bluuebunny/crossref_metadata_2025_split huggingface dataset:
Urine Cultures
Authors: Yarbrough Melanie L. 
Published: January 2025

Abstract
Urine culture results are reported semiquantitatively, as the colony count is used to guide the microbiological significance of bacteriuria. Thoughtful design and implementation of a urine reflex algorithm may improve diagnostic stewardship by increasing probability of a positive culture and decreasing overutilization of urine culture in cases of asymptomatic bacteriuria. Accordingly, interpretation of bacteria growing from urinary stone culture must take into account organism identification (e.g., urease producer, traditional uropathogen, traditional skin bacteria) and the mechanism by which the stone was obtained, in conjunction with concurrent urine culture results. Urinary stone disease is the result of urinary tract calcification leading to the formation of large mineral deposits. The exact molecular mechanism leading to the formation of urinary stones is unknown; however, there is a well‐understood association between the presence of bacteria within the genitourinary tract and formation of struvite stones.
Leptospira
Culture
Authors: Galloway Renee L. 
Published: January 2025

Abstract

Leptospirosis is a zoonosis caused by spirochetes of the genus
Leptospira
.
Leptospira
serovars that are antigenically related are further grouped into serogroups, primarily to simplify serologic diagnosis. Infection with
Leptospira
in humans may result in a wide spectrum of symptoms, ranging from mild, undifferentiated febrile illness to severe multiorgan system disease, with jaundice, renal failure, cardiac complications, severe pulmonary hemorrhagic syndrome, and high mortality. Clinical recognition of leptospirosis is difficult because leptospires can affect many different organ systems, resulting in a nonspecific clinical presentation. Consequently, leptospirosis is often misdiagnosed as influenza, malaria, aseptic meningitis, encephalitis, dengue fever, hepatitis, or gastroenteritis. Direct dark‐field smears are not recommended for leptospirosis diagnosis due to their lack of sensitivity. Leptospires are aerobic bacteria that can be cultivated at 30 degree Celsius in media containing either rabbit serum or bovine serum albumin and fatty acids.
Bartonella
Culture
Authors: Clarridge Jill E. , Harrington Amanda T. 
Published: January 2025

Abstract

The genus
Bartonella
comprises Gram‐negative short rod‐shaped bacteria that belong to the α‐2 subgroup of
Proteobacteria
. Depending on the level of host adaptation,
Bartonella
infection in the reservoir host ranges from asymptomatic to clinical manifestations with low morbidity and limited mortality or, rarely, life‐threatening disease, such as endocarditis. There are several methods of diagnosing bartonellosis in clinical specimens: serology, direct visualization, molecular methods such as polymerase chain reaction, and culture. Collection in ethylenediaminetetraacetic acid tubes or an Isolator tube system is the preferred method for culturing
Bartonella
species from blood. Detection of
Bartonella
species from clinical specimens using molecular methods has been shown to be more sensitive than culture for all specimen types and especially useful for cases in which lymphadenectomy or biopsy is not feasible or serologic results are equivocal.
Identification of Gram‐Positive Bacteria
Authors: Bernard Kathryn 
Published: January 2025

Abstract
Unlike in the case of Gram‐negative bacilli, it can be difficult to definitively identify Gram‐positive cocci and bacilli to the genus and species levels. Gram‐positive bacilli have been difficult to identify because pathogens have to be discerned from hundreds of validly named species that are found in the environment or are part of the normal microbiota of the human body, including the skin, mucosal membranes, oropharynx, and genitourinary and gastrointestinal tracts, and the taxonomy of such agents is both evolving and being augmented. For species‐level identification of viridans group streptococci, enterococci, and corynebacteria, commercial kits are often easier to perform than standard tube biochemical tests, but both approaches have limitations in accuracy. Because of the lack of unique colony morphologies for many Gram‐positive microorganisms, the Gram stain must be performed on isolates for identification. Gram‐variable microorganisms are considered Gram positive.
Identification of Gram‐Negative Bacteria
Authors: Munson Erik , Podzorski Raymond P. 
Published: January 2025

