Perspective on Clinically-Relevant Antimicrobial Resistant Enterobacterales in Food: Closing the Gaps Using Genomics

Abstract

Antimicrobial resistance is one of the most important public health concerns—it causes 700,000 deaths annually according to the World Health Organization (WHO). Enterobacterales such as E. coli and Klebsiella pneumoniae, have become resistant to many relevant antimicrobials including carbapenems and extended spectrum cephalosporins. These clinically relevant resistant Enterobacterales (CRRE) members are now globally distributed in the environment including different food types (meats, produce, dairy). Unlike known foodborne pathogens, CRRE are not usually part of most food surveillance systems. However, numerous reports of CRRE highlight the importance of these bacteria in food and have been shown to contribute to the overall crisis of antimicrobial resistance. This is especially important in the context of carriage of these pathogens by immuno-compromised individuals. CRRE infections upon consumption of contaminated food could colonize the human gastrointestinal tract and eventually be a source of systemic infections such as urinary tract infections or septicemia. While different aspects need to be considered to elucidate this, whole genome sequencing along with metadata could be used to understand genomic relationships of CRRE obtained from foods and humans, including isolates from clinical infections. Once robust scientific data is available on the role of CRRE in food, countries could move forward to better survey and control CRRE in food.

ESKAPE and Beyond: The Burden of Coinfections in the COVID-19 Pandemic

“…Globally, K. pneumoniae has been repeatedly identified over the past 30 years as the most common enterobacteria linked to the spread of extended-spectrum β-lactamase (ESBL) genes in hospital settings. Importantly, patients infected with carbapenem-resistant K. pneumoniae have a fourfold higher risk of death than patients infected with antibiotic-susceptible K. pneumoniae [ 70 ]. In recent years, carbapenem-resistant Enterobacterales (CRE) have become an increasingly frequent etiological agent of HAIs and present a major clinical impact due to the limited therapeutic options available.…”

“…Resistance to carbapenems is often caused by the production of carbapenemases. The main species of enterobacteria carrying carbapenemases are K. pneumoniae , Enterobacter spp., and E. coli [ 70 , 76 ]. In conjunction with carbapenemases, mutations in porin genes have been reported to impede the diffusion of antibiotics across their membranes thereby reducing the periplasmic concentration of antibiotics, leading to carbapenem resistance in some cases [ 78 , 79 ].…”