Microbial Genomics最新文献

{"title":"Longitudinal genomic surveillance of a UK intensive care unit shows a lack of patient colonisation by multi-drug-resistant Gram-negative bacterial pathogens.","authors":"Ann E Snaith, Robert A Moran, Rebecca J Hall, Anna Casey, Liz Ratcliffe, Willem van Schaik, Tony Whitehouse, Alan McNally","doi":"10.1099/mgen.0.001314","DOIUrl":"10.1099/mgen.0.001314","url":null,"abstract":"<p><p>Vulnerable patients in an intensive care unit (ICU) setting are at high risk of infection from bacteria including gut-colonising <i>Escherichia coli</i> and <i>Klebsiella</i> species. Complex ICU procedures often depend on successful antimicrobial treatment, underscoring the importance of understanding the extent of patient colonisation by multi-drug-resistant organisms (MDROs) in large UK ICUs. Previous work on ICUs globally uncovered high rates of colonisation by transmission of MDROs, but the situation in UK ICUs is less understood. Here, we investigated the diversity and antibiotic resistance gene (ARG) carriage of bacteria present in one of the largest UK ICUs at the Queen Elizabeth Hospital Birmingham (QEHB), focusing primarily on <i>E. coli</i> as both a widespread commensal and a globally disseminated multi-drug-resistant pathogen. Samples were taken during highly restrictive coronavirus disease 2019 (COVID-19) control measures from May to December 2021. Whole-genome and metagenomic sequencing were used to detect and report strain-level colonisation of patients, focusing on <i>E. coli</i> sequence types (STs), their colonisation dynamics and antimicrobial resistance gene carriage. We found a lack of multi-drug resistance (MDR) in the QEHB. Only one carbapenemase-producing organism was isolated, a <i>Citrobacter</i> carrying <i>bla</i> _KPC-2. There was no evidence supporting the spread of this strain, and there was little evidence overall of nosocomial acquisition or circulation of colonising <i>E. coli</i>. Whilst 22 different <i>E. coli</i> STs were identified, only 1 strain of the pandemic ST131 lineage was isolated. This ST131 strain was non-MDR and was found to be a clade A strain, associated with low levels of antibiotic resistance. Overall, the QEHB ICU had very low levels of pandemic or MDR strains, a result that may be influenced in part by the strict COVID-19 control measures in place at the time. Employing some of these infection prevention and control measures where reasonable in all ICUs might therefore assist in maintaining low levels of nosocomial MDR.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 11","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533117/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142569126","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":"Uncovering the transcriptome-wide RNA modifications in <i>Acinetobacter baumannii</i>.","authors":"Kah Ern Ten, Sadequr Rahman, Hock Siew Tan","doi":"10.1099/mgen.0.001327","DOIUrl":"10.1099/mgen.0.001327","url":null,"abstract":"<p><p>Despite being a major human pathogen, limited studies have reported RNA modifications in <i>Acinetobacter baumannii</i>. These post-transcriptional modifications play crucial regulatory roles in bacteria and have also been shown to modulate bacterial virulence. Using nanopore sequencing, we characterized RNA modifications in a virulent <i>A. baumannii</i> strain (Ab-C98) under free-living (mid-exponential phase <i>in vitro</i> culture) and during an early stage of infection (3 h post-infection) in <i>Galleria mellonella</i> larvae. Analysis revealed that m⁵C methylations are essential for ribosome synthesis, while m⁶A and Ψ are involved in metabolic pathways and translation processes. Iron-chelating genes <i>exbD</i> (m⁵C and m⁶A) and <i>feoB</i> (m⁶A and Ψ) and RNA polymerase subunit <i>rpoC</i> (m⁶A and Ψ) were selectively modified during infection. This first transcriptome-wide study highlights the potential regulatory roles of m⁵C, m⁶A and Ψ modifications in <i>A. baumannii</i> during infection.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 11","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11578064/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142676031","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":"Population-level whole-genome sequencing of <i>Ascochyta rabiei</i> identifies genomic loci associated with isolate aggressiveness.","authors":"Niloofar Vaghefi, Ido Bar, Jonathan Wanderley Lawley, Prabhakaran Thanjavur Sambasivam, Melody Christie, Rebecca Ford","doi":"10.1099/mgen.0.001326","DOIUrl":"https://doi.org/10.1099/mgen.0.001326","url":null,"abstract":"<p><p>Ascochyta blight caused by the ascomycete <i>Ascochyta rabiei</i> poses a major biotic threat to chickpea (<i>Cicer arietinum</i>) industries worldwide and incurs substantial costs to the Australian multimillion-dollar chickpea industry in both disease control and yield loss. The fungus was introduced to Australia in the 1970s from an unknown source population and, within a few decades, successfully established in all Australian agroecological chickpea-growing regions. Although genetically highly clonal, a broad range of phenotypic variation in terms of aggressiveness exists among the Australian <i>A. rabiei</i> isolates. More recently, highly aggressive isolates capable of causing severe disease symptoms on moderate to highly resistant chickpea cultivars have increased in frequency. To identify genetic loci potentially associated with <i>A. rabiei</i> aggressiveness on Australian chickpea cultivars, we performed deep genome sequencing of 230 isolates collected from a range of agroecological chickpea-growing regions between 2013 and 2020. Population genetic analyses using genome-wide SNP data identified three main clusters of genetically closely related isolates in Australia. Phylogenetic analyses showed that highly aggressive phenotypes developed multiple times independently throughout the phylogeny. The results point to a minor contribution of multiple genetic regions and most likely epigenomic variations to aggressiveness of <i>A. rabiei</i> isolates on Australian chickpea cultivars.