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ABSTRACT: Background: The rapid and global spread of Escherichia coli carrying mcr-type genes at the human-animal-environmental interface has become a serious global public health problem. Objective: To perform a genomic investigation of a colistin-resistant E. coli strain (14005RM) causing urinary tract infection, using a hybrid de novo assembly of Illumina/Nanopore sequence data, presenting phylogenomic insights into the relationship with mcr-1-positive strains circulating at the human-animal-environmental interface, in Brazil. Methods: Genomic DNA was sequenced using both the Illumina NexSeq and Nanopore MinION platforms. De novo hybrid assembly was performed by Unicycler. Genomic data were assessed by in silico prediction and bioinformatic tools. Results: The genome assembly size was 5 333 039 bp. The mcr-1.5-positive E. coli strain 14005RM belongs to the sequence type ST354 and presented a broad resistome (antibiotics, heavy metals, disinfectants, and glyphosate) and virulome. The mcr-1.5 gene was carried by an IncI2 plasmid (p14005RM, sizing 65,458 kb). Full genome SNP-based phylogenetic analysis reveals that mcr-1.5-producing E. coli strain 14005RM is highly related (> 98% identity) to colistin-resistant mcr-1.1-positive ST354 lineages associated with urinary tract infections in Brazil since 2015. Conclusion: Mobile colistin resistance within the Brazilian One Health microbiosphere is mediated by mcr gene variants propagated by IncX4, IncHI2, and IncI2 plasmids, circulating among global clones of E. coli.

The emergence of Klebsiella (K.) pneumoniae as a leading cause of nosocomial infections in Southeast Asia is of concern. Vietnam has an outstanding position with regard to antimicrobialresistant (AMR) pathogens and is a hotspot for carbapenem-resistant K. pneumoniae. In the current study, 19 clinical K. pneumoniae strains isolated from patients in Vietnam were tested for antibiotic susceptibility, and their genome sequences were analyzed to investigate potential resistance profiles, genotypes, AMR determinants, and virulence-associated genes. More than half of the isolates were multidrug-resistant (MDR), displaying resistance to ciprofloxacin, levofloxacin, chloramphenicol, piperacillin, cefotaxime, ceftazidime, and cefepime. Carbapenem- resistance was detected in 47% (n=9) of isolates. Five isolates were assigned to sequence type (ST) 23 by multi-locus sequence typing (MLST). These ST23 strains exhibited determinants characteristic of hypervirulent strains and were sensitive to all antibiotics tested except for one strain, which was resistant to chloramphenicol and trimethoprim/sulfamethoxazole. All isolates had AMR determinants that conferred resistance to aminoglycosides and ß-lactams. Single nucleotide variants of oqxA and oqxB conferring resistance to phenicol/quinolone, ompK37 and ompA conferring resistance to beta-lactams, and lptD conferring resistance to rifamycin, were found in all isolates. Additionally, 95% of the isolates (n=18) carried fosA genes; however, only two were resistant to fosfomycin. Five isolates carried genes conferring resistance to colistin; only one carried mcr-1.1 and showed resistance to colistin. One hundred thirty virulence-associated genes were identified. The current study demonstrated an inverse relationship between the number of detected virulence determinants and antibiotic resistance. Several well-known resistance genes have been identified but did not mediate resistance, which could be due to insufficient levels or lack of expression. A comprehensive study of the genotypic findings of AMR determinants and virulence with phenotypic data is required. The presence of hypervirulent K. pneumoniae carrying specific virulomes is a growing problem, and monitoring of virulence characteristics of K. pneumoniae is important. [ABSTRACT FROM AUTHOR]

