Microbial Genomics最新文献

{"title":"Phylogenetic diversity of putative nickel-containing carbon monoxide dehydrogenase-encoding prokaryotes in the human gut microbiome.","authors":"Yuka Adachi Katayama, Ryoma Kamikawa, Takashi Yoshida","doi":"10.1099/mgen.0.001285","DOIUrl":"10.1099/mgen.0.001285","url":null,"abstract":"<p><p>Although the production of carbon monoxide (CO) within the human body has been detected, only two CO-utilizing prokaryotes (CO utilizers) have been reported in the human gut. Therefore, the phylogenetic diversity of the human gut CO-utilizing prokaryotes remains unclear. Here, we unveiled more than a thousand representative genomes containing genes for putative nickel-containing CO dehydrogenase (pCODH), an essential enzyme for CO utilization. The taxonomy of genomes encoding pCODH was expanded to include 8 phyla, comprising 82 genera and 248 species. In contrast, putative molybdenum-containing CODH genes were not detected in the human gut microbial genomes. pCODH transcripts were detected in 97.3 % (<i>n</i>=110) of public metatranscriptome datasets derived from healthy human faeces, suggesting the ubiquitous presence of prokaryotes bearing transcriptionally active pCODH genes in the human gut. More than half of the pCODH-encoding genomes contain a set of genes for the autotrophic Wood-Ljungdahl pathway (WLP). However, 79 % of these genomes commonly lack a key gene for the WLP, which encodes the enzyme that synthesizes formate from CO₂, suggesting that potential human gut CO-utilizing prokaryotes share a degenerated gene set for WLP. In the other half of the pCODH-encoding genomes, seven genes, including putative genes for flavin adenine dinucleotide-dependent NAD(P) oxidoreductase (FNOR), ABC transporter and Fe-hydrogenase, were found adjacent to the pCODH gene. None of the putative genes associated with CO-oxidizing respiratory machinery, such as energy-converting hydrogenase genes, were found in pCODH-encoding genomes. This suggests that the human gut CO utilization is not for CO removal, but potentially for fixation and/or biosynthesis, consistent with the harmless yet continuous production of CO in the human gut. Our findings reveal the diversity and distribution of prokaryotes with pCODH in the human gut microbiome, suggesting their potential contribution to microbial ecosystems in human gut environments.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11338639/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142017965","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":"Whole-genome sequencing of Western Canadian <i>Borrelia</i> spp. collected from diverse tick and animal hosts reveals short-lived local genotypes interspersed with longer-lived continental genotypes.","authors":"Jennifer N Russell, Min-Kuang Lee, Miguel I Uyaguari-Diaz, Ashton N Sies, Danae M Suchan, William Hsiao, Erin Fraser, Muhammad G Morshed, Andrew D S Cameron","doi":"10.1099/mgen.0.001276","DOIUrl":"10.1099/mgen.0.001276","url":null,"abstract":"<p><p>Changing climates are allowing the geographic expansion of ticks and their animal hosts, increasing the risk of <i>Borrelia</i>-caused zoonoses in Canada. However, little is known about the genomic diversity of <i>Borrelia</i> from the west of the Canadian Rockies and from the tick vectors <i>Ixodes pacificus</i>, <i>Ixodes auritulus</i> and <i>Ixodes angustus</i>. Here, we report the whole-genome shotgun sequences of 51 <i>Borrelia</i> isolates from multiple tick species collected on a range of animal hosts between 1993 and 2016, located primarily in coastal British Columbia. The bacterial isolates represented three different species from the Lyme disease-causing <i>Borrelia burgdorferi sensu lato</i> genospecies complex [<i>Borrelia burgdorferi sensu stricto</i> (<i>n</i>=47), <i>Borrelia americana</i> (<i>n</i>=3) and <i>Borrelia bissettiae</i> (<i>n</i>=1)]. The traditional eight-gene multi-locus sequence typing (MLST) strategy was applied to facilitate comparisons across studies. This identified 13 known <i>Borrelia</i> sequence types (STs), established 6 new STs, and assigned 5 novel types to the nearest sequence types. <i>B. burgdorferi</i> s. s. isolates were further differentiated into ten <i>ospC</i> types, plus one novel <i>ospC</i> with less than 92 % nucleotide identity to all previously defined <i>ospC</i> types. The MLST types resampled over extended time periods belonged to previously described STs that are distributed across North America. The most geographically widespread ST, ST.12, was isolated from all three tick species. Conversely, new <i>B. burgdorferi</i> s. s. STs from Vancouver Island and the Vancouver region were only detected for short periods, revealing a surprising transience in space, time and host tick species, possibly due to displacement by longer-lived genotypes that expanded across North America.This article contains data hosted by Microreact.