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 11","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142692751","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":"Erratum: Development and implementation of a Core Genome Multilocus Sequence Typing (cgMLST) scheme for <i>Haemophilus influenzae</i>.","authors":"Made Ananda Krisna, Keith A Jolley, William Monteith, Alexandra Boubour, Raph L Hamers, Angela B Brueggemann, Odile B Harrison, Martin C J Maiden","doi":"10.1099/mgen.0.001304","DOIUrl":"https://doi.org/10.1099/mgen.0.001304","url":null,"abstract":"","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 10","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142469635","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":"Tn<i>4661</i>-mediated transfer of <i>bla</i> _CTX-M-15 from <i>Klebsiella michiganensis</i> to an outbreak clone of <i>Pseudomonas aeruginosa</i>.","authors":"Katelyn V Bartlett, Ting L Luo, Ana C Ong, Rosslyn A Maybank, William Stribling, Bernadette Thompson, Aubrey Powell, Yoon I Kwak, Jason W Bennett, Francois Lebreton, Patrick T Mc Gann","doi":"10.1099/mgen.0.001303","DOIUrl":"https://doi.org/10.1099/mgen.0.001303","url":null,"abstract":"<p><p>Carriage of CTX-M-type extended-spectrum β-lactamase (ESBL) is rare in <i>Pseudomonas aeruginosa</i>. During routine surveillance of an endemic ST-621 <i>P. aeruginosa</i> at a large hospital, isolate MRSN 100690 carrying <i>bla</i> _CTX-M-15 was cultured from a patient (P2). This was the first detection of this ESBL in the endemic ST-621 lineage. All 1 488 bacterial isolates collected from the same facility in the 12 months prior to the incidence of 100 690 were screened for the presence of <i>bla</i> _CTX-M-15. A set of 183 isolates was identified, in which corresponding patient metadata was evaluated for spatiotemporal overlaps with P2. The resulting three isolates, along with 100 690, were long-read sequenced using the Oxford Nanopore MinION platform to determine a potential donor of <i>bla</i> _CTX-M-15. The screen revealed a single <i>Klebsiella michiganensis</i> isolate, MRSN 895358, which carried an IncA/C2 plasmid harbouring <i>bla</i> _CTX-M-15. Notably, the patient harbouring 895358, P1, occupied the same hospital room as P2 9 months prior. Genomic alignment revealed that both isolates shared an identical 80.8 kb region containing the IncA/C2 plasmid replicon and <i>bla</i> _CTX-M-15. This region was plasmid bound in 895 358, but chromosomally bound in 100 690 due to Tn<i>4661</i>-mediated transposition. ESBL <i>bla</i> _CTX-M-15 was acquired and subsequently integrated into the chromosome of a ST-621 <i>P. aeruginosa</i>, likely initiated by plasmid transfer from a <i>K. michiganensis</i> strain.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 10","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11482538/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142469640","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":"A host shift as the origin of tomato bacterial canker caused by <i>Clavibacter michiganensis</i>.","authors":"Alan Guillermo Yañez-Olvera, Ambar Grissel Gómez-Díaz, Nelly Sélem-Mojica, Lorena Rodríguez-Orduña, José Pablo Lara-Ávila, Vanina Varni, Florencia Alcoba, Valentina Croce, Thierry Legros, Alberto Torres, Alfonso Torres Ruíz, Félix Tarrats, Adriaan Vermunt, Thorben Looije, Angélica Cibrian-Jaramillo, Miryam Valenzuela, María Inés Siri, Francisco Barona-Gomez","doi":"10.1099/mgen.0.001309","DOIUrl":"10.1099/mgen.0.001309","url":null,"abstract":"<p><p>The Actinomycetota (formerly Actinobacteria) genus <i>Clavibacter</i> includes phytopathogens with devasting effects in several crops. <i>Clavibacter michiganensis</i>, the causal agent of tomato bacterial canker, is the most notorious species of the genus. Yet, its origin and natural reservoirs remain elusive, and its populations show pathogenicity profiles with unpredictable plant disease outcomes. Here, we generate and analyse a decade-long genomic dataset of <i>Clavibacter</i> from wild and commercial tomato cultivars, providing evolutionary insights that directed phenotypic characterization. Our phylogeny situates the last common ancestor of <i>C. michiganensis</i> next to <i>Clavibacter</i> isolates from grasses rather than to the sole strain we could isolate from wild tomatoes. Pathogenicity profiling of <i>C. michiganensis</i> isolates, together with <i>C. phaseoli</i> and <i>C. californiensis</i> as sister taxa and the wild tomato strain, was found to be congruent with the proposed phylogenetic relationships. We then identified gene enrichment after the evolutionary event, leading to the appearance of the <i>C. michiganesis</i> clade, including known pathogenicity factors but also hitherto unnoticed genes with the ability to encode adaptive traits for a pathogenic lifestyle. The holistic perspective provided by our evolutionary analyses hints towards a host shift event as the origin of <i>C. michiganensis</i> as a tomato pathogen and the existence of pathogenic genes that remain to be characterized.