bluuebunny/crossref_metadata_2025 huggingface dataset:
PROGRAM LITERASI SDN 193 PEKANBARU, SDN 190 PEKANBARU, SDN 181 PEKANBARU, SDN 177 PEKANBARU
Authors: Emelia  , Januarita Ulfa Silviana  , Nabila Safni Ranti  , Putri Rahma Dani Hasibuan  , Febrina Dafit
Published: July 2023

Latar Belakang : Program literasi telah menjadi perhatian penting dalam pendidikan di seluruh dunia, termasuk di Indonesia.

Tujuan : Penelitian ini bertujuan untuk menginvestigasi implementasi program literasi di sekolah dasar di daerah Riau, dengan fokus pada empat sekolah dasar yaitu SDN 193 Pekanbaru, SDN 190 Pekanbaru, SDN 181 Pekanbaru, dan SDN 177 Pekanbaru.

Metode : Penelitian ini menggunakan metode pendekatan kualitatif dengan metode pengumpulan data berupa observasi kelas, wawancara dengan guru dan siswa, serta analisis dokumen terkait program literasi.

Hasil dan Pembahasan : Dari hasil analisis Program literasi yang dilakukan di sekolah dasar juga telah berhasil mengembangkan minat baca siswa. Dengan menerapkan pendekatan yang menarik dan interaktif, siswa menjadi lebih tertarik untuk membaca buku dan materi bacaan lainnya. Mereka mulai menikmati kegiatan membaca dan melihatnya sebagai kesenangan daripada tugas yang membosankan. Hal ini berdampak positif pada kebiasaan membaca siswa di luar lingkungan sekolah.

Kesimpulan : Dari hasil penelitian dengan melakukan pengamaan di SDN 193, SDN 190, SDN 181, dan SDN 177 Pekanbaru, dapat dilihat bahwa sejauh ini program literasi yang telah dijalankan adalah jenis literasi baca tulis dan literasi budaya dan kewargaan. Pihak sekolah merancang tahapan pelaksanaan mulai dari pembiasaan, pengembangan, dan pembelajaran dengan sebermutu mungkin. Tahap-tahap ini juga disesuaikan dengan kebutuhan dan kondisi peserta didik di lingkungan sekolah.
S100 Beta as a Marker of Section Hepatic Encephalopathy: A Case-control Study
Authors: Chandey Manish , Singh Parminder , Kukreja Sahiba , Mohan Gurinder
Published: July 2023

Introduction: Hepatic Encephalopathy (HE) is a term used to describe a reversible syndrome of impaired brain function involving a complex spectrum of non specific neurological and psychiatric manifestations occurring in patients of severe acute or Chronic Liver Disease (CLD). The current clinical standard employed is psychometric analysis by computing Psychometric Hepatic Encephalopathy Score (PHES), which is cumbersome to perform. Hence, this necessitates the requirement of a serum biomarker which could correlate with the grades of HE. Following a metabolic injury, the earliest response involving the glial response and astrocyte activation results in the secretion of S100 Beta. Hence, estimation of serum S100 beta levels is considered as a strong marker of Central Nervous System (CNS) injury. Aim: To verify S100 Beta as a marker of HE. Materials and Methods: This was a case-control study conducted from 1st April 2021 to 31st July 2022. All diagnosed cases of cirrhosis of liver in the Medicine Department of a tertiary care hospital of North India. A total of 40 age and sex matched healthy controls were recruited after due consent and application of exclusion criteria. They were subjected to psychometric analysis (Five pen and paper tests) and on basis of PHES were divided into four groups on the basis of grades of encephalopathy. Serum samples of patients were run for all routine biochemical parameters in line with Child Turcotte Pugh (CTP) score and S100 Beta levels estimation. Statistical analysis was done to find correlation between S100 Beta levels, PHES and CTP score. Results: A total of 150 patients and 40 controls were recruited in the study. A progressive deterioration of PHES score was found in the various groups of the study population with worsening of grade of HE. S100 Beta levels correlated with the PHES and also Receiver Operating Characteristic (ROC) curve analysis showed that the sensitivity of the marker stood at 92.7% and specificity at 84.8%. S100 Beta levels could fairly differentiate between patients with and without HE. Hence, S100 Beta levels correlated more with grades of HE than with hepatic functional status (CTP Score). At higher grades of HE when it becomes more clinically apparent, S100 Beta levels would help, when other causes of behaviour changes like psychiatric illness coexist or cannot be ruled out. In the diagnosis of low-grade HE whenever neuro psychometric tests are suboptimal, or when competing psychiatric differential diagnoses are in place, S100 beta levels would have a role over and above the PHES score. Conclusion: Currently, psychometric analysis holds to be the best clinical standard for diagnosis of HE. S100 Beta holds promising results as a marker for establishing a liquid diagnosis of HE.
Post-fire behavior of RC columns repaired with square hollow section steel tube and RC concrete jackets
Authors: Belakhdar Ahmed Rafik , Dimia Mohamed Salah , Baghdadi Mohamed
Published: July 2023

