Microbial Genomics最新文献

{"title":"The hidden RNA viruses in <i>Blattodea</i> (cockroaches and termites).","authors":"Haoming Wu, Wenxin Li, Jingyan Fan, Shengsheng Jiang, Jiaxin Li, Peng Hu, Zejun Yu, Yang Li, Rui Pang, Huan Wu","doi":"10.1099/mgen.0.001265","DOIUrl":"10.1099/mgen.0.001265","url":null,"abstract":"<p><p>The insect order <i>Blattodea</i> (cockroaches and termites) has drawn substantial research attention for their dietary habits and lifestyle of living with or around humans. In the present study, we focused on the discovery of RNA viruses hidden in <i>Blattodea</i> insects using the publicly available RNA sequencing datasets. Overall, 136 distinctive RNA viruses were identified from 36 <i>Blattodea</i> species, of which more than 70 % were most closely related to the invertebrate-associated viral groups within <i>Picornavirales</i>, <i>Sobelivirales</i>, <i>Bunyaviricetes</i>, <i>Jingchuvirales</i>, <i>Durnavirales</i>, <i>Lispiviridae</i>, <i>Orthomyxoviridae</i>, <i>Permutotetraviridae</i>, <i>Flaviviridae</i> and <i>Muvirales</i>. Several viruses were associated with pathogens of vertebrates (<i>Paramyxoviridae</i>), plants (<i>Tymovirales</i>), protozoa (<i>Totiviridae</i>), fungi (<i>Narnaviridae</i>) and bacteria (<i>Norzivirales</i>). Collectively, 93 complete or near-complete viral genomes were retrieved from the datasets, and several viruses appeared to have remarkable temporal and spatial distributions. Interestingly, the newly identified <i>Periplaneta americana</i> dicistrovirus displayed a remarkable distinct bicistronic genome arrangement from the well-recognized dicistroviruses with the translocated structural and non-structural polyprotein encoding open reading frames over the genome. These results significantly enhance our knowledge of RNA virosphere in <i>Blattodea</i> insects, and the novel genome architectures in dicistroviruses and other RNA viruses may break our stereotypes in the understanding of the genomic evolution and the emergence of potential novel viral species.</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/PMC11316551/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141734553","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":"Giants' cooperation: a draft genome of the giant ciliate <i>Muniziella cunhai</i> suggests its ecological role in the capybara's digestive metabolism.","authors":"Franciane Cedrola, Marcus Vinicius Xavier Senra, Millke Jasmine Arminini Morales, Priscila Fregulia, Lucas Canesin, Roberto Júnio Pedroso Dias, Vera Nisaka Solferini","doi":"10.1099/mgen.0.001263","DOIUrl":"10.1099/mgen.0.001263","url":null,"abstract":"<p><p>Several hundred ciliate species live in animals' guts as a part of their microbiome. Among them, <i>Muniziella cunhai</i> (Trichostomatia, Pycnotrichidae), the largest described ciliate, is found exclusively associated with <i>Hydrochoerus hydrochaeris</i> (capybara), the largest known rodent reaching up to 90 kg. Here, we present the sequence, structural and functional annotation of this giant microeukaryote macronuclear genome and discuss its phylogenetic placement. The 85 Mb genome is highly AT rich (GC content 25.71 %) and encodes a total of 11 397 protein-coding genes, of which 2793 could have their functions predicted with automated functional assignments. Functional annotation showed that <i>M. cunhai</i> can digest recalcitrant structural carbohydrates, non-structural carbohydrates, and microbial cell walls, suggesting a role in diet metabolization and in microbial population control in the capybara's intestine. Moreover, the phylogenetic placement of <i>M. cunhai</i> provides insights on the origins of gigantism in the subclass Trichostomatia.</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/PMC11316547/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141492560","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":"Geographical distribution, disease association and diversity of <i>Klebsiella pneumoniae</i> K/L and O antigens in India: roadmap for vaccine development.","authors":"Varun Shamanna, Srikanth Srinivas, Natacha Couto, Geetha Nagaraj, Shyama Prasad Sajankila, Harshitha Gangaiah Krishnappa, Kavitha Arakalgud Kumar, David M Aanensen, Ravikumar Kadahalli Lingegowda, Nihr Global Health Research Unit On Genomic Surveillance-India Consortium","doi":"10.1099/mgen.0.001271","DOIUrl":"10.1099/mgen.0.001271","url":null,"abstract":"<p><p><i>Klebsiella pneumoniae</i> poses a significant healthcare challenge due to its multidrug resistance and diverse serotype landscape. This study aimed to explore the serotype diversity of 1072 <i>K</i>. <i>pneumoniae</i> and its association with geographical