bluuebunny/crossref_metadata_2025 huggingface dataset:
Internalisasi Nilai-Nilai Kepahlawanan Syaikhona Muhammad Kholil Sebagai Upaya Meningkatkan Jiwa Nasionalisme dan Patriotisme pada Generasi Muda
Authors: Suherlin Suherlin , Annisa Nur , Rusdiana Erma
Published: July 2023

Pengusulan gelar pahlawan Syaikhona Mohammad Kholil menjadi momen penting untuk membangkitkan kembali nilai-nilai nasionalisme dan patriotisme generasi muda. Pendidikan karakter untuk mencintai negara merupakan salah satu hal yang harus ditanamkan bagi generasi muda sedini mungkin. Karakter untuk mencinta bangsa dan negara merupakan fondasi awal untuk membentukan karakter jiwa nasionalisme dan upaya membangkitkan rasa nasionalisme pada generasi muda Indonesia. Penelitian tentang internalisasi nilai-nilai kepahlawanan ini bertujuan mengkaji strategi dan metode internalisasi nilai nasionalisme dan patriotisme serta memasukkan ketokohan Syaikhona Muhammad Kholil Syaikhona pada kurikulum sekolah menengah sebagai upaya meningkatkan jiwa nasionalisme dan patriotisme pada generasi muda. Penelitian ini dilaksanakan di Kabupaten Bangkalan pada tahun 2021. Data primer diperoleh melalui wawancara (interview) terstuktur dan tak terstruktur dengan responden atau informan adalah guru, Kepala Sekolah dan siswa. Selain itu dilakukan pula serangkaian FGD untuk memperoleh masukan dari para stakeholders. Hasil penelitian menunjukkan nilai-nilai karakter yang ditanamkan oleh Saikhona Muhammad Kholil melalui pendidikan pesantren memiliki ciri khas dalam pembelajaran karakter yang bernilai islami sekaligus menanamkan nasionalisme
Importance of Carotenoids and Phytoestrogens in Gonad Maturity of Various Types of Fish
Authors: Iskandar  , Saputra Muhamad Erpan , Anna Zuzy
Published: July 2023

Aims: The purpose of this article is to examine the potential for adding combinations of carotenoids and phytoestrogen in their feed to the maturity of gonads of different kinds of fish. The method of writing used is the library study, with the journal search stages, journal selection, journal analysis, and journal synthesis. Based on the review of several related journals. The presence of carotenoids and of estrogen in the reproductive process of fish is highly profitable. The carotenoid compound, which is a provitamin a, will help in the development of oocytes primarily with the accumulation of vitellogenin and maintaining fatty acids in the oocytes. Meanwhile, the presence of phytogenic that have structures like endogenous estradiol will assist in synthesizing and producing vitellogenin in the liver. So the size of oocytes would accelerate and impact the rapid ripening of the fish. After a maximum Estrogen measure, a full-flesh-based phytoestrogen will act like a hoflavon to give a MIH signal to be received by the surface of oocyte then passes to the cytoplasm to encourage maturation promoting factor (MPF) that causes germinal vesicle breakdown (GVBD) to the fish's egg. The presence of easily obtained carotenoids and phytoestrogen provided potential additives.

Conclusion: The combination of carotenoids and phytoestrogens in feed has the potential to make a considerable contribution to gonadal maturity and reproduction in fish.
Screening for Osteoporosis to Prevent Fractures
Authors: Kahwati Leila C. , Kistler Christine E. , Booth Graham , Sathe Nila , Gordon Rachel D’Amico , Okah Ebiere , Wines Roberta C. , Viswanathan Meera
Published: January 2025

Importance

Fragility fractures result in significant morbidity.

Objective

To review evidence on osteoporosis screening to inform the US Preventive Services Task Force.

Data Sources

PubMed, Embase, Cochrane Library, and trial registries through January 9, 2024; references, experts, and literature surveillance through July 31, 2024.

Study Selection

Randomized clinical trials (RCTs) and systematic reviews of screening; pharmacotherapy studies for primary osteoporosis; predictive and diagnostic accuracy studies.

Data Extraction and Synthesis

Two reviewers assessed titles/abstracts, full-text articles, study quality, and extracted data; when at least 2 similar studies were available, meta-analyses were conducted.

