Microbial Genomics最新文献

{"title":"Corrigendum: Identification of genes influencing the evolution of <i>Escherichia coli</i> ST372 in dogs and humans.","authors":"Paarthiphan Elankumaran, Glenn F Browning, Marc S Marenda, Amanda Kidsley, Marwan Osman, Marisa Haenni, James R Johnson, Darren J Trott, Cameron J Reid, Steven P Djordjevic","doi":"10.1099/mgen.0.001286","DOIUrl":"10.1099/mgen.0.001286","url":null,"abstract":"","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 8","pages":""},"PeriodicalIF":5.4,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11561579/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142017964","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":"Molecular characterization of <i>Streptococcus pyogenes</i> (StrepA) non-invasive isolates during the 2022-2023 UK upsurge.","authors":"Jennifer N Hall, Saikou Y Bah, Henna Khalid, Alison Brailey, Sarah Coleman, Tracey Kirk, Naveed Hussain, Mark Tovey, Roy R Chaudhuri, Steve Davies, Lisa Tilley, Thushan de Silva, Claire E Turner","doi":"10.1099/mgen.0.001277","DOIUrl":"10.1099/mgen.0.001277","url":null,"abstract":"<p><p>At the end of 2022 into early 2023, the UK Health Security Agency reported unusually high levels of scarlet fever and invasive disease caused by <i>Streptococcus pyogenes</i> (StrepA or group A <i>Streptococcus</i>). During this time, we collected and genome-sequenced 341 non-invasive throat and skin <i>S. pyogenes</i> isolates identified during routine clinical diagnostic testing in Sheffield, a large UK city. We compared the data with that obtained from a similar collection of 165 isolates from 2016 to 2017. Numbers of throat-associated isolates collected peaked in early December 2022, reflecting the national scarlet fever upsurge, while skin infections peaked later in December. The most common <i>emm</i>-types in 2022-2023 were <i>emm</i>1 (28.7 %), <i>emm</i>12 (24.9 %) and <i>emm</i>22 (7.7 %) in throat and <i>emm</i>1 (22 %), <i>emm</i>12 (10 %), <i>emm</i>76 (18 %) and <i>emm</i>49 (7 %) in skin. While all <i>emm</i>1 isolates were the M1_UK lineage, the comparison with 2016-2017 revealed diverse lineages in other <i>emm</i>-types, including <i>emm</i>12, and emergent lineages within other types including a new acapsular <i>emm</i>75 lineage, demonstrating that the upsurge was not completely driven by a single genotype. The analysis of the capsule locus predicted that only 51 % of throat isolates would produce capsule compared with 78% of skin isolates. Ninety per cent of throat isolates were also predicted to have high NADase and streptolysin O (SLO) expression, based on the promoter sequence, compared with only 56% of skin isolates. Our study has highlighted the value in analysis of non-invasive isolates to characterize tissue tropisms, as well as changing strain diversity and emerging genomic features which may have implications for spillover into invasive disease and future <i>S. pyogenes</i> upsurges.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 8","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11318961/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141917084","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":"<i>GWarrange</i>: a pre- and post- genome-wide association studies pipeline for detecting phenotype-associated genome rearrangement events.","authors":"Yi Ling Tam, Sarah Cameron, Andrew Preston, Lauren Cowley","doi":"10.1099/mgen.0.001268","DOIUrl":"10.1099/mgen.0.001268","url":null,"abstract":"<p><p>The use of <i>k</i>-mers to capture genetic variation in bacterial genome-wide association studies (bGWAS) has demonstrated its effectiveness in overcoming the plasticity of bacterial genomes by providing a comprehensive array of genetic variants in a genome set that is not confined to a single reference genome. However, little attempt has been made to interpret <i>k</i>-mers in the context of genome rearrangements, partly due to challenges in the exhaustive and high-throughput identification of genome structure and individual rearrangement events. Here, we present <i>GWarrange</i>, a pre- and post-bGWAS processing methodology that leverages the unique properties of <i>k</i>-mers to facilitate bGWAS for genome rearrangements. Repeat sequences are common instigators of genome rearrangements through intragenomic homologous recombination, and they are commonly found at rearrangement boundaries. Using whole-genome sequences, repeat sequences are replaced by short placeholder sequences, allowing the regions flanking repeats to be incorporated into relatively short <i>k</i>-mers. Then, locations of flanking regions in significant <i>k</i>-mers are mapped back to complete genome sequences to visualise genome rearrangements. Four case studies based on two bacterial species (<i>Bordetella pertussis</i> and <i>Enterococcus faecium</i>) and a simulated genome set are presented to demonstrate the ability to identify phenotype-associated rearrangements. <i>GWarrange</i> is available at https://github.com/DorothyTamYiLing/GWarrange.