Microbial Genomics最新文献

{"title":"High intra-laboratory reproducibility of nanopore sequencing in bacterial species underscores advances in its accuracy.","authors":"Mostafa Y Abdel-Glil, Christian Brandt, Mathias W Pletz, Heinrich Neubauer, Lisa D Sprague","doi":"10.1099/mgen.0.001372","DOIUrl":"10.1099/mgen.0.001372","url":null,"abstract":"<p><p>Nanopore sequencing is a third-generation technology known for its portability, real-time analysis and ability to generate long reads. It has great potential for use in clinical diagnostics, but thorough validation is required to address accuracy concerns and ensure reliable and reproducible results. In this study, we automated an open-source workflow (freely available at https://gitlab.com/FLI_Bioinfo/nanobacta) for the assembly of Oxford Nanopore sequencing data and used it to investigate the reproducibility of assembly results under consistent conditions. We used a benchmark dataset of five bacterial reference strains and generated eight technical sequencing replicates of the same DNA using the Ligation and Rapid Barcoding kits together with the Flongle and MinION flow cells. We assessed reproducibility by measuring discrepancies such as substitution and insertion/deletion errors, analysing plasmid recovery results and examining genetic markers and clustering information. We compared the results of genome assemblies with and without short-read polishing. Our results show an average reproducibility accuracy of 99.999955% for nanopore-only assemblies and 99.999996% when the short reads were used for polishing. The genomic analysis results were highly reproducible for the nanopore-only assemblies without short read in the following areas: identification of genetic markers for antimicrobial resistance and virulence, classical MLST, taxonomic classification, genome completeness and contamination analysis. Interestingly, the clustering information results from the core genome SNP and core genome MLST analyses were also highly reproducible for the nanopore-only assemblies, with pairwise differences of up to two allele differences in core genome MLST and two SNPs in core genome SNP across replicates. After polishing the assemblies with short reads, the pairwise differences for cgMLST were 0 and for cgSNP were 0-1 SNP across replicates. These results highlight the advances in sequencing accuracy of nanopore data without the use of short reads.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 3","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11927881/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143674069","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":"Metagenomic insights into taxonomic and functional patterns in shallow coastal and deep subseafloor sediments in the Western Pacific.","authors":"Jiarui Sun, Miho Hirai, Yoshihiro Takaki, Paul N Evans, Takuro Nunoura, Christian Rinke","doi":"10.1099/mgen.0.001351","DOIUrl":"10.1099/mgen.0.001351","url":null,"abstract":"<p><p>Marine sediments are vast, underexplored habitats and represent one of the largest carbon deposits on our planet. Microbial communities drive nutrient cycling in these sediments, but the full extent of their taxonomic and metabolic diversity remains to be explored. Here, we analysed shallow coastal and deep subseafloor sediment cores from 0.01 to nearly 600 metres below the seafloor, in the Western Pacific Region. Applying metagenomics, we identified several taxonomic clusters across all samples, which mainly aligned with depth and sediment type. Inferring functional patterns provided insights into possible ecological roles of the main microbial taxa. These included <i>Chloroflexota</i>, the most abundant phylum across all samples, whereby the classes <i>Dehalococcoida</i> and <i>Anaerolineae</i> dominated deep-subsurface and most shallow coastal sediments, respectively. <i>Thermoproteota</i> and <i>Asgardarchaeota</i> were the most abundant phyla among Archaea, contributing to high relative abundances of Archaea reaching over 50% in some samples. We recovered high-quality metagenome-assembled genomes for all main prokaryotic lineages and proposed names for three phyla, i.e. <i>Tangaroaeota</i> phyl. nov. (former RBG-13-66-14), <i>Ryujiniota</i> phyl. nov. (former UBA6262) and <i>Spongiamicota</i> phyl. nov. (former UBA8248). Metabolic capabilities across all samples ranged from aerobic respiration and photosynthesis in the shallowest sediment layers to heterotrophic carbon utilization, sulphate reduction and methanogenesis in deeper anoxic sediments. We also identified taxa with the potential to be involved in nitrogen and sulphur cycling and heterotrophic carbon utilization. In summary, this study contributes to our understanding of the taxonomic and functional diversity in benthic prokaryotic communities across marine sediments in the Western Pacific Region.