Publications by authors named "Derek Pickard"

108 Publications

Identification of Natural Mutations Responsible for Altered Infection Phenotypes of Salmonella enterica Clinical Isolates by Using Cell Line Infection Screens.

Appl Environ Microbiol 2021 01 4;87(2). Epub 2021 Jan 4.

Institute of Biotechnology, Faculty Environment and Natural Sciences, BTU Cottbus-Senftenberg, Senftenberg, Germany.

The initial steps of pathogenesis involve adhesion to and invasion into host epithelial cells. While well-studied for serovar Typhimurium, the factors contributing to this process in other, host-adapted serovars remains unexplored. Here, we screened clinical isolates of serovars Gallinarum, Dublin, Choleraesuis, Typhimurium, and Enteritidis for adhesion to and invasion into intestinal epithelial cell lines of human, porcine, and chicken origins. Thirty isolates with altered infectivity were used for genomic analyses, and 14 genes and novel mutations associated with high or low infectivity were identified. The functions of candidate genes included virulence gene expression regulation and cell wall or membrane synthesis and components. The role of several of these genes in adhesion to and invasion into cells has not previously been investigated. The genes (encoding a stringent response regulator) and (encoding a vancomycin high-temperature exclusion protein) were selected for further analyses, and we confirmed their roles in adhesion to and invasion into host cells. Furthermore, transcriptomic analyses were performed for Enteritidis and Typhimurium, with two highly infective and two marginally infective isolates for each serovar. Expression profiles for the isolates with altered infection phenotypes revealed the importance of type 3 secretion system expression levels in the determination of an isolate's infection phenotype. Taken together, these data indicate a new role in cell host infection for genes or gene variants previously not associated with adhesion to and invasion into the epithelial cells. is a foodborne pathogen affecting over 200 million people and resulting in over 200,000 fatal cases per year. Its adhesion to and invasion into intestinal epithelial cells represent one of the first and key steps in the pathogenesis of salmonellosis. Still, around 35 to 40% of bacterial genes have no experimentally validated function, and their contribution to bacterial virulence, including adhesion and invasion, remains largely unknown. Therefore, the significance of this study is in the identification of new genes or gene allelic variants previously not associated with adhesion and invasion. It is well established that blocking adhesion and/or invasion would stop or hamper bacterial infection; therefore, the new findings from this study could be used in future developments of anti- therapy targeting genes involved in these key processes. Such treatment could be a valuable alternative, as the prevalence of antibiotic-resistant bacteria is increasing very rapidly.
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http://dx.doi.org/10.1128/AEM.02177-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7783345PMC
January 2021

The architecture and stabilisation of flagellotropic tailed bacteriophages.

Nat Commun 2020 07 27;11(1):3748. Epub 2020 Jul 27.

Infection & Immunity Program, Biomedicine Discovery Institute & Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia.

Flagellotropic bacteriophages engage flagella to reach the bacterial surface as an effective means to increase the capture radius for predation. Structural details of these viruses are of great interest given the substantial drag forces and torques they face when moving down the spinning flagellum. We show that the main capsid and auxiliary proteins form two nested chainmails that ensure the integrity of the bacteriophage head. Core stabilising structures are conserved in herpesviruses suggesting their ancestral origin. The structure of the tail also reveals a robust yet pliable assembly. Hexameric rings of the tail-tube protein are braced by the N-terminus and a β-hairpin loop, and interconnected along the tail by the splayed β-hairpins. By contrast, we show that the β-hairpin has an inhibitory role in the tail-tube precursor, preventing uncontrolled self-assembly. Dyads of acidic residues inside the tail-tube present regularly-spaced motifs well suited to DNA translocation into bacteria through the tail.
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http://dx.doi.org/10.1038/s41467-020-17505-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7385642PMC
July 2020

Publisher Correction: Comparative genomics of Salmonella enterica serovar Enteritidis ST-11 isolated in Uruguay reveals lineages associated with particular epidemiological traits.

Sci Rep 2020 May 13;10(1):8207. Epub 2020 May 13.

Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Av. Alfredo Navarro 3051, CP, 11600, Montevideo, Uruguay.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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http://dx.doi.org/10.1038/s41598-020-63863-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217900PMC
May 2020

Genomic surveillance of ST131 identifies local expansion and serial replacement of subclones.

Microb Genom 2020 04 20;6(4). Epub 2020 Mar 20.

School of Biotechnology, Dublin City University, Dublin 9, Ireland.

sequence type 131 (ST131) is a pandemic clone that is evolving rapidly with increasing levels of antimicrobial resistance. Here, we investigated an outbreak of ST131 producing extended spectrum β-lactamases (ESBLs) in a long-term care facility (LTCF) in Ireland by combining data from this LTCF (=69) with other Irish (=35) and global (=690) ST131 genomes to reconstruct the evolutionary history and understand changes in population structure and genome architecture over time. This required a combination of short- and long-read genome sequencing, assembly, read mapping, ESBL gene screening, plasmid alignment and temporal phylogenetics. We found that Clade C was the most prevalent (686 out of 794 isolates, 86 %) of the three major ST131 clades circulating worldwide (A with , B with , C with ), and was associated with the presence of different ESBL alleles, diverse plasmids and transposable elements. Clade C was estimated to have emerged in . 1985 and subsequently acquired different ESBL gene variants ( vs ). An ISEcpmediated transposition of the gene further increased the diversity within Clade C. We discovered a local clonal expansion of a rare C2 lineage (C2_8) with a chromosomal insertion of at the gene. This was acquired from an IncFIA plasmid. The C2_8 lineage clonally expanded in the Irish LTCF from 2006, displacing the existing C1 strain (C1_10), highlighting the potential for novel ESBL-producing ST131 with a distinct genetic profile to cause outbreaks strongly associated with specific healthcare environments.
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http://dx.doi.org/10.1099/mgen.0.000352DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7276707PMC
April 2020

Comparative genomics of Salmonella enterica serovar Enteritidis ST-11 isolated in Uruguay reveals lineages associated with particular epidemiological traits.

Sci Rep 2020 02 27;10(1):3638. Epub 2020 Feb 27.

Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Av. Alfredo Navarro 3051, CP, 11600, Montevideo, Uruguay.