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 7","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11316554/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141559146","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":"Delivery mode is a larger determinant of infant gut microbiome composition at 6 weeks than exposure to peripartum antibiotics.","authors":"Sophie M Leech, Danielle J Borg, Kym M Rae, Sailesh Kumar, Vicki L Clifton, Marloes Dekker Nitert","doi":"10.1099/mgen.0.001269","DOIUrl":"10.1099/mgen.0.001269","url":null,"abstract":"<p><p><b>Background.</b> Previous research has shown that delivery mode can shape infant gut microbiome composition. However, mothers delivering by caesarean section routinely receive prophylactic antibiotics prior to delivery, resulting in antibiotic exposure to the infant via the placenta. Previously, only a small number of studies have examined the effect of delivery mode versus antibiotic exposure on the infant gut microbiome with mixed findings.<b>Objective.</b> We aimed to determine the effect of delivery mode compared to antibiotic use during labour and delivery on the infant and maternal gut microbiome at 6 weeks post-partum.<b>Methodology.</b> Twenty-five mother-infant dyads were selected from the longitudinal Queensland Family Cohort Study. The selected dyads comprised nine vaginally delivered infants without antibiotics, seven vaginally delivered infants exposed to antibiotics and nine infants born by caesarean section with routine maternal prophylactic antibiotics. Shotgun-metagenomic sequencing of DNA from stool samples collected at 6 weeks post-partum from mother and infant was used to assess microbiome composition.<b>Results.</b> Caesarean section infants exhibited decreases in <i>Bacteroidetes</i> (ANCOM-BC <i>q</i><0.0001, MaAsLin 2 <i>q</i>=0.041), changes to several functional pathways and altered beta diversity (<i>R</i> ²=0.056, <i>P=</i>0.029), while minimal differences due to antibiotic exposure were detected. For mothers, caesarean delivery (<i>P=</i>0.0007) and antibiotic use (<i>P</i>=0.016) decreased the evenness of the gut microbiome at 6 weeks post-partum without changing beta diversity. Several taxa in the maternal microbiome were altered in association with antibiotic use, with few differentially abundant taxa associated with delivery mode.<b>Conclusion.</b> For infants, delivery mode appears to have a larger effect on gut microbiome composition at 6 weeks post-partum than intrapartum antibiotic exposure. For mothers, both delivery mode and intrapartum antibiotic use have a small effect on gut microbiome composition at 6 weeks post-partum.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 7","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11316550/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141590718","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":"Five centuries of genome evolution and multi-host adaptation of <i>Campylobacter jejuni</i> in Brazil.","authors":"Ana Beatriz Garcez Buiatte, Stephanie S R Souza, Leticia Roberta Martins Costa, Phelipe Augusto Borba Martins Peres, Roberta Torres de Melo, Simone Sommerfeld, Belchiolina Beatriz Fonseca, Nicole I Zac Soligno, Odion O Ikhimiukor, Paulo Marcel Armendaris, Cheryl P Andam, Daise Aparecida Rossi","doi":"10.1099/mgen.0.001274","DOIUrl":"10.1099/mgen.0.001274","url":null,"abstract":"<p><p>Consumption of raw, undercooked or contaminated animal food products is a frequent cause of <i>Campylobacter jejuni</i> infection. Brazil is the world's third largest producer and a major exporter of chicken meat, yet population-level genomic investigations of <i>C. jejuni</i> in the country remain scarce. Analysis of 221 <i>C</i>. <i>jejuni</i> genomes from Brazil shows that the overall core and accessory genomic features of <i>C. jejuni</i> are influenced by the identity of the human or animal source. Of the 60 sequence types detected, ST353 is the most prevalent and consists of samples from chicken and human sources. Notably, we identified the presence of diverse <i>bla</i> genes from the OXA-61 and OXA-184 families that confer beta-lactam resistance as well as the operon <i>cmeABCR</i> related to multidrug efflux pump, which contributes to resistance against tetracyclines, macrolides and quinolones. Based on limited data, we estimated the most recent common ancestor of ST353 to the late 1500s, coinciding with the time the Portuguese first arrived in Brazil and introduced domesticated chickens into the country. We identified at least two instances of ancestral chicken-to-human infections in ST353. The evolution of <i>C. jejuni</i> in Brazil was driven by the confluence of clinically relevant genetic elements, multi-host adaptation and clonal population growth that coincided with major socio-economic changes in poultry farming.