bluuebunny/crossref_metadata_2025_split huggingface dataset:
Processing Specimens for Fungal Culture
Authors: Abdolrasouli Alireza , Howell Susan 
Published: January 2025

Abstract

When a specimen is suspected to contain a fungal etiologic agent, it should be processed for fungal culture, regardless of direct microscopic findings. Recovery of fungal pathogens in culture often provides definitive diagnosis of mycotic disease, identifies the etiologic agent of infection, and allows evaluation of in
vitro
testing of susceptibility to antifungal agents. In general, sensitivity of fungal culture can be increased by using specific fungal media as opposed to bacteriological media. Some specimens may require pretreatment prior to culture. There are several categories of culture media employed for the recovery of fungi from clinical specimens. This chapter summarizes the minimum recommendations for selection of culture media. It presents a general guide on incubation conditions, including duration and temperature, for fungal cultures. Personnel working in the mycology laboratory should be aware of the potential dangers when working with fungal organisms and exercise appropriate safety measures.
Phenotypic Identification of Molds
Authors: Cañete‐Gibas Connie F. , Wiederhold Nathan P. 
Published: January 2025

Abstract
“Mold” is an informal term signifying a fungus growing mostly or entirely in the form of diffuse filaments and usually producing an asexual reproductive state or a sexual state that is not a large, complex fruiting body. Morphologic characteristics learned from cultures can sometimes even be recognized in direct specimens, making possible a rapid preliminary identification, with more time‐consuming techniques directed toward confirmation. Morphological classification schemes for ascomycetous and basidiomycetous molds focus on conidial ontogeny, that is, the process by which asexual propagules form. Ascomycota make up most of the mold fungi of the medical laboratory, including all the dimorphic fungi, the dermatophytes, and common opportunistic molds that normally produce septate filaments in tissue. Dimorphic fungi are thermal or thermal‐nutritional dimorphic systemic pathogens that convert from a mold phase in ordinary culture or the environment to a budding yeast phase in the host or under special growth conditions at 37°C.
Introduction
Authors: Garcia Lynne S. 
Published: January 2025

Abstract
Good microscopes and light sources are mandatory for the examination of specimens for parasites. Identification of the majority of organisms depends on morphologic differences, most of which must be seen by using stereoscopic or regular microscopes. Either a table or floor model centrifuge, which should be able to accommodate 15‐ml centrifuge tubes, is acceptable. The centrifuge should have adjustable speed settings. Although a fume hood is not required, many laboratories prefer to keep their staining reagents and formalin in a fume hood. Any laboratory doing diagnostic work in parasitology should have a calibrated microscope available for precise measurements. Measurements are made with a micrometer disk that is placed in the ocular of the microscope; the disk is usually calibrated as a line divided into 50 units. The standard safety considerations of any clinical laboratory should be practiced in a parasitology laboratory.
Other Specimens from the Intestinal Tract and the Urogenital System
Authors: Morris Heather R. , Pritt Bobbi S , Garcia Lynne S. 
Published: January 2025

Abstract

Enterobius vermicularis is a parasitic nematode that inhabits the large intestine. The clear cellulose tape preparation has traditionally been the procedure of choice for collecting perianal specimens. The direct wet mount is primarily used to detect motile parasites that are found in the colon. The permanent stained smear is used primarily to detect parasites in the colon. When considering intestinal protozoa, permanent stained smears usually confirm structures seen on wet specimen examinations. Some organisms may be difficult to recover in the stool, particularly those normally found in the duodenum. An alternative approach to routine stool examinations is to sample the duodenal contents. The traditional method for detecting
Trichomonas vaginalis
infections is by detecting live motile flagellates from direct saline mounts of clinical specimens such as urethral or vaginal discharge. Some parasites may be found in the urine, and their detection is enhanced by concentration using centrifugation.
Gross Examination of Helminths and Arthropods
Authors: Mathison Blaine A. 
Published: January 2025

Abstract
Partial and intact arthropods and helminths are frequently submitted to the diagnostic laboratory for identification. Whole helminths and arthropods, or parts thereof, should be placed in a liquid medium as quickly as possible to preserve important diagnostic morphologic features and kill possible pathogens carried by the organisms. Adult and larval helminths may be recovered from a variety of specimens, including but not limited to stool; specimens obtained from the lungs, eyes, and biliary tree; specimens obtained from the gastrointestinal tract during colonoscopy and endoscopy; and helminths coughed up or expelled via the nose or mouth. There are several factors which may make proper identification and reporting challenging to the technologist, including but not limited to the condition of the specimen submitted, differentiating clinically relevant organisms from incidental findings of nonparasitic organisms, and determining how far to take an identification and how the organism should be reported.
Shell Vial/Multiwell Plate Culture for Rapid Virus Isolation
Authors: Mehta Ninad , Ginocchio Christine C. 
Published: January 2025

Abstract
Virus culture has long been considered the gold standard for the diagnosis of viral infections. Conventional tube/flask culture systems were the mainstay of clinical virology laboratories in the past. To further increase culture sensitivity and speed of viral detection for hard‐to‐cultivate or slow‐growing viruses, the centrifugation‐enhanced shell vial method was developed. This chapter describes the basic procedure for virus isolation in shell vial or multiwell plate cultures. Detection of viruses in cell culture is the most challenging and technically demanding of the traditional viral diagnostic technologies. With the advent of many sensitive and relatively simple molecular and antigen‐based assays for virus detection, the use of cell culture has declined dramatically worldwide. This procedure focuses on rapid centrifugation‐enhanced cultures. 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.
Selection, Maintenance, and Serial Propagation of Uninoculated Monolayer Cell Cultures
Authors: Hodinka Richard L. 
Published: January 2025

Abstract
The majority of diagnostic laboratories that continue to perform virus isolation in cell culture obtain the requisite cells from a commercial vendor, already seeded in the vessels that will be inoculated with clinical specimens. Alternatively, they receive them in a near‐ready state, with minimal manipulations required before the cell monloayers are ready to inoculate. Few laboratories still maintain onsite seed stocks of various cell types that are continuously passaged and routinely used to prepare cell cultures for virus isolation and identification. For those that choose to do so, it is imperative that they have the appropriate facilities and adhere strictly to detailed, well‐established protocols, to ensure an uninterrupted supply of healthy cell cultures for diagnostic purposes. The rate of cell division usually slows down as the monolayer becomes increasingly denser and more confluent and the nutrients in the growth medium are consumed.
Detection of
Brucella
spp. Antibodies
Authors: Stoddard Robyn A. 
Published: January 2025

Abstract

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

Abstract

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

Abstract

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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract

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

Abstract

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

Abstract

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

Abstract
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

Abstract
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.