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Molecular Microbial Diagnostic Methods: Pathways to Implementation for the Food and Water Industry was developed by recognized and experienced highlevel scientists.It's a comprehensive and detailed reference that uncovers industry needs for the use of molecular methods by providing a brief history of water and food analysis for the pathogens of.

This manual is a practical guide, for use by laboratory workers in health centres and district hospitals, to the procedures to be followed in obtaining specimens, isolating and identifying bacteria, and assessing their resistance to antibiotics. It covers bacteriological investigation of blood, cerebrospinal fluid, urine, stool, sputum, pharyngeal and genital specimens, and purulent exudates. Particular attention is given to the need for quality control of all laboratory procedures. A list of media and reagents needed for the isolation and identification of the most common bacterial pathogens is included, together with an indication of their relative importance for the intermediary laboratory. This list is intended for adaptation to local circumstances. This second edition has been updated in many areas, including a greatly enhanced section on stool specimens and a new section on serological tests.

Semen analysis is the cornerstone of male fertility evaluation with WHO guidelines providing the basis for procedural standardization and reference values worldwide. The first WHO manual was published in 1980, and five editions have been subsequently released over the last four decades. The 6th Edition was published in July 2021. In this review, we identify the key changes of this 6th Edition. Additionally, we evaluate the utility of this 6th Edition in clinical practice using SWOT (strengths, weaknesses, opportunities, and threats) analysis. This new Edition has made the analysis of basic semen parameters more robust, taking into account the criticisms and grey areas of the previous editions. The tests assessing sperm DNA fragmentation and seminal oxidative stress are well-described. The main novelty is that this latest edition abandons the notion of reference thresholds, suggesting instead to replace them with “decision limits”. While this seems attractive, no decision limits are proposed for either basic semen parameters, or for extended or advanced parameters. This critical review of the 6th Edition of the WHO laboratory manual combined with a SWOT analysis summarizes the changes and novelties present in this new Edition and provides an in-depth analysis that could help its global use in the coming years.

Background Human brucellosis is an infectious zoonotic disease caused by Brucella spp. It is one of the most public health problems that remains largely neglected in developing counties, including Saudi Arabia. Brucellosis is particularly prevalent among rural people who have constant contact with livestock. Methods A cross-sectional sero-epidemiological study conducted in Aseer Central Hospital, South Saudi Arabia, between 2014 and 2018 among 7567 patients. Serum samples were analyzed for Brucella antibodies using slide agglutination test. Serology results and patient’s demographic data were analyzed by GraphPad Prism. Results were presented as mean ± SEM and differences between two groups were assessed by t-test and p  < 0.05 was considered significant. Results The prevalence of brucellosis among the admitted suspected 7567 cases was 12.8% (10.4–15.7%; CI 95%). The highest prevalence rate was detected during 2015, the rate decreased to the lowest level during the last three years ( p  < 0.05). Higher rate of brucellosis was observed among males than females (p < 0.05) and most cases were reported during summer season (p < 0.05). The highest prevalence rate was observed in age group 21–40 year old (40.5%) followed by 41–60 years (27.7%). The lowest prevalence rate was noticed in old and young children (15 and 3%, respectively). Cross-transmission of brucellosis was seen within family (1%) and high titers (> 1280) was noticed in 22% of the hospitalized patients. The major symptoms were fatigue, hyperhidrosis, fever and joint pain. Conclusion Our findings showed a high prevalence of human brucellosis among suspected patients in Aseer region. This indicates that clinical suspicion is a valid criterion and the endemic nature of the disease. The disease status requires early laboratory detection and confirmation to start prompt treatment to decrease patients suffering.

