Access microbiology最新文献

{"title":"A prospective study on the evaluation of a novel immunochromatographic card for the rapid detection of five carbapenemase enzymes in metallo-beta-lactamase producers.","authors":"Jyotsna Agarwal, Vikramjeet Singh, Avneesh Sharma, Manodeep Sen, Anupam Das","doi":"10.1099/acmi.0.001024.v3","DOIUrl":"10.1099/acmi.0.001024.v3","url":null,"abstract":"<p><p><b>Objective.</b> To evaluate the performance of a novel immunochromatographic (IC) card test (TRURAPID^® O.K.N.V.I. RESIST-5) for rapid detection of five carbapenemase enzymes in metallo-beta-lactamase (MBL)-producing organisms, compared to real-time PCR and an Advanced Expert System (AES). <b>Methods.</b> Clinically isolated 100 non-duplicates of multidrug-resistant Gram-negative bacilli expressing MBL production were tested using the novel IC card, real-time PCR and the Vitek-2 AES. Sensitivity, specificity and turnaround time were evaluated. <b>Results.</b> The novel IC card showed high sensitivity for detecting NDM (93%) and KPC (91.7%) carbapenemases, but lower sensitivity for OXA-48 (60%), VIM (67%) and IMP (33%) compared to PCR. It had a rapid turnaround time of 15-20 min versus 5-7 h for PCR and 18-22 h for AES. <b>Conclusion.</b> The novel IC card offers a rapid, cost-effective approach for detecting carbapenemases, particularly NDM and KPC, in clinical microbiology practice. It may be beneficial in resource-limited settings where these enzymes are prevalent. Considering the limited sensitivity for the IMP and VIM genes, this warrants confirmatory testing by PCR. Further evaluation is needed to assess its role as a screening or confirmatory test, especially during nosocomial outbreaks.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12451311/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145132974","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diagnostic stewardship - optimization of superficial wound swab cultures can reduce the environmental impact of the microbiology laboratory.","authors":"Callum Goolden, Robert J Shorten","doi":"10.1099/acmi.0.000977.v3","DOIUrl":"10.1099/acmi.0.000977.v3","url":null,"abstract":"<p><p><b>Introduction.</b> Optimization of diagnostic testing is essential for the sustainable delivery of laboratory services. To date, little consideration has been given to the potential benefits of diagnostic stewardship to laboratories looking to reduce their environmental footprint. <b>Hypothesis.</b> Implementing a pre-analytical diagnostic stewardship intervention for the testing of superficial wound swabs would result in a measurable reduction in the environmental footprint of the microbiology laboratory. <b>Aim.</b> To assess the consequential impact of a diagnostic stewardship intervention on test volume, carbon footprint and quantity of non-recyclable plastic waste generated. <b>Methodology.</b> Superficial wound swabs received in the absence of clinical details suggestive of active skin and soft tissue infection were rejected by the laboratory. The carbon footprint of testing was estimated using Publicly Available Specification 2050:2011 methodology in a cradle-to-grave, attributional life-cycle assessment within a defined system boundary. The mass of laboratory plastic waste was calculated through the accurate weighing of associated laboratory consumables. <b>Results.</b> The intervention resulted in a reduction of 35.77 kg CO₂e and 9.06 kg of unrecyclable plastic waste over an 8-day period without measurable patient harm. <b>Conclusion.</b> This study demonstrates, in relation to specific testing pathways, that the optimization of microbiology laboratory diagnostic testing can result in a reduction in greenhouse gas emissions and non-recyclable plastic waste generation without negatively impacting patient care.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12408188/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145002470","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A multi-centre study on epidemiology and clinical characteristics of human metapneumovirus infection in Sri Lanka from 2021 to 2024.","authors":"Shiyamalee Arunasalam, Ishani De Silva, Udeshika Sathgurupathi, Veranja Liyanapathirana, Wasana Kudagammana, Faseeha Noordeen, Thulani Pattiyakumbura, Saranga Sumathipala, Rohitha Muthugala","doi":"10.1099/acmi.0.001022.v3","DOIUrl":"10.1099/acmi.0.001022.v3","url":null,"abstract":"<p><p><b>Introduction.</b> Human metapneumovirus (hMPV), first identified in 2001, is one of the major respiratory pathogens causing acute respiratory tract infections (ARTIs). In Sri Lanka, data on epidemiology and clinical characteristics of hMPV infections are limited. In this study, we aimed to investigate the epidemiology and clinical characteristics of hMPV infection in adults and children with ARTIs in different locations in Sri Lanka from January 2021 to December 2023. <b>Methods.</b> A total of 1,582 respiratory samples from patients with ARTIs were enrolled from four tertiary care hospitals. Nasopharyngeal swab samples were subjected to real-time reverse transcriptase PCR to test for hMPV using a commercial multiplex assay. Demographic and clinical data were extracted from the patients' clinical records. A selected subset of positive samples was subjected to genomic sequencing using an amplicon-based approach with the Respiratory Pathogen ID/AMR Library Prep and Enrichment Kit using the Illumina platform. <b>Results.