The global epidemic of multidrug resistant Salmonella Typhimurium DT104 provides an important example, both in terms of the agent and its resistance, of a widely disseminated zoonotic pathogen. Here, with an unprecedented national collection of isolates collected contemporaneously from humans and animals, and including a sample of internationally derived isolates, we have used whole genome sequencing to dissect the phylogenetic relationships of the bacterium and its antimicrobial resistance genes through the course of an epidemic. Contrary to current tenets supporting a single homogeneous epidemic, we demonstrate that the bacterium and its resistance genes were largely maintained within animal and human populations separately, and that there was limited transmission, in either direction. We also show considerable variation in the resistance profiles, in contrast to the largely stable bacterial core genome, further emphasizing the critical importance of integrated genotypic datasets in understanding the ecology of bacterial zoonoses and antimicrobial resistance.

CmeABC, a resistance-nodulation-division (RND) type of efflux pump, contributes to Campylobacter resistance to a broad spectrum of antimicrobial agents and is also essential for Campylobacter colonization of the animal intestinal tract by mediation of bile resistance. As one of the main systems for Campylobacter adaptation to different environments, CmeABC is likely subject to control by regulatory elements. We describe the identification of a transcriptional repressor for CmeABC. Insertional mutagenesis of cmeR, an open reading frame immediately upstream of the cmeABC operon, resulted in overexpression of cmeABC, as determined by transcriptional fusion (P cmeABC-lacZ ) and immunoblotting with CmeABC-specific antibodies. Overexpression of the efflux pump was correlated with a moderate increase in the level of resistance of the cmeR mutant to several antimicrobials. In vitro, recombinant CmeR bound specifically to the promoter region of cmeABC, precisely, to the inverted repeat sequences in the cmeABC promoter. A single nucleotide deletion between the two half sites of the inverted repeat reduced the level of CmeR binding to the promoter sequence and resulted in overexpression of cmeABC. Together, these findings indicate that cmeR encodes a transcriptional repressor that directly interacts with the cmeABC promoter and modulates the expression of cmeABC. Mutation either in CmeR or in the inverted repeat impedes the repression and leads to enhanced production of the MDR efflux pump.

CmeDEF interacts with CmeABC in conferring antimicrobial resistance and maintaining cell viability in C. jejuni. CmeABC is the predominant efflux pump in C. jejuni, whereas CmeDEF plays a secondary role in conferring intrinsic resistance to antimicrobials.

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Insertion sequences (ISs) are the simplest transposable elements and are widely distributed in bacteria. It has long been thought that IS excision rarely occurs in bacterial cells because most bacteria exhibit no end-joining activity to regenerate donor DNA after IS excision. Recently, however, we found that excision of IS629, an IS3 family member, occurs frequently in Escherichia coli O157. In this paper, we describe a protein IS-excision enhancer (IEE) that promotes IS629 excision from the O157 genome in an IS transposase-dependent manner. Various types of genomic deletions are also generated on IEE-mediated IS excision, and IEE promotes the excision of other IS3 family members and ISs from several other IS families. These data and the phylogeny of IEE homologues found in a broad range of bacteria suggest that IEE proteins have coevolved with IS elements and have pivotal roles in bacterial genome evolution by inducing IS removal and genomic deletion.

Many bacterial pathogens encode ADP-ribosyltransferase toxins. The authors identified an ADP-ribosyltransferase toxin homologue (ArtA, ArtB) in Salmonella enterica serovar Typhimurium (S. typhimurium) DT104. ArtA is most homologous to a putative pertussis-like toxin subunit present in Salmonella typhi (STY1890) and Salmonella paratyphi A (SPA1609), while ArtB shows homology to a hypothetical periplasmic protein of S. typhi (STY1364) and S. paratyphi A (SPA1188), and a putative pertussis-like toxin subunit in S. typhi (STY1891) and S. paratyphi A (SPA1610). The artA gene was detected from the phage particle fraction upon mitomycin C induction, and the flanking region of artAB contains a prophage-like sequence, suggesting that these putative toxin genes reside within a prophage. Southern blotting analysis revealed that artA is conserved in 12 confirmed DT104 strains and in four related strains which are not phage-typed but are classified into the same group as DT104 by both amplified-fragment length polymorphism and pulsed-field gel electrophoresis. Except for one strain, NCTC 73, all 13 S. typhimurium strains which were classified into different groups from that of DT104 lacked the artA locus. The results suggest that phage-mediated recombination has resulted in the acquisition of art genes in S. typhimurium DT104 strains.

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