Whole-Genome Assessment of Clinical Acinetobacter baumannii Isolates Uncovers Potentially Novel Factors Influencing Carbapenem Resistance

Kiran Javkar; Hugh Rand; Maria Hoffmann; Yan Luo; Saul Sarria; Nagarajan Thirunavukkarasu; Christine A Pillai; Patrick McGann; J Kristie Johnson; Errol Strain; Mihai Pop

doi:10.3389/fmicb.2021.714284

Whole-Genome Assessment of Clinical Acinetobacter baumannii Isolates Uncovers Potentially Novel Factors Influencing Carbapenem Resistance

Front Microbiol. 2021 Oct 1:12:714284. doi: 10.3389/fmicb.2021.714284. eCollection 2021.

Authors

Affiliations

¹ Department of Computer Science, University of Maryland, College Park, MD, United States.
² Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park, MD, United States.
³ Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, Department of Health and Human Services, College Park, MD, United States.
⁴ Center for Veterinary Medicine, United States Food and Drug Administration, Department of Health and Human Services, Laurel, MD, United States.
⁵ Multidrug Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, United States.
⁶ Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, United States.

Abstract

Carbapenems-one of the important last-line antibiotics for the treatment of gram-negative infections-are becoming ineffective for treating Acinetobacter baumannii infections. Studies have identified multiple genes (and mechanisms) responsible for carbapenem resistance. In some A. baumannii strains, the presence/absence of putative resistance genes is not consistent with their resistance phenotype-indicating the genomic factors underlying carbapenem resistance in A. baumannii are not fully understood. Here, we describe a large-scale whole-genome genotype-phenotype association study with 349 A. baumannii isolates that extends beyond the presence/absence of individual antimicrobial resistance genes and includes the genomic positions and pairwise interactions of genes. Ten known resistance genes exhibited statistically significant associations with resistance to imipenem, a type of carbapenem: blaOXA-23, qacEdelta1, sul1, mphE, msrE, ant(3")-II, aacC1, yafP, aphA6, and xerD. A review of the strains without any of these 10 genes uncovered a clade of isolates with diverse imipenem resistance phenotypes. Finer resolution evaluation of this clade revealed the presence of a 38.6 kbp conserved chromosomal region found exclusively in imipenem-susceptible isolates. This region appears to host several HTH-type DNA binding transcriptional regulators and transporter genes. Imipenem-susceptible isolates from this clade also carried two mutually exclusive plasmids that contain genes previously known to be specific to imipenem-susceptible isolates. Our analysis demonstrates the utility of using whole genomes for genotype-phenotype correlations in the context of antibiotic resistance and provides several new hypotheses for future research.

Keywords: Acinetobacter baumanni; antibiotic resistance; genomic association studies; multiple genome alignment; whole-genome comparison.

Grants and funding

R01 AI100947/AI/NIAID NIH HHS/United States