Salmonella enterica serovar Enteritidis is a major cause of foodborne disease in Uruguay since 1995. We used a genomic approach to study a set of isolates from different sources and years. Whole genome phylogeny showed that most of the strains are distributed in two major lineages (E1 and E2), both belonging to MLST sequence type 11 the major ST among serovar Enteritidis. Strikingly, E2 isolates are over-represented in periods of outbreak abundance in Uruguay, while E1 span all epidemic periods. Both lineages circulate in neighbor countries at the same timescale as in Uruguay, and are present in minor numbers in distant countries. We identified allelic variants associated with each lineage. Three genes, ycdX, pduD and hsdM, have distinctive variants in E1 that may result in defective products. Another four genes (ybiO, yiaN, aas, aceA) present variants specific for the E2 lineage. Overall this work shows that S. enterica serovar Enteritidis strains circulating in Uruguay have the same phylogenetic profile than strains circulating in the region, as well as in more distant countries. Based on these results we hypothesize that the E2 lineage, which is more prevalent during epidemics, exhibits a combination of allelic variants that could be associated with its epidemic ability.
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http://dx.doi.org/10.1038/s41598-020-60502-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7046640PMC
February 2020

Genomic analysis on broiler-associated strains and exploratory caecal microbiome investigation reveals key factors linked to poultry necrotic enteritis.

Anim Microbiome 2019 Oct;1:12

Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK.

Background: is a key pathogen in poultry-associated necrotic enteritis (NE). To date there are limited Whole Genome Sequencing based studies describing broiler-associated in healthy and diseased birds. Moreover, changes in the caecal microbiome during NE is currently not well characterised. Thus, the aim of this present study was to investigate virulence factors linked to health and diseased chickens, including identifying putative caecal microbiota signatures associated with NE.

Results: We analysed 88 broiler chicken genomes (representing 66 publicly available genomes and 22 newly sequenced genomes) using different phylogenomics approaches and identified a potential hypervirulent and globally-distributed clone spanning 20-year time-frame (1993-2013). These isolates harbored a greater number of virulence genes (including toxin and collagen adhesin genes) when compared to other isolates. Further genomic analysis indicated exclusive and overabundant presence of important NE-linked toxin genes including and in NE-associated broiler isolates. Secondary virulence genes including , , and collagen adhesin genes , and were also enriched in the NE-linked genomes. Moreover, an environmental isolate obtained from farm animal feeds was found to encode , suggesting potential reservoirs of NetB-positive strains (toxinotype G). We also analysed caecal samples from a small sub-set of 11 diseased and healthy broilers for exploratory microbiome investigation using 16S rRNA amplicon sequencing, which indicated a significant and positive correlation in genus within the wider microbiota of those broilers diagnosed with NE, alongside reductions in beneficial microbiota members.

Conclusions: These data indicate a positive association of virulence genes including , and variants linked to NE-linked isolates. Potential global dissemination of specific hypervirulent lineage, coupled with distinctive microbiome profiles, highlights the need for further investigations, which will require a large worldwide sample collection from healthy and NE-associated birds.
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http://dx.doi.org/10.1186/s42523-019-0015-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7000242PMC
October 2019

Phylogenetic Analysis Indicates a Longer Term Presence of the Globally Distributed H58 Haplotype of Salmonella Typhi in Southern India.

Clin Infect Dis 2020 Nov;71(8):1856-1863

Department of Medicine, Univesity of Cambridge, Cambridge, United Kingdom.

Background: Typhoid fever caused by Salmonella Typhi is a major public health concern in low-/middle-income countries. A recent study of 1900 global S. Typhi indicated that South Asia might be the site of the original emergence of the most successful and hypervirulent clone belonging to the 4.3.1 genotype. However, this study had limited samples from India.

Methods: We analyzed 194 clinical S. Typhi, temporal representatives from those isolated from blood and bone marrow cultures in southern India, over 26 years (1991-2016). Antimicrobial resistance (AMR) testing was performed for most common clinical agents. Whole-genome sequencing and SNP-level analysis was conducted. Comparative genomics of Vellore isolates was performed to infer transmission and AMR events.

Results: We identified multidrug-resistance (MDR)-associated clade 4.3.1 as the dominant genotype. We detected 4.3.1 S. Typhi as early as 1991, the earliest to be reported form India, and the majority were fluoroquinolone resistant and not MDR. MDR was not detected at all in other genotypes circulating in Vellore. Comparison with global S. Typhi showed 2 Vellore subgroups (I and II) that were phylogenetically highly related to previously described South Asia (subgroup I, II) and Southeast Asia (subgroup II) clades.

Conclusions: 4.3.1 S. Typhi has dominated in Vellore for 2 decades. Our study would assist public health agencies in better tracking of transmission and persistence of this successful clade in India and globally. It informs clinicians of the AMR pattern of circulating clone, which would add confidence to their prophylactic/treatment decision making and facilitate efficient patient care.
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http://dx.doi.org/10.1093/cid/ciz1112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7643746PMC
November 2020

A Genome-Wide Knockout Screen in Human Macrophages Identified Host Factors Modulating Infection.

mBio 2019 10 8;10(5). Epub 2019 Oct 8.

Wellcome Sanger Institute, Hinxton, United Kingdom

A genome-scale CRISPR knockout library screen of THP-1 human macrophages was performed to identify loss-of-function mutations conferring resistance to uptake. The screen identified 183 candidate genes, from which 14 representative genes involved in actin dynamics (, , , , , , and ), glycosaminoglycan metabolism (), receptor signaling ( and ), lipid raft formation (), calcium transport ( and ), and cholesterol metabolism () were analyzed further. For some of these pathways, known chemical inhibitors could replicate the resistance phenotype, indicating their potential as targets for host-directed therapy. The screen indicated a role for the relatively uncharacterized gene in both invasion and macrophage differentiation. Upon differentiation, mutant macrophages were hyperinflammatory and did not exhibit characteristics typical of macrophages, including atypical morphology and inability to interact and phagocytose bacteria/particles. Immunoprecipitation confirmed an interaction of NHLRC2 with FRYL, EIF2AK2, and KLHL13. exploits macrophages to gain access to the lymphatic system and bloodstream to lead to local and potentially systemic infections. With an increasing number of antibiotic-resistant isolates identified in humans, infections have become major threats to public health. Therefore, there is an urgent need to identify alternative approaches to anti-infective therapy, including host-directed therapies. In this study, we used a simple genome-wide screen to identify 183 candidate host factors in macrophages that can confer resistance to infection. These factors may be potential therapeutic targets against infections.
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http://dx.doi.org/10.1128/mBio.02169-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6786873PMC
October 2019

The flagellotropic bacteriophage YSD1 targets Salmonella Typhi with a Chi-like protein tail fibre.