distribution, disease severity and antimicrobial/virulence patterns in India. Whole-genome sequencing was performed on the Illumina platform, and genomic analysis was carried out using the Kleborate tool. The analysis revealed a total of 78 different KL types, among which KL64 (<i>n</i>=274/1072, 26 %), KL51 (<i>n</i>=249/1072, 24 %), and KL2 (<i>n</i>=88/1072, 8 %) were the most prevalent. In contrast, only 13 distinct O types were identified, with O1/O2v1 (<i>n</i>=471/1072, 44 %), O1/O2v2 (<i>n</i>=353/1072, 33 %), and OL101 (<i>n</i>=66/1072, 6 %) being the predominant serotypes. The study identified 114 different sequence types (STs) with varying serotypes, with ST231 being the most predominant. O serotypes were strongly linked with STs, with O1/O2v1 predominantly associated with ST231. Simpson's diversity index and Fisher's exact test revealed higher serotype diversity in the north and east regions, along with intriguing associations between specific serotypes and resistance profiles. No significant association between KL or O types and disease severity was observed. Furthermore, we found the specific association of virulence factors yersiniabactin and aerobactin (<i>P</i><0.05) with KL types but no association with O antigen types (<i>P</i>>0.05). Conventionally described hypervirulent clones (i.e. KL1 and KL2) in India lacked typical virulent markers (i.e. aerobactin), contrasting with other regional serotypes (KL51). The cumulative distribution of KL and O serotypes suggests that future vaccines may have to include either ~20 KL or four O types to cover >85 % of the carbapenemase-producing Indian <i>K. pneumoniae</i> population. The results highlight the necessity for comprehensive strategies to manage the diverse landscape of <i>K. pneumoniae</i> strains across different regions in India. Understanding regional serotype dynamics is pivotal for targeted surveillance, interventions, and tailored vaccine strategies to tackle the diverse landscape of <i>K. pneumoniae</i> infections across India. This article contains data hosted by Microreact.</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/PMC11316559/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141734552","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":"PHA4GE quality control contextual data tags: standardized annotations for sharing public health sequence datasets with known quality issues to facilitate testing and training.","authors":"Emma J Griffiths, Inês Mendes, Finlay Maguire, Jennifer L Guthrie, Bryan A Wee, Sarah Schmedes, Kathryn Holt, Chanchal Yadav, Rhiannon Cameron, Charlotte Barclay, Damion Dooley, Duncan MacCannell, Leonid Chindelevitch, Ilene Karsch-Mizrachi, Zahra Waheed, Lee Katz, Robert Petit Iii, Mugdha Dave, Paul Oluniyi, Muhammad Ibtisam Nasar, Amogelang Raphenya, William W L Hsiao, Ruth E Timme","doi":"10.1099/mgen.0.001260","DOIUrl":"10.1099/mgen.0.001260","url":null,"abstract":"&lt;p&gt;&lt;p&gt;As public health laboratories expand their genomic sequencing and bioinformatics capacity for the surveillance of different pathogens, labs must carry out robust validation, training, and optimization of wet- and dry-lab procedures. Achieving these goals for algorithms, pipelines and instruments often requires that lower quality datasets be made available for analysis and comparison alongside those of higher quality. This range of data quality in reference sets can complicate the sharing of sub-optimal datasets that are vital for the community and for the reproducibility of assays. Sharing of useful, but sub-optimal datasets requires careful annotation and documentation of known issues to enable appropriate interpretation, avoid being mistaken for better quality information, and for these data (and their derivatives) to be easily identifiable in repositories. Unfortunately, there are currently no standardized attributes or mechanisms for tagging poor-quality datasets, or datasets generated for a specific purpose, to maximize their utility, searchability, accessibility and reuse. The Public Health Alliance for Genomic Epidemiology (PHA4GE) is an international community of scientists from public health, industry and academia focused on improving the reproducibility, interoperability, portability, and openness of public health bioinformatic software, skills, tools and data. To address the challenges of sharing lower quality datasets, PHA4GE has developed a set of standardized contextual data tags, namely fields and terms, that can be included in public repository submissions as a means of flagging pathogen sequence data with known quality issues, increasing their discoverability. The contextual data tags were developed through