bluuebunny/crossref_metadata_2025_split huggingface dataset:
Introduction
Authors: Wengenack Nancy L. 
Published: January 2025

Abstract
This part introduction presents an overview of the key concepts discussed in the subsequent chapters. The part presents the standard operating procedures for technologies that currently constitute standard of care for mycobacterial diseases. Mycobacteria are important human pathogens. Tuberculosis (TB), caused by Mycobacterium tuberculosis, remains a major global public health problem. The gold standard for diagnosing mycobacterial infections involves routine culture methods using both solid and liquid media and acid‐fast smear microscopy. Traditional liquid and agar culture technologies to detect growth in the presence of antimycobacterial drugs remain the standard of practice for susceptibility testing. Next‐generation sequencing molecular technologies are in the pipeline for the early detection of TB and drug‐resistant strains and promise enhanced sensitivity and expanded target product profiles but are not yet routinely available to most diagnostic laboratories.
Susceptibility Testing by TREK Sensititre Microdilution Plates
Authors: Escuyer Vincent E. , Salfinger Max , Elliott Barbara Brown , Parrish Nikki , Armstrong Derek 
Published: January 2025

Abstract

This chapter provides the information on antimicrobial susceptibility testing for rapidly growing nontuberculous mycobacteria, slowly growing nontuberculous mycobacteria, and the
Mycobacterium tuberculosis
complex using broth microdilution. Antimicrobial susceptibility testing is performed on rapidly growing mycobacteria isolated from clinical specimens by using a broth microdilution method with the Thermo Fisher Scientific Sensititre 96‐well plate for rapidly growing mycobacteria. The intended use of the Thermo Fisher Scientific Sensititre SLOWMYCO2 broth microdilution plate is the determination of MICs of antimicrobial agents against slowly growing nontuberculous mycobacteria. This test determines MIC breakpoints via broth microdilution of the NTM in Mueller Hinton broth containing specific concentrations of recommended antimicrobial agents. The MICs of antibiotics used to treat
Mycobacterium tuberculosis
complex infections can be determined by the broth microdilution 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.
Specimen Selection, Collection, and Transport
Authors: Abdolrasouli Alireza , Howell Susan 
Published: January 2025

Abstract
Suitable specimen selection, proper specimen collection, and timely specimen transport must be performed to ensure the successful detection and recovery of the etiologic agent of a fungal infection. To establish or confirm the diagnosis of a suspected fungal infection, it is essential for the clinician to provide the laboratory with adequate and relevant specimens for examination. Mycological investigation of clinical specimens usually includes direct microscopic examination, culture, detection of fungal antigens, study of the host's antibody response to a specific fungal pathogen, and molecular assays. Collection and transport of clinical specimens for fungal investigation are similar to those for bacteria; however, a larger volume of sample is usually preferred. Environmental contamination of clinical specimens can occur during collection, transport, and processing in the laboratory. Delay in processing samples may result in an overgrowth of bacterial contaminants and impede recovery of fungal pathogens.
Macroscopic and Microscopic Examination of Fecal Specimens
Authors: Chan Wilson W. 
Published: January 2025

Abstract
In the diagnosis of parasitic infections, the age of the fecal specimen is key. The physical characteristics of a fresh fecal specimen may aid in determining the possible organisms present. Fecal specimens may be described as formed, semiformed, soft, loose, or watery. When the fresh specimen is examined visually in the collection container, macroscopic helminth forms may be seen. The microscopic examination of a direct smear has several purposes: to assess the worm burden of a patient, to provide a quick diagnosis of a heavily infected specimen, to check organism motility, and to observe parasites that may be lost in concentration techniques. Fecal concentration has become a routine procedure as part of the complete ova and parasite examination, particularly for human clinical specimens. The zinc flotation procedure separates protozoan cysts and most helminth eggs from excess debris through the use of a liquid with a high specific gravity.
Special Stains for Coccidia and Microsporidia
Authors: Mathison Blaine A. , Garcia Lynne S. , Leal Sixto M. 
Published: January 2025

