Microbial Genomics最新文献

{"title":"Phylogenetic distribution and longitudinal persistence of plasmids in <i>Mycobacterium abscessus</i>.","authors":"Trieu Le, Josephine M Bryant","doi":"10.1099/mgen.0.001807","DOIUrl":"10.1099/mgen.0.001807","url":null,"abstract":"<p><p><i>Mycobacterium abscessus,</i> a non-tuberculous mycobacterium, is a cause of severe respiratory infections, notably in individuals with underlying lung conditions. Its high levels of intrinsic and acquired antimicrobial resistance make it particularly difficult to treat and horizontally acquired genetic elements may facilitate the spread of resistance. A small number of plasmids have been identified in this species, but their distribution, transmission dynamics across subspecies and clonal lineages remain poorly characterized. We analysed short-read genomic data from 3,060 <i>M</i>. <i>abscessus</i> isolates, including longitudinal samples, to characterize plasmid diversity and dynamics. Using a graph-based pan-genome approach, we identified 28 plasmids, including 15 previously unreported plasmids, mapped their distribution onto the species phylogeny and assessed their functional potential. Overall, 23.1% of isolates carried at least one plasmid, with higher prevalence in dominant circulating clones (DCCs) compared with non-DCCs. Plasmid carriage varied across subspecies and clonal backgrounds, and plasmids encoded numerous genes which may be linked to bacterial adaptation. Several plasmids persisted across multiple time points within individual patients, suggesting they can be highly stable over the course of a chronic infection.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 9","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13552800/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148912773","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic epidemiology and antimicrobial resistance profile of <i>Shigella</i> isolated from diarrhoea diseases in under-five children in Blantyre, Malawi.","authors":"Grace Thandekire Sibande, Charlotte E Chong, Anmol Kiran, Belson Kutambe, Mary Charles, Victor Maiden, Kate S Baker, Jennifer Cornick","doi":"10.1099/mgen.0.001838","DOIUrl":"10.1099/mgen.0.001838","url":null,"abstract":"<p><p>Antimicrobial resistance (AMR) in <i>Shigella</i> is rising globally, complicating shigellosis management. Whole-genome sequence analysis (WGSA) has advanced our understanding of AMR and transmission dynamics, yet contemporary whole-genome sequencing data from <i>Shigella</i> in sub-Saharan Africa remain scarce. In this study, we applied WGSA to 27 <i>Shigella</i> isolates collected from children presenting with diarrhoea at Ndirande Health Centre in Malawi (2022-2023), as part of the Enterics for Global Health <i>Shigella</i> surveillance study. Serotyping, AMR profiling and phylogenetic analysis revealed <i>Shigella sonnei</i> as the dominant serogroup, with distinct genetic clustering relative to global reference strains among <i>S. sonnei</i>, <i>Shigella flexneri</i> and <i>Shigella boydii</i>. We identified 16 AMR genes linked to ten antimicrobial classes with <i>qnrS1</i> and <i>qnrB19</i> genes conferring resistance to fluoroquinolone, alongside IncFIB(K) and IncFII plasmid replicon markers. Importantly, no azithromycin resistance determinants were detected both genotypically and phenotypically, providing baseline evidence that warrants continued surveillance of current first-line treatment. However, the detection of fluoroquinolone resistance genes with plasmid replicon markers in the absence of phenotypic resistance might indicate a silent reservoir with epidemic potential. This is the first contemporary <i>Shigella</i> data from a large-scale diarrhoea disease surveillance study in Malawi, providing essential baseline information for guiding antibiotic treatment and future vaccine development efforts, contributing to the efforts to combat shigellosis in Malawi and other similar regions.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 9","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13566845/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148945158","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic analysis of prophage prevalence and diversity in the bovine mastitis pathogen <i>Streptococcus uberis</i>.","authors":"Thomas Smith-Zaitlik, Logan L Newstead, Katrina Henderson, Colin Mason, Nuno Silva, Geoffrey Foster, Alison S Low, Alastair Macrae, David L Gally, Gavin K Paterson","doi":"10.1099/mgen.0.001849","DOIUrl":"10.1099/mgen.0.001849","url":null,"abstract":"<p><p>The prevalence and diversity of prophages carried by the major global bovine mastitis pathogen, <i>Streptococcus uberis</i>, are poorly characterized. Bacteriophages (phages) are viruses which can infect and kill bacteria. Prophages, phages that have integrated into the bacterial genome, can have a profound impact on the fitness of their host cell. Here, we analysed the prophage content of 661 <i>S</i>. <i>uberis</i> genomes, including 345 newly sequenced isolates. Using PhiSpy, we identified 766 prophages, which formed 2 distinct clades postulated to correspond to full-length and satellite prophages, respectively. Putative full-length prophages had larger genomes and encoded more structural and lytic genes. Putative satellite prophages, which are reliant on helper phages for their replication and lysis, had smaller genomes, fewer structural genes and no lysins. Genomic and phylogenetic differences between the clades suggested that these satellite prophages were distinct from the full-length prophages, rather than being cryptic remnants of the latter. We identified a diverse repertoire of prophage-encoded endolysins with potential as novel therapeutics. Finally, we contextualized our <i>S. uberis</i> prophages within the broader phylogeny of <i>Streptococcus</i> phages, by aligning them with 1,078 publicly available phage genomes. The same division between putative full-length and satellite phages was maintained in this larger <i>Streptococcus</i> phage phylogeny of 1,844 phages. Our findings underline the prevalence and diversity of prophages within <i>S. uberis</i> and lay the foundations for furthering our understanding of phage-host interactions in this significant veterinary pathogen.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 9","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13619156/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149069891","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optimizing culture-free approaches to recover high-quality <i>Mycobacterium tuberculosis</i> genomic variation.","authors":"Katharine S Walter, Paulo César Pereira Dos Santos, Allison Carey, Salika M Shakir, Caroline Colijn, Ted Cohen, Barun Mathema, Julio Croda, Jason R Andrews","doi":"10.1099/mgen.0.001806","DOIUrl":"10.1099/mgen.0.001806","url":null,"abstract":"<p><p><b>Background.</b> <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>) genomic epidemiology often relies on culturing patient sputum, a time- and labour-intensive process. Hybrid capture approaches have been successfully used to enrich <i>Mtb</i> DNA from complex clinical samples, yet the accuracy of variant identification from captured samples has not been systematically evaluated.<b>Methods.</b> We created artificial strain mixtures of two well-characterized <i>Mtb</i> isolates such that the minor strain comprised 0-50% of <i>Mtb</i> DNA and serially diluted the <i>Mtb</i> DNA into human DNA to simulate diagnostic samples with different sputum smear burdens (32 samples). We also prospectively collected paired <i>Mtb</i> diagnostic cultures and sputum submitted to a national diagnostic laboratory (seven sample pairs). We performed hybrid capture and Illumina whole-genome sequencing for all samples. For the artificial strain mixtures, we measured hybrid capture efficiency, the percentage of total reads mapping to <i>Mtb</i> and performance of fixed and minority variant identification. For the diagnostic samples, we compared the number, identity and minor allele frequencies of minority variants identified in the cultured and hybrid-captured samples.<b>Results.</b> In the artificial strain mixture experiment, hybrid capture efficiency was 97% when <i>Mtb</i> comprised 0.01% of the input DNA. SNP identification via hybrid capture had a sensitivity ≥91% and precision ≥97% for <i>Mtb</i> lineages 4.1.2.1 and 4.9, excluding PE/PPE genes, when <i>Mtb</i> comprised 0.01% of input DNA. Observed minor allele frequencies were closely correlated (<i>r</i>=0.62 to <i>r</i>=0.79, <i>P</i><0.001) with input minor allele frequencies across all dilutions. Among paired diagnostic samples, hybrid capture efficiency was high, 95%. However, four of the seven captured sputum samples were overwhelmed with <i>Pseudomonas</i> contamination, which comprised >25% of sequence reads. We did not detect a significant difference in the number of minority variants identified in cultured (median, 14; range, 10-18) and hybrid-captured samples (median: 17 variants, range 9-47, <i>P</i>=0.25) and minor allele frequencies were correlated (<i>r</i>=0.87, <i>P</i><0.001) outside of PE/PPE genes.<b>Conclusions.</b> Hybrid capture of diagnostic sputum samples efficiently recovers accurate <i>Mtb</i> whole-genome sequences. Minority variant detection is robust in controlled mixtures but shows reduced concordance in clinical samples, highlighting the need for further validation in real-world settings.