bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interferon Gamma Release Assays for Latent Tuberculosis Infection
Authors: Costales Cristina , Banaei Niaz 
Published: January 2025

Abstract

Tuberculosis (TB) is a major global infectious cause of death and an enormous public health challenge. TB causes a wide spectrum of disease in humans that ranges from asymptomatic infection to symptomatic disease, which creates difficulty in TB control efforts. Control of the infection relies on multiple components of the immune system, including activation of lung macrophages, which play a key role in the innate response by phagocytosis and sequestration of
M. tuberculosis
bacilli within the phagosome.
M. tuberculosis
has evolved numerous strategies to evade elimination by the host response. States of immunosuppression such as HIV coinfection, antitumor necrosis factor drug regimens, or older age during latent infection are all risk factors for progression to active disease.
Molecular Methods for Identification of Microorganisms
Authors: Greninger Alexander L. , Hillyard David R. , Reimer Larry G. , Mehta Ninad , Mallory Melanie A. , Schlaberg Robert , Pettengill Matthew A. , Tang Yi‐Wei , Nguyen Nang , Pinsky Benjamin A. , Schutzbank Ted E. , Graf Erin H. 
Published: January 2025

Abstract
Human immunodeficiency virus‐1 (HIV‐1) ribonucleic acid is most often used for confirmation of HIV‐1 infection down stream of fourth‐generation antigen‐antibody screening assays and for quantitative viral load monitoring. For individuals with virologic failure, resistance testing is recommended at designated plasma viral concentrations, which are routinely monitored as part of patient care. Whole blood and plasma are acceptable specimen types for HIV resistance testing. Human papillomavirus types infecting the mucosal squamous cell epithelium are categorized into three general groups: the high‐risk (HR) group, the low‐risk (LR) group, and members of the indeterminate risk group for which insufficient information exists for classification as the HR or LR type. Herpes simplex virus 1 (HSV‐1), HSV‐2, and varicella‐zoster virus are members of the alphaherpes virus subfamily that exhibit neurotropism.
Introduction
Authors: Miller J. Michael 
Published: January 2025

Abstract
Epidemiologic and infection control microbiology brings together the best of microbiology science and medical expertise, most often through a team of infection preventionists (IP) focused on preventing hospital‐associated infections and keeping patients safe. The role of the IP team includes providing surveillance and prevention of hospital‐acquired infections, continuing education to the staff, outbreak control using epidemiology skills, protecting employees and visitors, advising on new products and procedures, and engaging with antibiotic stewardship. The Centers for Disease Control and Prevention (CDC) hosts the National Healthcare Safety Network, which is the most widely used health care‐associated infection tracking network. This chapter features a description of the role of the CDC‐sponsored Antimicrobial Resistance Laboratory Network and its role in addressing the issue of current and emerging resistance of microbial pathogens.
Laboratory Support for Infection Prevention: Collaboration with Benefits for All
Authors: Johnson J. Kristie 
Published: January 2025

Abstract
The modern discipline of hospital infection control (infection prevention [IP]) began in the 1970s, was refined in the 1980s, and has continued to evolve as an integral part of the health care provider's overall program of continuous quality improvement. Concomitant with the evolution of infection prevention programs (IPPs) has been the evolution of health care, with the introduction of new modalities of care that carry with them a high risk for health care‐associated infections (HAIs). The ever‐increasing complexity and sophistication of modern medical care pose challenges for both the IPP and the clinical microbiology laboratory (CML). In addition to performing their traditional roles in the CML, laboratory personnel play major roles in areas of critical importance to the IPP: surveillance, detection and management of HAI outbreaks, antimicrobial stewardship, diagnostic stewardship, deliberation of the infection control committee, and education.
CLIA Certification and Accreditation, ISO 15189 Accreditation, and Proficiency Testing
Authors: Stang Heather L. 
Published: January 2025

Abstract
Clinical laboratories can ensure the quality of testing and result reporting through laboratory certification and accreditation. The Centers for Medicare & Medicaid Services (CMS), which administers the Clinical Laboratory Improvement Amendments of 1988 (CLIA) program, can issue a certificate of accreditation based on the laboratory's meeting certification requirements for a CMS‐approved accreditation organization. While the CLIA certificate of accreditation is one way of meeting the required quality standards for U.S. laboratories, meeting an International Organization for Standardization (ISO) accreditation standard is another option for international laboratories or U.S. laboratories aspiring to higher levels of quality. ISO 15189 provides an overview of the quality management system standards and includes additional quality and competence criteria in medical laboratories. Proficiency testing (PT) is an essential part of a laboratory's quality system, and clinical laboratories use PT to verify test accuracy and reliability.
Individualized Quality Control Plan
Authors: Bryant Kendall , Sharp Susan 
Published: January 2025

