Journal of medical microbiology最新文献

{"title":"Use of TaqMan array card to investigate bacterial isolates in diabetic foot ulcers.","authors":"Sarah Johnson-Lynn, Martin D Curran, Candice Allen, Katherine M Webber, Mailis Maes, Matthew Routledge, David A Enoch, Andrew H N Robinson, Anthony P Coll","doi":"10.1099/jmm.0.002113","DOIUrl":"https://doi.org/10.1099/jmm.0.002113","url":null,"abstract":"<p><p>Diabetic foot disease is a major public health problem, with an annual National Health Service (NHS) expenditure exceeding £1 billion. Infection increases the risk of major amputation fivefold. Due to the polymicrobial nature of diabetic foot infections, it is often difficult to correctly and rapidly isolate pathological organisms with conventional culture techniques and deliver appropriate narrow-spectrum antimicrobials. Rapid DNA-based technology, using multi-channel arrays, offers a quicker alternative and has previously been used effectively in other settings. We undertook a prospective cohort study of deep tissue samples taken from diabetic foot ulcers (DFUs), comparing samples processed by conventional culture and real-time PCR TaqMan array card (TAC). Fifty samples were taken from 39 patients. The ulcers were of variable chronicity prior to sampling (range: 1-113 weeks) and were sited on the heel (3), midfoot (6) and forefoot (41). TAC results were available an average of 4.3 days earlier than culture results. Seventeen samples had the same organisms detected on culture and TAC. Sixteen of these 17 had additional organisms detected by TAC. The most frequent organisms detected by TAC that were not detected by culture were staphylococci, <i>Enterobacter</i> spp., <i>Pseudomonas</i> spp. and fungi. TAC rapidly and accurately detects clinically relevant organisms from DFUs, providing earlier results than standard culture. This may enable earlier rationalization of antimicrobials and infection control interventions.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"75 4","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13089970/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147719317","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":"Face mask sampling for the detection of microbes in expelled aerosols and the impact of airway clearance on microbial yield in children with cystic fibrosis: a feasibility trial.","authors":"Naomi A Dayman, Deepa Patel, Anika Wisniewska, Eve Fletcher, Molla Imaduddin Ahmed, Deborah Modha, Michael R Barer, Erol A Gaillard","doi":"10.1099/jmm.0.002150","DOIUrl":"10.1099/jmm.0.002150","url":null,"abstract":"<p><p><b>Background.</b> Early identification of pulmonary exacerbations is vital for the management of cystic fibrosis (CF). Non-invasive airway sampling in preschool children can be inaccurate. Face mask sampling (FMS) is a novel non-invasive approach that can be used to assess microbial airway pathogens in patients with CF.<b>Methods.</b> Prospective cross-sectional study in children with CF. Children wore a suitably sized face mask fitted with two strips of a polyvinyl alcohol sampling matrix for a period of 15 min. Routine microbiology sampling using cough swab, sputum and/or bronchoalveolar lavage was completed following FMS. Children then completed their routine airway clearance with their physiotherapist. Following this, a separate face mask was worn for a further 15 min, after which further routine microbiology sampling (cough swab or sputum) was completed. The face masks were stored at room temperature before transfer and processing in the laboratory to quantify bacterial burden and identify key pathogens such as <i>Mycobacterium abscessus</i> and <i>Pseudomonas aeruginosa</i>.<b>Results.</b> Eleven children (six male, median age 12 years, range 1-16 years), from the Leicester CF cohort were included. All patients tolerated the FMS. Nine face mask samples from 11 participants isolated respiratory pathogens, including <i>M. abscessus</i> (<i>n</i>=3). <i>P. aeruginosa</i> was not detected on face mask samples. There was a trend towards an increase in microbial yield (prGen16s) following airway clearance (<i>n</i>=5), but this did not reach statistical significance.<b>Conclusions.