Genomic Characterization of a Uropathogenic Escherichia coli ST405 Isolate Harboring blaCTX-M-15-Encoding IncFIA-FIB Plasmid, blaCTX-M-24-Encoding IncI1 Plasmid, and Phage-Like Plasmid

Yao, Mianzhi; Zhu, Qianhui; Zou, Jin; Shenkutie, Abebe Mekuria; Hu, Songnian; Qu, Jiuxin; He, Zilong; Leung, Polly H.M.

doi:10.3389/fmicb.2022.845045

Cited by 7 publications

(4 citation statements)

References 60 publications

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“…In this sense, UPEC strains have been extensively associated with the production of ESBL, especially the CTX-M group, whose presence is associated with co-resistance to aminoglycosides and fluoroquinolones [61] , as it was found in UTI-U7. bla CTX-M-15 has been reported as the most prevalent ARG in UPEC strains [60] – [64] . In addition to the bla CTX-M-15 and bla OXA-1 variants, no other determinants encoding beta-lactamase was found in the genomic sequence of the UTI-U7 isolate.…”

Section: Discussionmentioning

confidence: 99%

Genomic characterization of a multidrug-resistant uropathogenic Escherichia coli and evaluation of Echeveria plant extracts as antibacterials

Castañeda-Meléndrez,

Magaña-Lizárraga,

Martínez-Valenzuela

et al. 2024

AIMSMICRO

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<abstract> Uropathogenic <italic>Escherichia coli</italic> (UPEC) is the most common bacterial agent associated with urinary tract infections, threatening public health systems with elevated medical costs and high morbidity rates. The successful establishment of the infection is associated with virulence factors encoded in its genome, in addition to antibacterial resistance genes, which could limit the treatment and resolution of the infection. In this sense, plant extracts from the genus <italic>Echeveria</italic> have traditionally been used to treat diverse infectious diseases. However, little is known about the effects of these extracts on bacteria and their potential mechanisms of action. This study aims to sequence a multidrug-resistant UPEC isolate (UTI-U7) and assess the multilocus sequence typing (MLST), virulence factors, antimicrobial resistance profile, genes, serotype, and plasmid content. Antimicrobial susceptibility profiling was performed using the Kirby-Bauer disk diffusion. The antibacterial and anti-adherent effects of the methanol extracts (ME) of <italic>Echeveria</italic> (<italic>E. craigiana</italic>, <italic>E. kimnachii</italic>, and <italic>E. subrigida</italic>) against UTI-U7 were determined. The isolate was characterized as an O25:H4-B2-ST2279-CH40 subclone and had resistant determinants to aminoglycosides, β-lactams, fluoroquinolones/quinolones, amphenicols, and tetracyclines, which matched with the antimicrobial resistance profile. The virulence genes identified encode adherence factors, iron uptake, protectins/serum resistance, and toxins. Identified plasmids belonged to the IncF group (IncFIA, IncFIB, and IncFII), alongside several prophage-like elements. After an extensive genome analysis that confirmed the pathogenic status of UTI-U7 isolate, <italic>Echeveria</italic> extracts were tested to determine their antibacterial effects; as an extract, <italic>E. subrigida</italic> (MIC, 5 mg/mL) displayed the best inhibitory effect. However, the adherence between UTI-U7 and HeLa cells was unaffected by the ME of the <italic>E. subrigida</italic> extract. </abstract>

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Section: Discussionmentioning

confidence: 99%

Genomic characterization of a multidrug-resistant uropathogenic Escherichia coli and evaluation of Echeveria plant extracts as antibacterials

Castañeda-Meléndrez,

Magaña-Lizárraga,

Martínez-Valenzuela

et al. 2024

AIMSMICRO

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“…The results were visualized using the Interactive Tree Of Life (iTOL) platform (https://itol.embl.de) (Letunic and Bork, 2021). In addition, multiple circular alignments were applied to compare the similarity and heterogeneity of plasmids carrying bla NDM-1 /bla OXA58 -like using the BLAST Ring Image Generator (BRIG) version 0.95 (https://brig.sourceforge.net/) (Yao et al, 2022). Differences in the gene content of these plasmids were determined through pan-genome analysis using Roary (Rapid large-scale prokaryote pan-genome analysis) version 3.11.2 (http://sanger-pathogens.github.io/Roary) (Page et al, 2015), which operates on annotated assemblies in GFF3 format produced by Prokka (rapid prokaryotic genome annotation) version 1.14.5 (http://www.vicbioinformatics.com/software.prokka .shtml) (Seemann, 2014).…”

Section: Phylogenetic Analysis and Circular Alignment Of Carbapenemas...mentioning

confidence: 99%

Carbapenemase genes distribution in clonal lineages of Acinetobacter baumannii: a comprehensive study on plasmids and chromosomes

Beig,

Badmasti,

Solgi

et al. 2023

Front. Cell. Infect. Microbiol.

