bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of irrigation frequencies on nutrient uptake, growth and yield of pomegranate (Punica granatum) grown on heavy textured soils of semi-arid region
Authors: MARATHE R A , BABU K DHINESH , CHAUDHARI D T
Published: July 2023

This study evaluates the influence of different irrigation frequencies on the nutrient uptake, growth and yield performance of pomegranate (Punica granatum L.) cv. Bhagwa. The experiment was conducted during 2010–13 at National Research Centre on Pomegranate, Solapur, Maharashtra, India. The treatments were consisted of replenishment of irrigation on every day and cumulative irrigation after 1, 2, 3, 4 and 5 days interval. The results revealed that, increase in irrigation interval increased moisture spread in horizontal as well as vertical direction. Horizontal and vertical moisture spread was restricted up to 40 and 60 cm, respectively, in daily irrigation and 40 and 75 cm, respectively at 1 day irrigation interval treatment. Maximum leaf content of N (2.09%) and K (0.93%) was found in irrigation interval at 2 days while P (0.164%) at 3 days irrigation interval treatment. Higher nutrient uptake at 2 and 3 days irrigation interval resulted in attaining significantly higher vegetative growth of the plants. However, scheduling of irrigation frequency did not show effect on growth of the plants during pre-bearing period. Lowest leaf temperature (98.5o F) and highest leaf chlorophyll content (59.61) was recorded in 1 day irrigation interval treatment. Highest fruit yield (4.32 t/ha) was obtained in 2 days irrigation interval treatment. Application of irrigation at 4 and 5 days interval resulted in drastic reduction in fruit yield, which also had very high fruit cracking (11.6 and 15.5%, respectively).
EXPLORING THE RELATIONSHIP BETWEEN COMMUNICATION, WORK CULTURE, ORGANIZATIONAL COMMITMENT, AND MOTIVATION ON EMPLOYEE PERFORMANCE AT KRAMAT COMMUNITY HEALTH CENTER
Authors: Yoga Rizki Ramadhani  , Cucu Herawati  , A.D.Achmad
Published: July 2023

Purpose of the study — To test and find out the causal relationship of several factors that influence employee performanceResearch method— This research is a quantitative research with regression. The population in this study were employees of the Kramat Community Health Center, Tegal Regency, Central Java Province, with a total of 68 employees. Data was collected by questionnaire and document study, after which the data was tested for validity and reliability.Result— The results of the study show that Communication, Work Culture, Organizational Commitment and Motivation affect Employee Performance simultaneously. The coefficient of multiple determination in this study uses the adjusted R square value because the independent variables in this study are more than 2 in estimating the effect of the two independent variables studied. From the data the adjusted R Square value is 0.598, this means that together the influence of the variables X1, X2, X3, X4 is 59.8% on the Y variable or in other words the influence of the independent variables (Communication, Work Culture, Organizational Commitment and Motivation) to the dependent variable (Performance) of 59.8% while the remaining 40.2% is caused by other variables that are not included in the research frameworkConclusion— Communication, Work Culture, Organizational Commitment, and Motivation have a significant effect on Employee Performance. The adjusted R-squared value of 0.598 indicates that these variables explain 59.8% of the variation in performance. Practical implications of the study include the importance of organizations focusing on improving communication, work culture, organizational commitment, and motivation to enhance employee performance. Social implications include the potential for improved productivity and job satisfaction in the workforce.
IMPLEMENTATION OF THE PROBLEM-POSING LEARNING METHOD TO INCREASE STUDENT’S ACTIVE PARTICIPATION IN MATHEMATICS
Authors: Etik Rohmatika Etik Rohmatika
Published: July 2023

Purpose: This study aims to analyse the impact of the implementation of Problem-Posing Learning method to the student’s active participation and study results in Mathematics subject.

Research Methodology: This study uses Classroom Action Research and Paired t-test by using the pre-test and post-test score.

Results: The application of problem-posing learning method can increase students’ active participation and grade in Mathematics subject.

Limitations: This study analyses the impact of Problem-Posing Learning method in Mathematics subject.

