bluuebunny/crossref_metadata_2025_split huggingface dataset:
Culture Media for Anaerobes
Authors: Bard Jennifer Dien , Copsey‐Mawer Sarah , Precit Mimi 
Published: January 2025

Abstract

Selection of media is key to the recovery of anaerobic organisms from clinical specimens. Primary culture media are those onto which direct specimens are inoculated and may be enriched, nonselective, selective, or differential to allow for the initial recovery of clinically significant anaerobes and inhibition of facultative anaerobe overgrowth. Subculture of anaerobes from primary media to secondary media that are selective and/or differential aids in further identification of clinically significant anaerobes. Proper selection of the initial media used during specimen processing of anaerobic bacteriology aids in the overall accuracy of the workup and assists in recognition of key phenotypic characteristics including colonial morphology. As some anaerobes can be highly sensitive to oxygen exposure, it is recommended that prereduced, anaerobically sterilized media be used to inoculate clinical specimens. Anaerobes have a wide range of nutritional needs, but most strict anaerobes require hemin and vitamin K
1
.
Incubation Techniques for Anaerobic Bacteriology Specimens
Authors: Morris Trefor E. 
Published: January 2025

Abstract
This chapter describes the various environmental methods and incubation conditions used for anaerobic bacteriology specimens once a properly selected, collected, and transported specimen arrives in the laboratory. Ideally, the specimen is processed immediately on arrival in the laboratory and incubated under anaerobic conditions to prevent further exposure to oxygen. In general, growing cultures must not be exposed to oxygen for examination of culture media until after 48 h of incubation, since anaerobes are most sensitive to oxygen during the log phase of growth. One of the obvious advantages of using an anaerobic chamber/workstation is that technologists can inspect inoculated media without removing them from the anaerobic environment. The choice of incubation systems is influenced by cost, the number of anaerobic cultures performed, and laboratory space limitations. The anaerobic environment is monitored with a methylene blue strip or resazurin indicator.
Anaerobic Gram‐Negative Bacilli
Authors: She Rosemary C. , Church Deirdre L. 
Published: January 2025

Abstract

The anaerobic Gram‐negative bacteria are part of the microbiota of the oral cavity, gastrointestinal tract, and urogenital tract. Many taxonomic changes have been instituted based on newer biochemical and molecular sequencing considerations. Many of the bile‐sensitive species of Gram‐negative bacilli, such as
Prevotella
and
Porphyromonas spp.
, make up a large percentage of the normal microbiota in the oral cavity and are involved in many different types of oral infections. The pigmented anaerobic Gram‐negative bacilli include members of the genera
Prevotella
,
Porphyromonas
, and
Alistipes
. The chapter includes a few additional Gram‐negative rods of human pathogenicity. It also helps the laboratory staff to perform all analyses, including appropriate quality control recommendations, from the receipt of the specimen (anaerobic Gram‐negative bacilli) through processing, testing, interpretation, presentation of the final report, and subsequent consultation.
Anaerobic Gram‐Positive Bacilli
Authors: Bernard Kathryn , Hamula Camille 
Published: January 2025

Abstract

Anaerobic Gram‐positive bacilli of clinical relevance in human infections are divided into two distinct groups: sporeforming Gram‐positive anaerobic bacilli, including
Clostridium sensu stricto
and allied genera, and a group of asporogenic, anaerobic Gram‐positive bacilli (Grampositive rods (GPRs)). Many of these anaerobic GPRs are part of the normal microbiota of the oral cavity, gastrointestinal tract, genitourinary tract, and skin. They can, however, be associated with skin and soft tissue infections, periodontitis and other oral infections, pulmonary infections (usually in combination with other aerobes and anaerobes), genitourinary tract infections, and, in the case of
Cutibacterium acnes
, infected CSF shunts, prosthetic joint infections, and endophthalmitis. Many of the nonsporeformers are aerotolerant and are often resistant to metronidazole, an antimicrobial agent that is usually effective against most other anaerobes.
Clostridioides
(
Clostridium
)
difficile
as a Pathogen Involved in Antimicrobial Agent‐Associated Diarrhea, Colitis, and Pseudomembranous Colitis
Authors: Carroll Karen C. , Paulick Ashley L. 
Published: January 2025

