The Resistance Mechanism Governs Physiological Adaptation of Escherichia coli to Growth With Sublethal Concentrations of Carbapenem.

Franca Schäfer,Dirk Schlüter,Marius Vital,Stefan Ziesing,Sabrina Woltemate,Pia Görner,Robert Geffers,Christina Brandenberger

doi:10.3389/fmicb.2021.812544

Abstract

Factors governing resistance in carbapenem-resistant Enterobacteriaceae are manifold. Despite ample research efforts, underlying molecular mechanisms are still only partly understood. Furthermore, little is known on (eco)physiological consequences from resistance acquisition originating from distinct mechanisms in respective bacteria.In this study, we examined physiological adaptation of Escherichia coli clinical isolates exhibiting two distinct resistance mechanisms–either carrying a carbapenemase (n = 4, CARB) or alterations in porin-encoding genes (n = 6, POR)–during growth with sublethal concentrations of ertapenem in chemostat culture. Basic growth parameters based on optical density and flow-cytometric analyses as well as global gene expression patterns using RNA-Seq were recorded. We demonstrate that strategies to deal with the antibiotic were distinct between strains of the two groups, where (increased) expression of carbapenemases was the major response in CARB, whereas wide-spread alterations in gene-expression that promoted a survival-like phenotype was observed in POR. The response in POR was accompanied with “costs of resistance” resulting in reduced growth efficiencies compared with CARB that are intrinsic to that group and were also observed during growth without antibiotic challenge, however, at lower levels. All strains showed similar minimal inhibitory concentrations and did not form phylogenetic groups, indicating that results cannot be attributed to distinct resistance levels or phylogenetic relationships, but are indeed based on the resistance mechanism.

Highlights

Gram-negative bacteria are a common cause of life-threatening diseases with Enterobacteriaceae, such as Klebsiella spp. and Escherichia coli, playing a major role (Vincent et al, 2009)
We performed experiments in chemostat culture, i.e., steady-state growth in continuous culture, with and without the addition of ertapenem at sublethal concentrations in order to elucidate physiological adaptations of E. coli to grow with carbapenems
Throughout this study we were interested in response differences between bacteria exhibiting a carbapenemase gene (n = 4) and those characterized by alterations in the porin-encoding genes ompC/F (n = 6), referred to as CARB and porin encoding genes (POR), respectively, in the following text

Summary

Introduction

Gram-negative bacteria are a common cause of life-threatening diseases with Enterobacteriaceae, such as Klebsiella spp. and Escherichia coli, playing a major role (Vincent et al, 2009). Most prominent are carbapenemases that act by cleaving the antibiotic They belong to three of the four Ambler classes of β-lactams: class A carbapenemases includes KPC, GES, IMI, SME, class B contains the metallo-β-lactamases (VIM, IMP, NDM), and class D represent the OXAs, among which OXA-48 is the most frequent carbapenemase in Enterobacteriaceae (Nordmann and Poirel, 2014). Another prominent resistance mechanism to carbapenems are alterations of the main porins OmpC and OmpF (Nikaido, 2003). A combination of additional mechanisms, such as expression of extendedspectrum β-lactamases (ESBLs) or enzymes of the AmpC-group, increased antibiotic efflux, and target modification of penicillin binding proteins, are believed to contribute to carbapenem resistance in those strains (Adler et al, 2016; Mmatli et al, 2020)

Methods

Results

Conclusion