Mol Microbiol 2019 12 9;112(6):1831-1846. Epub 2019 Oct 9.

Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia.

The discovery of a Salmonella-targeting phage from the waterways of the United Kingdom provided an opportunity to address the mechanism by which Chi-like bacteriophage (phage) engages with bacterial flagellae. The long tail fibre seen on Chi-like phages has been proposed to assist the phage particle in docking to a host cell flagellum, but the identity of the protein that generates this fibre was unknown. We present the results from genome sequencing of this phage, YSD1, confirming its close relationship to the original Chi phage and suggesting candidate proteins to form the tail structure. Immunogold labelling in electron micrographs revealed that YSD1_22 forms the main shaft of the tail tube, while YSD1_25 forms the distal part contributing to the tail spike complex. The long curling tail fibre is formed by the protein YSD1_29, and treatment of phage with the antibodies that bind YSD1_29 inhibits phage infection of Salmonella. The host range for YSD1 across Salmonella serovars is broad, but not comprehensive, being limited by antigenic features of the flagellin subunits that make up the Salmonella flagellum, with which YSD1_29 engages to initiate infection.
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http://dx.doi.org/10.1111/mmi.14396DOI Listing
December 2019

Phylogenomic analysis of gastroenteritis-associated in England and Wales over a 7-year period indicates distribution of clonal toxigenic strains in multiple outbreaks and extensive involvement of enterotoxin-encoding (CPE) plasmids.

Microb Genom 2019 10 20;5(10). Epub 2019 Sep 20.

Gut Microbes and Health, Quadram Institute Bioscience, Norwich NR4 7UQ, UK.

is a major enteric pathogen known to cause gastroenteritis in human adults. Although major outbreak cases are frequently reported, only limited whole-genome sequencing (WGS) based studies have been performed to understand the genomic epidemiology and virulence gene content of outbreak-associated strains. We performed phylogenomic analysis on 109 . isolates (human and food) obtained from disease cases in England and Wales between 2011 and 2017. Initial findings highlighted the enhanced discriminatory power of WGS in profiling outbreak strains, when compared to the current Public Health England referencing laboratory technique of fluorescent amplified fragment length polymorphism analysis. Further analysis identified that isogenic strains were associated with nine distinct care-home-associated outbreaks over the course of a 5-year interval, indicating a potential common source linked to these outbreaks or transmission over time and space. As expected, the enterotoxin gene was encoded in all but 4 isolates (96.3 %; 105/109), with virulence plasmids encoding (particularly pCPF5603 and pCPF4969 plasmids) extensively distributed (82.6 %; 90/109). Genes encoding accessory virulence factors, such as beta-2 toxin, were commonly detected (46.7 %; 51/109), and genes encoding phage proteins were also frequently identified. Overall, this large-scale genomic study of gastroenteritis-associated suggested that three major -encoding (toxinotype F) genotypes underlie these outbreaks: strains carrying (1) pCPF5603 plasmid, (2) pCPF4969 plasmid and (3) chromosomal- strains. Our findings substantially expanded our knowledge on type F involved in human-associated gastroenteritis, with further studies required to fully probe the dissemination and regional reservoirs of this enteric pathogen, which may help devise effective prevention strategies to reduce the food-poisoning disease burden in vulnerable patients, such as the elderly.
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http://dx.doi.org/10.1099/mgen.0.000297DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6861862PMC
October 2019

Genomic Analysis of BEC/CPILE-Positive, Toxinotype D and E Strains Isolated from Healthy Children.

Toxins (Basel) 2019 09 19;11(9). Epub 2019 Sep 19.

Gut Microbes & Health, Quadram Institute Bioscience, Norwich NR4 7UQ, UK.

toxinotype D, toxinotype E, and gastroenteritis-linked BEC/CPILE-positive strains have never been reported in healthy children. We isolated, whole-genome sequenced and bioinformatically characterised three isolates-type D (IQ1), type E (IQ2) and BEC/CPILE-positive (IQ3), recovered from the stools of three healthy two-year-olds, which were further compared to 128 genomes available from NCBI. The analysis uncovered a previously under-described putative toxin gene (alveolysin) encoded by isolates IQ2 and IQ3, which appeared to be a clade-specific trait associated with strains from domestic animals. A plasmid analysis indicated that the iota-toxin was encoded on a near-intact previously described plasmid pCPPB-1 in type E strain IQ2. The BEC genes and were carried on a near-identical pCPOS-1 plasmid previously associated with Japanese gastroenteritis outbreaks. Furthermore, a close phylogenetic relatedness was inferred between the French type E isolates cp515.17 and newly sequenced IQ2, suggesting geographical links. This study describes novel isolates from healthy individuals which encode important toxin genes, indicating the potential spread of these veterinary and clinically important strains and mobile genetic elements, and highlights areas for future research.
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http://dx.doi.org/10.3390/toxins11090543DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6783817PMC
September 2019

An African Salmonella Typhimurium ST313 sublineage with extensive drug-resistance and signatures of host adaptation.

Nat Commun 2019 09 19;10(1):4280. Epub 2019 Sep 19.

Department of Biomedical Sciences, Institute of Tropical Medicine, Nationalestraat 155, 2000, Antwerp, Belgium.