Abstract

Clostridioides (Clostridium) difficile
is a major cause of health care‐associated diarrhea and the primary pathogen responsible for pseudomembranous colitis. Recent epidemiological trends note decreases in health care‐acquired
C. difficile
as a possible consequence of decreased fluoroquinolone use and increases in cases in the community in individuals lacking traditional risk factors. While
C. difficile
colitis was originally dubbed “clindamycin‐associated pseudomembranous colitis”, any antimicrobial agent, including those used to treat the infection itself (i.e., metronidazole and vancomycin), can be a risk factor. Disease results from action of toxins produced by the bacteria.
C. difficile
produces two toxins: toxin A, a weakly cytopathic toxin, is predominantly responsible for the enterotoxic activity of the organism, and toxin B, a potent cytotoxin, appears to play a major role in human disease.
Preanalytical Considerations and Laboratory Processing of Samples for Blood Culture
Authors: Tibbetts Robert J. , Harrington Amanda T. 
Published: January 2025

Abstract
This chapter presents the preanalytical considerations and laboratory processing of samples for blood culture. Bloodstream infection and sepsis remain one of the most significant causes of morbidity and mortality worldwide. Establishing an etiologic diagnosis for bloodstream infections is an essential role of clinical microbiology laboratories. The number of blood culture bottles collected and the volume of blood collected in each bottle also significantly impact recovery of organisms and interpretation of results. The volume of blood obtained for culture is typically determined using an age‐ or weight‐based calculation. Adequate volume of blood is the single most important factor in the laboratory detection of microorganisms in the bloodstream, regardless of age; when blood culture is optimized to the recommended volumes, the more likely a culture will be positive. Blood culture collection prior to administration of antimicrobials is essential for optimal organism recovery.
Quality Control and Quality Assurance for Blood Cultures
Authors: Martinez Raquel M. 
Published: January 2025

Abstract
Because of the impact on patient care, blood cultures are considered among the most important microbiology tests performed. Quality control (QC) begins with acquiring a blood culture instrument and associated blood culture media, then verifying and validating the performance for clinical use. Like QC, quality assurance (QA) programs are essential to ensure accurate and reliable results. For blood cultures to perform as intended, specific preanalytical, analytical, and postanalytical criteria must be met. The volume of blood collected for culture is the most critical of all the quality benchmarks, as it is the most significant factor impacting culture positivity. The analytical QA metrics specific to blood cultures, such as percent contamination and percent positivity, are directly impacted by the preanalytical variables including fill volume and the number of bottles submitted. Higher rates of contamination are associated with certain specimen types, such as line draws, lower‐extremity venipuncture, and arterial puncture.
Specialized Processing of Blood
Authors: Chamberland Robin R. 
Published: January 2025

Abstract

Transfusable blood components, including platelets, red blood cells, and plasma, pose a risk of transfusion‐transmitted bacterial infection (TTBI). Platelet products are associated with the highest risk of TTBI of all transfusable blood components, with an overall rate of 1.95 per 10
5
units transfused. This chapter focuses on the microbiologic evaluation of transfusion reaction. In cases of suspected TTBI, the transfusion should be stopped, and the port should be covered or the tubing clamped. The component bag containing any residual product should be placed in a sealed plastic bag and transported to the laboratory immediately for culture. Culture of transfused blood products should always be accompanied by concurrent blood cultures performed for the patient experiencing a transfusion reaction. The chapter focuses on the specimen collection, transport, and handling, materials, quality control, interpretation, reporting results and limitations of procedure.
Identification of Highly Pathogenic Bacteria by MALDI‐TOF MS
Authors: Tran Anthony 
Published: January 2025

Abstract
The use of matrix‐assisted laser desorption ionization–time of flight mass spectrometry (MALDI‐TOF MS) for identification of pathogenic bacteria and fungi has become popular in diagnostic microbiology and public health laboratories due to its accuracy and speed of microorganism identification. Based on the presence or absence of organisms in the MALDI‐TOF MS library, testing of select agents may yield no identification or misidentifications. A biological risk assessment should be conducted prior to implementation of MALDI‐TOF MS to mitigate the risks to the laboratorian conducting the test. The biological risk assessment should be reviewed periodically as well as any time changes to the instrument or the MALDI‐TOF MS. This chapter focuses on the specimen collection, reagents and equipment, calibration and quality control, reporting results and limitations of procedure.
Agar Dilution MIC Test
Authors: Patel Samir N. 
Published: January 2025