This paper investigates numerically fire-exposed reinforced concrete (RC) columns. As a first step, the study examined the effects of exposing the columns to fire for 60 minutes according to the ISO 834 fire standard on the column's residual load-bearing capacity by considering some decisive geometrical parameters such as the column height and its cross-sectional area. The second step consisted of investigating the effectiveness of the strengthening technique utilized by incorporating composite jackets, considering different strengths of concrete, in order to improve the post-fire behavior of these columns. The results showed that the longer the column is exposed to fire, the lower its bearing capacity. However, it was also found that increasing the column cross-sectional area can reduce the percentage of load-bearing capacity. Finally, it was revealed that the strengthening method used herein allowed restoring the capacity of the columns exposed to fire for a period of one hour by up to 180%.
ROLE OF BREASTFEEDING IN PROTECTION AGAINST RESPIRATORY TRACT INFECTIONS IN CHILDREN
Authors: Sajjad Ahmad  , Shazia Liaquat  , Qurat-ul-Ain  , Aleena Malik  , Malik Sania Ali
Published: July 2023

Objectives:

To assess the role of breastfeeding in prevention of respiratory tract infections in children less than 5 years of age.Materials and Methods:

A case control study on a total population of 100, taken throughnon-probability convenience sampling from Pediatrics ward of KTH, equally divided in 50 cases and 50 control. Cases were the patients suff ering from any respiratory tract infection admitted in the pediatric wards of KTH and controls were the patients admitted in same wards due to any disease other than respiratory tract infection. Data collected by questionnaires which were filled by interviewing the cases and control group. Later the data was entered and analyzed by using software SPSS.16.Results: It was found that 45 out of 50(90%) in controls were breast fed as compared to 35 out of 50 (70%) in cases; OR: 3.8 with CI of 0.8-6.8).children who received supplemental feeds in first 6 months of life were 51 ( 51%), participants who were vaccinated were 69(69%), Low socioeconomic participants were60(60%), participants who were receiving passive smoking were32 (32%) , colostrum was given to more no. of children 38 out of 50(76%) as compared to cases 36 out of 50(72%), 57(57%) of the mothers included in the study were illiterate.Conclusion: It was concluded that risk of respiratory tract infections was less in those children (under 5 years of age) who were breast fed and vaccinated.
EVALUATION OF REMOVAL OF GUTTA PERCHA POINTS AND SEALER WITH HEDSTROM FILES ALONE AND AUGMENTED BY CHLOROFORM
Authors: Shahid Ilyas  , Mumtaz ul Islam  , Ali Hamad Khan  , Hanzala Waqar  , Sadeeq Ahmad  , Atta  Elahi
Published: July 2023

Objectives: To compare time dependent value and potential for eff ectiveness of Hedstrom files alone and facilitated with chloroform to retrieve the obturated material from root canals.Materials and Methods: First premolars, single rooted teeth (n=20) were used. Root canals of specimen teeth obturated following standard protocol, specimens incubated at 37º C for one month in humid conditions in an incubator. Re-treatment was performed with H files alone (group A) and facilitated with chloroform (group B). Time spent for removal of material for both groups was recorded. To inspect the remaining material in the root canals specimens were splitted longitudinally. Photographs of the splitted specimens were taken for confi rmation and record. Results: Mean values showed a marked difference in two protocols which were confirmed by independent t test which provided highly signifi cant value. Conclusion: Hedstrom files alone (not aided by chloroform) are efficient for removal of materials from obturated root canals in terms of efficacy and time.
MUCORMYCOSIS IN COVID-19 AND NON COVID-19 PATIENTS: A COMPARATIVE CROSS SECTIONAL STUDY
Authors: Izaz Muhammad , Bibi Amara , Rehman Basheer
Published: July 2023

Background:

Recently, there have been a growing number of incidences of fungal infections, such as mucormycosis, in people with COVID-19 all over the world. The spread of Mucormycosis is very fast and delay in treatment could be fatal. This study compared Mucormycosis in COVID-19 patients versus non-COVID-19 patients.

Material and Methods:

This cross-sectional study was conducted in the Department of Oral and Maxillofacial Surgery, Khyber College of Dentistry Peshawar Pakistan from July 2021 to December 2021. A total of 50 cases of Mucormycosis were included by dividing into two groups. One of the groups had a positive history of COVID-19 infection while the second group had negative COVID-19 history. Diagnosis of Mucormycosis was confirmed on histopathology or fungal culture. For group 1, a history of COVID-19 infection was confirmed from patient records having positive COVID PCR within 2 months of the onset of Mucormycosis. For group 2, no COVID-19 infection was confirmed from the absence of signs and symptoms such as cough, fever,body achess and no contact with COVID-19-positive patient within 6 months of the onset of Mucormycosis. A logistic regression model was applied to determine the predictors of Mucormycosis while multi-logistic regression was run to see potential confounders.

Results:

Out of the total 50 patients,the  mean age of the patients was 50+9.45S.D. Steroids usage was high in COVID-19 positive patients [15 (60%),P value;0.001] while pus discharge was low 5(20%) in CoVID-19 patients in contrast toNon-COVID-199 Patients which was high[17 (68%):P value;0.001].

Multivariate Logistic regression analysis showed that the adjusted odds ratio (OR) for female patients was 2.74 (95 % CI 0.66-4.25) as compared to male patients. Similarly, patients with steroid use have about 3.58 times higher odds of catching the disease as compared to non-steroid use (95 % CI 1.066-19.3).  The OR for pus discharge was 0.40 (95 % CI 0.08-2.00), Left side 0.45 (95 % CI 0.06-2.9,) and Bilateral 0.93 (95 % CI 0.14-6.17).

