Biology subjects

Sanders, I. M. J. G.

Publications and source records attributed to Sanders, I. M. J. G..

3 recordsLinked to original sources

bioRxiv2024

Antimicrobial susceptibility testing of Clostridioides difficile: a dual-site study of three different media and three therapeutic antimicrobials

ObjectivesIncreasing resistance to antimicrobials used for the treatment of Clostridioides difficile infections necessitates reproducible antimicrobial susceptibility testing. Current guidelines take a one-size-fits-all approach and/or offer limited guidance. We investigated how the choice of medium affects measured MIC values across two sites. MethodsWe determined MIC values for the antimicrobials fidaxomicin, metronidazole and vancomycin for a representative collection of European C. difficile strains (n=235) using agar dilution on three different media: Brucella Blood Agar (BBA), Fastidious Anaerobe Agar supplemented with horseblood (FAA-HB) and Wilkins-Chalgren (WC) agar. The study was conducted at two sites to compare reproducibility. Useability (ease of preparation of the media as well as read-out of the assay) was assessed through a survey. ResultsWe found that all media result in highly consistent aggregated MIC data for all antibiotics, with MIC50 and MIC90 within 2-fold of each other across sites. For fidaxomin, MIC values on WC were lower than on the other media. Metronidazole showed the lowest MIC on BBA, and the highest on WC. For vancomycin, there was little difference between media. Though absolute values for individual isolates differed between sites, identified resistant isolates were similar. Results obtained on FAA-HB were most consistent between sites and results obtained on WC showed the most divergence. FAA-HB was positively evaluated in the usability survey. ConclusionsThis study shows medium-dependent differences in C. difficile MICs for at least two antimicrobials across two sites. We suggest the use of FAA-HB to align with general EUCAST recommendations for susceptibility testing of anaerobic bacteria and deposited reference strains for standard susceptibility testing of C. difficile to increase interlaboratory reproducibility.

microbiology↗

bioRxiv2024

Metagenomic global survey and in-depth genomic analyses of Ruminococcus gnavus reveal differences across host lifestyle and health status

Ruminococcus gnavus is a highly prevalent gut bacterium (present in >90% of healthy individuals), of which increased abundance is associated with chronic inflammatory diseases, most notably Crohns disease. Nevertheless, its global distribution has not been investigated and little is known about intraspecies genomic variation. Through a large-scale survey of 12,791 gut metagenomes, we recapitulated known associations with metabolic diseases and inflammatory bowel disease. We uncover a higher prevalence and abundance of R. gnavus in Westernized populations and observe relative abundances of up to 83% in newborns and infants. Next, we built a collection of existing and newly cultured R. gnavus isolates (N = 45) from both healthy individuals and Crohns disease patients and subjected these to PacBio circular consensus sequencing to greatly expand the number of complete R. gnavus genomes. Analysis of these genomes as well as publicly available high quality draft genomes (total > 300 genomes) revealed multiple clades which separated Crohns-derived isolates from healthy-derived isolates. Functional analyses of genes predicted to constitute R. gnavus virulence factors could not explain this separation. Bacterial GWAS revealed that Crohns-derived isolates were enriched in genes related to mobile elements and putative mucin foraging. Together, we present one of the largest complete genome collections of any commensal gut microbe and provide novel biological insights into the global distribution and genomic variation of R. gnavus.

microbiology↗

bioRxiv2022

Clostridioides difficile PCR ribotype 151 is polyphyletic and includes pathogenic isolates from cryptic clade C-II with mono-toxin pathogenicity loci that can escape routine diagnostics

We report a patient case with pseudomembranous colitis associated with a mono-toxin producing Clostridioides difficile belonging to the very rarely diagnosed PCR ribotype (RT) 151. The infection was difficult to diagnose, since the isolate and the feces sample tested negative for toxin-encoding genes using a routine commercial test. This prompted us to sequence n = 11 RT151s from various geographical regions to study their genomic characteristics and relatedness. By including whole genome sequence data from other sources, we could further place these isolates into the phylogenetic tree of C. difficile and assign them to their respective clades. These analyses revealed that 1) RT151s are polyphyletic with isolates falling into clades 1, and cryptic clades C-I and C-II 2) RT151 contains both non-toxigenic and toxigenic isolates and 3) RT151 C-II isolates contained mono-toxin pathogenicity loci (PaLoc). Additional analysis with PacBio circular consensus sequencing revealed that the isolate from our patient case report contains a novel PaLoc insertion site, lacked tcdA and a had significantly divergent tcdB sequence that might explain the failure of the diagnostic test. The study is noteworthy as 1) RT151 encompasses both typical and cryptic clades and 2) conclusive evidence for CDI due to clade C-II isolates was hitherto lacking.

microbiology↗