Main Outcomes and Measures

Hip, clinical vertebral, major osteoporotic, and total fractures; mortality; harms; accuracy.

Results

Three RCTs and 3 systematic reviews reported benefits of screening in older, higher-risk women. Two RCTs used 2-stage screening: Fracture Risk Assessment Tool estimate with bone mineral density (BMD) testing if risk threshold exceeded. One RCT used BMD plus additional tests. Screening was associated with reduced hip (pooled relative risk [RR], 0.83 [95% CI, 0.73-0.93]; 3 RCTs; 42 009 participants) and major osteoporotic fracture (pooled RR, 0.94 [95% CI, 0.88-0.99]; 3 RCTs; 42 009 participants) compared with usual care. Corresponding absolute risk differences were 5 to 6 fewer fractures per 1000 participants screened. The discriminative accuracy of risk assessment instruments to predict fracture or identify osteoporosis varied by instrument and fracture type; most had an area under the curve between 0.60 and 0.80 to predict major osteoporotic fracture, hip fracture, or both. Calibration outcomes were limited. Compared with placebo, bisphosphonates (pooled RR, 0.67 [95% CI, 0.45-1.00]; 6 RCTs; 12 055 participants) and denosumab (RR, 0.60 [95% CI, 0.37-0.97] from the largest RCT [7808 participants]) were associated with reduced hip fractures. Compared with placebo, no statistically significant associations were observed for adverse events.

Conclusions and Relevance

Screening in higher-risk women 65 years or older was associated with a small absolute risk reduction in hip and major fractures compared with usual care. No evidence evaluated screening with BMD alone or screening in men or younger women. Risk assessment instruments, BMD alone, or both have poor to modest discrimination for predicting fracture. Osteoporosis treatment with bisphosphonates or denosumab over several years was associated with fracture reductions and no meaningful increase in adverse events.
Screening for Osteoporosis to Prevent Fractures
Authors:   US Preventive Services Task Force, Nicholson Wanda K. , Silverstein Michael , Wong John B. , Chelmow David , Coker Tumaini Rucker , Davis Esa M. , Jaén Carlos Roberto , Krousel-Wood Marie , Lee Sei , Li Li , Mangione Carol M. , Ogedegbe Gbenga , Rao Goutham , Ruiz John M. , Stevermer James , Tsevat Joel , Underwood Sandra Millon , Wiehe Sarah
Published: January 2025

Importance

Osteoporotic fractures are associated with psychological distress, subsequent fractures, loss of independence, reduced ability to perform activities of daily living, and death.

Objective

The US Preventive Services Task Force (USPSTF) commissioned a systematic review to evaluate the evidence on the benefits and harms of screening for osteoporosis to prevent fractures in adults 40 years or older with no known diagnosis of osteoporosis or history of fragility fracture.

Population

Adults 40 years or older without known osteoporosis or history of fragility fractures.

Evidence Assessment

The USPSTF concludes with moderate certainty that screening for osteoporosis to prevent osteoporotic fractures in women 65 years or older has moderate net benefit. The USPSTF concludes with moderate certainty that screening for osteoporosis to prevent osteoporotic fractures in postmenopausal women younger than 65 years at increased risk has moderate net benefit. The USPSTF concludes that the evidence is insufficient and the balance of benefits and harms for screening for osteoporosis to prevent osteoporotic fractures in men cannot be determined.

Recommendation

The USPSTF recommends screening for osteoporosis to prevent osteoporotic fractures in women 65 years or older. (B recommendation) The USPSTF recommends screening for osteoporosis to prevent osteoporotic fractures in postmenopausal women younger than 65 years who are at increased risk for an osteoporotic fracture as estimated by clinical risk assessment. (B recommendation) The USPSTF concludes that the current evidence is insufficient to assess the balance of benefits and harms of screening for osteoporosis to prevent osteoporotic fractures in men. (I statement)
Respiratory Tract Cultures
Authors: Alby Kevin , Smedberg Jason R. , Lindsay Diane S. J. , Ricci Maria L. , Yarbrough Melanie L. , Burnham Carey‐Ann D. , Leber Amy L. , Bateman Allen C. , Gonzalez Mark D. , Pence Morgan A.
Published: January 2025