Conclusion:

Covid-19 seems to havea  causal, coincidental or contributory role in the  development of Mucormycosis in the background of comorbidities such as diabetes. The role of Covid-19 needs to be specified and its association with Mucormycosis needs to be established. Furtherlarge-scalee studies are required where the association of COVID-19,the  role of dia,betethe s and use of steroids with the development of mucormycosis would be understood clearly.
PROSPECTS FOR THE USE OF MINI-INVASIVE TECHNOLOGIES IN THE SURGICAL TREATMENT OF RECTAL FISTULAS
Authors: Firsyk T. M.
Published: July 2023

Summary. The search for the optimal method of surgical treatment of fistulas of the rectum is an important issue of modern surgery. The main complications after operations are the recurrence of the disease and anal incontinence. The reasons for such complications are not only the incorrect choice of the surgical technique, but also technical errors in their implementation. The proposed methods of surgical interventions are characterized by a combination of radical excision of the fistula tract and minimal impact on the anal sphincter.

Objective. To analyze the results of surgical treatment of rectal fistulas using minimally invasive technologies and to determine the prospects of their use.

Materials and methods. The study consisted retro- and prospective analysis of surgical treatment of patients with various types of rectal fistulae. The advantages of using minimally invasive methods (the modified method LIFT and excision anal fistulas with biowelding) were revealed.

Results. The use of the proposed methods demonstrated high efficiency and reduced rates of postoperative complications.

Conclusions. The effectiveness of the techniques consists in the minimal damaging effect on the muscle structures of the anal complex. This reduces the risk of insufficiency of the anal sphincter in the postoperative period. The use of minimally invasive techniques reduce the duration of surgery, the number of hospital days, and the overall wound healing time.
Disputes and their Settlement Machinery in Tea Plantation Industry in North Bengal
Authors: Anand Dev , R. Sengupta Palas
Published: July 2023

Industrial disputes are fairly common in the workplace. Industrial disputes were the matter of concern from last so many years. The industrial dispute in tea plantations began in 1848 when workers of the Assam Company India limited went on strike against the delay in payment of wages. Failure in implementation of the provisions of Plantation Labour Act, 1951 related to welfare of tea workers in West Bengal are the main reasons of disputes in the tea plantation Industry. Low wages, bonus issue, poor working condition, limited healthcare facilities and poor living condition are some factors contributing to industrial disputes in tea plantation industries of the West Bengal.
Cuidados em saúde bucal de pacientes com necessidades especiais
Authors: Bell Kamila Sostena , Franco Ana Beatriz Aiélo , Delfino Mateus Machado , Scannavino Fábio Luiz Ferreira , Martins Alex Tadeu , Santos Fabiano de Sant’Ana dos
Published: July 2023

Objetivo: analisar as percepções e conhecimentos sobre cuidados para saúde bucal dos pais e ou cuidadores dos pacientes com necessidades especiais atendidos no curso de Odontologia do UNIFEB, Barretos, São Paulo, Brasil. Material e Métodos: estudo descritivo, quantitativo e de amostra por conveniência e aplicação de questionário. Os dados foram armazenados e analisados por meio de estatística descritiva. Resultados: a amostra mostrou que 26,6% dos entrevistados eram homens e 73,4% mulheres com idade média igual a 50,2 anos. Em relação à quando se deve iniciar a higiene bucal do paciente, 13,3% responderam ser antes de 1 mês de vida, 43,3% de 1 a 5 anos, 10% de 1 a 6 meses e 26,7% entre 7 a 12 meses e os outros 6,7% não souberam responder. Quanto ao que usar para fazer a higiene bucal no primeiro ano de vida, 10% não souberam responder, 53,3% afirmaram ser com a utilização de uma gaze/frauda, 26,7% disseram ser com a escova e 10% responderam ser com a utilização de outro meio de escovação. Após o primeiro ano de vida, 70% dos participantes responderam que a higienização deve ser feita com a escova dental, 13,3% não souberam responder e 13,3% disseram ser feita com a utilização da gaze/frauda. Conclusão: os cuidadores reconhecem a necessidade dos cuidados bucais, porém a maioria não sabe como realizar de forma correta.
Theoretical-conceptual clarifications on dental phobia
Authors: Brancoveanu Romica
Published: July 2023

Dental phobia is defined as a persistent, unrealistic reaction to a specific dental stimulus that results in partial or complete avoidance of the perceived danger. A person with dental phobia will avoid dental care at all costs until the physical problem or psychological burden of the phobia becomes unbearable. This phobia, in itself, causes a lot of stress and a negative impact on other aspects of the dentophobic patient’s life. Dental fear, it is described, as of lower intensity than dental phobia and is a protective reaction to some danger suggested by the dental environment. The literature also describes dental anxiety as a reaction to an unknown danger. Most people experience some degree of dental anxiety, especially if they are about to have something done to them that has never been done to them before in the dental office.
Digital Meditation to Target Employee Stress
Authors: Radin Rachel M. , Vacarro Julie , Fromer Elena , Ahmadi Sarah E. , Guan Joanna Y. , Fisher Sarah M. , Pressman Sarah D. , Hunter John F. , Sweeny Kate , Tomiyama A. Janet , Hofschneider Lauren Tiongco , Zawadzki Matthew J. , Gavrilova Larisa , Epel Elissa S. , Prather Aric A.
Published: January 2025

Importance

Mindfulness meditation may improve well-being among employees; however, effects of digital meditation programs are poorly understood.

Objective

To evaluate the effects of digital meditation vs a waiting list condition on general and work-specific stress and whether greater engagement in the intervention moderates these effects.