Contribution:  The results contribute to the education field in terms of effective learning model to increase students’ active participation and study results.
Perbuatan Melawan Hukum dalam Perjanjian Pinjam Nama Perusahaan untuk Mengikuti Tender Pengadaan Barang dan Jasa Pemerintah Dihubungkan dengan Kuhperdata
Authors: Dibrata Shintadewi , Afriana Anita , Faisal Pupung
Published: July 2023

Proses tender pengadaan barang dan jasa pemerintah sangat rawan akan terjadinya penyelewengan salah satunya yaitu praktik pinjam nama perusahaan. Penelitian ini memiliki tujuan untuk mengetahui bagaimana akibat hukum dari pinjam nama perusahaan dan perlindungan hukum bagi pemilik perusahaan yang nama perusahaanya dipinjam untuk mengikuti tender pengadaan barang dan jasa pemerintah berdasarkan KUHPerdata. Penelitian ini dilakukan dengan menggunakan metode pendekatan yuridis normatif yang mana melakukan penelitian dengan menggunakan kepustakaan sebagai bahan penelitian. Berdasarkan penelitian yang dilakukan mendapatkan hasil bahwa akibat hukum dari pinjam nama perusahaan untuk mengikuti tender pengadaan barang dan jasa pemerintah mewajibkan “Pihak Pemilik Perusahaan” untuk mengganti kerugian kepada Negara/Daerah sebagai pemilik pekerjaan (bouwheer). Perlindungan hukum bagi pemilik perusahaan yaitu melakukan Gugatan Perbuatan Melawan Hukum kepada pihak peminjam nama perusahaan ketika pengerjaan proyek tidak dilaksanakan sesuai kesepakatan yang menjadi tanggung jawabnya.
Registros multiprofissionais antes e depois da implantação de sistema informatizado sobre sepse
Authors: Gonçalves Luciana Schleder , Amaro Maria Luiza de Medeiros
Published: July 2023

Objetivo: Comparar os registros multiprofissionais de preenchimento do protocolo institucional de sepse no prontuário eletrônico, antes e depois da implantação de um sistema informatizado de alerta. Método: Foi empregado o método de estudo quasi experimental, sem grupo controle e com desenho pré e pós intervenção, em que foram comparados os registros da equipe multidisciplinar de um hospital do sul do Brasil com prontuário eletrônico. Resultados: A amostra compreendeu 209 protocolos: 107 do período anterior (janeiro a maio/2018) e 102 do período após (julho a novembro/2018) a implantação do sistema informatizado de alertas. No período pós implantação do sistema foram identificados resultados significativos na frequência e média de verificação de sinais vitais por paciente (p<0,001).Conclusão: Houve diferença no cumprimento dos registros de preenchimento do protocolo institucional de sepse após a implantação do sistema informatizado de alerta.
Resenha do livro “A nova infância em análise”
Authors: Green Lauro Caldas
Published: July 2023

Resenha do livro “A nova infância em análise”, de Celso Gutfreind.
A (Re) Construção dos Vínculos em uma Família Reconstituída e com Adoção Tardia
Authors: Gomes Elenice Alves , Silva Thais Angélica Garcia
Published: July 2023

O artigo parte de muitos questionamentos sobre a família contemporânea e suas transformações, sobretudo no que se refere aos vínculos, como se constroem, se constituem e como podem ser fortalecidos. É sobre uma pesquisa qualitativa fundamentada teórica e metodologicamente na teoria sistêmica de um caso clínico de uma família composta por quatro membros, encaminhada por um Serviço do Hospital das Clínicas de Ribeirão Preto/SP a um instituto formador de terapeutas familiares sistêmicos na mesma cidade.  O objetivo foi compreender a dificuldade em construir novos vínculos num determinado tipo de família, que denominaremos de Borges e auxiliá-la no fortalecimento dos seus relacionamentos. A família inicialmente composta por um par conjugal heterossexual adotou tardiamente um casal de irmãos com quatro e três anos; posteriormente, a mãe adotiva adoeceu e morreu e o pai adotivo reconstituiu essa família com um novo casamento, quando as crianças já estavam transitando da puberdade para a adolescência.
Haemogram and Iron Profile in Children Suffering from Severe Acute Malnutrition at a Tertiary Care Centre, Bhopal: A Cross-sectional Study
Authors: Rose Naina
Published: July 2023