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 3","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11920076/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657757","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":"Using gut microbiome metagenomic hypervariable features for diabetes screening and typing through supervised machine learning.","authors":"Xavier Chavarria, Hyun Seo Park, Singeun Oh, Dongjun Kang, Jun Ho Choi, Myungjun Kim, Yoon Hee Cho, Myung-Hee Yi, Ju Yeong Kim","doi":"10.1099/mgen.0.001365","DOIUrl":"10.1099/mgen.0.001365","url":null,"abstract":"<p><p>Diabetes mellitus is a complex metabolic disorder and one of the fastest-growing global public health concerns. The gut microbiota is implicated in the pathophysiology of various diseases, including diabetes. This study utilized 16S rRNA metagenomic data from a volunteer citizen science initiative to investigate microbial markers associated with diabetes status (positive or negative) and type (type 1 or type 2 diabetes mellitus) using supervised machine learning (ML) models. The diversity of the microbiome varied according to diabetes status and type. Differential microbial signatures between diabetes types and negative group revealed an increased presence of <i>Brucellaceae</i>, <i>Ruminococcaceae</i>, <i>Clostridiaceae</i>, <i>Micrococcaceae</i>, <i>Barnesiellaceae</i> and <i>Fusobacteriaceae</i> in subjects with diabetes type 1, and <i>Veillonellaceae</i>, <i>Streptococcaceae</i> and the order <i>Gammaproteobacteria</i> in subjects with diabetes type 2. The decision tree, elastic net, random forest (RF) and support vector machine with radial kernel ML algorithms were trained to screen and type diabetes based on microbial profiles of 76 subjects with type 1 diabetes, 366 subjects with type 2 diabetes and 250 subjects without diabetes. Using the 1000 most variable features, tree-based models were the highest-performing algorithms. The RF screening models achieved the best performance, with an average area under the receiver operating characteristic curve (AUC) of 0.76, although all models lacked sensitivity. Reducing the dataset to 500 features produced an AUC of 0.77 with sensitivity increasing by 74% from 0.46 to 0.80. Model performance improved for the classification of negative-status and type 2 diabetes. Diabetes type models performed best with 500 features, but the metric performed poorly across all model iterations. ML has the potential to facilitate early diagnosis of diabetes based on microbial profiles of the gut microbiome.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 3","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11893737/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143597339","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":"Progressive evolution of <i>Streptococcus equi</i> from <i>Streptococcus equi</i> subsp. <i>zooepidemicus</i> and adaption to equine hosts.","authors":"Hayley J Wilson, Jiangbao Dong, Andries J van Tonder, Christopher Ruis, Noémie Lefrancq, Abigail McGlennon, Carla Bustos, Sara Frosth, Albertine Léon, Adam M Blanchard, Matthew Holden, Andrew S Waller, Julian Parkhill","doi":"10.1099/mgen.0.001366","DOIUrl":"10.1099/mgen.0.001366","url":null,"abstract":"<p><p><i>Streptococcus equi</i> subsp. <i>equi</i> causes the equine respiratory disease 'strangles', which is highly contagious, debilitating and costly to the equine industry. <i>S. equi</i> emerged from the ancestral <i>Streptococcus equi</i> subsp. <i>zooepidemicus</i> and continues to evolve and disseminate globally. Previous work has shown that there was a global population replacement around the beginning of the twentieth century, obscuring the early genetic events in this emergence. Here, we have used large-scale genomic analysis of <i>S. equi</i> and its ancestor <i>S. zooepidemicus</i> to identify evolutionary events, leading to the successful expansion of <i>S. equi</i>. One thousand two hundred one whole-genome sequences of <i>S. equi</i> were recovered from