</b> FMS systems are feasible for children and young people with CF. They may provide an effective method to detect exhaled lower airway pathogens including non-tuberculous mycobacteria. The effect of physiotherapy on the exhaled microbiome needs to be explored further.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"75 4","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13061336/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147640948","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":"Dynamic procalcitonin-guided antibiotic stewardship among cancer patients in the UK.","authors":"Dowan Kwon, Philip Williams, Helen Winter","doi":"10.1099/jmm.0.002145","DOIUrl":"10.1099/jmm.0.002145","url":null,"abstract":"<p><p><b>Introduction.</b> Procalcitonin has been recognized as a tool for effective antibiotic stewardship to reduce unnecessary antibiotic use; however, its effectiveness remains unknown in the oncology setting, where infections are common and antibiotics are frequently prescribed.<b>Gap statement.</b> The utility of procalcitonin for effective antibiotic stewardship in people with solid organ cancers is unknown.<b>Aim.</b> To evaluate the role of procalcitonin dynamics in solid organ cancer patients with suspected bacterial infections in predicting clinical outcomes and guiding antibiotic therapy decisions.<b>Methodology.</b> A single-centre evaluation was conducted at the Bristol Haematology and Oncology Centre, studying consecutive admissions of adult patients with solid organ cancer over a 3-month period. In a population in which serum procalcitonin levels were sporadically measured to guide antibiotic therapy, they were measured as standard care on admission and at 48 hours for patients admitted with a suspected bacterial infection. A threshold of 0.25 ng ml^-1 was used to distinguish between low and high procalcitonin levels. Cases that had persistently low procalcitonin levels were retrospectively analysed for the potential identification of patients who could have had their antibiotic treatment ceased 48 hours into the antibiotic course.<b>Results.</b> Seventy-seven cases with procalcitonin readings were recorded. Seventy (90.9%) cases received intravenous antibiotics during admission. Twenty-seven (35.1%) cases had persistently low procalcitonin, defined as <0.25 ng ml^-1 on consecutive measurements, interpreted as unlikely to have bacterial infection as suggested from previous literature. No objective microbiological evidence of bacterial infection was observed in these cases. Retrospective clinician reviews of the 27 cases showed antibiotic therapy for 16 of the 27 cases could have been stopped 48 h into the admission, equivalent to a total reduction of up to 83/778 (10.7%) antibiotic days.<b>Conclusion.</b> Procalcitonin could provide a helpful adjunct for clinicians to consider antibiotic stewardship and help reduce unnecessary antibiotic use in the oncology setting.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"75 4","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13056215/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147635570","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 murine sinonasal infection model recapitulates key features of clinical chronic rhinosinusitis.","authors":"Emily J Vanderpool, Kendra P Rumbaugh","doi":"10.1099/jmm.0.002152","DOIUrl":"10.1099/jmm.0.002152","url":null,"abstract":"<p><p><b>Introduction.</b> Chronic rhinosinusitis is a difficult-to-treat, recurrent inflammatory condition of the nose and paranasal sinuses with global prevalence. Despite its impact on patient quality of life and its cost to the healthcare system, the pathogenesis of chronic rhinosinusitis (CRS) remains poorly understood. Additionally, while the presence of bacteria in CRS has been confirmed by numerous studies, their influence on disease symptoms is unclear. Disease-relevant models can help resolve these questions.<b>Hypothesis.</b> We hypothesized that bacterial inoculation could drive CRS-associated symptoms in a murine model.<b>Aim.</b> To characterize host-microbe interactions in a murine model of sinonasal bacterial infection.<b>Methodology.