Introduction: There is a high global prevalence of malnutrition in India, with anaemia and infection being the major co-morbidities in these patients. Iron deficiency is one of the most common causes of anaemia worldwide, which has its complications. However, data regarding haematological and iron profiles among Severe Acute Malnutrition (SAM) children in India is very limited. Aim: To study the iron profile and haemogram in children with SAM and its comparison with various associated complications. Materials and Methods: This observational cross-sectional study was conducted in the Department of Paediatrics, Gandhi Medical College, Bhopal, Madhya Pradesh, India, from March 2021 to September 2022. Children aged between six months to five years, fulfilling the World Health Organisation (WHO) criteria of SAM in this study were included and clinical and haematological data were collected, including growth parameters, haemogram, peripheral smear, Red Blood Cell (RBC) indices, reticulocyte counts, and iron profile. Categorical variables were analysed using the Chi-square test or Fisher’s-exact test. Continuous variables were assessed using the Analysis of Variance (ANOVA) or t-test. Results: Total of 175 children (80 girls and 95 boys) with SAM were enrolled in the study and data was analysed. 87% of the study population had anaemia. Most SAM children with complications had severe anaemia (51.9%) with a higher prevalence of microcytic anaemia followed by macrocytic anaemia compared to SAM without complications with normocytic anaemia. On comparing the haemogram, it was revealed that Hemoglobin (Hb), Packed Cells Volume (PCV), Red Blood Cells (RBC), Mean Corpuscular Haemoglobin (MCH), and Mean Corpuscular Haemoglobin Concentration (MCHC) were significantly low in SAM patients with complications. While the iron status of SAM patients with complications revealed low serum iron levels and transferrin saturation while ferritin and Total Iron-Binding Capacity (TIBC) were increased. Conclusion: Anaemia was observed to be highly prevalent in SAM children with complications. The most common type of anaemia was microcytic hypochromic, followed by macrocytic type. Serum iron levels were significantly lower in SAM patients with complications (p-value <0.001).
Esophageal Candida Infection and Esophageal Cancer Risk in Patients With Achalasia
Authors: Guo Xiaopei , Lam Suk Yee , Janmaat Vincent T. , de Jonge Pieter Jan F. , Hansen Bettina E. , Leeuwenburgh Ivonne , Peppelenbosch Maikel P. , Spaander Manon C. W. , Fuhler Gwenny M.
Published: January 2025

Importance

Patients with achalasia face a higher risk of developing esophageal cancer (EC), but the surveillance strategies for these patients remain controversial due to the long disease duration and the lack of identified risk factors.

Objective

To investigate the prevalence of esophageal Candida infection among patients with achalasia and to assess the association of Candida infection with EC risk within this population.

Design, Setting, and Participants

This retrospective cohort study included patients with achalasia diagnosed at or referred for treatment and monitoring to the Erasmus University Medical Center in Rotterdam, the Netherlands, between January 1, 1980, and May 31, 2024. Data analysis was conducted from August 1 to October 31, 2024.

Exposure

Esophageal Candida infection.

Main Outcomes and Measures

The primary outcomes were the prevalence of esophageal Candida infection and its association with EC development among patients with achalasia. Associations were estimated using time-dependent Cox proportional hazards regression models with esophageal Candida infection as a time-varying covariate, adjusting for age at diagnosis and sex.

Results

This study included 234 patients with achalasia (median [IQR] age at diagnosis, 45 [32-63] years; 117 [50%] male), with a median follow-up time of 13 (4-22) years. Esophageal Candida infection was identified in 29 patients (12%), while EC was observed in 24 patients (10%). Esophageal cancer risk analysis was performed for 207 patients with 2 or more consecutive endoscopy follow-up visits (median [IQR] age at diagnosis, 43 [32-60] years; 104 [50%] male). The median (IQR) follow-up time for this subgroup was 16 (9-26) years. Among these patients, esophageal Candida infection was independently associated with an increased risk of EC (adjusted hazard ratio [AHR], 8.24 [95% CI, 2.97-22.89]). Additionally, age at diagnosis (AHR, 1.06 [95% CI, 1.03-1.10]) and male sex (AHR, 3.34 [95% CI, 1.08-10.36]) were independently associated with EC risk.

Conclusions and Relevance

This retrospective cohort study found that prior esophageal Candida infection, older age at diagnosis, and male sex were associated with increased risk of EC among patients with achalasia. These findings provide an important rationale for optimizing the monitoring of patients with achalasia.
Introduction
Authors: Harrington Amanda T. , Yarbrough Melanie L.
Published: January 2025

The aerobic bacteriology encompasses procedures used for the culture of aerobic and facultative anaerobic bacteria that are routinely recovered from human clinical specimens as well as specialized procedures for more fastidious organisms. This chapter reflects common associations between selected organisms at a particular site of infection. Each procedure provides information on isolation and recognition of these bacteria as well as their clinical relevance. The chapter concludes with procedures for rapid and streamlined identification of many common and important aerobic bacteria. While the tables and flowcharts in these procedures are designed to identify clinically important microorganisms using minimal phenotypic testing, in many cases, additional testing is needed for a specific species‐level identification. With the application of newer technologies such as total laboratory automation and artificial intelligence processes procedures for recovery and identification of aerobic bacteria within the clinical microbiology laboratory will continue to evolve.
Staining Procedures
Authors: Dallas Steven D. , Harrington Amanda T.
Published: January 2025

