bluuebunny/crossref_metadata_2025_split huggingface dataset:
Processing Specimens for Anaerobic Culture
Authors: Morris Trefor E. 
Published: January 2025

Abstract
This chapter presents the procedure for processing specimens for anaerobic culture. This procedure describes the steps for processing a specimen for anaerobic culture once received within the laboratory. The overarching aim is to complete these steps within the shortest possible timeframe so that there is no loss of organism viability. Ideally, all processing should take place within an anaerobic chamber, as this allows all stages to occur within an anaerobic environment. All specimens should be examined macroscopically (visually), with reference made to any significant characteristics, and microscopically via Gram stain. The procedure includes the steps, such as visual examination, microscopic examination via Gram stain, specimen preparation, inoculation of media, and incubation.
Examination of Primary Culture Plates for Anaerobic Bacteria
Authors: Morris Trefor E. 
Published: January 2025

Abstract
The goal of processing primary culture plates is to isolate significant anaerobic organisms from the original specimen for identification and susceptibility testing when it is indicated. Comparison of culture results with what was seen on the original Gram stain of the specimen is critical. When culture plates are evaluated, all morphotypes observed in the original Gram stain should match the aerobes and anaerobes recovered. It is important to remember that anaerobic culture media permit facultatively anaerobic bacteria to grow. All bacterial isolates must be subjected to aerotolerance testing before being designated as anaerobes. Special precautions must be taken to avoid exposure of culture plates to oxygen during examination. A maximum of 20 min of exposure is recommended, as beyond this, some oxygen‐sensitive anaerobes will be killed. In addition, reduced culture media may become oxidized when exposed to air beyond this period, making the media unsuitable for isolation of fastidious anaerobes.
Introduction
Authors: Harrington Amanda T. , McElvania Erin 
Published: January 2025

Abstract
Blood culture remains one of the most critical functions of the clinical microbiology laboratory, aiding in the diagnosis of bloodstream infection and therapy management for patients. Culture of blood specimens is largely accomplished using commercial, continuously monitored blood culture systems, and aerobic and anaerobic bacteria, fungi, and mycobacteria can be recovered using these methods. Postanalytical communication and coordination with clinical care teams, especially those who prescribe antibiotics, result in improved patient care, such as reducing the interval of time to effective treatment. Gram staining remains a cornerstone of clinical microbiology practice and is a useful and rapid tool for preliminary identification of organisms from blood culture specimens. The procedure for quality control and quality assurance for blood culture provides guidance on verification of continuous‐monitoring blood culture systems as well as recommended strategies for monitoring quality of blood culture processes using standard metrics, such as contamination rates.
MALDI‐TOF MS for Identification of Acid‐Fast Bacilli and Aerobic Actinomycetes
Authors: Zelazny Adrian M. , Balada‐Llasat Joan‐Miquel 
Published: January 2025

Abstract
This chapter describes the use of matrix‐assisted laser desorption ionization–time of flight mass spectrometry (MALDI‐TOF MS) for the identification of mycobacteria, Nocardia, and other aerobic actinomycetes after growth in culture. It evaluates the MALDI‐TOF MS technique results in a spectral profile that relates to the mass‐to‐charge ratio of the organism. Direct spotting or on‐target extraction is not advised for myco‐bacteria due to safety concerns and the cell wall properties of this microorganism group. For these reasons, tube extraction protocols are recommended and typically involve mechanical disruption via bead beating, sonication, and/ or vortexing in ethanol, formic acid, and/or acetonitrile. The extracted proteins are then spotted onto the target plate for MALDI‐TOF MS analysis, where the microbial profile is then compared with a reference database; matching algorithms are used to determine the organism's identity.
Specimen Examination and Primary Isolation
Authors: Bell Melissa E. , Sussland Zdenek 
Published: January 2025