Abstract

Cryptosporidium
spp.,
Cyclospora cayetanensis
,
Cystoisospora belli
,
Sarcocystis hominis
, and
Sarcocystis suihominis
have been recognized as causes of severe diarrhea in immunocompetent hosts but can also cause severe diarrhea in immunocompromised hosts.
Cryptosporidium
spp.,
C. cayetanensis
, and
C. belli
can also cause ectopic infections in immunocompromised hosts. Oocysts in clinical specimens may be difficult to detect without special staining. Modified acid‐fast stains are recommended for demonstrating these organisms, although oocysts of
Sarcocystis
species will not retain the stain. Modified acid‐fast stains stain the
Cyclospora
oocysts from light pink to deep red, and some of the oocysts will contain granules or have a bubbly appearance, often being described as looking like “wrinkled cellophane.”
Sputum, Aspirates, and Biopsy Material
Authors: Leal Sixto M. 
Published: January 2025

Abstract

A direct smear can be used to detect large or motile organisms from the lung. Although
cryptosporidium
spp. are difficult to see in a direct mount, examination of smears stained with modified acid‐fast stains may provide confirmation of pulmonary cryptosporidiosis. Expectorated sputum specimens are collected after patient instruction in the appropriate measures to take to ensure quality specimens, including mouth wash before expectorating and exclusion of saliva from specimens. If parasite involvement is low on the differential diagnosis, the majority of aspirates and bronchoscopy specimens will be submitted only for standard cytology and microbial culture. Biopsy specimens are sometimes recommended for the diagnosis of tissue parasites. This chapter presents a list of stains for identifying parasites in various tissues. Biopsy specimens are invasive and costly and characterized by a small volume that may not accurately represent the entire infectious lesion.
Culture
Authors: Ali Ibne Karim M. , Visvesvara Govinda , Secor W. Evan , Lawrence Justin J. , Sapp Sarah G.H. 
Published: January 2025

Abstract

Acanthamoeba
,
Naegleria
, and
Balamuthia
are free‐living soil and freshwater amebae. Members of the genera
Acanthamoeba
and
Naegleria
can be easily cultivated in the laboratory either monoxenically or axenically. In contrast,
Balamuthia mandrillaris
cannot be cultivated with bacterial species, although it can be cultured with an associated mammalian cell such as human lung fibroblasts or monkey kidney cells. This chapter focuses on the culture growth of
Naegleria
and
Acanthamoeba
species in clinical specimens only. Cultivation is a more sensitive method than direct wet mounts for the diagnosis of trichomoniasis, but it is less sensitive than tests that detect antigen or nucleic acid.
Trypanosoma cruzi
, which causes Chagas disease, is a major public health problem in Latin America. An important consideration for choosing culture conditions for cultivating
Leishmania
spp. and
Trypanosoma cruzi
is that different media have different effects upon the phenotype, infectivity, and overall culture longevity of the desired organism.
Quality Control and Quality Assurance in Clinical Virology
Authors: Mostafa Heba H. 
Published: January 2025

Abstract
An efficient clinical virology laboratory aims at delivering accurate results in a timely manner. Appropriate procedures must be in place to ensure that this mission is achieved efficiently and with highest quality. Each step in this process is governed systematically by a multifaceted quality management system (QMS) of policies, processes, and procedures used by the laboratory to meet the accreditation and certification requirements and to maintain a high‐quality operation. The scope of QMS in the clinical virology laboratory extends in focus beyond quality control (QC) and quality assurance (QA) as it includes all aspects of laboratory management and the technical operations to ensure sustained monitoring of quality and patient safety. This procedure provides information on the different aspects of QA and QC measures in the clinical virology laboratory as a part of the overall QMS.
Preparation of Cell Culture Media and Supplemental Components
Authors: Hodinka Richard L. 
Published: January 2025