Specimens from the upper respiratory tract (throat specimens, nasopharyngeal swabs, and nasal discharges) can be easily obtained but are contaminated with resident microbiota. Infections of the lower respiratory tract are the sixth leading cause of mortality in the United States, with 2 to 3 million cases per year, resulting in 500,000 hospitalizations. The purpose of the culture of respiratory secretions from cystic fibrosis (CF) patients is to isolate organisms associated with CF pulmonary disease so that appropriate interventions may be taken. Tympanocentesis and culture of the middle ear fluid are valuable tools for definitive diagnosis, guiding therapy, and evaluating treatment failures. In many laboratories in areas of low endemicity, culture‐based testing specifically for
Corynebacterium diphtheriae
has been discontinued due to the lack of requests and limitations in media shelf life.
Culture Media for Anaerobes
Authors: Bard Jennifer Dien , Copsey‐Mawer Sarah , Precit Mimi
Published: January 2025

Selection of media is key to the recovery of anaerobic organisms from clinical specimens. Primary culture media are those onto which direct specimens are inoculated and may be enriched, nonselective, selective, or differential to allow for the initial recovery of clinically significant anaerobes and inhibition of facultative anaerobe overgrowth. Subculture of anaerobes from primary media to secondary media that are selective and/or differential aids in further identification of clinically significant anaerobes. Proper selection of the initial media used during specimen processing of anaerobic bacteriology aids in the overall accuracy of the workup and assists in recognition of key phenotypic characteristics including colonial morphology. As some anaerobes can be highly sensitive to oxygen exposure, it is recommended that prereduced, anaerobically sterilized media be used to inoculate clinical specimens. Anaerobes have a wide range of nutritional needs, but most strict anaerobes require hemin and vitamin K
1
.
Incubation Techniques for Anaerobic Bacteriology Specimens
Authors: Morris Trefor E.
Published: January 2025

This chapter describes the various environmental methods and incubation conditions used for anaerobic bacteriology specimens once a properly selected, collected, and transported specimen arrives in the laboratory. Ideally, the specimen is processed immediately on arrival in the laboratory and incubated under anaerobic conditions to prevent further exposure to oxygen. In general, growing cultures must not be exposed to oxygen for examination of culture media until after 48 h of incubation, since anaerobes are most sensitive to oxygen during the log phase of growth. One of the obvious advantages of using an anaerobic chamber/workstation is that technologists can inspect inoculated media without removing them from the anaerobic environment. The choice of incubation systems is influenced by cost, the number of anaerobic cultures performed, and laboratory space limitations. The anaerobic environment is monitored with a methylene blue strip or resazurin indicator.
Anaerobic Gram‐Negative Bacilli
Authors: She Rosemary C. , Church Deirdre L.
Published: January 2025

The anaerobic Gram‐negative bacteria are part of the microbiota of the oral cavity, gastrointestinal tract, and urogenital tract. Many taxonomic changes have been instituted based on newer biochemical and molecular sequencing considerations. Many of the bile‐sensitive species of Gram‐negative bacilli, such as
Prevotella
and
Porphyromonas spp.
, make up a large percentage of the normal microbiota in the oral cavity and are involved in many different types of oral infections. The pigmented anaerobic Gram‐negative bacilli include members of the genera
Prevotella
,
Porphyromonas
, and
Alistipes
. The chapter includes a few additional Gram‐negative rods of human pathogenicity. It also helps the laboratory staff to perform all analyses, including appropriate quality control recommendations, from the receipt of the specimen (anaerobic Gram‐negative bacilli) through processing, testing, interpretation, presentation of the final report, and subsequent consultation.
Anaerobic Gram‐Positive Bacilli
Authors: Bernard Kathryn , Hamula Camille
Published: January 2025

