bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitative aspects of septicemia
Authors: Yagupsky P , Nolte F S
Published: June 2016

For years, quantitative blood cultures found only limited use as aids in the diagnosis and management of septic patients because the available methods were cumbersome, labor intensive, and practical only for relatively small volumes of blood. The development and subsequent commercial availability of lysis-centrifugation direct plating methods for blood cultures have addressed many of the shortcomings of the older methods. The lysis-centrifugation method has demonstrated good performance relative to broth-based blood culture methods. As a result, quantitative blood cultures have found widespread use in clinical microbiology laboratories. Most episodes of clinical significant bacteremia in adults are characterized by low numbers of bacteria per milliliter of blood. In children, the magnitude of bacteremia is generally much higher, with the highest numbers of bacteria found in the blood of septic neonates. The magnitude of bacteremia correlates with the severity of disease in children and with mortality rates in adults, but other factors play more important roles in determining the patient's outcome. Serial quantitative blood cultures have been used to monitor the in vivo efficacy of antibiotic therapy in patients with slowly resolving sepsis, such as disseminated Mycobacterium avium-M. intracellulare complex infections. Quantitative blood culture methods were used in early studies of bacterial endocarditis, and the results significantly contributed to our understanding of the pathophysiology of this disease. Comparison of paired quantitative blood cultures obtained from a peripheral vein and the central venous catheter has been used to help identify patients with catheter-related sepsis and is the only method that does not require removal of the catheter to establish the diagnosis. Quantitation of bacteria in the blood can also help distinguish contaminated from truly positive blood cultures; however, no quantitative criteria can invariably differentiate contamination from bacteremia.
Some infectious causes of diarrhea in young farm animals
Authors: Holland R E
Published: June 2016

Escherichia coli, rotaviruses, and Cryptosporidium parvum are discussed in this review as they relate to enteric disease in calves, lambs, and pigs. These microorganisms are frequently incriminated as causative agents in diarrheas among neonatal food animals, and in some cases different strains or serotypes of the same organism cause diarrhea in humans. E. coli causes diarrhea by mechanisms that include production of heat-labile or heat-stable enterotoxins and synthesis of potent cytotoxins, and some strains cause diarrhea by yet undetermined mechanisms. Rotaviruses and C. parvum induce various degrees of villous atrophy. Rotaviruses infect and replicate within the cytoplasm of enterocytes, whereas C. parvum resides in an intracellular, extracytoplasmic location. E. coli, rotavirus, and C. parvum infections are of concern to producers, veterinarians, and public health officials. These agents are a major cause of economic loss to the producer because of costs associated with therapy, reduced performance, and high morbidity and mortality rates. Moreover, diarrheic animals may harbor, incubate, and act as a source to healthy animals and humans of some of these agents.
Rhodococcus equi: an animal and human pathogen
Authors: Prescott J F
Published: June 2016

Recent isolations of Rhodococcus equi from cavitatory pulmonary disease in patients with AIDS have aroused interest among medical microbiologists in this unusual organism. Earlier isolations from humans had also been in immunosuppressed patients following hemolymphatic tumors or renal transplantation. This organism has been recognized for many years as a cause of a serious pyogranulomatous pneumonia of young foals and is occasionally isolated from granulomatous lesions in several other species, in some cases following immunosuppression. The last decade has seen many advances in understanding of the epidemiology, pathogenesis, diagnosis, treatment, and immunity to infection in foals. The particular susceptibility of the foal is not understood but can be explained in part by a combination of heavy challenge through the respiratory route coinciding with declining maternally derived antibody in the absence of fully competent foal cellular immune mechanisms. R. equi is largely a soil organism but is widespread in the feces of herbivores. Its growth in soil is considerably improved by simple nutrients it obtains from herbivore manure. About one-third of human patients who have developed R. equi infections had contact in some way with herbivores or their manure. Others may have acquired infection from contact with soil or wild bird manure. R. equi is an intracellular parasite, which explains the typical pyogranulomatous nature of R. equi infections, the predisposition to infection in human patients with defective cell-mediated immune mechanisms, and the efficacy of antimicrobial drugs that penetrate phagocytic cells.
Functions and activities of the Area Committee on Microbiology of the National Committee for Clinical Laboratory Standards
Authors: Washington J A
Published: June 2016

The Area Committee on Microbiology of the National Committee for Clinical Laboratory Standards has responsibility for the development of guidelines and standards in the field of clinical microbiology. Through the consensus process, representatives from government, industry, and professional societies have developed standards on antibacterial susceptibility testing (M2, M7, and M11), antimycobacterial susceptibility testing (M24), quality assurance on commercially prepared microbiological culture media (M22), evaluation of production lots of dehydrated Mueller-Hinton agar (M6), and preparation and testing of fetal bovine serum for use as cell culture growth supplement (M25) and guidelines on bactericidal tests (M26), protection of laboratory workers from infections transmitted by blood, body fluids, and tissue (M29), blood film examination for parasites (M15), and development of in vitro susceptibility testing criteria and quality control parameters (M23).
Nucleic acid detection systems for enteroviruses
Authors: Rotbart H A
Published: June 2016

