effective against many bacterial agents, including Leptospira Adherence to this preventive medicine likely contributed to disease avoidance in these individuals Borreliae General Characteristics The genus Borrelia comprises several species of spirochetes that are morphologically similar but have different pathogenic tahir99 VRG 532 PART II  Laboratory Identification of Significant Isolates an adequate immune response The disease recurs several days to weeks later, following a less severe but similar course The spirochetemia worsens during the febrile periods and wanes between recurrences FIGURE 23-2  Appearance of Borrelia recurrentis (arrows) in blood (Giemsa stain, ×850) properties and host ranges Most species cause relapsing fever, with the notable exception of Lyme borreliosis, which is caused by several species in the Borrelia burgdorferi sensu lato complex All pathogenic Borrelia are arthropod-borne The borreliae are highly flexible organisms varying in thickness from 0.2 to 0.5 µm and in length from to 20 µm The spirals vary in number from to 10 per organism and are much less tightly coiled than those of the leptospires (Figure 23-2) Unlike the leptospires and treponemes, the borreliae stain easily and can be visualized by bright field microscopy Electron microscopy shows the same general features as are seen with the treponemes—long, periplasmic flagella (15 to 20/cell) coated with sheaths of protoplasm and periplasm The borreliae are typically cultivated in the clinical laboratory using Kelly medium Clinically Significant Species A number of borreliae, including Borrelia recurrentis and Borrelia duttonii, cause relapsing fever The complex B burgdorferi sensu lato causes a spectrum of syndromes known as Lyme disease Borrelia recurrentis and Similar Borreliae Virulence Factors As the disease name suggests, relapsing fever is characterized by acute febrile episodes that subside spontaneously but tend to recur over a period of weeks Borrelia spp responsible for this disease first evade complement by acquiring and displaying suppressive complement regulators, C4b-binding protein and factor H The relapses are potentiated by antigenic variation; the borreliae systematically change their surface antigens, thereby rendering specific antibody production ineffective in completely clearing the organisms Clinical Manifestations After an incubation period of to 15 days, a massive spirochetemia develops and remains at varying levels of severity during the entire course of relapsing fever The infection is accompanied by sudden high temperature, rigors, severe headache, muscle pains, and weakness The febrile period lasts about to days and ends abruptly with the development of Epidemiology Relapsing fever can be tick-borne (endemic relapsing fever) or louse-borne (epidemic relapsing fever) The tick-borne borreliae are transmitted by a large variety of soft ticks of the genus Ornithodoros Species-specific borreliae often bear the same epithet as their vectors (e.g., Ornithodoros hermsii transmits Borrelia hermsii) Tick-borne borreliae are widely distributed throughout the Eastern and Western hemispheres, and transmission to a vertebrate host takes place via infected saliva during tick attachment Louse-borne fever is transmitted via the body louse, Pediculus humanus, and humans are the only reservoir The borreliae infect the hemolymph of the louse Unlike tickborne disease, transmission of the louse-borne disease occurs when infected lice are crushed and scratched into the skin rather than through the bite of an infected arthropod Relapsing fever is best prevented by control of exposure to the arthropod vectors For tick-borne relapsing fever, exposure control includes wearing protective clothing, rodent control, and the use of repellents For louseborne relapsing fever, control is best achieved by good personal and public hygiene, especially improvements in overcrowding and delousing Laboratory Diagnosis Microscopic Examination.  Diagnosis of borreliosis is readily made by observing Giemsa- or Wright-stained blood smears of blood taken during the febrile period Relapsing fever is the only spirochetal disease in which the organisms are visible in blood with bright-field microscopy The appearance of the spirochete among the red cells is characteristic (Figure 23-2) Isolation and Identification.  Borreliae can be recovered using Kelly medium or animal inoculation (involving suckling Swiss mice or suckling rats), but it is rarely attempted B recurrentis, B hermsii, Borrelia parkeri, Borrelia turicatae, and Borrelia hispanica have been successfully cultivated Antigenic variation in the spirochetes that cause relapsing fever makes the serodiagnosis of their diseases difficult and impractical Antimicrobial Susceptibility Borreliae are susceptible to many antimicrobial agents; however, tetracyclines are the drugs of choice because they reduce the relapse rate and rid the central nervous system of spirochetes Studies indicate that up to 39% of patients treated with antimicrobial agents experience fever, chills, headache, and myalgia believed to be caused by the sudden release of endotoxin from the spirochetes, a condition referred to as Jarisch-Herxheimer reaction Borrelia burgdorferi Virulence Factors Bacterial spread may occur by the organism’s ability to bind plasminogen and urokinase-type plasminogen activator to its surface This binding could convert plasminogen to plasmin, which is a potent protease and could facilitate tissue invasion tahir99 VRG CHAPTER 23  The Spirochetes Binding factor H allows for complement evasion and immune system suppression and might explain, in part, why IgM antibody does not peak for to weeks In vitro, the organism can stimulate proinflammatory cytokines such as tumor necrosis factor and interferons, which can be important in controlling disease but may also contribute to inflammatory manifestations as untreated disease progresses Clinical Manifestations Lyme borreliosis is a complex disease that can generally be divided into three stages Early infection includes two stages, the first of which is localized (stage 1) About 60% of patients exhibit erythema migrans (EM), the classic skin lesion that is normally found at the site of the tick bite It begins as a red macule and expands to form large annular erythema with partial central clearing, sometimes described as having a target appearance Regional lymphadenopathy is common with minor constitutional symptoms Stage is early disseminated and produces widely variable symptoms that include secondary skin lesions, migratory joint and bone pain, alarming neurologic and cardiac pathology, splenomegaly, and severe malaise and fatigue Late manifestations, or late persistent infections (stage 3), focus on the cardiac, musculoskeletal, and neurologic systems Arthritis is the most common symptom, occurring weeks to years later Epidemiology Organisms are transmitted via the bite of infected Ixodes ticks, so most cases occur during June through September, when more people are involved in outdoor activities and ticks are more active Lyme disease was first described after an outbreak among children in Lyme, Connecticut, in 1975 A total of 33,097 cases were reported in the United States in 2011 At least three species of B burgdorferi sensu lato cause Lyme disease (Lyme borreliosis) B burgdorferi sensu stricto occurs in North America B garinii and B afzelii have been confirmed in Asia, and all three species have caused disease in Europe Protective clothing and repellents should be worn in areas in which tick exposure is intense Attached ticks should be removed immediately because pathogen transmission is associated with the length of attachment Laboratory Diagnosis Specimen Collection and Handling.  The most common and productive specimen collected for the laboratory diagnosis of B burgdorferi sensu lato infection is serum for serology Other tests have too many limitations (e.g., polymerase chain reaction) or have not been adequately validated (e.g., urine antigen, CD57 lymphocyte) Serologic Tests.  Diagnosis follows a two-tiered approach in which the first step is an immunofluorescent antibody (IFA) or enzyme immunoassay (EIA) screen Positive or equivocal results are confirmed with IgM and/or just IgG Western blot, depending on whether symptoms were present for longer than 30 days (IgG only) Western blot confirmation of IgM antibody presence includes reactivity for two of the three following bands—24, 39, and 41 kDa Confirmation of IgG antibody presence is acceptable when five of the scored bands are present—18, 21, 28, 30, 39, 41, 45, 58, 66, and 93 kDa If serology is negative 533 and symptoms are consistent with Lyme disease, a convalescent serum should be obtained and tested Antimicrobial Susceptibility Early diagnosis and antimicrobial treatment are important for preventing neurologic, cardiac, and joint abnormalities that can occur late in the disease Doxycycline and amoxicillin are equally effective in treating early stages of Lyme disease without complications For refractile or late stages, prolonged treatment with ceftriaxone has been effective Treponemes General Characteristics Pathogenic treponemes are thin, spiral organisms about 0.1 to 0.2 µm in thickness and to 20  µm in length They are difficult to visualize with a bright field microscope because they are so thin, but they can be seen very easily using dark field microscopy The spirals are regular and angular, with to 14 spirals per organism (Figure 23-3) Three periplasmic flagella are inserted into each end of the cell The ends are pointed and covered with a sheath The cells are motile, with graceful flexuous movements in liquid Clinically Significant Species The genus Treponema comprises four microorganisms that are pathogenic for humans—T pallidum subsp pallidum, the causative agent of syphilis; T pallidum subsp pertenue, the causative agent of yaws; T pallidum subsp endemicum, the causative agent of endemic syphilis; and Treponema carateum, the causative agent of pinta The four pathogenic strains exhibit a high degree of DNA homology and shared antigens At least six nonpathogenic species have been identified in the normal microbiota, and they are particularly prominent in the oral cavity Treponema pallidum Subsp pallidum Virulence Factors Treponema pallidum subsp pallidum has the ability to cross intact mucous membranes and the placenta, disseminate FIGURE 23-3  Scanning electron micrograph of Treponema pallidum Two treponemes are shown adjacent to an erythrocyte (Nichols strain, ×2500) tahir99 VRG 534 PART II  Laboratory Identification of Significant Isolates throughout the body, and infect almost any organ system It has also been postulated that antigenic variation of cell surface proteins contributes to the organism’s ability to evade host immune response and establish persistent infection Clinical Manifestations Treponema pallidum subsp pallidum causes syphilis The word “syphilis” comes from a poem written in 1530 that described a mythical shepherd named Syphilus who was afflicted with the disease as punishment for cursing the gods The poem represented the compendium of knowledge at the time regarding the disease Treponema pallidum subsp pallidum transmission normally occurs during direct sexual contact with an individual who has an active primary or secondary syphilitic lesion Consequently, the genital organs—the vagina and cervix in females, and the penis in males—are the usual sites of inoculation Syphilis can also be acquired by nongenital contact with a lesion (e.g., on the lip) or transplacental transmission to a fetus, resulting in congenital syphilis After bacterial invasion through a break in the epidermis or penetration through intact mucous membranes, the natural course of syphilis can be divided into primary, secondary, and tertiary stages based on the clinical manifestations Coinfection with human immunodeficiency virus (HIV) can result in variation of the natural course of the disease Furthermore, ulcers caused by syphilis may contribute to the efficiency of HIV transmission in populations with high rates of both infections Syphilis has a wide variety of clinical manifestations, which gave rise to the name the “great imitator.” Primary Stage of Syphilis.  After inoculation, the spirochetes multiply rapidly and disseminate to local lymph nodes and other organs via the bloodstream The primary lesion develops 10 to 90 days after infection and is a result of an inflammatory response to the infection at the site of the inoculation The lesion, known as a chancre, is typically a single erythematous lesion that is nontender but firm, with a clean surface and raised border The lesion is teeming with treponemes and is extremely infectious Because the chancre is commonly found on the cervix or vaginal wall and is nontender, the lesion might not be obvious The lesion can also be found in the anal canal of both genders and remain undetected No systemic signs or symptoms are evident in the primary stages of the disease Secondary Stage of Syphilis.  Approximately to 12 weeks after development of the primary lesion, the patient may experience secondary disease, with clinical symptoms of fever, sore throat, generalized lymphadenopathy, headache, lesions of the mucous membranes, and rash The rash can present as macular, papular, follicular, papulosquamous, or pustular and is unusual in that it can also occur on the palms and soles All secondary lesions of the skin and mucous membranes are highly infectious The secondary stage can last for several weeks and can relapse It might also be mild and go unnoticed by the patient Tertiary Stage of Syphilis.  