Plasmids shape the diverse accessory resistomes of Escherichia coli ST131
| Autor: | Hawriya Al-Foori, Caitriona Woods, Arun Gonzales Decano, Tim Downing, Shane Power, Louisse P. Mirabueno, Leigh Campbell, Cian Smyth, Kevin Ellison, Nghia T.H. Tran, Alexander D. Rahm, Maddy Nelson, Zoe Vance, Buthaina Al-Awadi, Genevieve Smith |
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| Přispěvatelé: | Laboratoire de Géométrie Algébrique et Applications à la Théorie de l'Information (GAATI), Université de la Polynésie Française (UPF) |
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
Genome Variation Detection
sequence type Human Microbiome Project ST131 Operon UTI Fimbria extended-spectrum beta-lactamase extra-intestinal pathogenic E. coli incompatibility medicine.disease_cause Genome topological data analysis Plasmid ST131. Abbreviations: AMR single nucleotide polymorphism General Materials Science CTX-M ComputingMilieux_MISCELLANEOUS 2. Zero hunger Genetics ExPEC 0303 health sciences HGT ST Inc fimbrial [MATH.MATH-KT]Mathematics [math]/K-Theory and Homology [math.KT] horizontal gene transfer Research Article SNP biology_other Biology cefotaximase TDA 03 medical and health sciences plasmid evolution medicine Escherichia coli Microbiome antimicrobial resistance Gene 030304 developmental biology 030306 microbiology HMP MGE mobile genetic element SIAS infection Resistome Sequence Identity and Similarity ESBL Microbial Evolution and Epidemiology Mobile genetic elements urinary tract infection |
| Zdroj: | Access Microbiology Access Microbiology, Microbiology Society, 2020, ⟨10.1099/acmi.0.000179⟩ |
| ISSN: | 2516-8290 |
| DOI: | 10.1101/2020.05.07.081380 |
| Popis: | The human gut microbiome includes beneficial, commensal and pathogenic bacteria that possess antimicrobial resistance (AMR) genes that exchange these predominantly through conjugative plasmids. Escherichia coli is a significant component of the gastrointestinal microbiome and is typically non-pathogenic in this niche. In contrast, extra-intestinal pathogenic E. coli (ExPEC) including ST131 may occupy other environments like the urinary tract or bloodstream where they express genes enabling AMR and host cell adhesion like type 1 fimbriae. The extent to which commensal E. coli and uropathogenic ExPEC ST131 share AMR genes remains understudied at a genomic level, and here we examined this using a preterm infant resistome. Here, individual ST131 had small differences in AMR gene content relative to a larger shared resistome. Comparisons with a range of plasmids common in ST131 showed that AMR gene composition was driven by conjugation, recombination and mobile genetic elements. Plasmid pEK499 had extended regions in most ST131 Clade C isolates, and it had evidence of a co-evolutionary signal based on protein-level interactions with chromosomal gene products, as did pEK204 that had a type IV fimbrial pil operon. ST131 possessed extensive diversity of selective type 1, type IV, P and F17-like fimbriae genes that was highest in subclade C2. The structure and composition of AMR genes, plasmids and fimbriae vary widely in ST131 Clade C and this may mediate pathogenicity and infection outcomes.Data SummaryThe following files are available on the FigShare project “Plasmids_ST131_resistome_2020” : The set of 794 AMR genes derived from [74] are available (with their protein sequence translation) at FigShare at doi: dx.doi.org/10.6084/m9.figshare.11961402. The AMR gene profiles per sample determined by their BLAST sequence similarity results against CARD are available at FigShare at doi: dx.doi.org/10.6084/m9.figshare.11961612. This dataset includes the PlasmidFinder results. It also includes other AMR database comparisons (ARG-ANNOT, ResFinder, MegaRes, VFDB and VirulenceFinder). The BLAST sequence similarity results for the fim, pil, pap and ucl operons’ genes versus 4,071 E. coli ST131 assemblies from Decano & Downing (2019) are available at FigShare at doi: dx.doi.org/10.6084/m9.figshare.11961711. The genome sequences and annotation files for reference genomes NCTC13441, EC958 and SE15, along with the assembled contigs for 83972 and 3_2_53FAA are available at FigShare at doi: dx.doi.org/10.6084/m9.figshare.11961813. The 4,071 E. coli ST131 genome assemblies from Decano & Downing (2019) are available at FigShare at doi: 10.6084/m9.figshare.11962278 (the first 1,680 assemblies) and at doi: dx.doi.org/10.6084/m9.figshare.11962557 (the second 2,391 assemblies). |
| Databáze: | OpenAIRE |
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