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BackgroundThe global spread of plasmids carrying carbapenemase genes within carbapenem resistant Acinetobacter baumannii (CRAB) strains poses a worldwide public health issue. In this study, we conducted a comprehensive genetic analysis of plasmids and chromosomes harboring the major carbapenemase genes (blaNDM, blaKPC, blaVIM, blaIMP, blaGES, blaOXA-58-like, blaOXA-24/40-like, blaOXA-143-like, and blaOXA-23-like) in CRAB strains using bioinformatic tools.MethodsWe retrieved plasmids and chromosomes carrying the major carbapenemase genes from GenBank. The size, replicon type, and conjugal apparatus of the plasmids were also determined. Furthermore, allele types, co-existence of other antimicrobial resistance genes alongside carbapenemases in plasmids or chromosomes, co-occurrence of carbapenemase genes, gene repetition, and sequence types (ST) of whole genomes were characterized.ResultsThe database contained 113 plasmids and 38 chromosomes harboring carbapenemase genes. This investigation revealed that blaNDM and blaOXA-58-like were the predominant allele types in both the plasmids and chromosomes. Nine (7.96%) plasmids with blaNDM-1 were potentially conjugative. The most common replicon types of the plasmids were R3-T1, R3-T8, R3-T2, R3-T23, and RP-T1. The analysis revealed that blaNDM-1 and blaOXA-58-like genes possessed the highest variety of co-existence with other antibiotic resistance genes. The co-occurrence of dual carbapenemases was identified in 12 plasmids and 19 chromosomes. Carbapenemase gene repetitions were identified in 10 plasmids and one chromosome. Circular alignment revealed that the plasmids carrying the co-occurrence of blaNDM-1 and blaOXA-58 were more homogeneous. However, there was heterogeneity in certain regions of these plasmids. According to the minimum spanning tree (MST) results, the majority of the plasmids belonged to the genomes of ST2Pas, ST1Pas, ST422Pas, ST622Pas, and ST85Pas.ConclusionA. baumannii appears to have a strong ability for genome plasticity to incorporate carbapenemase genes on its plasmids and chromosomes to develop resistance against carbapenems. Mobilizable plasmids harboring carbapenemases significantly contribute to the dissemination of these genes. The genetic structure of the plasmids revealed a strong associations of class I integrons, ISAba-like structures, Tn4401 elements, and aac (6′)-Ib with carbapenemases. Furthermore, gene repetition may also be associated with carbapenem heteroresistance.

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“…The mechanism involved in conferring evolutionary advantage is underpinned by several complex molecular pathways currently being elucidated (14); it would eventually result in phage-plasmids with AMR genes being positively selected. For instance, phageplasmids carrying extended-spectrum beta-lactamase (ESBL) and colistin resistance genes have been identified in Escherichia coli (12,(15)(16)(17)(18)(19)(20)(21)(22), Klebsiella pneumoniae (23) and Salmonella enterica (13,(24)(25)(26) to date. Among S. enterica, reports suggest that phageplasmids are associated more specifically with the AMR genes blaCTX-M-15 (25), blaCTX-M-27 (24,26) and mcr-1 (26).…”

Section: Introductionmentioning

confidence: 99%

Presence of phage-plasmids in multiple serovars ofSalmonella enterica

Nair,

Barker,

Bird

et al. 2024

Preprint

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Evidence is accumulating in the literature that the horizontal spread of antimicrobial resistance (AMR) genes mediated by bacteriophages and bacteriophage-like plasmid (phage-plasmid) elements is much more common than previously envisioned. For instance, we recently identified and characterised a circular P1-like phage-plasmid harbouring a blaCTX-M-15 gene conferring extended-spectrum beta-lactamase (ESBL) resistance in S. Typhi. As the prevalence and epidemiological relevance of such mechanisms has never been systematically assessed in Enterobacterales, in this study we carried out a follow-up retrospective analysis of UK Salmonella isolates previously sequenced as part of routine surveillance protocols between 2016 and 2021. Using a high-throughput bioinformatics pipeline we screened 47,784 isolates for the presence of the P1 lytic replication gene repL, identifying 226 positive isolates from 25 serovars and demonstrating that phage-plasmid elements are more frequent than previously thought. The affinity for phage-plasmids appears highly serovar-dependent, with several serovars being more likely hosts than others; most of the positive isolates (170/226) belonged to S. Typhimurium ST34 and ST19. The phage-plasmids ranged between 85.8-99.5kb in size, with an average length of 92.6kb; detailed analysis indicated a high amount of diversity in gene content and genomic architecture. 132 phage-plasmids had the p0111 plasmid replication type, and 94 the IncY type; phylogenetic analysis indicated that both horizontal and vertical gene transmission mechanisms are likely to be involved in phage-plasmid propagation. Finally, phage-plasmids were present in isolates that were resistant and non-resistant to antimicrobials. In addition to providing a first comprehensive view of the presence of phage-plasmids in Salmonella, our work highlights the need for a better surveillance and understanding of phage-plasmids as AMR carriers, especially through their characterisation with long-read sequencing.

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Genomic Characterization of a Uropathogenic Escherichia coli ST405 Isolate Harboring blaCTX-M-15-Encoding IncFIA-FIB Plasmid, blaCTX-M-24-Encoding IncI1 Plasmid, and Phage-Like Plasmid

Cited by 7 publications

References 60 publications

Genomic characterization of a multidrug-resistant uropathogenic <i>Escherichia coli</i> and evaluation of <i>Echeveria</i> plant extracts as antibacterials

Genomic characterization of a multidrug-resistant uropathogenic <i>Escherichia coli</i> and evaluation of <i>Echeveria</i> plant extracts as antibacterials

Carbapenemase genes distribution in clonal lineages of Acinetobacter baumannii: a comprehensive study on plasmids and chromosomes

Presence of phage-plasmids in multiple serovars ofSalmonella enterica

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