Abstract
The Gram‐negative bacteria are a heterogeneous group of organisms consisting of numerous families, genera, and species, many of which cause serious disease and endotoxic shock. The accurate, rapid identification of Gram‐negative bacilli, coccobacilli, and diplococci makes it possible to provide timely, meaningful treatment and diagnosis of disease. Commercial kit‐based identification systems do an excellent job of identifying most pathogens with minimal work and are often a major tool in the laboratory's identification system. Deciding when to use a commercial system and which system to use for identification is key to success in providing the identification in a timely manner. The speed of identification and extremely low reagent cost make the technology a desirable means of organism identification in the clinical microbiology setting. In the course of the potential rapid identification of Gram‐negative coccobacilli and Gram‐negative bacilli, the clinical microbiology laboratory may encounter isolates that are potential agents of bioterrorism.
Introduction
Authors: Schuetz Audrey N. 
Published: January 2025

Abstract
Anaerobic bacteria are a significant component of the normal microbiota of the human host. There are anaerobes present on most body surfaces and mucous membranes; they exist in large numbers throughout the entire gastrointestinal tract, from the mouth to the colon; and they are found in large numbers in the female genitourinary tract. Anaerobic bacteria can cause a wide variety of infections, including wound infections as a result of trauma or surgery; abscesses of the liver, brain, lung, and other local sites; appendicitis; peritonitis; chronic otitis media and sinusitis; endophthalmitis; bacteremia; endocarditis; myonecrosis; gas gangrene; and dental and oral infections. This chapter discusses resurgence of Lemierre's syndrome and the increased association of newly named and emerging anaerobes with many types of infections. It describes acceptable specimen collection, transport, and inoculation for anaerobe recovery. The chapter provides situational examples outlining the extent to which anaerobe work‐up should be followed.
Specimen Selection, Collection, and Transport for Anaerobic Culture
Authors: Harriott Melphine M. , Brown Kristen L. 
Published: January 2025

Abstract
Proper collection of specimens, to avoid contamination with organisms of the normal microbiota, and prompt transport to the laboratory for processing are essential. This is especially true for specimens sent to the laboratory for anaerobic culture. The laboratory director and staff must provide health care personnel with guidelines for the optimal type and amount of clinical specimens that are needed for anaerobic culture, including the appropriate methods for specimen collection. Patient care units, clinics, emergency rooms, and satellite facilities should be provided with appropriate collection and transport devices and complete instructions for their use. The ideal transport system should maintain the viability of the anaerobes during transport without allowing the overgrowth of members of the normal microbiota that are not a part of the pathogenic process. Good communication between the clinical microbiology laboratory and the clinical staff will ensure that collection and transport are optimal.
A Practical Guide to the Workup of Anaerobic Cultures
Authors: Shannon Samantha K. , Pence Morgan A. 
Published: January 2025

Abstract
This chapter provides a practical guidance to the workup of anaerobic cultures. When a specimen is sent to the laboratory in an appropriate container and from an appropriate site with a request for anaerobe testing, a Gram stain should be performed and reported. All specimens for which anaerobe culture is requested should undergo simultaneous aerobic culture. Workup of anaerobic cultures should be completed while taking into account the corresponding aerobic culture. In cultures with three or more organisms, workup may focus on the bacteria with the highest potential to be pathogenic. The extent of workup of anaerobes may vary based on whether the specimen was collected from a nonsterile site or a sterile site. The chapter provides the information of identification of anaerobic bacteria isolated from nonsterile sites. Identification procedures that require a week or more to complete may be of academic interest only.
Commercial Kit and Rapid Enzymatic Systems for the Identification of Anaerobes
Authors: Valencia‐Shelton Frances , Bard Jennifer Dien 
Published: January 2025