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11296321/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141875283","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":"Capturing clinically relevant <i>Campylobacter</i> attributes through direct whole genome sequencing of stool.","authors":"Bilal Djeghout, Thanh Le-Viet, Leonardo de Oliveira Martins, George M Savva, Rhiannon Evans, David Baker, Andrew Page, Ngozi Elumogo, John Wain, Nicol Janecko","doi":"10.1099/mgen.0.001284","DOIUrl":"https://doi.org/10.1099/mgen.0.001284","url":null,"abstract":"<p><p><i>Campylobacter</i> is the leading bacterial cause of infectious intestinal disease, but the pathogen typically accounts for a very small proportion of the overall stool microbiome in each patient. Diagnosis is even more difficult due to the fastidious nature of <i>Campylobacter</i> in the laboratory setting. This has, in part, driven a change in recent years, from culture-based to rapid PCR-based diagnostic assays which have improved diagnostic detection, whilst creating a knowledge gap in our clinical and epidemiological understanding of <i>Campylobacter</i> genotypes - no isolates to sequence. In this study, direct metagenomic sequencing approaches were used to assess the possibility of replacing genome sequences with metagenome sequences; metagenomic sequencing outputs were used to describe clinically relevant attributes of <i>Campylobacter</i> genotypes. A total of 37 diarrhoeal stool samples with <i>Campylobacter</i> and five samples with an unknown pathogen result were collected and processed with and without filtration, DNA was extracted, and metagenomes were sequenced by short-read sequencing. Culture-based methods were used to validate <i>Campylobacter</i> metagenome-derived genome (MDG) results. Sequence output metrics were assessed for <i>Campylobacter</i> genome quality and accuracy of characterization. Of the 42 samples passing quality checks for analysis, identification of <i>Campylobacter</i> to the genus and species level was dependent on <i>Campylobacter</i> genome read count, coverage and genome completeness. A total of 65% (24/37) of samples were reliably identified to the genus level through <i>Campylobacter</i> MDG, 73% (27/37) by culture and 97% (36/37) by qPCR. The <i>Campylobacter</i> genomes with a genome completeness of over 60% (<i>n</i>=21) were all accurately identified at the species level (100%). Of those, 72% (15/21) were identified to sequence types (STs), and 95% (20/21) accurately identified antimicrobial resistance (AMR) gene determinants. Filtration of stool samples enhanced <i>Campylobacter</i> MDG recovery and genome quality metrics compared to the corresponding unfiltered samples, which improved the identification of STs and AMR profiles. The phylogenetic analysis in this study demonstrated the clustering of the metagenome-derived with culture-derived genomes and revealed the reliability of genomes from direct stool sequencing. Furthermore, <i>Campylobacter</i> genome spiking percentages ranging from 0 to 2% total metagenome abundance in the ONT MinION sequencer, configured to adaptive sequencing, exhibited better assembly quality and accurate identification of STs, particularly in the analysis of metagenomes containing 2 and 1% of <i>Campylobacter jejuni</i> genomes. Direct sequencing of <i>Campylobacter</i> from stool samples provides clinically relevant and epidemiologically important genomic information without the reliance on cultured genomes.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142109155","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":"Development of the Pneumococcal Genome Library, a core genome multilocus sequence typing scheme, and a taxonomic life identification number barcoding system to investigate and define pneumococcal population structure.","authors":"Melissa J Jansen van Rensburg, Duncan J Berger, Iman Yassine, David Shaw, Andy Fohrmann, James E Bray, Keith A Jolley, Martin C J Maiden, Angela B Brueggemann","doi":"10.1099/mgen.0.001280","DOIUrl":"10.1099/mgen.0.001280","url":null,"abstract":"<p><p>Investigating the genomic epidemiology of major bacterial pathogens is integral to understanding transmission, evolution, colonization, disease, antimicrobial resistance and vaccine impact. Furthermore, the recent accumulation of large numbers