Population structure and pangenome analysis of Enterobacter bugandensis uncover the presence of blaCTX-M-55, blaNDM-5 and blaIMI-1, along with sophisticated iron acquisition strategies

Filipe P Matteoli; Hemanoel Passarelli-Araujo; Francisnei Pedrosa-Silva; Fabio L Olivares; Thiago M Venancio

doi:10.1016/j.ygeno.2019.07.003

Population structure and pangenome analysis of Enterobacter bugandensis uncover the presence of bla_CTX-M-55, bla_NDM-5 and bla_IMI-1, along with sophisticated iron acquisition strategies

Genomics. 2020 Mar;112(2):1182-1191. doi: 10.1016/j.ygeno.2019.07.003. Epub 2019 Jul 4.

Authors

Filipe P Matteoli¹, Hemanoel Passarelli-Araujo², Francisnei Pedrosa-Silva¹, Fabio L Olivares³, Thiago M Venancio⁴

Affiliations

¹ Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Brazil.
² Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Brazil; Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
³ Núcleo de Desenvolvimento de Insumos Biológicos para a Agricultura (NUDIBA), UENF, Brazil; Laboratório de Biologia Celular e Tecidual, Centro de Biociências e Biotecnologia, UENF, Brazil.
⁴ Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Brazil. Electronic address: thiago.venancio@gmail.com.

PMID: 31279858
DOI: 10.1016/j.ygeno.2019.07.003

Abstract

Enterobacter bugandensis is a recently described species that has been largely associated with nosocomial infections. We report the genome of a non-clinical E. bugandensis strain, which was integrated with publicly available genomes to study the pangenome and general population structure of E. bugandensis. Core- and whole-genome multilocus sequence typing allowed the detection of five E. bugandensis phylogroups (PG-A to E), which contain important antimicrobial resistance and virulence determinants. We uncovered several extended-spectrum β-lactamases, including bla_CTX-M-55 and bla_NDM-5, present in an IncX replicon type plasmid, described here for the first time in E. bugandensis. Genetic context analysis of bla_NDM-5 revealed the resemblance of this plasmid with other IncX plasmids from other bacteria from the same country. Three distinctive siderophore producing operons were found in E. bugandensis: enterobactin (ent), aerobactin (iuc/iut), and salmochelin (iro). Our findings provide novel insights on the lifestyle, physiology, antimicrobial, and virulence profiles of E. bugandensis.

Keywords: Beta-lactamase; Core genome; Drug resistance; Genomic island; Virulence.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Bacterial Proteins / genetics*
Bacterial Proteins / metabolism
Enterobacter / genetics*
Enterobacter / metabolism
Enterobactin / analogs & derivatives
Enterobactin / genetics
Enterobactin / metabolism
Genome, Bacterial*
Hydroxamic Acids / metabolism
Iron / metabolism*
Operon
beta-Lactamases / genetics*
beta-Lactamases / metabolism

Substances

Bacterial Proteins
Hydroxamic Acids
salmochelin
aerobactin
Enterobactin
Iron
beta-Lactamases

Supplementary concepts

Enterobacter bugandensis