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Metagenomics has been transformative in our understanding of the diversity and function of soil microbial communities. Applying long read sequencing to whole genome shotgun metagenomics has the potential to revolutionise soil microbial ecology through improved taxonomic classification, functional characterisation and metagenome assembly. However, optimisation of robust methods for long read metagenomics of environmental samples remains undeveloped. In this study, Oxford Nanopore sequencing using samples from five commercially available soil DNA extraction kits was compared across four soil types, in order to optimise read length and reproducibility for comparative long read soil metagenomics. Average extracted DNA lengths varied considerably between kits, but longer DNA fragments did not translate consistently into read lengths. Highly variable decreases in the length of resulting reads from some kits were associated with poor classification rate and low reproducibility in microbial communities identified between technical repeats. Replicate samples from other kits showed more consistent conversion of extracted DNA fragment size into read length and resulted in more congruous microbial community representation. Furthermore, extraction kits showed significant differences in the community representation and structure they identified across all soil types. Overall, the QIAGEN DNeasy PowerSoil Pro Kit displayed the best suitability for reproducible long-read WGS metagenomic sequencing, although further optimisation of DNA purification and library preparation may enable translation of higher molecular weight DNA from other kits into longer read lengths. These findings provide a novel insight into the importance of optimising DNA extraction for achieving replicable results from long read metagenomic sequencing of environmental samples.

Hydatidosis, also known as cystic echinococcosis, is a widespread zoonosis, caused by a tapeworm of the genus Echinococcus. It presents a significant public health concern, particularly in endemic areas. The occurrence of disseminated hydatid disease is uncommon, even in regions where it is endemic, with an incidence ranging from 1-8%. The definitive diagnosis relies on a parasitological method. In this work, we present an unusual case of disseminated hydatid disease that was diagnosed in the central parasitology-mycology laboratory of 'The Ibn Sina University Hospital'. This is a 21-year-old patient residing in a rural area, who presented with heaviness-type pain in the right hypochondrium, accompanied with nausea and vomiting. During the examination, the patient mentioned the contact with dogs. Abdominal radiography (ultrasound and CT) revealed findings suggestive of multiple hydatid cysts located in the liver and peritoneum. This suspicion was confirmed by positive hydatid serology. After 9 months of treatment with albendazole, the patient underwent surgery for excision of the cysts shown on the x-ray, as well as other cysts incidentally discovered intraoperatively at the pelvic and rectal levels. All of the extracted specimens were sent to the parasitology laboratory. The direct examination, along with the viability test, revealed the presence of hooks and scolex of non-viable Echinococcus granulosus. Disseminated hydatidosis is a rare but serious presentation, and the positive diagnosis relies on several epidemiological, clinical, radiological and parasitological arguments. Medical and surgical treatments play a crucial role in determining the patient's prognosis.

Introduction. Enteric pathogens contribute significantly to morbidity in a developing country such as India. Early and prompt diagnosis of diarrhoeal diseases can reduce the mortality rate, particularly in children. The pattern of sensitivity to antimicrobials for the common pathogens can vary from time to time. The present study was conducted to study the pathogen distribution and antimicrobial susceptibility pattern during the study period (January 2010 to December 2023). Hypothesis/gap statement. Studying the changing trend in the antimicrobial sensitivity pattern of diarrhoeal pathogens over a decade can help to plan future treatment options. Aim. This study was undertaken to provide insights into the changing pattern of pathogen distribution and antimicrobial susceptibility for enteric pathogens over 14 years. Methods. A retrospective observational cohort analysis was conducted on all the stool pathogens isolated from the samples received in the microbiology department of a tertiary care hospital from 2010 to 2023. The demographic details, stool microscopy, culture reports, and antimicrobial susceptibility patterns were noted. Results. A total of 18 336 stool specimens were received in the microbiology laboratory between January 2010 and December 2023, of which 1354 specimens had diarrhoeal pathogens grown in culture. Out of these 1354 specimens, 591 (44%) had Salmonella, 471 (35%) Shigella, 181 (13%) Vibrio cholerae, and 80 (6%) Aeromonas species. Among these pathogens, susceptibility to ceftriaxone was seen in 93% (552 isolates) of Salmonella species, 89% (420 isolates) of Shigella species, and 95% (171 isolates) of Vibrio cholerae; 91% (73 isolates) of Aeromonas species were susceptible to chloramphenicol. Some major parasites were also observed on microscopy. Conclusion. Timely diagnosis of diarrhoeal pathogens can be life-saving for patients at the extremes of age, i.e. in children and the elderly. Pathogens can exhibit a changing susceptibility pattern to antibiotics, which should be regularly observed to plan future therapy.