</b> <i>Staphylococcus aureus</i> and/or <i>Pseudomonas aeruginosa</i> were inoculated in the nasal cavity of Swiss Webster, C57Bl/6, Balb/c and B6.Cg-<i>Prkdc</i> ^scid/SzJ severe combined immunodeficient (SCID) mice. Systemic cytokine response was quantified with a multiplexed enzyme-linked immunosorbent assay, and local histological alterations were quantified using haematoxylin and eosin as well as Alcian Blue-Periodic Acid-Schiff-stained sinonasal sections.<b>Results.</b> Intranasal bacterial inoculation induced symptoms of CRS in murine sinonasal cavities. Dual species inoculation generated a unique response compared to single species. Repeated inoculations did not result in bacterial clearance from immunological priming. While Swiss Webster and C57Bl/6 mice demonstrated the greatest magnitude of responses, Balb/c mice demonstrated a protective response, generally downregulating cytokines and attempting to prevent further tissue damage. SCID mice demonstrated effective clearance of <i>P. aeruginosa</i> by innate immunity, but maintenance of <i>S. aureus</i>.<b>Conclusion.</b> Pathogenic bacteria are able to persist and drive the development of symptoms associated with clinical CRS in a murine model. Bacterial interactions and host factors influence CRS-associated inflammation. By investigating host responses from a number of mouse genetic backgrounds, the heterogeneity of disease presentation in CRS can be modelled, and strategies for infection management can be evaluated as potential therapeutic targets.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"75 4","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13061426/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147641024","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":"Comparable efficacy of bictegravir/emtricitabine/tenofovir alafenamide and doravirine/lamivudine/tenofovir disoproxil fumarate in therapy-naive Human Immunodeficiency Virus adults with very high baseline viraemia.","authors":"Leonardo Calza, Maddalena Giglia, Claudio Rigamonti, Alberto Zuppiroli, Domenico Marzolla, Isabella Bon, Pierluigi Viale","doi":"10.1099/jmm.0.002119","DOIUrl":"10.1099/jmm.0.002119","url":null,"abstract":"<p><p><b>Introduction.</b> Clinical trials and observational studies of co-formulated regimens bictegravir/emtricitabine/tenofovir alafenamide (BIC/F/TAF) and doravirine/lamivudine, tenofovir disoproxil fumarate (DOR/3TC/TDF) demonstrated potent efficacy in both antiretroviral therapy-naive and -experienced patients, but data on efficacy in naive people with high-level Human Immunodeficiency Virus (HIV) viraemia are still lacking.<b>Hypothesis.</b> BIC/F/TAF and DOR/3TC/TDF have comparable effectiveness in naive people with high-level viraemia.<b>Aim.</b> To compare the effectiveness of BIC/F/TAF and DOR/3TC/TDF in naive people with high-level viraemia.<b>Methodology.</b> We performed a retrospective cohort study of adult people living with HIV, who were naive to antiretroviral therapy, had baseline HIV-1 RNA >500,000 copies ml^-1 and initiated the co-formulated regimen BIC/F/TAF or DOR/3TC/TDF. Virological efficacy, changes in immunological parameters and safety profiles after 12 months of treatment were evaluated.<b>Results.</b> Inclusion criteria were met by 78 patients: 43 in the BIC/F/TAF group and 35 in the DOR/3TC/TDF group. Baseline characteristics were similar in both groups: median age was 45.2 years, median HIV RNA was 5.95 log₁₀, median CD4 T lymphocyte count was 383 cells mm^-3 and 22 patients (28%) had HIV RNA >10⁶ copies ml^-1. After 12 months, virological efficacy was comparable: HIV RNA <20 copies ml^-1 was obtained in 40 patients (93%) in the BIC/F/TAF group and in 31 (89 %) in the DOR/3TC/TDF group. The median increase in CD4 T lymphocyte count was comparable between groups (+139 and +117 cells mm^-3, respectively), such as incidence of adverse events, while median increase in low-density lipoprotein cholesterol and weight gain was significantly greater in the BIC/F/TAF group (weight change, +1.64 kg vs. +0.85 kg; <i>P</i>=0.013).<b>Conclusion.</b> In this real-life cohort, BIC/F/TAF and DOR/3TC/TDF showed high and comparable virological efficacy in naive patients with baseline HIV RNA above 500,000 copies ml^-1.