of whole genome sequences for many bacterial species enhances the development of robust genome-wide typing schemes to define the overall bacterial population structure and lineages within it. Using the previously published data, we developed the Pneumococcal Genome Library (PGL), a curated dataset of 30 976 genomes and contextual data for carriage and disease pneumococci recovered between 1916 and 2018 in 82 countries. We leveraged the size and diversity of the PGL to develop a core genome multilocus sequence typing (cgMLST) scheme comprised of 1222 loci. Finally, using multilevel single-linkage clustering, we stratified pneumococci into hierarchical clusters based on allelic similarity thresholds and defined these with a taxonomic life identification number (LIN) barcoding system. The PGL, cgMLST scheme and LIN barcodes represent a high-quality genomic resource and fine-scale clustering approaches for the analysis of pneumococcal populations, which support the genomic epidemiology and surveillance of this leading global pathogen.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11321556/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141976130","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":"Complete genome of the Medicago anthracnose fungus, <i>Colletotrichum destructivum</i>, reveals a mini-chromosome-like region within a core chromosome.","authors":"Nicolas Lapalu, Adeline Simon, Antoine Lu, Peter-Louis Plaumann, Joëlle Amselem, Sandrine Pigné, Annie Auger, Christian Koch, Jean-Félix Dallery, Richard J O'Connell","doi":"10.1099/mgen.0.001283","DOIUrl":"10.1099/mgen.0.001283","url":null,"abstract":"<p><p><i>Colletotrichum destructivum</i> (<i>Cd</i>) is a phytopathogenic fungus causing significant economic losses on forage legume crops (<i>Medicago</i> and <i>Trifolium</i> species) worldwide. To gain insights into the genetic basis of fungal virulence and host specificity, we sequenced the genome of an isolate from <i>Medicago sativa</i> using long-read (PacBio) technology. The resulting genome assembly has a total length of 51.7 Mb and comprises ten core chromosomes and two accessory chromosomes, all of which were sequenced from telomere to telomere. A total of 15, 631 gene models were predicted, including genes encoding potentially pathogenicity-related proteins such as candidate-secreted effectors (484), secondary metabolism key enzymes (110) and carbohydrate-active enzymes (619). Synteny analysis revealed extensive structural rearrangements in the genome of <i>Cd</i> relative to the closely related Brassicaceae pathogen, <i>Colletotrichum higginsianum</i>. In addition, a 1.2 Mb species-specific region was detected within the largest core chromosome of <i>Cd</i> that has all the characteristics of fungal accessory chromosomes (transposon-rich, gene-poor, distinct codon usage), providing evidence for exchange between these two genomic compartments. This region was also unique in having undergone extensive intra-chromosomal segmental duplications. Our findings provide insights into the evolution of accessory regions and possible mechanisms for generating genetic diversity in this asexual fungal pathogen.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11338638/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142017963","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":"Detection of novel orthoparamyxoviruses, orthonairoviruses and an orthohepevirus in European white-toothed shrews.","authors":"Viola C Haring, Benedikt Litz, Jens Jacob, Michael Brecht, Markus Bauswein, Julia Sehl-Ewert, Marta Heroldova, Claudia Wylezich, Donata Hoffmann, Rainer G Ulrich, Martin Beer, Florian Pfaff","doi":"10.1099/mgen.0.001275","DOIUrl":"10.1099/mgen.0.001275","url":null,"abstract":"<p><p>While the viromes and immune systems of bats and rodents have been extensively studied, comprehensive data are lacking for insectivores (order Eulipotyphla) despite their wide geographic distribution. Anthropogenic land use and outdoor recreational activities, as well as changes in the range of shrews, may lead to an expansion of the human-shrew interface with the risk of spillover infections, as reported for Borna disease virus 1. We investigated the virome of 45 individuals of 4 white-toothed shrew species present in Europe, using metagenomic RNA sequencing of tissue and intestine pools. Moderate to high abundances of sequences related to the families <i>Paramyxoviridae</i>, <i>Nairoviridae</i>, <i>Hepeviridae</i> and <i>Bornaviridae</i> were detected. Whole genomes were determined for novel orthoparamyxoviruses (<i>n</i>=3), orthonairoviruses (<i>n</i>=2) and