Bloodstream infections by Salmonella enterica serovar Typhimurium constitute a major health burden in sub-Saharan Africa (SSA). These invasive non-typhoidal (iNTS) infections are dominated by isolates of the antibiotic resistance-associated sequence type (ST) 313. Here, we report emergence of ST313 sublineage II.1 in the Democratic Republic of the Congo. Sublineage II.1 exhibits extensive drug resistance, involving a combination of multidrug resistance, extended spectrum β-lactamase production and azithromycin resistance. ST313 lineage II.1 isolates harbour an IncHI2 plasmid we name pSTm-ST313-II.1, with one isolate also exhibiting decreased ciprofloxacin susceptibility. Whole genome sequencing reveals that ST313 II.1 isolates have accumulated genetic signatures potentially associated with altered pathogenicity and host adaptation, related to changes observed in biofilm formation and metabolic capacity. Sublineage II.1 emerged at the beginning of the 21st century and is involved in on-going outbreaks. Our data provide evidence of further evolution within the ST313 clade associated with iNTS in SSA.
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http://dx.doi.org/10.1038/s41467-019-11844-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6753159PMC
September 2019

Diagnostic host gene signature for distinguishing enteric fever from other febrile diseases.

EMBO Mol Med 2019 10 30;11(10):e10431. Epub 2019 Aug 30.

Department of Paediatrics, Centre for Clinical Vaccinology and Tropical Medicine, Oxford Vaccine Group, Oxford, UK.

Misdiagnosis of enteric fever is a major global health problem, resulting in patient mismanagement, antimicrobial misuse and inaccurate disease burden estimates. Applying a machine learning algorithm to host gene expression profiles, we identified a diagnostic signature, which could distinguish culture-confirmed enteric fever cases from other febrile illnesses (area under receiver operating characteristic curve > 95%). Applying this signature to a culture-negative suspected enteric fever cohort in Nepal identified a further 12.6% as likely true cases. Our analysis highlights the power of data-driven approaches to identify host response patterns for the diagnosis of febrile illnesses. Expression signatures were validated using qPCR, highlighting their utility as PCR-based diagnostics for use in endemic settings.
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http://dx.doi.org/10.15252/emmm.201910431DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6783646PMC
October 2019

Rapid transcriptional responses to serum exposure are associated with sensitivity and resistance to antibody-mediated complement killing in invasive Typhimurium ST313.

Wellcome Open Res 2019 25;4:74. Epub 2019 Apr 25.

Institute of Immunology and Immuotherapy, University of Birmingham, Birmingham, UK.

: Typhimurium ST313 exhibits signatures of adaptation to invasive human infection, including higher resistance to humoral immune responses than gastrointestinal isolates. Full resistance to antibody-mediated complement killing (serum resistance) among nontyphoidal is uncommon, but selection of highly resistant strains could compromise vaccine-induced antibody immunity. Here, we address the hypothesis that serum resistance is due to a distinct genotype or transcriptome response in . Typhimurium ST313. : Six . Typhimurium ST313 bloodstream isolates, three of which were antibody resistant, were studied. Genomic content (single nucleotide polymorphisms and larger chromosomal modifications) of the strains was determined by Illumina and PACBIO sequencing, and functionally characterized using RNA-seq, transposon directed insertion site sequencing (TraDIS), targeted gene deletion and transfer of selected point mutations in an attempt to identify features associated with serum resistance.   : Sequence polymorphisms in genes from strains with atypical serum susceptibility when transferred from strains that were highly resistant or susceptible to a strain that exhibited intermediate susceptibility did not significantly alter serum killing phenotype. No large chromosomal modifications typified serum resistance or susceptibility. Genes required for resistance to serum identified by TraDIS and RNA-seq included those involved in exopolysaccharide synthesis, iron scavenging and metabolism. Most of the down-regulated genes were associated with membrane proteins. Resistant and susceptible strains had distinct transcriptional responses to serum, particularly related to genes responsible for polysaccharide biosynthesis. There was higher upregulation of locus genes, involved in the biosynthesis of colanic acid exopolysaccharide, in susceptible strains and increased expression of , a regulator of very long-chain lipopolysaccharide in resistant strains. : Clinical isolates of . Typhimurium ST313 exhibit distinct antibody susceptibility phenotypes that may be associated with changes in gene expression on exposure to serum.
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http://dx.doi.org/10.12688/wellcomeopenres.15059.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6560496PMC
April 2019

Genomic and Functional Analysis of Emerging Virulent and Multidrug-Resistant Lineage Sequence Type 648.

Antimicrob Agents Chemother 2019 06 24;63(6). Epub 2019 May 24.

Institute of Microbiology and Epizootics, Free University Berlin, Berlin, Germany

The pathogenic extended-spectrum-beta-lactamase (ESBL)-producing lineage ST648 is increasingly reported from multiple origins. Our study of a large and global ST648 collection from various hosts (87 whole-genome sequences) combining core and accessory genomics with functional analyses and experiments suggests that ST648 is a nascent and generalist lineage, lacking clear phylogeographic and host association signals. By including large numbers of ST131 ( = 107) and ST10 ( = 96) strains for comparative genomics and phenotypic analysis, we demonstrate that the combination of multidrug resistance and high-level virulence are the hallmarks of ST648, similar to international high-risk clonal lineage ST131. Specifically, our , , and results demonstrate that ST648 is well equipped with biofilm-associated features, while ST131 shows sophisticated signatures indicative of adaption to urinary tract infection, potentially conveying individual ecological niche adaptation. In addition, we used a recently developed NFDS (negative frequency-dependent selection) population model suggesting that ST648 will increase significantly in frequency as a cause of bacteremia within the next few years. Also, ESBL plasmids impacting biofilm formation aided in shaping and maintaining ST648 strains to successfully emerge worldwide across different ecologies. Our study contributes to understanding what factors drive the evolution and spread of emerging international high-risk clonal lineages.
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http://dx.doi.org/10.1128/AAC.00243-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6535536PMC
June 2019

Publisher Correction: Clonal analysis of Salmonella-specific effector T cells reveals serovar-specific and cross-reactive T cell responses.

Nat Immunol 2019 Apr;20(4):514

MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.

