bluuebunny/crossref_metadata_2025 huggingface dataset:
Detection of
Brucella
spp. Antibodies
Authors: Stoddard Robyn A.
Published: January 2025

Brucellosis is a zoonotic disease that is found in domestic and wild animals and transmitted to humans through contact with or ingestion of infected animal products. Brucellosis is caused by the small facultative, intracellular, Gram‐negative coccobacilliin the genus
Brucella
. Laboratory diagnosis of brucellosis can be performed through either direct detection methods, including culture or nucleic acid amplification testing, or via indirect, anti‐
Brucella
antibody detection using serologic assays. The interpretation of serologic results for anti‐
Brucella
antibodies is best performed in the context of the individual patient history, including clinical signs, exposure or risk of exposure, and course of infection. Microagglutination test and tube agglutination test can provide presumptive evidence of brucellosis, but laboratory confirmation should be considered in combination with other clinical, laboratory, and epidemiologic findings. The only specimen that can be used for testing is serum.
Laboratory Diagnosis of Syphilis
Authors: Fakile Yetunde F. , Cao Weiping , Shukla Mayur , Pillay Allan
Published: January 2025

Syphilis is a sexually transmitted disease caused by the spirochete
Treponema pallidum
subsp.
pallidum
and is easily cured with antimicrobial therapy. If untreated, syphilis can progress through five stages of infection: primary, secondary, early latent, late latent, and tertiary. The laboratory diagnosis of syphilis is usually based on serologic testing. Serologic testing is recommended for persons with symptoms or signs of infection, persons with an infected sex partner, pregnant women, sexually active men who have sex with men, sexually active HIV‐infected persons, and persons in at‐risk populations. Serologic test results should be interpreted in the context of the patient's medical history, physical examination findings, history of prior treatment for syphilis, and sexual history. Commonly used FDA‐cleared nontreponemal serologic tests include the Venereal Diseases Research Laboratory and rapid plasma reagin tests. Trep‐Sure enzyme immunoassay is a qualitative treponemal test for the serologic detection of antitreponemal antibodies.
Epstein‐Barr Virus Serology
Authors: Miller Linda E.
Published: January 2025

Epstein‐Barr virus (EBV) is a doublestranded DNA virus of the family
Herpesviridae
. Infection with EBV is ubiquitous, with almost 100% of the world's population showing serologic evidence of infection by age 40. Clinical laboratory testing for EBV infection includes serologic tests, molecular techniques, and antigen detection by immunohistochemistry. Serologic tests are mainly used for diagnosis of IM, while quantitative nucleic acid amplification is recommended for detection and monitoring of patients with PTLD, EBV‐associated lymphomas, and nasopharyngeal carcinoma. This chapter covers serologic tests for detection of EBV infections and in particular for diagnosis of IM. Serology tests for EBV detect one of two types of antibodies: heterophile antibodies or EBV‐specific antibodies. Heterophile antibodies are defined by their ability to react with similar antigens from unrelated species. The chapter covers quality control principles for analytical tests. With postanalytical considerations, it provides attention to common test limitations, interpretive challenges, and results reporting.
Serologic Testing for Hepatitis Viruses
Authors: Parikh Bijal A. , Anderson Neil W.
Published: January 2025

Hepatitis A virus (HAV) is a common and serious cause of infectious hepatitis worldwide. While HAV is transmitted via a fecal‐oral route, the exact mechanism of transmission is directly related to the level of endemicity in a region. The symptoms of HAV are impossible to distinguish from other forms of infectious and noninfectious hepatitis, necessitating accurate diagnostic testing. The cornerstone for HAV diagnosis is serologic testing. Serologic tests for HAV are available in three different formats: HAV IgM, HAV IgG, and HAV total antibody. The primary role of HAV IgM testing is to diagnose acute HAV infection, whereas the primary role of HAV IgG and HAV total antibody tests is to establish immune status, regardless of whether it is naturally derived or via vaccination. HAV IgM is a component of the Centers for Medicare and Medicaid Services‐approved serologic testing panel for acute viral hepatitis.
General Aspects of Molecular Diagnostics
Authors: Cybulski Robert J. , Chiaruttini Jessica , Lee Mark J. , Lieberman Joshua A. , Salipante Stephen J. , Binnicker Matthew J. , Hill Jill N. , Stevenson Jeffrey B. , Bard Jennifer Dien , Truong Thao T.
Published: January 2025

Preanalytical considerations for molecular testing encompass a large breadth of topics, from those directly related to the testing sample to those related to human error. Inappropriate test selection or test utilization is among the most consequential yet least considered preanalytical factors responsible for unsatisfactory or unsatisfying results. A minimum requirement for enabling successful specimen collection among clinical staff is the publication of hospital‐specific guides. In addition to proactive steps to avoid error‐introducing variance, such as publication of lab test menus and specimen handling guidance, general education, case‐specific consultation, etc., there is a need to establish means of detecting, monitoring, and responding to variance. The emergence of the Coronavirus disease 2019 pandemic, which resulted in the declaration of a public health emergency in the United States on 30 January 2020, thrust molecular diagnostic testing into the spotlight as a key component of the early pandemic response.
Syndromic Panels
Authors: Couturier Marc R. , Raible Kevin , Cintrón Melvilí , Babady N. Esther , Bard Jennifer Dien , Van Tam T.
Published: January 2025