clinical samples or from data available in public databases. Seventy-four whole-genome sequences representative of the diversity of <i>S. zooepidemicus</i> were used to compare the gene content and examine the evolutionary emergence of <i>S. equi</i>. A dated Bayesian phylogeny was constructed, and ancestral state reconstruction was used to determine the order and timing of gene gain and loss events between the different species and between different <i>S. equi</i> lineages. Additionally, a newly developed framework was used to investigate the fitness of different <i>S. equi</i> lineages. We identified a novel <i>S. equi</i> lineage, comprising isolates from donkeys in Chinese farms, which diverged nearly 300 years ago, after the emergence of <i>S. equi</i> from <i>S. zooepidemicus</i>, but before the global sweep. Ancestral state reconstruction demonstrated that phage-encoded virulence factors <i>slaA</i>, <i>seeL</i> and <i>seeM</i> were acquired by the global <i>S. equi</i> after the divergence of the basal donkey lineage. We identified the equibactin locus in both <i>S. equi</i> populations, but not <i>S. zooepidemicus</i>, reinforcing its role as a key <i>S. equi</i> virulence mechanism involved in its initial emergence. Evidence of a further population sweep beginning in the early 2000s was detected in the UK. This clade now accounts for more than 80% of identified UK cases since 2016. Several sub-lineages demonstrated increased fitness, within which we identified the acquisition of a new, fifth prophage containing additional toxin genes. We definitively show that acquisition of the equibactin locus was a major determinant in <i>S. equi</i> becoming an equid-exclusive pathogen, but that other virulence factors were fixed by the population sweep at the beginning of the twentieth century. Evidence of a secondary population sweep in the UK and acquisition of further advantageous genes implies that <i>S. equi</i> is continuing to adapt, and therefore, continued investigations are required to determine further risks to the equine industry.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 3","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143730740","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":"The utility of integrating nanopore sequencing into routine HIV-1 drug resistance surveillance.","authors":"Daniel Bugembe Lule, Deogratius Ssemwanga, Pontiano Kaleebu, Damien C Tully","doi":"10.1099/mgen.0.001375","DOIUrl":"10.1099/mgen.0.001375","url":null,"abstract":"<p><p>HIV continues to be a significant global public health concern. In 2022, an estimated 29.8 million people living with HIV received antiretroviral treatment (ART). From this, an estimated 10-15% of individuals living with HIV have drug-resistant strains of the virus. Testing for resistance to antiretroviral drugs is recommended before initiating ART. However, such services are often inaccessible due to costs and the need for complex laboratory infrastructure. The assessment of HIV drug resistance (HIVDR) relies on genotyping sequencing and algorithms to interpret genotypic resistance test results. Genotypic assays involve Sanger sequencing of the reverse transcriptase (<i>RT</i>), protease (<i>PR</i>) and integrase (<i>IN</i>) genes of circulating RNA in plasma to detect mutations that are known to confer drug resistance. While state-of-the-art sequencing technologies have swept the globe and enhanced our global pandemic response capabilities, they are still sparingly used for HIVDR surveillance. The scale-up of ART, especially in low- and middle-income countries, necessitates the establishment of cheap, expeditious and decentralized methods for HIVDR monitoring. Here, we outline how one low-capital next-generation sequencing platform, namely, nanopore sequencing, could augment efforts in expanding HIVDR surveillance efforts, especially in resource-limited settings. We discuss that because of its versatility, nanopore sequencing can accelerate HIVDR surveillance in conjunction with scaling up ART efforts and outline some of the challenges that need to be considered before its widespread and routine adaptation to detect drug resistance rapidly.