1
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Lu T, Das S, Howlader DR, Picking WD, Picking WL. Shigella Vaccines: The Continuing Unmet Challenge. Int J Mol Sci 2024; 25:4329. [PMID: 38673913 PMCID: PMC11050647 DOI: 10.3390/ijms25084329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Shigellosis is a severe gastrointestinal disease that annually affects approximately 270 million individuals globally. It has particularly high morbidity and mortality in low-income regions; however, it is not confined to these regions and occurs in high-income nations when conditions allow. The ill effects of shigellosis are at their highest in children ages 2 to 5, with survivors often exhibiting impaired growth due to infection-induced malnutrition. The escalating threat of antibiotic resistance further amplifies shigellosis as a serious public health concern. This review explores Shigella pathology, with a primary focus on the status of Shigella vaccine candidates. These candidates include killed whole-cells, live attenuated organisms, LPS-based, and subunit vaccines. The strengths and weaknesses of each vaccination strategy are considered. The discussion includes potential Shigella immunogens, such as LPS, conserved T3SS proteins, outer membrane proteins, diverse animal models used in Shigella vaccine research, and innovative vaccine development approaches. Additionally, this review addresses ongoing challenges that necessitate action toward advancing effective Shigella prevention and control measures.
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Affiliation(s)
- Ti Lu
- Department of Veterinary Pathobiology and Bond Life Science Center, University of Missouri, Columbia, MO 65201, USA; (D.R.H.); (W.D.P.)
| | - Sayan Das
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD 21201, USA;
| | - Debaki R. Howlader
- Department of Veterinary Pathobiology and Bond Life Science Center, University of Missouri, Columbia, MO 65201, USA; (D.R.H.); (W.D.P.)
| | - William D. Picking
- Department of Veterinary Pathobiology and Bond Life Science Center, University of Missouri, Columbia, MO 65201, USA; (D.R.H.); (W.D.P.)
| | - Wendy L. Picking
- Department of Veterinary Pathobiology and Bond Life Science Center, University of Missouri, Columbia, MO 65201, USA; (D.R.H.); (W.D.P.)
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2
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Wang X, Yu D, Chui L, Zhou T, Feng Y, Cao Y, Zhi S. A Comprehensive Review on Shiga Toxin Subtypes and Their Niche-Related Distribution Characteristics in Shiga-Toxin-Producing E. coli and Other Bacterial Hosts. Microorganisms 2024; 12:687. [PMID: 38674631 PMCID: PMC11052178 DOI: 10.3390/microorganisms12040687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Shiga toxin (Stx), the main virulence factor of Shiga-toxin-producing E. coli (STEC), was first discovered in Shigella dysenteriae strains. While several other bacterial species have since been reported to produce Stx, STEC poses the most significant risk to human health due to its widespread prevalence across various animal hosts that have close contact with human populations. Based on its biochemical and molecular characteristics, Shiga toxin can be grouped into two types, Stx1 and Stx2, among which a variety of variants and subtypes have been identified in various bacteria and host species. Interestingly, the different Stx subtypes appear to vary in their host distribution characteristics and in the severity of diseases that they are associated with. As such, this review provides a comprehensive overview on the bacterial species that have been recorded to possess stx genes to date, with a specific focus on the various Stx subtype variants discovered in STEC, their prevalence in certain host species, and their disease-related characteristics. This review provides a better understanding of the Stx subtypes and highlights the need for rapid and accurate approaches to toxin subtyping for the proper evaluation of the health risks associated with Shiga-toxin-related bacterial food contamination and human infections.
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Affiliation(s)
- Xuan Wang
- School of Public Health, Ningbo University, Ningbo 315000, China; (X.W.); (T.Z.); (Y.F.)
| | - Daniel Yu
- School of Public Health, Univeristy of Alberta, Edmonton, AB T6G 2R3, Canada;
| | - Linda Chui
- Alberta Precision Laboratories-ProvLab, Edmonton, AB T6G 2J2, Canada;
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2B7, Canada
| | - Tiantian Zhou
- School of Public Health, Ningbo University, Ningbo 315000, China; (X.W.); (T.Z.); (Y.F.)
| | - Yu Feng
- School of Public Health, Ningbo University, Ningbo 315000, China; (X.W.); (T.Z.); (Y.F.)
| | - Yuhao Cao
- School of Basic Medical Sciences, Ningbo University, Ningbo 315000, China;
| | - Shuai Zhi
- School of Public Health, Ningbo University, Ningbo 315000, China; (X.W.); (T.Z.); (Y.F.)
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3
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Zhang X, Payne M, Kaur S, Lan R. Improved Genomic Identification, Clustering, and Serotyping of Shiga Toxin-Producing Escherichia coli Using Cluster/Serotype-Specific Gene Markers. Front Cell Infect Microbiol 2022; 11:772574. [PMID: 35083165 PMCID: PMC8785982 DOI: 10.3389/fcimb.2021.772574] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/03/2021] [Indexed: 11/16/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) have more than 470 serotypes. The well-known STEC O157:H7 serotype is a leading cause of STEC infections in humans. However, the incidence of non-O157:H7 STEC serotypes associated with foodborne outbreaks and human infections has increased in recent years. Current detection and serotyping assays are focusing on O157 and top six (“Big six”) non-O157 STEC serogroups. In this study, we performed phylogenetic analysis of nearly 41,000 publicly available STEC genomes representing 460 different STEC serotypes and identified 19 major and 229 minor STEC clusters. STEC cluster-specific gene markers were then identified through comparative genomic analysis. We further identified serotype-specific gene markers for the top 10 most frequent non-O157:H7 STEC serotypes. The cluster or serotype specific gene markers had 99.54% accuracy and more than 97.25% specificity when tested using 38,534 STEC and 14,216 non-STEC E. coli genomes, respectively. In addition, we developed a freely available in silico serotyping pipeline named STECFinder that combined these robust gene markers with established E. coli serotype specific O and H antigen genes and stx genes for accurate identification, cluster determination and serotyping of STEC. STECFinder can assign 99.85% and 99.83% of 38,534 STEC isolates to STEC clusters using assembled genomes and Illumina reads respectively and can simultaneously predict stx subtypes and STEC serotypes. Using shotgun metagenomic sequencing reads of STEC spiked food samples from a published study, we demonstrated that STECFinder can detect the spiked STEC serotypes, accurately. The cluster/serotype-specific gene markers could also be adapted for culture independent typing, facilitating rapid STEC typing. STECFinder is available as an installable package (https://github.com/LanLab/STECFinder) and will be useful for in silico STEC cluster identification and serotyping using genome data.
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Affiliation(s)
- Xiaomei Zhang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Michael Payne
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Sandeep Kaur
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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4
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AB 5 Enterotoxin-Mediated Pathogenesis: Perspectives Gleaned from Shiga Toxins. Toxins (Basel) 2022; 14:toxins14010062. [PMID: 35051039 PMCID: PMC8779504 DOI: 10.3390/toxins14010062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/12/2022] [Accepted: 01/12/2022] [Indexed: 02/01/2023] Open
Abstract
Foodborne diseases affect an estimated 600 million people worldwide annually, with the majority of these illnesses caused by Norovirus, Vibrio, Listeria, Campylobacter, Salmonella, and Escherichia coli. To elicit infections in humans, bacterial pathogens express a combination of virulence factors and toxins. AB5 toxins are an example of such toxins that can cause various clinical manifestations, including dehydration, diarrhea, kidney damage, hemorrhagic colitis, and hemolytic uremic syndrome (HUS). Treatment of most bacterial foodborne illnesses consists of fluid replacement and antibiotics. However, antibiotics are not recommended for infections caused by Shiga toxin-producing E. coli (STEC) because of the increased risk of HUS development, although there are conflicting views and results in this regard. Lack of effective treatment strategies for STEC infections pose a public health threat during outbreaks; therefore, the debate on antibiotic use for STEC infections could be further explored, along with investigations into antibiotic alternatives. The overall goal of this review is to provide a succinct summary on the mechanisms of action and the pathogenesis of AB5 and related toxins, as expressed by bacterial foodborne pathogens, with a primary focus on Shiga toxins (Stx). The role of Stx in human STEC disease, detection methodologies, and available treatment options are also briefly discussed.