After the secondary stage heals, individuals are not contagious; however, relapses of secondary syphilis occur in about 25% of untreated patients Following the secondary stage, patients enter latent syphilis, when clinical manifestations are absent Latency within year of infection is referred to as early latent, whereas latency greater than year is late latent syphilis Approximately one third of untreated patients exhibit a biologic cure, losing serologic reactivity Another third remain latent for life but have reactive serology The remaining third ultimately develop tertiary or late syphilis, generally decades later Symptoms of tertiary syphilis include the development of granulomatous lesions (gummas) in skin, bones, and liver (benign tertiary syphilis), degenerative changes in the central nervous system (neurosyphilis), and syphilitic cardiovascular lesions, particularly aortitis, aneurysms, and aortic valve insufficiency Patients in the tertiary stage are usually not infectious In the United States and most developed countries, the tertiary stage of disease is not often seen because most patients are adequately treated with antimicrobial agents before the tertiary stage is reached Congenital Syphilis.  Treponemes can be transmitted from an infected mother to her fetus by crossing the placenta Congenital syphilis affects many body systems and is therefore severe and mutilating Early-onset congenital syphilis, onset at less than years of age, is characterized by mucocutaneous lesions, osteochondritis, anemia, hepatosplenomegaly, and central nervous system involvement and occurs when mothers have early syphilis during pregnancy Late-onset congenital syphilis results following pregnancies when mothers have chronic, untreated infections Symptoms of late onset congenital syphilis occur after years of age but generally are not apparent until the second decade of life Symptoms include interstitial keratitis, bone and tooth deformities, eighth nerve deafness, neurosyphilis, and other tertiary manifestations Epidemiology Treponema pallidum subsp pallidum is an exclusively human pathogen under natural conditions Syphilis was first recognized in Europe at the end of the fifteenth century, when it reached epidemic proportions Two theories have been proposed concerning the introduction of syphilis to Europe The first theory suggests that Christopher Columbus’ crew brought the disease from the West Indies back to Europe The second theory suggests that the disease was endemic in Africa and transported to Europe via the migration of armies and civilians The venereal transmission of syphilis was not recognized until the eighteenth century The causative agent of syphilis was not discovered until 1905 The incidence of syphilis in the United States dropped through the 1990s, and the fewest cases since reporting began in 1941 (31,618) was reached in 2000 However, since 2000 the disease has increased, peaking at 46,290 cases in 2008 The next years saw only a slight decrease from the peak number of cases at 44,830 in 2009 and 46,042 in 2011 High-risk sexual behavior and coinfection with HIV continue to complicate syphilis control efforts Educating people about sexually transmitted diseases, including the proper use of barrier contraceptives, reporting each case of syphilis to the public health authorities for contact investigation, and treating all sexual contacts of persons infected with syphilis are cornerstones of syphilis control efforts Serologic screening of high-risk populations should be performed, and to avoid congenital syphilis, pregnant women should have serologic examinations early and late in their pregnancy Laboratory Diagnosis Specimen Collection and Handling.  Lesions of primary and secondary syphilis typically contain large numbers of tahir99 VRG CHAPTER 23  The Spirochetes spirochetes The surface of primary or secondary lesions is cleaned with saline and gently abraded with dry, sterile gauze; bleeding should not be induced Serous transudate is placed onto a slide, diluting with nonbacteriocidal saline if the preparation is too thick A coverslip is added and the slide is transported immediately to a laboratory where dark field microscopy is performed Oral lesions should not be examined because numerous nonpathogenic spirochetes present in these specimens will lead to misinterpretation Culture methods are not available and dark field microscopy equipment and expertise are uncommon, so serology is the normal basis of diagnosis Microscopic Examination.  Organisms are too thin to be observed by bright field microscopy, so spirochetes are illuminated against a dark background Dark field microscopy requires considerable skill and experience; however, demonstration of motile treponemes in material from the chancre is diagnostic for primary syphilis Serologic Tests.  Serology is the primary method used for the laboratory diagnosis of syphilis Two major types of serologic tests exist, nontreponemal tests and treponemal tests Both have lower sensitivities in the primary stage, but approach 100% in the secondary stage of syphilis The treponemal tests retain a very high sensitivity in the tertiary stage as well A coinfection with HIV can result in false-negative serologic test results Comparisons between CSF and serum antibody responses can be helpful in potential cases of neurosyphilis With congenital syphilis, comparing antibody responses in the mother’s and baby’s serum can aid diagnosis The nontreponemal tests detect reaginic antibodies that develop against lipids released from damaged cells Although they are biologically nonspecific and known to react with organisms of other diseases and conditions (causing false-positive reactions), the nontreponemal tests are excellent screening tests The antigen used is a cardiolipin-lecithin complex made from bovine hearts The two nontreponemal tests widely used today are the Venereal Disease Research Laboratory (VDRL) and rapid plasma reagin (RPR) tests These tests are inexpensive to perform, demonstrate rising and falling reagin titers, and correlate with the clinical status of the patient The VDRL test uses a cardiolipin antigen that is mixed with the patient’s serum or CSF Flocculation occurs in a positive reaction and is observed microscopically The RPR test is more commonly used; it uses carbon particles and is read macroscopically When mixed with a positive serum on a disposable card, the black charcoal particles clump together with the cardiolipin-antibody complexes The flocculation is easily observed without a microscope Reactive or weakly reactive sera should undergo titration and be tested with treponemal tests The treponemal tests detect antibodies specific for treponemal antigens Historically, they have been used to confirm positive nontreponemal test results, although some laboratories use reverse sequence syphilis screening In this strategy, automated treponemal test–positive sera is tested with nontreponemal and a second treponemal assay This algorithm resulted in higher numbers of false-positives in five laboratories studied from 2006 to 2010, so the CDC continues to recommend the original approach Treponemal tests are also helpful in the detection of late-stage infections because the titers remain high and usually not drop in response to therapy, as the nontreponemal test 535 results Consequently, treponemal tests are also not useful in following therapy or detecting reinfection The treponemal antigens used are spirochetes derived from rabbit testicular lesions Two commonly used treponemal test methods are the Treponema pallidum–particulate agglutination (TP-PA) Test (Fujirebio America, Fairfield, NJ) and EIAs The TP-PA test uses gelatin particles sensitized with T pallidum antigens Agglutination indicates the presence of anti-treponemal antibodies EIA kits are simple to perform, commercially available, and comparable to other treponemal tests The fluorescent treponemal antibody absorption (FTA-ABS) assay utilizes a fluorescent-labeled anti-human antibody that detects patient antitreponemal antibodies bound to treponema affixed to a commercially prepared slide Because of subjectivity in reading the samples and the use of expensive fluorescent microscopy, the FTA-ABS test has become less frequently used in favor of the EIAs Antimicrobial Susceptibility Penicillin is the drug of choice for treating patients with syphilis It is the only proven therapy that has been widely used for patients with neurosyphilis, congenital syphilis, and syphilis during pregnancy Resistant strains have not developed Longacting penicillin such as benzathine penicillin is preferred Alternative regimens for patients who are allergic to penicillin and not pregnant include doxycycline, tetracycline, and chloramphenicol A typical Jarisch-Herxheimer reaction and exacerbation of cutaneous lesions can occur within hours following treatment Other Treponemal Diseases Three nonvenereal treponemal diseases—yaws, pinta, and endemic syphilis—occur in different geographic locations These treponematoses are found in developing countries in which hygiene is poor, little clothing is worn, and direct skin contact is common because of overcrowding All three diseases have primary and secondary stages, but tertiary manifestations are uncommon All diseases respond well to penicillin or tetracycline These infections are rarely transmitted by sexual contact, and congenital infections not occur Yaws Yaws is a spirochetal disease caused by T pallidum subsp pertenue It is endemic in the humid, tropical belt, the tropical regions of Africa, parts of South America, India, and Indonesia, and many of the Pacific Islands It is not seen in the United States The course of yaws resembles that of syphilis, but the early stage lesions are elevated, granulomatous nodules Endemic Syphilis Endemic syphilis (bejel) is caused by T pallidum subsp endemicum and closely resembles yaws in clinical manifestations It is found in the Middle East and the arid, hot areas of the world The primary and secondary lesions are usually papules that often go unnoticed They can progress to gummas of the skin, bones, and nasopharynx Dark field microscopy is not useful because of normal oral spirochetal biota Poor hygienic conditions are important in perpetuating these infections Endemic syphilis is transmitted by direct contact or sharing contaminated eating utensils tahir99 VRG 536 PART II  Laboratory Identification of Significant Isolates Pinta Pinta, caused by T carateum, is found in the tropical regions of Central and South America It is acquired by person to person contact and is rarely transmitted by sexual intercourse Lesions begin as scaling, painless papules and are followed by an erythematous rash that becomes hypopigmented with time Points to Remember ■ ■ ■ ■ ■ ■ ■ ■ Spirochetes are slender, flexuous, helically shaped bacteria Leptospires are most likely to enter the human host through small breaks in the skin or intact mucosa The incubation period of leptospirosis is usually 10 to 12 days but ranges from to 30 days after inoculation The onset of clinical illness is generally abrupt, with nonspecific, influenza-like constitutional symptoms such as fever, chills, headache, severe myalgia, and malaise The pathogenic borreliae commonly are arthropod-borne (by a tick or louse) and cause relapsing fever and Lyme disease B recurrentis and similar species cause relapsing fever The relapses are caused by immune evasion, including antigenic variation During the course of a single infection, borreliae systematically change their surface antigens During the febrile period, diagnosis of relapsing fever is readily made by Giemsa or Wright staining of blood smears Relapsing fever is the only spirochetal disease in which the organisms are visible in blood with bright field microscopy Laboratory diagnosis of Lyme borreliosis caused by B burgdorferi sensu lato is accomplished by a two-tiered serology Initial positive or equivocal EIA results are confirmed with Western blot Treponemes can cross the placenta and be transmitted from an infected mother to her fetus Congenital syphilis affects many body systems and is therefore severe and mutilating All pregnant women should have serologic testing for syphilis early in pregnancy Learning Assessment Questions What are the general characteristics of spirochetes? What risk factors are associated with Borrelia spp endemic relapsing fever infection? Which tickborne species of Borrelia is associated with a skin rash or lesion? What is the significance on infectious disease transmission of finding partially engorged ticks attached to the skin? What is the test of choice for the laboratory diagnosis of relapsing fever borreliosis? Name the four strains of the genus Treponema that are pathogenic for humans What are the stages of a Treponema pallidum subsp pallidum infection? Is the final stage usually seen in developed countries? Where are most cases of leptospiroses contracted within the United States, and why is this important when considering the typical incubation period of the infection? Compare the difference(s) between treponemal and nontreponemal tests for syphilis 10 What is the recommended methodology for laboratory diagnosis of Lyme borreliosis? BIBLIOGRAPHY Aguero-Rosenfeld ME, et al: Diagnosis of Lyme borreliosis, Clin Microbiol Rev 18:484, 2005 Centers for Disease Control and Prevention: Discordant results from reverse sequence syphilis screening—five laboratories, United States, 2006–2010, MMWR 60:133, 2011 Available at: http://www.cdc.gov/ mmwr/preview/mmwrhtml/mm6005a1.htm?s_cid=mm6005a1_w Accessed November 14, 2013 Centers for Disease Control and Prevention: Lyme disease: resources for clinicians: diagnosis, treatment, and testing, 2013 Available at: http://www.cdc.gov/lyme/healthcare/clinicians.html Accessed June 30, 2013 Centers for Disease Control and Prevention: 2010 sexually transmitted disease surveillance Available at: http://www.cdc.gov/std/stats10/ syphilis.htm Accessed September 4, 2012 Centers for Disease Control and Prevention: Sexually transmitted diseases treatment guidelines, 2010, MMWR 59(RR-12):1, 2010 Available at: http://www.cdc.gov/mmwr/preview/mmwrhtml/mm6131a3 