Design, Setting, and Participants

This randomized clinical trial included a volunteer sample of adults (aged ≥18 years) employed at a large academic medical center who reported mild to moderate stress, had regular access to a web-connected device, and were fluent in English. Exclusion criteria included being a regular meditator. Participants were recruited from May 16, 2018, through September 28, 2019, and completed baseline, 8-week, and 4-month measures assessing stress, job strain, burnout, work engagement, mindfulness, depression, and anxiety. Data were analyzed from March 2023 to October 2024.

Intervention

Participants were randomized 1:1 to a digital meditation program or the waiting list control condition. Participants in the intervention group were instructed to complete 10 minutes of meditation per day for 8 weeks. The control group was instructed to continue their normal activities and not add any meditation during the study period.

Main Outcomes and Measures

The primary outcome measure was change in Perceived Stress Scale (PSS) score at 8 weeks. Secondary outcome measures included changes in job strain, measured as work effort-reward imbalance.

Results

A total of 1458 participants (mean [SD] age, 35.54 [10.30] years; 1178 [80.80%] female) were included. Those randomized to meditation (n = 728) vs waiting list (n = 730) showed improvements in PSS (Cohen d, 0.85; 95% CI, 0.73-0.96) and in all secondary outcome measures (eg, job strain: Cohen d, 0.34; 95% CI, 0.23-0.46) at 8 weeks. These improvements were maintained at 4 months after randomization (PSS: Cohen d, 0.71; 95% CI, 0.59-0.84; job strain: Cohen d, 0.37; 95% CI, 0.25-0.50). Those using the app from 5 to 9.9 min/d vs less than 5 min/d showed greater reduction in stress (mean PSS score difference, −6.58; 95% CI, −7.44 to −5.73).

Conclusions and Relevance

The findings suggest that a brief, digital mindfulness-based program is an easily accessible and scalable method for reducing perceptions of stress. Future work should seek to clarify mechanisms by which such interventions contribute to improvements in work-specific well-being.

Trial Registration

ClinicalTrials.gov Identifier: NCT03527303
Biochemical Tests for the Identification of Aerobic Bacteria
Authors: Davis Richard E. , Pezzlo Marie T.
Published: January 2025

Acetamide agar is used to test an organism‐s ability to utilize acetamide by deamination. The medium contains acetamide as the sole carbon source and inorganic ammonium salts as the sole source of nitrogen. Growth is indicative of a positive test for acetamide utilization. When the bacterium metabolizes acetamide by the enzymatic action of an acylamidase, the ammonium salts are broken down to ammonia, which increases alkalinity. Acetate agar is used to test an organism‐s ability to utilize acetate. Antimicrobial disks dropped onto agar can help identify bacteria based on their susceptibility or resistance to certain antibiotics. Antibiotic disks used for organism identification should not be used to report or infer clinical sensitivity of an isolate. The butyrate test is a rapid test for the detection of the enzyme butyrate esterase.
Staphylococcus aureus
, the most pathogenic of the staphylococci, is separated from other species by the presence of coagulase.
Processing Specimens for Anaerobic Culture
Authors: Morris Trefor E.
Published: January 2025

This chapter presents the procedure for processing specimens for anaerobic culture. This procedure describes the steps for processing a specimen for anaerobic culture once received within the laboratory. The overarching aim is to complete these steps within the shortest possible timeframe so that there is no loss of organism viability. Ideally, all processing should take place within an anaerobic chamber, as this allows all stages to occur within an anaerobic environment. All specimens should be examined macroscopically (visually), with reference made to any significant characteristics, and microscopically via Gram stain. The procedure includes the steps, such as visual examination, microscopic examination via Gram stain, specimen preparation, inoculation of media, and incubation.
Examination of Primary Culture Plates for Anaerobic Bacteria
Authors: Morris Trefor E.
Published: January 2025

The goal of processing primary culture plates is to isolate significant anaerobic organisms from the original specimen for identification and susceptibility testing when it is indicated. Comparison of culture results with what was seen on the original Gram stain of the specimen is critical. When culture plates are evaluated, all morphotypes observed in the original Gram stain should match the aerobes and anaerobes recovered. It is important to remember that anaerobic culture media permit facultatively anaerobic bacteria to grow. All bacterial isolates must be subjected to aerotolerance testing before being designated as anaerobes. Special precautions must be taken to avoid exposure of culture plates to oxygen during examination. A maximum of 20 min of exposure is recommended, as beyond this, some oxygen‐sensitive anaerobes will be killed. In addition, reduced culture media may become oxidized when exposed to air beyond this period, making the media unsuitable for isolation of fastidious anaerobes.
Introduction
Authors: Harrington Amanda T. , McElvania Erin
Published: January 2025

Blood culture remains one of the most critical functions of the clinical microbiology laboratory, aiding in the diagnosis of bloodstream infection and therapy management for patients. Culture of blood specimens is largely accomplished using commercial, continuously monitored blood culture systems, and aerobic and anaerobic bacteria, fungi, and mycobacteria can be recovered using these methods. Postanalytical communication and coordination with clinical care teams, especially those who prescribe antibiotics, result in improved patient care, such as reducing the interval of time to effective treatment. Gram staining remains a cornerstone of clinical microbiology practice and is a useful and rapid tool for preliminary identification of organisms from blood culture specimens. The procedure for quality control and quality assurance for blood culture provides guidance on verification of continuous‐monitoring blood culture systems as well as recommended strategies for monitoring quality of blood culture processes using standard metrics, such as contamination rates.
MALDI‐TOF MS for Identification of Acid‐Fast Bacilli and Aerobic Actinomycetes
Authors: Zelazny Adrian M. , Balada‐Llasat Joan‐Miquel
Published: January 2025

