Microbial Genomics最新文献

{"title":"Cobalt starvation affects multiple cellular processes in <i>Desulfofundulus kuznetsovii</i> TPOSR during alcohol oxidation.","authors":"Lukas Friedeheim, Sjef Boeren, Irene Sánchez-Andrea, Alfons J M Stams, Diana Z Sousa","doi":"10.1099/mgen.0.001771","DOIUrl":"10.1099/mgen.0.001771","url":null,"abstract":"<p><p>Cobalt influences the methanol metabolism of <i>Desulfofundulus kuznetsovii</i> TPOSR, specifically by modulating the activity of one of its alcohol dehydrogenases (ADH), Adh1. However, the effects of cobalt on the broader proteome of strain TPOSR, as well as the utilization of alcohols besides methanol, remain unexplored. Here, proteomic analyses of strain TPOSR grown with and without cobalt on different alcohol substrates show that cobalt starvation impacts multiple cellular processes, including cobalamin biosynthesis, iron-sulphur cluster assembly and, most prominently, energy metabolism as indicated by altered abundances of hydrogenases and NAD(P)-dependent oxidoreductases. Despite the presence of six ADH-encoding genes in the genome, Adh1 is the dominant ADH during growth not only on methanol but also on several primary alcohols and diols (ethanol, 1-propanol, 1,2-propanediol, 1,3-propanediol, butanol, pentanol and heptanol). Enzymatic assays with purified Adh1 confirm activity with these substrates, except 1,3-propanediol, and show no activity toward secondary alcohols (2-propanol and 2-butanol). Comparative proteomics analyses of other sulphate-reducing microorganisms (SRMs), namely <i>Desulfofundulus australicum</i> and <i>Solidesulfovibrio carbinolicus</i>, further indicate that methanol and ethanol oxidation in SRMs is mediated by a single ADH/AOR pair. Together, these findings highlight the central role of cobalt in alcohol metabolism in strain TPOSR and identify conserved ADH/AOR enzymes as promising candidates for biotechnological applications.</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/PMC13541210/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148887917","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":"Comparative genomics approaches to identify genomic regions associated with the antimicrobial activity of <i>Pseudomonas protegens</i> PBL3.","authors":"Shilu Dahal, Chia Sin Liew, Jean-Jack Riethoven, Clemencia M Rojas","doi":"10.1099/mgen.0.001827","DOIUrl":"10.1099/mgen.0.001827","url":null,"abstract":"<p><p>The environmental bacterium <i>Pseudomonas protegens</i> PBL3 has antagonistic activity against the plant pathogenic bacterium <i>Burkholderia glumae</i>, an important pathogen in rice. The antimicrobial activity of <i>P. protegens</i> PBL3 was found in the bacteria-free secreted fraction (secretome), but the specific molecules, as well as the genetic basis of that activity, have not been identified. In this study, we integrated genomic information with antimicrobial assays on <i>P. protegens</i> PBL3 and additional six <i>Pseudomonas</i> spp. strains, to identify putative genomic regions in <i>P. protegens</i> PBL3 associated with antimicrobial activity. We hypothesized that <i>Pseudomonas</i> spp. strains with antimicrobial activity against <i>B. glumae</i> have conserved genes with <i>P. protegens</i> PBL3 that are absent in strains lacking activity. Comparative genomics analyses with anvi'o and progressiveMauve, and using <i>P. protegens</i> PBL3 as the reference genome, revealed 188 genes uniquely present in antimicrobial-producing strains. Seven of those genes were annotated as biosynthetic gene clusters predicted to encode secondary metabolites; additional genes were grouped into 25 contiguous clusters with functions annotated as secretion, signal transduction, regulation, transport/efflux, carbohydrate metabolism and one with an additional uncharacterized function. Altogether, this study uncovered a complex and multi-functional network of candidate genes, suggesting that the antimicrobial activity in <i>P. protegens</i> PBL3 is not limited to biosynthetic pathways but also involves additional regulatory, metabolic and export modules to synthesize and deploy antimicrobials.</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/PMC13541209/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148887893","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":"Applications of transposon-insertion sequencing for understanding bacterial physiology.","authors":"Emily C A Goodall, Stineke van Houte","doi":"10.1099/mgen.0.001796","DOIUrl":"10.1099/mgen.0.001796","url":null,"abstract":"<p><p>Transposon-insertion sequencing (Tn-seq) couples transposon mutagenesis with next-generation sequencing to identify the transposon insertion site for thousands of mutants in parallel. It is a powerful technology with a myriad of uses beyond the identification of essential genes required for a cell to grow and divide. Tn-seq is particularly useful as a high-throughput method to assign function to function-unknown genes, which have increased steadily with the abundance of newly sequenced bacterial genomes. Tn-seq has now been adapted for use in over 100 bacterial species. Here, we summarize the applications of Tn-seq for querying bacterial physiology and discuss some of the possible applications for the future.