an orthohepevirus. The novel paramyxovirus, tentatively named Hasua virus, was phylogenetically related to the zoonotic Langya virus and Mòjiāng virus. The novel orthonairoviruses, along with the potentially zoonotic Erve virus, fall within the shrew-borne Thiafora virus genogroup. The highest viral RNA loads of orthoparamyxoviruses were detected in the kidneys, in well-perfused organs for orthonairoviruses and in the liver and intestine for orthohepevirus, indicating potential transmission routes. Notably, several shrews were found to be coinfected with viruses from different families. Our study highlights the virus diversity present in shrews, not only in biodiversity-rich regions but also in areas influenced by human activity. This study warrants further research to characterize and assess the clinical implications and risk of these viruses and the importance of shrews as reservoirs in European ecosystems.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11293873/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141860203","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":"Comparison of gene-by-gene and genome-wide short nucleotide sequence-based approaches to define the global population structure of <i>Streptococcus pneumoniae</i>.","authors":"Alannah C King, Narender Kumar, Kate C Mellor, Paulina A Hawkins, Lesley McGee, Nicholas J Croucher, Stephen D Bentley, John A Lees, Stephanie W Lo","doi":"10.1099/mgen.0.001278","DOIUrl":"10.1099/mgen.0.001278","url":null,"abstract":"<p><p>Defining the population structure of a pathogen is a key part of epidemiology, as genomically related isolates are likely to share key clinical features such as antimicrobial resistance profiles and invasiveness. Multiple different methods are currently used to cluster together closely related genomes, potentially leading to inconsistency between studies. Here, we use a global dataset of 26 306 <i>Streptococcus pneumoniae</i> genomes to compare four clustering methods: gene-by-gene seven-locus MLST, core genome MLST (cgMLST)-based hierarchical clustering (HierCC) assignments, life identification number (LIN) barcoding and k-mer-based PopPUNK clustering (known as GPSCs in this species). We compare the clustering results with phylogenetic and pan-genome analyses to assess their relationship with genome diversity and evolution, as we would expect a good clustering method to form a single monophyletic cluster that has high within-cluster similarity of genomic content. We show that the four methods are generally able to accurately reflect the population structure based on these metrics and that the methods were broadly consistent with each other. We investigated further to study the discrepancies in clusters. The greatest concordance was seen between LIN barcoding and HierCC (adjusted mutual information score=0.950), which was expected given that both methods utilize cgMLST, but have different methods for defining an individual cluster and different core genome schema. However, the existence of differences between the two methods shows that the selection of a core genome schema can introduce inconsistencies between studies. GPSC and HierCC assignments were also highly concordant (AMI=0.946), showing that k-mer-based methods which use the whole genome and do not require the careful selection of a core genome schema are just as effective at representing the population structure. Additionally, where there were differences in clustering between these methods, this could be explained by differences in the accessory genome that were not identified in cgMLST. We conclude that for <i>S. pneumoniae</i>, standardized and stable nomenclature is important as the number of genomes available expands. Furthermore, the research community should transition away from seven-locus MLST, whilst cgMLST, GPSC and LIN assignments should be used more widely. However, to allow for easy comparison between studies and to make previous literature relevant, the reporting of multiple clustering names should be standardized within the research.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11353345/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142080741","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":"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":"https://doi.org/10.1099/mgen.0.001286","url":null,"abstract":"","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","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":null,"pages":null},"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":null,"pages":null},"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}