In the version of this article initially published, the first affiliation lacked 'MRC'; the correct name of the institution is 'MRC Weatherall Institute of Molecular Medicine'. Two designations (SP110Y and ST110H) were incorrect in the legend to Fig. 6f,h,i. The correct text is as follows: for panel f, "...loaded with either the CdtB(105-125)SP110Y (DRB4*SP110Y) or the CdtB(105-125)ST110H (DRB4*ST110H) peptide variants..."; for panel h, "...decorated by the DRB4*SP110Y tetramer (lower-right quadrant), the DRB4*ST110H (upper-left quadrant)..."; and for panel i, "...stained ex vivo with DRB4*SP110Y, DRB4*ST110H...". In Fig. 8e, the final six residues (LTEAFF) of the sequence in the far right column of the third row of the table were missing; the correct sequence is 'CASSYRRTPPLTEAFF'. In the legend to Fig. 8d, a designation (HLyE) was incorrect; the correct text is as follows: "(HlyE?)." Portions of the Acknowledgements section were incorrect; the correct text is as follows: "This work was supported by the UK Medical Research Council (MRC) (MR/K021222/1) (G.N., M.A.G., A.S., V.C., A.J.P.),...the Oxford Biomedical Research Centre (A.J.P., V.C.),...and core funding from the Singapore Immunology Network (SIgN) (E.W.N.) and the SIgN immunomonitoring platform (E.W.N.)." Finally, a parenthetical element was phrased incorrectly in the final paragraph of the Methods subsection "T cell cloning and live fluorescence barcoding"; the correct phrasing is as follows: "...(which in all cases included HlyE, CdtB, Ty21a, Quailes, NVGH308, and LT2 strains and in volunteers T5 and T6 included PhoN)...". Also, in Figs. 3c and 4a, the right outlines of the plots were not visible; in the legend to Fig. 3, panel letter 'f' was not bold; and in Fig. 8f, 'ND' should be aligned directly beneath DRB4 in the key and 'ND' should be removed from the diagram at right, and the legend should be revised accordingly as follows: "...colors indicate the HLA class II restriction (gray indicates clones for which restriction was not determined (ND)). Clonotypes are grouped on the basis of pathogen selectivity (continuous line), protein specificity (dashed line) and epitope specificity; for ten HlyE-specific clones (pixilated squares), the epitope specificity was not determined...". The errors have been corrected in the HTML and PDF versions of the article.
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http://dx.doi.org/10.1038/s41590-019-0357-6DOI Listing
April 2019

The golden death bacillus Chryseobacterium nematophagum is a novel matrix digesting pathogen of nematodes.

BMC Biol 2019 02 28;17(1):10. Epub 2019 Feb 28.

School of Veterinary Medicine, University of Glasgow, Scotland, UK.

Background: Nematodes represent important pathogens of humans and farmed animals and cause significant health and economic impacts. The control of nematodes is primarily carried out by applying a limited number of anthelmintic compounds, for which there is now widespread resistance being reported. There is a current unmet need to develop novel control measures including the identification and characterisation of natural pathogens of nematodes.

Results: Nematode killing bacilli were isolated from a rotten fruit in association with wild free-living nematodes. These bacteria belong to the Chryseobacterium genus (golden bacteria) and represent a new species named Chryseobacterium nematophagum. These bacilli are oxidase-positive, flexirubin-pigmented, gram-negative rods that exhibit gelatinase activity. Caenorhabditis elegans are attracted to and eat these bacteria. Within 3 h of ingestion, however, the bacilli have degraded the anterior pharyngeal chitinous lining and entered the body cavity, ultimately killing the host. Within 24 h, the internal contents of the worms are digested followed by the final digestion of the remaining cuticle over a 2-3-day period. These bacteria will also infect and kill bacterivorous free-living (L1-L3) stages of all tested parasitic nematodes including the important veterinary Trichostrongylids such as Haemonchus contortus and Ostertagia ostertagi. The bacteria exhibit potent collagen-digesting properties, and genome sequencing has identified novel metalloprotease, collagenase and chitinase enzymes representing potential virulence factors.

Conclusions: Chryseobacterium nematophagum is a newly discovered pathogen of nematodes that rapidly kills environmental stages of a wide range of key nematode parasites. These bacilli exhibit a unique invasion process, entering the body via the anterior pharynx through the specific degradation of extracellular matrices. This bacterial pathogen represents a prospective biological control agent for important nematode parasites.
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http://dx.doi.org/10.1186/s12915-019-0632-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6394051PMC
February 2019

Resistance mechanisms and population structure of highly drug resistant Klebsiella in Pakistan during the introduction of the carbapenemase NDM-1.

Sci Rep 2019 02 20;9(1):2392. Epub 2019 Feb 20.

Department of Microbiology and Immunology, The University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.

Klebsiella pneumoniae is a major threat to public health with the emergence of isolates resistant to most, if not all, useful antibiotics. We present an in-depth analysis of 178 extended-spectrum beta-lactamase (ESBL)-producing K. pneumoniae collected from patients resident in a region of Pakistan, during the period 2010-2012, when the now globally-distributed carbapenemase bla-NDM-1 was being acquired by Klebsiella. We observed two dominant lineages, but neither the overall resistance profile nor virulence-associated factors, explain their evolutionary success. Phenotypic analysis of resistance shows few differences between the acquisition of resistance genes and the phenotypic resistance profile, including beta-lactam antibiotics that were used to treat ESBL-positive strains. Resistance against these drugs could be explained by inhibitor-resistant beta-lactamase enzymes, carbapenemases or ampC type beta-lactamases, at least one of which was detected in most, but not all relevant strains analysed. Complete genomes for six selected strains are reported, these provide detailed insights into the mobile elements present in these isolates during the initial spread of NDM-1. The unexplained success of some lineages within this pool of highly resistant strains, and the discontinuity between phenotypic resistance and genotype at the macro level, indicate that intrinsic mechanisms contribute to competitive advantage and/or resistance.
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http://dx.doi.org/10.1038/s41598-019-38943-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6382945PMC
February 2019

Draft Genome Sequences of Two Multidrug-Resistant Salmonella enterica Serovar Typhimurium Clinical Isolates from Uruguay.

Microbiol Resour Announc 2018 Aug 2;7(4). Epub 2018 Aug 2.

Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, UDELAR, Montevideo, Uruguay.

Multidrug-resistant Salmonella enterica isolates are an increasing problem worldwide; nevertheless, the mechanisms responsible for such resistance are rarely well defined. Multidrug-resistant S. enterica serovar Typhimurium isolates ST3224 and ST827 were collected from two patients. The characteristics of both genomes and antimicrobial resistance genes were determined using next-generation sequencing.
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http://dx.doi.org/10.1128/MRA.00917-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6256424PMC
August 2018

Functional analysis of Salmonella Typhi adaptation to survival in water.