The enteroviruses comprise nearly 70 human pathogens responsible for a wide array of diseases including poliomyelitis, meningitis, myocarditis, and neonatal sepsis. Current diagnostic tests for the enteroviruses are limited in their use by the slow growth, or failure to grow, of certain serotypes in culture, the antigenic diversity among the serotypes, and the low titer of virus in certain clinical specimens. Within the past 6 years, applications of molecular cloning techniques, in vitro transcription vectors, automated nucleic acid synthesis, and the polymerase chain reaction have resulted in significant progress toward nucleic acid-based detection systems for the enteroviruses that take advantage of conserved genomic sequences across many, if not all, serotypes. Similar approaches to the study of enteroviral pathogenesis have already produced dramatic advances in our understanding of how these important viruses cause their diverse clinical spectra.
Epidemiology of human listeriosis
Authors: Schuchat A , Swaminathan B , Broome C V
Published: June 2016

During the 1980s, investigation of several large epidemics of listeriosis confirmed that transmission of L. monocytogenes in food causes human disease. Progress in laboratory detection and subtyping of the organism has enhanced our ability to compare human and environmental isolates of L. monocytogenes. Transmission by foodborne organisms is now recognized as causing both epidemic and sporadic listeriosis. Continued study of dietary risk factors associated with listeriosis is needed in order to develop dietary recommendations for the expanding population at increased risk of disease. Current research application of new molecular methods to the study of L. monocytogenes may improve the ability to diagnose pregnancy-associated disease and permit the rapid detection and control of L. monocytogenes in the food supply.
Biological safety cabinetry
Authors: Kruse R H , Puckett W H , Richardson J H
Published: June 2016

The biological safety cabinet is the one piece of laboratory and pharmacy equipment that provides protection for personnel, the product, and the environment. Through the history of laboratory-acquired infections from the earliest published case to the emergence of hepatitis B and AIDS, the need for health care worker protection is described. A brief description with design, construction, function, and production capabilities is provided for class I and class III safety cabinets. The development of the high-efficiency particulate air filter provided the impetus for clean room technology, from which evolved the class II laminar flow biological safety cabinet. The clean room concept was advanced when the horizontal airflow clean bench was manufactured; it became popular in pharmacies for preparing intravenous solutions because the product was protected. However, as with infectious microorganisms and laboratory workers, individual sensitization to antibiotics and the advent of hazardous antineoplastic agents changed the thinking of pharmacists and nurses, and they began to use the class II safety cabinet to prevent adverse personnel reactions to the drugs. How the class II safety cabinet became the mainstay in laboratories and pharmacies is described, and insight is provided into the formulation of National Sanitation Foundation standard number 49 and its revisions. The working operations of a class II cabinet are described, as are the variations of the four types with regard to design, function, air velocity profiles, and the use of toxins. The main certification procedures are explained, with examples of improper or incorrect certifications. The required levels of containment for microorganisms are given. Instructions for decontaminating the class II biological safety cabinet of infectious agents are provided; unfortunately, there is no method for decontaminating the cabinet of antineoplastic agents.
Factors promoting acute and chronic diseases caused by yersiniae
Authors: Brubaker R R
Published: June 2016

The experimental system constructed with the medically significant yersiniae provides a powerful basic model for comparative study of factors required for expression of acute versus chronic disease. The system exploits the close genetic similarity between Yersinia pestis, the etiological agent of bubonic plague, and enteropathogenic Yersinia pseudotuberculosis and Yersinia enterocolitica. Y. pestis possesses three plasmids, of which one, shared by the enteropathogenic species, mediates a number of virulence factors that directly or indirectly promote survival within macrophages and immunosuppression. The two remaining plasmids are unique and encode functions that promote acute disease by enhancing bacterial dissemination in tissues and resistance to phagocytosis by neutrophils and monocytes. These properties are replaced in the enteropathogenic yersiniae by host cell invasins and an adhesin which promote chronic disease; the latter are cryptic in Y. pestis. Additional distinctions include specific mutational losses in Y. pestis which result in loss of fitness in natural environments plus gain of properties that facilitate transmission and infection via fleabite.
Histoplasma variation and adaptive strategies for parasitism: new perspectives on histoplasmosis
Authors: Eissenberg L G , Goldman W E
Published: June 2016