Abstract
Biochemical systems for identification of anaerobes rely on the metabolic breakdown of substrates and the production of end products during the growth of the isolated organism. There is currently one commercially packaged kit system that uses this method for the identification of commonly isolated anaerobic bacteria in the clinical microbiology laboratory: the API 20A system. The API 20A requires overnight incubation, whereas rapid identification of anaerobes can be accomplished with commercially available microsystems that detect preformed enzymes of isolate suspension within a few hours. Database and numerical identification profiles are provided by the manufacturer for each system. Identification of anaerobes to the species level was reported at 74% with rapid enzymatic systems, compared to 50% with API 20A. The use of rapid methods such as matrix‐assisted laser desorption ionization–time‐of‐flight mass spectrometry has certainly replaced biochemicals and enzymatic reactions in many laboratories.
MALDI‐TOF MS for Filamentous Fungi Identification
Authors: Hanson Kimberly E. , Sobczyk Juliana , Snavely Emily 
Published: January 2025

Abstract
Identification of fungi in the clinical microbiology laboratory has traditionally relied on a combination of phenotypic characteristics, including colony morphology, microscopic examination, growth characteristics, and biochemical reactions. Sequencing‐based approaches require specialized molecular expertise, can be costly, and are relatively slow. Matrix‐assisted laser desorption ionization‐time of flight (MALDI‐TOF) mass spectrometry (MS) is a more rapid and inexpensive methodology that has been used for the identification of microorganisms, including molds, in the microbiology laboratory. Organisms are identified by using intact cells or cell protein extracts which are ionized into charged molecules using a laser. By measuring the mass to charge ratio of the ionized molecules, a spectral fingerprint is generated. These spectral fingerprints are then compared with a database of known spectra from reference organisms to generate an accurate, species‐level identification. This chapter describes protocols for application of MALDI‐TOF MS to identify filamentous fungi in the clinical microbiology laboratory.
Disk Diffusion Testing
Authors: Ransom Eric M. , Burnham Carey‐Ann D. , Matuschek Erika 
Published: January 2025

Abstract
The goal of antimicrobial susceptibility testing (AST) is to provide useful information to assist clinicians with the selection of antimicrobial therapy for patient care. An AST reference method that is widely used worldwide is disk diffusion testing. Disk diffusion testing was originally described by AW Bauer and colleagues in 1966. The method uses a standardized inoculum of bacteria swabbed onto the surface of an agar plate, most commonly Mueller‐Hinton agar. This chapter describes how to perform disk diffusion testing and describes testing guidance from CLSI and EUCAST. It provides troubleshooting tips, quality control information, and a disk diffusion reading guide. Both CLSI and EUCAST have developed standardized disk diffusion methods calibrated to the reference MIC method. While both disk diffusion methods are based on the same basic methodology, there are important differences. These include the supplements in media for fastidious organisms, disk contents for some antimicrobial agents, and interpretive categories.
Screening Tests for Detection of High‐Level Mupirocin Resistance in
Staphylococcus aureus
Authors: Hemarajata Peera 
Published: January 2025

Abstract

High‐level mupirocin resistance (HLMR) in
Staphylococcus aureus
is defined by a mupirocin MIC of ≥512 μg/ml and is associated with the presence of plasmidencoded
mupA
or, less commonly,
mupB
genes in these isolates. Screening methods for detection of HLMR include assessing growth at a high concentration of mupirocin by broth microdilution or by disk diffusion using a 200‐μg mupirocin disk. Mupirocin ointment use is associated with increased rate of HLMR in
S. aureus
and, in particular, methicillin‐resistant
S. aureus
(MRSA). Failure of attempted MRSA decolonization using mupirocin may result in selection for genetic elements conferring resistance to other classes of antimicrobials.
Detection of Inducible Clindamycin Resistance in
Staphylococcus
spp.,
Streptococcus Pneumoniae
, and
Streptococcus
spp. Beta‐Hemolytic Group
Authors: Bard Jennifer Dien 
Published: January 2025

Abstract

Inducible clindamycin resistance (ICR) in staphylococci and streptococci can be detected by agar disk diffusion (D‐zone test) or broth microdilution methods. Prior to reporting clindamycin results, the CLSI recommends testing for ICR in all staphylococci,
Streptococcus pneumoniae
, and beta‐hemolytic streptococci that are resistant to erythromycin and susceptible or intermediate to clindamycin. Isolates with ICR should be reported as clindamycin resistant alongside a comment stating that the isolate is presumed to be resistant to clindamycin based on the presence of ICR, as determined by testing clindamycin in combination with erythromycin. It is best to perform the ICR test concurrently with individual tests for erythromycin and clindamycin, especially with the MIC method. 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.
AmpC Beta‐Lactamase Testing
Authors: Yee Rebecca , Simner Patricia J. 
Published: January 2025