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 8","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13485273/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148794586","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The genome, transcriptome and metabolome of <i>Aspergillus welwitschiae</i> Ocstreb1 from wild halophytic rice, <i>Oryza coarctata</i>, indicates its distinctiveness.","authors":"Nishat Tamanna, Md Nafis Ul Alam, Arifa Akhter Airin, Habibul Bari Shozib, Md Rakibul Islam, Zeba I Seraj","doi":"10.1099/mgen.0.001804","DOIUrl":"https://doi.org/10.1099/mgen.0.001804","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Aspergillus welwitschiae&lt;/i&gt; is a widespread fungus with diverse roles as a plant mutualist, opportunistic human pathogen and industrial enzyme producer. The endophytic strain AwOcstreb1, isolated from halophytic rice (&lt;i&gt;Oryza coarctata&lt;/i&gt;), promotes growth in commercial rice under normal and saline conditions. Despite its significance, genomic and metabolic resources for &lt;i&gt;A. welwitschiae&lt;/i&gt; remain limited, with no complete genome information available for endophytic strains within the species. Moreover, the close relationship of this species to &lt;i&gt;Aspergillus niger&lt;/i&gt; complicates its taxonomic resolution. We performed whole-genome and transcriptomic sequencing of AwOcstreb1 cultured on potato dextrose agar, along with -MS-based volatile metabolite profiling. Comparative analyses included simple sequence repeat (SSR), transposable element (TE; including starships) and carbohydrate-active enzyme (CAZyme) profiling across &lt;i&gt;A. welwitschiae&lt;/i&gt; strains. Evolutionary relationships with &lt;i&gt;A. niger&lt;/i&gt; were examined using average nucleotide identity (ANI) and orthologous gene clustering, supported by phylogenomic reconstruction. Genes for mycotoxin production and plant growth-promoting traits were also searched in this strain. The AwOcstreb1 genome is 37.7 Mb with 13,242 predicted genes, of which 66.6% were actively expressed under potato dextrose agar growth. The genome harbours 5,126 SSRs, 19,434 TEs and a CAZyme composition similar to other &lt;i&gt;A. welwitschiae&lt;/i&gt; strains. Although established marker genes such as CaM and β-tubulin identify AwOcstreb1 as &lt;i&gt;A. welwitschiae&lt;/i&gt;, whole-genome ANI and orthologous gene-based analyses place &lt;i&gt;A. welwitschiae&lt;/i&gt; strains within the broader &lt;i&gt;A. niger&lt;/i&gt; species complex, suggesting that it represents a population-level group rather than a clearly separated species, a view that is still not widely adopted. Synteny analysis showed that the AwOcstreb1 genes are highly collinear with those of &lt;i&gt;A. niger&lt;/i&gt;. Genes involved in phosphate and zinc solubilization and siderophore biosynthesis were detected, whereas ochratoxin A biosynthetic genes were absent. Although the presence of fumonisin genes was detected, only a trace amount of the toxin was detected both in culture as well as rice grains. Among 172 strain-specific orthogroups, several encode intrinsically disordered, secreted or membrane-associated proteins that are potentially linked to endophytic lifestyle adaptations. Volatile metabolite profiling identified compounds such as 17-pentatriacontene, eicosane and octanal, each linked to known biological sources and potential functions, such as antifungal, antibacterial and anti-inflammatory activities. Several additional metabolites were also identified, whose biological roles need further investigation. This integrated omics study provides foundational insights into the endophytic potential and genomic distinctiveness of AwOcstreb1. This work opens new avenues for exploring &lt;i&gt;A. welwit","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 8","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148679164","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Stop codon reassignment to tryptophan in members of the bacterial phylum <i>Actinomycetota</i>.","authors":"Donovan H Parks, Pierre-Alain Chaumeil, Maria Chuvochina, Philip Hugenholtz","doi":"10.1099/mgen.0.001767","DOIUrl":"10.1099/mgen.0.001767","url":null,"abstract":"<p><p>Reassignment of stop codons is a significant evolutionary event with recoding of UGA to tryptophan being previously identified in only three bacterial phyla, the <i>Bacillota</i>, <i>Pseudomonadota</i> and <i>Verrucomicrobiota</i>. Here, we present genomic evidence of this reassignment in a fourth bacterial phylum, the <i>Actinomycetota</i>, specifically in the family <i>Eggerthellaceae</i>. We identify the UGA stop-to-tryptophan reassignment in 34 metagenome-assembled genomes recovered from the stool samples of diverse mammalian hosts, including equids and primates. Canonical markers for this reassignment are consistently observed including conserved UGA codons aligning to tryptophan, loss of release factor 2 (<i>prfB</i>) and presence of a tRNA^Trp(UCA) gene. We infer that this reassignment occurred at least twice as the lineages containing reassigned genomes are paraphyletic, forming two distinct groups separated by a third lineage with strains that use UGA as a stop codon. These lineages represent three new <i>Eggerthellaceae</i> genera for which we propose the type species <i>Equivita altericodex</i>, <i>Gorillivita intestinalis</i> and <i>Tapirivita inops</i> reflecting isolation source and genomic properties. Organisms representing these genera have reduced genomes and complete or partial loss of biosynthetic pathways, suggesting increasing host dependency and a transition to obligate symbiosis. This likely facilitated stop codon reassignment in <i>Equivita</i> and <i>Gorillivita</i> and suggests <i>Tapirivita</i> is primed for reassignment. This work expands the known phylogenetic diversity of UGA stop-to-tryptophan reassignment in the bacterial domain and establishes the <i>Eggerthellaceae</i> as a new focal point for understanding the evolutionary drivers of genetic code plasticity.