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 10","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11521342/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142546262","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":"Ethylene and epoxyethane metabolism in methanotrophic bacteria: comparative genomics and physiological studies using <i>Methylohalobius crimeensis</i>.","authors":"Noah Toppings, Meghan Marshall, Angela V Smirnova, Andriy Sheremet, Anthony S Pasala, Felix C Nwosu, Morgan Hepburn, Ian Lewis, Nicholas V Coleman, Peter F Dunfield","doi":"10.1099/mgen.0.001306","DOIUrl":"https://doi.org/10.1099/mgen.0.001306","url":null,"abstract":"<p><p>The genome of the methanotrophic bacterium <i>Methylohalobius crimeensis</i> strain 10Ki contains a gene cluster that encodes a putative coenzyme-M (CoM)-dependent pathway for oxidation of epoxyethane, based on homology to genes in bacteria that grow on ethylene and propylene as sole substrates. An alkene monooxygenase was not detected in the <i>M. crimeensis</i> genome, so epoxyethane is likely produced from co-oxidation of ethylene by the methane monooxygenase enzyme. Similar gene clusters were detected in about 10% of available genomes from aerobic methanotrophic bacteria, primarily strains grown from rice paddies and other wetlands. The sparse occurrence of the gene cluster across distant phylogenetic groups suggests that multiple lateral gene transfer events have occurred in methanotrophs. In support of this, the gene cluster in <i>M. crimeensis</i> was detected within a large genomic island predicted using multiple methods. Growth studies, reverse transcription-quantitative PCR (RT-qPCR) and proteomics were performed to examine the expression of these genes in <i>M. crimeensis</i>. Growth and methane oxidation activity were completely inhibited by the addition of >0.5% (v/v) ethylene to the headspace of cultures, but at 0.125% and below, the inhibition was only partial, and ethylene was gradually oxidized. The <i>etnE</i> gene encoding epoxyalkane:CoM transferase was strongly upregulated in ethylene-exposed cells based on RT-qPCR. Proteomics analysis confirmed that EtnE and nine other proteins encoded in the same gene cluster became much more predominant after cells were exposed to ethylene. The results suggest that ethylene is strongly inhibitory to <i>M. crimeensis</i>, but the bacterium responds to ethylene exposure by expressing an epoxide oxidation system similar to that used by bacteria that grow on alkenes. In the obligate methanotroph <i>M. crimeensis</i>, this system does not facilitate growth on ethylene but likely alleviates toxicity of epoxyethane formed through ethylene co-oxidation by particulate methane monooxygenase. The presence of predicted epoxide detoxification systems in several other wetland methanotrophs suggests that co-oxidation of ambient ethylene presents a stress for methanotrophic bacteria in these environments and that epoxyethane removal has adaptive value.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 10","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11507031/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142503569","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":"Microbial genetic potential differs among cryospheric habitats of the Damma glacier.","authors":"Maomao Feng, Serina Robinson, Weihong Qi, Arwyn Edwards, Beat Stierli, Marcel van der Heijden, Beat Frey, Gilda Varliero","doi":"10.1099/mgen.0.001301","DOIUrl":"10.1099/mgen.0.001301","url":null,"abstract":"<p><p>Climate warming has led to glacier retreat worldwide. Studies on the taxonomy and functions of glacier microbiomes help us better predict their response to glacier melting. Here, we used shotgun metagenomic sequencing to study the microbial functional potential in different cryospheric habitats, i.e. surface snow, supraglacial and subglacial sediments, subglacial ice, proglacial stream water and recently deglaciated soils. The functional gene structure varied greatly among habitats, especially for snow, which differed significantly from all other habitats. Differential abundance analysis revealed that genes related to stress responses (e.g. chaperones) were enriched in ice habitat, supporting the fact that glaciers are a harsh environment for microbes. The microbial metabolic capabilities related to carbon and nitrogen cycling vary among cryospheric habitats. Genes related to auxiliary activities were overrepresented in the subglacial sediment, suggesting a higher genetic potential for the degradation of recalcitrant carbon (e.g., lignin). As for nitrogen cycling, genes related to nitrogen fixation were more abundant in barren proglacial soils, possibly due to the presence of Cyanobacteriota in this habitat. Our results deepen our understanding of microbial processes in glacial ecosystems, which are vulnerable to ongoing global warming, and they have implications for downstream ecosystems.