This chapter presents two primary applications of the Gram stain in clinical microbiology. The first and most immediately impactful application is to detect and differentiate microorganisms including bacteria, yeast, fungi, and even some parasites directly from specimens. The second application is to confirm and describe bacterial growth from solid or liquid culture media as the first step in bacterial identification flowcharts. Bacteria stain is either Gram positive or Gram negative on the basis of differences in cell wall composition and architecture. The acridine orange fluorescent stain is an adjunct to or confirmatory test for the Gram stain, of use especially when direct specimen Gram stain results are inconclusive. The detection of leukocytes, predominantly neutrophils, in methylene blue‐stained fecal specimens assists in the diagnosis of infectious diarrhea. Dark‐field microscopy is used to demonstrate the presence of motile spirochetes of
Treponema pallidum
in lesions or aspirates in early‐stage syphilis prior to healing of lesions.
Ocular Cultures
Authors: Burd Eileen M.
Published: January 2025

Ocular infections can lead to serious morbidity and blindness. Superficial eye infections are commonly treated empirically; however, effective management of unresponsive, recurrent, or severe superficial infections and of inner‐eye infections requires identification of the specific etiology. Culture of clinical samples remains the gold standard for definitive etiologic diagnosis. The amount of specimen collected from the eye is very small, and it is common for ophthalmologists to inoculate culture media in the patient care area rather than transport the specimen to the laboratory for processing. Nucleic acid amplification tests have been successfully used for ocular specimens and are preferred for detection of viruses and organisms that are difficult to culture, such as Chlamydia, Toxoplasma gondii, Acanthamoeba, etc. Ophthalmologists are trained on the proper collection of specimens, but it is also the responsibility of the laboratory director or designee to provide physicians and caregivers with proper specimen collection instructions.
Urine Cultures
Authors: Yarbrough Melanie L.
Published: January 2025

Urine culture results are reported semiquantitatively, as the colony count is used to guide the microbiological significance of bacteriuria. Thoughtful design and implementation of a urine reflex algorithm may improve diagnostic stewardship by increasing probability of a positive culture and decreasing overutilization of urine culture in cases of asymptomatic bacteriuria. Accordingly, interpretation of bacteria growing from urinary stone culture must take into account organism identification (e.g., urease producer, traditional uropathogen, traditional skin bacteria) and the mechanism by which the stone was obtained, in conjunction with concurrent urine culture results. Urinary stone disease is the result of urinary tract calcification leading to the formation of large mineral deposits. The exact molecular mechanism leading to the formation of urinary stones is unknown; however, there is a well‐understood association between the presence of bacteria within the genitourinary tract and formation of struvite stones.
Leptospira
Culture
Authors: Galloway Renee L.
Published: January 2025

Leptospirosis is a zoonosis caused by spirochetes of the genus
Leptospira
.
Leptospira
serovars that are antigenically related are further grouped into serogroups, primarily to simplify serologic diagnosis. Infection with
Leptospira
in humans may result in a wide spectrum of symptoms, ranging from mild, undifferentiated febrile illness to severe multiorgan system disease, with jaundice, renal failure, cardiac complications, severe pulmonary hemorrhagic syndrome, and high mortality. Clinical recognition of leptospirosis is difficult because leptospires can affect many different organ systems, resulting in a nonspecific clinical presentation. Consequently, leptospirosis is often misdiagnosed as influenza, malaria, aseptic meningitis, encephalitis, dengue fever, hepatitis, or gastroenteritis. Direct dark‐field smears are not recommended for leptospirosis diagnosis due to their lack of sensitivity. Leptospires are aerobic bacteria that can be cultivated at 30 degree Celsius in media containing either rabbit serum or bovine serum albumin and fatty acids.
Bartonella
Culture
Authors: Clarridge Jill E. , Harrington Amanda T.
Published: January 2025