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5
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Zhi S, Parsons BD, Szelewicki J, Yuen YTK, Fach P, Delannoy S, Li V, Ferrato C, Freedman SB, Lee BE, Pang XL, Chui L. Identification of Shiga-Toxin-Producing Shigella Infections in Travel and Non-Travel Related Cases in Alberta, Canada. Toxins (Basel) 2021; 13:toxins13110755. [PMID: 34822539 PMCID: PMC8618429 DOI: 10.3390/toxins13110755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 01/21/2023] Open
Abstract
It has long been accepted that Shiga toxin (Stx) only exists in Shigella dysenteriae serotype 1. However, in recent decades, the presence of Shiga toxin genes (stx) in other Shigella spp. have been reported. We screened 366 Shigella flexneri strains from Alberta, Canada (2003 to 2016) for stx and 26 positive strains were identified. These isolates are highly related with the majority originating from the Dominican Republic and three isolates with Haiti origin. Both phylogenetic and spanning tree analysis of the 26 Alberta and 29 stx positive S. flexneri originating from the U.S., France, Canada (Quebec) and Haiti suggests that there are geographic specific distribution patterns (Haiti and Dominican Republic clades). This study provides the first comprehensive whole genome based phylogenetic analysis of stx positive S. flexneri strains as well as their global transmission, which signify the public health risks of global spreading of these strains.
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Affiliation(s)
- Shuai Zhi
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315000, China;
- School of Medicine, Ningbo University, Ningbo 315000, China
| | - Brendon D. Parsons
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2B7, Canada; (B.D.P.); (J.S.); (Y.T.K.Y.); (X.-L.P.)
| | - Jonas Szelewicki
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2B7, Canada; (B.D.P.); (J.S.); (Y.T.K.Y.); (X.-L.P.)
| | - Yue T. K. Yuen
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2B7, Canada; (B.D.P.); (J.S.); (Y.T.K.Y.); (X.-L.P.)
| | - Patrick Fach
- Agency for Food, Environmental and Occupational Health and Safety (ANSES), Food Safety Laboratory, COLiPATH Research Unit & IDPA Genomics Platform, FR-94700 Maisons-Alfort, France; (P.F.); (S.D.)
| | - Sabine Delannoy
- Agency for Food, Environmental and Occupational Health and Safety (ANSES), Food Safety Laboratory, COLiPATH Research Unit & IDPA Genomics Platform, FR-94700 Maisons-Alfort, France; (P.F.); (S.D.)
| | - Vincent Li
- Alberta Precision Laboratories-ProvLab, Edmonton, AB T6G 2J2, Canada;
| | - Christina Ferrato
- Alberta Precision Laboratories-ProvLab, Calgary, AB T2N 4W4, Canada;
| | - Stephen B. Freedman
- Alberta Children’s Hospital, Division of Pediatric Emergency Medicine and Gastroenterology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada;
- Alberta Children’s Hospital Research Institute, Department of Emergency Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Bonita E. Lee
- Department of Pediatrics, Faculty of Medicine & Dentistry, Women and Children’s Health Research Institute, Stollery Children’s Hospital, University of Alberta, Edmonton, AB T6G 1C9, Canada;
| | - Xiao-Li Pang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2B7, Canada; (B.D.P.); (J.S.); (Y.T.K.Y.); (X.-L.P.)
- Alberta Precision Laboratories-ProvLab, Edmonton, AB T6G 2J2, Canada;
| | - Linda Chui
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2B7, Canada; (B.D.P.); (J.S.); (Y.T.K.Y.); (X.-L.P.)
- Alberta Precision Laboratories-ProvLab, Edmonton, AB T6G 2J2, Canada;
- Correspondence:
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6
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Pinto G, Sampaio M, Dias O, Almeida C, Azeredo J, Oliveira H. Insights into the genome architecture and evolution of Shiga toxin encoding bacteriophages of Escherichia coli. BMC Genomics 2021; 22:366. [PMID: 34011288 PMCID: PMC8136144 DOI: 10.1186/s12864-021-07685-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 05/07/2021] [Indexed: 11/18/2022] Open
Abstract
Background A total of 179 Shiga toxin-producing Escherichia coli (STEC) complete genomes were analyzed in terms of serotypes, prophage coding regions, and stx gene variants and their distribution. We further examined the genetic diversity of Stx-converting phage genomes (Stx phages), focusing on the lysis-lysogeny decision and lytic cassettes. Results We show that most STEC isolates belong to non-O157 serotypes (73 %), regardless the sources and geographical regions. While the majority of STEC genomes contain a single stx gene (61 %), strains containing two (35 %), three (3 %) and four (1 %) stx genes were also found, being stx2 the most prevalent gene variant. Their location is exclusively found in intact prophage regions, indicating that they are phage-borne. We further demonstrate that Stx phages can be grouped into four clusters (A, B, C and D), three subclusters (A1, A2 and A3) and one singleton, based on their shared gene content. This cluster distribution is in good agreement with their predicted virion morphologies. Stx phage genomes are highly diverse with a vast number of 1,838 gene phamilies (phams) of related sequences (of which 677 are orphams i.e. unique genes) and, although having high mosaicism, they are generally organized into three major transcripts. While the mechanisms that guide lysis–lysogeny decision are complex, there is a strong selective pressure to maintain the stx genes location close to the lytic cassette composed of predicted SAR-endolysin and pin-holin lytic proteins. The evolution of STEC Stx phages seems to be strongly related to acquiring genetic material, probably from horizontal gene transfer events. Conclusions This work provides novel insights on the genetic structure of Stx phages, showing a high genetic diversity throughout the genomes, where the various lysis-lysogeny regulatory systems are in contrast with an uncommon, but conserved, lytic system always adjacent to stx genes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07685-0.
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Affiliation(s)
- Graça Pinto
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal.,INIAV, IP-National Institute for Agrarian and Veterinary Research, Rua dos Lagidos, Lugar da Madalena, Vairão, Vila do Conde, Portugal
| | - Marta Sampaio
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Oscar Dias
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Carina Almeida
- INIAV, IP-National Institute for Agrarian and Veterinary Research, Rua dos Lagidos, Lugar da Madalena, Vairão, Vila do Conde, Portugal
| | - Joana Azeredo
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal.
| | - Hugo Oliveira
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal.
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7
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Haksar D, Asadpoor M, Heise T, Shi J, Braber S, Folkerts G, Ballell L, Rodrigues J, Pieters RJ. Fighting Shigella by Blocking Its Disease-Causing Toxin. J Med Chem 2021; 64:6059-6069. [PMID: 33909975 PMCID: PMC8154557 DOI: 10.1021/acs.jmedchem.1c00152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
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Shiga toxin is an
AB5 toxin produced by Shigella species, while related toxins are produced
by Shiga toxin-producing Escherichia coli (STEC). Infection by Shigella can lead to bloody diarrhea followed
by the often fatal hemolytic uremic syndrome (HUS). In the present
paper, we aimed for a simple and effective toxin inhibitor by comparing
three classes of carbohydrate-based inhibitors: glycodendrimers, glycopolymers,
and oligosaccharides. We observed a clear enhancement in potency for
multivalent inhibitors, with the divalent and tetravalent compounds
inhibiting in the millimolar and micromolar range, respectively. However,
the polymeric inhibitor based on galabiose was the most potent in
the series exhibiting nanomolar inhibition. Alginate and chitosan
oligosaccharides also inhibit Shiga toxin and may be used as a prophylactic
drug during shigella outbreaks.
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Affiliation(s)
- Diksha Haksar
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Mostafa Asadpoor
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Torben Heise
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Jie Shi
- Diseases of the Developing World (DDW), Global Health R&D, GlaxoSmithKline, Tres Cantos, 28760 Madrid, Spain
| | - Saskia Braber
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Gert Folkerts
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Lluis Ballell
- Diseases of the Developing World (DDW), Global Health R&D, GlaxoSmithKline, Tres Cantos, 28760 Madrid, Spain
| | - Janneth Rodrigues
- Diseases of the Developing World (DDW), Global Health R&D, GlaxoSmithKline, Tres Cantos, 28760 Madrid, Spain
| | - Roland J Pieters
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
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8
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Sváb D, Falgenhauer L, Horváth B, Maróti G, Falgenhauer J, Chakraborty T, Tóth I. Genome Analysis of a Historical Shigella dysenteriae Serotype 1 Strain Carrying a Conserved Stx Prophage Region. Front Microbiol 2021; 11:614793. [PMID: 33488558 PMCID: PMC7819885 DOI: 10.3389/fmicb.2020.614793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/09/2020] [Indexed: 11/13/2022] Open
Abstract
Shigella dysenteriae are significant agents of bacillary dysentery, accounting for a considerable number of illnesses with high morbidity worldwide. The Shiga toxin (Stx) encoded by a defective prophage is the key virulence factor of S. dysenteriae type 1 (SD1) strains. Here we present the full genome sequence of an SD1 strain HNCMB 20080 isolated in 1954, compare it to other sequenced SD1 genomes, and assess the diversity of Stx-prophages harbored by previously sequenced SD1 strains. The genome of HNCMB 20080 consists of a chromosome sized 4,393,622 bp containing 5,183 CDSs, as well as two small plasmids. Comparative genomic analysis revealed a high degree of uniformity among SD1 genomes, including the structure of Stx prophage regions, which we found to form two subgroups termed PT-I and PT-II. All PT-I strains are members of the sequence type (ST) 146 or ST260, while the only PT-II harboring strain, Sd1617 proved to be ST untypeable. In accordance with data from previous reports, the Stx1 prophage could not be induced from HNCMB 20080. Our cumulative data do not support the notion that stx-harboring phages in STEC are derived from historical SD1 isolates.