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 3","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11925199/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143664009","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":"Multi-strain carriage and intrahost diversity of <i>Staphylococcus aureus</i> among Indigenous adults in the USA.","authors":"Julia Webb, Eleonora Cella, Catherine G Sutcliffe, Catherine Johnston, Sayf Al-Deen Hassouneh, Mohammad Jubair, Dennie Parker Riley, Carol Tso, Robert C Weatherholtz, Laura L Hammitt, Taj Azarian","doi":"10.1099/mgen.0.001367","DOIUrl":"10.1099/mgen.0.001367","url":null,"abstract":"<p><p><i>Staphylococcus aureus</i> (SA) is an opportunistic pathogen and human commensal that is frequently present in the upper respiratory tract, gastrointestinal tract and skin. While SA can cause diseases ranging from minor skin infections to life-threatening bacteraemia, it can also be carried asymptomatically. Indigenous individuals in the Southwest USA experience high rates of invasive SA disease. As carriage is the most significant risk factor for disease, understanding the dynamics of SA carriage, and in particular co-carriage of multiple strains, is important to develop strategies to prevent transmission in vulnerable communities. Here, we investigated SA co-carriage and intrahost evolution by sampling several colonies from multiple anatomical sites and whole-genome sequencing (WGS) on 310 SA isolates collected from 60 Indigenous adults participating in a cross-sectional carriage study. We assessed the richness and diversity of SA isolates <i>via</i> differences in multilocus sequence type, core-genome SNPs and genome content. Using WGS data, we identified 95 distinct SA intra-subject lineages (ISLs) among 60 participants; co-carriage was detected in 42% (25/60). Notably, two participants each carried four distinct SA ISLs. Variation in antibiotic resistance determinants among carried strains was identified among 42% (25/60) of participants. Lastly, we found unequal distribution of clonal complex by body site, suggesting that certain lineages may be adapted to specific anatomical sites. Together, these findings suggest that co-carriage may occur more frequently than previously appreciated and further our understanding of SA intrahost diversity during carriage, which has implications for surveillance activities and epidemiological investigations.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 3","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11909137/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143630612","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 characterization of <i>Streptococcus pneumoniae</i> isolates obtained from carriage and disease among paediatric patients in Addis Ababa, Ethiopia.","authors":"Abel Abera Negash, Ana Ferreira, Daniel Asrat, Abraham Aseffa, Piet Cools, Leen Van Simaey, Mario Vaneechoutte, Stephen D Bentley, Stephanie W Lo","doi":"10.1099/mgen.0.001376","DOIUrl":"https://doi.org/10.1099/mgen.0.001376","url":null,"abstract":"<p><p><b>Background and aims.</b> Despite the introduction of pneumococcal conjugate vaccines (PCVs), <i>Streptococcus pneumoniae</i> still remains an important cause of morbidity and mortality, especially among children under 5 years in sub-Saharan Africa. We sought to determine the distribution of serotypes, lineages and antimicrobial resistance of <i>S. pneumoniae</i> from carriage and disease among children presenting to health facilities, 5-6 years after the introduction of PCV10 in Ethiopia.<b>Methods.</b> Whole-genome sequencing (WGS) was performed on 103 <i>S. pneumoniae</i> (86 from nasopharyngeal swabs, 4 from blood and 13 from middle ear discharge) isolated from children aged <15 years at 3 healthcare facilities in Addis Ababa, Ethiopia, from September 2016 to August 2017. Using the WGS data, serotypes were predicted, isolates were assigned to clonal complexes, global pneumococcal sequence clusters (GPSCs) were inferred and screening for alleles and mutations that confer resistance to antibiotics was performed using multiple bioinformatic pipelines.<b>Results.