htm?s_cid=mm6131a3_w Accessed November 14, 2013 Centers for Disease Control and Prevention: Summary of notifiable diseases—United States, 2011, MMWR 60(53):1, 2013 Available at: http://www.cdc.gov/mmwr/preview/mmwrhtml/mm6053a1.htm Accessed November 13, 2013 Hawaii Department of Health Communicable Disease Division: Communicable disease report, September/October 2004 Personal communication for 2004 leptospirosis data Kassutto S, Doweiko JP: Syphilis in the HIV era, Emerg Infect Dis 10:1471, 2004 Available at: http://wwwnc.cdc.gov/eid/article/10/8/ 03-1107_article.htm Accessed November 14, 2013 Katz AR, et al: Leptospirosis in Hawaii, USA, 1999–2008, Emerg Inf Dis 17:221, 2011 Available at: http://wwwnc.cdc.gov/eid/article/ 17/2/10-1109_article.htm Accessed November 14, 2013 Levett PN: Leptospira In Versalovic J, et al, editors: Manual of clinical microbiology, ed 10, Washington, DC, 2011, ASM Press, p 916 Lo Y-C, et al: Severe leptospirosis similar to pandemic (H1N1) 2009, Florida and Missouri, USA, Emerg Infect Dis 17:1145, 2011 Available at: http://wwwnc.cdc.gov/eid/article/17/6/10-0980_article.htm Accessed November 14, 2013 Meri T, et al: Relapsing fever spirochetes Borrelia recurrentis and B duttonii acquire complement regulators C4b-binding protein and factor H, Infect Immun 74:4157, 2006 Radolf JD, et al: Treponema and Brachyspira, human host–associated spirochetes In Versalovic J, et al, editors: Manual of clinical microbiology, ed 10, Washington, DC, 2011, ASM Press, p 941 Schriefer ME: Borrelia In Versalovic J, et al, editors: Manual of clinical microbiology, ed 10, Washington, DC, 2011, ASM Press, p 924 Sejvar JB, et al: Leptospirosis in “Eco-Challenge” athletes, Malaysian Borneo, 2000, Emerg Infect Dis 9:702, 2003 Available at: http://wwwnc.cdc.gov/eid/article/9/6/02-0751_article.htm Accessed November 14, 2013 Steere AC: Borrelia burgdorferi (Lyme disease, Lyme borreliosis) In Mandell GL, et al, editors: Mandell, Douglas, and Bennett’s principles and practice of infectious diseases, ed 7, Philadelphia, 2010, Churchill Livingstone Elsevier, p 3071 tahir99 VRG CHAPTER 24   Chlamydia, Rickettsia, and Similar Organisms Donald C Lehman and Connie R Mahon* CHAPTER OUTLINE ■ CHLAMYDIACEAE General Characteristics Chlamydia trachomatis Chlamydophila pneumoniae Chlamydophila psittaci ■ RICKETTSIACEAE AND SIMILAR ORGANISMS Rickettsia Orientia Anaplasmataceae Coxiella OBJECTIVES After reading and studying this chapter, you should be able to: List the members of the family Chlamydiaceae Discuss the unique growth cycle of Chlamydia, describing elementary and reticulate bodies Compare and contrast Chlamydia and Rickettsia and distinguish them from other bacteria and viruses Discuss the most important human diseases caused by the Chlamydia, Chlamydophila, and Rickettsia, species and similar microorganisms Describe the modes of transmission for each species of Chlamydia, Chlamydophila, Rickettsia, and similar microorganisms Compare the epidemiology and pathogenesis of the serovars of Chlamydia trachomatis Evaluate the available assays for the laboratory diagnosis of C trachomatis and Chlamydophila pneumoniae infections Discuss the problems with serologic cross-reactivity among the rickettsial species For the following human rickettsial diseases, link the causative agent and compare the mode of transmission to humans: • Louse-borne typhus • Rocky Mountain spotted fever • Scrub typhus 10 Compare the laboratory methods available for the diagnosis of rickettsioses 11 Compare the characteristics of the Rickettsia and Coxiella and the diseases they cause Case in Point vaginal delivery in the parking lot of a local hospital Eye discharge and cell scrapings were cultured Routine bacterial cultures were negative; however, a rapid nucleic acid amplification test was diagnostic A 7-day-old newborn girl was brought by her grandmother to the emergency department of a large city hospital She had been discharged days after birth, with the last nursing note indicating that the child was “fussy.” The child presented to the emergency department with a fever of 39° C, loss of appetite, a profuse yellow discharge from the right eye, and general irritability Medical history revealed the mother to be a 17-year-old intravenous drug abuser with no prenatal care, who had a *My comments are my own and not represent the views of the Health Resources and Services Administration of the Department of Health and Human Services Issues to Consider After reading the patient’s case history, consider: ■ The various organisms that can be recovered from exudative material from newborns ■ The clinical infections and disease spectrum associated with these organisms ■ How these organisms are transmitted and the risk factors associated with the diseases produced ■ The appropriate methods of laboratory diagnosis tahir99 VRG 537 538 PART II  Laboratory Identification of Significant Isolates Key Terms Brill-Zinsser disease Bubo Elementary body (EB) Human granulocytic anaplasmosis (HGA) Human monocytic ehrlichiosis (HME) Lymphogranuloma venereum (LGV) Morulae Pelvic inflammatory disease (PID) Reiter syndrome Reticulate body (RB) Trachoma T he genus Chlamydia is in the family Chlamydiaceae; members of the family share selected characteristics (Table 24-1) and have a unique life cycle Within the genus Chlamydia, four species were previously recognized— C pecorum, C pneumoniae, C psittaci, and C trachomatis All except C pecorum have been associated with human disease Based on analysis of 16S and 23S rRNA gene sequences, a revised taxonomic classification has been accepted The family Chlamydiaceae now consists of two genera: (1) Chlamydia to include C trachomatis; and (2) Chlamydophila to include C pneumoniae, C psittaci, and C pecorum Other named species TABLE of Chlamydia exist, but they are rarely isolated from humans The creation of a second genus was somewhat controversial and is still being debated Therefore, readers may find both taxonomic classifications in published literature The term rickettsiae can specifically refer to the genus Rickettsia or it can refer to a group of organisms included in the order Rickettsiales There has been significant reorganization in the order Rickettsiales in recent years The order includes the families Rickettsiaceae and Anaplasmataceae The family Rickettsiaceae includes the genera Rickettsia and Orientia The family Anaplasmataceae includes the genera Ehrlichia, Anaplasma, Cowdria, Neorickettsia, and Wolbachia As a result of this reorganization, Coxiella has been removed from the family Rickettsiaceae Chlamydiaceae General Characteristics As shown in Table 24-2, initial differentiation of the Chlamydia spp was based on selected characteristics of the growth cycle, susceptibility to sulfa drugs, accumulation of glycogen in inclusions, and DNA relatedness Table 24-2 also lists additional properties of the Chlamydiaceae species that have helped further differentiate the three human species on the basis of natural host, major diseases, and number of antigenic variants (i.e., serovars) 24-1  Comparative Properties of Microorganisms Organisms Characteristic Typical Bacteria Chlamydiae Rickettsiae Mycoplasmas Viruses + − + + + + − + + + + − + + + + + + − − + + − + + − − + + + − + − + − − − − + − DNA and RNA Obligate intracellular parasites Peptidoglycan in cell wall Growth on nonliving medium Contain ribosomes Sensitivity to antimicrobial agents Sensitivity to interferon Binary fission (replication) +, Characteristic is present; −, characteristic is absent TABLE 24-2  Initial Differentiation of Chlamydiaceae Species Properties Inclusion morphology Glycogen in inclusions Elementary body morphology Sulfa drug sensitivity DNA relatedness (against C pneumoniae) Natural hosts Major human diseases Number of serovars Chlamydia trachomatis Chlamydophila pneumoniae Chlamydophila psittaci Round, vacuolar + Round + 10% Humans Sexually transmitted diseases Trachoma Lymphogranuloma venereum 20 Round, dense − Pear-shaped − 100% Humans Pneumonia Pharyngitis Bronchitis Variable shape, dense − Round − 10% Birds, lower animals Pneumonia FUO FUO, Fever of unknown origin; +, characteristic is present; −, characteristic is absent tahir99 VRG 10 1064 INDEX Minimal inhibitory concentration (MIC), 100, 275-276, 279, 297 agar dilution MIC test, 282, 282f breakpoint MIC panels, 281 broth macrodilution MIC tests, 280, 307f broth microdilution MIC tests, 280-282, 280f-281f, 281t, 285, 286t-287t on-scale MIC endpoints, 299 tube dilution, 280 Minimal media, 13 Minimum bactericidal concentration (MBC), 306-308, 306t, 307f Minocycline, 761-762 MIO test See Motility-indole-ornithine test Mission statement, 100-102 Mitsubishi Gas Chemical America, 505 Mixed acid fermentation, 16, 183 MLEE See Multilocus enzyme electrophoresis MLST See Multilocus sequence typing MLVA See Multilocus variable number of tandem repeat analysis MNV See Milker’s nodule virus Mobiluncus spp., 502 Moccasin foot, 597 Modified Robbins cell, 762 Modified Thayer-Martin medium, 377t Moeller decarboxylase base medium, 187 Moellerella wisconsensis, 440 Moist heat, 62-63 Mold, 590, 612, 821-822 Molecular beacons, 237, 239-240, 239f Molecular diagnostics, 227 Molecular probes complementarity of, 228 concentration of, 228 length of, 228 nucleic acid hybridization reaction and, 228 for resistance identification, 310 selection of, 228-229 Mollicutes, 552-556, 556t Molluscum contagiosum, 825, 825f, 929, 929f MOMP See Major outer membrane protein Monkeypox, 702-703 Monobactams, 259, 259f, 260t Monoclonal antibodies, 201-202, 202f Monocytes, 36, 36t Monograph system, 68 Monomicrobial infections, 133, 135 Mononucleosis, 220, 698 Moraxella catarrhalis, 150f, 487-488, 766-767 characteristics of, 380t general characteristics of, 373, 374f, 374t overview of, 384, 384f Moraxella nonliquefaciens, 487 Moraxella osloensis, 487 Moraxella spp., 150f, 487-488 Moraxella urethralis, 487-488 Morbillivirus spp., 711-712 Morganella morganii, 432, 432t Morphology, 10-12, 134t Morulae, 550, 550f, 952 Mosquitos, 708-709 Motility organelles, 10 Motility test, 189, 357-358, 358f, 513 Motility-indole-ornithine test (MIO test), 187, 190 Mouth, flora of, 25, 26b MR test See Methyl red test mRNA See Messenger RNA MRSA See Methicillin-resistant Staphylococcus aureus MRSE See Methicillin-resistant Staphylococcus epidermidis MSSA See Methicillin-sensitive Staphylococcus aureus Mucocutaneous leishmaniasis, 646 Mucor spp., 607, 607f Mucorales, 592-593, 593f, 606-608, 815 Mucormycosis, 815 Mueller-Hinton agar, 282-284, 461, 526 MUG test, 193t Multidrug and toxic effects family (MATE), 264 Multidrug resistance (MDR), 255, 567 Multidrug-resistant tuberculosis (MDR TB), 567 Multilocus enzyme electrophoresis (MLEE), 246-247 Multilocus sequence typing (MLST), 246, 248 Multilocus variable number of tandem repeat analysis (MLVA), 246, 248 Multiplex PCR, 231, 242, 242f Multispecies biofilms, 753, 753f Multispot HIV-1/2 Rapid Test, 715 Mumps viruses, 711, 859 Mupirocin, 809-810 Murine typhus, 548, 951-952 Murray-Washington method, for contamination assessment, 136 Musculoskeletal infections, 874 Mutations, 20 chromosomal, 267 LPS, 263 Mutualism, 24 MX4000 system, 237 Mycelia, 4-5, 590, 590f Mycetomas, 362, 594, 599-600, 600f, 600t, 813-814, 813t, 814f Mycobacterial infection, 816-817, 860, 866 Mycobacterium africanum, 573t Mycobacterium avium complex (MAC), 567-568 Mycobacterium avium subsp paratuberculosis, 568 Mycobacterium bovis, 567, 573t Mycobacterium chelonae-Mycobacterium abscessus, 571, 573t dermatologic manifestations of, 820f Mycobacterium fallax, 573t Mycobacterium fortuitum, 571-572, 573t Mycobacterium genavense, 569 Mycobacterium haemophilum, 569 Mycobacterium kansasii, 147f, 568-569, 569f Mycobacterium leprae, 572, 572f, 820-821 Mycobacterium malmoense, 569, 569f Mycobacterium marinum, 569-570, 570f Mycobacterium scrofulaceum, 570, 570f Mycobacterium simiae, 570 Mycobacterium smegmatis, 572 Mycobacterium spp., 147f See also Nontuberculosis mycobacterium acid-fast cell wall of, 8-9 acid-fast staining of, 131b-132b biochemical identification of, 582f-585f, 583-585 blood and, 577, 880 chromatography and, 586 chronic pneumonia and, 793-794, 794f colony morphology and, 582 dermatologic manifestations of, 820-821 disinfectants and, 575 general characteristics of, 564 Gram staining of, 578, 579t tahir99 VRG Mycobacterium spp (Continued) identification of aerobic, 364t inhibitory tests of, 585-586 isolation and identification of, 572-586, 573t, 582f-583f laboratory identification of, 581-586, 581b laboratory safety considerations for, 575 MAC growth of, 586 media and isolation methods for, 578-581, 579t overview of, 564 photoreactivity of, 583, 583b specimens and, 576-578, 576b stool samples and, 577 temperature and, 583 urease test and, 585, 585f urine and, 576-577 usual clinical significance of, 564b Mycobacterium szulgai, 570-571 Mycobacterium tuberculosis, 147f, 564-567, 573t, 729 AMTD and, 586 clinical significance of, 565-567 dermatologic manifestations of, 820 extrapulmonary tuberculosis and, 566 identification of, 566, 566f immunodiagnosis of, 587-588 multidrug-resistant, 567 nodular lymphangitis and, 817 nucleic acid amplification and hybridization tests for, 586 PCR and identification of, 586 primary tuberculosis and, 565 reactivation tuberculosis and, 565-566 serologic testing and, 587-588 skin testing and, 587 susceptibility testing of, 586-587 Mycobacterium ulcerans, 571, 573t Mycobacterium xenopi, 571 Mycoplasma fermentans, 556-557 Mycoplasma genitalium, 556 Mycoplasma hominis, 553, 555-556, 556t, 561t Mycoplasma orale, 559, 560f Mycoplasma pneumoniae, 553-555, 555f, 557-560, 557t, 561t Mycoplasma salivarium, 556-557, 559, 560f Mycoplasma spp clinical infections associated with, 554-557, 555f, 556t general characteristics of, 553-554, 553f-554f, 553t, 555t indigenous to humans, 555t laboratory diagnosis of, 557-560, 557t, 558f laboratory diagnosis