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Affiliation(s)
- Domonkos Sváb
- Institue for Veterinary Medical Research, Centre for Agricultural Research, Martonvásár, Hungary
| | - Linda Falgenhauer
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany.,German Centre for Infection Research, Site Giessen-Marburg-Langen, Giessen, Germany
| | | | - Gergely Maróti
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary.,Faculty of Water Sciences, University of Public Service, Baja, Hungary
| | - Jane Falgenhauer
- German Centre for Infection Research, Site Giessen-Marburg-Langen, Giessen, Germany.,Institute for Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany.,Institute for Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - István Tóth
- Institue for Veterinary Medical Research, Centre for Agricultural Research, Martonvásár, Hungary
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9
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Abstract
Numerous bacteriophages-viruses of bacteria, also known as phages-have been described for hundreds of bacterial species. The Gram-negative Shigella species are close relatives of Escherichia coli, yet relatively few previously described phages appear to exclusively infect this genus. Recent efforts to isolate Shigella phages have indicated these viruses are surprisingly abundant in the environment and have distinct genomic and structural properties. In addition, at least one model system used for experimental evolution studies has revealed a unique mechanism for developing faster infection cycles. Differences between these bacteriophages and other well-described model systems may mirror differences between their hosts' ecology and defense mechanisms. In this review, we discuss the history of Shigella phages and recent developments in their isolation and characterization and the structural information available for three model systems, Sf6, Sf14, and HRP29; we also provide an overview of potential selective pressures guiding both Shigella phage and host evolution.
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Affiliation(s)
- Sundharraman Subramanian
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Kristin N Parent
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Sarah M Doore
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA.,BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan 48824, USA;
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10
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Carretero-Vicario O, Taravillo I, Corbella L, Catalan M, Garfia C, Martinez MT, Chaves F, Orellana MA. Shigella sonnei bacteraemia in a cystic fibrosis patient: case report and literature review. Access Microbiol 2020; 2:acmi000102. [PMID: 34568758 PMCID: PMC8459098 DOI: 10.1099/acmi.0.000102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/12/2019] [Indexed: 11/18/2022] Open
Affiliation(s)
| | - Irene Taravillo
- Department of Microbiology, Instituto de Investigación Hospital 12 de Octubre, Madrid, Spain
| | - Laura Corbella
- Unit of Infectious Diseases, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Mercedes Catalan
- Intensive Medicine Service, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Cristina Garfia
- Unit of Cystic Fibrosis, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - M. Teresa Martinez
- Unit of Cystic Fibrosis, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Fernando Chaves
- Department of Microbiology, Instituto de Investigación Hospital 12 de Octubre, Madrid, Spain
- Department of Microbiology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - M. Angeles Orellana
- Department of Microbiology, Hospital Universitario 12 de Octubre, Madrid, Spain
- Department of Microbiology, Instituto de Investigación Hospital 12 de Octubre, Madrid, Spain
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11
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Joseph A, Cointe A, Mariani Kurkdjian P, Rafat C, Hertig A. Shiga Toxin-Associated Hemolytic Uremic Syndrome: A Narrative Review. Toxins (Basel) 2020; 12:E67. [PMID: 31973203 PMCID: PMC7076748 DOI: 10.3390/toxins12020067] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 01/13/2020] [Accepted: 01/17/2020] [Indexed: 01/28/2023] Open
Abstract
The severity of human infection by one of the many Shiga toxin-producing Escherichia coli (STEC) is determined by a number of factors: the bacterial genome, the capacity of human societies to prevent foodborne epidemics, the medical condition of infected patients (in particular their hydration status, often compromised by severe diarrhea), and by our capacity to devise new therapeutic approaches, most specifically to combat the bacterial virulence factors, as opposed to our current strategies that essentially aim to palliate organ deficiencies. The last major outbreak in 2011 in Germany, which killed more than 50 people in Europe, was evidence that an effective treatment was still lacking. Herein, we review the current knowledge of STEC virulence, how societies organize the prevention of human disease, and how physicians treat (and, hopefully, will treat) its potentially fatal complications. In particular, we focus on STEC-induced hemolytic and uremic syndrome (HUS), where the intrusion of toxins inside endothelial cells results in massive cell death, activation of the coagulation within capillaries, and eventually organ failure.
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Affiliation(s)
- Adrien Joseph
- Department of Nephrology, AP-HP, Hôpital Tenon, F-75020 Paris, France; (A.J.); (C.R.)
| | - Aurélie Cointe
- Department of Microbiology, AP-HP, Hôpital Robert Debré, F-75019 Paris, France; (A.C.); (P.M.K.)
| | | | - Cédric Rafat
- Department of Nephrology, AP-HP, Hôpital Tenon, F-75020 Paris, France; (A.J.); (C.R.)
| | - Alexandre Hertig
- Department of Renal Transplantation, Sorbonne Université, AP-HP, Hôpital Pitié Salpêtrière, F-75013 Paris, France
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12
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Ahamed ST, Roy B, Basu U, Dutta S, Ghosh AN, Bandyopadhyay B, Giri N. Genomic and Proteomic Characterizations of Sfin-1, a Novel Lytic Phage Infecting Multidrug-Resistant Shigella spp. and Escherichia coli C. Front Microbiol 2019; 10:1876. [PMID: 31507544 PMCID: PMC6714547 DOI: 10.3389/fmicb.2019.01876] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 07/30/2019] [Indexed: 12/14/2022] Open
Abstract
Shigellosis is a public health threat in developed as well as developing countries like “India.” While antibiotic therapy is the mainstay of treatment for shigellosis, current emergence of multidrug-resistant strains of Shigella spp. has posed the problem more challenging. Lytic bacteriophages which destroy antibiotic resistant Shigella spp. have great potential in this context and hence their identification and detailed characterization is necessary. In this study we presented the isolation and a detailed characterization of a novel bacteriophage Sfin-1, which shows potent lytic activity against multidrug-resistant isolates of Shigella flexneri, Shigella dysenteriae, Shigella sonnei obtained from clinical specimens from shigellosis patients. It is also active against Escherichia coli C. The purified phage is lytic in nature, exhibited absorption within 5–10 min, a latent period of 5–20 min and burst size of ∼28 to ∼146 PFU/cell. The isolated phage shows stability in a broad pH range and survives an hour at 50°C. Genome sequencing and phylogenetic analyses showed that Sfin-1 is a novel bacteriophage, which is very closely related to T1-like phages (89.59% identity with Escherichia virus T1). In silico analysis indicates that Sfin-1 genome consists of double stranded linear DNA of 50,403 bp (GC content of 45.2%) encoding 82 potential coding sequences, several potential promoters and transcriptional terminators. Under electron microscopy, Sfin-1 shows morphology characteristics of the family Siphoviridae with an isometric head (61 nm) and a non-contractile tail (155 nm). This is most likely the first report of a lytic bacteriophage that is active against three of the most virulent multidrug-resistant Shigella species and therefore might have a potential role in phage therapy of patients infected with these organisms.
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Affiliation(s)
- Sk Tousif Ahamed
- Department of Microbiology, Acharya Prafulla Chandra College, Kolkata, India
| | - Banibrata Roy
- Department of Microbiology, Acharya Prafulla Chandra College, Kolkata, India
| | - Utpal Basu
- Department of Molecular Biology and Biotechnology, University of Kalyani, Kalyani, India
| | - Shanta Dutta
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - A N Ghosh
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata, India
| | | | - Nabanita Giri
- Department of Microbiology, Acharya Prafulla Chandra College, Kolkata, India
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Response to Questions Posed by the Food and Drug Administration Regarding Virulence Factors and Attributes that Define Foodborne Shiga Toxin-Producing Escherichia coli (STEC) as Severe Human Pathogens †. J Food Prot 2019; 82:724-767. [PMID: 30969806 DOI: 10.4315/0362-028x.jfp-18-479] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
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- NACMCF Executive Secretariat, * U.S. Department of Agriculture, Food Safety and Inspection Service, Office of Public Health Science, PP3, 9-178, 1400 Independence Avenue S.W., Washington, D.C. 20250-3700, USA
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15
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Lee MS, Tesh VL. Roles of Shiga Toxins in Immunopathology. Toxins (Basel) 2019; 11:E212. [PMID: 30970547 PMCID: PMC6521259 DOI: 10.3390/toxins11040212] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 04/04/2019] [Accepted: 04/05/2019] [Indexed: 12/20/2022] Open
Abstract
Shigella species and Shiga toxin-producing Escherichia coli (STEC) are agents of bloody diarrhea that may progress to potentially lethal complications such as diarrhea-associated hemolytic uremic syndrome (D+HUS) and neurological disorders. The bacteria share the ability to produce virulence factors called Shiga toxins (Stxs). Research over the past two decades has identified Stxs as multifunctional toxins capable of inducing cell stress responses in addition to their canonical ribotoxic function inhibiting protein synthesis. Notably, Stxs are not only potent inducers of cell death, but also activate innate immune responses that may lead to inflammation, and these effects may increase the severity of organ injury in patients infected with Stx-producing bacteria. In the intestines, kidneys, and central nervous system, excessive or uncontrolled host innate and cellular immune responses triggered by Stxs may result in sensitization of cells to toxin mediated damage, leading to immunopathology and increased morbidity and mortality in animal models (including primates) and human patients. Here, we review studies describing Stx-induced innate immune responses that may be associated with tissue damage, inflammation, and complement activation. We speculate on how these processes may contribute to immunopathological responses to the toxins.