Abstract
The agar dilution MIC test is a quantitative method for the determination of in vitro activity of an antimicrobial agent against bacterial isolates, such as aerobic and anaerobic bacteria. Following incubation using conditions appropriate for the test organisms, the MIC is determined by observing the lowest concentration of antimicrobial agent that inhibits visible growth of each test isolate. MICs obtained are interpreted as susceptible, intermediate, susceptible dose‐dependent, resistant, or non‐susceptible based on criteria defined by the CLSI or by the European Committee on Antimicrobial Susceptibility Testing. Recommendations for performance of the agar dilution method for susceptibility testing of aerobic bacteria are found in the CLSI M07 standard and include procedures for both non‐fastidious and fastidious organisms. The chapter covers proper quality control principles for analytical tests. With postanalytical considerations, it provides attention to common test limitations, interpretive challenges, and results reporting.
Beta‐Lactamase Tests
Authors: Campeau Shelley , Deak Eszter 
Published: January 2025

Abstract

Beta‐lactamases are important mediators of bacterial resistance to beta‐lactam agents. The beta‐lactamase tests detect penicillinases where detection predicts resistance to the penicillinase‐labile penicillins. Routine beta‐lactamase tests are performed directly from bacterial colonies and are based on visual detection of the end products of beta‐lactamase hydrolysis, demonstrated with a colorimetric reaction. Direct beta‐lactamase testing can be performed on Gram‐negative and Grampositive anaerobes other than the
Bacteroides fragilis
group, as organisms in the
B. fragilis
group are beta‐lactamase producers and predictably resistant to penicillin, amoxicillin, and ampicillin. For direct beta‐lactamase tests, coagulase‐negative staphylococci may require induction to demonstrate a positive beta‐lactamase reaction.
Preparation of Routine Media and Reagents Used in Antimicrobial Susceptibility Testing
Authors: Lonsway David R. 
Published: January 2025

Abstract
McFarland turbidity standards are used to standardize the approximate number of the book bacteria in a liquid suspension by visually comparing the turbidity of a test suspension with the turbidity of a McFarland standard. Aliquots of antimicrobial stock solutions are incorporated into broth or agar medium for antimicrobial susceptibility tests. Stock solutions are prepared from laboratory reference standard‐grade antimicrobial powders. These are assayed for the amount of active agent present, and this is expressed as potency or activity, which is usually defined in terms of micrograms of active drug per milligram. Specific agar and broth media used for routine disk diffusion, agar dilution, and broth dilution susceptibility tests are prepared from commercially available dehydrated components. Although these media have shown fairly good reproducibility through many years of testing, they are undefined media, and there may be subtle performance differences among batches and lots.
Media and Methods Used for Phenotypic Characterization of Aerobic Actinomycetes
Authors: Bell Melissa E. , Sussland Zdenek , Mochon A. Brian 
Published: January 2025

Abstract
Aerobic actinomycetes can be identified to the genus level using a variety of conventional phenotypic characteristics. Despite most laboratories lacking access to some of Gordon's oxidative agar slants and media containing purine‐related compounds, the examination of microscopic and macroscopic morphologies combined with a few common physiologic tests can give a presumptive identification to the genus or even species level in most cases. This chapter provides an illustration of a schematic flowchart for the tentative phenotypic identification of medically important aerobic actinomycetes and related genera. The use of Gram‐stained and modified acid‐fast smears and colonial morphology, especially the presence/absence of aerial hyphae and growth in lysozyme broth, will presumptively identify most aerobic actinomycetes to at least the genus level.
General Mycobacterial Procedures
Authors: Wengenack Nancy L. 
Published: January 2025