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 8","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13462651/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148701681","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic epidemiology reveals geographically structured co-circulation of AFR10 and AFR13 <i>Vibrio cholerae</i> lineages driving cholera outbreaks in Tanzania (2022-2024).","authors":"Ibrahim I Mauki, Reuben Abednego, Lawrence Mapunda, Maria Ezekiely Kelly, Monica Fredrick Francis, Jackson Mushumbusi, Dennis Mrosso Kado, Feliciana Rawile, Boaz Wadugu, Hamisi Swalehe, Modest Benard, Edna Mgimba, Seif Abdul, Ambele Mwafulango, Tolbert Sonda, Calvin Sindato, Paul Kazyoba, Nyambura Moremi","doi":"10.1099/mgen.0.001813","DOIUrl":"https://doi.org/10.1099/mgen.0.001813","url":null,"abstract":"<p><p>Cholera remains a persistent public health challenge in Tanzania, with recurrent outbreaks across multiple regions overwhelming the health systems. Despite the ongoing surveillance to control the transmission, limited genomic characterization of circulating <i>Vibrio cholerae</i> strains has constrained traceability of outbreak sources and transmission dynamics including virulence determinants and antimicrobial resistance profiles to guide clinical and public health interventions. We conducted a genome analysis of 144 archived isolates from 2022 to 2024 cholera outbreaks from 16 regions across Tanzania. Sequencing was performed using Oxford Nanopore platforms. Comprehensive bioinformatics analysis was applied including genome assembly, multi-locus sequence typing, resistance gene detection, virulence profiling and phylogenetic reconstruction. Of 144 isolates, sequencing confirmed 119 to be <i>V. cholerae</i>, of which 109 (91.6%) belonged to sequence type ST69. Phylogenetic analysis identified two distinct transmission lineages: AFR10 (formerly T10) and AFR13 (formerly T13), demonstrating marked geographic stratification. AFR10 isolates clustered predominantly around Lake Tanganyika basin, bordering the Democratic Republic of the Congo and Zambia, whereas AFR13 isolates were widely distributed across different zones of Tanzania. All isolates harboured key virulence genes (<i>ctxA, ctxB, tcpA</i>) and multiple resistance genes conferring resistance to co-trimoxazole and macrolides. The <i>catB gene</i> was found to be silenced in these isolates. Notably, tetracycline resistance genes (<i>tetA/B/C</i>) were absent. The <i>qacEdelta</i> gene was only detected in AFR13 isolates and has been linked to resistance to quaternary ammonium compounds (antiseptics and disinfectants) in Gram-negative bacteria from other studies. These findings demonstrate the co-circulation of two sublineages (AFR10 and AFR13) of the seventh pandemic El Tor lineage with distinct geographic distribution, suggesting both localized persistence and regional circulation. The observed genotypic and phenotypic susceptibility to tetracycline supports the continued use of doxycycline as a first-line therapy in adults. However, the detected macrolide resistance (an alternative treatment for children) and resistance genes associated with reduced susceptibility to antiseptics underscore the need for extensive monitoring. Strengthened national and cross-border genomic surveillance is essential for effective cholera control.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 8","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13485274/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148794584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Erratum: Home is where the host is: evolutionary history of geographic spread, host switching and adaptive genomic signatures in two generalist group B <i>Streptococcus</i> clonal groups.","authors":"Antonia Hilbig, Chiara Crestani, Timothy Barkham, Swaine L Chen, Jiaying Ho, Claudia Cobo-Angel, Alejandro Ceballos-Marquez, Wanna Sirimanapong, Syafinaz Amin-Nordin, Nguyen Ngoc Phuoc, Tatiana Castro Abreu Pinto, Laura Oliveira, Chiara Anna Garbarino, Matteo Ricchi, Tiziana Lembo, Samantha Lycett, Roman Biek, Taya Forde, Ruth Nicolet Zadoks","doi":"10.1099/mgen.0.001820","DOIUrl":"10.1099/mgen.0.001820","url":null,"abstract":"","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 8","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13505958/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148819107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Skuas