In Vivo Evolution of Bacterial Resistance in Two Cases of Enterobacter aerogenes Infections during Treatment with Imipenem

Abstract

Infections caused by multidrug resistant (MDR) bacteria are a major concern worldwide. Changes in membrane permeability, including decreased influx and/or increased efflux of antibiotics, are known as key contributors of bacterial MDR. Therefore, it is of critical importance to understand molecular mechanisms that link membrane permeability to MDR in order to design new antimicrobial strategies. In this work, we describe genotype-phenotype correlations in Enterobacter aerogenes, a clinically problematic and antibiotic resistant bacterium. To do this, series of clinical isolates have been periodically collected from two patients during chemotherapy with imipenem. The isolates exhibited different levels of resistance towards multiple classes of antibiotics, consistently with the presence or the absence of porins and efflux pumps. Transport assays were used to characterize membrane permeability defects. Simultaneous genome-wide analysis allowed the identification of putative mutations responsible for MDR. The genome of the imipenem-susceptible isolate G7 was sequenced to closure and used as a reference for comparative genomics. This approach uncovered several loci that were specifically mutated in MDR isolates and whose products are known to control membrane permeability. These were omp35 and omp36, encoding the two major porins; rob, encoding a global AraC-type transcriptional activator; cpxA, phoQ and pmrB, encoding sensor kinases of the CpxRA, PhoPQ and PmrAB two-component regulatory systems, respectively. This report provides a comprehensive analysis of membrane alterations relative to mutational steps in the evolution of MDR of a recognized nosocomial pathogen.

Altered Outer Membrane Transcriptome Balance with AmpC Overexpression in Carbapenem-Resistant Enterobacter cloacae

“…The authors described decreased expression of both ompF (5-fold) and ompC (500-fold) genes in resistant strains. The decrease in expression level of both major OM proteins was also recorded in the report published by Koyano et al (2013), Philippe et al (2015) and Jaskulski et al (2013). …”

Next-generation sequencing based hospital outbreak investigation yields insight into Klebsiella aerogenes population structure and determinants of carbapenem resistance and virulence

“…However, the primary mechanisms underlying carbapenem non-susceptibility in K. aerogenes are thought to be carbapenemase independent and mediated by mutations affecting regulation of chromosomal AmpC β-lactamase expression and membrane permeability (2). The latter has been well documented in K. aerogenes with reports describing mutations impacting porin function/expression that can arise in vivo during antibiotherapy (6), be reversible (2), and present complex diagnostic and therapeutic management challenges (7).…”

Genomic analysis unveils important aspects of population structure, virulence, and antimicrobial resistance inKlebsiella aerogenes

“…For example, CC3 has a higher number of virulence genes when compared to resistance genes. It is important to note that more than 50% of the CC3 isolates derive from hospital outbreaks [2, 7, 47–49]. We hypothesize that, due to the sympatric lifestyle of K. aerogenes (i.e.…”