Abstract

Tubercular bacilli may be present in a variety of specimens that will be sent to the clinical mycobacterial laboratory for processing. Procedures that potentially may generate an aerosol, such as specimen processing, must be conducted in a biological safety cabinet until the specimen is inactivated. Sodium citrate is included in the digestion mixture to bind the heavy metal ions present in the specimen that could inactivate the
N
‐Acetyl‐L‐cysteine. Specimens requiring decontamination include sputum, induced sputum, bronchial alveolar lavage fluid, bronchial wash fluid, skin and soft tissue specimens, gastric lavage specimens, and urine and other body fluids, such as ascites and peritoneal fluid. Specimens from the respiratory tract are typically contaminated with large numbers of respiratory microbiota that must be significantly reduced in quantity to optimize the recovery of smaller numbers of acid‐fast bacilli.
Nucleic Acid Amplification Procedures for Identification from Specimens
Authors: Baron Ellen Jo , Gnanashanmugam Devasena 
Published: January 2025

Abstract

This chapter covers nucleic acid amplification procedures for identification from specimens. These tests include: Cepheid Xpert MTB/RIF test, Xpert MTB/RIF Ultra test, and Cepheid Xpert MTB/XDR test. Several studies have shown that results from one Xpert® MTB/RIF assay are more predictive of pulmonary tuberculosis in previously undiagnosed patients; thus, the U.S. National Tuberculosis Controllers Association has issued a guideline on use of this assay for patient diagnostic and infection prevention interventions. The Xpert MTB/RIF Ultra test demonstrates a higher sensitivity in M. tuberculosis complex detection than the Xpert MTB/RIF test, and using melt curve analysis to identify RIF resistance‐associated mutations may allow for more accurate RIF resistance detection in some regions. The Xpert MTB/XDR test is an
in vitro
diagnostic test for the detection of extensively drug‐resistant Mycobacterium tuberculosis complex.
Antifungal Susceptibility Testing
Authors: Wiederhold Nathan P. , Lockhart Shawn R. 
Published: January 2025

Abstract

Antifungal susceptibility testing (AFST) is performed as part of clinical diagnostic testing in order to provide information to clinicians that may help guide treatment in patients with fungal infections. AFST is used during the preclinical development of investigational agents to determine the scope of in vitro activity and the potency of an agent. The AFST methods primarily used for both yeasts and molds, including those standardized by Clinical and Laboratory Standards Institute (CLSI) and European Committee on Antimicrobial Susceptibility Testing (EUCAST), are broth dilution formats that quantitatively measure the
in vitro
activity of an antifungal agent against a fungal isolate. In order to make AFST less costly and more readily available to clinical microbiology laboratories, CLSI has developed standards for disk diffusion testing similar to those used for testing of bacteria that grow aerobically. Gradient diffusion testing is also available, although this method has not been standardized by CLSI or EUCAST.
Collection and Preservation of Fecal Specimens
Authors: Couturier Marc R. 
Published: January 2025

Abstract
One of the most important steps in the diagnosis of intestinal parasites is the proper collection of specimens. Fresh specimens are mandatory for the recovery of motile trophozoites. Fecal specimens for parasite examination that cannot be processed and examined in the recommended time should be placed in an appropriate fixative/preservative. Many commonly used fixatives, such as formalin and other aldehydes, also make the specimen more susceptible to staining. Ethanol is a commonly used preservative. In outpatient situations, it may be necessary for a specimen to be shipped to the laboratory for examination. Only fecal specimens in appropriate fixative should be shipped, as any delays in examination may result in deterioration of parasitic organisms.
Conventional Tube Cell Culture for Primary Virus Isolation
Authors: Hodinka Richard L. , Relich Ryan F. 
Published: January 2025

Abstract
For decades, cell culture was considered the reference standard in diagnostic virology laboratories for the primary isolation and identification of viruses from clinical specimen. Virus culture has played a significant role in the identification and knowledge of novel and clinically relevant human viruses such as metapneumovirus, severe acute respiratory syndrome coronavirus, human coronavirus NL63, Middle East respiratory syndrome coronavirus, and SARS‐CoV‐2. For the isolation of human pathogenic viruses, monolayer cultures of permissive mammalian cells are generally used. Several variables can influence the virus susceptibility of cell cultures and therefore their sensitivity for virus detection. In conventional virus cultures, isolation of viruses is traditionally performed by inoculating clinical specimens into prepared monolayers of cultured cells adhered to the inside of glass or plastic test tubes. The chapter covers proper quality control principles for analytical tests. With postanalytical considerations, it provides attention to common test limitations, interpretive challenges, and results reporting.
Tests for Direct Detection of Viruses in Clinical Specimens
Authors: Hodinka Richard L. , Banerjee Dithi , Selvarangan Rangaraj , Thomas Lynita , Glaser Laurel J. 
Published: January 2025