as sentinels of high pathogenicity avian influenza H5N1 on the Antarctic Peninsula in the 2024/2025 austral summer.","authors":"Michelle Wille, Will Abbott, Darrel Day, Yi-Mo Deng, Xiaomin Dong, Ted Gibson, Ryan Hope-Inglis, Michelle McCulley, Ida Olsson, Arvind Varsani, Teri Visentin, Matthew Walters, Meagan Dewar","doi":"10.1099/mgen.0.001724","DOIUrl":"https://doi.org/10.1099/mgen.0.001724","url":null,"abstract":"<p><p>Despite Antarctica's geographic isolation, the first incursion of high pathogenicity avian influenza (HPAI) H5N1 was detected in the 2023/2024 austral summer. Surveillance for HPAI H5N1 in Antarctica remains patchy due to logistical, financial and infrastructure challenges, with many suspected cases remaining unconfirmed and few viral genome sequences available to date. Through the 2024/2025 austral summer, we undertook five sampling expeditions to the South Shetland Islands and Antarctic Peninsula facilitated by cruise ships/operators. Across more than 500 faecal environmental samples collected from apparently healthy penguins and marine mammals, we found no detectable evidence of HPAI H5N1. However, HPAI H5N1 was detected in all but one of the skua carcasses sampled, which, in most cases, were found within metres of penguin sub-colonies. All HPAI H5N1 viral genome sequences from skuas on the Antarctic Peninsula fell within a single lineage, which included those genomes from skuas sampled in the 2024/2025 season from the South Shetland Islands. Genomes were in a different clade to those from the Antarctic Peninsula collected in the 2023/2024 austral summer. Our results confirm that although the prevalence may be low, HPAI H5N1 is recurring in Antarctica, emphasizing the need for ongoing surveillance to monitor and mitigate threats to wildlife, even in the planet's most isolated regions.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 8","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13476044/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148760554","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic diversity of <i>Pseudomonas aeruginosa</i> causing bacteremic pneumonia in an intensive care unit, with emergence of an OXA-796-producing NDM-1 ST773 isolate.","authors":"Kihyun Lee, Hyemin Chung, Kuenyoul Park, Sang-Ho Choi, Heungsup Sung","doi":"10.1099/mgen.0.001815","DOIUrl":"10.1099/mgen.0.001815","url":null,"abstract":"<p><p><i>Pseudomonas aeruginosa</i> bacteremic pneumonia carries exceptionally high mortality, yet there is a paucity of genomic characterization of the strains causing this infection. We performed hybrid sequencing (Illumina and Oxford Nanopore) of 12 non-redundant <i>P. aeruginosa</i> isolates from patients with severe bacteremic pneumonia admitted to the intensive care unit of a tertiary hospital between 2015 and 2023. The 12 isolates were assigned to nine distinct sequence types, suggesting that severe bacteremic pneumonia can arise from diverse <i>P. aeruginosa</i> lineages rather than being dominated by a single specialized or high-risk clone. In the combined dataset of our isolates and publicly available Korean <i>P. aeruginosa</i> genomes, type III secretion system exotoxin genotypes <i>exoU</i> and <i>exoS</i> showed a mutually exclusive and phylogenetically segregated distribution, as previously reported, with both genotypes represented among bacteremic pneumonia isolates. Carbapenemase genes were detected in only one isolate, PA22 (ST773), which harboured <i>bla</i> _NDM-1 together with <i>bla</i> _OXA-796 and was the only isolate displaying phenotypic carbapenem resistance and multidrug resistance. To assess the clonal relationship between <i>bla</i> _NDM-1-positive PA22 and the carbapenemase-negative ST773 isolate PA20 and to track the evolution of PA22 resistome within a broader epidemiological context, we investigated the population structure of a global ST773 dataset. Core genome MLST-based minimum spanning trees revealed a deep bifurcation within ST773, separating <i>bla</i> _NDM-1-positive and carbapenemase-negative lineages. Korean ST773 isolates formed two distinct clusters within the NDM-1-positive lineage, with the PA22-containing cluster phylogenetically proximal to isolates from the United States. Within the NDM-1-positive Korean cluster, <i>bla</i> _OXA-796 was located in conserved class 1 integron gene cassette arrays that exhibit ongoing structural diversification among closely related isolates, evidenced by variable integration of IS110 elements. Our findings demonstrate that severe bacteremic pneumonia arises from phylogenetically diverse <i>P. aeruginosa</i> lineages and provide genomic context for the NDM-1-producing ST773 clone that is rapidly emerging in Korea.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 8","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13446753/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148679178","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}