Abstract
Clinical Laboratory Improvement Amendments (CLIA) regulations require testing QC strains on each new lot/shipment of substrates/reagents to verify positive and negative reactivity. Individualized quality control plans (IQCPs) are limited to nonwaived tests that employ an internal QC system and can also be used for microbiology media and reagents used for microbial identification and susceptibility testing. CLIA regulates that laboratories must follow all manufacturer instructions for commercial tests. Risk assessment identifies areas where errors or failures could occur in preanalytical, analytical, and postanalytical assay steps. The assessment should include an analysis of potential risk for harm to the patient if an error were to occur and be reported. A laboratory's own data, whether new or historical, can be used to help determine potential risks. QC plan defines the control mechanisms in place for detecting or preventing errors. QA establishes a system for continually monitoring the effectiveness of the IQCP.
Laboratory Records
Authors: Hensley Rhonda 
Published: January 2025

Abstract
Records serve at least four purposes. First, they document what has transpired without recourse to memory, second, they serve as a point of reference for developing the facts regarding any incident, third, they assist in the recognition of trends and the resolution of problems, and final, they establish the laboratory's credibility. Whether laboratory records are stored electronically, in a paper‐based system, or a hybrid of both, they need to be accessible and retrievable in a timely manner. Paper copies may be scanned and stored, and after verifying that the electronic copy replicates the paper copy, the paper record may be destroyed. Records may be used to identify trends or shifts in testing and/or testing personnel. Quality control records of control values for procedures, tests, and equipment are used to detect and identify problems and trends within the laboratory.
Preparation and Quality Control of Laboratory Water
Authors: Hensley Rhonda 
Published: January 2025

Abstract
This chapter describes the methods of preparation and quality control testing of water used in microbiology laboratories and to provide water specifications published by CLSI. Classification of water is based not on the method of preparation, which is typically how most individuals characterize water, but on a series of tests the water passes. The recommendations found in this procedure are largely based upon those published by the CLSI and focus on purified water used to make reagents, buffers, diluents, and water used in instrumentation. Each laboratory must verify that water used is acceptable for the procedure and does not impede specificity, accuracy, or precision. The construction and design of a water distribution system significantly influence the quality of the end product. The chapter covers proper quality control principles for analytical tests. Each laboratory must establish a periodic maintenance schedule to monitor water quality based on risk and practicality.
Pipette and Loop Calibration
Authors: Hensley Rhonda 
Published: January 2025

Abstract
The volume of fluid picked up by a calibrated loop depends on the volume and shape of the container holding the liquid and the direction and depth in which the loop is immersed. Quantitative loops are less accurate than pipettors yet are a convenient way to set up a semiquantitative culture or dilution. The same pipette tips used for laboratory testing should be used for performance verification, since the tip design affects volume of pipetting. Pipettors aspirate and expel by an air displacement or positive‐displacement mechanism. Air displacement pipettors are more commonly used in microbiology. Manual pipettors are lightweight cylindrical tools consisting of a handheld mechanical handle for volume adjustment and calibration and a delivery shaft that fits disposable tips. Pipettors are approximately 10 in. long and deliver microliter to milliliter volumes. On automated pipettors, the mechanical handle is replaced with instrumentation.
Introduction
Authors: Relich Ryan F. 
Published: January 2025

Abstract
This part introduction presents an overview of the key concepts discussed in the subsequent chapters. The part deals with basic strategies and procedures for the prevention, containment, and management of laboratory‐associated infections (LAIs) in the clinical microbiology laboratory and is designed to help laboratories formulate their own bench procedures. Clinical laboratory workers are at high risk for occupational exposure to infectious agents. LAIs can result from exposure to contaminated blood, tissues, cultures of microorganisms, and other biohazardous materials present in the laboratory environment. Laboratory practices that can reduce the risk of LAIs include strict and consistent adherence to standard precautions, appropriate use of PPE and safety devices, regular decontamination of laboratory work surfaces, and appropriate disposal of infectious wastes. A renewed interest in improving safety in laboratory has occurred because of the recognition of new infectious agents, emergence of antimicrobial resistance, development of new diagnostic and treatment methods, and threat of agents of bioterrorism.
Biohazard Containment
Authors: Relich Ryan F. , Bell Drew 
Published: January 2025

Abstract
In addition to implementing standard microbiological procedures and practices, management of the biohazards associated with working with pathogens includes physical barriers and administrative controls. Physical barriers include primary safety equipment and secondary facility design. Biosafety levels (BSLs) are numerical designations assigned to microbiological and biomedical laboratories based upon the pathogenicity, virulence, transmissibility, treatability, preventability, and occupational risks associated with the agent(s) handled in the laboratory. BSLs range from BSL‐1 to BSL‐4 and are based on the increased risk associated with the types of microorganisms encountered. The biological safety cabinet (BSC) is the most important primary containment device in the clinical microbiology laboratory, and class II cabinets are the most commonly used types of BSC in this environment. 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.
Laboratory Instrumentation and Equipment
Authors: Buchan Blake W. , Capraro Gerald A. 
Published: January 2025

