Comparative Genomics Reveals a Well-Conserved Intrinsic Resistome in the Emerging Multidrug-Resistant Pathogen Cupriavidus gilardii

Abstract

The Gram-negative bacterium Cupriavidus gilardii is an emerging multidrug-resistant pathogen found in many environments. However, little is known about this species or its antibiotic resistance mechanisms. We used biochemical tests, antibiotic susceptibility experiments, and whole-genome sequencing to characterize an environmental C. gilardii isolate. Like clinical isolates, this isolate was resistant to meropenem, gentamicin, and other antibiotics. Resistance to these antibiotics appeared to be related to the large number of intrinsic antibiotic resistance genes found in this isolate. As determined by comparative genomics, this resistome was also well conserved in the only two other C. gilardii strains sequenced to date. The intrinsic resistome of C. gilardii did not include the colistin resistance gene mcr-5, which was in a transposon present only in one strain. The intrinsic resistome of C. gilardii was comprised of (i) many multidrug efflux pumps, such as a homolog of the Pseudomonas aeruginosa MexAB-OprM pump that may be involved in resistance to meropenem, other β-lactams, and aminoglycosides; (ii) a novel β-lactamase (OXA-837) that decreases susceptibility to ampicillin but not to other β-lactams tested; (iii) a new aminoglycoside 3-N-acetyltransferase [AAC(3)-IVb, AacC10] that decreases susceptibility to gentamicin and tobramycin; and (iv) a novel partially conserved aminoglycoside 3ʺ-adenylyltransferase [ANT(3ʺ)-Ib, AadA32] that decreases susceptibility to spectinomycin and streptomycin. These findings provide the first mechanistic insight into the intrinsic resistance of C. gilardii to multiple antibiotics and its ability to become resistant to an increasing number of drugs during therapy. IMPORTANCE Cupriavidus gilardii is a bacterium that is gaining increasing attention both as an infectious agent and because of its potential use in the detoxification of toxic compounds and other biotechnological applications. In recent years, however, there has been an increasing number of reported infections, some of them fatal, caused by C. gilardii. These infections are hard to treat because this bacterium is naturally resistant to many antibiotics, including last-resort antibiotics, such as carbapenems. Moreover, this bacterium often becomes resistant to additional antibiotics during therapy. However, little is known about C. gilardii and its antibiotic resistance mechanisms. The significance of our research is in providing, for the first time, whole-genome information about the natural antibiotic resistance genes found in this bacterium and their conservation among different C. gilardii strains. This information may provide new insights into the appropriate use of antibiotics in combating infections caused by this emerging pathogen.

Diversity and Function of Wolf Spider Gut Microbiota Revealed by Shotgun Metagenomics

“…Cupriavidus gilardii is an emerging multidrug-resistant Gramnegative pathogen found in many environments (Ruiz et al, 2019). It is Cu-resistant (Huang et al, 2019).…”

Urban and agricultural soils in Southern California are a reservoir of carbapenem‐resistant bacteria

“…None of the soil CR Cupriavidus isolates characterized in this study produced carbapenemases. A related species, C. gilardii , is intrinsically resistant to carbapenems despite also not producing carbapenemases likely because of its large array of multidrug efflux pumps (Ruiz, McCarley, Espejo, Cooper, & Harmon, 2019).…”

MCR-5-Producing Colistin-Resistant Cupriavidus gilardii Strain from Well Water in Batna, Algeria

“… Cupriavidus gilardii is a glucose-nonfermenting Gram-negative bacterium (GNB) that belongs to the Burkholderiaceae family. It was previously classified as Ralstonia gilardii and Wautersia gilardii ( 9 ). The gene was fully amplified by standard PCR and sequenced using BigDye terminator chemistry on an ABI 3500xl automated sequencer (Applied Biosystems, Foster City, CA, USA).…”

“…All detected hits are presented in Table 1 . In addition to the mcr-5.1 colistin resistance gene, we identified a class D β-lactamase which was highly similar (90.84% similarity with the reference sequence) to the OXA-837 enzyme and a putative aminoglycoside inactivation enzyme, “ aac(3)-IVa .” Interestingly, these two antibiotic resistance genes have been found to be well conserved in C. gilardii genomes ( 9 ). Furthermore, several conserved multidrug efflux pumps were detected, which could explain the multidrug resistance phenotype observed in our isolate.…”

“…C. gilardii is gaining increasing attention as an emerging pathogen, and several studies have reported its role in human infections, including perirectal inflammation, bloodstream infection, muscular abscess, and catheter sepsis ( 15 ). In terms of antibiotic resistance, it has been suggested that C. gilardii is intrinsically resistant to ertapenem, meropenem, ampicillin, amoxicillin-clavulanate, gentamicin, tobramycin, and streptomycin, while it is susceptible to imipenem and cefotaxime and intermediately resistant to spectinomycin ( 9 ). In a study carried out on 39 Cupriavidus clinical isolates, including six C. gilardii strains, the authors tested the MICs of these strains against 20 antibiotics by BMD, and the results showed that two C. gilardii strains were resistant to colistin and four were imipenem resistant.…”