of, result interpretation, 561, 562t overview of, 552-553 serologic testing and, 560, 561t susceptibility testing and, 560-561 Mycoses, 592 agents of opportunistic, 606-611 cutaneous, 594, 596-598, 597f-598f skin and, 593-594, 593f subcutaneous, 594, 598-601, 599f-602f, 601b superficial, 593-596, 595f-596f systemic, 594, 601-606, 602f-606f, 602t-603t Mycosis, 162f Myonecrosis, 500-501 Myotis occultus, 707 Myroides spp., 490-491 N NAATs See Nucleic acid amplification tests Naegleria fowleri, 639-640, 639t, 640f NAG See N-acetyl-d-glucosamine Nails, 597, 615 NALC See N-acetyl-L-cysteine Nalidixic acid, 256t-257t NAM See N-acetyl-d-muramic acid NANB hepatitis, 720 Nanobiotechnology, 248-251, 271-272 Nanoencapsulation, 271-272 Nanomedicine, 251 Nanoshells, 272 Nanotubes, 272 NAP test, 585-586 Narrow spectrum antimicrobial activity, 259-260, 260t NASBA See Nucleic acid sequence-based amplification Nasopharyngeal aspirates, 417, 546 Nasopharyngeal carcinoma, 699 Nasopharynx, flora of, 26, 26b, 766, 767b National Fire Protection Association (NFPA), 80 National laboratories, 90 National Science Advisory Board for Biosecurity (NSABB), 748 National Select Agents Registry Program (NSAR), 730 Natural immunity See Innate immunity NDA See New drug application Necator americanus, 676-678 Necrosis, infectious causes of, 807 Necrotizing fasciitis (NF), 332, 813 Necrotizing soft infection, 813, 813f Negative predictive value (NPV), 106-107 Negri bodies, 692 Neighbor-joining method, 249 Neisseria cinerea, 385, 386f Neisseria elongata, 388 Neisseria flavescens, 385 Neisseria gonorrhoeae, 171, 373, 903-906, 905f See also Gonorrhea carbohydrate utilization for, 380 characteristics of, 380t clinical infections of, 375 collection and transportation of, 376, 376f colony morphology of, 377, 377f definitive identification for, 378-380, 379t direct microscopic examination of, 376, 376f epidemiology of, 375 immunoassays and, 380 incubation of, 377 laboratory diagnosis of, 376-381, 376f-378f, 377t, 379t-380t microscopic morphology of, 377-378, 378f NAATs and, 381 overview of, 374-381 oxidase test and, 378, 378f pharyngitis and, 375 resistance and, 381 susceptibility testing and, 288 treatment of, 381 Neisseria lactamica, 385-386, 387f Neisseria meningitidis, 24, 150f clinical infections of, 382-383, 382f direct microscopic examination of, 383, 383f epidemiology of, 382 laboratory diagnosis of, 383, 383f laboratory-acquired disease and, 383-384 INDEX Neisseria meningitidis (Continued) overview of, 382-384, 385t susceptibility testing and, 288 treatment for, 384 vaccine for, 384 Neisseria mucosa, 386-387 Neisseria polysaccharea, 387 Neisseria sicca, 387, 388f Neisseria spp., 150f colony morphology and, 386t commensal, 385-388, 385t-387t differential tests for, 387t general characteristics of, 373, 374f, 374t pathogenic species of, 373-384 virulence factors of, 373, 375f Neisseria subflava, 388, 388f Neisseria weaveri, 388 Neonatal herpes, 697, 913 Neonates bacteremia density in adults compared to, 875 Chlamydia trachomatis and, 541, 541t genital mollicutes and, 555-556, 556t immunocompromised patients and, 940 Neoplasia, 756 Nested PCR, 231, 242 Neuraminidase inhibitors, 711 Neurosyphilis, 534 Neutralization assays, 210-211 Neutropenia, 608, 799, 936 Neutrophils, 798 New drug application (NDA), 68 New World arenaviruses, 704-705 New York City medium, 377t NF See Necrotizing fasciitis NFPA See National Fire Protection Association NGU See Nongonococcal urethritis Niacin test, 584, 584f 9/11 attacks, 748 Nitazoxanide, 659 Nitrate disk, 514 Nitrate reduction test, 189, 584, 584f NLF See Nonlactose fermenters Nocardia spp., 148f, 150f acid-fast cell wall and, 8-9 overview of, 361-363, 362f-363f, 364t virulence factors of, 362 Nocardioform, 364 Nocardiopsis spp., 150f Nocardiosis, 148f, 816 Nodular lymphangitis (lymphocutaneous syndrome), 815-817, 816b, 816f actinomycosis and, 817, 817f causes of, 816b mycobacterial infection, 816-817 Mycobacterium tuberculosis and, 817 nocardiosis, 816 NTM and, 816-817 sporotrichosis, 815-816, 816f Nomenclature, overview of, Non-A, non-B hepatitis (NANB hepatitis), 720 Non-chromogens, 568 Nonfermentative gram-negative bacilli See also specific genera biochemical characteristics and identification of, 475-478, 476t, 477f, 479f-480f carbohydrates and, 475 clinical infections from, 475, 475b clinically significant species of, 478-488 tahir99 VRG 1065 Nonfermentative gram-negative bacilli (Continued) general characteristics of, 475-478, 478b less commonly encountered, 488-492 MAC and, 476, 477f taxonomic changes for, 476, 476t Nongonococcal urethritis (NGU), 541, 555, 903 Nonhemolytic organisms, 172 Nonlactose fermenters (NLF), 171, 171f, 182-185, 442 Nonoxidizers, 475 Nonroutine specimens, 123 Nonselective media, 119 Nonsusceptible organisms, 279, 288, 297 Nontreponemal antibody tests, 916-917 Nontuberculosis mycobacterium (NTM) clinically significant, 567-572 dermatologic manifestations of, 820, 820f nodular lymphangitis and, 816-817 overview of, 564 pneumonia and, 792 rapidly growing species of, 571-572, 583f slowly growing species of, 567-571, 582f Nontypeable H influenzae (NTHi), 392 Normal biota, of respiratory tract, 766-768, 767b Noroviruses, 706, 706f North American blastomycosis See Blastomycosis Northern blotting, 229-230 Norwalk virus, 841 Norwegian scabies, 829f Nose, flora of, 26, 26b Nosocomial bacteremia, 870 Nosocomial infections, 316, 769 Novobiocin susceptibility test, 322-323, 323f NPV See Negative predictive value NRTIs See Nucleoside analogue reverse transcriptase inhibitors NSABB See National Science Advisory Board for Biosecurity NSAR See National Select Agents Registry Program NTHi See Nontypeable H influenzae NTM See Nontuberculosis mycobacterium Nuclear peripheral chromatin, 629 5’ nuclease assay, 237-239, 238f Nucleic acid amplification tests (NAATs), 520, 880-881, 905-906 See also Polymerase chain reaction bDNA detection for, 231, 244, 244f Chlamydia spp and, 544 cycling probe technology for, 231, 245, 245f hybrid capture for, 231, 244-245, 245f invader chemistry and, 245 Mycobacterium tuberculosis and, 586 NASBA for, 231, 242-243, 243f Neisseria gonorrhoeae and, 381 ocular infections and, 973 procedures of, 230-245 signal amplification methods and, 243-245 steps in, 231, 231t TMA for, 230-231, 243 tuberculosis and, 793 viral infections and, 693 Nucleic acid hybridization applications of, 230 formats, 229-230 in-solution, 230 ISH, 230 Mycobacterium tuberculosis and, 586 overview and techniques of, 227-230, 227f, 229f reaction variables, 228 solid support, 229 1066 INDEX Nucleic acid probe assays, 347 Nucleic acid sequence-based amplification (NASBA), 231, 242-243, 243f Nucleocapsid, 689 Nucleolus, 10 Nucleoprotein, 709 Nucleoside analogue reverse transcriptase inhibitors (NRTIs), 716 Numeric codes, 190-191 Nutrient media, 13 Nutritional resources, 12-14, 754 Nutritionally variant streptococci See Abiotrophia spp.; Granulicatella spp Nymphs, 950 O O antigen, 422, 434, 434f Obama, Barack, 747 Obesumbacterium proteus, 441 Obligate aerobes, 14, 496, 496t Obligate anaerobes, 14, 496, 496t Obligate intracellular parasites, 690 Occult (unsuspected) bacteremia, 869 Occupational Safety and Health Administration (OSHA), 73-74, 89 Ocular herpes, 697 Ocular infections, 385t See also Blepharitis; Conjunctivitis; Keratitis Acinetobacter spp and, 484 biofilms and, 970-971, 970t, 971f chlamydial, 960-961, 960f of cornea, 963-966 culture and, 972-973, 973t, 974f direct microscopic examination and, 971-972, 972f, 972t endophthalmitis, 956, 968, 968b, 969f episclera and, 966 of eyelids, 962-963 general concepts of, 956-959 HIV and, 969-970, 970f host protective mechanisms and, 957 indigenous microbial flora and, 957, 957t of intraocular chambers, 968, 968b laboratory diagnosis of, 971-976 of lacrimal apparatus, 967, 967b microorganisms associated with, 958b NAATs and, 973 ocular structures and, 956-957, 956f of orbit, 966-967 of retina, 968-970 scleritis, 966 smears and, 972t specimens and, 971, 971f virulence factors of, 958-959, 958b Ocular medications, contaminated, 975, 975b Odor, colony morphology and, 175-176 Odynophagia, 777 O/F basal medium (OFBM), 183, 184f, 184t OF media See Oxidative-fermentative media O/F tests See Oxidation-fermentation test OFBM See O/F basal medium OIAs See Optical immunoassays Old World arenaviruses, 704-705 Oligella spp., 487-488 Oligonucleotide primers, 227-228, 231-233, 231t, 233t Omsk hemorrhagic fever, 746 Onchocerca volvulus, 682-683, 682t Onchocerciasis, 827, 827f Oncosphere See Hexacanth embryo On-scale MIC endpoints, 299 Onychomycosis, 597 Oocyst, 659-662 Opaque density, 174, 175f Ophthalmia neonatorum, 375 Ophthalmic drops, 975 Opportunistic infections, 25, 768 Opportunistic pathogens Coccidioides immitis and, 792-793 diarrhea and, 848 endogenous, 934 exogenous, 934 immunocompromised patients and, 933-934, 934t overview of, 29-30, 30t respiratory tract infections and, 796 Opportunists, 27 Opsonins, 36, 791 Opsonization, 36 Optical immunoassays (OIAs), 217, 217f Optochin susceptibility test, 346, 346f Oral herpes, 697 Ora-Quick Advance Rapid HIV-1/2 Antibody Test, 715, 924 Orbit infections, 966-967 Orbital cellulitis, 774, 966 Orf virus, 825 Organ culture, 694 Organ transplantation, 938 Organic material, 61-62 Oriental sore See Leishmaniasis Orientia spp., 547, 549 Ornithine, 187 Oropharyngeal candidiasis, 616 Oropharyngeal infections, 375 Oropharynx, flora of, 26, 26b, 766, 767b Orthomyxoviridae, 709-711 Ortho-nitrophenyl-β-D-galactopyranoside test (ONPG test), 185, 185f, 193t, 383 Orthostatic changes, 838 ORYX, 94 Oseltamivir (Tamiflu), 711 OSHA See Occupational Safety and Health Administration Osler nodes, 830 Osteomyelitis, 319, 385t OTC drug See Over-the-counter drug Otitis externa, 481 Otitis media, 769 causes of, 775 clinical manifestations of, 776 complications with, 776 epidemiology of, 775 laboratory diagnosis of, 776 overview of, 771t, 775-776 pathogenesis of, 775-776 treatment of, 776 Ouchterlony gel diffusion See Double immunodiffusion Outbreak investigations, 52-56 antibiograms and, 54, 55t cultures and serology for, 54 epidemiologic curve of, 52-53, 53f laboratory support for, 54-55, 55t local, 52, 52f PGFE and, 54-55 steps of, 53-54, 54t widespread, 52-53, 53f tahir99 VRG Outbreaks, 49 Outcome monitors, 102 Over-the-counter drug (OTC drug), 68 Oxacillin, 256t-257t, 280t, 286t, 289-290, 290f, 324-325 Oxacillin screen plate, 290 Oxalic acid, 578 Oxazolidinones, 262 Oxidase test, 189-190, 193t, 378, 378f, 476, 477f Oxidation, 17, 17f, 183 See also Respiration Oxidation-fermentation test (O/F tests), 183, 184f, 184t, 320-321 Oxidative-fermentative media (OF media), 475 Oxidizers, 475 Oxoid Signal system, 877 P PA See Protective antigen Pace system, 230 Packaging and shipping, infectious substances and, 90 PAD See Phenylalanine deaminase Paecilomyces spp., 609, 609f PAM See Primary amebic meningoencephalitis Pantoea spp., 429-430, 430f Panton-Valentine leukocidin (PVL), 31, 317, 786 PAP See Population analysis profile Papanicolaou smear, 692 Papillomaviridae dermatologic manifestations of, 825-826 koilocytes and, 702 overview of, 702, 702t Papules, 806 Parachlorometaxylenol (PCMX), 67 Paracoccidioides brasiliensis, 602t-603t, 605-606, 606f Paracoccus yeei, 489 Para-dimethylaminobenzaldehyde (PDAB), 188-189, 189f Paradoxic effect, 308 Paragonimus westermani, 665-666, 665t, 666f, 862 Parainfluenza viruses (PIVs), 711 Paramyxoviridae, 711-713 hMPV, 712-713 measles virus, 711-712, 712f mumps virus, 711 PIVs, 711 RSV, 691, 693, 712 Parapneumonic effusions (PPEs), 787 Parasafe, 627 Parasites, 26 See also specific parasites blepharitis and, 963 blood and tissue, 630 central nervous system infections and, 861-862 conjunctivitis and, 962 CSF and, 630, 866, 866f diarrhea and, 845-846 ectoparasites, 826, 828, 829f EIAs and, 631 general concepts and laboratory methods with, 626-632 immunologic diagnosis of, 630-631 intestinal and urogenital, 629-630 keratitis and, 640, 965-966, 966f medically important, 632-662, 632t microscopic examination of, 163 overview of, 4, 626 QC and, 631-632 skin manifestations of, 826-828 Parasites (Continued) stool samples and, 626-629, 627t, 628f viruses as obligate intracellular, 690 Parasitism, 24 Parinaud oculoglandular conjunctivitis, 540 Paronychia, 809t, 811 Paroxysmal phase, of pertussis, 416 Parrot fever, 547 Parvoviridae, 703-704 Parvovirus B19 infection, 822 Pasteurella spp., 391, 391f, 403-404, 404f, 405t Pasteurellosis, 403-404, 943-944 Pasteurization, 63 PathoGene system, 230 Pathogenesis adherence to host cells and tissues and, 31, 32f, 770 endotoxins and, 32-34 exotoxins and, 32-33, 33t extracellular toxins and enzymes production and, 32-34 intracellular survival and proliferation and, 32 microbial factors contributing to, 29-30, 30t microbial flora role in, 27 phagocytosis evasion and, 30-31, 31t transmission routes and, 43-45, 43t, 44f Pathogenic bacteria, Pathogenic microorganisms, 766-768, 768b Pathogenicity, 29, 756-758, 756b Patient preoperative skin preparation, 68, 69t, 70 Patient-collect specimens, 112-114 Paul-Bunnell heterophile antibody test, 699-700 PBF See Phenotype biofilm PBPs See Penicillin-binding proteins PCMX See Parachlorometaxylenol PCR See Polymerase chain reaction PCV7 vaccine, 337 PDAB See Para-dimethylaminobenzaldehyde PEA See Phenylethyl alcohol Pectobacterium spp., 433 Pediculosis, 828 Pediococcus spp., 342 Pelvic inflammatory disease (PID), 375, 541, 904, 928-929 Penems, 259, 260t Penetration, viral replication and, 690-691 Penicillin, 535, 557, 917 Penicillinase-producing Neisseria gonorrhoeae (PPNG), 288, 381 Penicillinase-resistant penicillins, 285 Penicillin-binding proteins (PBPs), 263 β-lactam antibiotics and, 259 oxacillin resistance and, 324-325 Penicillins chemical structure of, 259, 259f disk-diffusion testing and, 285 overview of, 256t-257t for Streptococcus pneumoniae, 285, 347 susceptibility testing and, 