The genus
Bartonella
comprises Gram‐negative short rod‐shaped bacteria that belong to the α‐2 subgroup of
Proteobacteria
. Depending on the level of host adaptation,
Bartonella
infection in the reservoir host ranges from asymptomatic to clinical manifestations with low morbidity and limited mortality or, rarely, life‐threatening disease, such as endocarditis. There are several methods of diagnosing bartonellosis in clinical specimens: serology, direct visualization, molecular methods such as polymerase chain reaction, and culture. Collection in ethylenediaminetetraacetic acid tubes or an Isolator tube system is the preferred method for culturing
Bartonella
species from blood. Detection of
Bartonella
species from clinical specimens using molecular methods has been shown to be more sensitive than culture for all specimen types and especially useful for cases in which lymphadenectomy or biopsy is not feasible or serologic results are equivocal.
Identification of Gram‐Positive Bacteria
Authors: Bernard Kathryn
Published: January 2025

Unlike in the case of Gram‐negative bacilli, it can be difficult to definitively identify Gram‐positive cocci and bacilli to the genus and species levels. Gram‐positive bacilli have been difficult to identify because pathogens have to be discerned from hundreds of validly named species that are found in the environment or are part of the normal microbiota of the human body, including the skin, mucosal membranes, oropharynx, and genitourinary and gastrointestinal tracts, and the taxonomy of such agents is both evolving and being augmented. For species‐level identification of viridans group streptococci, enterococci, and corynebacteria, commercial kits are often easier to perform than standard tube biochemical tests, but both approaches have limitations in accuracy. Because of the lack of unique colony morphologies for many Gram‐positive microorganisms, the Gram stain must be performed on isolates for identification. Gram‐variable microorganisms are considered Gram positive.
Identification of Gram‐Negative Bacteria
Authors: Munson Erik , Podzorski Raymond P.
Published: January 2025

The Gram‐negative bacteria are a heterogeneous group of organisms consisting of numerous families, genera, and species, many of which cause serious disease and endotoxic shock. The accurate, rapid identification of Gram‐negative bacilli, coccobacilli, and diplococci makes it possible to provide timely, meaningful treatment and diagnosis of disease. Commercial kit‐based identification systems do an excellent job of identifying most pathogens with minimal work and are often a major tool in the laboratory's identification system. Deciding when to use a commercial system and which system to use for identification is key to success in providing the identification in a timely manner. The speed of identification and extremely low reagent cost make the technology a desirable means of organism identification in the clinical microbiology setting. In the course of the potential rapid identification of Gram‐negative coccobacilli and Gram‐negative bacilli, the clinical microbiology laboratory may encounter isolates that are potential agents of bioterrorism.
Introduction
Authors: Schuetz Audrey N.
Published: January 2025

Anaerobic bacteria are a significant component of the normal microbiota of the human host. There are anaerobes present on most body surfaces and mucous membranes; they exist in large numbers throughout the entire gastrointestinal tract, from the mouth to the colon; and they are found in large numbers in the female genitourinary tract. Anaerobic bacteria can cause a wide variety of infections, including wound infections as a result of trauma or surgery; abscesses of the liver, brain, lung, and other local sites; appendicitis; peritonitis; chronic otitis media and sinusitis; endophthalmitis; bacteremia; endocarditis; myonecrosis; gas gangrene; and dental and oral infections. This chapter discusses resurgence of Lemierre's syndrome and the increased association of newly named and emerging anaerobes with many types of infections. It describes acceptable specimen collection, transport, and inoculation for anaerobe recovery. The chapter provides situational examples outlining the extent to which anaerobe work‐up should be followed.
Specimen Selection, Collection, and Transport for Anaerobic Culture
Authors: Harriott Melphine M. , Brown Kristen L.
Published: January 2025

Proper collection of specimens, to avoid contamination with organisms of the normal microbiota, and prompt transport to the laboratory for processing are essential. This is especially true for specimens sent to the laboratory for anaerobic culture. The laboratory director and staff must provide health care personnel with guidelines for the optimal type and amount of clinical specimens that are needed for anaerobic culture, including the appropriate methods for specimen collection. Patient care units, clinics, emergency rooms, and satellite facilities should be provided with appropriate collection and transport devices and complete instructions for their use. The ideal transport system should maintain the viability of the anaerobes during transport without allowing the overgrowth of members of the normal microbiota that are not a part of the pathogenic process. Good communication between the clinical microbiology laboratory and the clinical staff will ensure that collection and transport are optimal.
A Practical Guide to the Workup of Anaerobic Cultures
Authors: Shannon Samantha K. , Pence Morgan A.
Published: January 2025