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 7","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11316555/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141727402","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":"Evidence of <i>Lactobacillus</i> strains shared between the female urinary and vaginal microbiota.","authors":"Haley Atkins, Baani Sabharwal, Leah Boger, Natalie Stegman, Alexander Kula, Alan J Wolfe, Swarnali Banerjee, Catherine Putonti","doi":"10.1099/mgen.0.001267","DOIUrl":"10.1099/mgen.0.001267","url":null,"abstract":"<p><p><i>Lactobacillus</i> species are common inhabitants of the 'healthy' female urinary and vaginal communities, often associated with a lack of symptoms in both anatomical sites. Given identification by prior studies of similar bacterial species in both communities, it has been hypothesized that the two microbiotas are in fact connected. Here, we carried out whole-genome sequencing of 49 <i>Lactobacillus</i> strains, including 16 paired urogenital samples from the same participant. These strains represent five different <i>Lactobacillus</i> species: <i>L. crispatus</i>, <i>L. gasseri</i>, <i>L. iners</i>, <i>L. jensenii</i>, and <i>L. paragasseri</i>. Average nucleotide identity (ANI), alignment, single-nucleotide polymorphism (SNP), and CRISPR comparisons between strains from the same participant were performed. We conducted simulations of genome assemblies and ANI comparisons and present a statistical method to distinguish between unrelated, related, and identical strains. We found that 50 % of the paired samples have identical strains, evidence that the urinary and vaginal communities are connected. Additionally, we found evidence of strains sharing a common ancestor. These results establish that microbial sharing between the urinary tract and vagina is not limited to uropathogens. Knowledge that these two anatomical sites can share lactobacilli in females can inform future clinical approaches.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 7","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11316553/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141469297","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":"Rapid identification and subsequent contextualization of an outbreak of methicillin-resistant <i>Staphylococcus aureus</i> in a neonatal intensive care unit using nanopore sequencing.","authors":"Rhys T White, Sarah Bakker, Megan Burton, M Leticia Castro, Christine Couldrey, Kristin Dyet, Alexandra Eustace, Chad Harland, Samantha Hutton, Donia Macartney-Coxson, Claire Tarring, Charles Velasco, Emma M Voss, John Williamson, Max Bloomfield","doi":"10.1099/mgen.0.001273","DOIUrl":"10.1099/mgen.0.001273","url":null,"abstract":"<p><p>Outbreaks of methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) are well described in the neonatal intensive care unit (NICU) setting. Genomics has revolutionized the investigation of such outbreaks; however, to date, this has largely been completed retrospectively and has typically relied on short-read platforms. In 2022, our laboratory established a prospective genomic surveillance system using Oxford Nanopore Technologies sequencing for rapid outbreak detection. Herein, using this system, we describe the detection and control of an outbreak of sequence-type (ST)97 MRSA in our NICU. The outbreak was identified 13 days after the first MRSA-positive culture and at a point where there were only two known cases. Ward screening rapidly defined the extent of the outbreak, with six other infants found to be colonized. There was minimal transmission once the outbreak had been detected and appropriate infection control measures had been instituted; only two further ST97 cases were detected, along with three unrelated non-ST97 MRSA cases. To contextualize the outbreak, core-genome single-nucleotide variants were identified for phylogenetic analysis after <i>de novo</i> assembly of nanopore data. Comparisons with global (<i>n</i>=45) and national surveillance (<i>n</i>=35) ST97 genomes revealed the stepwise evolution of methicillin resistance