Abstract
At present, most diagnostic virology laboratories that continue to perform some level of cell culture for virus isolation purchase media and supplemental components from commercial sources rather than preparing these materials from basic constituent ingredients. Commercial products of high quality and consistency come premixed and prepackaged and require minimal manipulations by the laboratory to complete the medium before it is ready to use. Many types of synthetic (artificial) media have been developed, modified, and enriched to support the growth of certain cell types, resulting in the availability of a variety of medium formulations for a range of cell culture applications. The basic components of cell culture medium include vitamins, amino acids, carbohydrates, proteins and peptides, fatty acids and lipids, and basic and trace elements as a supply of nutrients needed for cells to survive and grow in culture.
Hemagglutination Inhibition Assay for Quantitative Measurement of Antibody Responses to Influenza Virus
Authors: Young Stephen , Pinsky Benjamin A. 
Published: January 2025

Abstract
Hemagglutination inhibition (HAI) is a traditional laboratory method which continues to be used in public health and research laboratories and by vaccine manufacturers as a primary method for global influenza seroepidemiologic surveillance to determine the distribution and prevalence of influenza in given populations, antigenically characterize influenza viruses that may be selected for use in seasonal influenza vaccines, compare antigenic changes among current and previously circulating influenza viruses, and monitor the effectiveness of annual vaccines and newly developed vaccine candidates to induce an antibody response. In the past, when performing the HAI test, specialized equipment was used in the titration of either virus or antibody. The HAI test is accomplished by making serial 2‐fold dilutions of a patient's serum, mixing and incubating each dilution with a fixed amount of either virus particles or isolated viral hemagglutinin, and then adding a suspension of red blood cells.
Cytomegalovirus Serology
Authors: Prince Harry E. 
Published: January 2025

Abstract

Human cytomegalovirus (CMV), also known as human herpesvirus 5, is a member of the family
Herpesviridae
. CMV infections in healthy children and adults are primarily asymptomatic, although in young healthy adults, they can mimic Epstein‐Barr virus‐mediated infectious mononucleosis syndrome. CMV is shed in a variety of body fluids, including tears, saliva, breast milk, urine, blood, vaginal secretions, and semen; hence, it can be transmitted by intimate personal contact and is more prevalent in conditions of crowding. One of the most serious consequences of CMV infection is congenital infection in infants due to transplacental viral transmission during pregnancy. The laboratory diagnosis of CMV infection can be established by histologic or cytologic detection of classic CMV tissue pathology, isolation of the virus in cell culture, direct detection of viral antigen or nucleic acids, and/or serologic assays. Serologic assays are routinely used for screening purposes and are also valuable adjuncts for CMV diagnosis.
Human Immunodeficiency Virus Serology
Authors: Kaleta Erin J. 
Published: January 2025

Abstract
Human immunodeficiency virus (HIV) is a positive‐sense, enveloped retrovirus in the lentivirus subgroup. Two distinct HIV viruses exist, HIV‐1 and HIV‐2, and among these two groups, there is a great deal of genetic diversity that distinguishes subgroups and clades of HIV viruses. HIV‐1 can be broken down into the subgroup M, the divergent group O, and the more recent groups N and P. Subgroup M accounts for most HIV infections and includes clades A, B, C, D, F, G, H, J, and K. HIV‐2 can be broken down into groups A to H, although A and B are most common. The structure of HIV includes viral RNA contained within the viral capsid, which is composed of core structural proteins; the capsid is surrounded by a lipid bilayer containing protruding surface glycoproteins that are responsible for host cell recognition and binding.
Serologic Diagnosis of Arbovirus Infections
Authors: Collins Matthew H. , Pelc Rebecca S. 
Published: January 2025

Abstract
Arthropod‐borne viruses (ARBV), transmitted by ticks or mosquitoes, are a subset of vectorborne diseases, which in recent years have been on the rise in the United States. New pathogenic ARBV continue to emerge, being identified either in human cases or through vector surveillance over the last few decades. Many ARBV infections are clinically inapparent, but all can cause a nonspecific fever and/or rash illness. Many of the ARBV endemic in the United States are also capable of causing neurologic manifestations, such as meningitis and encephalitis. The possible causes of acute neurologic illness are numerous, some of which are reversible with targeted treatment. The presymptomatic incubation period is typically less than 15 days for most ARBV. The timing and magnitude of antibody responses can be altered by prior infection with the same or similar virus.
Serologic Diagnosis of Chagas Disease
Authors: Whitman Jeffrey D. , Bern Caryn 
Published: January 2025