Environ Microbiol 2018 11;20(11):4079-4090

The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

Contaminated water is a major risk factor associated with the transmission of Salmonella enterica serovar Typhi (S. Typhi), the aetiological agent of human typhoid. However, little is known about how this pathogen adapts to living in the aqueous environment. We used transcriptome analysis (RNA-seq) and transposon mutagenesis (TraDIS) to characterize these adaptive changes and identify multiple genes that contribute to survival. Over half of the genes in the S. Typhi genome altered expression level within the first 24 h following transfer from broth culture to water, although relatively few did so in the first 30 min. Genes linked to central metabolism, stress associated with arrested proton motive force and respiratory chain factors changed expression levels. Additionally, motility and chemotaxis genes increased expression, consistent with a scavenging lifestyle. The viaB-associated gene tviC encoding a glcNAc epimerase that is required for Vi polysaccharide biosynthesis was, along with several other genes, shown to contribute to survival in water. Thus, we define regulatory adaptation operating in S. Typhi that facilitates survival in water.
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http://dx.doi.org/10.1111/1462-2920.14458DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6282856PMC
November 2018

Microevolution of epidemiological highly relevant non-O157 enterohemorrhagic Escherichia coli of serogroups O26 and O111.

Int J Med Microbiol 2018 Dec 10;308(8):1085-1095. Epub 2018 Aug 10.

Robert Koch-Institute, Berlin, Germany. Electronic address:

Enterohemorrhagic Escherichia coli (EHEC) are a cause of bloody diarrhea, hemorrhagic colitis (HC) and the potentially fatal hemolytic uremic syndrome (HUS). While O157:H7 is the dominant EHEC serotype, non-O157 EHEC have emerged as serious causes of disease. In Germany, the most important non-O157 O-serogroups causing one third of EHEC infections, including diarrhea as well as HUS, are O26, O103, O111 and O145. Interestingly, we identified EHEC O-serogroups O26 and O111 in one single sequence type complex, STC29, that also harbours atypical enteropathogenic E. coli (aEPEC). aEPEC differ from typical EHEC merely in the absence of stx-genes. These findings inspired us to unravel a putative microevolutionary scenario of these non-O157 EHEC by whole genome analyses. Analysis of single nucleotide polymorphisms (SNPs) of the maximum common genome (MCG) of 20 aEPEC (11 human/ 9 bovine) and 79 EHEC (42 human/ 36 bovine/ 1 food source) of STC29 identified three distinct clusters: Cluster 1 harboured strains of O-serogroup O111, the central Cluster 2 harboured only O26 aEPEC strains, while the more heterogeneous Cluster 3 contained both EHEC and aEPEC strains of O-serogroup O26. Further combined analyses of accessory virulence associated genes (VAGs) and insertion sites for mobile genetic elements suggested a parallel evolution of the MCG and the acquisition of virulence genes. The resulting microevolutionary model suggests the development of two distinct EHEC lineages from one common aEPEC ancestor of ST29 by lysogenic conversion with stx-converting bacteriophages, independent of the host species the strains had been isolated from. In conclusion, our cumulative data indicate that EHEC of O-serogroups O26 and O111 of STC29 originate from a common aEPEC ancestor and are bona fide zoonotic agents. The role of aEPEC in the emergence of O26 and O111 EHEC should be considered for infection control measures to prevent possible lysogenic conversion with stx-converting bacteriophages as major vehicle driving the emergence of EHEC lineages with direct Public Health consequences.
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http://dx.doi.org/10.1016/j.ijmm.2018.08.003DOI Listing
December 2018

Transposon Insertion Sequencing Elucidates Novel Gene Involvement in Susceptibility and Resistance to Phages T4 and T7 in O157.

mBio 2018 07 24;9(4). Epub 2018 Jul 24.

Wellcome Trust Sanger Institute, Hinxton, Cambridge United Kingdom.

Experiments using bacteriophage (phage) to infect bacterial strains have helped define some basic genetic concepts in microbiology, but our understanding of the complexity of bacterium-phage interactions is still limited. As the global threat of antibiotic resistance continues to increase, phage therapy has reemerged as an attractive alternative or supplement to treating antibiotic-resistant bacterial infections. Further, the long-used method of phage typing to classify bacterial strains is being replaced by molecular genetic techniques. Thus, there is a growing need for a complete understanding of the precise molecular mechanisms underpinning phage-bacterium interactions to optimize phage therapy for the clinic as well as for retrospectively interpreting phage typing data on the molecular level. In this study, a genomics-based fitness assay (TraDIS) was used to identify all host genes involved in phage susceptibility and resistance for a T4 phage infecting Shiga-toxigenic O157. The TraDIS results identified both established and previously unidentified genes involved in phage infection, and a subset were confirmed by site-directed mutagenesis and phenotypic testing of 14 T4 and 2 T7 phages. For the first time, the entire operon was implicated in phage susceptibility and, conversely, the stringent starvation protein A gene () was shown to provide phage resistance. Identifying genes involved in phage infection and replication should facilitate the selection of bespoke phage combinations to target specific bacterial pathogens. Antibiotic resistance has diminished treatment options for many common bacterial infections. Phage therapy is an alternative option that was once popularly used across Europe to kill bacteria within humans. Phage therapy acts by using highly specific viruses (called phages) that infect and lyse certain bacterial species to treat the infection. Whole-genome sequencing has allowed modernization of the investigations into phage-bacterium interactions. Here, using O157 and T4 bacteriophage as a model, we have exploited a genome-wide fitness assay to investigate all genes involved in defining phage resistance or susceptibility. This knowledge of the genetic determinants of phage resistance and susceptibility can be used to design bespoke phage combinations targeted to specific bacterial infections for successful infection eradication.
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http://dx.doi.org/10.1128/mBio.00705-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6058288PMC
July 2018

ESBL-plasmid carriage in enhances in vitro bacterial competition fitness and serum resistance in some strains of pandemic sequence types without overall fitness cost.

Gut Pathog 2018 15;10:24. Epub 2018 Jun 15.