This review summarizes the biology of Histoplasma capsulatum in relation to a wide variety of corresponding pathologies in histoplasmosis. Features of these disease syndromes can be explained in part by natural variations within the fungal population and adaptations made by individual organisms to specific environments. H. capsulatum grows as mycelia and conidia in the soil; once inhaled, the organism undergoes a dramatic morphological and physiological conversion to a yeast form. The yeasts proliferate within the phagolysosomes of macrophages, using a variety of specific strategies for intracellular survival. Even avirulent strains or variants are able to avoid being killed by macrophages and instead establish inapparent or persistent infections. The ingested avirulent organisms assume enlarged shapes similar in appearance to those seen in histological sections of tissues from patients with histoplasmosis. Respiratory tract epithelial cells also appear to play a role in persistence: within them yeasts undergo phenotypic switching akin to the phase variation observed in other pathogens. This particular change involves the loss or modification of cell wall alpha-(1,3)-glucan, which is also correlated with the spontaneous appearance of avirulent variants. The repertoire of adaptive responses and natural variations within this species probably evolved from the need to adjust to a wide range of dynamic environments. In combination with the immune status of the host, these characteristics of H. capsulatum appear to influence the epidemiology, extent, and persistence of histoplasmosis.
Applications of cellular fatty acid analysis
Authors: Welch D F
Published: June 2016

More than ever, new technology is having an impact on the tools of clinical microbiologists. The analysis of cellular fatty acids by gas-liquid chromatography (GLC) has become markedly more practical with the advent of the fused-silica capillary column, computer-controlled chromatography and data analysis, simplified sample preparation, and a commercially available GLC system dedicated to microbiological applications. Experience with applications in diagnostic microbiology ranges from substantial success in work with mycobacteria, legionellae, and nonfermentative gram-negative bacilli to minimal involvement with fungi and other nonbacterial agents. GLC is a good alternative to other means for the identification of mycobacteria or legionellae because it is rapid, specific, and independent of other specialized testing, e.g., DNA hybridization. Nonfermenters show features in their cellular fatty acid content that are useful in identifying species and, in some cases, subspecies. Less frequently encountered nonfermenters, including those belonging to unclassified groups, can ideally be characterized by GLC. Information is just beginning to materialize on the usefulness of cellular fatty acids for the identification of gram-positive bacteria and anaerobes, despite the traditional role of GLC in detecting metabolic products as an aid to identification of anaerobes. When species identification of coagulase-negative staphylococci is called for, GLC may offer an alternative to biochemical testing. Methods for direct analysis of clinical material have been developed, but in practical and economic terms they are not yet ready for use in the clinical laboratory. Direct analysis holds promise for detecting markers of infection due to an uncultivable agent or in clinical specimens that presently require cultures and prolonged incubation to yield an etiologic agent.
Immunodiagnosis of aspergillosis
Authors: Kurup V P , Kumar A
Published: June 2016

Aspergillus species are ubiquitous fungi and have been implicated as the causative agents of a variety of lung disorders in humans. These disorders include allergic, saprophytic, and systemic manifestations. The allergic disorders mainly affect atopic persons, and invasive or systemic diseases affect immunosuppressed individuals. Immunodiagnosis can help the practitioner diagnose these diseases. Demonstration of circulating antibodies is a useful criterion, but the lack of dependable and standardized antigens is a limiting factor in the diagnosis of most Aspergillus-induced diseases. Despite this limitation, however, immunodiffusion and enzyme-linked immunosorbent assays have been widely used for the detection of antibodies in the sera of patients with aspergillosis. Similarly, crude and semipurified antigens are being used to demonstrate skin hypersensitivity in patients, and several methods have been useful in the detection of antigenemia in patients with invasive aspergillosis. With a growing number of reports on the incidence of aspergillosis and an increase in the number of immunosuppressed individuals in the population, more rapid methods and more reliable reagents for immunodiagnosis are needed. With recent attempts at obtaining reliable reagents for through hybridoma technology and molecular biological techniques, substantial progress toward efficient immunodiagnosis may be achieved.
Bacterial vaginosis
Authors: Spiegel C A
Published: June 2016

Bacterial vaginosis (BV) is the most common of the vaginitides affecting women of reproductive age. It appears to be due to an alteration in the vaginal ecology by which Lactobacillus spp., the predominant organisms in the healthy vagina, are replaced by a mixed flora including Prevotella bivia, Prevotella disiens, Porphyromonas spp., Mobiluncus spp., and Peptostreptococcus spp. All of these organisms except Mobiluncus spp. are also members of the endogenous vaginal flora. While evidence from treatment trials does not support the notion that BV is sexually transmitted, recent studies have shown an increased risk associated with multiple sexual partners. It has also been suggested that the pathogenesis of BV may be similar to that of urinary tract infections, with the rectum serving as a reservoir for some BV-associated flora. The organisms associated with BV have also been recognized as agents of female upper genital tract infection, including pelvic inflammatory disease, and the syndrome BV has been associated with adverse outcome of pregnancy, including premature rupture of membranes, chorioamnionitis, and fetal loss; postpartum endometritis; cuff cellulitis; and urinary tract infections. The mechanisms by which the BV-associated flora causes the signs of BV are not well understood, but a role for H2O2-producing Lactobacillus spp. in protecting against colonization by catalase-negative anaerobic bacteria has been recognized. These and other aspects of BV are reviewed.
The hypnozoite and relapse in primate malaria
Authors: Cogswell F B
Published: June 2016