Abstract

Aerobic actinomycetes cause a variety of infections in humans, including respiratory, cutaneous, and disseminated infections, with a marked tropism to the central nervous system, from a primary pulmonary infection. This chapter outlines practical procedures that can be used to establish the presence of clinically important aerobic actinomycetes. These include members of several genera:
Actinomadura
,
Dermatophilus
,
Gordonia
,
Nocardia
,
Nocardiopsis
,
Rhodococcus
,
Streptomyces
,
Tsukamurella
,
Segniliparus
, and, to a lesser extent,
Amycolata
,
Amycolatopsis
,
Dietzia
,
Micromonospora
,
Saccharopolyspora
,
Saccharomonospora
,
Thermoactinomyces
, and
Williamsia
. The genera
Gordonia
,
Nocardia
,
Rhodococcus
, and
Tsukamurella
, and the microbiologically closely related genera
Mycobacterium
and
Corynebacterium
are collectively known as the mycolic acid‐containing genera, or “mycolata”. 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. The selection of media for the isolation of the aerobic actinomycetes depends primarily on the specimen type.
Molecular Susceptibility Testing for
Mycobacterium tuberculosis
Authors: Musser Kimberlee A. , Halse Tanya A. 
Published: January 2025

Abstract
Pyrosequencing (PSQ) technology is a rapid real‐time method for sequencing small segments of genomic deoxyribonucleic acid (DNA), often referred to as nucleic acid sequencing‐by‐synthesis. PSQ can be utilized for the molecular detection of mutations associated with drug resistance for Mycobacterium tuberculosis complex (MTBC). PSQ, when utilized directly on clinical specimens, has been shown to shorten the time to treatment of multidrug‐resistant tuberculosis (MDR‐TB) to as much as 5 weeks earlier and has influenced clinicians' decisions to devise effective TB drug regimens. The technology utilizes polymerase chain reaction products amplified from primary clinical samples or cultures to yield single‐stranded DNA to which a sequencing primer can be annealed. Sequences derived from pyrograms are compared to a library of known sequences to determine if the sample has mutations and resistance is predicted or if it has no mutations and susceptibility is suggested.
Full Identification of Yeasts
Authors: Zhang Sean X. , Memon Warda 
Published: January 2025

Abstract
In an era of increasing resistance of yeast species to antifungal agents and a widening range of species capable of causing diseases, there is almost no situation in which identification to species level is not warranted. Recently, matrix‐assisted laser desorption ionization‐time of flight mass spectroscopy (MALDI‐TOF MS) has been introduced as a method with the potential to identify a wide range of bacteria and fungi. MALDI‐TOF MS has been applied in clinical laboratories to identify a variety of clinically important yeasts. This chapter presents the methods which take advantage of phenotypic features of various yeast species. It provides some of the characteristics of various pathogenic yeasts. Supplemental tests can sometimes provide the single result that identifies an organism. Carbon assimilation, in practical terms, is the ability to use a sole carbon substrate for growth; thus, an organism that assimilates a substrate will show growth or increased turbidity.
Serologic Methods for Diagnosis of
Coccidioides
Infections
Authors: Lindsley Mark D. 
Published: January 2025

Abstract

Coccidioides species are thermally dimorphic fungal pathogens endemic primarily to the southwestern region of the United States, parts of northern Mexico, and Central and South America. It has recently been noted that the region of endemicity in the United States is expanding northward and these species are present in southern Washington State and northern Utah. Two species have been recognized,
Coccidioides immitis
and
Coccidioides posadasii
, which are phenotypically indistinguishable and can be differentiated only by molecular analysis. In the environment,
Coccidioides
spp. are found in soil in desert conditions. The mold grows in a filamentous form and reproduces by forming arthroconidia which break off from the hyphae. Definitive diagnosis of coccidioidomycosis is made through culture or histopathology. Tissue for histopathological diagnosis may be difficult to obtain, often requiring surgery. Therefore, serologic methods are more frequently employed, as serum can be obtained through less invasive venipuncture and is often the only material for diagnosis.
Introduction
Authors: Greninger Alexander L. , Naccache Samia N. 
Published: January 2025