Molecular testing for gastrointestinal (GI) pathogens is a rapidly developing field; until recently, it was only of interest to researchers and large reference laboratories. Traditional stool culture, direct antigen detection, scanning electron microscopy, and light microscopy have long been the standard diagnostic approaches for GI pathogens. Syndromic respiratory panels can be divided into two groups, those targeting pathogens associated with upper respiratory tract infections and those targeting pathogens associated with lower respiratory tract infections (LRTI). LRTI includes a wider range of syndromes, and each syndrome is traditionally associated with different, primarily bacterial etiologies. In addition to identification of pathogens, management of LRTI relies more heavily on antimicrobial susceptibility test results. Diagnostic testing for meningitis and encephalitis pathogens, particularly viral etiologies, has progressed from traditional culture to various molecular detection methods. The FilmArray meningitis/encephalitis panel is the only molecular panel that is Food and Drug Administration cleared and commercially available in the United States.
Microbiological Sampling for Pharmacies that Compound Sterile Preparations
Authors: Livesay Hannah N. , Weissfeld Alice , Schaeffer Fran , DeGarmo Meredith , Vance Paula , Terry Pamela
Published: January 2025

Over 100 years have passed since the 1906 Pure Food and Drug Act led to the creation of the U.S. Food and Drug Administration, which established the United States Pharmacopeia as the official standard for drugs in the United States. Compounding settings include hospitals, free‐standing compounding pharmacies, outpatient infusion centers, home health care services, ambulatory care services, physician offices, and nursing homes. The Microbial Pharmacy Surveillance Program consists of microbiology testing performed to determine the presence of microbial growth in compounded sterile preparations (CSPs) or the potential for microbial contamination of CSPs. Aseptic work practice assessment and evaluation is performed via gloved fingertip sampling of compounding personnel for all risk levels, because direct touch contamination is the most likely source of microorganisms introduced into CSPs prepared by humans.
Biological Safety and Biohazard Prevention
Authors: Relich Ryan F. , Demkowicz Ryan
Published: January 2025

Many different categories of hazards are encountered from the time a clinical specimen is collected until it and any cultures or other derivatives of it are disposed of. Management of biohazardous spills depends on the infectious agent, the quantity of the material spilled, and whether an aerosol was generated. The management of risks posed by working with pathogens is accomplished by the development and implementation of standard procedures and practices for handling infectious material that will minimize or eliminate the threat of microbial transmission within the laboratory. Routine decontamination and cleaning of the work environment are the responsibilities of all laboratory workers. The laboratory biosafety plan should include recommendations on frequent and careful hand hygiene and recognize the importance of this mitigation tool in the risk assessment for handling pathogens. Hand hygiene rituals are described in some religious texts.
Levels of Laboratory Biosafety
Authors: Pentella Michael A.
Published: January 2025

Biohazard levels (BSLs) are a means to determine the safety precautions necessary to work with specific pathogens in the laboratory environment. The purpose of biosafety levels is to inform laboratory personnel about the level of biohazardous risk and necessary biocontainment precautions that should be in place in a laboratory setting. The classification of BSL demonstrates the ascending risk containment and is referred to as BSL‐1, BSL‐2, BSL‐3, and BSL‐4. Each level progresses to higher controls to reduce the risk of exposure. Risk assessment is an essential part of the process of determining the biosafety procedures and biosafety level at which laboratory work should be conducted. Laboratory‐acquired infections have been caused by a wide variety of microorganisms.
Melioidosis (
Burkholderia pseudomallei
) and Glanders (
Burkholderia mallei
)
Authors: Egan Christina , Perry Michael J.
Published: January 2025

Burkholderia mallei
is the etiologic agent of glanders, a febrile illness typically seen in equines, i.e., horses, mules, and donkeys. It is a nonmotile, aerobic Gram‐negative coccobacillus, which may or may not be oxidase positive or grow on MacConkey agar.
Burkholderia pseudomallei
was thought to cause a glanders‐like illness in humans.
B. pseudomallei
is an oxidase‐positive, aerobic Gram‐negative bacillus that is straight or slightly curved. The recent sequencing of the genomes suggests that
B. mallei
is a recently evolved clone of
B. pseudomallei
.
B. mallei
infections can present either as cutaneous or systemic. 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.
Smallpox and Other Poxviruses
Authors: Arrroyocazurro Miguel A.
Published: January 2025

Poxviruses are of great veterinary and human importance and infect numerous vertebrate and invertebrate animals, including humans. The clinical presentation similarity of smallpox to many vesicular and pustular rash illnesses, including varicella, herpes simplex, drug reactions, and erythema multiforme, represents a major challenge for public health officials. Smallpox is caused by the variola virus, which emerged in human populations thousands of years ago. Monkeypox is a zoonotic disease that is endemic to central and western Africa. Orthopoxviruses that are closely related to vaccinia virus have repeatedly caused zoonotic infections in humans across the world, such as buffalopox and other vaccinia related viruses. The epidemiology and natural history of yatapoxviruses are poorly understood. Parapoxviruses are widespread pathogens that can infect a variety of different mammals, including humans. Molluscum contagiosum virus is the sole member of the genus
Molluscipoxvirus
.
Q Fever—
Coxiella burnetii
Authors: Schaecher Kurt E.
Published: January 2025