</b> hMPV infection was identified in 1.64% (26/1,582) of patients, with the majority being children under 5 years of age. The co-infection rate was 0.34% with other respiratory viruses. The most common clinical presentation in hMPV infection included acute upper respiratory tract infection with fever, cough and cold and sore throat. <b>Conclusion.</b> hMPV is an important respiratory pathogen in children, causing ARTIs. hMPV-infected patients showed a range of respiratory symptoms with varying severity ranging from common cold to life-threatening lower respiratory tract infections. Continuous surveillance on hMPV infection may help in monitoring the hMPV activity, which will help in tracking the emergence of hMPV infections.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12451297/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145133263","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Potential role of gut bacteria in the development of hepatocellular carcinoma.","authors":"Bingqing Yan, Yuchao Wang, Ziqi Wang, Ailong Huang, Xiuxiu Jin, Tiantian Jiang, Hong Xue, Zheyu Shen, Shifang Wang, Haiyan Xu, Renfei Zhu","doi":"10.1099/acmi.0.000859.v6","DOIUrl":"10.1099/acmi.0.000859.v6","url":null,"abstract":"<p><p>Liver cancer is the fourth most deadly cancer, and early detection and timely treatment apparently play a crucial role in it. Intestinal bacteria affect the development of liver cancer through various pathways. In this study, the gut bacteria of liver cancer patients are analysed in detail by using metagenomic sequencing technology, and some of the bacterial species and metabolic pathways that may affect the development of liver cancer have been identified. Additionally, we identified bacterial factors that may impact key clinical indicators of the tumour. The findings of this study provide a scientific foundation for understanding the mechanisms underlying liver cancer development. This study freshened insights into clinical treatment strategies for liver cancer.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12369552/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144985104","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative evaluation of GeneXpert and reverse transcription polymerase chain reaction for SARS-CoV-2 diagnosis: a retrospective study.","authors":"Ashish William, Yogita Rai, Deepti Rawat, Sanjib Gogoi, Megh Singh Dhakad, Manoj Jais, Ravinder Kaur","doi":"10.1099/acmi.0.000643.v5","DOIUrl":"10.1099/acmi.0.000643.v5","url":null,"abstract":"<p><p><b>Background.</b> The novel coronavirus disease 2019 (COVID-19) has highlighted vulnerabilities in healthcare systems and has brought the world to a standstill single-handedly. Diagnostic testing for COVID-19 is critical for understanding epidemiology, contact tracing, case management and controlling the transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Real-time reverse transcription PCR test, the gold standard test, involves fairly complex steps and takes nearly 24-48 h to generate the results. GeneXpert is a rapid nucleic-acid-detection-based test approved by the Indian Council of Medical Research, which can shorten the turnaround time significantly. <b>Aim.</b> The study aimed to compare the performance of GeneXpert against the gold standard real-time reverse transcription PCR for SARS-CoV-2. <b>Materials and methods.</b> This retrospective study was conducted at a tertiary care centre from 25 March 2020 to 8 December 2020. The nasopharyngeal/oropharyngeal swabs that were sent to the Viral Research and Diagnostic Laboratory for testing of SARS-CoV-2 by GeneXpert [cartridge-based nucleic acid amplification test (CBNAAT)] were included for the study. A total of 270 samples (220 samples positive and 50 samples negative for SARS-CoV-2 by GeneXpert) were simultaneously tested for real-time reverse transcription PCR. Real-time reverse transcription PCR was considered as gold standard test (reference) for calculating the sensitivity and specificity of the GeneXpert (CBNAAT) test. <b>Results.</b> Out of the total samples tested (<i>n</i>=270) for SARS-CoV-2, 220 were positive, and 50 were negative for SARS-CoV-2 by GeneXpert. Among 220 GeneXpert SARS-CoV-2-positive samples, 118 (53.64%) were also positive by real-time reverse transcription PCR, while 102 (46.36%) showed negative results by real-time reverse transcription PCR. However, 50 GeneXpert negative samples showed 100% agreement with real-time reverse transcription PCR, i.e. they were also negative by real-time reverse transcription PCR. The GeneXpert sensitivity and specificity for COVID-19 were seen to be 100% (95% CI: 96.92-100%) and 32.89% (95% CI: 25.50-40.97%), respectively, as compared to the gold standard real-time reverse transcription PCR test. The positive predictive value and negative predictive value of GeneXpert for COVID-19 were found to be 53.64% and 100%, respectively. <b>Conclusion.</b> This study highlights that the GeneXpert test is highly sensitive and found to be useful in emergency and challenging situations for rapidly ruling out negative cases. However, due to its relatively low specificity, positive results should be confirmed with real-time reverse transcription PCR. Therefore, it can serve as a valuable tool for patients requiring urgent care by facilitating early diagnosis and management of COVID-19, ultimately contributing to preventing morbidity and mortality.