Epidemic Clostridioides difficile Ribotype 027 Lineages: Comparisons of Texas Versus Worldwide Strains

Abstract

BackgroundThe epidemic Clostridioides difficile ribotype 027 strain resulted from the dissemination of 2 separate fluoroquinolone-resistant lineages: FQR1 and FQR2. Both lineages were reported to originate in North America; however, confirmatory large-scale investigations of C difficile ribotype 027 epidemiology using whole genome sequencing has not been undertaken in the United States.MethodsWhole genome sequencing and single-nucleotide polymorphism (SNP) analysis was performed on 76 clinical ribotype 027 isolates obtained from hospitalized patients in Texas with C difficile infection and compared with 32 previously sequenced worldwide strains. Maximum-likelihood phylogeny based on a set of core genome SNPs was used to construct phylogenetic trees investigating strain macro- and microevolution. Bayesian phylogenetic and phylogeographic analyses were used to incorporate temporal and geographic variables with the SNP strain analysis.ResultsWhole genome sequence analysis identified 2841 SNPs including 900 nonsynonymous mutations, 1404 synonymous substitutions, and 537 intergenic changes. Phylogenetic analysis separated the strains into 2 prominent groups, which grossly differed by 28 SNPs: the FQR1 and FQR2 lineages. Five isolates were identified as pre-epidemic strains. Phylogeny demonstrated unique clustering and resistance genes in Texas strains indicating that spatiotemporal bias has defined the microevolution of ribotype 027 genetics.Conclusions Clostridioides difficile ribotype 027 lineages emerged earlier than previously reported, coinciding with increased use of fluoroquinolones. Both FQR1 and FQR2 ribotype 027 epidemic lineages are present in Texas, but they have evolved geographically to represent region-specific public health threats.

In Vitro Activity of Omadacycline, a New Tetracycline Analog, and Comparators against Clostridioides difficile

“…A convenience sample of 16 isolates from five distinct ribotypes underwent DNA extraction using either the QIAamp DNA minikit (Qiagen, Venlo, The Netherlands) or AnaPrep automated DNA extractor (BioChain Institute Inc., Newark, CA) as previously described ( 22 ). DNA was quantified by NanoDrop (Thermo Fisher Scientific, Waltham, MA) and Qubit (Thermo Fisher Scientific, Waltham, MA), and DNA quality was assessed using a BioAnalyzer (Agilent Technologies Inc., Santa Clara, CA).…”

Origin, genomic diversity and microevolution of the Clostridium difficile B1/NAP1/RT027/ST01 strain in Costa Rica, Chile, Honduras and Mexico

“…Most introductions corresponded to isolates from the FQR2 lineage, which has been recognized as the most widely distributed in the world [ 10 ]. However, newer studies report that the prevalence of the FQR1 and FQR2 lineages is similar in North America [ 56 ]. The most recent common ancestor analysis performed showed that the B1/NAP1/RT027/ST01 strain arrived in LA between 1998 and 2005 from North America (FQR1 and FQR2), Western Europe (FQR1 and FQR2) and Northern Europe (FQR2), confirming the rapid global dissemination of the FQR lineages after their emergence [ 10 ].…”

In vitro activity of eravacycline against common ribotypes of Clostridioides difficile

“…A convenience sample of isolates from six distinct ribotypes underwent DNA extraction using either the QIAamp DNA Mini Kit (QIAGEN, Venlo, the Netherlands) or the AnaPrep automated DNA extractor (BioChain Institute Inc., Newark, CA, USA) as previously described. 17 DNA was quantified by NanoDrop (Thermo Fisher Scientific, Waltham, MA, USA) and Qubit (Thermo Fisher Scientific, Waltham, MA, USA) and DNA quality was assessed using a BioAnalyzer (Agilent Technologies Inc., Santa Clara, CA, USA). DNA libraries were prepared according to Illumina’s protocols, multiplexed on a flow cell and run on a NextSeq (Illumina Inc., San Diego, CA, USA) using paired-end sequencing.…”