Convergent Loss of ABC Transporter Genes From Clostridioides difficile Genomes Is Associated With Impaired Tyrosine Uptake and p-Cresol Production

Abstract

We report the frequent, convergent loss of two genes encoding the substrate-binding protein and the ATP-binding protein of an ATP-binding cassette (ABC) transporter from the genomes of unrelated Clostridioides difficile strains. This specific genomic deletion was strongly associated with the reduced uptake of tyrosine and phenylalanine and production of derived Stickland fermentation products, including p-cresol, suggesting that the affected ABC transporter had been responsible for the import of aromatic amino acids. In contrast, the transporter gene loss did not measurably affect bacterial growth or production of enterotoxins. Phylogenomic analysis of publically available genome sequences indicated that this transporter gene deletion had occurred multiple times in diverse clonal lineages of C. difficile, with a particularly high prevalence in ribotype 027 isolates, where 48 of 195 genomes (25%) were affected. The transporter gene deletion likely was facilitated by the repetitive structure of its genomic location. While at least some of the observed transporter gene deletions are likely to have occurred during the natural life cycle of C. difficile, we also provide evidence for the emergence of this mutation during long-term laboratory cultivation of reference strain R20291.

A publicly accessible database for Clostridioides difficile genome sequences supports tracing of transmission chains and epidemics

“…For Illumina sequencing, genomic DNA was extracted from bacterial isolates by using the DNeasy Blood and Tissue kit (Qiagen), and libraries were prepared as described previously [46] and sequenced on an Illumina NextSeq 500 machine using a Mid-Output kit (Illumina) with 300 cycles. For generating complete genome sequences, we applied SMRT long-read sequencing on an RSII instrument (Pacific Biosciences) in combination with Illumina sequencing as reported previously [46]. All genome sequencing data were submitted to the European Nucleotide Archive (www.ebi.ac.uk/ena) under study numbers PRJEB33768, PRJEB33779 and PRJEB33780.…”

“…Sequencing reads were mapped to the reference genome sequence from C. difficile strain R20291 (sequence accession number FN545816) by using BWA-MEM and sequence variation was detected by applying VarScan2 as reported previously [46]. Sequence variation likely generated by recombination was detected through analysis with ClonalFrameML [47] and removed prior to determination of pairwise sequence distances [15] and to construction of maximum-likelihood phylogenetic trees with RAxML (version 8.2.9) [48].…”

Day and Night: Metabolic Profiles and Evolutionary Relationships of Six Axenic Non-Marine Cyanobacteria

“…2018). The Wilcoxon–Mann–Whitney test using Benjamini–Hochberg correction was used for statistical analyses (Steglich et al. 2018).…”

Predictive regulatory and metabolic network models for systems analysis ofClostridioides difficile

“…Recent studies also suggest that CD630_ 08760 may function as a tyrosine transporter per its homology to the CodY-regulated neighbor gene, CD630_08730 (36). Furthermore, Steglich et al (37) observed decreases in tyrosine uptake and Stickland fermentation in clinical isolates lacking CD630_08760 and CD630_08780.…”