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Affiliation(s)
- Moo-Seung Lee
- Environmental Diseases Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea.
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 127 Gajeong-ro, Yuseong-gu, Daejeon 34113, Korea.
| | - Vernon L Tesh
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA.
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Abstract
The history of Shigella, the causative agent of bacillary dysentery, is a long and fascinating one. This brief historical account starts with descriptions of the disease and its impact on human health from ancient time to the present. Our story of the bacterium starts just before the identification of the dysentery bacillus by Kiyoshi Shiga in 1898 and follows the scientific discoveries and principal scientists who contributed to the elucidation of Shigella pathogenesis in the first 100 years. Over the past century, Shigella has proved to be an outstanding model of an invasive bacterial pathogen and has served as a paradigm for the study of other bacterial pathogens. In addition to invasion of epithelial cells, some of those shared virulence traits include toxin production, multiple-antibiotic resistance, virulence genes encoded on plasmids and bacteriophages, global regulation of virulence genes, pathogenicity islands, intracellular motility, remodeling of host cytoskeleton, inflammation/polymorphonuclear leukocyte signaling, apoptosis induction/inhibition, and "black holes" and antivirulence genes. While there is still much to learn from studying Shigella pathogenesis, what we have learned so far has also contributed greatly to our broader understanding of bacterial pathogenesis.
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In Silico Serotyping Based on Whole-Genome Sequencing Improves the Accuracy of Shigella Identification. Appl Environ Microbiol 2019; 85:AEM.00165-19. [PMID: 30709819 DOI: 10.1128/aem.00165-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 01/25/2019] [Indexed: 12/21/2022] Open
Abstract
Bacteria of the genus Shigella, consisting of 4 species and >50 serotypes, cause shigellosis, a foodborne disease of significant morbidity, mortality, and economic loss worldwide. Classical Shigella identification based on selective media and serology is tedious, time-consuming, expensive, and not always accurate. A molecular diagnostic assay does not distinguish Shigella at the species level or from enteroinvasive Escherichia coli (EIEC). We inspected genomic sequences from 221 Shigella isolates and observed low concordance rates between conventional designation and molecular serotyping: 86.4% and 80.5% at the species and serotype levels, respectively. Serotype determinants for 6 additional serotypes were identified. Examination of differentiation gene markers commonly perceived as characteristic hallmarks in Shigella showed high variability among different serotypes. Using this information, we developed ShigaTyper, an automated workflow that utilizes limited computational resources to accurately and rapidly determine 59 Shigella serotypes using Illumina paired-end whole-genome sequencing (WGS) reads. Shigella serotype determinants and species-specific diagnostic markers were first identified through read alignment to an in-house curated reference sequence database. Relying on sequence hits that passed a threshold level of coverage and accuracy, serotype could be unambiguously predicted within 1 min for an average-size WGS sample of ∼500 MB. Validation with WGS data from 380 isolates showed an accuracy rate of 98.2%. This pipeline is the first step toward building a comprehensive WGS-based analysis pipeline of Shigella spp. in a field laboratory setting, where speed is essential and resources need to be more cost-effectively dedicated.IMPORTANCE Shigella causes diarrheal disease with serious public health implications. However, conventional Shigella identification methods are laborious and time-consuming and can be erroneous due to the high similarity between Shigella and enteroinvasive Escherichia coli (EIEC) and cross-reactivity between serotyping antisera. Further, serotype interpretation is complicated for inexperienced users. To develop an easier method with higher accuracy based on whole-genome sequencing (WGS) for Shigella serotyping, we systematically examined genomic information of Shigella isolates from 53 serotypes to define rules for differentiation and serotyping. We created ShigaTyper, an automated pipeline that accurately and rapidly excludes non-Shigella isolates and identifies 59 Shigella serotypes using Illumina paired-end WGS reads. A serotype can be unambiguously predicted at a data processing speed of 538 MB/min with 98.2% accuracy from a regular laptop. Once it is installed, training in bioinformatics analysis and Shigella genetics is not required. This pipeline is particularly useful to general microbiologists in field laboratories.
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The Evasive Enemy: Insights into the Virulence and Epidemiology of the Emerging Attaching and Effacing Pathogen Escherichia albertii. Infect Immun 2018; 87:IAI.00254-18. [PMID: 30373891 DOI: 10.1128/iai.00254-18] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 10/18/2018] [Indexed: 01/10/2023] Open
Abstract
The diarrheic attaching and effacing (A/E) pathogen Escherichia albertii was first isolated from infants in Bangladesh in 1991, although the bacterium was initially classified as Hafnia alvei Subsequent genetic and biochemical interrogation of these isolates raised concerns about their initial taxonomic placement. It was not until 2003 that these isolates were reassigned to the novel taxon Escherichia albertii because they were genetically more closely related to E. coli, although they had diverged sufficiently to warrant a novel species name. Unfortunately, new isolates continue to be mistyped as enteropathogenic E. coli (EPEC) or enterohemorrhagic E. coli (EHEC) owing to shared traits, most notably the ability to form A/E lesions. Consequently, E. albertii remains an underappreciated A/E pathogen, despite multiple reports demonstrating that many provisional EPEC and EHEC isolates incriminated in disease outbreaks are actually E. albertii Metagenomic studies on dozens of E. albertii isolates reveal a genetic architecture that boasts an arsenal of candidate virulence factors to rival that of its better-characterized cousins, EPEC and EHEC. Beyond these computational comparisons, studies addressing the regulation, structure, function, and mechanism of action of its repertoire of virulence factors are lacking. Thus, the paucity of knowledge about the epidemiology, virulence, and antibiotic resistance of E. albertii, coupled with its misclassification and its ability to develop multidrug resistance in a single step, highlights the challenges in combating this emerging pathogen. This review seeks to synthesize our current but incomplete understanding of the biology of E. albertii.
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Yang C, Wang H, Ma H, Bao R, Liu H, Yang L, Liang B, Jia L, Xie J, Xiang Y, Dong N, Qiu S, Song H. Characterization and Genomic Analysis of SFPH2, a Novel T7virus Infecting Shigella. Front Microbiol 2018; 9:3027. [PMID: 30619123 PMCID: PMC6302001 DOI: 10.3389/fmicb.2018.03027] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/22/2018] [Indexed: 11/13/2022] Open
Abstract
Shigellosis, caused by Shigella, is a major global health concern, with nearly 164.7 million cases and over a million deaths occurring annually worldwide. Shigella flexneri is one of the most common subgroups of Shigella with a high incidence of multidrug-resistance. The phage therapy approach is an effective method for controlling multidrug-resistant bacteria. However, only a few Shigella phages have been described to date. In this study, a novel lytic bacteriophage SFPH2 was isolated from a sewage sample obtained from a hospital in Beijing, China, using a multidrug-resistant S. flexneri 2a strain (SF2) isolated from the fecal sample of a dysentery patient. SFPH2 is a member of the Podoviridae virus family with an icosahedral capsid and a short, non-contractile tail. It was found to be stable over a wide range of temperatures (4–50°C) and pH values (pH 3–11). Moreover, SFPH2 could infect two other S. flexneri serotypes (serotypes 2 variant and Y). High-throughput sequencing revealed that SFPH2 has a linear double-stranded DNA genome of 40,387 bp with 50 open reading frames. No tRNA genes were identified in the genome. Comparative analysis of the genome revealed that the SFPH2 belongs to the subfamily Autographivirinae and genus T7virus. The genome shows high similarity with other enterobacterial T7virus bacteriophages such as Citrobacter phage SH4 (95% identity and 89% coverage) and Cronobacter phage Dev2 (94% identity and 92% coverage). A comparison of the fiber proteins showed that minor differences in the amino acid residues might specify different protein binding regions and determine host species. In conclusion, this is the first report of a T7virus that can infect Shigella; SFPH2 has a functional stability under a wide range of temperatures and pH values, showing the potential to be widely applied to control Shigella–associated clinical infections and reduce the transmission rates of S. flexneri serotype 2a and its variants in the environment.
