Genomic insights into the fate of colistin resistance and Acinetobacter baumannii during patient treatment

Abstract

Bacterial whole-genome sequencing (WGS) of human pathogens has provided unprecedented insights into the evolution of antibiotic resistance. Most studies have focused on identification of resistance mutations, leaving one to speculate on the fate of these mutants once the antibiotic selective pressure is removed. We performed WGS on longitudinal isolates of Acinetobacter baumannii from patients undergoing colistin treatment, and upon subsequent drug withdrawal. In each of the four patients, colistin resistance evolved via mutations at the pmr locus. Upon colistin withdrawal, an ancestral susceptible strain outcompeted resistant isolates in three of the four cases. In the final case, resistance was also lost, but by a compensatory inactivating mutation in the transcriptional regulator of the pmr locus. Notably, this inactivating mutation reduced the probability of reacquiring colistin resistance when subsequently challenged in vitro. On face value, these results supported an in vivo fitness cost preventing the evolution of stable colistin resistance. However, more careful analysis of WGS data identified genomic evidence for stable colistin resistance undetected by clinical microbiological assays. Transcriptional studies validated this genomic hypothesis, showing increased pmr expression of the initial isolate. Moreover, altering the environmental growth conditions of the clinical assay recapitulated the classification as colistin resistant. Additional targeted sequencing revealed that this isolate evolved undetected in a patient undergoing colistin treatment, and was then transmitted to other hospitalized patients, further demonstrating its stability in the absence of colistin. This study provides a unique window into mutational pathways taken in response to antibiotic pressure in vivo, and demonstrates the potential for genome sequence data to predict resistance phenotypes.

Preservation of Acquired Colistin Resistance in Gram-Negative Bacteria

“…The colistinresistant mutants had a colistin MIC of Ն64 g/ml. Rapid development of colistin resistance in some bacterial species has previously been reported (12,17,18). A previous mutant prevention concentration study also indicated that colistin resistance can be readily induced during drug therapy by single-step mutation in A. baumannii, P. aeruginosa, and K. pneumoniae (19).…”

Old drug, new findings: colistin resistance and dependence of Acinetobacter baumannii

“…Adams et al [40] Park et al [41] Lesho et al [42] Beceiro et al [44] Rolain et al [46] Kim et al [48] Arroyo et al [34] Snitkin et al [47] Choi et al [43] Choi et al [45] Colistin resistance and dependence in A. baumannii sule polysaccharide (CPS) and efflux pumps [54,55]. For CPS production, reduced production of CPS in colistin-resistant mutants was observed in Klebsiella pneumoniae, which is a contradictory finding [56].…”

Antibiotic resistance mechanisms of Myroides sp.

“…Genomic sequencing revealed comprehensive drug-resistance mechanisms, such as a 41.6-kb closely related antibiotic resistance island in the chromosome (Huang et al, 2012), the horizontally transmittable carbapenem resistance gene (bla ) containing a plasmid (in isolate MDR-TJ, with 454 Titanium) among different A. baumannii strains (Huang et al, 2012;Lee et al, 2013), a list of antimicrobial resistance-associated genes (with 454 and SOLiD) (Rolain et al, 2013), a diversified resistance gene list (with Illumina Hiseq2000) (Tan et al, 2013), and longitudinally evolved antibiotic resistance gene mutations and mutational pathways under pressure from the antibiotic colistin (with 454 Titanium) (Snitkin et al, 2013). Since its invention by Rothberg et al (2011), Ion Torrent sequencing technology has been successfully applied to complete genomic sequencing, such as in Clostridium sp.…”