</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/PMC13541208/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148887922","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":"Transcriptomic shift in ethanol and amino acid metabolic genes regulated by Med15 during alcoholic fermentation.","authors":"David G Cooper, Emma Grunkemeyer, Jan S Fassler","doi":"10.1099/mgen.0.001811","DOIUrl":"10.1099/mgen.0.001811","url":null,"abstract":"<p><p>Organisms that thrive in extreme environments provide natural experiments in evolution, revealing the genetic regulators that orchestrate complex phenotypic change. Wine yeast (WY) are specialized strains that are adapted to survive in the wine making environment while producing high concentrations of ethanol. In addition to large genomic changes that differentiate WY from yeast used in other industries, SNP and polyglutamine tract polymorphism in the transcriptional regulator Med15 are associated with the fermentation efficiency and stress response phenotypes of WY. In this study, we investigated the transcriptional differences during wine fermentation in transgenic lab strain yeast having integrated WY <i>MED15</i> alleles. Compared to the unmodified lab strain (<i>MED15</i> _LAB), the same strain in which the <i>MED15</i> locus was replaced with a <i>MED15</i> allele from yeast isolated from palm wine, the fermented sap of palm (oil, date, coconut) trees (<i>MED15</i> _WY23), exhibited enhanced expression of amino acid biosynthesis genes as well as stress resistance and metabolic adaptation genes. Our experimental data confirm the role of arginine in efficient fermentation and suggest that certain <i>MED15</i> alleles alter the expression patterns of arginine pathway genes in some cases improving carbon flux under nitrogen stress. The global benefits conferred by natural polymorphisms in a single transcriptional regulator highlight Med15 as a target for engineering of strains devoted to various types of alcohol production.</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/PMC13541290/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148887949","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":"Presence of globally prominent multidrug-resistant genotypes of <i>Salmonella enterica</i> serovar Typhi in New York State, 2016-2023.","authors":"Samantha K Lindberg, Ana Beatriz Garcez Buiatte, Odion O Ikhimiukor, Leticia Roberta Martins Costa, Samantha E Wirth, Kimberlee A Musser, Lisa A Mingle, Cheryl P Andam","doi":"10.1099/mgen.0.001816","DOIUrl":"10.1099/mgen.0.001816","url":null,"abstract":"<p><p>The human-restricted enteric pathogen <i>Salmonella enterica</i> serovar Typhi (<i>S</i>. Typhi) is the causative agent of the life-threatening typhoid fever. Although <i>S</i>. Typhi incidence is relatively low in the USA, routine surveillance of <i>S</i>. Typhi is critical to track the emergence and spread of high-risk lineages in non-endemic areas. In this study, we analysed 151 genomes of <i>S</i>. Typhi isolates from patients who were clinically confirmed with typhoid fever across New York State between 2016 and 2023. We used the GenoTyphi classification scheme and identified established multidrug-resistant and extensively drug-resistant lineages. We detected the presence of the globally widespread genotype 4.3.1 (haplotype 58) and its derivative 4.3.1.1.P1, which recently emerged in Pakistan, as well as the Bangladesh-restricted lineages 3.3.2.Bd1 and 3.3.2.Bd2 in our dataset. Ten mutations and 14 acquired genes associated with antimicrobial resistance (AMR) were present across the entire population, with 86.8% of the genomes possessing at least one of these AMR determinants. The <i>gyrA</i> S83F mutation conferring quinolone and triclosan resistance was the most frequently detected (94 genomes). Combinations of <i>dfrA7+catA1</i> (resistance to trimethoprim and chloramphenicol, respectively) and <i>sul2+aph(3″)-Ib+aph(6)-Id</i> (resistance to sulphonamide and aminoglycosides, respectively) co-occurred frequently and were associated with IncQ and IncY plasmid replicons. Phylogenetic contextualization against a global dataset of 1,643 genomes from 20 countries across five continents, including other parts of the USA, from the same time period showed geographic intermingling, suggesting the spread of high-risk genotypes of international origins to New York State. Altogether, these findings reveal the presence of globally dominant resistant genotypes that are likely facilitated by human travel in New York State, where typhoid fever is not endemic. Long-term genomic surveillance is critical to AMR profiling, identifying genotypic shifts in regional <i>S</i>. Typhi populations, monitoring transmission routes and guiding effective public health interventions.</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/PMC13537747/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148880989","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":"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":"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}