285-288 Penicillium marneffei, 606 Penicillium spp., 609, 610f Pentose phosphate pathway, 15, 16f, 17b Peptidoglycan biosynthesis of, 259, 259f overview of, 256t-257t structure of, 258-259, 259f Pepto-Bismol, 846-848, 852 Peptone-yeast extract-glucose (PYG), 518 Peptostreptococcus spp., 503 INDEX Peracetic acid, 67-68 Performance improvement (PI), 94 See also Quality control benchmarking and, 103 customer concept and, 102-103 fixing process and, 103 indicators of, 102 monitors established for, 102, 102b problem-action form for, 102, 102t Q-probes and, 103 vision and mission statements for, 100-102 Perihepatitis, 375 Perinatal period, 940 Periodontitis, 402-403, 403f, 759 Peripheral chromatin, 629 Periplasmic flagella, 530 Periplasmic space, Perithecia, 610-611 Peritonitis, 484 Peritrichous flagella, 9-10, 9f Permanently stained smears, 629 Persistent effect, 67 Persister cells, 264, 308, 755 Personal protective equipment (PPE), 74, 75f, 575 Personnel competency, 100, 101f Pertussis, 415-416 Bordetella spp and, 416-417 catarrhal phase of, 416 causes of, 778 clinical manifestations of, 778 complications with, 778 convalescent phase of, 416 epidemiology of, 778 laboratory diagnosis of, 417-419, 418b, 418f, 778-779 overview of, 771t, 778-779 paroxysmal phase of, 416 pathogenesis of, 778 treatment of, 779 Pertussis toxin (PT), 416 Petechiae, 807, 819 PGFE See Pulsed-field gel electrophoresis pH bacterial growth and, 13-14 disinfection, sterilization and, 62 gastric, 836 nucleic acid hybridization reactions and, 228 Phaeoacremonium spp., 591f Phaeohyphomycosis, subcutaneous, 600-601, 601b, 601f, 814-815 Phaeoid hyphae, 591, 591f Phaeoid saprophytes, 610-611 Phage See Bacteriophage Phagocytes, 31 Phagocytosis attachment and, 36 capsules and resistance of, 30-31, 31t as host resistance factor, 36-37, 36t IgG and, 36 ingestion and, 36-37, 37f killing and, 37 pathogenesis and evasion of, 30-31, 31t virulence and evasion of, 30-31, 31t Pharyngitis, 545, 767 Arcanobacterium spp and, 360 causes of, 770-771, 771t clinical manifestations of, 771-772 complications with, 772 tahir99 VRG 1067 Pharyngitis (Continued) direct antigen detection assay for, 221-222, 222t epidemiology of, 770 group A streptococcal pharyngitis, 221-222, 222t, 331-332, 770, 772-773 laboratory diagnosis of, 772-773, 772f Neisseria gonorrhoeae and, 375 overview of, 770-773 pathogenesis of, 771 Streptococcus pyogenes and, 332 treatment of, 773 Phenicol, 256t-257t Phenolics, 66-67, 575 Phenotype biofilm (PBF), 753-754 Phenotype planktonic (PPL), 753-754 Phenotypes, 6, 18-19, 182 Phenylalanine deaminase (PAD), 187, 188f Phenylethyl alcohol (PEA), 367, 506, 507t Pheromones, 755 Phialides, 592, 592f Phialophora verrucosa, 599t Phoma spp., 611, 611f Phosphonoformic acid (foscarnet), 723 Photochromogens, 568, 569f Photoreactivity, Mycobacterium spp and, 583, 583b Photorhabdus luminescens, 443 Photorhabdus spp., 441 Phototrophs, 12 Phthiriasis, 828 Phthirus pubis, 166f Phyla, Physical barriers, 34-35 PI See Performance improvement Picornaviridae, 713-714 PID See Pelvic inflammatory disease Piedraia hortae, 595 Pigment, colony morphology and, 175, 175f-176f Pilus (pili), 10, 31, 32f Pinta, 533, 536 Pinworm See Enterobius vermicularis Pithomyces spp., 611, 612f PIVs See Parainfluenza viruses Plague infections bubonic, 438, 735-736, 736f, 949 causes of, 949, 949f clinical manifestations of, 949 life cycle of, 949 pneumonic, 438, 736, 800, 949 septicemic, 438, 736 Yersinia spp and, 438-439 Plaque, dental, 759 Plaques, 806 Plasma membrane (cell membrane), 7, 8f, 10 Plasmid profile analysis, 246 Plasmid-mediated quinolone resistance (PMAR), 270 Plasmids, 246 overview of, 20, 270 transformation and, 20, 21f Plasmodium falciparum, 650-651, 653t, 654-656, 655f Plasmodium knowlesi, 650 Plasmodium marlariae, 650, 653t, 654, 655f Plasmodium ovale, 650, 653t, 654, 655f Plasmodium spp clinical infections and, 651 comparisons of, 653t laboratory diagnosis of, 653-656 life cycles of, 651-653, 653f 1068 INDEX Plasmodium spp (Continued) overview of, 650-656 treatment for infections of, 651 Plasmodium vivax, 650, 653t, 654, 654f Plate reading, 170 See also Colony morphology Pleocytosis, 856 Pleomorphic gram-positive bacilli, 352 Pleomorphic shape, 10, 11f Plesiomonas spp clinical manifestations of, 467 epidemiology of, 466-467 gastroenteritis and, 467 key features of, 458t laboratory diagnosis of, 467 overview of, 466-468 susceptibility testing and, 467-468 Pleurisy, 566 Pleuropneumonia-like organism (PPLO), 554 PMAR See Plasmid-mediated quinolone resistance PMNs See Polymorphonuclear neutrophils Pneumococcal pneumonia, 142f Pneumocystis jirovecii, 163f, 224, 224f, 614, 614f, 924, 925f Pneumocystis spp., 613-614, 614f Pneumocytes, 614 Pneumonia, 385t, 545, 767, 785 See also Aspiration pneumonia; Community acquired pneumonia; Health care-associated pneumonia acute, 785-791 Aspergillus spp and, 792-793 bacteremia and, 873 blastomycosis and, 793 chronic, 792-796 Cryptococcus spp and, 792-793 empyema complications with, 337 fungi and, 792-793 Legionella spp and, 410 Mycobacterium spp and chronic, 793-794, 794f Mycoplasma pneumoniae and, 554-555, 555f NTM and, 792 primary atypical, 554 Pseudomonas aeruginosa and, 481 Streptococcus pneumoniae and, 336-338, 337f tuberculosis and, 792-796 Pneumonic plague, 438, 736, 800, 949 Pneumonitis, 362 Pneumovirus spp., 712 p-nitrophenyl-β-D-galactopyranoside test (PNPG test), 185 PNPG test See p-nitrophenyl-β-D-galactopyranoside test Polar flagella, 9-10, 9f Polioviruses, 713 Polyclonal antibody, 200-201 Polymerase chain reaction (PCR), 18, 227, 572-575 components of, 232-234, 233t contamination prevention and, 234, 234f Corynebacterium spp and, 353 electrophoresis and, 235-236, 235f laboratory applications of, 240-241 mechanism of, 231-232, 232f multiplex, 231, 242, 242f Mycobacterium tuberculosis identification and, 586 nested, 231, 242 overview of, 231-242 product analysis of, 234-240 real-time, 234, 236-240, 237f Polymerase chain reaction (PCR) (Continued) repetitive palindromic extragenic elements, 246-248 reverse transcription, 231, 241-242, 706 Polymers, surface, 9-10, 9f Polymicrobial bacteremia, 870 Polymicrobial infections, 135, 150f definition of, 133 microscopic examination of, 156 Polymorphic fungi, 592 Polymorphonuclear neutrophils (PMNs), 36-37, 36f, 133-137, 757 Polyvinyl alcohol (PVA), 627 Pontiac fever, 410 Population analysis profile (PAP), 290-291 Population studies, 203 Porins, 263 Pork tapeworm, 671-673 Porphyrin test, 396-397, 397f Porphyromonas spp., 503, 523 Posaconazole (POSA), 622 Positive predictive value (PPV), 106-107, 892-893 Postanalytic activity, 94, 94t Postsplenectomy, 938-939 Postzone, 207 Potassium hydroxide (KOH), 595, 595f, 615, 617 Potassium nitrate assimilation, 621 Potato dextrose agar, 617-618 Pott disease, 566 Poxviridae See also specific types as bioterror agent, 743-745, 745t cowpox and, 702 monkeypox and, 702-703 overview of, 702-703 smallpox, 702-703, 703f PPD See Purified protein derivative PPE See Personal protective equipment PPEs See Parapneumonic effusions PPi See Pyrophosphate PPL See Phenotype planktonic PPLO See Pleuropneumonia-like organism PPNG See Penicillinase-producing Neisseria gonorrhoeae PPV See Positive predictive value PRAS media See Prereduced, anaerobically sterilized media Preanalytic activity, 94, 94t Precipitation assays, 204-205, 205f Precision, 105 Precysts, 614 Predictive value of tests, 106-107, 107t Pregnancy ectopic, 375 immunocompromised patients and, 940 UTIs and, 888 Prereduced, anaerobically sterilized media (PRAS media), 504, 506, 506f Preseptal cellulitis, 966 Preservatives, for specimens, 115, 627, 627t Presurgical skin disinfection, 70 Prevalence, 51, 106 Preventive maintenance program, 95, 96f Prevotella melaninogenica, 175 Prevotella spp., 503, 523 Primary amebic meningoencephalitis (PAM), 639, 861 Primary atypical pneumonia, 554 Primary bacteremia, 869-870 Primary cell cultures, 694 Primary inoculations, 119 tahir99 VRG Primary tuberculosis, 565 Primer-dimers, 233 Primers, 227-228, 231-233, 231t, 233t Prions, 61, 61f, 723 Pristinamycin, 256t-257t Probe, 227-228 See also Molecular probes Probe-mediated stains, 129 ProbeTec, 544 Probe-Tec ET Legionella assay, 393 Problem-action form, 102, 102t Procalcitonin, 881 Process monitors, 102 Proctitis, 541, 919, 929-930 Proficiency testing, 100 Proglottids, 627, 667 Project BioShield, 748 Prokaryotes cell appendages of, 9-10, 9f cell structure of, 7-10, 8f-9f cell wall of, 7-9, 9f classification by, 6-7 eukaryotes compared to, 4, 4t, 5f, 7-10 ribosomes of, 4t, Promastigote stage, 645-646 Propionibacterium acnes, 24-25 Propionibacterium spp., 24-25, 148f, 521, 521f Propionic acid fermentation, 16 Prostatic secretions, 897 Prostatitis, 885b, 891 Prosthetic valve infection, 385t Proteases, 514-515 Protective antigen (PA), 365-366 Proteeae tribe, 431, 432t Protein A, 31, 316-317 Protein expression, 18-19 Protein synthesis inhibitors, 256t-257t Proteolytic enzymes, 514-515 Proteomics, 248-251 Proteus mirabilis, 24 Proteus spp., 173-174, 174f, 431-432, 432f, 432t Prot-fix, 627 Protozoa blood and tissue flagellates, 645-650, 646f central nervous system infections and, 861 ciliates, 641 intestinal amebae, 632 life cycle of, 632-639, 633f nonpathogenic intestinal flagellates, 645, 645f pathogenic intestinal and urogenital flagellates, 641-645, 642f, 643t, 644f-645f tissue amebae, 639-641, 639t Providencia spp., 432, 432t Prozone, 207 Prusiner, Stanley B., 723 PS23 vaccine, 337 Pseudallescheria boydii, 599-600, 600f, 813-814, 813t Pseudobacteremia, 869 Pseudocatalase reaction, 340 Pseudo-germ tubes, 620, 621f Pseudohyphae, 613, 621, 621f Pseudomembranous colitis, 502 Pseudomonads, 478, 483 Pseudomonal infectious disease, 154f Pseudomonas aeruginosa, 154f, 790 bacteremia and, 481 identifying characteristics of, 481-482, 482f overview of, 481-482, 481f pigment production and, 175, 175f Pseudomonas aeruginosa (Continued) pneumonia and, 481 resistance and, 263 scum produced by, 176, 177f treatment for infections of, 482 virulence factors of, 481 Pseudomonas alcaligene, 483-484 Pseudomonas fluorescens, 483 Pseudomonas luteola, 484 Pseudomonas mendocina, 483 Pseudomonas oryzihabitans, 484, 484f Pseudomonas pseudoalcaligenes, 483-484 Pseudomonas putida, 483 Pseudomonas spp., 478, 817 Pseudomonas stutzeri, 483, 483f Pseudopodia, Psittacosis, 547 Psychrobacter immobilis, 488 Psychrobacter spp., 487-488 Psychrophiles, 14 PT See Pertussis toxin Public health settings, 48, 51, 51t Puffballs, 176, 177f Pulmonary anthrax, 946 Pulsed-field gel electrophoresis (PGFE), 54-55, 246-247, 247f Purified protein derivative (PPD), 565, 794 Purines, 18, 18f Purpura, 807 Purpura fulminans, 812, 829 Purulence, 127, 135, 137 Pustules, 806 Putrescine, 187 PVA See Polyvinyl alcohol PVL See Panton-Valentine leukocidin Pyelonephritis, 885, 885b, 895, 897 PYG See Peptone-yeast extract-glucose PyloriTek test, 471 Pyocyanin, 481-482 Pyodermal infections, 332, 809-812, 809t Pyogenic streptococci See Streptococcus pyogenes Pyoverdin, 481-482 PYR hydrolysis test See Pyrrolidonyl-αnaphthylamide hydrolysis test Pyrazinamide (PZA), 567, 585, 585f Pyrimidines, 18, 18f Pyrophosphate (PPi), 250 Pyrosequencing, 248, 250 Pyrrolidonyl arylamidase test, 322 Pyrrolidonyl-α-naphthylamide hydrolysis test (PYR hydrolysis test), 193t, 333, 345, 345f Pyruvate, 15-17, 15f, 17f Pyuria, 892, 895 PZA See Pyrazinamide Q Q fever (query fever), 550-551, 742 QBC See Quantitative Buffy Coat QC See Quality control Qiagen, 906t qnr genes, 267, 270 Q-probes, 103 QRDR See Quinolone resistance-determining region QS See Quorum sensing Quality control (QC), 94 See also Performance improvement antimicrobial susceptibility and, 99-100, 99t for equipment, 95, 96t INDEX Quality control (QC) (Continued) general guidelines for establishing, 94-100 manual for, 100 media and, 95-98, 97f-98f, 98t in microscopic observations, 138 parasites and laboratory, 631-632 personnel competency and, 100, 101f reagents and, 98, 99f stock cultures and, 100 for susceptibility testing, 299-301, 299t-302t temperature and, 94-95 thermometer calibration and, 95, 95b Quantitative Buffy Coat (QBC), 631, 648-649, 653-654 Quantitative isolation, 120-121, 121f Quaternary ammonium compounds, 66 Query fever See Q fever Quinolone resistance-determining region (QRDR), 267 Quinolones, 260-261, 267 Quinupristin, 256t-257t, 262 Quorum sensing (QS), 755 R Rabbit, 738 Rabies, 692, 716-717 Radial immunodiffusion, 205, 205f Radiation methods, disinfection, sterilization and, 63 Radio-immunoassay (RIA), 219, 310-311 RADTs See Rapid antigen detection tests Ragpicker’s disease, 366, 732 Rahnella aquatilis, 441 Ralstonia pickettii, 492 Random amplified polymorphic DNA (RAPD), 246-247 RAPD See Random amplified polymorphic DNA Rapid antigen detection tests (RADTs), 772 RapID CB Plus system, 356 Rapid hippurate hydrolysis test, 193t Rapid method, 192 Rapid modified Wright-Giemsa stain, 129, 132b Rapid plasma reagin tests (RPR tests), 220, 220f, 535, 916-917 RapID STR panel, 344, 344f Rapid susceptibility testing, 302-303 R.A.P.I.D system, 237 Rapid tests, 191-196, 193f, 193t-194t, 195f-196f, 512-515 Rapid urease test, 193t RapID-ANA II, 517, 518f Rapid-Cycler system, 237 RASE See Recognized as safe and effective Rashes, 806 Rat bite fever, 819-820 Rats, 949, 949f Rayon, 691 RB See Reticulate body RBCs See Red blood cells RD cells See Rhabdomyosarcoma cells Reactivation tuberculosis, 565-566 Reagents, QC and, 98, 99f Reagin antibodies, 205 Reagin screen test (RST), 916-917 Real-time PCR, 234, 236-240, 237f Recognized as safe and effective (RASE), 68 Recombination, 20 Recrudescent typhus See Brill-Zinsser disease Red blood cells (RBCs), 330, 629-630, 652, 654-656 Reemerging pathogens, 57, 57b tahir99 VRG 1069 Reference laboratories, 90 Regan-Lowe transport medium, 417 Reiter syndrome, 541 Relapsing fever, 530, 532 Relative light units (RLUs), 230 Relenza, 711 Renal