Journal Article

Genome-based characterization of two Colombian clinical Providencia rettgeri isolates co-harboring NDM-1, VIM-2, and other β-lactamases

Duarte, Carolina, Donato, John, Barreto-Hernández, Emiliano, Piza-Buitrago, Adriana, Rincón, Verónica, Falquet, Laurent, Saavedra, Sandra Yamile, Reguero, María Teresa, Morero, Jaime

2020

Overview

Background Providencia rettgeri is a nosocomial pathogen associated with urinary tract infections and related to Healthcare-Associated Infection (HAI). In recent years isolates producing New Delhi Metallo-β-lactamase (NDM) and other β-lactamases have been reported that reduce the efficiency of clinical antimicrobial treatments. In this study, we analyzed antibiotic resistance, the presence of resistance genes and the clonal relationship of two P. rettgeri isolates obtained from male patients admitted to the same hospital in Bogotá – Colombia, 2015. Results Antibiotic susceptibility profile evaluated by the Kirby-Bauer method revealed that both isolates were resistant to third-generation carbapenems and cephalosporins. Whole-genome sequencing (Illumina HiSeq) followed by SPAdes assembling, Prokka annotation in combination with an in-house Python program and resistance gene detection by ResFinder identified the same six β-lactamase genes in both isolates: bla NDM-1 , bla VIM-2 , bla CTX-M-15 , bla OXA-10 , bla CMY-2 and bla TEM-1 . Additionally, various resistance genes associated with antibiotic target alteration ( arn A, Pmr E, Pmr F, Lpx A, Lpx C, gyr B, fol P, mur A, rpo B, rps L, tet 34) were found and four efflux pumps ( Ros AB, Emr D, mdt H and cml A). The additional resistance to gentamicin in one of the two isolates could be explained by a detected SNP in CpxA (Cys191Arg) which is involved in the stress response of the bacterial envelope. Genome BLAST comparison using CGView, the ANI value (99.99%) and the pangenome (using Roary) phylogenetic tree (same clade, small distance) showed high similarity between the isolates. The rMLST analysis indicated that both isolates were typed as rST-61,696, same as the RB151 isolate previously isolated in Bucaramanga, Colombia, 2013, and the FDAARGOS_330 isolate isolated in the USA, 2015. Conclusions We report the coexistence of the carbapenemase genes bla NDM-1 , and bla VIM-2 , together with the β-lactamase genes bla CTX-M-15 , bla OXA-10 , bla CMY-2 and bla TEM-1 , in P. rettgeri isolates from two patients in Colombia. Whole-genome sequence analysis indicated a circulation of P. rettgeri rST-61,696 strains in America that needs to be investigated further.

• Publisher: BioMed Central,Springer Nature B.V,BMC
• Subject: And bla TEM-1 / Annotations / Anti-Bacterial Agents - pharmacology / Antibiotic resistance / Antibiotics / Antiinfectives and antibacterials / Antimicrobial agents / Bacterial Proteins - genetics / beta-Lactam Resistance - genetics / beta-Lactamases - genetics / Biological Microscopy / Biomedical and Life Sciences / bla CMY-2 / bla CTX-M-15 / bla OXA-10 / Carbapenemase / Carbapenems / Cell division / Cephalosporins / Coexistence / Colombia / Drug resistance / Drug Resistance, Multiple, Bacterial - genetics / Efflux / Enterobacteriaceae Infections - microbiology / Gene sequencing / Genes / Genome, Bacterial - genetics / Genomes / genomics and proteomics / Gentamicin / Hospitals / Humans / Infections / Life Sciences / Male / Metallo-β-lactamase / Metallography / Microbial genetics / Microbial Sensitivity Tests / Microbiology / Mycology / Nosocomial infection / Nucleotide sequence / Parasitology / Patients / Phylogeny / Plasmids / Providencia - drug effects / Providencia - genetics / Providencia - isolation & purification / Providencia rettgeri / Research Article / RpoB protein / Single-nucleotide polymorphism / Urinary tract / Virology / Whole genome sequencing / β Lactamase