Genome sequencing reveals diversification of virulence factor content and possible host adaptation in distinct subpopulations of Salmonella enterica

<p>Abstract</p> <p>Background</p> <p>Divergence of bacterial populations into distinct subpopulations is often the result of ecological isolation. While some studies have suggested the existence of <it>Salmonella enterica </it>subsp. <it>enterica </it>subclades, evidence for these subdivisions has been ambiguous. Here we used a comparative genomics approach to define the population structure of <it>Salmonella enterica </it>subsp. <it>enterica</it>, and identify clade-specific genes that may be the result of ecological specialization.</p> <p>Results</p> <p>Multi-locus sequence analysis (MLSA) and single nucleotide polymorphisms (SNPs) data for 16 newly sequenced and 30 publicly available genomes showed an unambiguous subdivision of <it>S. enterica </it>subsp. <it>enterica </it>into at least two subpopulations, which we refer to as clade A and clade B. Clade B strains contain several clade-specific genes or operons, including a β-glucuronidase operon, a S-fimbrial operon, and cell surface related genes, which strongly suggests niche specialization of this subpopulation. An additional set of 123 isolates was assigned to clades A and B by using qPCR assays targeting subpopulation-specific SNPs and genes of interest. Among 98 serovars examined, approximately 20% belonged to clade B. All clade B isolates contained two pathogenicity related genomic islands, SPI-18 and a cytolethal distending toxin islet; a combination of these two islands was previously thought to be exclusive to serovars Typhi and Paratyphi A. Presence of β-glucuronidase in clade B isolates specifically suggests an adaptation of this clade to the vertebrate gastrointestinal environment.</p> <p>Conclusions</p> <p><it>S. enterica </it>subsp. <it>enterica </it>consists of at least two subpopulations that differ specifically in genes involved in host and tissue tropism, utilization of host specific carbon and nitrogen sources and are therefore likely to differ in ecology and transmission characteristics.</p

Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss

<p>Abstract</p> <p>Background</p> <p>The bacterial genus <it>Listeria </it>contains pathogenic and non-pathogenic species, including the pathogens <it>L. monocytogenes </it>and <it>L. ivanovii</it>, both of which carry homologous virulence gene clusters such as the <it>prfA </it>cluster and clusters of internalin genes. Initial evidence for multiple deletions of the <it>prfA </it>cluster during the evolution of <it>Listeria </it>indicates that this genus provides an interesting model for studying the evolution of virulence and also presents practical challenges with regard to definition of pathogenic strains.</p> <p>Results</p> <p>To better understand genome evolution and evolution of virulence characteristics in <it>Listeria</it>, we used a next generation sequencing approach to generate draft genomes for seven strains representing <it>Listeria </it>species or clades for which genome sequences were not available. Comparative analyses of these draft genomes and six publicly available genomes, which together represent the main <it>Listeria </it>species, showed evidence for (i) a pangenome with 2,032 core and 2,918 accessory genes identified to date, (ii) a critical role of gene loss events in transition of <it>Listeria </it>species from facultative pathogen to saprotroph, even though a consistent pattern of gene loss seemed to be absent, and a number of isolates representing non-pathogenic species still carried some virulence associated genes, and (iii) divergence of modern pathogenic and non-pathogenic <it>Listeria </it>species and strains, most likely circa 47 million years ago, from a pathogenic common ancestor that contained key virulence genes.</p> <p>Conclusions</p> <p>Genome evolution in <it>Listeria </it>involved limited gene loss and acquisition as supported by (i) a relatively high coverage of the predicted pan-genome by the observed pan-genome, (ii) conserved genome size (between 2.8 and 3.2 Mb), and (iii) a highly syntenic genome. Limited gene loss in <it>Listeria </it>did include loss of virulence associated genes, likely associated with multiple transitions to a saprotrophic lifestyle. The genus <it>Listeria </it>thus provides an example of a group of bacteria that appears to evolve through a loss of virulence rather than acquisition of virulence characteristics. While <it>Listeria </it>includes a number of species-like clades, many of these putative species include clades or strains with atypical virulence associated characteristics. This information will allow for the development of genetic and genomic criteria for pathogenic strains, including development of assays that specifically detect pathogenic <it>Listeria </it>strains.</p

Korelacije u bolničkoj smrtnosti bolesnika s akutnim koronarnim sindromom na Kosovu