transplantation, 888 Reoviridae, 704, 841 Repetitive palindromic extragenic elements PCR, 246-248 Replication, 18-19, 260-261 Reporters, 251 Reporting, 123, 124b of laboratories, 56, 56t microscopic observations and, 137, 138b susceptibility testing results of, 277-278, 278b Requisitions, 114-115 Resident microbial flora, 24, 68-69 Resistance See also Host resistance factors; Susceptibility testing acquired, 262, 265-270 bacteremia and, 871 biofilms and, 264 dissemination of, 270-271 efflux pumps and, 264-267, 264f Enterococcus spp and, 340-341 enzymatic inactivation and, 265, 265f, 266t, 268-270 enzymatic target site alteration and, 267-268 impermeability and, 263 induced, 264 innate, 264 intrinsic, 263-265 macrolide, 256t-257t, 261, 267, 325 mechanisms of, 262-270 molecular probes for identifying determinants of, 310 Neisseria gonorrhoeae and, 381 new target acquisition and, 268 origins of, 262-263 overview of, 255 Pseudomonas aeruginosa and, 263 Streptococcus pneumoniae and, 338 target site modification and, 267-268 Resistance nodulation cell division superfamily (RND), 264-265 Resistant organisms, 279, 280t Respiration, 15 Respiratory burst, 37 Respiratory diphtheriae, 351-352 Respiratory specimens, 615-616 Respiratory syncytial virus (RSV), 691, 693, 712, 775 Respiratory tract anaerobes and, 498 anatomy of, 766, 767f cleansing mechanisms of, 35 flora of, 26, 26b normal biota of, 766-768, 767b Respiratory tract infections See also specific infections age and, 768-769, 785t Aspergillus spp and, 799 barriers to, 766 bioterror agents and, 800 empiric antimicrobial therapy and, 769 general concepts of, 766-768 hemadsorption test and, 695 host defense evasion and, 770 host risk factors and, 768-769 in immunocompromised patients, 796-800, 796t 1070 INDEX Respiratory tract infections (Continued) infection-induced airway obstruction and, 769 lower, 779-796, 780t-781t opportunistic pathogens and, 796 pathogenic microorganisms distinguished from indigenous microbial flora in, 767-768, 768b reduced clearance of secretions and, 769 seasonal and community trends in, 769 toxin elaboration and, 770 upper, 770-779, 771t viral, 799 virulence factors and, 769-770 Respiratory viral infections, 222 Response plans, emergency, 57 Restriction enzymes, 21, 229, 246 Reticulate body (RB), 539 Retina infections, 968-970 Retinitis, 968-969, 969f Retroorbital abscesses, 774 Retroviridae, 714-716, 714f, 715b-716b, 716f Reveal G2 Rapid HIV-1 Antibody Test, 715 Reverse passive agglutination, 205-206 Reverse transcription-PCR, 231, 241-242, 706 RF See Rheumatoid factor Rhabditiform larva, 674t, 677, 678f, 680f Rhabdomyosarcoma cells (RD cells), 694-695 Rhabdoviridae, 716-717 Rhadinovirus spp., 701 Rheumatic fever, 333, 772 Rheumatoid factor (RF), 201 Rhinocerebral zygomycosis, 607 Rhinocladiella aquaspersa, 599t Rhinoscleroma, 429 Rhinosporidiosis, 813t, 815 Rhinosporidium seeberi, 815 Rhinoviruses, 714 Rhizoids, 173-174, 173f, 607 Rhizopus spp., 591f, 607, 607f Rhodococcus equi., 148f Rhodococcus spp., 364t, 365 Rhodotorula spp., 613 RIA See Radio-immunoassay Ribavirin, 712 Ribonuclease H (RNase H), 242-243 Ribonucleic acid (RNA) anatomy of, 18, 18f double-stranded, 5, 704 Northern blotting for, 229-230 single-stranded, 5, 704-717 viruses and, 5-6 Ribosomal RNA (rRNA), 261, 468, 518 Ribosomes of eukaryotes, 10 of prokaryotes, 4t, Ribotyping, 246 Rice grains, growth on, 620 Ricin, 728, 747 Ricin communis, 747 Rickettsia prowazekii, 547 Rickettsia spp., 547-549, 548f-549f comparative properties of, 538t dermatologic manifestations of, 819 general characteristics of, 951 laboratory diagnosis of, 549 overview of, 538, 951-952 spotted fever group, 951 transitional group of, 549 typhus group of, 548-549, 549f, 951-952 Rickettsiae akari, 549 Rickettsiae conorii, 548 Rickettsiae prowazekii, 549, 549f Rickettsiae typhi, 548-549 Rickettsialpox, 549, 951 Rifampin, 256t-257t, 261, 761-762 Rifamycins, 256t-257t, 261 Rifapentine, 256t-257t Rift Valley fever virus, 705, 746 Rimantadine, 711 Ringworm See Dermatophytosis Risk groups, 76, 76b Risus sardonicus, 501 Ritter disease, 317 River blindness, 827 RLUs See Relative light units RMSF See Rocky Mountain spotted fever RNA See Ribonucleic acid RNase H See Ribonuclease H RND See Resistance nodulation cell division superfamily Roche Amplicor, 544 Roche Molecular Diagnostics, 906t Rocky Mountain spotted fever (RMSF), 547-548, 548f, 819, 862, 951 Rodents, 735 Roseolovirus spp., 701 Roseomonas spp., 491, 492f Rotaviruses, 704, 841 Rothia dentocariosa, 356 Rotor Gene system, 237 Rough form, 173-174, 173f Roundworms, 673-676, 674t, 675f-677f, 679-684, 681f RPR tests See Rapid plasma reagin tests rRNA See Ribosomal RNA RST See Reagin screen test RSV See Respiratory syncytial virus Rubella, 220, 717, 822 Rubeola, 822 Rubivirus spp., 717 Rubulavirus spp., 711 S Sabin-Feldman dye test, 659 Sabouraud dextrose agar, 491, 617-618, 975 SAF See Sodium acetate-acetic acid-formalin Safety See Laboratory safety Safety data sheets (SDS), 81, 82f-88f, 88b Saline, 691 Salmonella spp antigens and, 434, 434f bacteremia and, 436 as bioterror agent, 728 classification of, 433-434, 434t clinical infections from, 434-436 diarrhea and, 842, 849-852 enteric fever and, 842 food poisoning and, 842 gastroenteritis and, 435, 842 laboratory diagnosis of, 849-852, 851f overview of, 433-436 serologic testing and, 452-453 virulence factors of, 434 Salmonellosis, 434-435 Salpingitis, 541 Salt tolerance test, 345-346 Salts, concentration of, 228 Sample preparation, 127-129, 127f-129f, 127t tahir99 VRG Sanger, Frederick, 249 Sapoviruses, 706 Saprobes, 590, 606 Saprophytes, 606 septate and hyaline, 608-610 septate and phaeoid, 610-611 Sarcoptes scabiei, 828, 829f SARS See Severe acute respiratory syndrome SARS-associated coronavirus (SARS-CoV), 706-707 SARS-CoV See SARS-associated coronavirus SAS See Sodium amylosulfate Satellitism, 392 SBA See Sheep blood agar SBT See Serum bactericidal test Scabies, 828, 829f Scalded skin syndrome (SSS), 316, 318 Scarlet fever, 332, 822, 830-831 SCB See StrepB Carrot Broth SCCmec See Staphylococcal cassette chromosome mec Schaeffer-Fulton stain, Schistosoma haematobium, 629, 664, 666, 667f Schistosoma japonicum, 664, 666, 667f Schistosoma mansoni, 667, 668f Schistosoma spp., 666-667, 667f Schistosomes, 663, 826 Schistosomiasis, 666-667 Schizogony, 651, 652f Schizont, 651-653 Schüffner’s stippling, 654, 655f Sclera, 966 Scleritis, 966 Scolex, 667 Scombroid, 846 Scopulariopsis spp., 609, 610f Scorpion primer, 237, 240, 240f Scotochromogens, 568, 570 Scrapie, 723 Screening, 108-109 Scum, 176, 177f SDS See Safety data sheets; Sodium dodecyl sulfate Seasonal trends, in respiratory tract infections, 769 SEB See Staphylococcal enterotoxin B Secondary bacteremia, 869-870 Secondary immune responses, 200-201, 201f Secretions, 769 Sedimentation, 628 Select biological agents, 404, 730, 730b Selective media, 13, 119 Selective reporting, 277t, 278, 278b Semmelweis, Ignatz, 64 SEN virus, 717-718, 723 Sensititre Automated Incubator Reader, 295, 295f Sensititre System, 194t, 195 Sensitivity, 105-106 Sentinel laboratories, 90 Sepsis See also Bacteremia biomarkers for, 881, 881b definition of, 869, 869t direct antigen detection assay for, 222-223 mortality and, 870 treatment for, 882 Septate saprophytes, 608-611 Sept-Chek AFB, 581, 581f September 11th attacks, 748 Septic shock, 869-870, 869t Septicemia Aeromonas spp and, 464 definition of, 869 Erysipelothrix rhusiopathiae and, 358-359 mortality and, 870 neutropenia and, 936 Vibrio vulnificus and, 460 Septicemic plague, 438, 736 Septi-Chek, 615 Sequencing, 249-250, 249f Sero-conversion, 201 Serologic testing agglutination assays and, 205-210, 206f-210f antibodies in, 200-204, 200t, 201f-203f antigen detection and, 204, 204f antigens and, 200 of Bordetella spp., 418-419 Campylobacter spp and, 471-472 Chlamydia spp detection with, 545t Chlamydia trachomatis detection with, 544-545, 545t commercial, 201 for congenital infections, 204 EBV and, 699-700, 700f, 700t false-negative, 201-203, 203f false-positive, 199, 202-203, 203f, 207 of fungal infections, 221 for HIV, 221 immune status testing, 203-204 labeled immunoassays and, 211-219 Legionella spp and, 414 Mycobacterium tuberculosis and, 587-588 Mycoplasma spp and, 560, 561t neutralization assays and, 210-211 population studies and, 203 precipitation assays, 204-205, 205f principles of, 204-219 Salmonella spp and, 452-453 Shigella spp and, 453 for streptococcus pyogenes, 220 of syphilis, 219-220, 220f, 535 Ureaplasma spp and, 560, 561t Vibrio spp and, 461 of viruses, 220-221, 695-696 Serology, 54, 199 Serotyping, 182 Serratia marcescens, 175, 176f, 430-431, 431f Serratia spp., 430-431, 431f Serum bactericidal test (SBT), 306t, 310 Sessile phenotype, 753 Severe acute respiratory syndrome (SARS), 689 coronaviridae and, 706-707 overview of, 784 Sexual reproduction, 592, 592f, 650-651, 652f Sexually transmitted infections (STIs), 51, 375, 391, 902-903, 902t-903t See also specific infections Shear stress, 754 Sheather sugar flotation method, 628-629 Shedding, 696 Sheep blood agar (SBA), 460, 482, 482f, 518-519 Shell vial culture, centrifugation-enhanced, 695 Sherlock Microbial Identification System, 194t, 195-196, 196f Shewanella spp., 492 Shiga toxin (Stx), 426-427 INDEX Shigella spp., 30 antigens and, 436t, 437 clinical infections with, 437 diarrhea and, 437, 842, 851, 851f laboratory diagnosis of, 851, 851f overview of, 436-437, 437f serologic testing and, 453 Shigellosis, 437 Shingles See Zoster Shipping infectious substances and, 90 of specimens, 116, 117f Shunt infections, 858 Sigmoidoscopy, 629 Signage, for laboratory safety, 81-88, 88f Signal amplification methods, 243-245 Silent genes, 18-19 Silent mutations, 20 Silica gel, 509 SIM medium See Sulfide-indole-motility medium Simple stains, 129 Sin Nombre virus, 705-706, 705t Single-stranded DNA (ssDNA), 5, 703-704 Single-stranded RNA (ssRNA), 5, 704-717 Sinusitis abscesses and, 774 acute, 773 causes of, 773 clinical manifestations of, 773-774, 774f complications of, 774 epidemiology of, 773 laboratory diagnosis of, 774-775 overview of, 771t, 773-775 pathogenesis of, 773 treatment of, 775 SIRS See Systemic inflammatory response syndrome 16S ribosomal RNA gene sequencing, 518 Skin anaerobes and, 498 anatomy of, 805, 806f bacteremia and, 873 as barrier against infection, 34-35 cancer patients and, 936 Erysipelothrix rhusiopathiae and, 358-359 FDA regulations on antiseptics and, 68-70, 69t flora of, 25, 25b, 805 microorganisms infecting or entering via, 34-35, 34t mycoses and, 593-594, 593f mycotic sample collection of, 615 patient preoperative preparation of, 68, 69t, 70 SSS and, 316, 318 Staphylococcus aureus infections with, 317-318 Skin and soft tissue infections See also specific disorders bite infections, 812 CPE and, 832 diabetic foot infections, 812, 812f fungi causing, 815 immune-mediated cutaneous disease and, 829-830 laboratory diagnosis and, 831-832 localized, 805-817, 806b-807b, 807t necrotizing, 813, 813f parasites and, 826-828 smears for, 831 SSSS and, 830 swabs for, 831 systemic bacterial infection, 817-821 systemic fungal infections, 821-822 tahir99 VRG 1071 Skin and soft tissue infections (Continued) toxin-mediated cutaneous disease and, 830-831 viral infections and, 822-826 Skin testing, 587 Skipped wells, 282 SLE See St Louis encephalitis Sleeping sickness, 647, 648f Slide cultures, 619 SLO See Streptolysin O Small colony variants, 315-316 Small intestine, 26-27, 27b, 836-837 Small multidrug resistance family (SMR), 264 Smallpox, 702-703, 703f, 743-745, 743f-744f, 745t SmartCycler system, 237, 238f, 241 Smears blood, 630 examining various areas of, 135 microscopic examination of, 140, 142 ocular infections and, 972t Papanicolaou, 692 permanently stained, 629 for skin and soft tissue infections, 831 from swabs, 127, 127f from thick, granular, or mucoid materials, 127-128, 128f from thick liquids or semisolids, 127, 128f from thin fluids, 128-129, 129f Tzanck, 692 Smooth form, 173-174, 173f SMR See Small multidrug resistance family SMZ See Sulfamethoxazole Sodium acetate-acetic acid-formalin (SAF), 627, 627t Sodium amylosulfate (SAS), 877 Sodium chloride tolerance, 586 Sodium dodecyl sulfate (SDS), 218, 513-514 Sodium hydroxide, 577-578 Sodium hypochlorite, 575 Sodium polyanethol sulfonate (SPS), 116, 875 Soft chancre See Chancroid Solid support hybridization, 229 Solid-phase immunosorbent assays (SPIAs), 213, 213f Southern blotting, 229, 229f, 246-247 Spanish flu, 710 Sparganosis, 673 Spaulding, E H., 62 Special potency antimicrobial disks, 513, 514f, 515t Species, Specific immunity See Adaptive immunity Specificity, 105-106, 200 Specimens anaerobe acceptable, 504t anaerobe unacceptable, 504b anaerobes selection, collection, transport, and processing of, 503-510, 504b, 504t-505t, 507t anticoagulants and, 116 bacteremia and, 874-876 biopsy, 630 Brucella spp and, 740, 740f catheterized collection of, 893, 897 collection of, 112-115, 113t communication of findings with, 123, 124b cutaneous anthrax and, 734 digestion and decontamination agents for, 577-578 holding or transport media and, 116 incubation of, 121 isolation techniques and, 119-121, 121f, 122t labeling of, 114-115 laboratory safety and processing, 76 1072 INDEX Specimens (Continued) macroscopic observations of, 118 microscopic observations of, 118-119 Mycobacterium spp and, 576-578, 576b mycology laboratory and, 614-617, 615t, 616f nonroutine, 123 ocular infections and, 971, 971f patient-collected, 112-114 preparation of, 119 preservatives for, 115, 627, 627t primary inoculation of, 119 prioritization of, 117-118, 117t receipt and processing of, 117-121 rejection of, 118, 896 requisitions and, 114-115 safety and, 115 shipping of, 116, 117f sputum for, 113t, 114 Staphylococcus spp collection and handling of, 319 stool samples for, 113t, 114 storage of, 115, 115t suprapubic aspiration and, 893-894, 897 from urine, 113t, 114 UTIs and, 