Abstract
Molecular testing is central to the operation of the clinical microbiology laboratory and is increasingly first‐line testing for many analytes. For high‐throughput testing, several fully robotic, mostly random‐access analyses are commercially available and have also become more widespread in labs seeking solutions to testing for severe acute respiratory syndrome coronavirus 2. With advanced molecular instrumentation being more accessible than ever and allowing improved performance and faster turnaround times than purely laboratory‐developed tests with separate extraction and amplification steps, the barrier to entry for molecular assays has been reduced considerably. Increasingly, specialized molecular laboratories are called on to develop next‐generation sequencing‐based assays, which for the most part necessitate laboratory‐developed testing protocols. Next‐generation sequencing technologies, which allow the detection of potentially all microbes in a specimen, bring with them augmented focus on classic molecular challenges in preanalytical, analytical, and postanalytical processes.
Packing and Shipping Infectious Substances
Authors: Pentella Michael A. 
Published: January 2025

Abstract
The requirements and regulations governing the transport of infectious substances by commercial carriers change often. Most regulations for the safe air transport of dangerous goods throughout the world originate as decisions made by the ICAO United Nations Committee of Experts. The IATA DGR requirements have become the most widely recognized, copied, and used packing and shipping guidelines in the world. An important non‐safety‐related benefit of adherence to these regulations and requirements is to reduce the exposure of the shipper to the risks of criminal and civil liability associated with the improper shipment of dangerous goods. IATA requirements and DOT regulations mandate the minimum standards for packing infectious substances that can pose a threat to humans, animals, or the environment. Shipping of all dangerous goods begins with classification of the substances.
Introduction to the 13th Edition of the
Manual of Clinical Microbiology
Authors: Carroll Karen C. , Pfaller Michael A. 
Published: January 2025

Abstract

This introduction presents an overview of the key concepts discussed in the subsequent chapters of this book. The book includes updated content on all aspects of microbiology, authored by world experts on each subject and edited by a highly committed team of volume and section editors working within the usual 4‐year publication cycle. It presents practical information for daily improvements in test utilization and ways to collaborate with antimicrobial stewardship teams. The book accommodates taxonomic changes among the
Enterobacterales
by reorganizing some of the existing chapters and creating a new separate chapter on
Salmonella
species. Antimicrobial resistance, particularly among Gram negative organisms, continues to challenge microbiology laboratories and clinicians.
Diagnostic Stewardship in Clinical Microbiology
Authors: Chew Ka‐lip , Chia Jonathan W. Z. , Vasoo Shawn 
Published: January 2025

Abstract

Patient evaluation begins with a thorough symptom review and history, followed by physical examination to develop differential diagnoses for the patient's clinical presentation. Diagnostic testing is subsequently requested to confirm or exclude specific diagnoses. Diagnostic stewardship may be defined as performing the right test for the right patient for the right reasons at the right time, with the right interpretation which results in the right treatment, optimizing patient care. The postanalytical phase involves final reporting and interpretation of results, as well as the clinician's application of the results to guide patient management. Underutilization of blood cultures can lead to missed diagnoses and delayed or inappropriate therapy. Diagnosing ventilator‐associated pneumonia is complicated by the frequent colonization of the respiratory tract with
Enterobacterales
and nonfermenting Gram‐negative bacilli. A diagnostic stewardship program should ensure value and implement evidence‐based practice in clinical microbiology, where attention is paid to both accuracy and optimal patient outcomes.
Laboratory Automation in Clinical Microbiology
Authors: McElvania Erin , Doern Christopher D. , Culbreath Karissa 
Published: January 2025

Abstract
The practice of clinical microbiology has been revolutionized by technological innovations such as the advent of molecular diagnostics and polymerase chain reaction, matrix‐assisted laser desorption ionization–time of flight mass spectrometry, and most recently laboratory automation. This chapter focuses on the automation of culture‐based bacteriology. It discusses the various components of culture‐based automation along with some important considerations for those looking to adopt automation in their microbiology laboratory, such as how to select the right system, change management, and system validation. The chapter also includes some details of each system for the purposes of facilitating a capability comparison. The automation of microbiological specimen processing improves the quality of plate streaking, avoids cross‐contamination, alleviates ergonomic issues, and reduces processing time and costs. Total laboratory automation will likely become commonplace in high‐volume laboratories and may eventually be found in smaller laboratories.
Mycobacterium
: Clinical and Laboratory Characteristics of Rapidly Growing Mycobacteria
Authors: Brown‐Elliott Barbara A. , Harrington Susan M. , Morimoto Kozo , Wallace, Richard J. 
Published: January 2025