Although the phenomenon of malarial relapse was known to the ancients, the mechanism has only recently been explained satisfactorily. The long-held hypothesis of a tissue "cycle" in primate malaria as a cause of relapse did not fit clinical and experimental observations. A latent stage for Plasmodium spp. in the liver, for which there is now extensive morphological and experimental confirmation, best explains both the relapse phenomenon and the long prepatent periods seen with some strains of Plasmodium vivax. These latent stages (hypnozoites) have been detected in three relapsing malarias and have been found to persist in the liver as uninucleate parasites for up to 229 days after sporozoite inoculation. They have been found in in vitro cultures of two species of Plasmodium, and their ultrastructure has been partially described.
Human infections due to Malassezia spp
Authors: Marcon M J , Powell D A
Published: June 2016

The genus Malassezia contains three member species: Malassezia furfur and Malassezia sympodialis, both obligatory lipophilic, skin flora yeasts of humans, and Malassezia pachydermatis, a nonobligatory lipophilic, skin flora yeast of other warm-blooded animals. Several characteristics suggest the basidiomycetous nature of these yeasts, although a perfect stage has not been identified. Classically, these organisms are associated with superficial infections of the skin and associated structures, including pityriasis versicolor and folliculitis. Recently, however, they have been reported as agents of more invasive human diseases including deep-line catheter-associated sepsis. The latter infection occurs in patients, primarily infants, receiving parenteral nutrition (including lipid emulsions) through the catheter. The lipids presumably provide growth factors required for replication of the organisms. It is unclear how deep-line catheters become colonized with Malassezia spp. Skin colonization with M. furfur is common in infants hospitalized in neonatal intensive care units, whereas colonization of newborns hospitalized in well-baby nurseries and of older infants is rarely observed. Catheter colonization, which may occur without overt clinical symptoms, probably occurs secondary to skin colonization, with the organism gaining access either via the catheter insertion site on the skin or through the external catheter hub (connecting port). There is little information on the colonization of hospitalized patients by M. sympodialis or M. pachydermatis. Diagnosis of superficial infections is best made by microscopic examination of skin scrapings following KOH, calcofluor white, or histologic staining. Treatment of these infections involves the use of topical or oral antifungal agents, and it may be prolonged. Diagnosis of Malassezia catheter-associated sepsis requires detection of the organism in whole blood smears or in buffy coat smears of blood drawn through the infected catheter or isolation of the organism from catheter or peripheral blood or the catheter tip. Culture of M. furfur from blood is best achieved with Isolator tubes and plating onto a solid medium supplemented with a lipid source. Appropriate treatment of patients requires removal of the infected catheter with or without temporary stoppage of lipid emulsions; administration of antifungal therapeutic agents does not appear to be necessary. Because many patients who develop Malassezia catheter-associated sepsis have severe underlying illnesses, caution must be exercised in attributing all clinical deterioration to Malassezia infection. Our better understanding of how these organisms cause disease awaits the development of a useful typing scheme for epidemiologic studies and further studies on microbial virulence factors and the role of the immune response in pathogenesis.
Intestinal capillariasis
Authors: Cross J H
Published: June 2016

Intestinal capillariasis caused by Capillaria philippinensis appeared first in the Philippines and subsequently in Thailand, Japan, Iran, Egypt, and Taiwan, but most infections occur in the Philippines and Thailand. As established experimentally, the life cycle involves freshwater fish as intermediate hosts and fish-eating birds as definitive hosts. Embryonated eggs from feces fed to fish hatch and grow as larvae in the fish intestines. Infective larvae fed to monkeys, Mongolian gerbils, and fish-eating birds develop into adults. Larvae become adults in 10 to 11 days, and the first-generation females produce larvae. These larvae develop into males and egg-producing female worms. Eggs pass with the feces, reach water, embryonate, and infect fish. Autoinfection is part of the life cycle and leads to hyperinfection. Humans acquire the infection by eating small freshwater fish raw. The parasite multiplies, and symptoms of diarrhea, borborygmus, abdominal pain, and edema develop. Chronic infections lead to malabsorption and hence to protein and electrolyte loss, and death results from irreversible effects of the infection. Treatment consists of electrolyte replacement and administration of an antidiarrheal agent and mebendazole or albendazole. Capillariasis philippinensis is considered a zoonotic disease of migratory fish-eating birds. The eggs are disseminated along flyways and infect the fish, and when fish are eaten raw, the disease develops.
Gardnerella vaginalis: characteristics, clinical considerations, and controversies
Authors: Catlin B W
Published: June 2016

