Clostridioides difficileMreE (PBP2) variants facilitate clinical disease during cephalosporin exposures

Abstract

Cephalosporins are the most common triggers of healthcare-associated Clostridioides difficile infections (CDI). Here, we confirm gene-level drivers of cephalosporin resistance and their roles in promoting disease. Genomic-epidemiologic analyses of 306 C. difficile isolates from a hospital surveillance program monitoring asymptomatic carriers and CDI patients identified prevalent third-generation cephalosporin resistance to ceftriaxone at >256 ug/mL in 26% of isolates. Resistance was associated with patient cephalosporin exposures 8-10 days before C. difficile detection. Genomic analyses identified variants in the mreE penicillin binding protein 2 (PBP2) associated with resistance to multiple beta-lactam classes. Transfer of variants into susceptible strain CD630 elevated resistance to first and third-generation cephalosporins. Transfer into the mouse-infective strain ATCC 43255 enabled disease when mice were exposed to 500ug/mL cefoperazone, a dose that inhibited the isogenic susceptible strain. Our findings establish roles of cephalosporins and mreE-cephalosporin-resistant variants in CDI and provide testable genetic loci for detecting resistance in patient strains.

Approaching pathogenicClostridiafrom a One Health perspective

“…Additional strain phenotypic data, including antibiograms, biochemical, or serologic strain typing also enhances available datasets to provide functional assessments of antibiotic resistance and known antigenic or biochemical properties 23,47,51 . The phenotypic analyses, particularly when conducted under a recognized international standards such as CLIA (Clinical Laboratory Improvement Amendments) 52 or ISO 15189 53 , offer means to correlate phenotypic findings from strains collected across geographic locations with genomic findings 39 .…”

“…For example, in C. difficile AMRFinderPlus has identified plasmid-borne genes that increase strain phenotypic resistance to metronidazole 68 . In contrast, many van gene homologs that are involved in C. difficile’s cell wall synthesis, promote phenotypic resistance to vancomycin in Enterococci and other species, but do not do so in C. difficile 47 . Similarly, chromosomal carriage of a class D beta-lactamase in C. difficile 69 was not associated with phenotypic resistance to multiple penicillin, cephalosporin, or carbapenem agents when tested in vitro 47 .…”

“…In contrast, many van gene homologs that are involved in C. difficile’s cell wall synthesis, promote phenotypic resistance to vancomycin in Enterococci and other species, but do not do so in C. difficile 47 . Similarly, chromosomal carriage of a class D beta-lactamase in C. difficile 69 was not associated with phenotypic resistance to multiple penicillin, cephalosporin, or carbapenem agents when tested in vitro 47 . The reasons for these differences may relate to differing functions of these genes in Clostridia versus other members of phylum Firmicutes, as well as the conditions that induce their expression in in vitro versus in vivo or ex vivo settings.…”

“…Isolate location data, which ranges from information provided at the level of country of origin to municipalities and geo-coordinates, also enhances strain tracking and capacity to provide context for newly contributed genomes. Incorporation of codified clinical data, such as ICD.10 (International Classification of Diseases 10th revision), Diagnosis Related Group (DRG) codes 46,47 , and ordered testing that identified isolates, particularly to distinguish surveillance testing for asymptomatic carriage of toxigenic strains versus association with active infections 48 , provides critical information when tracking strains over time as well as within and among sites and healthcare institutions. Under HIPAA (Health Insurance Portability and Accountability Act) 49 , healthcare institutions in the US are limited from providing full location and date/timestamps that are associated with clinical events, but with institutional review and approval may communicate anonymous or limited datasets (LDS) that note the country, state, and often city, first 2-3 digits of the zip code, relative to population density, and the strain year of origin 33,49,50 .…”