Abstract
An autoclave, or steam sterilizer, is an insulated pressure chamber in which saturated steam is used to elevate temperature above the normal boiling point of water. Autoclaves are used for sterilization of both culture media and heat‐stable supplies and the decontamination of infectious waste. A centrifuge produces centrifugal force that is used to separate particles of various densities. In the microbiology laboratory, centrifugation is used for concentrating microorganisms and cells, separating components of body fluids or mixed suspensions, and removing particulate matter. Laboratory personnel should be cognizant of hazards from compressed gases. A falling cylinder can cause physical injury to personnel. A safe and efficient way to transport specimens and materials from one point to another is through an automated and computerized pneumatic tube system. Clinical specimens and microorganism isolates are routinely stored for extended periods of time for retrieval and testing or before shipment to other laboratories.
Special Pathogens and Employee Safety
Authors: Simons Corrie C. , Capraro Gerald A. 
Published: January 2025

Abstract
At the point of electronic order entry, questions can be included that allow providers to specify the potential select agent or symptoms that raise suspicion for a high‐consequence pathogen. The use of some bacteria and viruses as biothreat agents presents additional risk to clinical microbiologists and imposes additional safety concerns for the laboratory. Clinical microbiology laboratories should consider implementing a policy of not accepting non‐human specimens (e.g., devices, fluids, medicines, eye drops, and animal specimens) and suspicious environmental specimens (e.g., powders, envelopes, papers, building materials, pouches, containers, books, and mail) into the laboratory for any type of examination or culture. Personnel are at higher risk for laboratory‐acquired infections, which can be transmitted to other employees, employees' families, and the general public. Prions cannot be cultured in the laboratory. Potential Creutzfeldt‐Jakob disease specimens can be classified by level of risk to laboratory workers.
General Introduction to Bioterrorism and Emerging Infectious Diseases
Authors: Rowlinson Marie‐Claire 
Published: January 2025

Abstract
The primary function of the Laboratory Response Network for Biological Threats is to respond to biological threats/bioterrorism and emerging infectious diseases. This chapter focuses on laboratory preparedness for bioterrorism‐associated biological agents, the challenges posed by emerging infectious diseases serve to highlight the importance of, and the need for, maintaining an integrated network of diagnostic laboratories that are capable of providing rapid detection of both. Bioterrorism events are classified as either overt or covert. In an overt event, the agent is announced. A covert event, which is more likely to occur, is unannounced and is much more of a challenge to detect. The detection of a covert event is likely to occur at the community/sentinel laboratory level. Health care institutions, including the laboratory, should have a preparedness plan that includes the recognition of the covert form of bioterrorism or a highly pathogenic or emerging infectious disease.
Brucella
spp.—Brucellosis
Authors: Rowlinson Marie‐Claire , Lee Philip A. 
Published: January 2025

Abstract

Brucella
species are fastidious, aerobic, small, Gram‐negative coccobacilli that are nonmotile and non‐spore forming and are the causative agent of brucellosis, a reportable disease in most countries.
Brucella abortus
,
Brucella melitensis
, and
Brucella suis
are considered “overlap” select agents because they pose a serious threat to public health and safety as well as to animal health and animal products. To identify
Brucella
to the genus level, some biochemical testing is needed; however, automated systems and manual biochemical test kits cannot accurately identify the organism, due to its minimal reactivity. Brucellosis is the most common zoonotic disease worldwide, and although the epidemiology has changed with livestock vaccination and pasteurization of dairy products, it continues to be endemic in certain areas of Latin America, Asia, Africa, and the Middle East, causing an estimated 500,000 human cases of brucellosis annually.
Tularemia—
Francisella tularensis
Authors: Schaecher Kurt E. 
Published: January 2025

Abstract

Francisella tularensis
is a fastidious, tiny, Gram‐negative coccobacillus and the etiological agent of tularemia.
F. tularensis
is a known risk for laboratory‐acquired infection. The identification of
F. tularensis
should not be attempted with commercial identification systems because of the potential of generating aerosols and the high probability of misidentification.
F. tularensis
is widespread throughout the Northern Hemisphere and is responsible for recent tularemia outbreaks in several countries, including Norway and Turkey.
F. tularensis
is a zoonotic pathogen with an extremely wide host range that includes mammals, birds, and amphibians. The primary hosts for
F. tularensis
are believed to be small rodents (hares, voles, muskrats).
F. tularensis
was actively pursued as a biological warfare agent by both the United States and the former Soviet Union.
Novel Influenza Viruses and Highly Pathogenic Coronaviruses
Authors: Loeffelholz Mike J. , Relich Ryan F. 
Published: January 2025

