Resolving colistin resistance and heteroresistance in Enterobacter species

Species within the <em>Enterobacter cloacae </em>complex (ECC)<em> </em>include globally important nosocomial pathogens. A three-year study of ECC in Germany identified <em>Enterobacter xiangfangensis</em> as the most common species (65.5%) detected, a result replicated by examining a global pool of 3246 isolates. Antibiotic resistance profiling revealed widespread resistance and heteroresistance to the antibiotic colistin and detected the mobile colistin resistance (<em>mcr</em>)-9 gene in 19.2% of all isolates. We show that resistance and heteroresistance properties depend on the chromosomal <em>arnBCADTEF</em> gene cassette whose products catalyze transfer of L-Ara4N to lipid A. Using comparative genomics, mutational analysis, and quantitative lipid A profiling we demonstrate that intrinsic lipid A modification levels are genospecies-dependent and governed by allelic variations in <em>phoPQ</em> and <em>mgrB</em>, that encode a two-component sensor-activator system and specific inhibitor peptide. By generating <em>phoPQ </em>chimeras and combining them with <em>mgrB</em> alleles, we show that interactions at the pH-sensing interface of the sensory histidine kinase <em>phoQ</em> dictate <em>arnBCADTEF</em> expression levels. To minimize therapeutic failures, we developed an assay that accurately detects colistin resistance levels for any ECC isolate.