Background: Faecal microbiota transplantation (FMT) is a highly effective treatment for Clostridioides difficile infection. Its use is backed by solid evidence, but application methods differ. Encapsulated FMT is a non-invasive, patient-friendly and scalable application method that may be preferred over colonoscopy or nasoduodenal tube application. Objectives: We describe a detailed protocol, the Glyprotect protocol, for producing glycerol-based capsules to increase FMT accessibility. Design: Using iterative quality improvement methods, we developed and validated the Glyprotect protocol as a reproducible protocol for cryopreserving minimally processed donor faeces in a standard hospital laboratory setting. Methods: We describe detailed standard operating procedures for producing glycerol-based capsules, including all necessary materials and troubleshooting guidelines. Capsule integrity was tested at various temperatures and pH levels. Flow cytometry was used to measure microbiota counts and dose accuracy. Results: The Glyprotect protocol has been used for more than 2500 capsule-based FMT treatments and complies with European tissue and cell standards. The protocol is optimised to preserve microbes and minimise modulation of the donated microbiota by removing debris and water, which also reduces the number of capsules needed per FMT treatment. The intestinal microbiota is preserved in glycerol for cryoprotection and to prevent capsule leakage. Each capsule contains 650 µL microbe–glycerol mass, estimated to contain an average of 2.5 × 108 non-specified bacteria. Conclusion: The Glyprotect protocol enables hospitals and tissue establishments to set up capsule production in a standard laboratory, improving patients’ access to FMT. The protocol facilitates the scalability of FMT services because capsule FMT is less time-consuming and less expensive than liquid-suspension FMT applied by colonoscopy or nasojejunal tube. Trial registration: Not applicable. Plain language summary A protocol for production of encapsulated donor faeces for faecal microbiota transplantation We provide a detailed description of how to produce encapsulated donor faeces for faecal microbiota transplantation (FMT). FMT is a highly effective treatment for diseases where the intestinal microbiota is compromised, in particular Clostridioides difficile infection. Encapsulated application is patient-friendly and non-invasive, but protocols for the production of FMT capsules have not been published or are not reproducible. We here provide detailed guidance for standard-equipped hospital laboratories to enable capsule production under the current regulatory framework for substances of human origin in Europe. The dissemination of this protocol will increase patients’ access to a life-saving therapy.

\"A Concise Manual of Pathogenic Microbiology is a quick and concise source of information on the causal agents of common infectious diseases. Divided into chapters based on broad taxonomic groupings or similarities between the causal agents, A Concise Manual of Pathogenic Microbiology lists important pathogenic taxa in each group, their natural habitats, the diseases they cause, microbiological highlights, laboratory diagnosis, and measures of prevention and control, including availability of vaccines and effective therapeutic agents\"--

The ability to prepare sterilized media is a critical capability of any microbiology lab. Diagnostic labs in low-resource settings, which lack autoclave facilities, are therefore severely limited in their ability to perform basic assays such as bacterial culture or biochemical tests. This investigation aimed to validate the use of a commercially available pressure cooker as an autoclave substitute to produce agar plates. First, a Geobacillus stearothermophilus biological indicator was used to confirm adequate sterilization. Next, the colony morphology of several important bacterial species were compared on MacConkey and 5% sheep’s blood agar plates prepared using the pressure cooker with those made in an autoclave. Finally, disc diffusion susceptibility testing was performed to determine whether the sterilization method impacts the inhibitory zone diameters. Overall, the morphology of colonies was similar on media prepared in both ways; key phenotypic characteristics (lactose fermentation, colour, shape, hemolysis and smell) were the same. Kirby-Bauer disc diffusion test results were nearly identical. These findings indicate that a commercially available pressure cooker may be suitable to prepare media in low-resource laboratories.

Developing and deploying new diagnostic tests are difficult, but the need to do so in response to a rapidly emerging pandemic such as COVID-19 is crucially important. During a pandemic, laboratories play a key role in helping healthcare providers and public health authorities detect active infection, a task most commonly achieved using nucleic acid-based assays. While the landscape of diagnostics is rapidly evolving, PCR remains the gold-standard of nucleic acid-based diagnostic assays, in part due to its reliability, flexibility and wide deployment. To address a critical local shortage of testing capacity persisting during the COVID-19 outbreak, our hospital set up a molecular-based laboratory developed test (LDT) to accurately and safely diagnose SARS-CoV-2. We describe here the process of developing an emergency-use LDT, in the hope that our experience will be useful to other laboratories in future outbreaks and will help to lower barriers to establishing fast and accurate diagnostic testing in crisis conditions.