Anaerobic Gram‐positive bacilli of clinical relevance in human infections are divided into two distinct groups: sporeforming Gram‐positive anaerobic bacilli, including
Clostridium sensu stricto
and allied genera, and a group of asporogenic, anaerobic Gram‐positive bacilli (Grampositive rods (GPRs)). Many of these anaerobic GPRs are part of the normal microbiota of the oral cavity, gastrointestinal tract, genitourinary tract, and skin. They can, however, be associated with skin and soft tissue infections, periodontitis and other oral infections, pulmonary infections (usually in combination with other aerobes and anaerobes), genitourinary tract infections, and, in the case of
Cutibacterium acnes
, infected CSF shunts, prosthetic joint infections, and endophthalmitis. Many of the nonsporeformers are aerotolerant and are often resistant to metronidazole, an antimicrobial agent that is usually effective against most other anaerobes.
Clostridioides
(
Clostridium
)
difficile
as a Pathogen Involved in Antimicrobial Agent‐Associated Diarrhea, Colitis, and Pseudomembranous Colitis
Authors: Carroll Karen C. , Paulick Ashley L.
Published: January 2025

Clostridioides (Clostridium) difficile
is a major cause of health care‐associated diarrhea and the primary pathogen responsible for pseudomembranous colitis. Recent epidemiological trends note decreases in health care‐acquired
C. difficile
as a possible consequence of decreased fluoroquinolone use and increases in cases in the community in individuals lacking traditional risk factors. While
C. difficile
colitis was originally dubbed “clindamycin‐associated pseudomembranous colitis”, any antimicrobial agent, including those used to treat the infection itself (i.e., metronidazole and vancomycin), can be a risk factor. Disease results from action of toxins produced by the bacteria.
C. difficile
produces two toxins: toxin A, a weakly cytopathic toxin, is predominantly responsible for the enterotoxic activity of the organism, and toxin B, a potent cytotoxin, appears to play a major role in human disease.
Preanalytical Considerations and Laboratory Processing of Samples for Blood Culture
Authors: Tibbetts Robert J. , Harrington Amanda T.
Published: January 2025

This chapter presents the preanalytical considerations and laboratory processing of samples for blood culture. Bloodstream infection and sepsis remain one of the most significant causes of morbidity and mortality worldwide. Establishing an etiologic diagnosis for bloodstream infections is an essential role of clinical microbiology laboratories. The number of blood culture bottles collected and the volume of blood collected in each bottle also significantly impact recovery of organisms and interpretation of results. The volume of blood obtained for culture is typically determined using an age‐ or weight‐based calculation. Adequate volume of blood is the single most important factor in the laboratory detection of microorganisms in the bloodstream, regardless of age; when blood culture is optimized to the recommended volumes, the more likely a culture will be positive. Blood culture collection prior to administration of antimicrobials is essential for optimal organism recovery.
Quality Control and Quality Assurance for Blood Cultures
Authors: Martinez Raquel M.
Published: January 2025

Because of the impact on patient care, blood cultures are considered among the most important microbiology tests performed. Quality control (QC) begins with acquiring a blood culture instrument and associated blood culture media, then verifying and validating the performance for clinical use. Like QC, quality assurance (QA) programs are essential to ensure accurate and reliable results. For blood cultures to perform as intended, specific preanalytical, analytical, and postanalytical criteria must be met. The volume of blood collected for culture is the most critical of all the quality benchmarks, as it is the most significant factor impacting culture positivity. The analytical QA metrics specific to blood cultures, such as percent contamination and percent positivity, are directly impacted by the preanalytical variables including fill volume and the number of bottles submitted. Higher rates of contamination are associated with certain specimen types, such as line draws, lower‐extremity venipuncture, and arterial puncture.
Specialized Processing of Blood
Authors: Chamberland Robin R.
Published: January 2025

Transfusable blood components, including platelets, red blood cells, and plasma, pose a risk of transfusion‐transmitted bacterial infection (TTBI). Platelet products are associated with the highest risk of TTBI of all transfusable blood components, with an overall rate of 1.95 per 10
5
units transfused. This chapter focuses on the microbiologic evaluation of transfusion reaction. In cases of suspected TTBI, the transfusion should be stopped, and the port should be covered or the tubing clamped. The component bag containing any residual product should be placed in a sealed plastic bag and transported to the laboratory immediately for culture. Culture of transfused blood products should always be accompanied by concurrent blood cultures performed for the patient experiencing a transfusion reaction. The chapter focuses on the specimen collection, transport, and handling, materials, quality control, interpretation, reporting results and limitations of procedure.
Identification of Highly Pathogenic Bacteria by MALDI‐TOF MS
Authors: Tran Anthony
Published: January 2025