Abstract

Rapidly growing mycobacteria (RGM) contain long‐chain fatty acids, known as mycolic acids, that can be quantitated with chromatographic techniques such as high‐performance liquid chromatography (HPLC). Prior to the molecular era, HPLC was used for identification of RGM species in most major reference laboratories. The RGM are opportunistic pathogens that cause disease in a variety of clinical settings. RGM may also cause bone and joint infections. Chronic lung infections with RGM, most often in nonsmoking older women with bronchiectasis, are sometimes associated with the
Mycobacterium avium
complex. The use of mycobacterial smears is a rapid and reasonably sensitive step in the diagnosis of RGM disease. PCR amplification and sequencing has been used to detect and identify nontuberculous mycobacteria in specimens from sterile sites, but these tests are generally limited to larger, reference laboratories. The adjunctive nonmolecular tests, including antimicrobial susceptibility tests, have been utilized for preliminary identification of the RGM.
Aggregatibacter
,
Capnocytophaga
,
Eikenella
,
Kingella
,
Pasteurella
, and Other Fastidious or Rarely Encountered Gram‐Negative Rods
Authors: Zbinden Reinhard 
Published: January 2025

Abstract

This chapter covers the bacterial genera that are taxonomically diverse and belong to the families
Cardiobacteriaceae
,
Flavobacteriaceae
,
Leptotrichiaceae
,
Neisseriaceae
,
Pasteurellaceae
, and
Porphyromonadaceae
; common traits justify their discussion as a group. The taxonomy of the family
Pasteurellaceae
has undergone important changes; the family consists of over 100 named species distributed in over 25 genera, of which 4 include human pathogens:
Actinobacillus
,
Aggregatibacter
,
Haemophilus
, and
Pasteurella
. The chapter focuses on species commonly isolated from humans. Direct microscopy of specimens or of positive blood cultures supported by clinical information may help identify the corresponding bacteria, e.g., the typical morphology of spindle‐shaped cells in the Gram stain in the context of a dog bite allows the presumptive identification of
C. canimorsus
. Phenotypic identification of fastidious Gram‐negative rods presents several challenges.
Haemophilus
Authors: Gonzalez Mark D. , Ledeboer Nathan A. 
Published: January 2025

Abstract

Haemophilus
spp. are members of the family
Pasteurellaceae
. Members of the
Haemophilus
genus are small, nonmotile, non‐spore‐forming, non‐acid‐fast, pleomorphic, Gram‐negative bacilli with fastidious growth requirements.
Haemophilus
spp. can be found as part of the commensal microbiota of mucous membranes in humans.
H. influenzae
may also be found as part of the commensal bacterial microbiota of the mucosal surfaces of the upper respiratory tract (URT) of many healthy individuals; however, asymptomatic colonization of the URT with encapsulated strains of
H. influenzae
type b is rare. Isolates of
H. influenzae
constitute a diverse group of organisms that cause a broad range of human diseases. Collection of specimens for the diagnosis of
Haemophilus
infections is predicated on the nature of the infection being evaluated.
Klebsiella
,
Enterobacter
,
Citrobacter
, and Selected Other
Enterobacteriaceae
Authors: Das Sanchita , Pierce Virginia M. , Frank Karen M. 
Published: January 2025

Abstract

The genera
Klebsiella
,
Enterobacter
,
Citrobacter
, and
Cronobacter
are commonly encountered in clinical laboratories and cause a range of infections in humans, including bacteremia, meningitis, wound infections, and infections of the respiratory and urinary tracts. This chapter contains information not only on the taxonomy, detection, and identification of these genera but also on the global issue of antimicrobial resistance, which is especially pertinent to this group of organisms.
Klebsiella pneumoniae
is a significant pathogen in both community and hospital settings.
Klebsiella granulomatis
is the agent of donovanosis or granuloma inguinale, a disease characterized by painless, slowly progressive, vascular genital ulcers.
Enterobacter
spp. are opportunistic pathogens that are found in the natural environment in habitats such as water, sewage, vegetables, and soil. They are also commensal bacteria in the human gastrointestinal tract. The detection of antimicrobial‐resistant organisms by laboratories is a critical step required for appropriate management of patients and infection prevention and control efforts.
Bartonella
Authors: Giladi Michael , Gutiérrez Ricardo , Harrus Shimon 
Published: January 2025