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"75 4","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13068290/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147647866","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":"Corrigendum: <i>Enterococcus faecalis</i> co-cultured with oral cancer cells exhibits higher virulence and promotes cancer cell survival, proliferation, and migration: an <i>in vitro</i> study.","authors":"Fida Fathima, Yuvarajan Subramaniyan, Akshatha Rai, Punchappady Devasya Rekha","doi":"10.1099/jmm.0.002141","DOIUrl":"10.1099/jmm.0.002141","url":null,"abstract":"","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"75 3","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12987659/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147461551","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":"Differences in gut microbiota and faecal metabolomics characteristics in preterm infants with feeding intolerance.","authors":"Jinya Wang, Jiejing Zhang, Ji Wang, Danqiong Lu, Shiwei Lai, Xinyu Wang","doi":"10.1099/jmm.0.002138","DOIUrl":"10.1099/jmm.0.002138","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;b&gt;Introduction.&lt;/b&gt; Feeding intolerance (FI) is one of the most common clinical issues in preterm infants, and there are currently no internationally unified diagnostic criteria.&lt;b&gt;Gap Statement.&lt;/b&gt; Screening valuable biomarkers and evaluating their diagnostic value for FI in preterm infants is of great significance.&lt;b&gt;Aim.&lt;/b&gt; This study aimed to identify and assess diagnostic biomarkers for feeding intolerance in preterm infants.&lt;b&gt;Methodology.&lt;/b&gt; This study included clinical data from 49 preterm infants admitted to a tertiary maternal and child health hospital in Zhejiang's coastal region (January to June 2024). Based on feeding assessments at day 21 postpartum recorded in electronic medical records, infants were divided into feeding-tolerant (FT, &lt;i&gt;n&lt;/i&gt;=34) and feeding-intolerant (FI, &lt;i&gt;n&lt;/i&gt;=15) groups. Patient data analysis incorporated maternal age, gestational age, parity, antibiotic use, pregnancy complications and neonatal factors (birth weight, Apgar scores, delivery/feeding methods, vomiting, abdominal distension, gastric residuals, kangaroo care and enema use). Faecal samples underwent microbiome and metabolomic profiling to identify diagnostic biomarkers.&lt;b&gt;Results.&lt;/b&gt; Baseline data showed no significant differences in maternal-infant characteristics between groups (&lt;i&gt;P&gt;&lt;/i&gt;0.05). Dynamic monitoring of feeding tolerance in 21-day-old preterm infants revealed that the incidence of vomiting, abdominal distension, abnormal intestinal morphology and gastric residual volume &gt;30% or &gt;2 ml kg&lt;sup&gt;-1&lt;/sup&gt; was significantly higher in the FI group than in the FT group (&lt;i&gt;P&lt;/i&gt;&lt;0.001), whereas there was no significant difference in the frequency of nasogastric feeding between the two groups (&lt;i&gt;P&lt;/i&gt;&gt;0.05). Microbial analysis revealed enrichment of &lt;i&gt;Escherichia&lt;/i&gt; (10.92%) and &lt;i&gt;Klebsiella&lt;/i&gt; (6.88%) in FT infants, while FI infants specifically harboured increased &lt;i&gt;Clostridium_P&lt;/i&gt; (3.93%), &lt;i&gt;Burkholderia&lt;/i&gt; (4.06%) and &lt;i&gt;Limosilactobacillus&lt;/i&gt; (4.94%). Metabolomic profiling identified significant pathway differences in ATP-binding cassette transporters (ABC transporters), carbohydrate digestion/absorption and propanoate metabolism. The receiver operating characteristic (ROC) analyses showed that metabolites arginine-proline (Arg-Pro, AUC=0.920), glutamic acid-arginine (Glu-Arg, AUC=0.873), lactaldehyde (AUC=0.900) and genera &lt;i&gt;Clostridium&lt;/i&gt;_&lt;i&gt;P&lt;/i&gt; (AUC=0.947), &lt;i&gt;Escherichia&lt;/i&gt; (AUC=0.765), &lt;i&gt;Staphylococcus&lt;/i&gt; (AUC=0.733) and &lt;i&gt;Bifidobacterium&lt;/i&gt; (AUC=0.851) exhibited robust predictive value for FI.&lt;b&gt;Conclusion.