consultations with the community including input from the International Nucleotide Sequence Data Collaboration (INSDC), and have been standardized using ontologies - community-based resources for defining the tag properties and the relationships between them. The standardized tags are agnostic to the organism and the sequencing technique used and thus can be applied to data generated from any pathogen using an array of sequencing techniques. The tags can also be applied to synthetic (lab created) data. The list of standardized tags is maintained by PHA4GE and can be found at https://github.com/pha4ge/contextual_data_QC_tags. Definitions, ontology IDs, examples of use, as well as a JSON representation, are provided. The PHA4GE QC tags were tested, and are now implemented, by the FDA's GenomeTrakr laboratory network as part of its routine submission process for SARS-CoV-2 wastewater surveillance. We hope that these simple, standardized tags will help improve communication regarding quality control in public repositories, in addition to making datasets of variable quality more easily identifiable. Suggestions for additional tags can be submitted to PHA4GE via the New Term Request Form in the GitHub repository. By providing ","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 6","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11261899/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141300996","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":"Prevalence and diversity of TAL effector-like proteins in fungal endosymbiotic <i>Mycetohabitans</i> spp.","authors":"Sara C D Carpenter, Adam J Bogdanove, Bhuwan Abbot, Jason E Stajich, Jessie K Uehling, Brian Lovett, Matt T Kasson, Morgan E Carter","doi":"10.1099/mgen.0.001261","DOIUrl":"10.1099/mgen.0.001261","url":null,"abstract":"<p><p>Endofungal <i>Mycetohabitans</i> (formerly <i>Burkholderia</i>) spp. rely on a type III secretion system to deliver mostly unidentified effector proteins when colonizing their host fungus, <i>Rhizopus microsporus</i>. The one known secreted effector family from <i>Mycetohabitans</i> consists of homologues of transcription activator-like (TAL) effectors, which are used by plant pathogenic <i>Xanthomonas</i> and <i>Ralstonia</i> spp. to activate host genes that promote disease. These '<i>Burkholderia</i> TAL-like (Btl)' proteins bind corresponding specific DNA sequences in a predictable manner, but their genomic target(s) and impact on transcription in the fungus are unknown. Recent phenotyping of Btl mutants of two <i>Mycetohabitans</i> strains revealed that the single Btl in one <i>Mycetohabitans endofungorum</i> strain enhances fungal membrane stress tolerance, while others in a <i>Mycetohabitans rhizoxinica</i> strain promote bacterial colonization of the fungus. The phenotypic diversity underscores the need to assess the sequence diversity and, given that sequence diversity translates to DNA targeting specificity, the functional diversity of Btl proteins. Using a dual approach to maximize capture of Btl protein sequences for our analysis, we sequenced and assembled nine <i>Mycetohabitans</i> spp. genomes using long-read PacBio technology and also mined available short-read Illumina fungal-bacterial metagenomes. We show that <i>btl</i> genes are present across diverse <i>Mycetohabitans</i> strains from Mucoromycota fungal hosts yet vary in sequences and predicted DNA binding specificity. Phylogenetic analysis revealed distinct clades of Btl proteins and suggested that <i>Mycetohabitans</i> might contain more species than previously recognized. Within our data set, Btl proteins were more conserved across <i>M. rhizoxinica</i> strains than across <i>M. endofungorum</i>, but there was also evidence of greater overall strain diversity within the latter clade. Overall, the results suggest that Btl proteins contribute to bacterial-fungal symbioses in myriad ways.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 6","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11261895/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141300997","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":"How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies.","authors":"George Bouras, Louise M Judd, Robert A Edwards, Sarah Vreugde, Timothy P Stinear, Ryan R Wick","doi":"10.1099/mgen.0.001254","DOIUrl":"10.1099/mgen.0.001254","url":null,"abstract":"<p><p>It is now possible to assemble near-perfect bacterial genomes using Oxford Nanopore Technologies (ONT) long reads, but short-read polishing is usually required for perfection. However, the effect of short-read depth on polishing performance is not well understood. Here, we introduce