1Institute of Microbiology and Epizootics, Veterinary Faculty, Freie Universität Berlin, Robert-von-Ostertag Str. 7-13, 14163 Berlin, Germany.

Background: Extended spectrum beta lactamase (ESBL)-producing extraintestinal pathogenic infections are of global interest because of their clinical and economic impact. The ESBL resistance genes disseminate through plasmids, and are found in successful global lineages such as ST131 and ST648. The carriage of plasmids has been suggested to result in a fitness burden, but recently it was shown that ESBL-plasmids enhanced virulence in pandemic ST131 and ST648 lineages without affecting their fitness. Herein, we investigated the influence of ESBL-plasmids on bacterial competition and serum resistance, both of which are essential characteristics of ExPEC during infections.

Methods: Triplets of ESBL-plasmid-carrying wildtype (WT), plasmid-cured variant (PCV) and transformant (T) of five ExPEC strains of ST131 and ST648 were used for bacterial competition experiments with colicin-producing commensal , competitive adhesion experiments and serum survival. In addition, resilience after SDS, acid, osmotic challenges and RNA sequence data were analyzed.

Results: In all five strains tested, ESBL-plasmid carriage did not negatively influence fitness in direct bacterial competition with commensal in vitro. That is, WTs did not show any disadvantages when compared to their isogenic plasmid-free PCV. For one strain we even found the opposite as PCV17433 was out-competed by a commensal strain, which suggests an even protective role of the ESBL-plasmid carried by the WT17433. Similarly, in the serum-resistance experiments, the PCVs of two strains (PCV17433 and PCV17887) were more sensitive to serum, unlike WTs and Ts. The observed inter-strain differences could be explained by the different genetic content of plasmids carried in those strains.

Conclusions: Overall, we found no compelling evidence for an increased burden resulting from the carriage of ESBL-plasmids in the absence of antimicrobial selection pressure in the strains of pandemic ST131 and ST648; rather, the possession of certain ESBL-plasmids was beneficial for some strains in regarding competition fitness and serum survival.
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http://dx.doi.org/10.1186/s13099-018-0243-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6003029PMC
June 2018

Morphological, genomic and transcriptomic responses of Klebsiella pneumoniae to the last-line antibiotic colistin.

Sci Rep 2018 06 29;8(1):9868. Epub 2018 Jun 29.

Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

Colistin remains one of the few antibiotics effective against multi-drug resistant (MDR) hospital pathogens, such as Klebsiella pneumoniae. Yet resistance to this last-line drug is rapidly increasing. Characterized mechanisms of col in K. pneumoniae are largely due to chromosomal mutations in two-component regulators, although a plasmid-mediated col mechanism has recently been uncovered. However, the effects of intrinsic colistin resistance are yet to be characterized on a whole-genome level. Here, we used a genomics-based approach to understand the mechanisms of adaptive col acquisition in K. pneumoniae. In controlled directed-evolution experiments we observed two distinct paths to colistin resistance acquisition. Whole genome sequencing identified mutations in two colistin resistance genes: in the known col regulator phoQ which became fixed in the population and resulted in a single amino acid change, and unstable minority variants in the recently described two-component sensor crrB. Through RNAseq and microscopy, we reveal the broad range of effects that colistin exposure has on the cell. This study is the first to use genomics to identify a population of minority variants with mutations in a col gene in K. pneumoniae.
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http://dx.doi.org/10.1038/s41598-018-28199-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6026146PMC
June 2018

Lysogenic conversion of atypical enteropathogenic Escherichia coli (aEPEC) from human, murine, and bovine origin with bacteriophage Φ3538 Δstx::cat proves their enterohemorrhagic E. coli (EHEC) progeny.

Int J Med Microbiol 2018 Oct 19;308(7):890-898. Epub 2018 Jun 19.

Institute for Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany; Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald - Insel Riems, Germany. Electronic address:

Bacteriophages play an important role in the evolution of bacterial pathogens. A phage-mediated transfer of stx-genes to atypical enteropathogenic E. coli (aEPEC) which are prevalent in different hosts, would convert them to enterohemorrhagic E. coli (EHEC). We decided to confirm this hypothesis experimentally to provide conclusive evidence that aEPEC isolated from different mammalian hosts are indeed progenitors of typical EHEC which gain the ability to produce Shiga-Toxin by lysogeny with stx-converting bacteriophages, utilizing the model phage Φ3538 Δstx::cat. We applied a modified in vitro plaque-assay, using a high titer of a bacteriophage carrying a deletion in the stx gene (Φ3538 Δstx::cat) to increase the detection of lysogenic conversion events. Three wild-type aEPEC strains were chosen as acceptor strains: the murine aEPEC-strain IMT14505 (sequence type (ST)28, serotype Ont:H6), isolated from a striped field mouse (Apodemus agrarius) in the surrounding of a cattle shed, and the human aEPEC-strain 910#00 (ST28, Ont:H6). The close genomic relationship of both strains implies a high zoonotic potential. A third strain, the bovine aEPEC IMT19981, was of serotype O26:H11 and ST21 (STC29). All three aEPEC were successfully lysogenized with phage Φ3538 Δstx::cat. Integration of the bacteriophage DNA into the aEPEC host genomes was confirmed by amplification of chloramphenicol transferase (cat) marker gene and by Southern-Blot hybridization. Analysis of the whole genome sequence of each of the three lysogens showed that the bacteriophage was integrated into the known tRNA integration site argW, which is highly variable among E. coli. In conclusion, the successful lysogenic conversion of aEPEC with a stx-phage in vitro underlines the important role of aEPEC as progenitors of EHEC. Given the high prevalence and the wide host range of aEPEC acceptors, their high risk of zoonotic transmission should be recognized in infection control measures.
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http://dx.doi.org/10.1016/j.ijmm.2018.06.005DOI Listing
October 2018

Clonal analysis of Salmonella-specific effector T cells reveals serovar-specific and cross-reactive T cell responses.

Nat Immunol 2018 07 20;19(7):742-754. Epub 2018 Jun 20.

MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.

