Genomic Characterization of Antimicrobial Resistance, Virulence, and Phylogeny of the Genus <i>Ochrobactrum</i>
Yael Yagel,
Stephanie Sestito,
Yair Motro,
Anat Shnaiderman-Torban,
Boris Khalfin,
Orly Sagi,
Shiri Navon-Venezia,
Amir Steinman,
Jacob Moran-Gilad
Affiliations
Yael Yagel
Microbiology, Advanced Genomics and Infection Control Applications Laboratory (MAGICAL), Department of Health Systems Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
Stephanie Sestito
Microbiology, Advanced Genomics and Infection Control Applications Laboratory (MAGICAL), Department of Health Systems Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
Yair Motro
Microbiology, Advanced Genomics and Infection Control Applications Laboratory (MAGICAL), Department of Health Systems Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
Anat Shnaiderman-Torban
Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 761001, Israel
Boris Khalfin
Microbiology, Advanced Genomics and Infection Control Applications Laboratory (MAGICAL), Department of Health Systems Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
Orly Sagi
Microbiology Lab, Soroka University Medical Center, Beer-Sheva 8410101, Israel
Shiri Navon-Venezia
Department of Molecular Biology and the Adelson School of Medicine, Ariel University, Ariel 40700, Israel
Amir Steinman
Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 761001, Israel
Jacob Moran-Gilad
Microbiology, Advanced Genomics and Infection Control Applications Laboratory (MAGICAL), Department of Health Systems Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
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.