The use of matrix‐assisted laser desorption ionization–time of flight mass spectrometry (MALDI‐TOF MS) for identification of pathogenic bacteria and fungi has become popular in diagnostic microbiology and public health laboratories due to its accuracy and speed of microorganism identification. Based on the presence or absence of organisms in the MALDI‐TOF MS library, testing of select agents may yield no identification or misidentifications. A biological risk assessment should be conducted prior to implementation of MALDI‐TOF MS to mitigate the risks to the laboratorian conducting the test. The biological risk assessment should be reviewed periodically as well as any time changes to the instrument or the MALDI‐TOF MS. This chapter focuses on the specimen collection, reagents and equipment, calibration and quality control, reporting results and limitations of procedure.
Agar Dilution MIC Test
Authors: Patel Samir N.
Published: January 2025

The agar dilution MIC test is a quantitative method for the determination of in vitro activity of an antimicrobial agent against bacterial isolates, such as aerobic and anaerobic bacteria. Following incubation using conditions appropriate for the test organisms, the MIC is determined by observing the lowest concentration of antimicrobial agent that inhibits visible growth of each test isolate. MICs obtained are interpreted as susceptible, intermediate, susceptible dose‐dependent, resistant, or non‐susceptible based on criteria defined by the CLSI or by the European Committee on Antimicrobial Susceptibility Testing. Recommendations for performance of the agar dilution method for susceptibility testing of aerobic bacteria are found in the CLSI M07 standard and include procedures for both non‐fastidious and fastidious organisms. 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.
Beta‐Lactamase Tests
Authors: Campeau Shelley , Deak Eszter
Published: January 2025

Beta‐lactamases are important mediators of bacterial resistance to beta‐lactam agents. The beta‐lactamase tests detect penicillinases where detection predicts resistance to the penicillinase‐labile penicillins. Routine beta‐lactamase tests are performed directly from bacterial colonies and are based on visual detection of the end products of beta‐lactamase hydrolysis, demonstrated with a colorimetric reaction. Direct beta‐lactamase testing can be performed on Gram‐negative and Grampositive anaerobes other than the
Bacteroides fragilis
group, as organisms in the
B. fragilis
group are beta‐lactamase producers and predictably resistant to penicillin, amoxicillin, and ampicillin. For direct beta‐lactamase tests, coagulase‐negative staphylococci may require induction to demonstrate a positive beta‐lactamase reaction.
Preparation of Routine Media and Reagents Used in Antimicrobial Susceptibility Testing
Authors: Lonsway David R.
Published: January 2025

McFarland turbidity standards are used to standardize the approximate number of the book bacteria in a liquid suspension by visually comparing the turbidity of a test suspension with the turbidity of a McFarland standard. Aliquots of antimicrobial stock solutions are incorporated into broth or agar medium for antimicrobial susceptibility tests. Stock solutions are prepared from laboratory reference standard‐grade antimicrobial powders. These are assayed for the amount of active agent present, and this is expressed as potency or activity, which is usually defined in terms of micrograms of active drug per milligram. Specific agar and broth media used for routine disk diffusion, agar dilution, and broth dilution susceptibility tests are prepared from commercially available dehydrated components. Although these media have shown fairly good reproducibility through many years of testing, they are undefined media, and there may be subtle performance differences among batches and lots.
Media and Methods Used for Phenotypic Characterization of Aerobic Actinomycetes
Authors: Bell Melissa E. , Sussland Zdenek , Mochon A. Brian
Published: January 2025

Aerobic actinomycetes can be identified to the genus level using a variety of conventional phenotypic characteristics. Despite most laboratories lacking access to some of Gordon's oxidative agar slants and media containing purine‐related compounds, the examination of microscopic and macroscopic morphologies combined with a few common physiologic tests can give a presumptive identification to the genus or even species level in most cases. This chapter provides an illustration of a schematic flowchart for the tentative phenotypic identification of medically important aerobic actinomycetes and related genera. The use of Gram‐stained and modified acid‐fast smears and colonial morphology, especially the presence/absence of aerial hyphae and growth in lysozyme broth, will presumptively identify most aerobic actinomycetes to at least the genus level.
General Mycobacterial Procedures
Authors: Wengenack Nancy L.
Published: January 2025