To tackle the complexity of cross-reactive and pathogen-specific T cell responses against related Salmonella serovars, we used mass cytometry, unbiased single-cell cloning, live fluorescence barcoding, and T cell-receptor sequencing to reconstruct the Salmonella-specific repertoire of circulating effector CD4 T cells, isolated from volunteers challenged with Salmonella enterica serovar Typhi (S. Typhi) or Salmonella Paratyphi A (S. Paratyphi). We describe the expansion of cross-reactive responses against distantly related Salmonella serovars and of clonotypes recognizing immunodominant antigens uniquely expressed by S. Typhi or S. Paratyphi A. In addition, single-amino acid variations in two immunodominant proteins, CdtB and PhoN, lead to the accumulation of T cells that do not cross-react against the different serovars, thus demonstrating how minor sequence variations in a complex microorganism shape the pathogen-specific T cell repertoire. Our results identify immune-dominant, serovar-specific, and cross-reactive T cell antigens, which should aid in the design of T cell-vaccination strategies against Salmonella.
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http://dx.doi.org/10.1038/s41590-018-0133-zDOI Listing
July 2018

A novel prophage identified in strains from Salmonella enterica serovar Enteritidis is a phylogenetic signature of the lineage ST-1974.

Microb Genom 2018 03 6;4(3). Epub 2018 Mar 6.

1​Instituto de Higiene, Facultad de Medicina, UDELAR, Montevideo, Uruguay.

Salmonella enterica serovar Enteritidis is a major agent of foodborne diseases worldwide. In Uruguay, this serovar was almost negligible until the mid 1990s but since then it has become the most prevalent. Previously, we characterized a collection of strains isolated from 1988 to 2005 and found that the two oldest strains were the most genetically divergent. In order to further characterize these strains, we sequenced and annotated eight genomes including those of the two oldest isolates. We report on the identification and characterization of a novel 44 kbp Salmonella prophage found exclusively in these two genomes. Sequence analysis reveals that the prophage is a mosaic, with homologous regions in different Salmonella prophages. It contains 60 coding sequences, including two genes, gogB and sseK3, involved in virulence and modulation of host immune response. Analysis of serovar Enteritidis genomes available in public databases confirmed that this prophage is absent in most of them, with the exception of a group of 154 genomes. All 154 strains carrying this prophage belong to the same sequence type (ST-1974), suggesting that its acquisition occurred in a common ancestor. We tested this by phylogenetic analysis of 203 genomes representative of the intraserovar diversity. The ST-1974 forms a distinctive monophyletic lineage, and the newly described prophage is a phylogenetic signature of this lineage that could be used as a molecular marker. The phylogenetic analysis also shows that the major ST (ST-11) is polyphyletic and might have given rise to almost all other STs, including ST-1974.
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http://dx.doi.org/10.1099/mgen.0.000161DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5885013PMC
March 2018

Comparison of Salmonella enterica Serovars Typhi and Typhimurium Reveals Typhoidal Serovar-Specific Responses to Bile.

Infect Immun 2018 03 20;86(3). Epub 2018 Feb 20.

MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom

serovars Typhi and Typhimurium cause typhoid fever and gastroenteritis, respectively. A unique feature of typhoid infection is asymptomatic carriage within the gallbladder, which is linked with Typhi transmission. Despite this, Typhi responses to bile have been poorly studied. Transcriptome sequencing (RNA-Seq) of Typhi Ty2 and a clinical Typhi isolate belonging to the globally dominant H58 lineage (strain 129-0238), as well as Typhimurium 14028, revealed that 249, 389, and 453 genes, respectively, were differentially expressed in the presence of 3% bile compared to control cultures lacking bile. genes, the operon, and putative sialic acid uptake and metabolism genes (t1787 to t1790) were upregulated in all strains following bile exposure, which may represent adaptation to the small intestine environment. Genes within the pathogenicity island 1 (SPI-1), those encoding a type IIII secretion system (T3SS), and motility genes were significantly upregulated in both Typhi strains in bile but downregulated in Typhimurium. Western blots of the SPI-1 proteins SipC, SipD, SopB, and SopE validated the gene expression data. Consistent with this, bile significantly increased Typhi HeLa cell invasion, while Typhimurium invasion was significantly repressed. Protein stability assays demonstrated that in Typhi the half-life of HilD, the dominant regulator of SPI-1, is three times longer in the presence of bile; this increase in stability was independent of the acetyltransferase Pat. Overall, we found that Typhi exhibits a specific response to bile, especially with regard to virulence gene expression, which could impact pathogenesis and transmission.
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http://dx.doi.org/10.1128/IAI.00490-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5820949PMC
March 2018

Preterm Infant-Associated Clostridium tertium, Clostridium cadaveris, and Clostridium paraputrificum Strains: Genomic and Evolutionary Insights.

Genome Biol Evol 2017 10;9(10):2707-2714

The Gut Health and Food Safety Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom.

Clostridium species (particularly Clostridium difficile, Clostridium botulinum, Clostridium tetani and Clostridium perfringens) are associated with a range of human and animal diseases. Several other species including Clostridium tertium, Clostridium cadaveris, and Clostridium paraputrificum have also been linked with sporadic human infections, however there is very limited, or in some cases, no genomic information publicly available. Thus, we isolated one C. tertium strain, one C. cadaveris strain and three C. paraputrificum strains from preterm infants residing within neonatal intensive care units and performed Whole Genome Sequencing (WGS) using Illumina HiSeq. In this report, we announce the open availability of the draft genomes: C. tertium LH009, C. cadaveris LH052, C. paraputrificum LH025, C. paraputrificum LH058, and C. paraputrificum LH141. These genomes were checked for contamination in silico to ensure purity, and we confirmed species identity and phylogeny using both 16S rRNA gene sequences (from PCR and in silico) and WGS-based approaches. Average Nucleotide Identity (ANI) was used to differentiate genomes from their closest relatives to further confirm speciation boundaries. We also analysed the genomes for virulence-related factors and antimicrobial resistance genes, and detected presence of tetracycline and methicillin resistance, and potentially harmful enzymes, including multiple phospholipases and toxins. The availability of genomic data in open databases, in tandem with our initial insights into the genomic content and virulence traits of these pathogenic Clostridium species, should enable the scientific community to further investigate the disease-causing mechanisms of these bacteria with a view to enhancing clinical diagnosis and treatment.
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http://dx.doi.org/10.1093/gbe/evx210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5647805PMC
October 2017