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 10","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11443553/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142349688","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":"AMRColab - a user-friendly antimicrobial resistance detection and visualization tool.","authors":"Su Datt Lam, Sabrina Di Gregorio, Mia Yang Ang, Emma Griffiths, Tengku Zetty Maztura Tengku Jamaluddin, Sheila Nathan, Hui-Min Neoh","doi":"10.1099/mgen.0.001308","DOIUrl":"10.1099/mgen.0.001308","url":null,"abstract":"<p><p>Antimicrobial resistance (AMR) poses a significant threat to global public health, with the potential to cause millions of deaths annually by 2050. Effective surveillance of AMR pathogens is crucial for monitoring and predicting their behaviour in response to antibiotics. However, many public health professionals lack the necessary bioinformatics skills and resources to analyse pathogen genomes effectively. To address this challenge, we developed AMRColab, an open-access bioinformatics analysis suite hosted on Google Colaboratory. AMRColab enables users with limited or no bioinformatics training to detect and visualize AMR determinants in pathogen genomes using a 'plug-and-play' approach. The platform integrates established bioinformatics tools such as AMRFinderPlus and hAMRonization, allowing users to analyse, compare and visualize trends in AMR pathogens easily. A trial run using methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) strains demonstrated AMRColab's effectiveness in identifying AMR determinants and facilitating comparative analysis across strains. A workshop was conducted and feedback from participants indicated high confidence in using AMRColab and a willingness to incorporate it into their research. AMRColab's user-friendly interface and modular design make it accessible to a diverse audience, including medical laboratory technologists, medical doctors and public health scientists, regardless of their bioinformatics expertise. Future improvements to AMRColab will include enhanced visualization tools, multilingual support and the establishment of an online community platform. AMRColab represents a significant step towards democratizing AMR surveillance and empowering public health professionals to combat AMR effectively.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 10","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11493187/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142469631","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":"Revisiting typing systems for group B <i>Streptococcus</i> prophages: an application in prophage detection and classification in group B <i>Streptococcus</i> isolates from Argentina.","authors":"Veronica Kovacec, Sabrina Di Gregorio, Mario Pajon, Chiara Crestani, Tomás Poklepovich, Josefina Campos, Uzma Basit Khan, Stephen D Bentley, Dorota Jamrozy, Marta Mollerach, Laura Bonofiglio","doi":"10.1099/mgen.0.001297","DOIUrl":"https://doi.org/10.1099/mgen.0.001297","url":null,"abstract":"<p><p>Group B <i>Streptococcus</i> (GBS) causes severe infections in neonates and adults with comorbidities. Prophages have been reported to contribute to GBS evolution and pathogenicity. However, no studies are available to date on the presence and diversity of prophages in GBS isolates from humans in South America. This study provides insights into the prophage content of 365 GBS isolates collected from clinical samples in the context of an Argentinean multicentric study. Using whole-genome sequence data, we implemented two previously proposed methods for prophage typing: a PCR approach (carried out <i>in silico</i>) coupled with a blastx-based method to classify prophages based on their prophage group and integrase type, respectively. We manually searched the genomes and identified 325 prophages. However, only 80% of prophages could be accurately categorized with the previous approaches. Integration of phylogenetic analysis, prophage group and integrase type allowed for all to be classified into 19 prophage types, which correlated with GBS clonal complex grouping. The revised prophage typing approach was additionally improved by using a blastn search after enriching the database with ten new genes for prophage group classification combined with the existing integrase typing method. This modified and integrated typing system was applied to the analysis of 615 GBS genomes (365 GBS from Argentina and 250 from public databases), which revealed 29 prophage types, including two novel integrase subtypes. Their characterization and comparative analysis revealed major differences in the lysogeny and replication modules. Genes related to bacterial fitness, virulence or adaptation to stressful environments were detected in all prophage types. Considering prophage prevalence, distribution and their association with bacterial virulence, it is important to study their role in GBS epidemiology. In this context, we propose the use of an improved and integrated prophage typing system suitable for rapid phage detection and classification with little computational processing.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 10","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11485964/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142469637","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}