within this ST97 subset. A distinct cluster comprising nine of the ten ST97-IVa genomes from the NICU was identified, with strains from 2020 to 2022 national surveillance serving as outgroups to this cluster. One ST97-IVa genome presumed to be part of the outbreak formed an outgroup and was retrospectively excluded. A second phylogeny was created using Illumina sequencing, which considerably reduced the branch lengths of the NICU isolates on the phylogenetic tree. However, the overall tree topology and conclusions were unchanged, with the exception of the NICU outbreak cluster, where differences in branch lengths were observed. This analysis demonstrated the ability of a nanopore-only prospective genomic surveillance system to rapidly identify and contextualize an outbreak of MRSA in a NICU.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 7","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11316549/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141534799","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 study of European <i>Clostridioides difficile</i> ribotype 002/sequence type 8.","authors":"Ines Dost, Mostafa Abdel-Glil, Søren Persson, Karen Loaiza Conza, Mónica Oleastro, Frederico Alves, Sven Maurischat, Anissa Scholtzek, Christelle Mazuet, Laure Diancourt, Tanel Tenson, Gernot Schmoock, Heinrich Neubauer, Stefan Schwarz, Christian Seyboldt","doi":"10.1099/mgen.0.001270","DOIUrl":"10.1099/mgen.0.001270","url":null,"abstract":"<p><p><i>Clostridioides difficile</i> has significant clinical importance as a leading cause of healthcare-associated infections, with symptoms ranging from mild diarrhoea to severe colitis, and possible life-threatening complications. <i>C. difficile</i> ribotype (RT) 002, mainly associated with MLST sequence type (ST) 8, is one of the most common RTs found in humans. This study aimed at investigating the genetic characteristics of 537 <i>C. difficile</i> genomes of ST8/RT002. To this end, we sequenced 298 <i>C</i>. <i>difficile</i> strains representing a new European genome collection, with strains from Germany, Denmark, France and Portugal. These sequences were analysed against a global dataset consisting of 1,437 ST8 genomes available through Enterobase. Our results showed close genetic relatedness among the studied ST8 genomes, a diverse array of antimicrobial resistance (AMR) genes and the presence of multiple mobile elements. Notably, the pangenome analysis revealed an open genomic structure. ST8 shows relatively low overall variation. Thus, clonal isolates were found across different One Health sectors (humans, animals, environment and food), time periods, and geographical locations, suggesting the lineage's stability and a universal environmental source. Importantly, this stability did not hinder the acquisition of AMR genes, emphasizing the adaptability of this bacterium to different selective pressures. Although only 2.4 % (41/1,735) of the studied genomes originated from non-human sources, such as animals, food, or the environment, we identified 9 cross-sectoral core genome multilocus sequence typing (cgMLST) clusters. Our study highlights the importance of ST8 as a prominent lineage of <i>C. difficile</i> with critical implications in the context of One Health. In addition, these findings strongly support the need for continued surveillance and investigation of non-human samples to gain a more comprehensive understanding of the epidemiology of <i>C. difficile</i>.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 7","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11316560/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141759633","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":"Mobile genetic element-driven genomic changes in a community-associated methicillin-resistant <i>Staphylococcus aureus</i> clone during its transmission in a regional community outbreak in Japan.","authors":"Katsuyuki Katahira, Yasuhiro Gotoh, Kentaro Kasama, Dai Yoshimura, Takehiko Itoh, Chieko Shimauchi, Akihiko Tajiri, Tetsuya Hayashi","doi":"10.1099/mgen.0.001272","DOIUrl":"10.1099/mgen.0.001272","url":null,"abstract":"<p><p>Community-associated methicillin-resistant <i>Staphylococcus aureus</i> (CA-MRSA) infections are now a public health concern in both community and healthcare settings worldwide. We previously identified a suspected case of a maternity clinic-centred outbreak of CA-MRSA skin infection in a regional community in Japan by PFGE-based analysis. In this study, we performed genome sequence-based analyses of 151 CA-MRSA isolates, which included not only outbreak-related isolates that we previously defined based on identical or