Coxiella burnetii
is the etiologic agent of Q fever.
C. burnetii
is phylogenetically related to
Pseudomonas
,
Francisella
, and
Legionella
, within the Legionella group of the
Gammaproteobacteria
subdivision. Q fever is a zoonotic disease, especially of parturient goats, sheep, or cattle and, occasionally, domestic cats. Q fever persists from a reservoir among wildlife, including mammals, birds, and arthropods. Geographic distribution of Q fever cases in the United States is most densely located in areas associated with sheep, goat, or cattle ranching. The chapter covers safety considerations, specimen collection, and specimen processing, incubation and examination of cultures for preanalytical considerations. For analytical considerations, it provides quality control and identification. With postanalytical considerations, the chapter also provides attention to summary/special considerations.
Clinical Laboratory Bioterrorism Readiness Plan
Authors: Uprety Priyanka
Published: January 2025

This chapter provides a model for clinical laboratories to use for developing a bioterrorism (BT) preparedness plan. The laboratory BT preparedness plan should be integrated into the institutional BT preparedness plan. In the United States, the Laboratory Response Network (LRN) serves as a consortium and partnership of laboratories that provide immediate and sustained laboratory testing and communication in support of public health emergencies, particularly in response to acts of bioterrorism and emerging infectious diseases. The LRN is composed of sentinel laboratories, reference laboratories, and national laboratories in addition to private and commercial clinical laboratories, and selected food, water, agricultural, military, and veterinary testing laboratories. Clinical laboratories play a critical role in the LRN. Their heightened awareness of the possibility of recovering the agents of bioterrorism from patient specimens and referral of suspect isolates to the appropriate public health reference laboratory is crucial.
Systems for Identification of Bacteria and Fungi
Authors: Heaton Phillip R. , Bhatti Micah M.
Published: January 2025

A proteomics‐based approach, matrix‐assisted laser desorption ionization‐time of flight mass spectrometry (MALDI‐TOF MS), was introduced in clinical microbiology laboratories between 2005 and 2010 as a highly reliable and much more rapid method for identifying bacteria and yeast. Advances in molecular tools have allowed proteomics and genomics to have a substantial role in the identification of bacteria and yeast in clinical laboratories. In many laboratories, MALDI‐TOF MS has become the primary method for bacteria and yeast identification, supplanting biochemical analysis, including automated methods. DNA target sequencing may be performed on organisms growing in pure culture. This is typically performed when automated systems in the laboratory are unable to yield an identification or they provide an unusual identification or one that conflicts with phenotypic characteristics. The use of artificial intelligence and machine learning has made its way into the clinical microbiology laboratory, largely due to the digitization of microbiology and increasing technology use.
Yersiniaceae
Authors: Kingry Luke C. , Gladney Lori , Petersen Jeannine M.
Published: January 2025

The family
Yersiniaceae
includes two well‐known pathogenic genera,
Serratia
and
Yersinia
, and multiple other genera which inhabit a wide range of ecological niches.
Serratia marcescens
is the
Serratia
species most often isolated from clinical specimens and can cause urinary tract infections, pneumonia, bloodstream infections, endocarditis, and wound infections. This chapter primarily focuses on the taxonomy, detection, and identification of
Serratia
and
Yersinia
.
Yersiniaceae
members are Gram‐negative rods that are non‐spore‐forming, oxidase‐negative, catalase‐positive facultative anaerobes which display nonfastidious growth. The
Yersiniaceae
are widely distributed throughout the environment and transmitted to humans via arthropod bites, contact with infected animals, ingestion of contaminated food or water, or exposure to hospital environments and medical procedures. Serology can be used as an adjunct in the diagnosis of disease due to
Yersinia enterocolitica
or
Yersinia pseudotuberculosis
. Many
S. marcescens
strains carry both chromosomally encoded and plasmid‐mediated resistance determinants for several different types of antimicrobials.
Pseudomonas
Authors: Høiby Niels , Bjarnsholt Thomas , Ciofu Oana
Published: January 2025

Pseudomonas
is a large and complex genus of Gram‐negative bacteria that is important because it includes species with both clinical and environmental implications.
Pseudomonas
spp. are conventionally described as aerobic species based on their growth in routine media used in the clinical microbiology laboratory, but several species are actually facultative aerobes. The identification of fluorescent and nonfluorescent pseudomonads has become less difficult with the availability of MALDI‐TOF MS technology, which has replaced conventional phenotypic identification systems in many clinical microbiology laboratories. However, phenotypic methods are still used in small laboratories, and it should be recognized that these methods also provide information about the physiological and biochemical capabilities of the bacteria, which may sometimes be important for the pathogenesis of infections. The frequent acquisition of antimicrobial resistance in
P. aeruginosa
limits the utility of antimicrobial susceptibility patterns as a tool in epidemiological typing.
Burkholderia
,
Stenotrophomonas
,
Ralstonia
,
Cupriavidus
,
Pandoraea
,
Brevundimonas
,
Comamonas
,
Delftia
, and
Acidovorax
Authors: Lipuma John J. , Currie Bart J. , Baird Robert W. , Vandamme Peter A. R.
Published: January 2025