Abstract

Bartonella
species are fastidious, Gram‐negative, coccobacillary or bacillary, small, arthropod‐borne bacteria that evolved from free‐living organisms and insect gut symbionts. This chapter focuses on the epidemiology, microbiology, clinical manifestations, and diagnosis of the three most common
Bartonella spp
;
B. bacilliformis
,
B. quintana
and
B. henselae
. Incidence of cat scratch disease is highest among those who live in the southern United States and among children 5 to 9 years of age. Trench fever, also known as 5‐day fever or quintan fever, is caused by
B. quintana
. Bacillary angiomatosis is characterized by neovascular proliferative lesions involving various organs. Infections caused by Bartonella spp. are uncommon among solid‐organ transplant recipients but both clinicians and clinical microbiologists should be aware of their unique characteristics.
Borrelia
Authors: Aguero‐Rosenfeld Maria E. , Sabljić Eva Ružić 
Published: January 2025

Abstract

Borrelia
species constitute a heterogeneous group of organisms that are maintained in nature in animal reservoirs and are transmitted via arthropod vectors.
Borrelia
species are agents of relapsing fever (RF), caused by the RF
Borrelia
group, and Lyme disease, caused by the Lyme borreliosis (LB)
Borrelia
group. A hallmark of
Borrelia
species is a segmented genome consisting of a linear chromosome and a mix of linear and circular plasmids. Although members of LB group of
Borrelia
have similar characteristics, they vary in their ability to cause disease in humans as well as in clinical manifestations. Acrodermatitis chronica atrophicans is a common late manifestation of LB in Europe. RF
Borrelia
can be detected in peripheral blood with blood films prepared from blood collected with EDTA. Variable major protein‐like sequences expressed is one of the most specific
Borrelia burgdorferi
antigens and has high significance in LB serology.
Chlamydia
Authors: Greub Gilbert , Munson Erik 
Published: January 2025

Abstract

This chapter focuses on the important human pathogens within the genus
Chlamydia
, as well as on
Parachlamydia acanthamoebae
,
Waddlia chondrophila
, and
Simkania negevensis
, for which evidence gathered over the past 20 years supports possible pathogenicity in humans. The taxonomy of
Chlamydiales
is rapidly evolving and progressively moving from a purely phenotypic taxonomy to a polyphasic taxonomy combining phenotypic, molecular, and phylogenetic characteristics.
Chlamydia
,
Parachlamydia
,
Waddlia
, and
Simkania
all present biphasic developmental stages with elementary body and reticulate body formation.
Chlamydia trachomatis
is the most common bacterial agent of sexually transmitted infection in the world.
Chlamydia psittaci
causes a wide variety of clinical conditions in humans, ranging from asymptomatic infection to severe, even fatal pneumonia and systemic infections. For
Chlamydia trachomatis
, one effective method for identification of the organism in cell culture is to stain the monolayers with species‐specific fluorescein‐conjugated monoclonal antibodies.
Ehrlichia
,
Anaplasma
, and Related Intracellular Bacteria
Authors: Theel Elitza S. , Pritt Bobbi S. 
Published: January 2025

Abstract

The family
Anaplasmataceae
in the order
Rickettsiales
is composed of several genera of clinically significant bacteria encompassing both human and veterinary pathogens. Members of the genera
Ehrlichia
and
Anaplasma
are the best known, having been recognized as agents of veterinary importance for over a century and as human pathogens since 1987. This chapter focuses on the clinically relevant members of the
Anaplasmataceae
, with particular emphasis on
Anaplasma phagocytophilum
and
Ehrlichia chaffeensis
, the most common human pathogens in this family. The family
Anaplasmataceae
contains small, nonmotile, pleomorphic, obligately intracellular bacteria that reside and propagate within host membrane‐derived vacuoles in the host cell cytoplasm. Like other rickettsiae, members of the
Anaplasmataceae
have a reduced genome size and rely on host cell machinery for survival. As with anaplasmosis, the spectrum of clinical presentations of
Ehrlichia chaffeensis
ehrlichiosis ranges from subclinical infection to life‐threatening disease.