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12369551/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144985095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Implementation of project management methodologies in microbiology research laboratories.","authors":"Piotr R Stempinski, Heather M Lamb, Jiaqi Qian","doi":"10.1099/acmi.0.001032.v3","DOIUrl":"10.1099/acmi.0.001032.v3","url":null,"abstract":"<p><p>The increasing complexity and collaborative nature of scientific research projects underscore the need to implement project management practices to manage resources and funding, ensure data quality and prevent delays in project progress. Here, we introduce three major project management methodologies, including agile, waterfall and hybrid approaches, and explore their suitability for biological and microbiological research laboratories. Variables that may influence choosing an appropriate strategy for managing projects are considered, including the size and experience of a research group. In the following article, we provide an overview of the five major stages of project planning and execution, focusing on implementing each of the discussed strategies in the research laboratory. Furthermore, we discuss the composition of the research team and outline the responsibilities assigned to each team member based on their role in the project. This paper highlights potential risks and challenges that may negatively impact research progress, underscoring the need for proper project planning. Applying proper project management methodologies is often neglected in academic research, leading to serious delays and waste of valuable resources.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12365402/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144985038","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Infection caused by a cryptic fungal species, Blastomyces gilchristii, in a tiger.","authors":"Sreekumari Rajeev, Porsha Reed, Alejandro Llanes, Rebekah Jones, Andrew Cushing, Linden E Craig, Brian Johnson","doi":"10.1099/acmi.0.001011.v3","DOIUrl":"10.1099/acmi.0.001011.v3","url":null,"abstract":"<p><p>Blastomycosis is a serious fungal disease affecting humans and animals. It is typically caused by the thermally dimorphic fungus, <i>Blastomyces dermatitidis</i>. In this report, we describe an infection caused by the cryptic fungal species, <i>Blastomyces gilchristii</i>, in a tiger (<i>Panthera tigris</i>).</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12365400/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144985119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Functional characterization of engineered bacterial biosensors for kynurenine detection.","authors":"Pisit Charoenwongwatthana, Halah Ahmed, Wojciech Cajdler, Jamie Coulter, Chien-Yi Chang","doi":"10.1099/acmi.0.001031.v5","DOIUrl":"10.1099/acmi.0.001031.v5","url":null,"abstract":"<p><p>The kynurenine (KYN) pathway is the major catabolic pathway for tryptophan in humans, producing several metabolites that influence health. In clinical settings, KYN levels serve as a valuable biomarker for the diagnosis and prognosis of inflammatory and neurological diseases. Nevertheless, KYN detection relies on mass spectrometry analysis, which requires specialized knowledge and expertise with high operational costs. The bacterial biosensor presents as a promising tool for rapid and cost-effective targeted substance detection due to its ease of genetic modification. Therefore, this study aimed to develop an engineered bacterial biosensor by integrating a genetic module in a plasmid designed for KYN detection harboured in an <i>Escherichia coli</i> chassis. The KYN biosensing component in the genetic module encodes a KYN pathway regulator (KynR) from <i>Pseudomonas aeruginosa</i>, driven by the <i>P_BAD</i> arabinose-inducible promoter. Upon expression, KynR would bind to the exogenous KYN and the bacterial responding <i>kyn</i> promoter to express the downstream green fluorescent protein gene to emit a fluorescence signal. However, despite successful induction by arabinose and the presence of KYN, biosensors with different gene orientations and genetic components failed to produce a significant fluorescence signal. These findings suggest that the sensitivity of <i>P. aeruginosa</i> KynR is insufficient to detect physiological levels of KYN. Further exploration of alternative biological sensing components is warranted.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12451312/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145133252","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genotypic study of isolated resistance to isoniazid in the Mycobacterium tuberculosis complex in a Moroccan hospital.","authors":"Amine Amri, Elmostafa Benaissa, Yassine Benlahlou, Fatna Bsaibis, Adil Maleb, Mariama Chadli, Mostafa Elouenass","doi":"10.1099/acmi.0.000928.v5","DOIUrl":"10.1099/acmi.0.000928.v5","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;b&gt;Introduction.