Many of the bacteria discussed in this chapter formerly belonged to the genus Pseudomonas; others were described and named after the taxonomic dissection of this genus to conform to a modern phylogeny‐based taxonomy.
Burkholderia
,
Ralstonia
,
Cupriavidus
,
Pandoraea
,
Brevundimonas
,
Comamonas
,
Delftia
, and
Acidovorax
species are aerobic, non‐spore‐forming, straight or slightly curved Gram‐negative rods. Several molecular genetic methods are available to assess the relatedness of isolates of these genera during nosocomial or community outbreak investigations. Of the organisms discussed in this chapter, serologic tests have been used clinically to diagnose only infections with
B. pseudomallei
. Given the uncertainty regarding the role(s)
Delftia
,
Acidovorax
, and
Brevundimonas
play in human infection, antimicrobial susceptibility testing of isolates from human specimens as a matter of routine may not be warranted.
Acinetobacter
,
Chryseobacterium
,
Moraxella
,
Branhamella
and Other Nonfermentative Gram‐Negative Rods
Authors: Cools Piet , Nemec Alexandr , Abeele Anne‐Marie van den , Kämpfer Peter
Published: January 2025

This chapter covers the organisms which belong to a group of taxonomically and phylogenetically diverse, Gram‐negative, non‐fermentative rods and coccobacilli. Most of the organisms are found in the environment, that is, soil and water. For each group of closely related species, the chapter presents their taxonomic history, addresses the clinical importance of the species, and describes the phenotypic data that are useful to differentiate this group from other groups and to differentiate the species within this group. It discusses antibiotic susceptibility characteristics and treatment options. Decisions regarding the significance of GNF in a clinical specimen must consider the clinical condition of the patient and the source of the specimen submitted for culture. Identification of GNF may be important to document health care‐related outbreaks linked to hospital environments or medical devices.
Legionella
Authors: Lindsay Diane S. J. , Ricci Maria Luisa
Published: January 2025

The family
Legionellaceae
is composed of a single genus,
Legionella
, and comprises 66 validly named species and three subspecies.
Legionella pneumophila
,
Legionella micdadei
,
Legionella bozemanii
, and
Legionella longbeachae
are the most important species from a clinical standpoint, with
L. pneumophila
causing more than 90% of Legionnaires' disease (LD) globally, apart from Australia and New Zealand, where
L. longbeachae
predominates. LD is a type of bacterial pneumonia caused by
L. pneumophila
and other
Legionella spp
. Identification of
Legionella spp
. in a clinical laboratory is optimally performed by observation of visual morphology, agglutination methods, and matrix‐assisted laser desorption ionization–time of flight mass spectrometry. Antimicrobial agents regarded as effective for treatment of LD are macrolides, fluoroquinolones, and, rarely, rifampin, all achieving adequate intracellular concentrations.
Approaches to the Identification of Anaerobic Bacteria
Authors: Boyanova Lyudmila , Medeiros José Augusto da Silva
Published: January 2025

This chapter focuses on important requirements of anaerobic microbiology and methods and techniques used in the diagnostic workflow. Anaerobic bacteria (anaerobes) can cause infections in all tissues and organs of the human body. The chapter summarizes some important recommendations for specimen collection and handling for diagnosing anaerobic infections. Moreover, since antibiotic resistance in anaerobes and the proportion of patients with immunosuppressive diseases or immunosuppressive therapy are constantly increasing, anaerobic microbiology is becoming increasingly important and must not be neglected in any hospital center or country. The disk diffusion method may facilitate susceptibility testing of anaerobes. However, all microbiology laboratories should, at the minimum, be able to culture and perform basic identification of anaerobes and refer uncommon isolates to a reference laboratory. Both clinicians and laboratory staff should be familiar with the requirements for collection and transport of clinical samples for anaerobic microbiology.
Clostridium, Clostridioides
, and Other Clostridia
Authors: Kuijper Ed J. , Reubsaet Frans A. G. , Barbut Frédéric
Published: January 2025

The genus
Clostridium
comprises obligately anaerobic (or occasionally aerotolerant), Gram‐positive rods commonly found in soil, water, and gastrointestinal tracts of insects and animals, as well as humans. Accurate, definitive identification is needed to better define the role of clostridia in disease, to aid the clinician in selecting optimal treatment, and for public health purposes (e.g., hospital‐acquired
Clostridioides difficile disease
). The isolation of a
Clostridium
species from a clinical specimen, even a blood culture, may or may not be significant clinically, and culture results should be interpreted in relation to the clinical findings for the patient. Identification of clostridia in specimens from sites of infection due to mixed organisms can be time‐consuming and expensive. Typing of
Clostridioides difficile
fosters understanding of the epidemiology of infections and has become increasingly important with the emergence of outbreaks caused by hypervirulent strains.
Helicobacter
Authors: Couturier Marc R.
Published: January 2025