893-894 viral infections and, 691 voided midstream collection of, 893 wounds and collection of, 112 Yersinia pestis and, 736-737 Spectinomycin, 261 Sphingobacterium spp., 490-491 Sphingomonas spp., 492, 493f SPIAs See Solid-phase immunosorbent assays Spills, chemical, 81 Spirochetes Borrelia spp and, 531-533 central nervous system infections and, 860 Leptospira spp and, 530-531, 530f overview of, 530 Treponema spp and, 533-536 virulence factors of, 530, 532 Spirochetes shape, 10, 11f Sporangiophores, 592-593, 593f, 607-608 Sporangiospores, 592-593, 593f Spores, 7, 662-663, 663f, 966 Sporicidal activity, 62 Sporoblasts, 661 Sporocysts, 661 Sporogony, 651, 652f, 653 Sporothrix schenckii, 601, 602f Sporotrichosis, 815-816, 816f Sporozoites, 651 Spot indole test, 193t, 513, 524 Spot tests, 220 Spotted fever, 547-548, 548f Spotted fever group, Rickettsia spp., 951 SPS See Sodium polyanethol sulfonate Sputum, 113t, 114, 136, 546, 576, 629-630, 666 ssDNA See Single-stranded DNA SSI See Surgical site infection ssRNA See Single-stranded RNA SSS See Scalded skin syndrome SSSS See Staphylococcal scalded skin syndrome St Louis encephalitis (SLE), 709, 862-863 Staining See also specific stains of acid-fast cell walls, 8-9 of capsules, microscopic observations and, 129, 130b-132b, 130t Standard precautions, 57, 73, 279 Staphaurex test, 323-324 Staphylocoagulase, 321-322 Staphylococcal cassette chromosome mec (SCCmec), 268 Staphylococcal coagglutination, 208-209, 208f, 210t Staphylococcal disease, 144f Staphylococcal enterotoxin B (SEB), 747 Staphylococcal enterotoxins, 747 Staphylococcal leukocidin See Panton-Valentine leukocidin Staphylococcal scalded skin syndrome (SSSS), 830 Staphylococcus aureus See also Methicillin-resistant Staphylococcus aureus clindamycin resistance in, 291, 291f cultural characteristics of, 320 cytolytic toxins and, 316-317 enterotoxins and, 316-317 enzymes and, 317 epidemiology of, 317 exfoliative toxins and, 316-317 food poisoning and, 318-319 infections caused by, 317-319 overview of, 316-319 oxacillin resistance in, 289-290 protein A and, 316-317 significance of, 316 skin and wound infections with, 317-318 TSST-1 and, 317 vancomycin resistance in, 289-290 virulence factors of, 316-317 Staphylococcus epidermidis, 316, 316t, 319, 890, 891t Staphylococcus hyicus, 316, 316t Staphylococcus intermedius, 316, 316t Staphylococcus lugdunensis, 319 Staphylococcus saprophyticus, 316, 316t, 319, 890, 891t Staphylococcus sciuri, 316, 316t Staphylococcus simulans, 316, 316t Staphylococcus spp., 127 clinically significant species of, 316-319, 316t differentiation of, 180f general characteristics of, 315-316, 315t-316t isolation and identification of, 320-324, 320f-323f, 321t-322t laboratory diagnosis and, 319-324 Micrococcus spp compared to, 315, 315t microscopic examination of, 319-320, 320f specimen collection and handling for, 319 susceptibility testing of, 324-325 Steer’s replicator, 282f Stenotrophomonas maltophilia, 485 Sterility, 375 Sterilization See also Disinfection biofilms and, 62 chemical methods of, 64, 64t contact time and, 62 disinfection compared to, 60 factors influencing degree of killing in, 60-62, 61f filtration methods and, 63 heat methods and, 62-63, 63t organic material and, 61-62 pH and, 62 physical methods of, 62-63, 63t radiation methods and, 63 temperature and, 62 STIs See Sexually transmitted infections Stock cultures, 100 Stock solutions, antimicrobial, 279-280 tahir99 VRG Stomach, flora of, 26-27, 27b Stool samples collection, handling, transportation of, 626-629 Enterobacteriaceae pathogens screened for in, 442-452, 442t, 443f, 452f macroscopic examination of, 627, 628f microscopic observation of, 628-629 Mycobacterium spp and, 577 parasites and, 626-629, 627t, 628f preservation of, 627, 627t specimen collection from, 113t, 114 Storage chemical, 81 of specimens, 115, 115t Strain typing and identification, 246-248 Strains, Strawberry cervix, 909, 910f Streamers, 176, 177f, 754 Strep throat, 332 StrepB Carrot Broth (SCB), 336 Streptococcal disease, 144f Streptococcal toxic shock syndrome (STSS), 332-333 Streptococcus agalactiae, 179f, 331t, 333-336, 334t, 335f, 857 Streptococcus anginosus, 338-339, 339t Streptococcus bovis, 331t, 338, 339t Streptococcus dysgalactiae, 331t Streptococcus equinus, 338 Streptococcus faecalis, 331t Streptococcus faecium, 331t Streptococcus mitis, 338, 339t Streptococcus mutans, 338, 339t Streptococcus pneumoniae, 150f, 158f, 331t bacterial meningitis and, 857, 857f colony morphology of, 177, 178f overview of, 336-338, 337f penicillins for, 285, 347 pneumonia and, 336-338, 337f resistance and, 338 susceptibility testing and, 285-288, 287f vaccines for, 337 Streptococcus pyogenes, 179f, 331t antigenic structure of, 331 clinical infections from, 332-333 exotoxins of, 332 laboratory diagnosis of, 333 pharyngitis and, 332 serologic testing for, 220 virulence factors of, 331-332 Streptococcus salivarius, 338, 339t Streptococcus spp antigens and, 331, 333, 336 biochemical identification of, 334t, 343-346, 343f-344f cell wall structure of, 329-330, 330f clinically significant, 330-342, 331t differentiation of, 177, 178f-180f general characteristics of, 329-330, 329f hemolysis and, 330, 330f, 330t, 342, 343f immunoassays and, 346-347, 347f laboratory diagnosis of, 342-348 Lancefield classification system and, 331t, 343 nucleic acid probe assays and, 347 physiologic characteristics of, 342-343 predictive values and, 107 susceptibility testing and, 285-288, 347-348 Streptococcus-like organisms, 341-342 Streptogramins, 256t-257t, 262, 269 Streptolysin O (SLO), 331-332 Streptolysin S, 331-332 Streptomyces spp., 364, 364t Streptomycin, 256t-257t, 567 Streptozyme test, 209, 209f Stridor, 777 Strongyloides stercoralis, 164f, 629-630 cancer patients and, 937 dermatologic manifestations of, 826-827 eggs and larvae of, 674t lack of growth in cultures of, 136 life cycle of, 679, 680f overview of, 678-679, 680f Strongyloidiasis, 849 STSS See Streptococcal toxic shock syndrome Stx See Shiga toxin Subcutaneous, 805, 806f Subcutaneous phaeohyphomycosis, 600-601, 601b, 601f, 814-815 Suboptimal specimens, 118 Substrata, 754 Subterminal spores, 500, 500f Sulcus, 759 Sulfamethoxazole (SMZ), 256t-257t, 260, 333 Sulfide-indole-motility medium (SIM medium), 190 Sulfur granules, 362, 363f Superficial candidiasis, 807-808 Superoxide anion, 497 Superoxide dismutase, 497 Suppurative lymph nodes, 394 Suprapubic aspiration, 893-894, 897 Sure-Vue Mono test kit, 209f Surface cultures, 55-56 Surface polymers, 9-10, 9f Surgical hand scrub, 68-70, 69t Surgical site infection (SSI), 48-49, 49t Surveillance, infection control and, 49-51, 49t Susceptibility testing Aeromonas spp and, 466 of agents of bioterrorism, 289 anaerobes and, 289, 525-526, 526t antifungal, 622-623 automated methods for, 293-297, 302 bacitracin, 344-345, 345f battery selection for, 277 of biofilms, 303 body site in, 276 Bordetella spp and, 419 Campylobacter spp and, 472 challenges with, 302-303 clindamycin resistance in Staphylococcus aureus and, 291, 291f dilutions and, 279-282, 280t-281t, 285, 286t-287t disk diffusion testing and, 282-285, 283f-285f, 286t-287t, 300t Enterococcus spp and, 291-292, 292t, 347-348 ESBLs and, 292-293, 292f Etest and, 289, 296-297, 296f fastidious organisms and, 285-289 Haemophilus influenzae and, 288, 397 Haemophilus parainfluenzae and, 288 Helicobacter pylori and, 288-289 host status in, 276 inoculum preparation and standardization for, 278-279, 279f-280f KPCs and, 293 Legionella spp and, 414 MAC and, 568 INDEX Susceptibility testing (Continued) MBC test and, 306-308, 306t, 307f McFarland turbidity standards and, 278-279 method selection for, 301-302 MRSA and, 289-290, 324-325 of Mycobacterium tuberculosis, 586-587 Mycoplasma spp and, 560-561 Neisseria gonorrhoeae, Neisseria meningitidis and, 288 novobiocin, 322-323, 323f optochin, 346, 346f oxacillin and, 289-290, 290f penicillins and, 285-288 Plesiomonas spp and, 467-468 presence of other bacteria and quality of specimen in, 276 QC for, 299-301, 299t-302t rapid, 302-303 reasons and indications for, 275-276 reporting results of, 277-278, 278b SBT and, 306t, 310 selection of agents for, 276-278, 277t, 278b Staphylococcus spp and, 324-325 Streptococcus pneumoniae and, 285-288, 287f Streptococcus spp and, 285-288, 347-348 synergy tests and, 306t, 308, 309f time-kill assays and, 306t, 308 Ureaplasma spp and, 560-561 UTI and, 899 vancomycin resistance in Staphylococcus aureus and, 289-290, 325 Vibrio spp and, 461-463 in vitro result interpretation and, 297 Susceptible organisms, 279, 280t Svedberg, Theodor, Svedberg units, Swabs, 112, 504, 546 flocked, 710-711 for skin and soft tissue infections, 831 smears from, 127, 127f Swarming, 173-174, 174f Swimmer’s itch See Cercarial dermatitis Swine flu See H1N1 influenza SYBR Green, 235, 237, 240 Sycosis barbae, 811 Symbionts, 24 Symbiosis, 24 Synanamorphs, 592 Syncephalastrum spp., 607-608, 607f Syncytia, 695 Synergism, 308, 309f Synergy tests, 306t, 308, 309f Syphilis, 530, 533 clinical manifestations of, 915-916, 915f-916f congenital, 534, 916 endemic, 533, 535 epidemiology of, 914-915, 915f laboratory diagnosis of, 916-917 latent, 916 neuro-, 534 overview of, 534, 914-917 primary stage of, 534 secondary stage of, 534 serologic testing of, 219-220, 220f, 535 tertiary stage of, 534 treatment for, 917 Systemic inflammatory response syndrome (SIRS), 869, 869t tahir99 VRG 1073 T T2H test, 586 Taches noire, 951 Tachypnea, 874 Tachyzoites, 657, 658f, 659 Taenia spp., 668-669, 670t, 671f-672f Tamiflu, 711 Tapeworms, 667-673, 669f-673f, 670t Taq DNA polymerase, 233-234, 233t TaqMan, 237-239, 238f Target, 227-228 Target site modification, 267-268 Targeted surveillance, 50 TAT See Turnaround time Tatumella ptyseos, 441 Taxa, Taxonomy, 6-7 TCA cycle See Tricarboxylic acid cycle TCBS agar See Thiosulfate citrate bile salt sucrose agar Tease mount, 619 Technical sensitivity, 105 Teicoplanin, 256t-257t Teleomorphs, 592 Telithromycin, 261-262 Tellurite reduction test, 585, 585f Temperate phage, 20 Temperature, 13-14, 228 disinfection, sterilization and, 62 Mycobacterium spp and, 583 QC and, 94-95 yeast identification and, 621 Template, 227-228, 233, 233t, 241 TEN See Toxic epidermal necrolysis Terminal spores, 500, 500f TestPack Strep A kit, 216f Tests See also specific tests analytic analysis of, 105 clinical analysis of, 105-106 efficiency of, 107-108 method selection and, 108-109, 108f operational analysis of, 106-108 validation of, 109 Tetanospasmin, 501 Tetanus, 500-501 Tetracyclines, 256t-257t, 261 Tetrahydrofolate (THF), 260, 260f Thayer-Martin medium, 377t Thermal cycler, 231, 233t, 234 Thermal injuries, 89 Thermometer calibration, 95, 95b Thermophiles, 14 Thermostable DNA polymerase, 233, 233t THF See Tetrahydrofolate Thiamine requirement, 619 Thioglycollate, 176, 177f, 507t Thiosulfate citrate bile salt sucrose agar (TCBS agar), 461 Threadworm See Strongyloides stercoralis Throat swabs, 546 Throat washings, 546 Ticks, 950 arboviruses and, 704 babesiosis and, 656-657 relapsing fever and, 532 RMSF and, 548, 548f Tigecycline, 761-762 1074 INDEX Time-kill assays, 306t, 308 Tinea capitis, 596-597, 808, 808f Tinea corporis, 808, 808f Tinea cruris, 808 Tinea nigra, 593-594, 596, 596f Tinea pedis, 597, 808 Tinea versicolor, 594-595, 808, 809f Tinidazole, 910 Tinsdale medium, 353f Tissue See also Skin and soft tissue infections amebae, 639-641, 639t culture, 694 infections with cestodes, 671-673 roundworms, 679-684, 681f specimens, 505, 615, 630 stains, 617, 618f TJC See The Joint Commission TMA See Transcription-mediated amplification TMP See Trimethoprim Tns See Transposons Tobramycin, 256t-257t Togaviridae, 717, 826 Tolerance, 42, 308 Toluidine red unheated serum test (TRUST), 916-917 Tonsillitis, 332 Topoisomerases, 260-261, 267 TORCH agents, 204 Total surveillance programs, 49-50 Toxic epidermal necrolysis (TEN), 318 Toxic megacolon, 838 Toxic shock syndrome (TSS), 316-318, 332-333, 830 Toxic shock syndrome toxin-1 (TSST-1), 317 Toxins See also Endotoxins; Exotoxins diphtheria, 350-353 pathogenesis and, 32-34 Vibrio spp and, 458, 459f virulence and, 32-34 Toxocara canis, 681 Toxocara cati, 681 Toxoplasma gondii, 164f, 937, 970, 970f life cycle of, 657-659, 658f overview of, 657-659, 657f Toxoplasmosis, 164f, 657 TP-PA test See Treponema pallidum-particulate agglutination test Trabulsiella guamensis, 441 Tracheal cytotoxin, 416 Trachoma, 540 Trailing growth, 281-282 Transcription, 18-19, 229-230, 261 Transcription-mediated amplification (TMA), 230-231, 243 Transduction, 20, 21f, 270 Transfer RNA (tRNA), 18-19, 261 Transformation, 20, 21f, 270 Transfusion-transmitted virus (TTV), 717-718, 723 Transgrow, 376 Transient bacteremia, 870 Transient flora, 24, 68 Transillumination, 172, 173f Translucent density, 174, 175f Transmissible spongiform encephalopathies (TSEs), 723 Transmission routes, 43-45, 43t, 44f Transmission-based precautions, 73 Transparent density, 174, 175f Transplant recipients, 698 Transport media, 13, 112, 115-116 Transposons (Tns), 270-271 Traveler’s diarrhea, 425-426, 642, 837, 846-848, 848f TREK Sensititre, 295, 295f Trematodes See Flukes Treponema pallidum, 219-220, 533-535, 533f, 818, 818f-819f, 914-915 Treponema pallidum-particulate agglutination test (TP-PA test), 535 Treponema spp., 533-536 Treponemal antibody tests, 916-917 Treponemal tests, 535 Triatomid bug, 649 Tribes, 421-422, 422t Tricarboxylic acid cycle (TCA cycle), 17, 17f Trichinella spiralis, 166f, 679-681, 681f Trichinosis, 166f, 966-967 Trichoderma spp., 610, 610f Trichomonas hominis, 643t, 645 Trichomonas vaginalis, 156f, 643t, 644-645 Trichomoniasis, 156f, 909-910, 909f-910f Trichophyton agars, 620 Trichophyton concentricum, 596 Trichophyton mentagrophytes, 598, 598f Trichophyton rubrum, 598, 598f Trichophyton schoenleinii, 596 Trichophyton spp., 596 Trichophyton tonsurans, 598 Trichosporon spp., 595, 595f Trichrome stain, 628-629 Trichuris