</b> The 103 <i>S</i>. <i>pneumoniae</i> isolates were assigned to 38 serotypes (including nontypeable) and 46 different GPSCs. The most common serotype was serotype 19A. Common GPSCs were GPSC1 [14.6% (15/103), sequence type (ST) 320, serotype 19A], GPSC268 [8.7% (9/103), ST 6882 and novel STs; serotypes 16F, 11A and 35A] and GPSC10 [8.7% (9/103), STs 2013, 230 and 8804; serotype 19A]. The four invasive isolates were serotype 19A (<i>n</i>=2) and serotype 33C (<i>n</i>=2). Resistance to penicillin (>0.06 µg ml^-1, CLSI meningitis cutoff) was predicted in 57% (59/103) of the isolates, and 43% (25/58) penicillin-binding protein allele combinations were predicted to be associated with penicillin resistance. Resistance mutations in <i>folA</i> (<i>I100L</i>) and/or <i>folP</i> (indel between fifty-sixth and sixty-seventh aa) were identified among 66% (68/103) of the isolates, whilst tetracycline (<i>tetM</i>) and macrolide (<i>ermB</i> and <i>mefA</i>) resistance genes were found in 46.6% (48/103), 20.4% (21/103) and 20.4% (21/103) of the isolates, respectively. Multidrug resistance (MDR) (≥3 antibiotic classes) was observed in 31.1% (32/103) of the isolates. GPSC1 and GPSC10 accounted for 46.8% (15/32) and 18.7% (6/32) of the overall MDR.<b>Conclusion.</b> Five to 6 years after the introduction of PCV10 in Ethiopia, the <i>S. pneumoniae</i> obtained from carriage and disease among paediatric patients showed diverse serotype and pneumococcal lineages. The most common serotype identified was 19A, expressed by the MDR lineages GPSC1 and GPSC10, which is not covered by PCV10 but is included in PCV13. Continued assessment of the impact of PCV on the population structure of <i>S. pneumoniae</i> in Ethiopia is warranted during and after PCV13 introduction.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 3","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657660","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 epidemiology of a multidrug-resistant <i>Shigella sonnei</i> outbreak in Tunisia (2022-2023) using whole-genome sequencing.","authors":"Fahmi Smaoui, Boutheina Ksibi, Senda Mezghani, Eya Guermazi, Fatma Charfi, Sonia Ktari, Nourelhouda Ben Ayed, Thouraya Kammoun, Héla Karray, Adnene Hammami","doi":"10.1099/mgen.0.001362","DOIUrl":"10.1099/mgen.0.001362","url":null,"abstract":"<p><p><b>Purpose.</b> The prevalence of multidrug-resistant (MDR) <i>Shigella sonnei</i> is increasing globally, raising concerns for public health. In 2022, an outbreak of MDR <i>S. sonnei</i> was observed in Tunisia. We aimed to evaluate the genetic profile of <i>S. sonnei</i> isolates during the outbreak, including their clonal relationship, antimicrobial determinants and connection to international strains.<b>Methods.</b> In this study, we sequenced the whole genome of 24 S. <i>sonnei</i> strains collected from South Tunisia between July 2022 and November 2023. Bioinformatic analysis was conducted to confirm species identification, assign sequence types, determine core genome sequence types, analyse phylogenetic relationships and identify antimicrobial resistance determinants. Phylodynamic and phylogeographic analyses were performed to trace the spatiotemporal spread of the outbreak genotype.<b>Results.</b> Our investigation revealed that 23 out of 24 isolates were grouped into the HC10-20662 genotype within the 3.6.3 subclade. All isolates carried the <i>blaCTX-M-15</i> gene associated with extended-spectrum beta-lactamase production, as well as the <i>dfrA1</i> and <i>qnrS1</i> genes, along with the D87G mutation in <i>gyrA</i>. Additionally, the s<i>ul2, tet(A</i>) and <i>mph(A</i>) resistance genes were present in most isolates (96%, 96 and 83, respectively). Phylogeographic analysis suggested that the outbreak genotype likely spread in Europe before being introduced into Tunisia.<b>Conclusion.</b> To the best of our knowledge, this is the first MDR <i>S. sonnei</i> outbreak in the country. The HC10-20662 genotype appears to be responsible for a multi-country outbreak, affecting both Tunisia and Europe. Continued genomic surveillance efforts, both nationally and internationally, are essential for monitoring the dynamic evolution and global spread of MDR <i>S. sonnei</i>.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 3","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11936343/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143573456","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":"Birmingham-group IncP-1<i>α</i> plasmids revisited: RP4, RP1 and RK2 are identical and their remnants can be detected in environmental isolates.","authors":"Vuong Van Hung Le, Zhuang Gong, Lorrie Maccario, Emma Bousquet, Boris Parra, Arnaud Dechesne, Søren J Sørensen, Joseph Nesme","doi":"10.1099/mgen.0.001381","DOIUrl":"10.1099/mgen.0.001381","url":null,"abstract":"<p><p>RP4, RP1, RK2 and R68 were isolated from the multidrug-resistant bacterial wound isolates in 1969 in the Birmingham Accident Hospital, Birmingham, England, and collectively