&lt;/b&gt; Our study demonstrates that bacterial genera such as &lt;i&gt;Staphylococcus&lt;/i&gt;, &lt;i&gt;Clostridium&lt;/i&gt;_&lt;i&gt;P&lt;/i&gt;, &lt;i&gt;Bifidobacterium&lt;/i&gt; and &lt;i&gt;Escherichia&lt;/i&gt; in the gut microbiota, along with metabolites including Arg-Pro, Glu-Arg and lactaldehyde identified in metabolomics, can serve as diagnostic criteria for feeding tolerance in preterm infants. &lt;i&gt;Klebsiella&lt;/i&gt; shows a certain degree of diagnos","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"75 3","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13021176/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147517802","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":"Assessment of SARS-CoV-2 genome sequence recovery from four lateral flow device products available in the UK.","authors":"Kuiama Lewandowski, Matthew Stokes, Alexandra Alexandridou, Abigail Fenwick, Mia L White, Jack Crook, Karly-Rai Rogers-Broadway, Catherine Ryan, Deborah A Williamson, Richard Vipond, Steven T Pullan","doi":"10.1099/jmm.0.002144","DOIUrl":"10.1099/jmm.0.002144","url":null,"abstract":"<p><p><b>Introduction.</b> Lateral flow tests have played a key role in the response to the COVID-19 pandemic and are likely to be a major component of diagnostic strategies to combat future outbreaks of infectious disease.<b>Gap Statement.</b> One challenge posed by widescale use of lateral flow tests in the community is the loss of sequence information to track virus evolution and epidemiology.<b>Aim.</b> Beyond their primary diagnostic function, it has been demonstrated that recovery of viral RNA from positive lateral flow devices (LFDs) for genome sequencing purposes is possible. We, therefore, aimed to assess the robustness and broader applicability of this process.<b>Methodology.</b> We evaluated SARS-CoV-2 RNA recovery and subsequent sequencing from eluates from the four major LFDs in use in the UK, testing both cultured virus and residual clinical nasal swab samples.<b>Results.</b> Our results demonstrated that sequencing from LFD eluates is possible, at clinically relevant titres, within a reasonable processing time frame post-use, and gave sequences concordant with routine methods. However, results varied across the four devices used.<b>Conclusion.</b> Our results highlight that if sequencing from LFD eluates is to be put into routine use, there is the requirement for refinement of existing or second-generation designs, optimized for sequencing as an intended output from positive tests.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"75 3","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13034076/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147505836","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":"Molecular epidemiology of rodent-borne <i>Leptospira</i> spp. in Sri Lanka: identification of novel sequence types and previously unrecognized reservoir animals.","authors":"Nipun Rathnayake, Kyosuke Takabe, Devinda Muthusinghe, Rydhnieya Vijeyakumaran, Pavani Senarathne, Nilanthi Dissanayake, Shuzo Urata, Kumiko Yoshimatsu, Yukihiro Akeda, Chandika Gamage, Nobuo Koizumi","doi":"10.1099/jmm.0.002133","DOIUrl":"10.1099/jmm.0.002133","url":null,"abstract":"<p><p><b>Introduction.</b> Leptospirosis is an important zoonotic disease globally, which is most prevalent in tropical regions. This disease is endemic in Sri Lanka, where the complex ecology of <i>Leptospira</i> spp., reservoir animals and environmental and occupational factors has resulted in a public health problem.<b>Gap Statement.</b> Although genomic analysis of <i>Leptospira</i> isolates has recently revealed the diversity of <i>Leptospira</i> spp. in Sri Lanka, the genetic relationship between human patients and reservoir animals remains unclear.<b>Aim.</b> This study investigated the genetic diversity of <i>Leptospira</i> spp. circulating in rodent populations in three districts of Sri Lanka: Kurunegala, Anuradhapura and Badulla.<b>Methodology.</b> <i>Leptospira</i> DNA was detected from rodent kidney tissue samples by real-time PCR, from which positive samples were subjected to <i>flaB</i> sequencing and multilocus sequencing typing (MLST).<b>Results.