The genus
Helicobacter
is classified in the family
Helicobacteriaceae
of the class
Epsilonproteobacteria
, formerly known as the epsilon subclass of the
Proteobacteria
, with
Helicobacter pylori
as the type species. There are five other genera in the family:
Sulfuricurvum
,
Sulfurimonas
,
Sulfurovum
,
Thiovulum
, and
Wolinella
. Phylogenetic analyses reliant on 16S rRNA gene sequences alone are insufficient for distinguishing closely related helicobacters, which have a high degree of natural transformation and genetic plasticity.
Helicobacter
species are isolated from the gastrointestinal and hepatobiliary tracts of a variety of mammalian and avian hosts. Laboratory tests requiring the collection of other types of specimen have been developed to assist in the diagnosis of
H. pylori
infection and may be undertaken under some circumstances.
H. pylori
is readily isolated by culture from gastric biopsy specimens.
Mycoplasma
and
Ureaplasma
Authors: Waites Ken B. , Bébéar Cécile
Published: January 2025

Mollicutes
are eubacteria that have evolved from
Clostridium
‐like Gram‐positive cells through genome reduction. The term “mycoplasma” is often used in a trivial way to refer to any members of the class
Mollicutes
, irrespective of whether they actually belong to the genus
Mycoplasma
. Mycoplasmas and ureaplasmas of human origin can be classified according to whether they utilize glucose, arginine, or urea. Attachment of
Mycoplasma pneumoniae
to host cells in the respiratory tract of humans is a prerequisite for colonization and infection. Urogenital mycoplasmas of clinical importance include
Mycoplasma genitalium
, a sexually transmitted pathogen, and
Mycoplasma hominis
and
Ureaplasma
spp., commensals of the human urogenital tract.
Ureaplasma
species have been shown to cause systemic and sometimes fatal infections leading to hyperammonemia in immunosuppressed persons who have undergone lung transplantation. Serology has been the most common laboratory means for diagnosis of
M. pneumoniae
respiratory tract infections.
Tropheryma whipplei
Authors: Geißdörfer Walter , Moter Annette , Bogdan Christian
Published: January 2025

Tropheryma whipplei
is the agent of classical Whipple disease, an infection originally described by the American pathologist George Hoyt Whipple in 1907 as intestinal lipodystrophy. Reasons are the rarity of the disease, the diversity and nonspecificity of symptoms, the fastidious nature of the pathogen, and the lack of serological tests. Data from two sequenced
T. whipplei
genomes reveal a small genome lacking key biosynthetic pathways. Whipple disease is a rare condition, with an estimated annual incidence of 1 case per 100,000 to 1,000,000. In classical Whipple disease, infection with
T. whipplei
probably occurs years before clinical manifestations point to the diagnosis.
T. whipplei
was detected in urine sediments by nucleic acid amplification testing in 9 of 12 patients and 10 of 13 patients with classical Whipple disease and in one patient with isolated endocarditis, but not in control persons, including healthy carriers.
Specimen Collection, Transport, and Processing: Virology
Authors: Dunn James J. , Pinsky Benjamin A.
Published: January 2025

This chapter describes preanalytical steps for viral diagnostics involving specimen selection, collection, transport, and processing, as well as details for collection of specific sample types. Depending on the specimen source and type of testing requested, it may be appropriate to place the sample in viral transport medium (VTM). Liquid specimens, such as amniotic fluid, blood, cerebrospinal fluid, urine, and bronchoalveolar lavage fluid, do not generally require VTM. Eye specimens include swabs or scrapings of the conjunctiva, corneal scrapings, and vitreous and aqueous fluids. An oral specimen provides a noninvasive means of detecting infection, and for some viruses, the onset of salivary shedding can indicate recent acquisition. Nonsterile specimens (e.g., upper respiratory tract, skin, lower genital tract, and stool) are obtained from sites that contain normal microbiota, or they are obtained from sterile sites but contact with nonsterile sites is unavoidable during specimen collection.
Reagents, Stains, Media, and Cell Cultures: Virology
Authors: Binnicker Matthew J.
Published: January 2025

This chapter describes the cell lines, reagents, stains, and media used in association with traditional tube and rapid viral culture techniques. In the era of molecular detection and quantification of viral pathogens, the applicability of viral isolation has been questioned. Quality control (QC) in the diagnostic virology laboratory is one component of quality assurance program and refers to the measures included in each assay to verify that the test is working properly and to ensure that a laboratory consistently produces accurate results. Essential to the QC process are the use of internal and external control material and the verification that these controls are performed in accordance with manufacturer criteria for acceptability, adherence to appropriate incubation time and temperatures for the assay, and ensuring that test kits are used prior to expiration. Several commercial sources provide reliable QC material for purchase, including specific strains, purified nucleic acid, antigens, antibodies, and other biological reagents.
Enteroviruses and Parechoviruses
Authors: Stellrecht Kathleen A. , Lamson Daryl M. , Romero José R.
Published: January 2025