Pypolca (with default and careful parameters) and Polypolish v0.6.0 (with a new careful parameter). We then show that: (1) all polishers other than Pypolca-careful, Polypolish-default and Polypolish-careful commonly introduce false-positive errors at low read depth; (2) most of the benefit of short-read polishing occurs by 25× depth; (3) Polypolish-careful almost never introduces false-positive errors at any depth; and (4) Pypolca-careful is the single most effective polisher. Overall, we recommend the following polishing strategies: Polypolish-careful alone when depth is very low (<5×), Polypolish-careful and Pypolca-careful when depth is low (5-25×), and Polypolish-default and Pypolca-careful when depth is sufficient (>25×).</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 6","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11261834/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141237827","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":"Plasmid genomic epidemiology of carbapenem-hydrolysing class D β-lactamase (CDHL)-producing <i>Enterobacterales</i> in Canada, 2010-2021.","authors":"Nicole Lerminiaux, Robyn Mitchell, Kevin Katz, Ken Fakharuddin, Erin McGill, Laura Mataseje","doi":"10.1099/mgen.0.001257","DOIUrl":"10.1099/mgen.0.001257","url":null,"abstract":"<p><p>Carbapenems are last-resort antibiotics for treatment of infections caused by multidrug-resistant <i>Enterobacterales</i>, but carbapenem resistance is a rising global threat due to the acquisition of carbapenemase genes. Oxacillinase-48 (<i>bla</i> _OXA-48)-type carbapenemases are increasing in abundance in Canada and elsewhere; these genes are frequently found on mobile genetic elements and are associated with specific transposons. This means that alongside clonal dissemination, <i>bla</i> _OXA-48-type genes can spread through plasmid-mediated horizontal gene transfer. We applied whole genome sequencing to characterize 249 <i>bla</i> _OXA-48-type-producing <i>Enterobacterales</i> isolates collected by the Canadian Nosocomial Infection Surveillance Program from 2010 to 2021. Using a combination of short- and long-read sequencing, we obtained 70 complete and circular <i>bla</i> _OXA-48-type-encoding plasmids. Using MOB-suite, four major plasmids clustered were identified, and we further estimated a plasmid cluster for 91.9 % (147/160) of incomplete <i>bla</i> _OXA-48-type-encoding contigs. We identified different patterns of carbapenemase mobilization across Canada, including horizontal transmission of <i>bla</i> _OXA-181/IncX3 plasmids (75/249, 30.1 %) and <i>bla</i> _OXA-48/IncL/M plasmids (47/249, 18.9 %), and both horizontal transmission and clonal transmission of <i>bla</i> _OXA-232 for <i>Klebsiella pneumoniae</i> ST231 on ColE2-type/ColKP3 plasmids (25/249, 10.0 %). Our findings highlight the diversity of OXA-48-type plasmids and indicate that multiple plasmid clusters and clonal transmission have contributed to <i>bla</i> _OXA-48-type spread and persistence in Canada.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 6","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11261825/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141419746","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":"Expansion of pneumococcal serotype 23F and 14 lineages with genotypic changes in capsule polysaccharide locus and virulence gene profiles post introduction of pneumococcal conjugate vaccine in Blantyre, Malawi.","authors":"Rory Cave, Akuzike Kalizang'oma, Chrispin Chaguza, Thandie S Mwalukomo, Arox Kamng'ona, Comfort Brown, Jacquline Msefula, Farouck Bonomali, Roseline Nyirenda, Todd D Swarthout, Brenda Kwambana-Adams, Neil French, Robert S Heyderman","doi":"10.1099/mgen.0.001264","DOIUrl":"10.1099/mgen.0.001264","url":null,"abstract":"<p><p>Since the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13) in Malawi in 2011, there has been persistent carriage of vaccine serotype (VT) <i>Streptococcus pneumoniae</i>, despite high vaccine coverage. To determine if there has been a genetic change within the VT capsule polysaccharide (cps) loci since the vaccine's introduction, we compared 1022 whole-genome-sequenced VT isolates from 1998 to 2019. We identified the clonal expansion of a multidrug-resistant, penicillin non-susceptible serotype 23F GPSC14-ST2059 lineage, a serotype 14 GPSC9-ST782 lineage and a novel serotype 14 sequence type GPSC9-ST18728 lineage. Serotype 23F GPSC14-ST2059 had an I253T mutation within the capsule oligosaccharide repeat unit polymerase Wzy protein, which is predicted <i>in silico</i> to alter the protein pocket cavity. Moreover, serotype 23F GPSC14-ST2059 had SNPs in the DNA binding sites