Abstract

Three viruses in the family
Orthomyxoviridae
cause influenza in humans: influenza virus types A and B, and influenza virus C. Influenza viruses are enveloped and have a segmented, single‐stranded, negative‐sense RNA genome. There are seven known human‐pathogenic coronaviruses, including the human coronaviruses (HCoV229E, HCoV‐NL63, HCoV‐OC43, and HCoV‐HKU1), Middle East respiratory syndrome coronavirus (MERS‐CoV), severe acute respiratory syndrome coronavirus (SARSCoV or SARS‐CoV‐1) and SARSCoV‐2. In humans, coronaviruses primarily cause respiratory tract diseases that range from mild nasopharyngitis to severe, life‐threatening pneumonia; however, many of these viruses have been found to cause extrapulmonary diseases as well. The chapter covers safety considerations, specimen collection, and methods 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.
Eastern Equine Encephalitis Virus
Authors: Vetter Sara M. 
Published: January 2025

Abstract

Eastern equine encephalitis virus (EEEV) is a member of the Alphavirus group in the family
Togaviridae
. It is an enveloped, positive‐sense RNA virus and is part of a group of other important arthropod‐borne viruses such as chikungunya virus and Ross River virus. EEEV is the etiological agent of eastern equine encephalitis (EEE) disease in humans and equines. The main mosquito vector is
Culiseta melanura
, which is found in the southeastern United States, Central America, and northern South America, but other “bridge vectors”, such as
Aedes
,
Culex
, and
Coquillettidia
, which feed on both birds and mammals, are responsible for infections in equines and humans. EEEV has been detected only in the Western Hemisphere, being found in eastern Canada and all U.S. states east of the Mississippi as well as several other states, including Arkansas, Minnesota, South Dakota, and Texas. Clinical manifestations of EEE infection vary from low‐grade fever to severe encephalitis, including death.
Immunoassays for the Diagnosis of Infectious Diseases
Authors: Theel Elitza S. 
Published: January 2025

Abstract
This chapter summarizes the common serologic testing methods used for detection of the humoral immune response to, or antigens released from, various infectious agents. It presents their application for the diagnosis of infectious diseases, including a discussion of the advantages and limitations of selected methods. An understanding of serologic immunoassays and their clinical utility requires an appreciation of the basic immunologic principles of humoral immunity. Serologic assays can be used for either screening or diagnostic purposes. Agglutination reactions utilize a particulate, insoluble antigen, in contrast to precipitation reactions, which are based on the interaction of soluble antigen and antibodies. The complement fixation assay is based on the interaction of immune complexes with components of the classical complement pathway. Another classic serologic technique is the neutralization assay. The term “enzyme immunoassay” is considered a general term that can be applied to any immunoassay which uses an enzyme label.
Investigation of Disease Outbreaks
Authors: Rolon Rebecca M. , Szymczak Wendy A. 
Published: January 2025

Abstract
This chapter reviews concepts associated with infectious diseases outbreaks, including disease surveillance, mechanisms used to detect outbreaks, and the epidemiological steps used to investigate an outbreak. It describes the role of the laboratory in outbreaks and includes examples where laboratory testing played a key role in the investigation of the outbreak. Outbreak investigations provide a unique opportunity for local authorities to provide enhanced education and awareness. Outbreak (or epidemic) intelligence is the process used to detect, verify, analyze, assess, and investigate signals that may represent a threat to public health. The chapter provides specific examples of how laboratories contributed to the SARS‐CoV‐2 outbreak response. In the recent SARS‐CoV‐2 pandemic, nucleic acid amplification and antigen detection assays have been used widely for virus identification from specimens, while WGS has been used for both the detection of and surveillance for emerging variants.
Molecular Epidemiology
Authors: MacCannell Duncan , Terry Fei Fan Ng , Chow Nancy , Jorba Jaume , Beck Andrew , Carleton Heather 
Published: January 2025

Abstract
The practice of infectious disease epidemiology has always been linked to advances in laboratory science, data analysis, and interpretation. This chapter is intended to serve as an introduction to molecular epidemiology and important terms and concepts associated with the field. It focuses on applications of these classical molecular epidemiologic techniques, and focuses on the increasing role and impact of genomic sequencing and bioinformatics in broad‐based pathogen identification, characterization, molecular surveillance, and outbreak response. The chapter discusses strategies for the development of molecular subtyping tools, including data analysis and interpretation, and comprehensive validation and quality control. All molecular subtyping methods show very high typeability with the organisms that they target. Data from ongoing molecular surveillance of viral and bacterial pathogens are used to decide on the most appropriate formulation for vaccines, and to assess for ongoing vaccine safety and effectiveness.