Enteroviruses (EVs) are members of the
Picornaviridae
family, with “pico” meaning very small, “rna” indicating an RNA genome, and “viridae” signifying viruses. Traditional criteria for taxonomy and identification of EVs to subgroups were based on patterns of replication in cell cultures, clinical syndromes, or disease and on disease manifestations in suckling mice. EVs and Parechoviruses (PeVs) cause a wide array of both localized and systemic infections that affect many organ systems in patients of all ages. Specimen selection is important for making a diagnosis of EV infection, as asymptomatic shedding, especially in stool, is common. Nucleic acid amplification tests, such as reverse transcriptase PCR, are the recommended method for the detection of EV and PeV because of their enhanced sensitivity and rapid turnaround times. In the clinical setting, situations may arise where EV serology is requested; such is the case for myocarditis and determination of congenital infection in pregnant women.
Coronaviruses
Authors: Mostafa Heba H. , Pinsky Benjamin A.
Published: January 2025

Coronaviruses (CoVs) are so called due to their striking crown of surface projections, reminiscent of the solar corona, which can be seen by electron microscopy. CoVs have been found in a wide range of domestic and wild mammals and birds; however, the particular diversity of strains found in birds and bats suggests that these animals are the natural reservoirs of CoVs, although this may also be the result of sampling bias. The major transmission route of HCoV is likely to be respiratory, although many animal CoVs also have a fecal‐oral route of transmission and can replicate in epithelial cells in both the respiratory and gastrointestinal tracts. HCoVs can be detected by nucleic acid amplification testing in a range of routine upper and lower respiratory tract specimens, such as nasopharyngeal (NP) swabs, NP aspirates, sputum, and bronchoalveolar lavage fluid.
Hepatitis C Virus
Authors: Slev Patricia
Published: January 2025

Hepatitis C virus (HCV) is classified within the family
Flaviviridae
in its own genus
Hepacivirus
. Phylogenetic analysis of helicase sequences has been used to probe its relatedness to other viruses in the family. Serum and plasma are acceptable for HCV nucleic acid amplification tests (NAATs) and serology tests. HCV core antigen detection/quantification tests have been developed as alternatives to HCV RNA assays. HCV genotypes and subtypes can be determined by commercial and laboratory‐developed NAATs based on a variety of biochemical methods. With the emergence of the simplified pangenotypic treatment algorithms for the treatment naive, the clinical utility of baseline testing for the presence of resistance‐associated substitutions (RASs) that are associated with direct‐acting antiviral (DAA) therapy failures has been greatly reduced. Sequencing is the diagnostic method of choice for RAS detection. Initiating DAA therapy is recommended for both acute and pediatric HCV infections.
Herpes Simplex Viruses and Herpes B Virus
Authors: Greninger Alexander L. , Morrow Rhoda Ashley , Jerome Keith R.
Published: January 2025

This chapter provides taxonomy, description of the agent, epidemiology and transmission, clinical significance, direct detection, isolation procedures, identification and typing, serologic tests, and antiviral susceptibilities of Herpes Simplex viruses (HSVs) and Herpes B virus. HSV infections occur worldwide with no seasonal distribution. Most HSV‐1 infections are acquired early in childhood as subclinical or unrecognized infections. Young children may present with classic primary HSV‐1 infection characterized by gingivostomatitis, fever, and marked submandibular lymphadenopathy. Herpes B virus is similar to HSV in terms of genome size and structure and in terms of virion morphology. Herpes B virus can be cultured in monkey kidney and chicken embryo cells. Detection of virus in patient samples without an intervening culture amplification step provides the most rapid diagnosis. Serodiagnosis of herpes B virus infections has been complicated by extensive cross‐reactivity with HSV‐1 and HSV‐2.
Human Herpesviruses 6A, 6B, and 7
Authors: Greninger Alexander L. , Sedlak Ruth Hall , Jerome Keith R.
Published: January 2025

Human herpesvirus (HHV) 6A, HHV‐6B, and HHV‐7 are three distinct virus species that make up the
Roseolovirus
genus. Like HHV‐6, HHV‐7 infection is highly prevalent and infects most individuals during childhood. HHV‐7 DNA has been detected more frequently and at higher loads in affected tissues from non‐immunocompromised patients with interstitial pneumonia. Interpreting HHV‐6 detection by PCR in clinical specimens is complicated by both the ubiquity of subclinical reactivation and inherited chromosomally integrated forms. HHV‐6A and HHV‐6B can be typed through the use of species‐specific monoclonal antibodies and species‐specific PCR assays. The most usual setting for HHV‐6 testing is in the context of immunosuppression, especially hematopoietic cell or solid organ transplantation. Like all herpesviruses, HHV‐7 establishes latency after primary infection, and thus reactivation can later occur, particularly in the setting of immunodeficiency. Cytomegalovirus viremia is also more frequent among recipients with inherited chromosomally integrated HHV‐6.
Human Herpesvirus 8
Authors: Dollard Sheila C. , Gunthel Clifford J.
Published: January 2025

Human herpesvirus 8 (HHV‐8) is classified in the genus
Rhadinovirus
of the subfamily
Gammaherpesvirinae
based on sequence and biological properties. The HHV‐8 genome is double‐stranded DNA approximately 160 kb long and contains over 85 genes, including several genes of host derivation. HHV‐8 is in the small group of DNA viruses that cause cancer in humans, along with Epstein‐Barr virus, human papillomavirus, and hepatitis B virus. Serum and plasma can be used interchangeably in most HHV‐8 serologic tests, and standard procedures for collection and storage of serum and plasma apply. Kaposi's sarcoma is normally a clinical diagnosis that does not involve laboratory testing other than possible histological examination of a lesion biopsy.
Adenoviruses
Authors: Heim Albert , Kajon Adriana E.
Published: January 2025