called Birmingham-group IncP-1<i>α</i> plasmids. These plasmids have been widely used as models to study different aspects of plasmid biology, develop genetic delivery systems and design plasmid vectors. Early studies showed that these plasmids conferred the same antibiotic resistance profile, had a similar size and were undistinguishable from each other using DNA heteroduplex electron microscopy and restriction endonuclease analyses. These observations have led to the widely held assumption that they are identical, although there has been no conclusive supporting evidence. In this work, we sequenced the plasmids RP1 and RP4 from our laboratory strain collection and compared these new sequences with the plasmids RP4 and RK2 assembled from a publicly available sequencing database, showing that the RP1, RP4 and RK2 plasmids are 60 095 bp in length and identical at the nucleotide resolution. Noteworthily, the plasmid sequence is highly conserved despite having been distributed to different labs over 50 years and propagated in different bacterial hosts, strengthening the previous observation that the bacterial host adapts to the RP4/RP1/RK2 plasmid rather than the opposite. In the updated RP4/RP1/RK2 sequence, we found a fusion gene, called <i>pecM-orf2</i>, that was formed putatively by a genetic deletion event. By searching for <i>pecM-orf2</i> in the National Center for Biotechnology Information database, we detected remnants of the RP4/RP1/RK2 plasmid that carry features of laboratory-engineered vectors in bacterial environmental isolates, either in their chromosome or as a plasmid. This suggests a leak of these plasmids from the laboratory into the environment, which may subsequently impact bacterial evolution and raises concerns about the biocontainment of engineered plasmids when being handled in laboratory settings.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 3","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11952213/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143730739","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":"Characterization of antibiotic determinants and heavy metal resistance genes in <i>Escherichia coli</i> from pigs in Catalonia.","authors":"Biel Garcias, William Monteith, Anna Vidal, Laia Aguirre, Ben Pascoe, Carolin M Kobras, Matthew D Hitchings, Samuel K Sheppard, Marga Martin, Laila Darwich","doi":"10.1099/mgen.0.001371","DOIUrl":"10.1099/mgen.0.001371","url":null,"abstract":"<p><p>More antibiotics are administered to livestock animals than to treat human infections. Industrialization, large animal densities and early weaning mean pigs are exposed to more antibiotics than any other livestock animal. Consequently, antimicrobial resistance (AMR) is common among commensal and pathogenic bacteria. Heavy metals (HMs) are also often used as feed additives for growth promotion and infection prevention alongside antimicrobials, and increased exposure to copper, zinc and cadmium can further encourage AMR through co-selection. In this study, we sequenced an archived collection of 112 <i>Escherichia coli</i> isolates from pigs in Catalonia using short- and long-read sequencing methods to detect AMR and HM tolerance genes. The most common AMR genes were <i>mdfA</i> (84.8%), <i>aph(3″)-Ib</i> (52.7%), <i>bla</i> _TEM-1B (45.6%) and <i>aph(6)-Id</i> (45.6%). Genes relevant to public health, such as the extended-spectrum <i>β</i>-lactamases (15.4%), <i>bla</i> _CTX-M type or <i>bla</i> _SHV, or mobile colistin resistance (<i>mcr</i>) genes (13.4%), such as <i>mcr-1</i>, were also found. HM tolerance genes were present in almost every genome but were rarely located in plasmids, and, in most cases, AMR and HM tolerance genes were not located on the same plasmids. Of the genes predicted to increase tolerance to HMs, only those with activity to mercury were co-located on plasmids alongside other AMR determinants. However, mercury is rarely used in pig farming and does not support a scenario where AMR and HM genes are co-selected. Finally, we identified the exclusive association between <i>mcr-4</i> and ColE10 plasmid, which may help target interventions to curtail its spread among pig <i>Escherichia coli</i>.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"11 3","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11937225/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143700884","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}