It has been demonstrated that pre-hospital emergency care reduces in-hospital mortality in patients admitted with acute coronary syndrome (ACS). The aim of this study was to analyze the relationship between pre-hospital emergency care and in-hospital mortality in ACS patients treated at the University Clinical Centre of Kosovo Emergency Department (UCCK ED). This observational clinical study included 1498 ACS patients treated at UCCK ED and followed-up by phone call for one year after discharge from the hospital. According to multivariate Cox regression analysis, age (HR=2.37, 95% CI 1.67-3.52), pre-hospital emergency care (HR=3.92, 95% CI 2.35-6.54), STEMI (HR=6.17, 95% CI 3.22-15.31), diabetes mellitus (HR=3.01, 95% CI 1.98-3.78), left ventricular ejection fraction <40% (HR=17.63, 95% CI 11.2-30.54) and ex-smoking (HR=2.34, 95% CI 1.57-3.85) were significant predictors of mortality in ACS patients. In-hospital mortality of patients admitted with ACS remains high in Kosovo as compared with developed countries. A better strategy for pre-hospital emergency care in Kosovo is recommended to save lives in these high-risk patients.Pokazano je da predbolnička hitna skrb smanjuje bolničku smrtnost u bolesnika s akutnim koronarnim sindromom (AKS). Cilj ove studije bio je analizirati odnos između predbolničke hitne skrbi i bolničke smrtnosti bolesnika s AKS-om liječenih na Odjelu za hitne slučajeve Univerzitetskog kliničkog centra Kosova (UKCK). Ovo opservacijsko kliničko istraživanje obuhvaćalo je 1498 bolesnika s AKS-om liječenih na Odjelu za hitne slučajeve UKCK, koji su praćeni godinu dana nakon otpusta telefonskim pozivom. Multivarijatna Coxova regresijska analiza pokazala je da su dob (HR=2,37, 95% CI 1,67-3,52), predbolnička hitna skrb (HR=3,92, 95% CI 2,35-6,54), STEMI (HR=6,17, 95% CI 3,22-15,31), šećerna bolest (HR=3,01, 95% CI 1,98-3,78), istisna frakcija lijeve klijetke <40% (HR=17,63, 95% CI 11,2-30,54) i pušenje (HR=2,34, 95% CI 1,57-3,85) značajni prediktori smrtnosti u bolesnika s AKS-om. Bolnička smrtnost bolesnika primljenih s AKS-om i dalje je visoka na Kosovu u usporedbi s razvijenim zemljama. Preporuča se bolja strategija za predbolničku hitnu skrb na Kosovu radi spašavanja života ovih bolesnika visokog rizika

Identification and Characterization of Novel <em>Salmonella</em> Mobile Elements Involved in the Dissemination of Genes Linked to Virulence and Transmission

<div><p>The genetic diversity represented by >2,500 different <em>Salmonella</em> serovars provides a yet largely uncharacterized reservoir of mobile elements that can contribute to the frequent emergence of new pathogenic strains of this important zoonotic pathogen. Currently, our understanding of <em>Salmonella</em> mobile elements is skewed by the fact that most studies have focused on highly virulent or common serovars. To gain a more global picture of mobile elements in <em>Salmonella</em>, we used prediction algorithms to screen for mobile elements in 16 sequenced <em>Salmonella</em> genomes representing serovars for which no prior genome scale mobile element data were available. From these results, selected mobile elements underwent further analyses in the form of validation studies, comparative analyses, and PCR-based population screens. Through this analysis we identified a novel plasmid that has two cointegrated replicons (IncI1-IncFIB); this plasmid type was found in four genomes representing different <em>Salmonella</em> serovars and contained a virulence gene array that had not been previously identified. A <em>Salmonella</em> Montevideo isolate contained an IncHI and an IncN2 plasmid, which both encoded antimicrobial resistance genes. We also identified two novel genomic islands (SGI2 and SGI3), and 42 prophages with mosaic architecture, seven of them harboring known virulence genes. Finally, we identified a novel integrative conjugative element (ICE) encoding a type IVb pilus operon in three non-typhoidal <em>Salmonella</em> serovars. Our analyses not only identified a considerable number of mobile elements that have not been previously reported in <em>Salmonella</em>, but also found evidence that these elements facilitate transfer of genes that were previously thought to be limited in their distribution among <em>Salmonella</em> serovars. The abundance of mobile elements encoding pathogenic properties may facilitate the emergence of strains with novel combinations of pathogenic traits.</p> </div

Phylogeny inferred with maximum likelihood of the IncI1 replicon.

<p>Maximum likelihood phylogeny conducted with IncI1 sequences for plasmids found in this study and currently available sequences. Analysis was conducted with RAxML. Two clades were observed (clade I and clade II), with clade I containing the <i>Salmonella</i> plasmids analyzed here.</p

Comparison, made using the Blast algorithm, of PSP3-like and P22-like phages.

<p>(A) Comparison of six phages that resemble PSP3; phages were identified in serovars Uganda, Johannesburg, Adelaide, Gaminara, Montevideo, and Urbana. Coding regions are represented as blue arrows and regions of homology are shaded in grey. (B) Comparison of six phages that resemble P22, identified in serovars Wandsworth, Mississippi, Rubislaw, Uganda, Johannesburg, and Montevideo. Coding regions are represented as orange arrows and regions of homology are shaded in grey.</p

Plasmids predicted and validated in this study.

<p>Plasmids predicted and validated in this study.</p

Isolates positive for type IVb pili, and/or IncI1-IncFIB replicons.

1<p>Isolates used for invasion assay are marked with ^a, isolates with completed whole genome sequences are marked with ^b, isolates were IncFIB and IncI1 replicons were identified by PCR and sequencing are marked with ^c (which could indicate the presence of both an IncI1 and an IncFIB plasmids or the presence of a cointegrated plasmid).</p