This chapter provides a practical guidance to the workup of anaerobic cultures. When a specimen is sent to the laboratory in an appropriate container and from an appropriate site with a request for anaerobe testing, a Gram stain should be performed and reported. All specimens for which anaerobe culture is requested should undergo simultaneous aerobic culture. Workup of anaerobic cultures should be completed while taking into account the corresponding aerobic culture. In cultures with three or more organisms, workup may focus on the bacteria with the highest potential to be pathogenic. The extent of workup of anaerobes may vary based on whether the specimen was collected from a nonsterile site or a sterile site. The chapter provides the information of identification of anaerobic bacteria isolated from nonsterile sites. Identification procedures that require a week or more to complete may be of academic interest only.
Commercial Kit and Rapid Enzymatic Systems for the Identification of Anaerobes
Authors: Valencia‐Shelton Frances , Bard Jennifer Dien
Published: January 2025

Biochemical systems for identification of anaerobes rely on the metabolic breakdown of substrates and the production of end products during the growth of the isolated organism. There is currently one commercially packaged kit system that uses this method for the identification of commonly isolated anaerobic bacteria in the clinical microbiology laboratory: the API 20A system. The API 20A requires overnight incubation, whereas rapid identification of anaerobes can be accomplished with commercially available microsystems that detect preformed enzymes of isolate suspension within a few hours. Database and numerical identification profiles are provided by the manufacturer for each system. Identification of anaerobes to the species level was reported at 74% with rapid enzymatic systems, compared to 50% with API 20A. The use of rapid methods such as matrix‐assisted laser desorption ionization–time‐of‐flight mass spectrometry has certainly replaced biochemicals and enzymatic reactions in many laboratories.
MALDI‐TOF MS for Filamentous Fungi Identification
Authors: Hanson Kimberly E. , Sobczyk Juliana , Snavely Emily
Published: January 2025

Identification of fungi in the clinical microbiology laboratory has traditionally relied on a combination of phenotypic characteristics, including colony morphology, microscopic examination, growth characteristics, and biochemical reactions. Sequencing‐based approaches require specialized molecular expertise, can be costly, and are relatively slow. Matrix‐assisted laser desorption ionization‐time of flight (MALDI‐TOF) mass spectrometry (MS) is a more rapid and inexpensive methodology that has been used for the identification of microorganisms, including molds, in the microbiology laboratory. Organisms are identified by using intact cells or cell protein extracts which are ionized into charged molecules using a laser. By measuring the mass to charge ratio of the ionized molecules, a spectral fingerprint is generated. These spectral fingerprints are then compared with a database of known spectra from reference organisms to generate an accurate, species‐level identification. This chapter describes protocols for application of MALDI‐TOF MS to identify filamentous fungi in the clinical microbiology laboratory.
Disk Diffusion Testing
Authors: Ransom Eric M. , Burnham Carey‐Ann D. , Matuschek Erika
Published: January 2025

The goal of antimicrobial susceptibility testing (AST) is to provide useful information to assist clinicians with the selection of antimicrobial therapy for patient care. An AST reference method that is widely used worldwide is disk diffusion testing. Disk diffusion testing was originally described by AW Bauer and colleagues in 1966. The method uses a standardized inoculum of bacteria swabbed onto the surface of an agar plate, most commonly Mueller‐Hinton agar. This chapter describes how to perform disk diffusion testing and describes testing guidance from CLSI and EUCAST. It provides troubleshooting tips, quality control information, and a disk diffusion reading guide. Both CLSI and EUCAST have developed standardized disk diffusion methods calibrated to the reference MIC method. While both disk diffusion methods are based on the same basic methodology, there are important differences. These include the supplements in media for fastidious organisms, disk contents for some antimicrobial agents, and interpretive categories.
Screening Tests for Detection of High‐Level Mupirocin Resistance in
Staphylococcus aureus
Authors: Hemarajata Peera
Published: January 2025

High‐level mupirocin resistance (HLMR) in
Staphylococcus aureus
is defined by a mupirocin MIC of ≥512 μg/ml and is associated with the presence of plasmidencoded
mupA
or, less commonly,
mupB
genes in these isolates. Screening methods for detection of HLMR include assessing growth at a high concentration of mupirocin by broth microdilution or by disk diffusion using a 200‐μg mupirocin disk. Mupirocin ointment use is associated with increased rate of HLMR in
S. aureus
and, in particular, methicillin‐resistant
S. aureus
(MRSA). Failure of attempted MRSA decolonization using mupirocin may result in selection for genetic elements conferring resistance to other classes of antimicrobials.
Detection of Inducible Clindamycin Resistance in
Staphylococcus
spp.,
Streptococcus Pneumoniae
, and
Streptococcus
spp. Beta‐Hemolytic Group
Authors: Bard Jennifer Dien
Published: January 2025