This chapter describes the use of matrix‐assisted laser desorption ionization–time of flight mass spectrometry (MALDI‐TOF MS) for the identification of mycobacteria, Nocardia, and other aerobic actinomycetes after growth in culture. It evaluates the MALDI‐TOF MS technique results in a spectral profile that relates to the mass‐to‐charge ratio of the organism. Direct spotting or on‐target extraction is not advised for myco‐bacteria due to safety concerns and the cell wall properties of this microorganism group. For these reasons, tube extraction protocols are recommended and typically involve mechanical disruption via bead beating, sonication, and/ or vortexing in ethanol, formic acid, and/or acetonitrile. The extracted proteins are then spotted onto the target plate for MALDI‐TOF MS analysis, where the microbial profile is then compared with a reference database; matching algorithms are used to determine the organism's identity.
Specimen Examination and Primary Isolation
Authors: Bell Melissa E. , Sussland Zdenek
Published: January 2025

Aerobic actinomycetes cause a variety of infections in humans, including respiratory, cutaneous, and disseminated infections, with a marked tropism to the central nervous system, from a primary pulmonary infection. This chapter outlines practical procedures that can be used to establish the presence of clinically important aerobic actinomycetes. These include members of several genera:
Actinomadura
,
Dermatophilus
,
Gordonia
,
Nocardia
,
Nocardiopsis
,
Rhodococcus
,
Streptomyces
,
Tsukamurella
,
Segniliparus
, and, to a lesser extent,
Amycolata
,
Amycolatopsis
,
Dietzia
,
Micromonospora
,
Saccharopolyspora
,
Saccharomonospora
,
Thermoactinomyces
, and
Williamsia
. The genera
Gordonia
,
Nocardia
,
Rhodococcus
, and
Tsukamurella
, and the microbiologically closely related genera
Mycobacterium
and
Corynebacterium
are collectively known as the mycolic acid‐containing genera, or “mycolata”. 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. The selection of media for the isolation of the aerobic actinomycetes depends primarily on the specimen type.
Molecular Susceptibility Testing for
Mycobacterium tuberculosis
Authors: Musser Kimberlee A. , Halse Tanya A.
Published: January 2025

Pyrosequencing (PSQ) technology is a rapid real‐time method for sequencing small segments of genomic deoxyribonucleic acid (DNA), often referred to as nucleic acid sequencing‐by‐synthesis. PSQ can be utilized for the molecular detection of mutations associated with drug resistance for Mycobacterium tuberculosis complex (MTBC). PSQ, when utilized directly on clinical specimens, has been shown to shorten the time to treatment of multidrug‐resistant tuberculosis (MDR‐TB) to as much as 5 weeks earlier and has influenced clinicians' decisions to devise effective TB drug regimens. The technology utilizes polymerase chain reaction products amplified from primary clinical samples or cultures to yield single‐stranded DNA to which a sequencing primer can be annealed. Sequences derived from pyrograms are compared to a library of known sequences to determine if the sample has mutations and resistance is predicted or if it has no mutations and susceptibility is suggested.
Full Identification of Yeasts
Authors: Zhang Sean X. , Memon Warda
Published: January 2025

In an era of increasing resistance of yeast species to antifungal agents and a widening range of species capable of causing diseases, there is almost no situation in which identification to species level is not warranted. Recently, matrix‐assisted laser desorption ionization‐time of flight mass spectroscopy (MALDI‐TOF MS) has been introduced as a method with the potential to identify a wide range of bacteria and fungi. MALDI‐TOF MS has been applied in clinical laboratories to identify a variety of clinically important yeasts. This chapter presents the methods which take advantage of phenotypic features of various yeast species. It provides some of the characteristics of various pathogenic yeasts. Supplemental tests can sometimes provide the single result that identifies an organism. Carbon assimilation, in practical terms, is the ability to use a sole carbon substrate for growth; thus, an organism that assimilates a substrate will show growth or increased turbidity.
Serologic Methods for Diagnosis of
Coccidioides
Infections
Authors: Lindsley Mark D.
Published: January 2025

Coccidioides species are thermally dimorphic fungal pathogens endemic primarily to the southwestern region of the United States, parts of northern Mexico, and Central and South America. It has recently been noted that the region of endemicity in the United States is expanding northward and these species are present in southern Washington State and northern Utah. Two species have been recognized,
Coccidioides immitis
and
Coccidioides posadasii
, which are phenotypically indistinguishable and can be differentiated only by molecular analysis. In the environment,
Coccidioides
spp. are found in soil in desert conditions. The mold grows in a filamentous form and reproduces by forming arthroconidia which break off from the hyphae. Definitive diagnosis of coccidioidomycosis is made through culture or histopathology. Tissue for histopathological diagnosis may be difficult to obtain, often requiring surgery. Therefore, serologic methods are more frequently employed, as serum can be obtained through less invasive venipuncture and is often the only material for diagnosis.
Introduction
Authors: Greninger Alexander L. , Naccache Samia N.
Published: January 2025