The clinical significance, Gram stain reaction, and genus affiliation of Gardnerella vaginalis have been controversial since Gardner and Dukes described the organism as the cause of "nonspecific vaginitis," a common disease of women which is now called bacterial vaginosis. The organism was named G. vaginalis when taxonomic studies showed that it was unrelated to bacteria in various genera including Haemophilus and Corynebacterium. Electron microscopy and chemical analyses have elucidated the organism's gram-variable reaction. Controversy over the etiology of bacterial vaginosis was largely resolved by (i) studies using improved media and methods for the isolation and identification of bacteria in vaginal fluids and (ii) standardization of criteria for clinical and laboratory diagnosis. Besides G. vaginalis, Mobiluncus spp., Mycoplasma hominis, and certain obligate anaerobes are now acknowledged as participants in bacterial vaginosis. The finding that G. vaginalis, Mobiluncus spp., and M. hominis inhabit the rectum indicates a potential source of autoinfection in addition to sexual transmission. Extravaginal infections with G. vaginalis are increasingly recognized, especially when the toxic anticoagulant polyanetholesulfonate is omitted from blood cultures and when urine cultures are incubated anaerobically for 48 h. The finding that mares harbor G. vaginalis suggests that an equine model can be developed for studies of Gardnerella pathogenesis.
Molecular and immunological diagnosis of echinococcosis
Authors: Gottstein B
Published: June 2016

Echinococcosis is an infectious disease of humans caused by the larval (metacestode) stage of the cestode species Echinococcus granulosus (cystic echinococcosis or hydatid disease) or Echinococcus multilocularis (alveolar echinococcosis or alveolar hydatid disease). Clinical manifestations depend primarily on localization and size of hepatic lesions and may include hepatomegaly, obstructive jaundice, or cholangitis. Prognostically, alveolar echinococcosis is considered similar to liver malignancies, including a lethality rate of 90% for untreated cases. Diagnosis is based on imaging techniques coupled with immunodiagnostic procedures. Antibody detection tests for E. multilocularis have markedly improved with the use of affinity-purified Em2 antigen and recombinant antigen II/3-10 in enzyme immunoassays. Antigens of corresponding quality for E. granulosus are still unavailable. The detection of circulating antigens and immune complexes in the sera of patients with cystic echinococcosis, the demonstration of in vitro lymphocyte proliferation in response to stimulation with Echinococcus antigens, and the discrimination of serum immunoglobulin isotype activity to various Echinococcus antigens in both cystic and alveolar echinococcosis have been suggested for diagnostic purposes as well as for monitoring patients after treatment. New diagnostic molecular tools include DNA probes for Southern hybridization tests and polymerase chain reaction for the amplification of E. multilocularis and E. granulosus species-specific DNA fragments.
Chagas' disease
Authors: Tanowitz H B , Kirchhoff L V , Simon D , Morris S A , Weiss L M , Wittner M
Published: June 2016

Chagas' disease, caused by Trypanosoma cruzi, is an important cause of morbidity in many countries in Latin America. The important modes of transmission are by the bite of the reduviid bug and blood transfusion. The organism exists in three morphological forms: trypomastigotes, amastigotes, and epimastigotes. The mechanism of transformation and differentiation is currently being explored, and signal transduction pathways of the parasites may be involved in this process. Parasite adherence to and invasion of host cells is a complex process involving complement, phospholipase, penetrin, neuraminidase, and hemolysin. Two clinical forms of the disease are recognized, acute and chronic. During the acute stage pathological damage is related to the presence of the parasite, whereas in the chronic stage few parasites are found. In recent years the roles of tumor necrosis factor, gamma interferon, and the interleukins in the pathogenesis of this infection have been reported. The common manifestations of chronic cardiomyopathy are arrhythmias and thromboembolic events. Autoimmune, neurogenic, and microvascular factors may be important in the pathogenesis of the cardiomyopathy. The gastrointestinal tract is another important target, and "mega syndromes" are common manifestations. The diagnosis and treatment of this infection are active areas of investigation. New serological and molecular biological techniques have improved the diagnosis of chronic infection. Exacerbations of T. cruzi infection have been reported for patients receiving immuno-suppressive therapy and for those with AIDS.
Tests for bactericidal effects of antimicrobial agents: technical performance and clinical relevance
Authors: Peterson L R , Shanholtzer C J
Published: June 2016

Bactericidal testing has been used for several decades as a guide for antimicrobial therapy of serious infections. Such testing is most frequently performed when bactericidal antimicrobial agent therapy is considered necessary (such as when treating infectious endocarditis or infection in an immunocompromised host). It has also been used to ensure that the infecting organism is killed by (not tolerant to) usually bactericidal compounds. However, few data are available to support the role of such tests in direct patient care. Several important variables affect the reproducibility of the test results; however, proposed reference methods are now available for performing the MBC test. With minor modifications, these can provide a standardized approach for laboratories that need to perform them. Currently, little evidence is available to support the routine use of such testing for the care of individual patients. However, testing of new (investigational) antimicrobial agents can be beneficial in determining their potential to provide bactericidal antimicrobial activity during clinical use. New methods to assess bactericidal activity are being developed, but as yet none have been rigorously tested in patient care settings; further, for most of these methods, little information is available as to which technical parameters affect their results. In clinical laboratories, all bactericidal tests must be performed with rigorously standardized techniques and adequate controls, bearing in mind the limitations of the currently available test procedures.
Antimicrobial susceptibility testing of Neisseria gonorrhoeae and implications for epidemiology and therapy
Authors: Fekete T
Published: June 2016

