Dissecting Colistin Resistance Mechanisms in Extensively Drug-Resistant Acinetobacter baumannii Clinical Isolates

Abstract

Nosocomial infections with Acinetobacter baumannii are a global problem in intensive care units with high mortality rates. Increasing resistance to first- and second-line antibiotics has forced the use of colistin as last-resort treatment, and increasing development of colistin resistance in A. baumannii has been reported. We evaluated the transcriptional regulator PmrA as potential drug target to restore colistin efficacy in A. baumannii. Deletion of pmrA restored colistin susceptibility in 10 of the 12 extensively drug-resistant A. baumannii clinical isolates studied, indicating the importance of PmrA in the drug resistance phenotype. However, two strains remained highly resistant, indicating that PmrA-mediated overexpression of the phosphoethanolamine (PetN) transferase PmrC is not the exclusive colistin resistance mechanism in A. baumannii. A detailed genetic characterization revealed a new colistin resistance mechanism mediated by genetic integration of the insertion element ISAbaI upstream of the PmrC homolog EptA (93% identity), leading to its overexpression. We found that eptA was ubiquitously present in clinical strains belonging to the international clone 2, and ISAbaI integration upstream of eptA was required to mediate the colistin-resistant phenotype. In addition, we found a duplicated ISAbaI-eptA cassette in one isolate, indicating that this colistin resistance determinant may be embedded in a mobile genetic element. Our data disprove PmrA as a drug target for adjuvant therapy but highlight the importance of PetN transferase-mediated colistin resistance in clinical strains. We suggest that direct targeting of the homologous PetN transferases PmrC/EptA may have the potential to overcome colistin resistance in A. baumannii. IMPORTANCE The discovery of antibiotics revolutionized modern medicine and enabled us to cure previously deadly bacterial infections. However, a progressive increase in antibiotic resistance rates is a major and global threat for our health care system. Colistin represents one of our last-resort antibiotics that is still active against most Gram-negative bacterial pathogens, but increasing resistance is reported worldwide, in particular due to the plasmid-encoded protein MCR-1 present in pathogens such as Escherichia coli and Klebsiella pneumoniae. Here, we showed that colistin resistance in A. baumannii, a top-priority pathogen causing deadly nosocomial infections, is mediated through different avenues that result in increased activity of homologous phosphoethanolamine (PetN) transferases. Considering that MCR-1 is also a PetN transferase, our findings indicate that PetN transferases might be the Achilles heel of superbugs and that direct targeting of them may have the potential to preserve the activity of polymyxin antibiotics.

Abundance of Colistin-Resistant, OXA-23- and ArmA-Producing Acinetobacter baumannii Belonging to International Clone 2 in Greece

“…Conversely, the mutation A226V in the histidine kinase A (phosphoacceptor) domain of PmrB was observed in all ColR isolates, and not in the ColS ones (Figure 1). This mutation has been described in several prior studies, associated with ColR strains (Arroyo et al, 2011;Mavroidi et al, 2015Mavroidi et al, , 2017Dortet et al, 2018;Trebosc et al, 2019).…”

“…Colistin resistance may also result from the overexpression of etpA, a pmrC homolog. This is mediated by insertional inactivation of a gene encoding an H-NS family transcriptional regulator (Lucas et al, 2018) or by integration of insertion sequence elements upstream of the eptA gene itself (Gerson et al, 2019;Potron et al, 2019;Trebosc et al, 2019).…”

Colistin and its role in the Era of antibiotic resistance: an extended review (2000–2019)

“…Very recently, Trebosc et al [52] showed the novel colistin resistance mechanism of A. baumannii mediated by genetic integration of the insertion element ISAbaI upstream of the PmrC homolog EptA (93% identity), leading to its overexpression. Besides, the detection of a duplicated ISAbaI-eptA cassette, suggesting that this colistin resistance determinant may be inserted in a mobile genetic element.…”

Clonal expansion of colistin-resistant Acinetobacter baumannii isolates in Cape Town, South Africa

“…The presence of the insertion sequence ISAba11 in lpxC or lpxA also causes inactivation of LPS production (Moffatt et al, 2011). Alternatively, phosphoethanolamine transferase overexpression can result from the integration of the ISAbaI upstream of a pmrC homolog eptA leading to colistin resistance (Trebosc et al, 2019).…”