Abstract
AmpC beta‐lactamases are Ambler class C beta‐lactamases, containing serine residues at their catalytic active site. AmpC beta‐lactamases can be expressed constitutively or induced in response to β‐lactam exposure. High‐level expression of AmpC beta‐lactamase can cause resistance to aminopenicillins, cephalosporins, cephamycins, monobactams, and sometimes cefepime and piperacillin‐tazobactam. This chapter describes three principal mechanisms of AmpC beta‐lactamase resistance: chromosomally encoded inducible resistance, noninducible chromosomal resistance, and acquired ampc beta‐lactamases. The European Committee on Antimicrobial Susceptibility Testing describes a method for detection of plasmid‐mediated AmpC among group 1 Enterobacterales that lack inducible AmpC for infection control or epidemiologic purposes only. This procedure describes a disk diffusion method for AmpC beta‐lactamase detection which requires two disks: cefoxitin alone and cefoxitin disk supplemented with cloxacillin. The chapter covers quality control principles for analytical tests. With postanalytical considerations, it provides attention to common test limitations, interpretive challenges, and results reporting.
Phenotypic Carbapenemase Detection Methods
Authors: Westblade Lars F. , Marino Jamie , Moore Nicholas M. , Poirel Laurent , Nordmann Patrice 
Published: January 2025

Abstract
The presence of a carbapenemase in an organism of interest may be assessed by phenotypic or genotypic assays. Phenotypic detection methods include broad carbapenemase detection methods that differentiate carbapenemase‐producing, carbapenem‐resistant Gram‐negative organisms from non‐carbapenemase‐producing, carbapenem‐resistant Gram‐negative organisms for which carbapenem resistance is mediated by other mechanisms. These tests include the carbapenem inactivation tests, which require overnight incubation e.g., the modified Hodge test and modified carbapenem inactivation method, or rapid colorimetric tests that exploit a carbapenemase dependent pH change due to hydrolysis of a carbapenem (e.g., Carba NP). Other phenotypic tests allow for identification and differentiation of metallo‐β‐lactamases from serine carbapenemases (e.g., the ethylenediaminetetraacetic acid‐modified carbapenem inactivation method and the combined disk test).
Introduction
Authors: Saubolle Michael A. 
Published: January 2025

Abstract

The group of bacteria known as aerobic actinomycetes is made up of Gram‐positive bacilli delineated by a vast array of heterogeneous and taxonomically divergent genera in the order
Actinomycetales
. Some genera contain mycolates and can be stained by the modified acid‐fast stain. The aerobic actinomycetes are found worldwide and are important components of natural and human‐made environments; some may be components of the human microbiome, while others may transiently contaminate or colonize superficial sites. Infection in humans is most frequently opportunistic, associated with either trauma, an immunocompromising condition, or the presence of a foreign object or device in the human host.
Nocardia
is the most common genus involved in human infections. The importance of identifying the
Nocardia
to the species level is due to many species having characteristic antimicrobial susceptibility profiles and some species having inconsistent and falsely resistant
in vitro
antimicrobial results.
Appendixes
Authors: Saubolle Michael A. , Bell Melissa E. , Sussland Zdenek 
Published: January 2025

Abstract

Comparatively, the aerobic actinomycetes are rarely encountered in human disease, although geographic variation of prevalence may be seen. Of this group of organisms, the
Nocardia
spp. are the most prevalent pathogens. Although there are 149 species recognized in the genus
Nocardia
at this time, in three studies spanning from 2006 to 2017 and including isolates (total of 4,973) from the United States and Europe, 6 species or complexes made up almost 80% of all isolates:
Nocardia nova
complex,
N. cyriacigeorgica
,
N. farcinica
complex,
N. abscessus
complex,
N. brasiliensis
, and
N. transvalensis
complex. An additional 3 species (
N. otitidiscaviarum
,
N. beijingensis
, and
N.pseudobrasiliensis
) increased that rate to approximately 93% of all species isolated.
Liquid Media Used for Isolation
Authors: Pfeltz Richard F. , Wengenack Nancy L. 
Published: January 2025