trichiuria, 674t, 675-676, 676f Triclosan, 67 Trimethoprim (TMP), 256t-257t, 260 Trimethoprim-sulfamethoxazole, 661 Triple sugar iron agar (TSI), 183-185, 184f-185f, 184t, 442, 442t, 452f, 475-476 Trismus, 501 Trisodium phosphate, 578 tRNA See Transfer RNA Tropheryma whipplei spp., 364t, 365 Trophozoites, 614, 626, 639 True pathogens, 29 TRUST See Toluidine red unheated serum test Trypanosoma brucei gambiense, 647 Trypanosoma brucei rhodesiense, 647 Trypanosoma cruzi, 649-650, 650f Trypanosoma spp., 630, 647-649, 648f Trypanosomiasis, 647-649 Trypomastigote stage, 630, 645-649 Trypticase soy broth, 691 TSEs See Transmissible spongiform encephalopathies Tsetse fly, 648, 648f TSI See Triple sugar iron agar TSS See Toxic shock syndrome TSST-1 See Toxic shock syndrome toxin-1 T-strain mycoplasma, 559 See also Ureaplasma spp Tsukamurella spp., 364-365, 364t TTV See Transfusion-transmitted virus Tube coagulase test, 321-322, 322f Tube dilution MIC, 280 Tuberculosis, 147f chronic pneumonia and, 792-796 extensively drug-resistant, 567 extrapulmonary, 566 meningitis, 566, 860, 866 miliary, 566 multidrug-resistant, 567 NAATs and, 793 overview of, 564 tahir99 VRG Tuberculosis (Continued) primary, 565 reactivation, 565-566 treatment of, 567, 794-795 Tuberculosis verrucosa cutis (TVC), 817 Tularemia, 800 aerosols and, 727 cause of, 946-947 clinical manifestations of, 738, 738f, 947 dermatologic manifestations of, 820 diagnosis of, 820 epidemiology of, 947 overview of, 406, 731, 737-739, 946-947 Tumbling motility, 357-358 Turbidity, 176, 177f, 278-279 Turnaround time (TAT), 693 TVC See Tuberculosis verrucosa cutis Tween 80 hydrolysis, 584 Type B gastritis, 469 Typhoid fevers, 435-436, 436f Typhus group, of Rickettsiae spp., 548-549, 549f Tzanck smear, 692 U Ulcers, infectious causes of, 807 Ulocladium spp., 611, 612f Umbilicate elevation, 174, 174f Umbonate elevation, 174, 174f Umbrella motility, 357, 358f Uncoating, 690-691 Undulant fever, 740, 947 UNG See Uracil-N-glycosylase Unheated serum reagin (USR), 916-917 Uni-Gold Recombigen HIV test, 715 Universal precautions, 73 Unsuspected bacteremia, 869 Unweighted pair group of method with arithmetic averages, 249 Upper respiratory tract infections, 770-779, 771t Upper urinary tract infection (U-UTI), 885b, 892t Uracil-N-glycosylase (UNG), 234 Urban cycle, 709 Urea breath test, 471, 845f Ureaplasma parvum, 555 Ureaplasma spp clinical infections associated with, 555-556, 556t laboratory diagnosis of, 557-560 laboratory diagnosis of, result interpretation, 561, 562t overview of, 552-553 serologic testing and, 560, 561t susceptibility testing and, 560-561 Ureaplasma urealyticum, 553, 555-556, 556t, 561t Urease test anaerobe identification and, 513 fungi and, 619 Mycobacterium spp and, 585, 585f overview of, 190, 190f, 193t yeasts and, 621 Urethritis, 541 causes of, 891, 892t, 903 clinical manifestations of, 555, 904-905, 905f definition of, 885b epidemiology of, 903-904, 904f gonococcal, 928 laboratory diagnosis of, 905-906, 905f nongonococcal, 541, 555, 903 overview of, 903-907 treatment of, 906-907 Urinary tract anatomy of, 885, 885f system of, 886, 886t Urinary tract infection (UTI), 48-49, 49t, 277, 316 Aerococcus spp and, 341 age and, 886-888, 887f, 887t antibiograms and, 899 bacteremia and, 873 bladder catheterization and, 888 causes of, 889-892, 892t clinical signs and symptoms of, 888-889, 889f colony counts historical background and, 892-893 cultures and, 887f, 896-898, 899t Escherichia coli and, 424-425 fungi and, 891, 895-896 gram-negative bacilli and, 890 gram-positive bacilli and, 891 gram-positive cocci and, 890-891 laboratory diagnosis of, 892-894 microbial detection of, 894-897 overview of, 885 pathogenesis of, 889-892, 890b, 890t-891t pregnancy and, 888 Pseudomonas fluorescens, Pseudomonas putida and, 483 renal transplantation and, 888 specimen collection and, 893-894 susceptibility testing and, 899 terms and abbreviations used for, 885b Urine additives to, 894 automated testing systems with, 896 comparative parameters for, 886t manual screening methods with, 895-896, 895t Mycobacterium spp and, 576-577 specimen collection from, 113t, 114 transport of, 894 volume of, 894 Urine antigen test, 413 Urogenital tract flagellates and, 641-645, 642f, 643t, 644f-645f mollicutes associated with diseases of, 555-556, 556t parasites and, 629-630 Uropathogenic Escherichia coli, 424-425, 425t USR See Unheated serum reagin UTI See Urinary tract infection U-UTI See Upper urinary tract infection V V factor, 391-392, 396, 396f, 398t Vaccines DPT, 501 genital warts and, 926-927 for influenza, 783 for Neisseria meningitidis, 384 polioviruses and, 713 safety and, 89 smallpox and, 703 for Streptococcus pneumoniae, 337 Vaccinia virus, 702, 743-744 Vaginosis, 361 Validation, of tests, 109 Vancomycin, 256t-257t, 289-290, 292, 347-348 Vancomycin agar screen plate, 292 Vancomycin-intermediate Staphylococcus aureus (VISA), 290-291, 325 Vancomycin-resistant enterococci (VRE), 292 INDEX Vancomycin-resistant Staphylococcus aureus (VRSA), 290-291, 325 VAP See Ventilator-associated pneumonia Variable number of tandem repeats (VNTRs), 248 Variant Creutzfeldt-Jakob disease (vCJD), 723 Variant viruses, 710 Varicella (chickenpox), 700, 743 Varicella-zoster infection, 166f, 692, 700-701, 937 Varicella-zoster virus (VZV), 700-701, 700f, 799, 823, 823f Variola major, 743 Variola minor, 743 Variola virus, 702-703, 703f, 743-745, 743f, 745t Vascular catheter tips, 123 Vasculitis, 819, 829-830, 830f vCJD See Variant Creutzfeldt-Jakob disease VDRL See Venereal Disease Research Laboratory Vectors, insect, 645-646, 646f, 649, 949, 949f VEE See Venezuelan equine encephalitis Veillonella spp., 503 Venereal Disease Research Laboratory (VDRL), 220, 535, 916-917 Venezuelan equine encephalitis (VEE), 717 Ventilation, laboratory safety and, 575 Ventilator-associated pneumonia (VAP), 48, 49t, 789-791, 935-936 Verification, antibiograms and, 300, 302t Vero cells, 559, 560f Verotoxin, 426-427 Verrucous dermatitidis See Chromoblastomycosis VersaTREK Culture System, 580-581, 878 Vesicles, 806, 809 VHF See Viral hemorrhagic fever Vi antigen, 422, 434, 434f Vibrio alginolyticus, 460 Vibrio cholerae, 45, 458-459, 459f Vibrio parahaemolyticus, 459-460 Vibrio spp antigens and, 458 clinical manifestations of, 456 definitive identification of, 461, 462t-463t dermatologic manifestations of, 817-818 diarrhea and, 843, 851-852, 851f general characteristics of, 456-458, 458t laboratory diagnosis of, 460-461, 851-852, 851f microscopic morphology of, 456, 457f overview of, 456-463 physiology of, 456-458, 457f, 458t presumptive identification of, 461 serologic testing and, 461 susceptibility testing and, 461-463 toxins and, 458, 459f Vibrio vulnificus, 460 Vietnamese time bomb, 741 Vine, 176, 177f Viral hemorrhagic fever (VHF), 745-746, 745f Viral hepatitis, 717-723, 718t, 927-928, 927f-928f Viral infections antiviral therapy for, 723, 724t causes of, 690t DFA test and, 692-693 diagnosis methods for, 692-696 EIAs and, 693, 693f laboratory diagnosis of, 691-696, 692t NAATs and, 693 specimen selection, collection and transport for, 691 Viremia, 713, 880 tahir99 VRG 1075 Virginia Polytechnic Institute (VPI), 518 Viridans streptococci, 338-340, 339f, 339t Virion, 689, 691 Virulence adherence to host cells and tissues and, 31, 32f, 769-770 anaerobes and, 499t of Bordetella pertussis, 416 Borrelia spp and, 532-533 of Corynebacterium diphtheriae, 350-351 definition of, 30 of Enterobacteriaceae, 422 of Enterococcus spp., 340 extracellular toxins and enzymes production and, 32-34 of Haemophilus influenzae, 392-393 intracellular survival and proliferation and, 32 of Legionella spp., 410 of Listeria monocytogenes, 356 microbial factors contributing to, 30 of Neisseria spp., 373, 375f of Nocardia spp., 362 ocular infections and, 958-959, 958b phagocytosis evasion and, 30-31, 31t Pseudomonas aeruginosa and, 481 respiratory tract infections and, 769-770 of Salmonella spp., 434 spirochetes and, 530, 532 of Staphylococcus aureus, 316-317 of Streptococcus pyogenes, 331-332 Vibrio parahaemolyticus and, 460 Viruses See also specific viruses antiviral therapy for, 723, 724t blepharitis and, 962-963 characteristics of, 689-691 CNS, 859b conjunctivitis and, 961, 961f CPE and, 692, 694-695, 695f cultures and, 694, 694t, 695f diarrhea and, 841 DNA, RNA and, 5-6 dsDNA, 696-703 dsRNA, 704 hepatitis, 717-723, 718t isolation of, 693-695 keratitis and, 964, 965b, 965f laboratory diagnosis of, 691-696, 692t meningitis and, 858-860, 858f, 859b microscopic examination of, 166 as obligate intracellular parasites, 690 overview and characteristics of, 5-6 overview of, 689 replication of, 690-691 respiratory, 222 respiratory tract infections and, 799 serologic testing of, 220-221, 695-696 skin manifestations of, 822-826 ssDNA, 703-704 ssRNA, 704-717 structure of, 689 taxonomy of, 689, 690t variant, 710 VISA See Vancomycin-intermediate Staphylococcus aureus Vision statement, 100-102 VITEK Systems, 194t, 195, 295-296, 296f, 478, 481 Vitritis, 158f VNTRs See Variable number of tandem repeats 1076 INDEX Voges-Proskauer test (VP test), 185-186, 186f, 275, 339, 346 Voided midstream collection, 893 Voriconazole (VORI), 622 VP test See Voges-Proskauer test VPI See Virginia Polytechnic Institute VRE See Vancomycin-resistant enterococci VRSA See Vancomycin-resistant Staphylococcus aureus Vulvovaginal candidiasis, 910-911 Vulvovaginitis See also Bacterial vaginosis; Candidiasis causes of, 908 overview of, 908-911 trichomoniasis, 156f, 909-910, 909f-910f W Wagatsuma agar, 460 WalkAway system, 193-195 Walking pneumonia See Primary atypical pneumonia Warts See Papillomaviridae Water cultures, 55, 55t sterility specimens, 123 transmission, 44-45 Waterhouse-Friderichsen syndrome, 382-383, 382f Waterless handrubs, 68-69 Waterless surgical handrubs, 69-70 Watson, James, 17 Wautersiella spp., 490-491 WEE See Western equine encephalitis Weeksella spp., 490-491 Wee-Tab Urease Test Tablet, 513 Weighted pair group of method with arithmetic averages, 249 Weil-Felix agglutination test, 549 Weil’s disease, 530-531, 949 West African Sleeping sickness, 647 West Nile virus (WNV), 689, 693, 709, 863, 865 Western blots, 218-219, 219f, 715, 716f, 924-925 Western equine encephalitis (WEE), 717 Wet mount preparations, 628, 831 Whipple disease, 365 Whooping cough, 152f, 415-417 See also Pertussis Wicker, Roger, 747 Widespread outbreaks, 52-53, 53f Winterbottom’s sign, 647-648 WNV See West Nile virus Wood’s lamp, 396, 615, 808-809 Woolsorter’s disease, 366, 732, 946 Work practice controls, 74 World War II, 744-745 Wounds Aeromonas spp and, 464 botulism and, 501 culture results from, 506-507, 508f mycotic sample collection of, 615 rabies and, 716-717 specimen collection and, 112 Staphylococcus aureus and, 317-318 Vibrio vulnificus and, 460 Wright-Giemsa stain, 129, 130t, 132b Wuchereria bancrofti, 681-682, 682t, 827-828 X X factor, 391-392, 396, 396f, 398t, 569 XDR-TB See Extensively drug-resistant tuberculosis Xenorhabdus nematophilus, 443 Xylose-lysine-desoxycholate agar (XLD agar), 421, 442-443, 443f Y Yaws, 535 Yeast infections, 611-613, 911 See also Candidiasis Yeastlike fungi, 612 Yeasts, 590 calcofluor white staining of, 132b carbohydrate assimilation and, 620-621 differentiating characteristics of, 613t general characteristics of, 612 molds compared to, 590, 612 overview of, 4-5, 611-613 scum produced by, 176, 177f temperature and identification of, 621 tests for identification of, 620-621, 620f-621f urease test and, 621 Yellow fever virus, 709, 746 Yersin, Alexandre, 735, 949 Yersinia enterocolitica, 438-439, 439t, 843-844, 851 Yersinia pestis, 154f, 949 as bioterror agent, 735-737, 735f buboes and, 736 clinical manifestations of, 736, 736f cultures and, 737, 737f tahir99 VRG Yersinia pestis (Continued) direct microscopic examination of, 737 overview of, 438, 439t presumptive identity tests for, 737 specimen collection and preparation for, 736-737 Yersinia pseudotuberculosis, 439, 439t Yersinia spp., 438-439, 439t, 851 Yokenella regensburgei, 441 Z Zanamivir (Relenza), 711 Zephiran, 578 Ziehl-Neelsen stain, 130t, 131b-132b, 578, 793, 831 Ziemann’s dots, 654 Zone diameter interpretive breakpoints, 282-283, 283f Zone of equivalence, 204 Zone of inhibition, 282, 297 Zoonoses, 43, 530 See also Anthrax; Plague infections; Rickettsia spp.; Severe acute respiratory syndrome; Tularemia African sleeping sickness, 647, 648f anaplasmataceae, 549-550, 550f, 952 arenaviridae and, 704-705 arthropods and, 45, 949-952 babesiosis, 656-657 brucellosis, 404-405, 740, 947-948 Capnocytophaga canimorsus infection, 944-945 cat scratch disease, 819, 945 definition of, 403 dermatologic manifestations of, 819-820 emerging, 952-954 erysipeloid, 944, 944f Leishmania spp as, 646-647, 647f, 828 leptospirosis, 530-531, 819, 948-949, 948f lyme borreliosis, 530-532, 818, 949-951, 950f overview of, 45, 45t, 943 pasteurellosis, 403-404, 943-944 rat bite fever, 819-820 RMSF, 547-548, 548f, 819, 862, 951 transmission by direct contact or inhalation, 945-949 transmission by scratches and bites, 943 Trypanosoma spp as, 647-649, 648f Zostavax, 701 Zoster (shingles), 700, 823 See also Varicella-zoster infection Zygomycota, 592-593, 607, 815 Zygospores, 592f This page intentionally left blank tahir99 VRG This page intentionally left blank tahir99 VRG ... IgM   IgG 10 15 20 25 35 40 +1 +2 +3 +3 +4 +3 +3 +4 +1 +2 +1 +1 104° F 104° F +2 + ≤8 104° F 100° F +3 + 1 02 F Absent +2 + 32 100° F Absent +2 + 64 Absent Absent +1 + 25 6 + 25 6 128 − − + − + +... approximately 0 .2 to 0.3 µm in diameter to tapered rods of approximately to 2 µm in length and 0 .2 to 0.3 µm in diameter Eight genera and over 20 0 species of mollicutes have been described Table 25 -2 compares... in 20 00 However, since 20 00 the disease has increased, peaking at 46 ,29 0 cases in 20 08 The next years saw only a slight decrease from the peak number of cases at 44,830 in 20 09 and 46,0 42 in 20 11