Molecular testing is central to the operation of the clinical microbiology laboratory and is increasingly first‐line testing for many analytes. For high‐throughput testing, several fully robotic, mostly random‐access analyses are commercially available and have also become more widespread in labs seeking solutions to testing for severe acute respiratory syndrome coronavirus 2. With advanced molecular instrumentation being more accessible than ever and allowing improved performance and faster turnaround times than purely laboratory‐developed tests with separate extraction and amplification steps, the barrier to entry for molecular assays has been reduced considerably. Increasingly, specialized molecular laboratories are called on to develop next‐generation sequencing‐based assays, which for the most part necessitate laboratory‐developed testing protocols. Next‐generation sequencing technologies, which allow the detection of potentially all microbes in a specimen, bring with them augmented focus on classic molecular challenges in preanalytical, analytical, and postanalytical processes.
Packing and Shipping Infectious Substances
Authors: Pentella Michael A.
Published: January 2025

The requirements and regulations governing the transport of infectious substances by commercial carriers change often. Most regulations for the safe air transport of dangerous goods throughout the world originate as decisions made by the ICAO United Nations Committee of Experts. The IATA DGR requirements have become the most widely recognized, copied, and used packing and shipping guidelines in the world. An important non‐safety‐related benefit of adherence to these regulations and requirements is to reduce the exposure of the shipper to the risks of criminal and civil liability associated with the improper shipment of dangerous goods. IATA requirements and DOT regulations mandate the minimum standards for packing infectious substances that can pose a threat to humans, animals, or the environment. Shipping of all dangerous goods begins with classification of the substances.
Introduction to the 13th Edition of the
Manual of Clinical Microbiology
Authors: Carroll Karen C. , Pfaller Michael A.
Published: January 2025

This introduction presents an overview of the key concepts discussed in the subsequent chapters of this book. The book includes updated content on all aspects of microbiology, authored by world experts on each subject and edited by a highly committed team of volume and section editors working within the usual 4‐year publication cycle. It presents practical information for daily improvements in test utilization and ways to collaborate with antimicrobial stewardship teams. The book accommodates taxonomic changes among the
Enterobacterales
by reorganizing some of the existing chapters and creating a new separate chapter on
Salmonella
species. Antimicrobial resistance, particularly among Gram negative organisms, continues to challenge microbiology laboratories and clinicians.
Diagnostic Stewardship in Clinical Microbiology
Authors: Chew Ka‐lip , Chia Jonathan W. Z. , Vasoo Shawn
Published: January 2025

Patient evaluation begins with a thorough symptom review and history, followed by physical examination to develop differential diagnoses for the patient's clinical presentation. Diagnostic testing is subsequently requested to confirm or exclude specific diagnoses. Diagnostic stewardship may be defined as performing the right test for the right patient for the right reasons at the right time, with the right interpretation which results in the right treatment, optimizing patient care. The postanalytical phase involves final reporting and interpretation of results, as well as the clinician's application of the results to guide patient management. Underutilization of blood cultures can lead to missed diagnoses and delayed or inappropriate therapy. Diagnosing ventilator‐associated pneumonia is complicated by the frequent colonization of the respiratory tract with
Enterobacterales
and nonfermenting Gram‐negative bacilli. A diagnostic stewardship program should ensure value and implement evidence‐based practice in clinical microbiology, where attention is paid to both accuracy and optimal patient outcomes.
Laboratory Automation in Clinical Microbiology
Authors: McElvania Erin , Doern Christopher D. , Culbreath Karissa
Published: January 2025

The practice of clinical microbiology has been revolutionized by technological innovations such as the advent of molecular diagnostics and polymerase chain reaction, matrix‐assisted laser desorption ionization–time of flight mass spectrometry, and most recently laboratory automation. This chapter focuses on the automation of culture‐based bacteriology. It discusses the various components of culture‐based automation along with some important considerations for those looking to adopt automation in their microbiology laboratory, such as how to select the right system, change management, and system validation. The chapter also includes some details of each system for the purposes of facilitating a capability comparison. The automation of microbiological specimen processing improves the quality of plate streaking, avoids cross‐contamination, alleviates ergonomic issues, and reduces processing time and costs. Total laboratory automation will likely become commonplace in high‐volume laboratories and may eventually be found in smaller laboratories.
Mycobacterium
: Clinical and Laboratory Characteristics of Rapidly Growing Mycobacteria
Authors: Brown‐Elliott Barbara A. , Harrington Susan M. , Morimoto Kozo , Wallace, Richard J.
Published: January 2025

Rapidly growing mycobacteria (RGM) contain long‐chain fatty acids, known as mycolic acids, that can be quantitated with chromatographic techniques such as high‐performance liquid chromatography (HPLC). Prior to the molecular era, HPLC was used for identification of RGM species in most major reference laboratories. The RGM are opportunistic pathogens that cause disease in a variety of clinical settings. RGM may also cause bone and joint infections. Chronic lung infections with RGM, most often in nonsmoking older women with bronchiectasis, are sometimes associated with the
Mycobacterium avium
complex. The use of mycobacterial smears is a rapid and reasonably sensitive step in the diagnosis of RGM disease. PCR amplification and sequencing has been used to detect and identify nontuberculous mycobacteria in specimens from sterile sites, but these tests are generally limited to larger, reference laboratories. The adjunctive nonmolecular tests, including antimicrobial susceptibility tests, have been utilized for preliminary identification of the RGM.
Aggregatibacter
,
Capnocytophaga
,
Eikenella
,
Kingella
,
Pasteurella
, and Other Fastidious or Rarely Encountered Gram‐Negative Rods
Authors: Zbinden Reinhard
Published: January 2025