In 1953, Rowe and colleagues described an “adenoid degeneration agent” that induced spontaneous deterioration of tissue cultures prepared from adenoids of children. In the mid1960s, human adenoviruses (HAdV) were found to cause tumors in rodents, prompting studies that revealed fundamental processes of molecular biology but failed to link the virus convincingly to human cancer. HAdV belong to the
Adenoviridae
family,
Mastadenovirus
genus. Adenoviruses are large, nonenveloped, icosahedral viruses 70 to 90 nm in diameter. Adenovirus infections can be epidemic, endemic, or sporadic, with the pattern of circulation, specific syndrome, and severity varying by type, population, and route of exposure. Adenovirus‐associated gastroenteritis is caused primarily by types 40 and 41 of species HAdV‐F, which are also known as the “enteric adenoviruses.”
Poxviruses
Authors: Satheshkumar P. S. , Olson Victoria A. , Damon Inger K.
Published: January 2025

All poxviruses belong to the family
Poxviridae
and subfamily
Chordopoxviridae
. All naturally occurring poxviruses that infect humans are sporadic zoonotic agents except the
Molluscipoxvirus
MCV, which is transmitted strictly between humans. The clinical appearance of human monkeypox, typified by that seen with the Congo Basin virus, is much like that of smallpox, with fever, a centrifugally distributed vesiculopustular rash, respiratory distress, and in some cases, death from systemic shock. In humans, cowpox lesions occur mainly on the fingers, with reddening and swelling. Human parapoxvirus infection is normally associated with an exposure to sheep, goats, and/or cattle. Electron microscopy could be a method for laboratory diagnosis of poxvirus infections. Serologic methods currently used to detect antibodies against human orthopoxviruses include enzyme‐linked immunosorbent assays, the virus neutralization test, Western blotting, and hemagglutination inhibition. The description of an orthopoxvirus immunoglobulin M assay offers great promise to enhance investigations of orthopoxvirus infection outbreaks, which are often semi‐retrospective.
Mechanisms of Resistance to Antiviral Agents
Authors: Shafer Robert W. , Boivin Guy , Howe Anita Y. M. , Chou Sunwen
Published: January 2025

Understanding the mechanisms of viral drug resistance is critical for clinical management of individuals receiving antiviral therapy, for developing new antiviral drugs, and for drug resistance surveillance. This chapter reviews the mechanisms of resistance to antiviral drugs used to treat infections by eight common viruses: herpes simplex, cytomegalovirus, varicella‐zoster virus, human immunodeficiency virus type 1, influenza A and B, hepatitis B, hepatitis C, and severe acute respiratory syndrome coronavirus 2. Drug‐resistant virus subpopulations may exist at low levels in clinical isolates or may arise only during drug exposure. The error‐prone polymerases in RNA viruses render the development of resistance more frequent than in DNA viruses. Drug‐resistant viruses are identified by in vitro passage experiments in which wild‐type viruses are cultured in increasing concentrations of an inhibitory drug and by ex vivo analysis of virus isolates obtained from individuals receiving antiviral therapy.
Susceptibility Test Methods: Viruses
Authors: Pinsky Benjamin A.
Published: January 2025

Testing for viral susceptibility, primarily via genotypic drug resistance mutation testing, is now standard practice for the management of viral infections for optimum patient care. Antiviral resistance is expressed as a drop in the efficacy of a drug to inhibit viral replication. The virus being treated is inherently resistant to the drug(s) being given. Alternatively, host biological and socio‐behavioral factors or inadequate dosing may influence therapeutic success. Host physiologic factors can interfere with a successful clinical response. Viral susceptibility testing can identify resistance and guide patient management strategies. The clinical category and status of the patient are important in determining whether antiviral resistance testing is indicated. Genotypic viral susceptibility testing requires knowledge of the mutations that confer antiviral resistance. FDA‐cleared genotypic antiviral resistance tests include software to analyze the raw sequence and render a resistance interpretation. The pharmaceutical industry is actively investigating and developing new antiviral drugs.
Taxonomy, Classification, and Nomenclature of Fungi
Authors: Cañete‐Gibas Connie F. , Wiederhold Nathan P.
Published: January 2025

Fungi form a clade of eukaryotic organisms that differ from other groups in several aspects. Fungi can be either multicellular or unicellular. The basic structural unit of multicellular fungi is a chain of multinucleate, tubular, filament‐like cells. Fungi that exist in the form of microscopic multicellular mycelium are commonly called molds. Identification of fungi solely by phenotypic characteristics requires familiarity with a range of different structures and terminology. However, the advent of rapid molecular and proteomic assays have transformed this process, facilitating the accurate identification of clinical isolates. In addition, these new methods of analysis are having a substantial impact on the taxonomy and nomenclature of fungi, including many medically important species. The advent of molecular phylogenetics has led to a revolution in microbial taxonomy. Yeasts are neither a natural nor a formal taxonomic group but are a growth form found in a wide range of unrelated ascomycetous and basidiomycetous fungi.
Specimen Collection, Transport, and Processing: Mycology
Authors: Berkow Elizabeth L. , Sexton D. Joseph
Published: January 2025