The string test is a screening method for detecting hypervirulent Klebsiella pneumoniae (hvKp). Agar media are used for string tests; however, the effect of the type of media on the test results remains unclear. We aimed to determine the optimal agar medium and cutoff value for the string test. We performed the string test on 99 Klebsiella strains using different agar media: sheep blood, chocolate, Drigalski's and MacConkey. The diagnostic accuracy was calculated in concordance with the rmpA, rmpA2 or iucA gene levels. The diagnostic accuracy rates for sheep blood, chocolate, Drigalski's and MacConkey agar were 0.79, 0.75, 0.73 and 0.64, respectively. When the cutoff was changed from 5 to 10 mm, the diagnostic accuracy rate for sheep blood agar decreased from 0.79 to 0.65. Our findings suggest that the type of agar medium impacts the string test results and sheep blood agar with a 5-mm cutoff is the optimal condition for detecting hvKp.

Staphylococcus aureus has been involved in transfusion-transmitted fatalities associated with platelet concentrates (PCs) due to its heightened pathogenicity enhanced by genome-encoded virulence and antibiotic resistance genes. This may be facilitated by mobile genetic elements (MGEs) that can cause rearrangements. Several factors contribute to S. aureus virulence, including the type VII secretion system (T7SS), composed of six core genes conserved across S. aureus strains. In this study, we conducted comparative genome analyses of five S. aureus isolates from PCs (CI/BAC/25/13 /W, PS/BAC/169/17 /W and PS/BAC/317/16 /W were detected during PCs screening with the BACT/ALERT automated culture system, and ATR-20003 and CBS2016-05 were missed during screening and caused septic transfusion reactions). Multiple alignments of the genomes revealed evidence of rearrangements involving phage Sa3int in PS/BAC/169/17 /W and PS/BAC/317/16 /W. While the former had undergone translocation of its immune evasion cluster (IEC), the latter had lost part of the phage, leaving behind the IEC. This observation highlights S. aureus genome plasticity. Unexpectedly, strain CBS2016-05 was found to encode a pseudo-type VII secretion system (T7SS) that had lost five of the conserved core genes (esxA, esaA, essA, esaB and essB) and contained a 5' truncated essC. Since these genes are essential for the function of the T7SS protein transport machinery, which plays a key role in S. aureus virulence, CBS2016-05 probably compensates by recruiting other export mechanisms and/or alternative virulence factors, such as neu-tralizing immunity proteins. This study unravels genome rearrangements in S. aureus isolated from PCs and reports the first S. aureus isolate lacking conserved T7SS core genes.

Oesophageal aspergillosis is a rare occurrence primarily documented in hematologic malignancies, and only rarely occurring among patients with solid tumours. In this case report, we present the unique case of an 81-year-old Lebanese man who had a remarkable medical history, including four solid tumours. The patient sought medical attention due to dysphagia and weight loss, prompting a gastroscopic examination that revealed a necrotic abscess at the oesophagogastric junction. Initial treatment with fluconazole and esomeprazole was administered, but the recurrence of similar symptoms led to a repeat gastroscopy, unveiling a diagnosis of Aspergillus oesophagitis. Intravenous voriconazole was promptly initiated; however, the patient developed a significant pericardial effusion and expired, with Aspergillus species identified in the pericardial fluid prior to patient expiring. This exceptional case emphasizes the importance of considering oesophageal aspergillosis in cancer patients who present with refractory symptoms such as epigastric pain, dysphagia, nausea, and vomiting, despite symptomatic treatment. Our findings underscore the need for increased awareness and the inclusion of gastrointestinal endoscopy as part of the diagnostic approach for this rare but potentially life-threatening condition.