This chapter covers the bacterial genera that are taxonomically diverse and belong to the families
Cardiobacteriaceae
,
Flavobacteriaceae
,
Leptotrichiaceae
,
Neisseriaceae
,
Pasteurellaceae
, and
Porphyromonadaceae
; common traits justify their discussion as a group. The taxonomy of the family
Pasteurellaceae
has undergone important changes; the family consists of over 100 named species distributed in over 25 genera, of which 4 include human pathogens:
Actinobacillus
,
Aggregatibacter
,
Haemophilus
, and
Pasteurella
. The chapter focuses on species commonly isolated from humans. Direct microscopy of specimens or of positive blood cultures supported by clinical information may help identify the corresponding bacteria, e.g., the typical morphology of spindle‐shaped cells in the Gram stain in the context of a dog bite allows the presumptive identification of
C. canimorsus
. Phenotypic identification of fastidious Gram‐negative rods presents several challenges.
Haemophilus
Authors: Gonzalez Mark D. , Ledeboer Nathan A.
Published: January 2025

Haemophilus
spp. are members of the family
Pasteurellaceae
. Members of the
Haemophilus
genus are small, nonmotile, non‐spore‐forming, non‐acid‐fast, pleomorphic, Gram‐negative bacilli with fastidious growth requirements.
Haemophilus
spp. can be found as part of the commensal microbiota of mucous membranes in humans.
H. influenzae
may also be found as part of the commensal bacterial microbiota of the mucosal surfaces of the upper respiratory tract (URT) of many healthy individuals; however, asymptomatic colonization of the URT with encapsulated strains of
H. influenzae
type b is rare. Isolates of
H. influenzae
constitute a diverse group of organisms that cause a broad range of human diseases. Collection of specimens for the diagnosis of
Haemophilus
infections is predicated on the nature of the infection being evaluated.
Klebsiella
,
Enterobacter
,
Citrobacter
, and Selected Other
Enterobacteriaceae
Authors: Das Sanchita , Pierce Virginia M. , Frank Karen M.
Published: January 2025

The genera
Klebsiella
,
Enterobacter
,
Citrobacter
, and
Cronobacter
are commonly encountered in clinical laboratories and cause a range of infections in humans, including bacteremia, meningitis, wound infections, and infections of the respiratory and urinary tracts. This chapter contains information not only on the taxonomy, detection, and identification of these genera but also on the global issue of antimicrobial resistance, which is especially pertinent to this group of organisms.
Klebsiella pneumoniae
is a significant pathogen in both community and hospital settings.
Klebsiella granulomatis
is the agent of donovanosis or granuloma inguinale, a disease characterized by painless, slowly progressive, vascular genital ulcers.
Enterobacter
spp. are opportunistic pathogens that are found in the natural environment in habitats such as water, sewage, vegetables, and soil. They are also commensal bacteria in the human gastrointestinal tract. The detection of antimicrobial‐resistant organisms by laboratories is a critical step required for appropriate management of patients and infection prevention and control efforts.
Bartonella
Authors: Giladi Michael , Gutiérrez Ricardo , Harrus Shimon
Published: January 2025

Bartonella
species are fastidious, Gram‐negative, coccobacillary or bacillary, small, arthropod‐borne bacteria that evolved from free‐living organisms and insect gut symbionts. This chapter focuses on the epidemiology, microbiology, clinical manifestations, and diagnosis of the three most common
Bartonella spp
;
B. bacilliformis
,
B. quintana
and
B. henselae
. Incidence of cat scratch disease is highest among those who live in the southern United States and among children 5 to 9 years of age. Trench fever, also known as 5‐day fever or quintan fever, is caused by
B. quintana
. Bacillary angiomatosis is characterized by neovascular proliferative lesions involving various organs. Infections caused by Bartonella spp. are uncommon among solid‐organ transplant recipients but both clinicians and clinical microbiologists should be aware of their unique characteristics.
Borrelia
Authors: Aguero‐Rosenfeld Maria E. , Sabljić Eva Ružić
Published: January 2025

Borrelia
species constitute a heterogeneous group of organisms that are maintained in nature in animal reservoirs and are transmitted via arthropod vectors.
Borrelia
species are agents of relapsing fever (RF), caused by the RF
Borrelia
group, and Lyme disease, caused by the Lyme borreliosis (LB)
Borrelia
group. A hallmark of
Borrelia
species is a segmented genome consisting of a linear chromosome and a mix of linear and circular plasmids. Although members of LB group of
Borrelia
have similar characteristics, they vary in their ability to cause disease in humans as well as in clinical manifestations. Acrodermatitis chronica atrophicans is a common late manifestation of LB in Europe. RF
Borrelia
can be detected in peripheral blood with blood films prepared from blood collected with EDTA. Variable major protein‐like sequences expressed is one of the most specific
Borrelia burgdorferi
antigens and has high significance in LB serology.
Chlamydia
Authors: Greub Gilbert , Munson Erik
Published: January 2025

This chapter focuses on the important human pathogens within the genus
Chlamydia
, as well as on
Parachlamydia acanthamoebae
,
Waddlia chondrophila
, and
Simkania negevensis
, for which evidence gathered over the past 20 years supports possible pathogenicity in humans. The taxonomy of
Chlamydiales
is rapidly evolving and progressively moving from a purely phenotypic taxonomy to a polyphasic taxonomy combining phenotypic, molecular, and phylogenetic characteristics.
Chlamydia
,
Parachlamydia
,
Waddlia
, and
Simkania
all present biphasic developmental stages with elementary body and reticulate body formation.
Chlamydia trachomatis
is the most common bacterial agent of sexually transmitted infection in the world.
Chlamydia psittaci
causes a wide variety of clinical conditions in humans, ranging from asymptomatic infection to severe, even fatal pneumonia and systemic infections. For
Chlamydia trachomatis
, one effective method for identification of the organism in cell culture is to stain the monolayers with species‐specific fluorescein‐conjugated monoclonal antibodies.
Ehrlichia
,
Anaplasma
, and Related Intracellular Bacteria
Authors: Theel Elitza S. , Pritt Bobbi S.
Published: January 2025