Carbapenem-resistant Enterobacter cloacae complex is a significant global healthcare threat, particularly carbapenemase-producing Enterobacter hormaechei (CPEH). From January 2017 to January 2021, twenty-two CPEH isolates from a regional teaching hospital in central Taiwan were identified with the carriage of carbapenemase genes bla KPC-2 , bla IMP-8 , and predominantly bla OXA-48 . Over 80% of these CPEH strains clustered into the high-risk ST78 lineage, carrying a bla OXA-48 IncL plasmid (pOXA48-CREH), nearly identical to the endemic plasmid pOXA48-KP in ST11 Klebsiella pneumoniae . This OXA-48-producing ST78 lineage disseminated clonally from 2018 to 2021 and transferred pOXA48-CREH to ST66 and ST90 E. hormaechei . An IMP-8-producing ST78 strain harbouring a bla IMP-8 -carrying pIncHI2 plasmid appeared in 2018, and by late 2020, a KPC-2-producing ST78 strain was identified after acquiring a novel bla KPC-2 -carrying IncFII plasmid. These findings suggest that the high-risk ST78 lineage of E . hormaechei has emerged as the primary driver behind the transmission of CPEH . ST78 has not only acquired various carbapenemase-gene-carrying plasmids but has also facilitated the transfer of pOXA48-CREH to other lineages. Continuous genomic surveillance and targeted interventions are urgently needed to control the spread of emerging CPEH clones in hospital settings.

Although previous studies using phenotypic or metagenomic approaches have revealed the patterns of antibiotic resistance genes (ARGs) in hospital effluents in local regions, limited information is available regarding the antibiotic resistome and plasmidome in human pathogenic bacteria in hospital effluents of megacity in China. To address this knowledge gap, we analyzed effluent samples from 166 hospitals across 13 geographical districts in Shanghai, China, using both cultivation-based approaches and metagenomics. A total of 357 strains were isolated from these samples, with the predominant species being Escherichia coli (n = 61), Aeromonas hydrophila (n = 57), Klebsiella pneumoniae (n = 48), and Aeromonas caviae (n = 42). Those identified indicator bacteria were classified into biosafety level 1 (BSL-1, 60 %) and BSL-2 (40 %). We identified 1237 ARG subtypes across 22 types, predominantly including beta-lactam, tetracycline, multidrug, polymyxin, and aminoglycoside resistance genes, using culture-enriched phenotypic metagenomics. Mobile genetic elements such as plasmids, transposons (tnpA), integrons (intI1), and insertion sequences (IS91) were abundant. We recovered 135 plasmids classified into mobilizable (n = 94) and non-mobilizable (n = 41) types. Additionally, 80 metagenome-assembled genomes (MAGs) were reconstructed from the hospital effluents for the assessment of ARG transmission risks, including genes for last-line antibiotics such as bla NDM , bla KPC , bla imiH , and mcr. This study is the first to comprehensively characterize and assess the risk of antimicrobial resistance levels and plasmidome in the hospital effluents of China's megacity, providing city-wide surveillance data and evidence to inform public health interventions., Competing Interests: Declaration of Competing Interest The authors declare that there are no conflicts of interest in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Background: The rapid and global spread of Escherichia coli carrying mcr-type genes at the human-animal-environmental interface has become a serious global public health problem., Objective: To perform a genomic investigation of a colistin-resistant E. coli strain (14005RM) causing urinary tract infection, using a hybrid de novo assembly of Illumina/Nanopore sequence data, presenting phylogenomic insights into the relationship with mcr-1-positive strains circulating at the human-animal-environmental interface, in Brazil., Methods: Genomic DNA was sequenced using both the Illumina NexSeq and Nanopore MinION platforms. De novo hybrid assembly was performed by Unicycler. Genomic data were assessed by in silico prediction and bioinformatic tools., Results: The genome assembly size was 5 333 039 bp. The mcr-1.5-positive E. coli strain 14005RM belongs to the sequence type ST354 and presented a broad resistome (antibiotics, heavy metals, disinfectants, and glyphosate) and virulome. The mcr-1.5 gene was carried by an IncI2 plasmid (p14005RM, sizing 65,458 kb). Full genome SNP-based phylogenetic analysis reveals that mcr-1.5-producing E. coli strain 14005RM is highly related (> 98% identity) to colistin-resistant mcr-1.1-positive ST354 lineages associated with urinary tract infections in Brazil since 2015., Conclusion: Mobile colistin resistance within the Brazilian One Health microbiosphere is mediated by mcr gene variants propagated by IncX4, IncHI2, and IncI2 plasmids, circulating among global clones of E. coli., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)