</b> Pathogenic <i>Leptospira</i> DNA was detected by real-time PCR in 33 of 257 kidney tissue samples (12.8%) from 4 rodent species: <i>Bandicota bengalensis</i>, <i>Mus booduga</i>, <i>Rattus rattus</i> and <i>Vandeleuria</i> sp. MLST and partial <i>flaB</i> sequencing of real-time PCR-positive samples identified <i>Leptospira borgpetersenii</i>, <i>Leptospira interrogans</i>, <i>Leptospira kirschneri</i> and <i>Leptospira licerasiae</i> in the rodent population. Five sequence types (STs), including two novel STs, ST389 and ST392, were identified. The novel STs of <i>L. interrogans</i> and <i>L. kirschneri</i> were genetically distinct from other STs detected in Sri Lanka. <i>R. rattus</i> and <i>M. booduga</i> were newly identified as the source of <i>L. interrogans</i> ST49 and of <i>L. borgpetersenii</i> ST144 and <i>L. licerasiae</i> infections in humans, respectively.<b>Conclusion.</b> This study identified the genetic diversity of <i>Leptospira</i> spp. in rodent populations and reservoir animals for human infections in Sri Lanka.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"75 3","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12967096/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147370915","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":"Evaluating the use of whole-genome sequencing and Sanger <i>emm</i> typing in guiding the identification and public health management of invasive group A <i>Streptococcus</i> clusters and outbreaks in England.","authors":"Kathrin Loosli, Juliana Coelho, Kartyk Moganeradj, Derren Ready, Charles R Beck, Nicola Love","doi":"10.1099/jmm.0.002146","DOIUrl":"10.1099/jmm.0.002146","url":null,"abstract":"<p><p><b>Introduction.</b> Sanger sequencing-based <i>emm</i> typing has traditionally been used in England to assess case relatedness when managing invasive group A <i>Streptococcus</i> (iGAS) outbreaks.<b>Gap statement.</b> While timely, <i>emm</i> typing can lack resolution. Whole-genome sequencing (WGS), offering greater strain discrimination, is increasingly used, but its comparative value for public health response has not been assessed.<b>Aim.</b> This study evaluates the added value of WGS over Sanger <i>emm</i> typing for group A <i>Streptococcus</i> (GAS) surveillance and outbreak detection, investigation and management in England.<b>Methodology.</b> The evaluation followed the Pathogen Genomics in Public Health Surveillance Evaluation (PG-PHASE) framework (full description in Appendix 1, Table S1). Interviews with laboratory staff and bioinformaticians, and a survey of UK Health Security Agency (UKHSA) health protection and epidemiology iGAS leads, provided insights into <i>emm</i> typing and WGS data use, utility, acceptability and appropriateness. Typing data from outbreak isolates collected between February 2018 and February 2024 were analysed to evaluate the concordance between Sanger <i>emm</i> typing and WGS-based single-nucleotide polymorphism (SNP) clusters. WGS strain diversity and SNP distances within <i>emm</i> types were assessed, using a five-SNP threshold for WGS clusters. The number of cases excluded from outbreaks by <i>emm</i> typing vs. WGS was compared.<b>Results.</b> Laboratory staff indicated that transitioning from a Sanger- to a WGS-based GAS typing service would result in more granular information to inform public health action. Survey participants acknowledged WGS benefits for relatedness resolution but raised concerns about longer turnaround times (a maximum of 14 vs. 5 days for WGS and the Sanger method, respectively) and highlighted the need for training in interpreting WGS data. Suggestions included more standardized, regular, cumulative WGS reports to improve clarity and usefulness. We analysed 178 epidemiologically linked GAS outbreaks, including 1,142 isolates. <i>Emm</i> typing excluded 217 unrelated isolates from 58 outbreaks, while WGS excluded a further 224 isolates (<i>n</i>=44 total) from 114 outbreaks.<b>Conclusion.</b> WGS improves outbreak management, particularly for protracted outbreaks and those with common <i>emm</i> types. WGS better automates and integrates reference laboratory services; however, current turnaround times reduce its benefits for immediate public health action. Our findings suggest that strengthening the timeliness of WGS reporting, co-designing reporting processes with data users and providing training in data interpretation will enhance WGS utility.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"75 3","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13016480/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147517854","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}