The family
Anaplasmataceae
in the order
Rickettsiales
is composed of several genera of clinically significant bacteria encompassing both human and veterinary pathogens. Members of the genera
Ehrlichia
and
Anaplasma
are the best known, having been recognized as agents of veterinary importance for over a century and as human pathogens since 1987. This chapter focuses on the clinically relevant members of the
Anaplasmataceae
, with particular emphasis on
Anaplasma phagocytophilum
and
Ehrlichia chaffeensis
, the most common human pathogens in this family. The family
Anaplasmataceae
contains small, nonmotile, pleomorphic, obligately intracellular bacteria that reside and propagate within host membrane‐derived vacuoles in the host cell cytoplasm. Like other rickettsiae, members of the
Anaplasmataceae
have a reduced genome size and rely on host cell machinery for survival. As with anaplasmosis, the spectrum of clinical presentations of
Ehrlichia chaffeensis
ehrlichiosis ranges from subclinical infection to life‐threatening disease.
Coxiella
Authors: Kersh Gilbert J. , Bleeker‐Rovers Chantal P.
Published: January 2025

Coxiella burnetii is a small, Gram‐negative rod that grows within a parasitophorous vacuole located in the cytoplasm of a host eukaryotic cell. It is a member of the
Gammaproteobacteria
. Transmission of C. burnetii to humans typically occurs by inhalation of the bacterium after it has been shed by animals. For chronic Q fever, where there is an identified nidus of infection, immunohistochemistry is an excellent method for the detection of C. burnetii antigens in tissue samples, particularly cardiac valve tissues that are colonized during chronic Q fever. Isolation of C. burnetii from human blood or tissue must be performed in a biosafety level 3 containment facility due to the low infectious dose of the agent and the potential for generating aerosols. Typing systems based on genetic differences between isolates are not standardized and are still undergoing development.
Susceptibility Test Methods: General Considerations
Authors: Turnidge John D. , Jorgensen James H. , Zimmer Barbara A.
Published: January 2025

Determination of the antimicrobial susceptibilities of significant bacterial isolates is one of the most important functions of the clinical microbiology laboratory. The main objective of susceptibility testing is to predict the likely outcome of treatment with the antimicrobial agents tested. Clinical microbiology laboratories can choose from among several conventional and novel methods for the performance of routine antibacterial susceptibility testing. A laboratory may choose to perform rapid detection of some resistance mechanisms by molecular testing or by rapid phenotypic testing. Breakpoints are the values that determine the categories of susceptibility. The approach to setting breakpoints varies by organization or regulatory body. Antimicrobial resistance is becoming widespread among a variety of clinically significant bacterial species. The advent of more readily available molecular techniques, especially whole‐genome sequencing, opens up the possibility of a major shift in the diagnostic laboratory, from phenotypic susceptibility testing to genotypic prediction of resistance.
Susceptibility Test Methods: Fastidious Bacteria
Authors: Humphries Romney M. , Bard Jennifer Dien
Published: January 2025

Most fastidious bacteria do not grow satisfactorily in standard
in vitro
susceptibility test systems that use unsupplemented media. This chapter summarizes the standard methods recommended by CLSI and EUCAST for antimicrobial susceptibility testing of
Streptococcus
spp.,
H. influenzae
,
N. gonorrhoeae
, and
N. meningitidis
. It summarizes methods for testing the infrequently isolated or fastidious bacteria included in CLSI guideline M45‐A3 and/or EUCAST clinical breakpoint tables. The chapter provides test methods and indications for testing and the reporting of results. Regional and global surveillance studies for antimicrobial resistance among respiratory pathogens including
H. influenzae
,
S. pneumoniae
, and
Moraxella catarrhalis
were conducted regularly. Several bacterial agents are identified as potential agents of bioterrorism by the CDC. The antimicrobial susceptibility patterns for most of these organisms are predictable, so susceptibility testing of naturally occurring isolates is often not necessary.
Human Immunodeficiency Viruses
Authors: Johnson Jeffrey , Masciotra Silvina , Owen S. Michele
Published: January 2025

Human immunodeficiency viruses (HIVs) are enveloped plus‐stranded RNA viruses. HIV viruses are classified based on phylogenetic relatedness of nucleotide sequences. Serum and plasma are the most common specimen types used for routine HIV antibody and antigen determinations in the laboratory. Because HIV can be isolated from the blood of the majority of HIV‐infected individuals, HIV culture was frequently utilized in the early years of the epidemic as a diagnostic or prognostic marker or for assessing the efficacy of antiviral therapy. Nucleic acid tests are needed for infant diagnosis because serologic tests are not useful for the detection of HIV infection in infants; maternal antibodies can persist in uninfected, HIV‐exposed infants until 18 months of age. Genotyping and variant calling information can identify nonsynonymous nucleotide mutations, termed drug resistance mutations, that code amino acid changes which can reduce the susceptibility of HIV to antiretroviral drugs.