&lt;/b&gt; Despite the introduction 40 years ago of effective and low-cost treatment for tuberculosis (TB), morbidity and mortality from this disease remain substantial worldwide. According to the WHO, TB is once again the leading cause of death worldwide from a single infectious agent. In 2023, TB caused ~1.25 million deaths, surpassing COVID-19. In Morocco, the number of new TB cases rose from 30,897 in 2017 to 35,000 in 2019, highlighting a concerning upward trend that underscores the persistent challenge TB poses to the country's public health system. The incidence of multidrug-resistant (MDR) or rifampicin (RIF)-resistant TB was estimated at 1.7 per 100,000 inhabitants. Isoniazid (INH) is a cornerstone of first-line TB treatment, and resistance to it, even in the absence of RIF resistance, is associated with delayed treatment response, higher rates of treatment failure or relapse and increased risk of progression to MDR-TB if not promptly identified and appropriately managed. Moreover, current diagnostic algorithms in many settings, including Morocco, may miss INH monoresistance due to their reliance on rapid molecular tests that primarily detect RIF resistance, further emphasizing the emerging threat of drug-resistant TB. Despite this, national data on INH monoresistance remain scarce. Given the increasing burden of TB and the critical importance of early detection of drug resistance, it is essential to better understand patterns of resistance beyond RIF. It is within this context that we conducted the present study, which aims to investigate INH resistance in TB cases (pulmonary or extrapulmonary, new or previously treated) over a period of 3 years. &lt;b&gt;Materials and methods.&lt;/b&gt; This is a retrospective study conducted at the Bacteriology Department of Mohammed V Military Instruction Hospital over a period of 3 years. Data were collected via the laboratory information system. Clinical samples underwent treatment using both conventional bacteriological methods and molecular techniques. The study of resistance to major anti-TB drugs was performed using the reverse hybridization technique, specifically the HAIN method (GenoType&lt;sup&gt;®&lt;/sup&gt; MTBDR plus by Hain Lifescience). Statistical analysis was performed using IBM SPSS Statistics 19 and Microsoft Excel 2019. &lt;b&gt;Results.&lt;/b&gt; The study involved 464 patients treated for pulmonary and extrapulmonary TB, including both new cases and those previously treated with positive cultures. The mean age of the patients was 42.2 years, with a range from 8 to 88 years. There was a predominance of males at 74%, with a sex ratio of 2.8. Pulmonary sputum samples accounted for 84.8% of the cases, whereas extrapulmonary samples represented only 15.2%, and the positivity rates for direct examination and culture across all samples were 74% and 100%, respectively. INH resistance had a prevalence of 9% (43 out of 464). Genetic mutations observed indicated that 63% of the clinical isolates resistant to","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12451310/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145133312","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Parapipe: a pipeline for parasite next-generation sequencing data analysis applied to Cryptosporidium.","authors":"Arthur V Morris, Guy Robinson, Rachel Chalmers, Simone Cacciò, Thomas Connor","doi":"10.1099/acmi.0.000993.v3","DOIUrl":"10.1099/acmi.0.000993.v3","url":null,"abstract":"<p><p><i>Cryptosporidium</i>, a protozoan parasite of significant public health concern, is responsible for severe diarrhoeal disease, particularly in immunocompromised individuals and young children in resource-limited settings. Analysis of whole-genome next-generation sequencing (NGS) data is critical in improving our understanding of <i>Cryptosporidium</i> epidemiology, transmission and diversity. However, effective analysis of NGS data in a public health context necessitates the development of robust, validated computational tools. We present Parapipe, an ISO-accreditable bioinformatic pipeline for high-throughput analysis of NGS data from <i>Cryptosporidium</i> and related taxa. Built using Nextflow DSL2 and containerized with Singularity, Parapipe is modular, portable, scalable and designed for use by public health laboratories. Using both simulated and real <i>Cryptosporidium</i> datasets, we demonstrate the power of Parapipe's genomic analysis for generating epidemiological insights. We highlight how whole-genome analysis yields substantially greater phylogenetic resolution than conventional <i>gp60</i> molecular typing in <i>Cryptosporidium parvum</i>. Uniquely, Parapipe facilitates the integration of mixed infection analysis and phylogenomic clustering with epidemiological metadata, representing a powerful tool in the investigation of complex transmission pathways and identification of outbreak sources. Parapipe significantly advances genomic surveillance of <i>Cryptosporidium</i>, offering a streamlined, reproducible analytical framework. By automating a complex workflow and delivering detailed genomic characterization, Parapipe provides a valuable tool for public health agencies and researchers, supporting efforts to mitigate the global burden of cryptosporidiosis.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12451305/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145133275","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}