Inducible clindamycin resistance (ICR) in staphylococci and streptococci can be detected by agar disk diffusion (D‐zone test) or broth microdilution methods. Prior to reporting clindamycin results, the CLSI recommends testing for ICR in all staphylococci,
Streptococcus pneumoniae
, and beta‐hemolytic streptococci that are resistant to erythromycin and susceptible or intermediate to clindamycin. Isolates with ICR should be reported as clindamycin resistant alongside a comment stating that the isolate is presumed to be resistant to clindamycin based on the presence of ICR, as determined by testing clindamycin in combination with erythromycin. It is best to perform the ICR test concurrently with individual tests for erythromycin and clindamycin, especially with the MIC method. The chapter covers proper quality control principles for analytical tests. With postanalytical considerations, it provides attention to common test limitations, interpretive challenges, and results reporting.
AmpC Beta‐Lactamase Testing
Authors: Yee Rebecca , Simner Patricia J.
Published: January 2025

AmpC beta‐lactamases are Ambler class C beta‐lactamases, containing serine residues at their catalytic active site. AmpC beta‐lactamases can be expressed constitutively or induced in response to β‐lactam exposure. High‐level expression of AmpC beta‐lactamase can cause resistance to aminopenicillins, cephalosporins, cephamycins, monobactams, and sometimes cefepime and piperacillin‐tazobactam. This chapter describes three principal mechanisms of AmpC beta‐lactamase resistance: chromosomally encoded inducible resistance, noninducible chromosomal resistance, and acquired ampc beta‐lactamases. The European Committee on Antimicrobial Susceptibility Testing describes a method for detection of plasmid‐mediated AmpC among group 1 Enterobacterales that lack inducible AmpC for infection control or epidemiologic purposes only. This procedure describes a disk diffusion method for AmpC beta‐lactamase detection which requires two disks: cefoxitin alone and cefoxitin disk supplemented with cloxacillin. The chapter covers quality control principles for analytical tests. With postanalytical considerations, it provides attention to common test limitations, interpretive challenges, and results reporting.
Phenotypic Carbapenemase Detection Methods
Authors: Westblade Lars F. , Marino Jamie , Moore Nicholas M. , Poirel Laurent , Nordmann Patrice
Published: January 2025

The presence of a carbapenemase in an organism of interest may be assessed by phenotypic or genotypic assays. Phenotypic detection methods include broad carbapenemase detection methods that differentiate carbapenemase‐producing, carbapenem‐resistant Gram‐negative organisms from non‐carbapenemase‐producing, carbapenem‐resistant Gram‐negative organisms for which carbapenem resistance is mediated by other mechanisms. These tests include the carbapenem inactivation tests, which require overnight incubation e.g., the modified Hodge test and modified carbapenem inactivation method, or rapid colorimetric tests that exploit a carbapenemase dependent pH change due to hydrolysis of a carbapenem (e.g., Carba NP). Other phenotypic tests allow for identification and differentiation of metallo‐β‐lactamases from serine carbapenemases (e.g., the ethylenediaminetetraacetic acid‐modified carbapenem inactivation method and the combined disk test).
Introduction
Authors: Saubolle Michael A.
Published: January 2025

The group of bacteria known as aerobic actinomycetes is made up of Gram‐positive bacilli delineated by a vast array of heterogeneous and taxonomically divergent genera in the order
Actinomycetales
. Some genera contain mycolates and can be stained by the modified acid‐fast stain. The aerobic actinomycetes are found worldwide and are important components of natural and human‐made environments; some may be components of the human microbiome, while others may transiently contaminate or colonize superficial sites. Infection in humans is most frequently opportunistic, associated with either trauma, an immunocompromising condition, or the presence of a foreign object or device in the human host.
Nocardia
is the most common genus involved in human infections. The importance of identifying the
Nocardia
to the species level is due to many species having characteristic antimicrobial susceptibility profiles and some species having inconsistent and falsely resistant
in vitro
antimicrobial results.
Appendixes
Authors: Saubolle Michael A. , Bell Melissa E. , Sussland Zdenek
Published: January 2025