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Affiliation(s)
- Chaojie Yang
- Institute of Disease Control and Prevention of PLA, Beijing, China
| | - Haiying Wang
- Joint Service Academy, National Defence University of People's Liberation Army, Beijing, China
| | - Hui Ma
- The 6th Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Renlong Bao
- Institute of Disease Control and Prevention of PLA, Beijing, China
| | - Hongbo Liu
- Institute of Disease Control and Prevention of PLA, Beijing, China
| | - Lang Yang
- Institute of Disease Control and Prevention of PLA, Beijing, China
| | - Beibei Liang
- Institute of Disease Control and Prevention of PLA, Beijing, China
| | - Leili Jia
- Institute of Disease Control and Prevention of PLA, Beijing, China
| | - Jing Xie
- Institute of Disease Control and Prevention of PLA, Beijing, China
| | - Ying Xiang
- Institute of Disease Control and Prevention of PLA, Beijing, China
| | - Nian Dong
- Institute of Disease Control and Prevention of PLA, Beijing, China
| | - Shaofu Qiu
- Institute of Disease Control and Prevention of PLA, Beijing, China
| | - Hongbin Song
- Institute of Disease Control and Prevention of PLA, Beijing, China
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Fogolari M, Mavian C, Angeletti S, Salemi M, Lampel KA, Maurelli AT. Distribution and characterization of Shiga toxin converting temperate phages carried by Shigella flexneri in Hispaniola. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2018; 65:321-328. [PMID: 30075254 PMCID: PMC6260934 DOI: 10.1016/j.meegid.2018.07.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/22/2018] [Accepted: 07/29/2018] [Indexed: 01/29/2023]
Abstract
Shigella infections account for a considerable burden of acute diarrheal diseases worldwide and remain a major cause of childhood mortality in developing countries. Although, all four species of Shigella (S. dysenteriae, S. flexneri, S. boydii, and S. sonnei) cause bacillary dysentery, historically only S. dysenteriae type 1 has been recognized as carrying the genes for Shiga toxin (stx). Recent epidemiological data, however, have suggested that the emergence of stx carrying S. flexneri strains may have originated from bacteriophage-mediated inter-species horizontal gene transfer in one specific geographical area, Hispaniola. To test this hypothesis, we analyzed whole genome sequences of stx-encoding phages carried by S. flexneri strains isolated in Haiti and S. flexneri S. boydii and S. dysenteriae strains isolated from international travelers who likely acquired the infection in Haiti or the Dominican Republic. Phylogenetic analysis showed that phage sequences encoded in the Shigella strains from Hispaniola were bacteriophage φPOC-J13 and they were all closely related to a phage isolated from a USA isolate, E. coli 2009C-3133 serotype O119:H4. In addition, despite the low genetic heterogeneity of phages from different Shigella spp. circulating in the Caribbean island between 2001 and 2014, two distinct clusters emerged in Haiti and the Dominican Republic. Each cluster possibly originated from phages isolated from S. flexneri 2a, and within each cluster several instances of horizontal phage transfer from S. flexneri 2a to other species were detected. The implications of the emergence of stx-producing non-S. dysenteriae type 1 Shigella species, such as S. flexneri, spans not only the basic science behind horizontal phage spread, but also extends to medical treatment of patients infected with this pathogen.
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Affiliation(s)
- Marta Fogolari
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy; Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Carla Mavian
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA; Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy
| | - Marco Salemi
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA; Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA.
| | | | - Anthony T Maurelli
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA; Department of Environmental and Global Health, University of Florida, Gainesville, FL, USA.
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Evolution of STEC virulence: Insights from the antipredator activities of Shiga toxin producing E. coli. Int J Med Microbiol 2018; 308:956-961. [DOI: 10.1016/j.ijmm.2018.07.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 06/29/2018] [Accepted: 07/10/2018] [Indexed: 11/17/2022] Open
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Li B, Liu H, Wang W. Multiplex real-time PCR assay for detection of Escherichia coli O157:H7 and screening for non-O157 Shiga toxin-producing E. coli. BMC Microbiol 2017; 17:215. [PMID: 29121863 PMCID: PMC5679507 DOI: 10.1186/s12866-017-1123-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 10/27/2017] [Indexed: 12/22/2022] Open
Abstract
Background Shiga toxin-producing Escherichia coli (STEC), including E. coli O157:H7, are responsible for numerous foodborne outbreaks annually worldwide. E. coli O157:H7, as well as pathogenic non-O157:H7 STECs, can cause life-threating complications, such as bloody diarrhea (hemolytic colitis) and hemolytic-uremic syndrome (HUS). Previously, we developed a real-time PCR assay to detect E. coli O157:H7 in foods by targeting a unique putative fimbriae protein Z3276. To extend the detection spectrum of the assay, we report a multiplex real-time PCR assay to specifically detect E. coli O157:H7 and screen for non-O157 STEC by targeting Z3276 and Shiga toxin genes (stx1 and stx2). Also, an internal amplification control (IAC) was incorporated into the assay to monitor the amplification efficiency. Methods The multiplex real-time PCR assay was developed using the Life Technology ABI 7500 System platform and the standard chemistry. The optimal amplification mixture of the assay contains 12.5 μl of 2 × Universal Master Mix (Life Technology), 200 nM forward and reverse primers, appropriate concentrations of four probes [(Z3276 (80 nM), stx1 (80 nM), stx2 (20 nM), and IAC (40 nM)], 2 μl of template DNA, and water (to make up to 25 μl in total volume). The amplification conditions of the assay were set as follows: activation of TaqMan at 95 °C for 10 min, then 40 cycles of denaturation at 95 °C for 10 s and annealing/extension at 60 °C for 60 s. Results The multiplex assay was optimized for amplification conditions. The limit of detection (LOD) for the multiplex assay was determined to be 200 fg of bacterial DNA, which is equivalent to 40 CFU per reaction which is similar to the LOD generated in single targeted PCRs. Inclusivity and exclusivity determinants were performed with 196 bacterial strains. All E. coli O157:H7 (n = 135) were detected as positive and all STEC strains (n = 33) were positive for stx1, or stx2, or stx1 and stx2 (Table 1). No cross reactivity was detected with Salmonella enterica, Shigella strains, or any other pathogenic strains tested. Conclusions A multiplex real-time PCR assay that can rapidly and simultaneously detect E. coli O157:H7 and screen for non-O157 STEC strains has been developed and assessed for efficacy. The inclusivity and exclusivity tests demonstrated high sensitivity and specificity of the multiplex real-time PCR assay. In addition, this multiplex assay was shown to be effective for the detection of E. coli O157:H7 from two common food matrices, beef and spinach, and may be applied for detection of E. coli O157:H7 and screening for non-O157 STEC strains from other food matrices as well.
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Affiliation(s)
- Baoguang Li
- Division of Molecular Biology, Center for Food Safety and Applied Nutrition, Food and Drug Administration, Laurel, MD, 20708, USA.
| | - Huanli Liu
- Branch of Microbiology, Office of Regulatory Affairs, Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Weimin Wang
- Division of Molecular Biology, Center for Food Safety and Applied Nutrition, Food and Drug Administration, Laurel, MD, 20708, USA
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Adams DA, Thomas KR, Jajosky RA, Foster L, Baroi G, Sharp P, Onweh DH, Schley AW, Anderson WJ. Summary of Notifiable Infectious Diseases and Conditions - United States, 2015. MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT 2017; 64:1-143. [PMID: 28796757 DOI: 10.15585/mmwr.mm6453a1] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The Summary of Notifiable Infectious Diseases and Conditions - United States, 2015 (hereafter referred to as the summary) contains the official statistics, in tabular and graphical form, for the reported occurrence of nationally notifiable infectious diseases and conditions in the United States for 2015. Unless otherwise noted, data are final totals for 2015 reported as of June 30, 2016. These statistics are collected and compiled from reports sent by U.S. state and territories, New York City, and District of Columbia health departments to the National Notifiable Diseases Surveillance System (NNDSS), which is operated by CDC in collaboration with the Council of State and Territorial Epidemiologists (CSTE). This summary is available at https://www.cdc.gov/MMWR/MMWR_nd/index.html. This site also includes summary publications from previous years.
