Genomic Characterization of Antimicrobial Resistance, Virulence, and Phylogeny of the Genus Ochrobactrum.

Yael Yagel,Anat Shnaiderman-Torban,Yair Motro,Amir Steinman,Jacob Moran-Gilad,Shiri Navon-Venezia,Stephanie Sestito,Orly Sagi,Boris Khalfin

doi:10.3390/antibiotics9040177

Abstract

Ochrobactrum is a ubiquitous Gram-negative microorganism, mostly found in the environment, which can cause opportunistic infections in humans. It is almost uniformly resistant to penicillins and cephalosporins through an AmpC-like β-lactamase enzyme class (OCH). We studied 130 assembled genomes, of which 5 were animal-derived isolates recovered in Israel, and 125 publicly available genomes. Our analysis focused on antimicrobial resistance (AMR) genes, virulence genes, and whole-genome phylogeny. We found that 76% of Ochrobactrum genomes harbored a blaOCH β-lactamase gene variant, while 7% harbored another AmpC-like gene. No virulence genes other than lipopolysaccharide-associated genes were found. Core genome multilocus sequence typing clustered most samples to known species, but neither geographical clustering nor isolation source clustering were evident. When analyzing the distribution of different blaOCH variants as well as of the blaOCH-deficient samples, a clear phylogenomic clustering was apparent for specific species. The current analysis of the largest collection to date of Ochrobactrum genomes sheds light on the resistome, virulome, phylogeny, and species classification of this increasingly reported human pathogen. Our findings also suggest that Ochrobactrum deserves further characterization to underpin its evolution, taxonomy, and antimicrobial resistance.

Highlights

The genus Ochrobactrum comprises a group of non-fermenting, aerobic, Gram-negative bacilli that are environmentally ubiquitous [1]
A total of 130 whole-genome sequences of Ochrobactrum isolates were available for analysis. This dataset comprises five novel isolates obtained from veterinary surveillance cultures in animals in Israel, 25 raw sequences obtained and assembled from the Sequence Read Archive (SRA) database, and 100 ready assemblies downloaded from the PATRIC database
Of the 125 publicly available genomes, 76% had metadata regarding the source of isolation, and 67% had data on geographic location (Table S1), but additional data on phenotypic antimicrobial resistance were not available

Summary

Introduction

The genus Ochrobactrum comprises a group of non-fermenting, aerobic, Gram-negative bacilli that are environmentally ubiquitous [1]. These bacteria have been isolated from soil, water, animal, and human sources—especially in gastric biopsies and from dialysis fluid [2,3,4,5]. While these species are infrequently the cause of human disease, they are associated with opportunistic central catheter-associated infections in immunocompromised human hosts [6]. These features, in combination with the genus’ close phylogenetic proximity to Brucella spp., a highly pathogenic group, have recently drawn considerable attention to the Ochrobactrum genus

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Discussion

Conclusion