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

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.

Vitamin A Deficiency in the Early-Life Periods Alters a Diversity of the Colonic Mucosal Microbiota in Rats

“…They are associated with opportunistic central catheter-associated infections in immunocompromised human hosts. Other reports of infections in humans include endocarditis, peritonitis, meningitis, osteomyelitis, endophthalmitis, septic arthritis, and bacteremia (33). The above data further indicates that VA deficiency of early-life stage (gestation and lactation) can enhance of Ochrobactrum abundance in the intestinal mucosa, which may increase the risk of infection.…”

Isolation, characterization, and interaction of lignin‐degrading bacteria from rumen of buffalo (Bubalus bubalis)

“…The genome analysis of 130 strains of Ochrobactrum spp. by Yagel et al [44] showed that there were limited virulence factors in the majority of these isolates, which proved that Ochrobactrum spp. are low virulence.…”

Induction of TLR4/TLR2 Interaction and Heterodimer Formation by Low Endotoxic Atypical LPS

“…For example, Porphyromonas gingivalis lipid A shows an antagonistic activity that enables the pathogen to evade TLR4-mediated bactericidal activity in macrophages, resulting in systemic inflammation ( 11 ). On the other hand, Brucella LPS is a poor TLR4 agonist and antigen-presenting cell activator ( 12 – 15 ), and its closely related species O. anthropi and O. intermedium are emerging as human opportunistic pathogens with mild virulence ( 16 ). Nevertheless, their immunomodulatory activity and the molecular basis of pathogen receptor involved in their interaction with the immune system are not fully understood.…”