Abstract

Chagas disease is caused by the protozoan parasite
Trypanosoma cruzi
. The primary route of infection is via host inoculation with feces from infected insect vectors. The infection has acute and chronic phases, which broadly represent active systemic replication and long‐term intracellular parasite persistence. This chapter focuses on serologic testing for chronic Chagas disease, as the acute phase is relatively brief and seldom suspected clinically. There are currently four tests cleared by the U.S. Food and Drug Administration for diagnosis of chronic
T. cruzi
infection. Three of these assays (Hemagen, Wiener, and Ortho) are 96‐well microplate ELISAs, and one is an operator‐interpreted immunochromatographic lateral flow assay. 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.
Serologic Testing for Toxoplasmosis
Authors: Pomares Christelle , Olson Kjerstie , Montoya José G. 
Published: January 2025

Abstract

Toxoplasma gondii is a protozoan intracellular parasite and the etiologic agent of toxoplasmosis. Toxoplasmosis exhibits a wide clinical spectrum, which ranges from an asymptomatic infection state to life‐threatening clinical manifestations. Initial
T. gondii
serologic testing can be performed in local or regional laboratories. Serum is the preferred material for testing. Negative and positive quality controls should be tested before patient samples. The dye test is a functional assay and regarded as the gold standard for the detection of
Toxoplasma
Immunoglobulin G antibodies. The Remington double‐sandwich Immunoglobulin M (IgM) enzyme‐linked immunosorbent assay (ELISA) is more sensitive than the IgM immunofluorescence test in diagnosing recently acquired infections and does not show false‐positive results due to antinuclear antibodies or rheumatoid factor. The IgM immunosorbent agglutination assay is more sensitive than the IgM ELISA and has been used effectively for diagnosis of congenital infection.
Molecular Methods for Epidemiological Typing of Microorganisms
Authors: Fisher Mark A. , Shakir Salika M. , Lopansri Bert K. 
Published: January 2025

Abstract
The increased availability of molecular methods for comparative analysis of genetic changes across microbial isolates has greatly expanded the ability of the clinical microbiologist to aid in the prevention and control of outbreaks. Pulsed‐field gel electrophoresis strain typing relies on changes in restriction sites, which can arise by single‐nucleotide changes or by large genomic rearrangements. Strain typing in the context of epidemiological investigation is based on several assumptions: that bacterial genomes are not static and that they undergo mutation at a given rate within a strain; that an outbreak is caused by a single strain, and subsequent isolates from different sources will have the same genotype; and that isolates not derived from the outbreak strain will have different genotypes. Ribotyping is a molecular method that was originally developed in 1986 by Grimont and Grimont for genotyping bacteria and adapted for use with PCR by multiple groups in the early 1990s.
Surveillance Cultures for Hospital‐Associated Infections
Authors: Gumbis Stephanie , Aubert Rachel D. , Sievert Dawn , Lainhart William D. , Pitout Johann D. , Bibbi Helen , Bourassa‐Blancette Sam , Lockhart Shawn R. , Green Daniel A. , Imlay Hannah , Hanson Kimberly E. 
Published: January 2025