Antimicrobial susceptibility testing (AST) of Neisseria gonorrhoeae has been under development since the early days of antimicrobial agents. However, it is rarely applied to clinical isolates today. The history of the various in vitro tests to determine the susceptibility of N. gonorrhoeae to antibiotics is rich with evidence that these results predict response to therapy for almost all agents tested. Further, AST is a useful and important aspect of strain characterization and disease epidemiology in conjunction with the more specific but laborious techniques of auxotyping, serotyping, and plasmid analysis. Current technology has overcome many of the objections to AST for N. gonorrhoeae with standardization of test media and the development of an accurate disk diffusion AST method that is suited to most clinical laboratories regardless of volume or level of technical expertise. Ironically, the very low level of resistance to the current primary treatment strategy in the United States, ceftriaxone or another potent cephalosporin, makes the use of AST somewhat superfluous.
Ureaplasma urealyticum intrauterine infection: role in prematurity and disease in newborns
Authors: Cassell G H , Waites K B , Watson H L , Crouse D T , Harasawa R
Published: June 2016

Ureaplasma urealyticum, a common commensal of the urogenital tract of sexually mature humans, is gaining recognition as an important opportunistic pathogen during pregnancy. While its etiologic significance in many aspects of adverse pregnancy remains controversial, recent evidence indicates that U. urealyticum in the absence of other organisms is a cause of chorioamnionitis. Furthermore, ureaplasmal infection of the chorioamnion is significantly associated with premature spontaneous labor and delivery. In at least some cases, it appears to be causal. Present evidence indicates that U. urealyticum is a cause of septicemia, meningitis, and pneumonia in newborn infants, particularly those born prematurely. There is strong but not definitive evidence that ureaplasmal infection of the lower respiratory tract can lead to development of chronic lung disease in very low-birth-weight infants. Although risk factors for colonization of the lower genitourinary tract have been identified, little information is available concerning risk factors for intrauterine infection and host immune responses to invasive infection. Recent establishment of animal models of respiratory and central nervous system diseases should provide an opportunity to evaluate risk factors, pathogenic mechanisms, and operative immune mechanisms. However, the most critical need is additional information concerning indications for diagnosis and treatment as well as efficacy of treatment.
Clostridium difficile: clinical disease and diagnosis
Authors: Knoop F C , Owens M , Crocker I C
Published: June 2016

Clostridium difficile is an opportunistic pathogen that causes a spectrum of disease ranging from antibiotic-associated diarrhea to pseudomembranous colitis. Although the disease was first described in 1893, the etiologic agent was not isolated and identified until 1978. Since clinical and pathological features of C. difficile-associated disease are not easily distinguished from those of other gastrointestinal diseases, including ulcerative colitis, chronic inflammatory bowel disease, and Crohn's disease, diagnostic methods have relied on either isolation and identification of the microorganism or direct detection of bacterial antigens or toxins in stool specimens. The current review focuses on the sensitivity, specificity, and practical use of several diagnostic tests, including methods for culture of the etiologic agent, cellular cytotoxicity assays, latex agglutination tests, enzyme immunoassay systems, counterimmunoelectrophoresis, fluorescent-antibody assays, and polymerase chain reactions.
Human immunodeficiency virus type 1 infection of the brain
Authors: Atwood W J , Berger J R , Kaderman R , Tornatore C S , Major E O
Published: June 2016

Direct infection of the central nervous system by human immunodeficiency virus type 1 (HIV-1), the causative agent of AIDS, was not appreciated in the early years of the AIDS epidemic. Neurological complications associated with AIDS were largely attributed to opportunistic infections that arose as a result of the immunocompromised state of the patient and to depression. In 1985, several groups succeeded in isolating HIV-1 directly from brain tissue. Also that year, the viral genome was completely sequenced, and HIV-1 was found to belong to a neurotropic subfamily of retrovirus known as the Lentivirinae. These findings clearly indicated that direct HIV-1 infection of the central nervous system played a role in the development of AIDS-related neurological disease. This review summarizes the clinical manifestations of HIV-1 infection of the central nervous system and the related neuropathology, the tropism of HIV-1 for specific cell types both within and outside of the nervous system, the possible mechanisms by which HIV-1 damages the nervous system, and the current strategies for diagnosis and treatment of HIV-1-associated neuropathology.
Antifungal susceptibility testing
Authors: Rex J H , Pfaller M A , Rinaldi M G , Polak A , Galgiani J N
Published: June 2016