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Affiliation(s)
- Deborah A Adams
- Division of Health Informatics and Surveillance, Office of Public Health Scientific Services, CDC
| | - Kimberly R Thomas
- Division of Health Informatics and Surveillance, Office of Public Health Scientific Services, CDC
| | - Ruth Ann Jajosky
- Division of Health Informatics and Surveillance, Office of Public Health Scientific Services, CDC
| | - Loretta Foster
- Division of Health Informatics and Surveillance, Office of Public Health Scientific Services, CDC
| | - Gitangali Baroi
- Division of Health Informatics and Surveillance, Office of Public Health Scientific Services, CDC
| | - Pearl Sharp
- Division of Health Informatics and Surveillance, Office of Public Health Scientific Services, CDC
| | - Diana H Onweh
- Division of Health Informatics and Surveillance, Office of Public Health Scientific Services, CDC
| | - Alan W Schley
- Division of Health Informatics and Surveillance, Office of Public Health Scientific Services, CDC
| | - Willie J Anderson
- Division of Health Informatics and Surveillance, Office of Public Health Scientific Services, CDC
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Volgers C, Savelkoul PHM, Stassen FRM. Gram-negative bacterial membrane vesicle release in response to the host-environment: different threats, same trick? Crit Rev Microbiol 2017; 44:258-273. [PMID: 28741415 DOI: 10.1080/1040841x.2017.1353949] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Bacteria are confronted with a multitude of stressors when occupying niches within the host. These stressors originate from host defense mechanisms, other bacteria during niche competition or result from physiological challenges such as nutrient limitation. To counteract these stressors, bacteria have developed a stress-induced network to mount the adaptations required for survival. These stress-induced adaptations include the release of membrane vesicles from the bacterial envelope. Membrane vesicles can provide bacteria with a plethora of immediate and ultimate benefits for coping with environmental stressors. This review addresses how membrane vesicles aid Gram-negative bacteria to cope with host-associated stress factors, focusing on vesicle biogenesis and the physiological functions. As many of the pathways, that drive vesicle biogenesis, confer we propose that shedding of membrane vesicles by Gram-negative bacteria entails an integrated part of general stress responses.
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Affiliation(s)
- Charlotte Volgers
- a Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM) , Maastricht University Medical Centre , Maastricht , The Netherlands
| | - Paul H M Savelkoul
- a Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM) , Maastricht University Medical Centre , Maastricht , The Netherlands.,b Department of Medical Microbiology and Infection Control , VU University Medical Center , Amsterdam , The Netherlands
| | - Frank R M Stassen
- a Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM) , Maastricht University Medical Centre , Maastricht , The Netherlands
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Sváb D, Bálint B, Vásárhelyi B, Maróti G, Tóth I. Comparative Genomic and Phylogenetic Analysis of a Shiga Toxin Producing Shigella sonnei (STSS) Strain. Front Cell Infect Microbiol 2017; 7:229. [PMID: 28611956 PMCID: PMC5447701 DOI: 10.3389/fcimb.2017.00229] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 05/17/2017] [Indexed: 01/26/2023] Open
Abstract
Shigella strains are important agents of bacillary dysentery, and in recent years Shigella sonnei has emerged as the leading cause of shigellosis in industrialized and rapidly developing countries. More recently, several S. sonnei and Shigella flexneri strains producing Shiga toxin (Stx) have been reported from sporadic cases and from an outbreak in America. In the present study we aimed to shed light on the evolution of a recently identified Shiga toxin producing S. sonnei (STSS) isolated in Europe. Here we report the first completely assembled whole genome sequence of a multidrug resistant (MDR) Stx-producing S. sonnei (STSS) clinical strain and reveal its phylogenetic relations. STSS 75/02 proved to be resistant to ampicillin, streptomycin, tetracycline, chloramphenicol, thrimetoprim, and sulfomethoxazol. The genome of STSS 75/02 contains a 4,891,717 nt chromosome and seven plasmids including the 214 kb invasion plasmid (pInv) harboring type III secretion system genes and associated effectors. The chromosome harbors 23 prophage regions including the Stx1 converting prophage. The genome carries all virulence determinants necessary for an enteroinvasive lifestyle, as well as the Stx1 encoding gene cluster within an earlier described inducible converting prophage. In silico SNP genotyping of the assembled genome as well as 438 complete or draft S. sonnei genomes downloaded from NCBI GenBank revealed that S. sonnei 75/02 belongs to the more recently diverged global MDR lineage (IIIc). Targeted screening of 1131 next-generation sequencing projects taken from NCBI Short Read Archive of confirms that only a few S. sonnei isolates are Stx positive. Our results suggest that the acquisition of Stx phages could have occurred in different environments as independent events and that multiple horizontal transfers are responsible for the appearance of Stx phages in S. sonnei strains.
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Affiliation(s)
- Domonkos Sváb
- Centre for Agricultural Research, Institute for Veterinary Medical Research, Hungarian Academy of SciencesBudapest, Hungary
| | | | | | - Gergely Maróti
- Biological Research Centre, Institute of Biochemistry, Hungarian Academy of SciencesSzeged, Hungary
| | - István Tóth
- Centre for Agricultural Research, Institute for Veterinary Medical Research, Hungarian Academy of SciencesBudapest, Hungary
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Doughan S, Uddayasankar U, Peri A, Krull UJ. A paper-based multiplexed resonance energy transfer nucleic acid hybridization assay using a single form of upconversion nanoparticle as donor and three quantum dots as acceptors. Anal Chim Acta 2017; 962:88-96. [DOI: 10.1016/j.aca.2017.01.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 12/31/2016] [Accepted: 01/06/2017] [Indexed: 12/15/2022]
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Lamba K, Nelson JA, Kimura AC, Poe A, Collins J, Kao AS, Cruz L, Inami G, Vaishampayan J, Garza A, Chaturvedi V, Vugia DJ. Shiga Toxin 1-Producing Shigella sonnei Infections, California, United States, 2014-2015. Emerg Infect Dis 2016; 22:679-86. [PMID: 26982255 PMCID: PMC4806944 DOI: 10.3201/eid2204.151825] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Shiga toxins (Stx) are primarily associated with Shiga toxin–producing Escherichia coli and Shigella dysenteriae serotype 1. Stx production by other shigellae is uncommon, but in 2014, Stx1-producing S. sonnei infections were detected in California. Surveillance was enhanced to test S. sonnei isolates for the presence and expression of stx genes, perform DNA subtyping, describe clinical and epidemiologic characteristics of case-patients, and investigate for sources of infection. During June 2014–April 2015, we identified 56 cases of Stx1-producing S. sonnei, in 2 clusters. All isolates encoded stx1 and produced active Stx1. Multiple pulsed-field gel electrophoresis patterns were identified. Bloody diarrhea was reported by 71% of case-patients; none had hemolytic uremic syndrome. Some initial cases were epidemiologically linked to travel to Mexico, but subsequent infections were transmitted domestically. Continued surveillance of Stx1-producing S. sonnei in California is necessary to characterize its features and plan for reduction of its spread in the United States.
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Kozyreva VK, Jospin G, Greninger AL, Watt JP, Eisen JA, Chaturvedi V. Recent Outbreaks of Shigellosis in California Caused by Two Distinct Populations of Shigella sonnei with either Increased Virulence or Fluoroquinolone Resistance. mSphere 2016; 1:e00344-16. [PMID: 28028547 PMCID: PMC5177732 DOI: 10.1128/msphere.00344-16] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 11/23/2016] [Indexed: 01/08/2023] Open
Abstract
Shigella sonnei has caused unusually large outbreaks of shigellosis in California in 2014 and 2015. Preliminary data indicated the involvement of two distinct bacterial populations, one from San Diego and San Joaquin (SDi/SJo) and one from the San Francisco (SFr) Bay area. Whole-genome analysis and antibiotic susceptibility testing of 68 outbreak and archival isolates of S. sonnei were performed to investigate the microbiological factors related to these outbreaks. Both SDi/SJo and SFr populations, as well as almost all of the archival S. sonnei isolates belonged to sequence type 152 (ST152). Genome-wide single nucleotide polymorphism (SNP) analysis clustered the majority of California (CA) isolates to an earlier described lineage III. Isolates in the SDi/SJo population had a novel lambdoid bacteriophage carrying genes encoding Shiga toxin (STX) that were most closely related to that found in Escherichia coli O104:H4. However, the STX genes (stx1A and stx1B) from this novel phage had sequences most similar to the phages from Shigella flexneri and S. dysenteriae. The isolates in the SFr population were resistant to ciprofloxacin due to point mutations in gyrA and parC genes and were related to the fluoroquinolone-resistant S. sonnei clade within lineage III that originated in South Asia. The emergence of a highly virulent S. sonnei strain and introduction of a fluoroquinolone-resistant strain reflect the changing traits of this pathogen in California. An enhanced monitoring is advocated for early detection of future outbreaks caused by such strains. IMPORTANCE Shigellosis is an acute diarrheal disease causing nearly half a million infections, 6,000 hospitalizations, and 70 deaths annually in the United States. S. sonnei caused two unusually large outbreaks in 2014 and 2015 in California. We used whole-genome sequencing to understand the pathogenic potential of bacteria involved in these outbreaks. Our results suggest the persistence of a local S. sonnei SDi/SJo clone in California since at least 2008. Recently, a derivative of the original clone acquired the ability to produce Shiga toxin (STX) via exchanges of bacteriophages with other bacteria. STX production is connected with more severe disease, including bloody diarrhea. A second population of S. sonnei that caused an outbreak in the San Francisco area was resistant to fluoroquinolones and showed evidence of connection to a fluoroquinolone-resistant lineage from South Asia. These emerging trends in S. sonnei populations in California must be monitored for future risks of the spread of increasingly virulent and resistant clones.