similar PFGE patterns but also other isolates obtained during the same period in the same region. Our analysis accurately defined 133 isolates as outbreak-related isolates, collectively called the TDC clone. They belonged to a CA-MRSA lineage in clonal complex (CC) 30, known as the South West Pacific (SWP) clone. A high-resolution phylogenetic analysis of these isolates combined with their epidemiological data revealed that the TDC clone was already present and circulating in the region before the outbreak was recognized, and only the isolates belonging to two sublineages (named SL4 and SL5) were directly involved in the outbreak. Long persistence in patients/carriers and frequent intrahousehold transmission of the TDC clone were also revealed by this analysis. Moreover, by systematic analyses of the genome changes that occurred in this CA-MRSA clone during transmission in the community, we revealed that most variations were associated with mobile genetic elements (MGEs). Variant PFGE types were generated by alterations of prophages and genomic islands or insertion sequence (IS)-mediated insertion of a plasmid or a sequence of unknown origin. Dynamic changes in plasmid content, which were linked to changes in antimicrobial resistance profiles in specific isolates, were generated by frequent gain and loss of plasmids, most of which were self-transmissible or mobilizable. The introduction of IS<i>256</i> by a plasmid (named pTDC02) into sublineage SL5 led to SL5-specific amplification of IS<i>256,</i> and amplified IS<i>256</i> copies were involved in some of the structural changes of chromosomes and plasmids and generated variations in the repertoire of virulence-related genes in limited isolates. These data revealed how CA-MRSA genomes change during transmission in the community and how MGEs are involved in this process.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 7","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11316552/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141627121","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":"Phylogenomic and genomic analysis reveals unique and shared genetic signatures of <i>Mycobacterium kansasii</i> complex species.","authors":"Edson Machado, Sidra Vasconcellos, Lia Gomes, Marcos Catanho, Jesus Ramos, Luciana de Carvalho, Telma Goldenberg, Paulo Redner, Paulo Caldas, Carlos Campos, Margareth Dalcolmo, Maria Cristina Lourenço, Elena Lasunskaia, Vinicius Mussi, Lizania Spinassé, Solange Vinhas, Leen Rigouts, Sari Cogneau, Pim de Rijk, Christian Utpatel, Jarmila Kaustova, Tridia van der Laan, Han de Neeling, Nalin Rastogi, Klavdia Levina, Marge Kütt, Igor Mokrousov, Viacheslav Zhuravlev, Ndivhu Makhado, Manca Žolnir-Dovč, Vera Jankovic, Jacobus de Waard, Maria Carolina Sisco, Dick van Soolingen, Stefan Niemann, Bouke C de Jong, Conor J Meehan, Philip Suffys","doi":"10.1099/mgen.0.001266","DOIUrl":"10.1099/mgen.0.001266","url":null,"abstract":"<p><p>Species belonging to the <i>Mycobacterium kansasii</i> complex (MKC) are frequently isolated from humans and the environment and can cause serious diseases. The most common MKC infections are caused by the species <i>M. kansasii</i> (<i>sensu stricto</i>), leading to tuberculosis-like disease. However, a broad spectrum of virulence, antimicrobial resistance and pathogenicity of these non-tuberculous mycobacteria (NTM) are observed across the MKC. Many genomic aspects of the MKC that relate to these broad phenotypes are not well elucidated. Here, we performed genomic analyses from a collection of 665 MKC strains, isolated from environmental, animal and human sources. We inferred the MKC pangenome, mobilome, resistome, virulome and defence systems and show that the MKC species harbours unique and shared genomic signatures. High frequency of presence of prophages and different types of defence systems were observed. We found that the <i>M. kansasii</i> species splits into four lineages, of which three are lowly represented and mainly in Brazil, while one lineage is dominant and globally spread. Moreover, we show that four sub-lineages of this most distributed <i>M. kansasii</i> lineage emerged during the twentieth century. Further analysis of the <i>M. kansasii</i> genomes revealed almost 300 regions of difference contributing to genomic diversity, as well as fixed mutations that may explain the <i>M. kansasii</i>'s increased virulence and drug resistance.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 7","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11316565/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141627122","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}