Abstract
Rapid solid‐phase immunoassays for direct detection of viral antigens in clinical specimens are commercially available and are most commonly used for influenza virus types A and B and respiratory syncytial virus (RSV). It is important to rapidly detect and distinguish disease caused by influenza viruses, RSV, or SARS‐CoV‐2 to provide early treatment with available antiviral therapy, improve clinical care and outcomes, and implement adequate infection control measures; for surveillance of communicable diseases; for outbreak containment; and to inform public health interventions. When using immunofluorescence assays, cells from submitted clinical specimens are fixed to the surface of glass slides and viral protein antigens within intact infected cells are detected using virus‐specific primary antibodies. The common staining techniques applied to cytologic and histologic specimens provide the initial assessment of viral infection. The detection of viruses in exfoliated cells and tissue plays a critical role in the diagnostic process.
Detection of
Francisella tularensis
Antibodies
Authors: Peterson Jeannine M. , Dietrich Elizabeth A. 
Published: January 2025

Abstract

Tularemia is a disease with multiple clinical forms, which results from infection by
Francisella tularensis
, a facultative Gram‐negative coccobacillus. Two subspecies of
F. tularensis
cause human infection:
Francisella tularensis
subsp.
tularensis
and
Francisella tularensis
subsp.
holarctica
. Serology can be used to aid diagnosis of all clinical forms of tularemia. The main antigen detected in
F. tularensis
serologic assays is lipopolysaccharide, a primary component of the bacterium's outer membrane. Testing formats include agglutination, ELISA, indirect immunofluorescence assay, and immunochromatographic assays. The agglutination test, using formalin‐inactivated bacteria, has long been used for detection of total anti‐
F. tularensis
antibodies and is still the standard method. ELISAs, using an
F. tularensis
LPS antigen extract, often separately detect IgM and IgG antibodies.
Detection of
Borrelia burgdorferi
Antibodies
Authors: Aguero‐Rosenfeld Maria E. 
Published: January 2025

Abstract

Lyme disease, or Lyme borreliosis (LB), is a multisystem disease caused by members of the
Borrelia burgdorferi sensu lato
complex and is transmitted through the bite of infected
Ixodes sp.
ticks.
B. burgdorferi sensu lato
is composed of several geno species that cause different manifestations of LB. B. burgdorferi is a motile, helically shaped bacterium with multiple endoflagella and with a complex antigenic composition. A tremendous amount of knowledge has been ascertained with respect to serologic testing for antibodies to
B. burgdorferi
since the original assays were developed. Depending on Food and Drug Administration approval, these assays may be used as either first‐tier or second‐tier tests in the standard two‐tiered testing or modified two‐tier testing algorithm. The most appropriate specimen for testing is serum. Interpretation guidelines are included in the manufacturer's package insert.
Serologic Tests for Diagnosis of
Histoplasma capsulatum
Authors: Slev Patricia , Rychert Jenna 
Published: January 2025

Abstract

Histoplasmosis is the most common endemic fungal infection in the United States, where it is endemic in the Ohio and Mississippi river valleys. Infection with Histoplasma capsulatum is generally due to environmental exposure and is not considered contagious between humans or animals. Diagnosis of histoplasmosis can be made by a variety of methods, including culture, molecular testing, histopathology, serology, and antigen detection in a variety of body fluids. There are four methods for
H. capsulatum
antibody detection: complement fixation (CF), immunodiffusion (ID), latex agglutination, and enzyme immunoassay. CF and ID are the reference standard serologic methods for detection of antibodies against
H. capsulatum
and should be performed in parallel for diagnosis. The chapter covers proper quality control principles for analytical tests. With postanalytical considerations, it provides attention to common test limitations, interpretive challenges, and results reporting.