Comparatively, the aerobic actinomycetes are rarely encountered in human disease, although geographic variation of prevalence may be seen. Of this group of organisms, the
Nocardia
spp. are the most prevalent pathogens. Although there are 149 species recognized in the genus
Nocardia
at this time, in three studies spanning from 2006 to 2017 and including isolates (total of 4,973) from the United States and Europe, 6 species or complexes made up almost 80% of all isolates:
Nocardia nova
complex,
N. cyriacigeorgica
,
N. farcinica
complex,
N. abscessus
complex,
N. brasiliensis
, and
N. transvalensis
complex. An additional 3 species (
N. otitidiscaviarum
,
N. beijingensis
, and
N.pseudobrasiliensis
) increased that rate to approximately 93% of all species isolated.
Liquid Media Used for Isolation
Authors: Pfeltz Richard F. , Wengenack Nancy L.
Published: January 2025

The use of liquid medium for isolation of mycobacteria and drug susceptibility testing of
Mycobacterium tuberculosis
complex was first introduced in 1980 as the BACTEC 460 radiometric system. The BACTEC MGIT automated system includes mycobacterial growth indicator tubes which contain liquid culture medium consisting of modified Middlebrook 7H9 broth, a separate growth supplement, and an antimicrobial agent mixture which is added separately to the medium. The antimicrobial agent mixture suppresses the growth of contaminating bacteria. The VersaTREK Myco culture system for the isolation of mycobacteria from clinical specimens consists of a modular arrangement of incubator and detection instruments and medium‐containing culture bottles. The VersaTREK instrument detects mycobacterial growth by automatically monitoring the rate of consumption of oxygen as a change in pressure within the headspace of the culture bottle. This chapter covers proper quality control principles for analytical tests. With postanalytical considerations, it provides attention to common test limitations, interpretive challenges, and results reporting.
Identification of Mycobacteria
Authors: Wengenack Nancy L. , Jonas‐Taggart Vivian , Vagnone Paula Snippes
Published: January 2025

This chapter provides the conventional biochemicals as a historical consideration, but their use has largely been eliminated from clinical laboratories and replaced with more rapid methods, including DNA probes, MALDI‐TOF mass spectrometry, and various molecular procedures. It also presents accuprobe mycobacterial culture identification tests. AccuProbe assays use a chemiluminescently labeled, singlestranded DNA probe that is complementary to the target organism's rRNA. The labeled DNA‐RNA hybrids are then measured in the Leader luminometer. The INNO‐LiPA MYCOBACTERIA v2 utilizes material from growing cultures that are suggestive of a mycobacterial species, from both solid and liquid media. 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.
Susceptibility Testing by Liquid Media Methods
Authors: Pfeltz Richard F. , Quinn Brigit , Wengenack Nancy L.
Published: January 2025

The BACTEC MGIT SIRE kit is a nonradiometric antimicrobial susceptibility testing (AST) system for testing
Mycobacterium tuberculosis
from isolated culture. It provides susceptibility results for streptomycin, isoniazid (INH), rifampin (RIF), and ethambutol (EMB). The BACTEC MGIT SIRE kit is a 4‐day to 13‐day qualitative test. The BACTEC MGIT 960 pyrazinamide (PZA) kit is a nonradiometric AST system for testing
Mycobacterium tuberculosis
from isolated culture against PZA. The BACTEC MGIT PZA kit is a 4‐day to21‐day qualitative test. The VersaTREK automated microbial detection system has been adapted for the performance of antimycobacterial susceptibility testing to the first‐line agents RIF, INH, EMB, and PZA with clinical isolates of
Mycobacterium tuberculosis
. This chapter focuses on the specimen, materials, quality control, results and interpretation, reporting results and limitations of procedure.
Introduction and General Considerations
Authors: Lockhart Shawn R. , Wiederhold Nathan P.
Published: January 2025

This part introduction presents an overview of the key concepts discussed in the subsequent chapters. The part brings together the contributions of well‐respected mycologists, whose expertise will help laboratories become more adept at identifying fungi, recognizing the significance of an isolated organism, and performing susceptibility testing. Fungi can cause severe illness, but they are often overlooked as causes of clinical disease and often considered only after other etiologies have been ruled out. Infections range in severity from cosmetic onychomycosis to life‐threatening disseminated disease. In some fungal diseases (histoplasmosis and coccidioidomycosis), the histopathology services may provide the first diagnostic evidence of the disease while the clinical laboratory provides confirmation of the etiology using culture or molecular methods. The appearance of the fungal organism in tissue, along with patient history, risk factors, and signs and symptoms, provides the best guidance about the likely etiology, but these should be confirmed whenever possible by culture.
Processing Specimens for Fungal Culture
Authors: Abdolrasouli Alireza , Howell Susan
Published: January 2025

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

“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

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

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

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

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

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.