Tubercular bacilli may be present in a variety of specimens that will be sent to the clinical mycobacterial laboratory for processing. Procedures that potentially may generate an aerosol, such as specimen processing, must be conducted in a biological safety cabinet until the specimen is inactivated. Sodium citrate is included in the digestion mixture to bind the heavy metal ions present in the specimen that could inactivate the
N
‐Acetyl‐L‐cysteine. Specimens requiring decontamination include sputum, induced sputum, bronchial alveolar lavage fluid, bronchial wash fluid, skin and soft tissue specimens, gastric lavage specimens, and urine and other body fluids, such as ascites and peritoneal fluid. Specimens from the respiratory tract are typically contaminated with large numbers of respiratory microbiota that must be significantly reduced in quantity to optimize the recovery of smaller numbers of acid‐fast bacilli.
Nucleic Acid Amplification Procedures for Identification from Specimens
Authors: Baron Ellen Jo , Gnanashanmugam Devasena
Published: January 2025

This chapter covers nucleic acid amplification procedures for identification from specimens. These tests include: Cepheid Xpert MTB/RIF test, Xpert MTB/RIF Ultra test, and Cepheid Xpert MTB/XDR test. Several studies have shown that results from one Xpert® MTB/RIF assay are more predictive of pulmonary tuberculosis in previously undiagnosed patients; thus, the U.S. National Tuberculosis Controllers Association has issued a guideline on use of this assay for patient diagnostic and infection prevention interventions. The Xpert MTB/RIF Ultra test demonstrates a higher sensitivity in M. tuberculosis complex detection than the Xpert MTB/RIF test, and using melt curve analysis to identify RIF resistance‐associated mutations may allow for more accurate RIF resistance detection in some regions. The Xpert MTB/XDR test is an
in vitro
diagnostic test for the detection of extensively drug‐resistant Mycobacterium tuberculosis complex.
Antifungal Susceptibility Testing
Authors: Wiederhold Nathan P. , Lockhart Shawn R.
Published: January 2025

Antifungal susceptibility testing (AFST) is performed as part of clinical diagnostic testing in order to provide information to clinicians that may help guide treatment in patients with fungal infections. AFST is used during the preclinical development of investigational agents to determine the scope of in vitro activity and the potency of an agent. The AFST methods primarily used for both yeasts and molds, including those standardized by Clinical and Laboratory Standards Institute (CLSI) and European Committee on Antimicrobial Susceptibility Testing (EUCAST), are broth dilution formats that quantitatively measure the
in vitro
activity of an antifungal agent against a fungal isolate. In order to make AFST less costly and more readily available to clinical microbiology laboratories, CLSI has developed standards for disk diffusion testing similar to those used for testing of bacteria that grow aerobically. Gradient diffusion testing is also available, although this method has not been standardized by CLSI or EUCAST.
Collection and Preservation of Fecal Specimens
Authors: Couturier Marc R.
Published: January 2025

One of the most important steps in the diagnosis of intestinal parasites is the proper collection of specimens. Fresh specimens are mandatory for the recovery of motile trophozoites. Fecal specimens for parasite examination that cannot be processed and examined in the recommended time should be placed in an appropriate fixative/preservative. Many commonly used fixatives, such as formalin and other aldehydes, also make the specimen more susceptible to staining. Ethanol is a commonly used preservative. In outpatient situations, it may be necessary for a specimen to be shipped to the laboratory for examination. Only fecal specimens in appropriate fixative should be shipped, as any delays in examination may result in deterioration of parasitic organisms.
Conventional Tube Cell Culture for Primary Virus Isolation
Authors: Hodinka Richard L. , Relich Ryan F.
Published: January 2025

For decades, cell culture was considered the reference standard in diagnostic virology laboratories for the primary isolation and identification of viruses from clinical specimen. Virus culture has played a significant role in the identification and knowledge of novel and clinically relevant human viruses such as metapneumovirus, severe acute respiratory syndrome coronavirus, human coronavirus NL63, Middle East respiratory syndrome coronavirus, and SARS‐CoV‐2. For the isolation of human pathogenic viruses, monolayer cultures of permissive mammalian cells are generally used. Several variables can influence the virus susceptibility of cell cultures and therefore their sensitivity for virus detection. In conventional virus cultures, isolation of viruses is traditionally performed by inoculating clinical specimens into prepared monolayers of cultured cells adhered to the inside of glass or plastic test tubes. 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.
Tests for Direct Detection of Viruses in Clinical Specimens
Authors: Hodinka Richard L. , Banerjee Dithi , Selvarangan Rangaraj , Thomas Lynita , Glaser Laurel J.
Published: January 2025