As in bacteriology, the goals of a good mycology laboratory are to accurately isolate and identify fungi suspected of causing infection. It is the laboratory's responsibility to ensure that specimens are appropriate for the requested test and to provide submitters with the guidelines for proper specimen selection, collection, and transport to the laboratory. This chapter provides general information related to fungal culture from various specimens and is based on historical practice that has been successful. Pretreatment of several specimen types is necessary to maximize the recovery of fungi. Abscess specimens should be collected from the active peripheral edge of open abscesses or aspirated from closed abscesses by use of a syringe. There are presently a wide variety of manual, biphasic, automated, and continuously monitoring systems for blood cultures, but no single commercial system or culture medium can detect all potential blood pathogens.
Reagents, Stains, and Media: Mycology
Authors: Lindsley Mark D.
Published: January 2025

A variety of stains, media, and reagents are available to the mycology laboratory for the detection, isolation, characterization, and identification of yeasts and moulds. Familiarity with the composition and characteristics of these materials is critical to the diagnostic approach when processing specimens from patients with suspected mycotic diseases. Many media are available for the primary inoculation and cultivation of fungi from clinical specimens. Chloramphenicol or gentamicin inhibits most bacterial contaminants, while cycloheximide inhibits most saprobic moulds. Dithiothreitol is a mucolytic agent that can be purchased commercially and has been used to prepare sputum specimens for detection of
Pneumocystis jirovecii
. Alcian blue is a mucopolysaccharide stain useful for visualizing the polysaccharide capsule produced by
Cryptococcus
species in histological sections of tissue. Methenamine silver stains are the most useful stains for visualizing fungi in tissue. Acetate ascospore agar is used for the cultivation of ascosporogenous yeasts such as
Saccharomyces cerevisiae
.
Agents of Systemic and Subcutaneous Mucormycosis and Entomophthoromycosis
Authors: Garcia‐Hermoso Dea , Alanio Alexandre , Lanternier Fanny , Lortholary Olivier
Published: January 2025

Mucormycosis and entomophthoromycosis are invasive fungal infections caused by environmental pauciseptate filamentous fungi. Entomophthoromycosis presents as subcutaneous infections with favorable outcome after prolonged azole therapy without surgery, although it is potentially associated with disfiguring lesions. Mucormycosis can develop in HIV‐infected patients and in intravenous‐drug users. The diagnosis of mucormycosis should be considered an emergency, because delaying therapy will affect outcome. One of the major differences between mucormycosis and entomophthoromycosis is that the former occurs mainly in predisposed individuals, whereas the latter occurs mostly in apparently immunocompetent hosts. Culture results should always be interpreted in light of the clinical presentation and along with the results of direct examination and/or histopathology. Therapeutic strategies for basidiobolomycosis and conidiobolomycosis are not standardized because of the lack of clinical trials for these rare infections.
Mechanisms of Resistance to Antiparasitic Agents
Authors: Bradbury Richard S. , Talundzic Eldin
Published: January 2025

Parasitic diseases rank among the most prevalent and severe diseases worldwide. The danger of depending on drugs as one of the primary tools for control is compounded by the relatively limited number of antiparasitic agents available. The complex biologic interactions between parasites and their hosts (and, at times, their vectors) significantly influence the emergence and expression of drug resistance. The development of resistance to all antimalarial drugs poses the greatest challenge for malaria control and prevention globally. Praziquantel is the only drug currently being used for treatment of schistosomiasis. The widespread use of albendazole, mebendazole, levamisole, and pyrantel in preventive chemotherapy programs to control soil‐transmitted helminth infections has raised concerns regarding the potential for the development of resistance in this group of intestinal nematodes. Public health interventions to correct these factors have not always been successful and would benefit from a better understanding of the drug resistance mechanisms used by parasites.
The Photoinduced Response of Antimony from Femtoseconds to Minutes
Authors: Walfort Sebastian , Holle Nils , Vehndel Julia , Yimam Daniel T. , Vollmar Niklas , Kooi Bart J. , Salinga Martin
Published: January 2025

As a phase change material (PCM), antimony exhibits a set of desirable properties that make it an interesting candidate for photonic memory applications. These include a large optical contrast between crystalline and amorphous solid states over a wide wavelength range. Switching between the states is possible on nanosecond timescales by applying short heating pulses. The glass state is reached through melting and rapid quenching through a supercooled liquid regime. While initial and final states are easily characterized, little is known about the optical properties on the path to forming a glass. Here we resolve the entire switching cycle of antimony with femtosecond resolution in stroboscopic optical pump‐probe measurements and combine the experimental results with ab‐initio molecular dynamics simulations. The glass formation process of antimony is revealed to be a complex multi‐step process, where the intermediate transient states exhibit distinct optical properties with even larger contrasts than those observed between crystal and glass. The provided quantitative understanding forms the basis for exploitation in high bandwidth photonic applications.