Abstract

The use of liquid medium for isolation of mycobacteria and drug susceptibility testing of
Mycobacterium tuberculosis
complex was first introduced in 1980 as the BACTEC 460 radiometric system. The BACTEC MGIT automated system includes mycobacterial growth indicator tubes which contain liquid culture medium consisting of modified Middlebrook 7H9 broth, a separate growth supplement, and an antimicrobial agent mixture which is added separately to the medium. The antimicrobial agent mixture suppresses the growth of contaminating bacteria. The VersaTREK Myco culture system for the isolation of mycobacteria from clinical specimens consists of a modular arrangement of incubator and detection instruments and medium‐containing culture bottles. The VersaTREK instrument detects mycobacterial growth by automatically monitoring the rate of consumption of oxygen as a change in pressure within the headspace of the culture bottle. This chapter covers proper quality control principles for analytical tests. With postanalytical considerations, it provides attention to common test limitations, interpretive challenges, and results reporting.
Identification of Mycobacteria
Authors: Wengenack Nancy L. , Jonas‐Taggart Vivian , Vagnone Paula Snippes 
Published: January 2025

Abstract
This chapter provides the conventional biochemicals as a historical consideration, but their use has largely been eliminated from clinical laboratories and replaced with more rapid methods, including DNA probes, MALDI‐TOF mass spectrometry, and various molecular procedures. It also presents accuprobe mycobacterial culture identification tests. AccuProbe assays use a chemiluminescently labeled, singlestranded DNA probe that is complementary to the target organism's rRNA. The labeled DNA‐RNA hybrids are then measured in the Leader luminometer. The INNO‐LiPA MYCOBACTERIA v2 utilizes material from growing cultures that are suggestive of a mycobacterial species, from both solid and liquid media. 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.
Susceptibility Testing by Liquid Media Methods
Authors: Pfeltz Richard F. , Quinn Brigit , Wengenack Nancy L. 
Published: January 2025

Abstract

The BACTEC MGIT SIRE kit is a nonradiometric antimicrobial susceptibility testing (AST) system for testing
Mycobacterium tuberculosis
from isolated culture. It provides susceptibility results for streptomycin, isoniazid (INH), rifampin (RIF), and ethambutol (EMB). The BACTEC MGIT SIRE kit is a 4‐day to 13‐day qualitative test. The BACTEC MGIT 960 pyrazinamide (PZA) kit is a nonradiometric AST system for testing
Mycobacterium tuberculosis
from isolated culture against PZA. The BACTEC MGIT PZA kit is a 4‐day to21‐day qualitative test. The VersaTREK automated microbial detection system has been adapted for the performance of antimycobacterial susceptibility testing to the first‐line agents RIF, INH, EMB, and PZA with clinical isolates of
Mycobacterium tuberculosis
. This chapter focuses on the specimen, materials, quality control, results and interpretation, reporting results and limitations of procedure.
Introduction and General Considerations
Authors: Lockhart Shawn R. , Wiederhold Nathan P. 
Published: January 2025

Abstract
This part introduction presents an overview of the key concepts discussed in the subsequent chapters. The part brings together the contributions of well‐respected mycologists, whose expertise will help laboratories become more adept at identifying fungi, recognizing the significance of an isolated organism, and performing susceptibility testing. Fungi can cause severe illness, but they are often overlooked as causes of clinical disease and often considered only after other etiologies have been ruled out. Infections range in severity from cosmetic onychomycosis to life‐threatening disseminated disease. In some fungal diseases (histoplasmosis and coccidioidomycosis), the histopathology services may provide the first diagnostic evidence of the disease while the clinical laboratory provides confirmation of the etiology using culture or molecular methods. The appearance of the fungal organism in tissue, along with patient history, risk factors, and signs and symptoms, provides the best guidance about the likely etiology, but these should be confirmed whenever possible by culture.