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Affiliation(s)
- Varvara K. Kozyreva
- Microbial Diseases Laboratory, California Department of Public Health, Richmond, California, USA
| | - Guillaume Jospin
- Genome Center, Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California, Davis, Davis, California, USA
| | - Alexander L. Greninger
- Microbial Diseases Laboratory, California Department of Public Health, Richmond, California, USA
| | - James P. Watt
- Division of Communicable Disease Control, California Department of Public Health, Richmond, California, USA
| | - Jonathan A. Eisen
- Genome Center, Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California, Davis, Davis, California, USA
| | - Vishnu Chaturvedi
- Microbial Diseases Laboratory, California Department of Public Health, Richmond, California, USA
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Dziewit L, Radlinska M. Two novel temperate bacteriophages co-existing in Aeromonas sp. ARM81 - characterization of their genomes, proteomes and DNA methyltransferases. J Gen Virol 2016; 97:2008-2022. [PMID: 27184451 DOI: 10.1099/jgv.0.000504] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Aeromonas species are causative agents of a wide spectrum of diseases in animals and humans. Although these bacteria are commonly found in various environments, little is known about their phages. Thus far, only one temperate Aeromonas phage has been characterized. Whole-genome sequencing of an Aeromonas sp. strain ARM81 revealed the presence of two prophage clusters. One of them is integrated into the chromosome and the other was maintained as an extrachromosomal, linear plasmid-like prophage encoding a protelomerase. Both prophages were artificially and spontaneously inducible. We separately isolated both phages and compared their genomes with other known viruses. The novel phages show no similarity to the previously characterized Aeromonas phages and might represent new evolutionary lineages of viruses infecting Aeromonadaceae. Apart from the comparative genomic analyses of these phages, complemented with their structural and molecular characterization, a functional analysis of four DNA methyltransferases encoded by these viruses was conducted. One of the investigated N6-adenine-modifying enzymes shares sequence specificity with a Dam-like methyltransferase of its bacterial host, while another one is non-specific, as it catalyzes adenine methylation in various sequence contexts. The presented results shed new light on the diversity of Aeromonas temperate phages.
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Affiliation(s)
- Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Monika Radlinska
- Department of Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
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30
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Carter CC, Fierer J, Chiu WW, Looney DJ, Strain M, Mehta SR. A Novel Shiga Toxin 1a-Converting Bacteriophage of Shigella sonnei With Close Relationship to Shiga Toxin 2-Converting Pages of Escherichia coli. Open Forum Infect Dis 2016; 3:ofw079. [PMID: 27419156 PMCID: PMC4943565 DOI: 10.1093/ofid/ofw079] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 04/15/2016] [Indexed: 11/22/2022] Open
Abstract
In recent studies, strains of non-dysenteriae 1 Shigella (NDS) expressing Shiga toxin have been reported. In this study, we report a novel stx1a-converting bacteriophage of Shigella sonnei associated with travel to Mexico. Phylogenetic comparison between this and other stx-converting phages suggests that toxigenic NDS strains have arisen through separate horizontal transfer events from toxigenic Escherichia coli.
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Affiliation(s)
- Christoph C Carter
- University of California San Diego; Veterans Affairs Medical Center, San Diego, California
| | - Joshua Fierer
- University of California San Diego; Veterans Affairs Medical Center, San Diego, California
| | - Wei Wei Chiu
- University of California San Diego; Veterans Affairs Medical Center, San Diego, California
| | - David J Looney
- University of California San Diego; Veterans Affairs Medical Center, San Diego, California
| | - Matthew Strain
- University of California San Diego; Veterans Affairs Medical Center, San Diego, California
| | - Sanjay R Mehta
- University of California San Diego; Veterans Affairs Medical Center, San Diego, California
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31
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The HC, Thanh DP, Holt KE, Thomson NR, Baker S. The genomic signatures of Shigella evolution, adaptation and geographical spread. Nat Rev Microbiol 2016; 14:235-50. [PMID: 26923111 DOI: 10.1038/nrmicro.2016.10] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Shigella spp. are some of the key pathogens responsible for the global burden of diarrhoeal disease. These facultative intracellular bacteria belong to the family Enterobacteriaceae, together with other intestinal pathogens, such as Escherichia coli and Salmonella spp. The genus Shigella comprises four different species, each consisting of several serogroups, all of which show phenotypic similarity, including invasive pathogenicity. DNA sequencing suggests that this similarity results from the convergent evolution of different Shigella spp. founders. Here, we review the evolutionary relationships between Shigella spp. and E . coli, and we highlight how the genomic plasticity of these bacteria and their acquisition of a distinctive virulence plasmid have enabled the development of such highly specialized pathogens. Furthermore, we discuss the insights that genotyping and whole-genome sequencing have provided into the phylogenetics and intercontinental spread of Shigella spp.
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Affiliation(s)
- Hao Chung The
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam
| | - Duy Pham Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam
| | - Kathryn E Holt
- Centre for Systems Genomics, University of Melbourne.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria 3052, Australia
| | - Nicholas R Thomson
- Bacterial Genomics, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.,Centre for Tropical Medicine and Global Health, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Stephen Baker
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, UK.,Department of Pathogen and Molecular Biology, The London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT, UK
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32
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Gray MD, Leonard SR, Lacher DW, Lampel KA, Alam MT, Morris JG, Ali A, LaBreck PT, Maurelli AT. Stx-Producing Shigella Species From Patients in Haiti: An Emerging Pathogen With the Potential for Global Spread. Open Forum Infect Dis 2015; 2:ofv134. [PMID: 26484357 PMCID: PMC4606844 DOI: 10.1093/ofid/ofv134] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 09/04/2015] [Indexed: 11/14/2022] Open
Abstract
Shiga toxins (Stx) are commonly produced by Shigella dysenteriae serotype 1 and Stx-producing Escherichia coli. However, the toxin genes have been detected in additional Shigella species. We recently reported the emergence of Stx-producing Shigella in travelers in the United States and France who had recently visited Hispaniola (Haiti and the Dominican Republic). In this study, we confirm this epidemiological link by identifying Stx-producing Shigella from Haitian patients attending clinics near Port-au-Prince. We also demonstrate that the bacteriophage encoding Stx is capable of dissemination to stx-negative Shigella species found in Haiti, suggesting that Stx-producing Shigella may become more widespread within that region.
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Affiliation(s)
- Miranda D. Gray
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda
| | - Susan R. Leonard
- US Food and Drug Administration, Center for Food Safety and Nutrition, Laurel, Maryland
| | - David W. Lacher
- US Food and Drug Administration, Center for Food Safety and Nutrition, Laurel, Maryland
| | - Keith A. Lampel
- US Food and Drug Administration, Center for Food Safety and Nutrition, Laurel, Maryland
| | - Meer T. Alam
- University of Florida, Emerging Pathogens Institute,
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville
| | | | - Afsar Ali
- University of Florida, Emerging Pathogens Institute,
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville
| | - Patrick T. LaBreck
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda
| | - Anthony T. Maurelli
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda
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33
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Tóth I, Sváb D, Bálint B, Brown-Jaque M, Maróti G. Comparative analysis of the Shiga toxin converting bacteriophage first detected in Shigella sonnei. INFECTION GENETICS AND EVOLUTION 2015; 37:150-7. [PMID: 26616675 DOI: 10.1016/j.meegid.2015.11.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 11/13/2015] [Accepted: 11/21/2015] [Indexed: 11/26/2022]
Abstract
Here we report the first complete nucleotide sequence of a Shiga toxin (Stx) converting phage from a Shigella sonnei clinical isolate that harbors stx1 operon, first identified in the chromosome of Shigella dysenteriae type 1. The phage named Shigella phage 75/02 Stx displayed Podoviridae morphology. It proved to be transferable to Escherichia coli K-12 strains, and cytotoxicity of the lysogenized strains was demonstrated in Vero cell cultures. Genomic analysis revealed that the prophage genome is circular and its size is 60,875 nt that corresponds to 76 ORFs. The genome of Shigella phage 75/02 Stx shows a great degree of mosaic structure and its architecture is related to lambdoid phages. All the deduced proteins, including the 37 hypothetical proteins showed significant homologies to Stx phage proteins present in databases. The phage uniformly inserted into the ynfG oxidoreductase gene framed by phage integrase and antirepressor genes in parental S. sonnei and in the three lysogenized K-12 strains C600, DH5α and MG1655. The Stx1 prophage proved to be stable in its bacterial hosts and remained inducible.
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Affiliation(s)
- István Tóth
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary.
| | - Domonkos Sváb
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary.
| | | | | | - Gergely Maróti
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary.