Acute respiratory infections (ARIs) are a serious public health concern across the world, causing considerable morbidity and mortality. Every year, around 13 million children under the age of five die. Approximately 95% of them are from developing nations, and ARIs are responsible for one-third of all deaths. Human Metapneumovirus (hMPV) is one of the causative agents associated with respiratory tract infections. There is lack of information about hMPV from the eastern region of Uttar Pradesh. At Indian Council of Medical Research- Regional Medical Research Centre, Gorakhpur (ICMR-RMRC, Gorakhpur) in Uttar Pradesh, India; we tested respiratory pathogens in under-five patients presenting with ARI and severe acute respiratory illness (SARI) through semi nested PCR. A total of 100 nasal and throat specimens were collected from the outdoor and indoor patient Departments (OPD) and (IPD) of Department of Paediatrics, BRD Medical College, Gorakhpur during February to April 2022. Out of 100 enrolled paediatric patients, 4(4%) were found to be hMPV positive. Among the patients who tested positive for hMPV, 25%(1/4) unfortunately died. The phylogenetic analysis of hMPV showed the close resemblance with the clade of Singapore and USA hMPV isolates. The study underlines the importance of hMPV as the cause of acute respiratory infections in children and the highlight the need for routine testing for this virus in laboratories. Further more comprehensive detailed study on various aspects of hMPV in this area is needed.

The coronavirus 2019 pandemic has highlighted the importance of physiologically relevant in vitro models to assist preclinical research. Here, we describe the adaptation of a human alveolus microphysiological system (MPS) model consisting of primary human alveolar epithelial and lung microvascular endothelial cells to study infection with SARS-CoV-2 at Biosafety Level 3 facility. This infection model recapitulates breathing-like stretch and culture of epithelial cells at the air-liquid interface and resulted in clinically relevant cytopathic effects including cell rounding of alveolar type 2 cells and disruption of the tight junction protein occludin. Viral replication was confirmed by immunocytochemical nucleocapsid staining in the epithelium and increased shedding of SARS-CoV-2 virus within 2 days post-infection, associated with changes in innate host immune responses. Together, these data demonstrate that, under the experimental conditions used in this work, this human alveolus MPS chip can successfully model SARS-CoV-2 infection of human alveolar lung cells.

The Bad Bugs Bookclub is a public engagement initiative that enables scientists (microbiologists) and non-scientists to discuss the role of infectious disease and microorganisms in novels of fiction. The bookclub began in 2009, but since 2020, the meetings have taken place online, enabling international membership and occasional author participation. The bookclub has been shown, through peer-reviewed publications, to have impact and value to its members. For each book (the number now exceeds 100), a reading guide (questions to provoke discussion) and a meeting report (narrative of the discussion) were produced. Previously hosted on a website, the reading guides from this rich archive and resource are now presented alongside this paper, which provides tips on how to run a similar reading group.

Present case report describes a case of an atypical oesophageal actinobacillosis in an adult cow presented to the university hospital with a history of inability to drink and swallow. Clinical examination revealed a five-inch swelling in the jugular groove. Skiagram revealed the presence of a small and slightly radio opaque round growth. Exploratory surgical excision of the growth was adapted as palliative treatment and the extirpated tissue was fixed in 10% buffered formalin. Histopathological examination revealed pyogranulomatous inflammation with radiating eosinophilic club shaped bodies surrounding small colonies of coccobacilli. Gram and Ziehl-Neelsen stains confirmed the presence of Gram-negative and non-acid-fast coccobacilli. Histopathology confirmed the pathognomonic lesion and proved to be a modality of choice for pathologists to reach at a diagnosis of atypical oesophageal actinobacillosis in a cow. After the exhaustive search of relevant literature on atypical actinobacillosis, the authors claim this to be the second report of oesophageal actinobacillosis worldwide.