Unlike antibacterial susceptibility testing, reliable antifungal susceptibility testing is still largely in its infancy. Many methods have been described, but they produce widely discrepant results unless such factors as pH, inoculum size, medium formulation, incubation time, and incubation temperature are carefully controlled. Even when laboratories agree upon a common method, interlaboratory agreement may be poor. As a result of numerous collaborative projects carried out both independently and under the aegis of the Subcommittee on Antifungal Susceptibility Testing of the National Committee for Clinical Laboratory Standards, the effects of varying these factors have been extensively studied and a standard method which minimizes interlaboratory variability during the testing of Candida spp. and Cryptococcus neoformans has been proposed. This review summarizes this work, reviews the strengths and weaknesses of the proposed susceptibility testing standard, and identifies directions for future work.
An overview of nosocomial infections, including the role of the microbiology laboratory
Authors: Emori T G , Gaynes R P
Published: June 2016

An estimated 2 million patients develop nosocomial infections in the United States annually. The increasing number of antimicrobial agent-resistant pathogens and high-risk patients in hospitals are challenges to progress in preventing and controlling these infections. While Escherichia coli and Staphylococcus aureus remain the most common pathogens isolated overall from nosocomial infections, coagulase-negative staphylococci (CoNS), organisms previously considered contaminants in most cultures, are now the predominant pathogens in bloodstream infections. The growing number of antimicrobial agent-resistant organisms is troublesome, particularly vancomycin-resistant CoNS and Enterococcus spp. and Pseudomonas aeruginosa resistant to imipenem. The active involvement and cooperation of the microbiology laboratory are important to the infection control program, particularly in surveillance and the use of laboratory services for epidemiologic purposes. Surveillance is used to identify possible infection problems, monitor infection trends, and assess the quality of care in the hospital. It requires high-quality laboratory data that are timely and easily accessible.
"The end of innocence" revisited: resistance of herpesviruses to antiviral drugs
Authors: Field A K , Biron K K
Published: June 2016

In the past 4 years, interest in drug-resistant herpesviruses has evolved from the realm of academic laboratory studies to that of great clinical importance. Recurrent and persistent infections due to the herpes simplex viruses, varicella-zoster virus, and human cytomegalovirus have been an unwelcome consequence of immunosuppression in graft recipients, cancer patients, and those suffering from AIDS. Treatment of these infections with the available antiviral drugs, such as acyclovir, ganciclovir, and foscarnet, has resulted in both clinical benefit and the emergence of drug-resistant variants. In addition, the role of Epstein-Barr virus is being clarified for an array of disease syndromes, and therapeutic approaches are beginning to emerge. In the present review, the emergence and clinical importance of drug resistance among the herpesviruses have been explored. Furthermore, particular attention has been focused on our understanding of the mechanisms of drug resistance and how that understanding will guide us in the development of more effective antiviral drugs and drug usage.
Adhesins and ligands involved in the interaction of Candida spp. with epithelial and endothelial surfaces
Authors: Hostetter M K
Published: June 2016

Adhesion of candidal species to the epithelium of the gastrointestinal or genitourinary tract stands as a critical first step in the pathogenesis of candidal infection. After colonization and replication at mucosal surfaces, Candida albicans and other pathogenic species may penetrate the mucosal barrier, enter the vascular tree, and disseminate hematogenously. The consequences of this pathogenic cascade evoke considerable morbidity and mortality, especially among immunocompromised patients. Thus, interactions of C. albicans and other candidal species with epithelium and endothelium may lead to serious consequences for the human host. This review evaluates candidate candidal adhesions for epithelial and endothelial surfaces, with emphasis on the specificity of the interaction, the inhibitors that have been employed, and the ligands that have been identified on mammalian cells or matrices. Three types of interactions are described: protein-protein interactions, lectin-like interactions, and incompletely defined interactions in which the adhesive ligand is as yet unidentified. Special attention is given to the roles of integrin-like proteins. Differences in the mechanisms of candidal attachment to epithelium and endothelium are delineated. Last, on the basis of the available literature, avenues of potentially fruitful investigation are proposed.
Adhesion and its role in the virulence of enteropathogenic Escherichia coli
Authors: Law D
Published: June 2016

Enteropathogenic Escherichia coli (EPEC) organisms are an important cause of diarrheal disease in young children. The virulence of EPEC is a multifactorial process and involves a number of distinct stages. Initial adherence to intestinal mucosa is mediated by fimbriae which bring about a distinct form of adhesion, localized adhesion. Intimate adhesion of the bacterium to the eukaryotic membrane occurs, resulting in the activation of signal transduction pathways. Microvilli are disrupted and effaced from the apical membrane which then cups around the organism to form pedestal structures, the attaching and effacing lesion. Diarrhea may be produced by alteration of the permeability of the apical membrane and also through a malabsorption mechanism. The pathways involved in the production of the attaching and effacing lesion are described. EPEC organisms were originally thought to belong to a number of distinct serogroups; it is now apparent that many isolates belonging to these serogroups are not pathogenic or belong to other pathogenic groups of E. coli. In addition, isolates falling outside of these serogroups are considered to be true EPEC. The definition of EPEC based on serotyping is inaccurate and should be replaced by methods that specifically detect the virulence properties of EPEC.
DNA fingerprinting of medically important microorganisms by use of PCR
Authors: van Belkum A
Published: June 2016

