Kingsley, R.A. et al. Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype. Genome Res. 19, 2279-2287

The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Cambridge, United Kingdom.
Genome Research (Impact Factor: 13.85). 11/2009; 19(12):2279-87. DOI: 10.1101/gr.091017.109
Source: PubMed

ABSTRACT Whereas most nontyphoidal Salmonella (NTS) are associated with gastroenteritis, there has been a dramatic increase in reports of NTS-associated invasive disease in sub-Saharan Africa. Salmonella enterica serovar Typhimurium isolates are responsible for a significant proportion of the reported invasive NTS in this region. Multilocus sequence analysis of invasive S. Typhimurium from Malawi and Kenya identified a dominant type, designated ST313, which currently is rarely reported outside of Africa. Whole-genome sequencing of a multiple drug resistant (MDR) ST313 NTS isolate, D23580, identified a distinct prophage repertoire and a composite genetic element encoding MDR genes located on a virulence-associated plasmid. Further, there was evidence of genome degradation, including pseudogene formation and chromosomal deletions, when compared with other S. Typhimurium genome sequences. Some of this genome degradation involved genes previously implicated in virulence of S. Typhimurium or genes for which the orthologs in S. Typhi are either pseudogenes or are absent. Genome analysis of other epidemic ST313 isolates from Malawi and Kenya provided evidence for microevolution and clonal replacement in the field.

Download full-text


Available from: Melita A Gordon, Aug 27, 2015
1 Follower
  • Source
    • "The BTP1 prophage is one of the distinguishing genetic features of the iNTS S. Typhimurium strain D23580 (Kingsley et al., 2009). Previously, a Salmonella-wide genome analysis for the occurrence of O-antigen modifying gtr operons determined that this prophage encoded an uncharacterized gtr operon (Davies et al., 2013). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Salmonella Typhimurium isolate D23580 represents a recently identified ST313 lineage of invasive non-Typhoidal Salmonellae (iNTS). One of the differences between this lineage and other non-iNTS S. Typhimurium isolates is the presence of prophage BTP1. This prophage encodes a gtrC gene, implicated in O-antigen modification. GtrC(BTP1) is essential for maintaining O-antigen length in isolate D23580, since a gtr(BTP1) mutant yields a short O-antigen. This phenotype can be complemented by gtrC(BTP1) or very closely related gtrC genes. The short O-antigen of the gtr(BTP1) mutant was also compensated by deletion of the BTP1 phage tailspike gene in the D23580 chromosome. This tailspike protein has a putative endorhamnosidase domain and thus may mediate O-antigen cleavage. Expression of the gtrC(BTP1) gene is, in contrast to expression of many other gtr operons, not subject to phase variation and transcriptional analysis suggests that gtrC is produced under a variety of conditions. Additionally, GtrC(BTP1) expression is necessary and sufficient to provide protection against BTP1 phage infection of an otherwise susceptible strain. These data are consistent with a model in which GtrC(BTP1) mediates modification of the BTP1 phage O-antigen receptor in lysogenic D23580, and thereby prevents superinfection by itself and other phage that use the same O-antigen co-receptor. This article is protected by copyright. All rights reserved.
    Molecular Microbiology 01/2015; 96(2). DOI:10.1111/mmi.12933 · 5.03 Impact Factor
  • Source
    • "Mobility of antibiotic resistance genes virulence and antibiotic resistance genes (Mulvey et al., 2006; Kingsley et al., 2009; Venturini et al., 2010). Many of these are likely to evolve in commensal bacterial populations that inhabit the gastrointestinal tracts of food-producing animals but are also in humans and are a cause for great concern. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Multiple antibiotic resistant pathogens represent a major clinical challenge in both the human and veterinary context. It is now well understood that the genes that encode resistance are context independent. That is, the same gene is commonly present in otherwise very disparate pathogens in both humans and production and companion animals, and among bacteria that proliferate in an agricultural context. This can be true even for pathogenic species or clonal types that are otherwise confined to a single host or ecological niche. It therefore follows that mechanisms of gene flow must exist to move genes from one part of the microbial biosphere to another. It is widely accepted that lateral (or horizontal) gene transfer (L(H)GT) drives this gene flow. LGT is relatively well understood mechanistically but much of this knowledge is derived from a reductionist perspective. We believe that this is impeding our ability to deal with the medical ramifications of LGT. Resistance genes and the genetic scaffolds that mobilize them in MDR bacteria of clinical significance are likely to have their origins in completely unrelated parts of the microbial biosphere. Resistance genes are increasingly polluting the microbial biosphere by contaminating environmental niche where previously they were not detected. More attention needs to be paid to the way that humans have, through the widespread application of antibiotics, selected for combinations of mobile elements that enhance the flow of resistance genes between remotely linked parts of the microbial biosphere. Attention also needs to be paid to those bacteria that link human and animal ecosystems. We argue that multiply antibiotic resistant commensal bacteria are especially important in this regard. More generally, the post genomics era offers the opportunity for understanding how resistance genes are mobilized from a one health perspective. In the long term, this holistic approach offers the best opportunity to better manage wh
    Frontiers in Microbiology 04/2013; 4:86. DOI:10.3389/fmicb.2013.00086 · 3.94 Impact Factor
  • Source
    • "2.3. S. Typhimurium bacterial isolate S. Typhimurium D23580, a well-characterized invasive clinical isolate of nontyphoidal Salmonella from Malawi (MacLennan et al., 2008; Kingsley et al., 2009) was used throughout the study. This strain is representative of 90% of invasive NTS isolates in Malawi. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Nontyphoidal Salmonellae (NTS) are a common cause of bacteraemia in children and HIV-infected adults in Sub-Saharan Africa. We have previously shown that antibodies play a key role in both bactericidal and cellular mechanisms of immunity to NTS, but found that high concentrations of antibody to Salmonella Typhimurium O antigen (OAg) in the serum of some HIV-infected African adults is associated with impaired killing of NTS. To further investigate the function of antibodies to the OAg NTS, we developed a method to purify these antibodies from human serum by affinity chromatography. Purified Salmonella Typhimurium OAg was activated with adipic acid dihydrazide (ADH) via two different chemistries before linking to N-hydroxysuccinamide-Sepharose resin: one ADH molecule was introduced per OAg chain on its terminal 3-deoxy-D-manno-octulosonic acid sugar (OAg-ADH), or multiple ADH molecules were attached along the OAg chain after oxidation with sodium periodate (OAgoxADH). Both resulting columns worked well when tested with commercial polyclonal anti-O:4,5 antibodies from rabbit serum. Over 90% of the applied antibodies bound to the resin and 89% of the linked antibodies were then eluted as detected by ELISA. OAg-ADH was preferred as the method for OAg derivatisation as it does not modify the saccharide chain and can be applied to OAg from different bacteria. Both columns were able to bind OAg-specific antibodies in human serum, but antibody recovery was initially low. Different elution buffers were tested and different amounts of OAg-ADH were linked to the resin to improve the yield. Optimal recovery (51%) was obtained by loading 1 mg of activated OAg per ml of resin and eluting with 0.1 M glycine, 0.1 M NaCl pH 2.4.The column matrix could be regenerated following elution with no detectible loss in performance for over ten uses. This method offers the potential to purify antibodies to Salmonella OAg from polyclonal serum following vaccination or natural exposure to Salmonella and so investigate the functionality and diversity of the antibody response to OAg.
    Journal of immunological methods 11/2012; 387(1-2). DOI:10.1016/j.jim.2012.10.015 · 2.01 Impact Factor
Show more