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34
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Bekal S, Pilon PA, Cloutier N, Doualla-Bell F, Longtin J. Identification of Shigella flexneri isolates carrying the Shiga toxin 1-producing gene in Quebec, Canada, linked to travel to Haiti. Can J Microbiol 2015; 61:995-6. [PMID: 26401981 DOI: 10.1139/cjm-2015-0538] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Sadjia Bekal
- a Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada.,b Département de Microbiologie, Infectiologie et immunologie, Université de Montréal, Montréal, Quebec, Canada
| | - Pierre A Pilon
- c Direction régionale de santé publique de Montréal, Quebec, Canada
| | - Nancy Cloutier
- a Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Florence Doualla-Bell
- a Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada.,d Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Quebec, Canada
| | - Jean Longtin
- a Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada.,e Centre de recherche en infectiologie de l'Université Laval, Quebec, Canada
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35
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Yang C, Li P, Su W, Li H, Liu H, Yang G, Xie J, Yi S, Wang J, Cui X, Wu Z, Wang L, Hao R, Jia L, Qiu S, Song H. Polymorphism of CRISPR shows separated natural groupings of Shigella subtypes and evidence of horizontal transfer of CRISPR. RNA Biol 2015; 12:1109-20. [PMID: 26327282 PMCID: PMC4829275 DOI: 10.1080/15476286.2015.1085150] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 07/30/2015] [Accepted: 08/15/2015] [Indexed: 10/23/2022] Open
Abstract
Clustered, regularly interspaced, short palindromic repeats (CRISPR) act as an adaptive RNA-mediated immune mechanism in bacteria. They can also be used for identification and evolutionary studies based on polymorphisms within the CRISPR locus. We amplified and analyzed 6 CRISPR loci from 237 Shigella strains belonging to the 4 species groups, as well as 13 Escherichia coli strains. The CRISPR-associated (cas) gene sequence arrays of these strains were screened and compared. The CRISPR sequences from Shigella were conserved among subtypes, suggesting that CRISPR may represent a new identification tool for the detection and discrimination of Shigella species. Secondary structure analysis showed a different stem-loop structure at the terminal repeat, suggesting a distinct recognition mechanism in the formation of crRNA. In addition, the presence of "self-target" spacers and polymorphisms within CRISPR in Shigella indicated a selective pressure for inhibition of this system, which has the potential to damage "self DNA." Homology analysis of spacers showed that CRISPR might be involved in the regulation of virulence transmission. Phylogenetic analysis based on CRISPR sequences from Shigella and E. coli indicated that although phenotypic properties maintain convergent evolution, the 4 Shigella species do not represent natural groupings. Surprisingly, comparative analysis of Shigella repeats with other species provided new evidence for CRISPR horizontal transfer. Our results suggested that CRISPR analysis is applicable for the detection of Shigella species and for investigation of evolutionary relationships.
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Affiliation(s)
- Chaojie Yang
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Peng Li
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Wenli Su
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Hao Li
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Hongbo Liu
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Guang Yang
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Jing Xie
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Shengjie Yi
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Jian Wang
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Xianyan Cui
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Zhihao Wu
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Ligui Wang
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Rongzhang Hao
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Leili Jia
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Shaofu Qiu
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Hongbin Song
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
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36
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Connor TR, Barker CR, Baker KS, Weill FX, Talukder KA, Smith AM, Baker S, Gouali M, Pham Thanh D, Jahan Azmi I, Dias da Silveira W, Semmler T, Wieler LH, Jenkins C, Cravioto A, Faruque SM, Parkhill J, Wook Kim D, Keddy KH, Thomson NR. Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri. eLife 2015; 4:e07335. [PMID: 26238191 PMCID: PMC4522646 DOI: 10.7554/elife.07335] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 07/04/2015] [Indexed: 12/15/2022] Open
Abstract
Shigella flexneri is the most common cause of bacterial dysentery in low-income countries. Despite this, S. flexneri remains largely unexplored from a genomic standpoint and is still described using a vocabulary based on serotyping reactions developed over half-a-century ago. Here we combine whole genome sequencing with geographical and temporal data to examine the natural history of the species. Our analysis subdivides S. flexneri into seven phylogenetic groups (PGs); each containing two-or-more serotypes and characterised by distinct virulence gene complement and geographic range. Within the S. flexneri PGs we identify geographically restricted sub-lineages that appear to have persistently colonised regions for many decades to over 100 years. Although we found abundant evidence of antimicrobial resistance (AMR) determinant acquisition, our dataset shows no evidence of subsequent intercontinental spread of antimicrobial resistant strains. The pattern of colonisation and AMR gene acquisition suggest that S. flexneri has a distinct life-cycle involving local persistence.
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Affiliation(s)
- Thomas R Connor
- Cardiff School of Biosciences, Cardiff, United Kingdom
- Pathogen Genomics, Wellcome Trust Sanger Centre, Cambridge, United Kingdom
| | | | - Kate S Baker
- Pathogen Genomics, Wellcome Trust Sanger Centre, Cambridge, United Kingdom
| | | | - Kaisar Ali Talukder
- Centre for Food and Water Borne Diseases, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Anthony M Smith
- Centre for Enteric Diseases, National Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephen Baker
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Malika Gouali
- Unité des Bactéries Pathogènes Entériques, Institut Pasteur, Paris, France
| | - Duy Pham Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ishrat Jahan Azmi
- Centre for Food and Water Borne Diseases, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Wanderley Dias da Silveira
- Department of Genetics, Evolution, and Bioagents, Institute of Biology, University of Campinas, São Paulo, Brazil
| | - Torsten Semmler
- Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie University, Berlin, Germany
- Robert Koch Institute, Berlin, Germany
| | - Lothar H Wieler
- Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie University, Berlin, Germany
- Robert Koch Institute, Berlin, Germany
| | - Claire Jenkins
- Gastrointestinal Bacteria Reference Unit, Public Health England, London, United Kingdom
| | | | - Shah M Faruque
- Centre for Food and Water Borne Diseases, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Julian Parkhill
- Pathogen Genomics, Wellcome Trust Sanger Centre, Cambridge, United Kingdom
| | - Dong Wook Kim
- Department of Pharmacy, School of Pharmacy, Hanyang University, Ansan, Republic of Korea
| | - Karen H Keddy
- Centre for Enteric Diseases, National Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicholas R Thomson
- Pathogen Genomics, Wellcome Trust Sanger Centre, Cambridge, United Kingdom
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
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37
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Gray MD, Lacher DW, Leonard SR, Abbott J, Zhao S, Lampel KA, Prothery E, Gouali M, Weill FX, Maurelli AT. Prevalence of Shiga toxin-producing Shigella species isolated from French travellers returning from the Caribbean: an emerging pathogen with international implications. Clin Microbiol Infect 2015; 21:765.e9-765.e14. [PMID: 25980352 DOI: 10.1016/j.cmi.2015.05.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 05/01/2015] [Accepted: 05/02/2015] [Indexed: 11/28/2022]
Abstract
Shiga toxins (Stxs) are potent cytotoxins that inhibit host cell protein synthesis, leading to cell death. Classically, these toxins are associated with intestinal infections due to Stx-producing Escherichia coli or Shigella dysenteriae serotype 1, and infections with these strains can lead to haemolytic-uraemic syndrome. Over the past decade, there has been increasing recognition that Stx is produced by additional Shigella species. We recently reported the presence and expression of stx genes in Shigella flexneri 2a clinical isolates. The toxin genes were carried by a new stx-encoding bacteriophage, and infection with these strains correlated with recent travel to Haiti or the Dominican Republic. In this study, we further explored the epidemiological link to this region by utilizing the French National Reference Centre for Escherichia coli, Shigella and Salmonella collection to survey the frequency of Stx-producing Shigella species isolated from French travellers returning from the Caribbean. Approximately 21% of the isolates tested were found to encode and produce Stx. These isolates included strains of S. flexneri 2a, S. flexneri Y, and S. dysenteriae 4. All of the travellers who were infected with Stx-producing Shigella had recently travelled to Haiti, the Dominican Republic, or French Guiana. Furthermore, whole genome sequencing showed that the toxin genes were encoded by a prophage that was highly identical to the phage that we identified in our previous study. These findings demonstrate that this new stx-encoding prophage is circulating within that geographical area, has spread to other continents, and is capable of spreading to multiple Shigella serogroups.
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Affiliation(s)
- M D Gray
- Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - D W Lacher
- US Food and Drug Administration, Laurel, MD, USA
| | - S R Leonard
- US Food and Drug Administration, Laurel, MD, USA
| | - J Abbott
- US Food and Drug Administration, Laurel, MD, USA
| | - S Zhao
- US Food and Drug Administration, Laurel, MD, USA
| | - K A Lampel
- US Food and Drug Administration, Laurel, MD, USA
| | - E Prothery
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, France
| | - M Gouali
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, France
| | - F-X Weill
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, France
| | - A T Maurelli
- Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
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