for the cps transcriptional repressors CspR and SpxR. Serotype 14 GPSC9-ST782 harbours a non-truncated version of the large repetitive protein (Lrp), containing a Cna protein B-type domain which is also present in proteins associated with infection and colonisation. These emergent lineages also harboured genes associated with antibiotic resistance, and the promotion of colonisation and infection which were absent in other lineages of the same serotype. Together these data suggest that in addition to serotype replacement, modifications of the capsule locus associated with changes in virulence factor expression and antibiotic resistance may promote vaccine escape. In summary, the study highlights that the persistence of vaccine serotype carriage despite high vaccine coverage in Malawi may be partly caused by expansion of VT lineages post-PCV13 rollout.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 6","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11261835/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141419805","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":"Model-driven characterization of functional diversity of <i>Pseudomonas aeruginosa</i> clinical isolates with broadly representative phenotypes.","authors":"Mohammad Mazharul Islam, Glynis L Kolling, Emma M Glass, Joanna B Goldberg, Jason A Papin","doi":"10.1099/mgen.0.001259","DOIUrl":"10.1099/mgen.0.001259","url":null,"abstract":"<p><p><i>Pseudomonas aeruginosa</i> is a leading cause of infections in immunocompromised individuals and in healthcare settings. This study aims to understand the relationships between phenotypic diversity and the functional metabolic landscape of <i>P. aeruginosa</i> clinical isolates. To better understand the metabolic repertoire of <i>P. aeruginosa</i> in infection, we deeply profiled a representative set from a library of 971 clinical <i>P. aeruginosa</i> isolates with corresponding patient metadata and bacterial phenotypes. The genotypic clustering based on whole-genome sequencing of the isolates, multilocus sequence types, and the phenotypic clustering generated from a multi-parametric analysis were compared to each other to assess the genotype-phenotype correlation. Genome-scale metabolic network reconstructions were developed for each isolate through amendments to an existing PA14 network reconstruction. These network reconstructions show diverse metabolic functionalities and enhance the collective <i>P. aeruginosa</i> pangenome metabolic repertoire. Characterizing this rich set of clinical <i>P. aeruginosa</i> isolates allows for a deeper understanding of the genotypic and metabolic diversity of the pathogen in a clinical setting and lays a foundation for further investigation of the metabolic landscape of this pathogen and host-associated metabolic differences during infection.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 6","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11261902/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141248300","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":"Estimating geographical spread of <i>Streptococcus pneumoniae</i> within Israel using genomic data.","authors":"Hsueh-Chien Raymond Cheng, Sophie Belman, Henrik Salje, Ron Dagan, Stephen D Bentley","doi":"10.1099/mgen.0.001262","DOIUrl":"10.1099/mgen.0.001262","url":null,"abstract":"<p><p>Understanding how pathogens spread across geographical space is fundamental for control measures such as vaccination. <i>Streptococcus pneumoniae</i> (the pneumococcus) is a respiratory bacterium responsible for a large proportion of infectious disease morbidity and mortality globally. Even in the post-vaccination era, the rates of invasive pneumococcal disease (IPD) remain stable in most countries, including Israel. To understand the geographical spread of the pneumococcus in Israel, we analysed 1174 pneumococcal genomes from patients with IPD across multiple regions. We included the evolutionary distance between pairs of isolates inferred using whole-genome data within a relative risk (RR) ratio framework to capture the geographical structure of <i>S. pneumoniae</i>. While we could not find geographical structure at the overall lineage level, the extra granularity provided by whole-genome sequence data showed that it takes approximately 5 years for invasive pneumococcal isolates to become fully mixed across the country.This article contains data hosted by Microreact.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 6","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11261897/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141443037","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}