Rapid solid‐phase immunoassays for direct detection of viral antigens in clinical specimens are commercially available and are most commonly used for influenza virus types A and B and respiratory syncytial virus (RSV). It is important to rapidly detect and distinguish disease caused by influenza viruses, RSV, or SARS‐CoV‐2 to provide early treatment with available antiviral therapy, improve clinical care and outcomes, and implement adequate infection control measures; for surveillance of communicable diseases; for outbreak containment; and to inform public health interventions. When using immunofluorescence assays, cells from submitted clinical specimens are fixed to the surface of glass slides and viral protein antigens within intact infected cells are detected using virus‐specific primary antibodies. The common staining techniques applied to cytologic and histologic specimens provide the initial assessment of viral infection. The detection of viruses in exfoliated cells and tissue plays a critical role in the diagnostic process.
Detection of
Francisella tularensis
Antibodies
Authors: Peterson Jeannine M. , Dietrich Elizabeth A.
Published: January 2025

Tularemia is a disease with multiple clinical forms, which results from infection by
Francisella tularensis
, a facultative Gram‐negative coccobacillus. Two subspecies of
F. tularensis
cause human infection:
Francisella tularensis
subsp.
tularensis
and
Francisella tularensis
subsp.
holarctica
. Serology can be used to aid diagnosis of all clinical forms of tularemia. The main antigen detected in
F. tularensis
serologic assays is lipopolysaccharide, a primary component of the bacterium's outer membrane. Testing formats include agglutination, ELISA, indirect immunofluorescence assay, and immunochromatographic assays. The agglutination test, using formalin‐inactivated bacteria, has long been used for detection of total anti‐
F. tularensis
antibodies and is still the standard method. ELISAs, using an
F. tularensis
LPS antigen extract, often separately detect IgM and IgG antibodies.
Detection of
Borrelia burgdorferi
Antibodies
Authors: Aguero‐Rosenfeld Maria E.
Published: January 2025

Lyme disease, or Lyme borreliosis (LB), is a multisystem disease caused by members of the
Borrelia burgdorferi sensu lato
complex and is transmitted through the bite of infected
Ixodes sp.
ticks.
B. burgdorferi sensu lato
is composed of several geno species that cause different manifestations of LB. B. burgdorferi is a motile, helically shaped bacterium with multiple endoflagella and with a complex antigenic composition. A tremendous amount of knowledge has been ascertained with respect to serologic testing for antibodies to
B. burgdorferi
since the original assays were developed. Depending on Food and Drug Administration approval, these assays may be used as either first‐tier or second‐tier tests in the standard two‐tiered testing or modified two‐tier testing algorithm. The most appropriate specimen for testing is serum. Interpretation guidelines are included in the manufacturer's package insert.
Serologic Tests for Diagnosis of
Histoplasma capsulatum
Authors: Slev Patricia , Rychert Jenna
Published: January 2025

Histoplasmosis is the most common endemic fungal infection in the United States, where it is endemic in the Ohio and Mississippi river valleys. Infection with Histoplasma capsulatum is generally due to environmental exposure and is not considered contagious between humans or animals. Diagnosis of histoplasmosis can be made by a variety of methods, including culture, molecular testing, histopathology, serology, and antigen detection in a variety of body fluids. There are four methods for
H. capsulatum
antibody detection: complement fixation (CF), immunodiffusion (ID), latex agglutination, and enzyme immunoassay. CF and ID are the reference standard serologic methods for detection of antibodies against
H. capsulatum
and should be performed in parallel for diagnosis. 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.
Interferon Gamma Release Assays for Latent Tuberculosis Infection
Authors: Costales Cristina , Banaei Niaz
Published: January 2025

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

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

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

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

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

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

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

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

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

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

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

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

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

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.