Abstract

Antibiotic and antifungal resistance (AR)—the ability of bacteria and fungi to defeat the drugs designed to kill them—is one of the greatest global public health challenges. Antibiotics and antifungals are among our most powerful tools for fighting life‐threatening infections. The threat of AR undermines progress in health care, food production, and life expectancy. The Centers for Disease Control and Prevention (CDC) is a leader in the fight against this global threat, driving aggressive action along with partners and facilitating collaborative responses to resistance through a One Health approach. State and local health care‐associated infection (HAI)/AR programs are essential to U.S. efforts to detect, prevent, respond to, and contain HAI and AR pathogens. In 2019, CDC evaluated the sensitivity and specificity of many carbapenem‐resistant
Enterobacterales
and
Pseudomonas aeruginosa
antimicrobial susceptibility testing phenotypes to determine which were most predictive of the presence of carbapenemase genes.
Infection Control in the Laboratory
Authors: Pentella Michael A. , Luethy Paul M. , Church Deirdre L. 
Published: January 2025

Abstract
The immunization of laboratory staff is an important component of the laboratory biosafety plan and occupational health services. Immunization is the primary means of preventing the acquisition of disease in workers who have the potential for exposure to various microbial agents in the laboratory workplace. Personal health status must be considered by the individual in electing to be vaccinated or deferring on vaccination. This chapter describes immunization practices and procedures for specific functions in the clinical and public health laboratory setting. Employees who decline a recommended vaccination may be required to complete a vaccination declination form for retention in their occupational health record. Risk for occupational HIV infection is modified not just by the general type of exposure but also by several specific factors, including the depth of the exposure, the exposure inoculum, and the exposed worker's immunological response.
Risk Assessment
Authors: Buchan Blake W. 
Published: January 2025

Abstract
Working in a clinical microbiology laboratory presents a number of potential hazards in the form of exposure to infectious biological agents, dangerous chemical reagents, and both manual and automated instrumentation capable of causing bodily harm. The collection of safety policies is referred to as a biosafety manual and should be unique to each laboratory, considering the personnel, facilities, test procedures, and biological and other risks inherent to that laboratory. The development of individualized and effective safety policies requires a multistep process formally known as a risk assessment. There are several laboratory‐focused resources that provide recommendations for the design of a risk assessment, as well as important considerations for risk mitigation strategies related to common biological, chemical, and mechanical hazards. These include publications by the U.S. Centers for Disease Control and Prevention, NIH, and the American Society for Microbiology. The primary goal of hazard characterization is to determine if the relative risk is acceptable or unacceptable.
Yersinia pestis
Authors: Sharp Susan 
Published: January 2025

Abstract

Yersinia pestis
is a nonmotile, slow‐growing, facultative organism classified in the order
Enterobacterales
. It appears as plump, Gram‐negative bacilli or coccobacilli that are seen mostly as single cells or pairs, which may exhibit bipolar staining from a direct specimen if stained with Wright stains.
Y. pestis
, the causative agent of plague, has a protracted history, being described in epidemics and pandemics since biblical times. Plague is a zoonotic disease transmitted ordinarily by animals and their infected fleas. Humans can acquire plague through the bite of infected fleas, direct contact with contaminated tissue, or inhalation. The chapter covers safety considerations, materials, specimen collection, and quality control principles for preanalytical considerations. For analytical considerations, it provides specimen processing, incubation and examination of cultures, and culture identification. With postanalytical considerations, the chapter also provides attention to common test limitations, interpretive challenges, and results reporting.
High‐Consequence Viral Pathogens
Authors: Relich Ryan F. 
Published: January 2025

Abstract
High‐consequence viruses comprise a growing list of pathogens that periodically cause outbreaks of infectious diseases that are characterized by severe symptomatology and high case fatality rates. Many of these agents are transmissible from person to person and elicit early signs and symptoms that overlap with more common diseases, resulting in the delayed implementation of infection control measures designed to prevent their spread. This chapter focuses on viruses that cause hemorrhagic fever, central nervous system diseases, and respiratory tract diseases. All known high‐consequence viruses originate in animals, and their spillover from reservoir species, intermediate hosts, and/or arthropod vectors precipitates outbreaks among humans. The expeditious diagnosis of high‐consequence viral diseases is paramount for implementation of appropriate patient treatment measures and containment of outbreaks. Arthropods, primarily ticks, serve as vectors of several dangerous viruses, including Crimean‐Congo hemorrhagic fever virus and tick‐borne encephalitis virus.