Selected segments of any DNA molecule can be amplified exponentially by PCR. This technique provides a powerful tool to detect and identify minimal numbers of microorganisms. PCR is applicable both in diagnosis and in epidemiology. By amplification of hypervariable DNA domains, differences can be detected even among closely related strains. PCR fingerprinting is a valuable tool for medical microbiologists, epidemiologists, and microbial taxonomists. The current state of PCR-mediated genotyping is reviewed, and a comparison with conventional molecular typing methods is included. Because of its speed and versatility, PCR fingerprinting will play an important role in microbial genetics, epidemiology, and systematics.
Transfusion-associated bacterial sepsis
Authors: Wagner S J , Friedman L I , Dodd R Y
Published: June 2016

The incidence of sepsis caused by transfusion of bacterially contaminated blood components is similar to or less than that of transfusion-transmitted hepatitis C virus infection, yet significantly exceeds those currently estimated for transfusion-associated human immunodeficiency and hepatitis B viruses. Outcomes are serious and may be fatal. In addition, transfusion of sterile allogenic blood can have generalized immunosuppressive effects on recipients, resulting in increased susceptibility to postoperative infection. This review examines the frequency of occurrence of transfusion-associated sepsis, the organisms implicated, and potential sources of bacteria. Approaches to minimize the frequency of sepsis are discussed, including the benefits and disadvantages of altering the storage conditions for blood. In addition, the impact of high levels of bacteria on the gross characteristics of erythrocyte and platelet concentrates is described. The potentials and limitations of current tests for detecting bacteria in blood are also discussed.
Paratuberculosis
Authors: Cocito C , Gilot P , Coene M , de Kesel M , Poupart P , Vannuffel P
Published: June 2016

Paratuberculosis (Johne's disease) is a chronic, wasting, widespread mycobacteriosis of ruminants. It involves extensive mycobacterial shedding, which accounts for the high contagiousness, and ends with a fatal enteritis. Decreases in weight, milk production, and fertility produce severe economic loss. The DNA of the etiological agent (Mycobacterium paratuberculosis) has a base composition (66 to 67% G+C) within the range of that of mycobacteria (62 to 70% G+C), a size (4.4 x 10(6) to 4.7 x 10(6) bp) larger than that of most pathogenic mycobacteria (2.0 x 10(6) to 4.2 x 10(6) bp), and a high relatedness (> 90%) to Mycobacterium avium DNA. However, the DNAs of the two organisms can be distinguished by restriction fragment length polymorphism analysis. M. paratuberculosis genes coding for a transposase, a cell wall-associated protein (P34), and two heat shock proteins have been cloned and sequenced. Nucleic acid probes (two of which are species specific) are used, after PCR amplification, for M. paratuberculosis identification in stools and milk. As in leprosy, with disease progression, cellular immune reactions decrease and humoral immune reactions increase. Cutaneous testing with sensitins, lymphocyte proliferation assays, and cytokine tests are used to monitor cellular immune reactions in paratuberculosis, but these tests lack specificity. Complement fixation, immunodiffusion, and enzymometric tests based on antibodies to M. paratuberculosis extracts, to mycobacterial antigen complex A36, to glycolipids, and to proteins help identify affected cattle but are not species specific. The carboxyl-terminal portion of the 34-kDa cell wall-associated A36 protein (P34) carries species-specific B-cell epitopes and is the basis for an enzyme-linked immunosorbent assay. Diagnostic tests for paratuberculosis are also used in Crohn's disease, a chronic human ileitis mimicking Johne's disease, in which isolates identified as M. paratuberculosis have been found.
Bronchoscopic diagnosis of pneumonia
Authors: Baselski V S , Wunderink R G
Published: June 2016

Lower respiratory tract infections are characterized by significant morbidity and mortality but also by a relative inability to establish a specific etiologic agent on clinical grounds alone. With the recognized shortcomings of expectorated or aspirated secretions toward establishing an etiologic diagnosis, clinicians have increasingly used bronchoscopy to obtain diagnostic samples. A variety of specimen types may be obtained, including bronchial washes or brushes, protected specimen brushings, bronchoalveolar lavage, and transbronchial biopsies. Bronchoscopy has been applied in three primary clinical settings, including the immunocompromised host, especially human immunodeficiency virus-infected and organ transplant patients; ventilator-associated pneumonia; and severe, nonresolving community- or hospital-acquired pneumonia in nonventilated patients. In each clinical setting, and for each specimen type, specific laboratory protocols are required to provide maximal information. These protocols should provide for the use of a variety of rapid microscopic and quantitative culture techniques and the use of a variety of specific stains and selective culture to detect unusual organism groups.