1
|
de Almeida OGG, Bertozzi BG, de Oliveira Rocha L, von Hertwig AM, Arroyo DMD, de Martinis ECP, Nascimento MS. Genomic-wide analysis of Salmonella enterica strains isolated from peanuts in Brazil. Int J Food Microbiol 2024; 420:110767. [PMID: 38820989 DOI: 10.1016/j.ijfoodmicro.2024.110767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 05/25/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
Peanut-based products have been associated with Salmonella foodborne outbreaks and/or recalls worldwide. The ability of Salmonella to persist for a long time in a low moisture environment can contribute to this kind of contamination. The objective of this study was to analyse the genome of five S. enterica enterica strains isolated from the peanut supply chain in Brazil, as well as to identify genetic determinants for survival under desiccation and validate these findings by phenotypic test of desiccation stress. The strains were in silico serotyped using the platform SeqSero2 as Miami (M2851), Javiana (M2973), Oranienburg (M2976), Muenster (M624), and Glostrup/Chomedey (M7864); with phylogenomic analysis support. Based on Multilocus Sequence Typing (MLST) the strains were assigned to STs 140, 1674, 321, 174, and 2519. In addition, eight pathogenicity islands were found in all the genomes using the SPIFinder 2.0 (SPI-1, SPI-2, SPI-3, SPI-5, SPI-9, SPI-13, SPI-14). The absence of a SPI-4 may indicate a loss of this island in the surveyed genomes. For the pangenomic analysis, 49 S. enterica genomes were input into the Roary pipeline. The majority of the stress related genes were considered as soft-core genes and were located on the chromosome. A desiccation stress phenotypic test was performed in trypticase soy broth (TSB) with four different water activity (aw) values. M2976 and M7864, both isolated from the peanut samples with the lowest aw, showed the highest OD570nm in TSB aw 0.964 and were statistically different (p < 0.05) from the strain isolated from the peanut sample with the highest aw (0.997). In conclusion, genome analyses have revealed signatures of desiccation adaptation in Salmonella strains, but phenotypic analyses suggested the environment influences the adaptive ability of Salmonella to overcome desiccation stress.
Collapse
Affiliation(s)
- Otávio Guilherme Gonçalves de Almeida
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas - Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café s/n, Ribeirão Preto 14040-903, Brazil
| | - Bruno Gerfi Bertozzi
- Departamento de Ciência e Nutrição de Alimentos, Faculdade de Engenharia de Alimentos, Universidade Estadual de Campinas, Rua Monteiro Lobato, 80, Campinas 13083-862, Brazil
| | - Liliana de Oliveira Rocha
- Departamento de Ciência e Nutrição de Alimentos, Faculdade de Engenharia de Alimentos, Universidade Estadual de Campinas, Rua Monteiro Lobato, 80, Campinas 13083-862, Brazil
| | - Aline Morgan von Hertwig
- Departamento de Engenharia e Tecnologia de Alimentos, Faculdade de Engenharia de Alimentos, Universidade Estadual de Campinas, Rua Monteiro Lobato, 80, Campinas 13083-862, Brazil
| | - Diana Mara Dias Arroyo
- Departamento de Engenharia e Tecnologia de Alimentos, Faculdade de Engenharia de Alimentos, Universidade Estadual de Campinas, Rua Monteiro Lobato, 80, Campinas 13083-862, Brazil
| | - Elaine Cristina Pereira de Martinis
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas - Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café s/n, Ribeirão Preto 14040-903, Brazil
| | - Maristela Silva Nascimento
- Departamento de Engenharia e Tecnologia de Alimentos, Faculdade de Engenharia de Alimentos, Universidade Estadual de Campinas, Rua Monteiro Lobato, 80, Campinas 13083-862, Brazil.
| |
Collapse
|
2
|
Trees E, Carleton HA, Folster JP, Gieraltowski L, Hise K, Leeper M, Nguyen TA, Poates A, Sabol A, Tagg KA, Tolar B, Vasser M, Webb HE, Wise M, Lindsey RL. Genetic Diversity in Salmonella enterica in Outbreaks of Foodborne and Zoonotic Origin in the USA in 2006-2017. Microorganisms 2024; 12:1563. [PMID: 39203405 PMCID: PMC11356229 DOI: 10.3390/microorganisms12081563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 07/23/2024] [Accepted: 07/26/2024] [Indexed: 09/03/2024] Open
Abstract
Whole genome sequencing is replacing traditional laboratory surveillance methods as the primary tool to track and characterize clusters and outbreaks of the foodborne and zoonotic pathogen Salmonella enterica (S. enterica). In this study, 438 S. enterica isolates representing 35 serovars and 13 broad vehicle categories from one hundred epidemiologically confirmed outbreaks were evaluated for genetic variation to develop epidemiologically relevant interpretation guidelines for Salmonella disease cluster detection. The Illumina sequences were analyzed by core genome multi-locus sequence typing (cgMLST) and screened for antimicrobial resistance (AR) determinants and plasmids. Ninety-three of the one hundred outbreaks exhibited a close allele range (less than 10 allele differences with a subset closer than 5). The remaining seven outbreaks showed increased variation, of which three were considered polyclonal. A total of 16 and 28 outbreaks, respectively, showed variations in the AR and plasmid profiles. The serovars Newport and I 4,[5],12:i:-, as well as the zoonotic and poultry product vehicles, were overrepresented among the outbreaks, showing increased variation. A close allele range in cgMLST profiles can be considered a reliable proxy for epidemiological relatedness for the vast majority of S. enterica outbreak investigations. Variations associated with mobile elements happen relatively frequently during outbreaks and could be reflective of changing selective pressures.
Collapse
Affiliation(s)
- Eija Trees
- Association of Public Health Laboratories, Bethesda, MD 20814, USA
| | | | - Jason P. Folster
- Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | | | - Kelley Hise
- Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Molly Leeper
- Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Thai-An Nguyen
- Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Angela Poates
- Association of Public Health Laboratories, Bethesda, MD 20814, USA
| | - Ashley Sabol
- Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Kaitlin A. Tagg
- Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Beth Tolar
- Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Michael Vasser
- Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Hattie E. Webb
- Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Matthew Wise
- Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | | |
Collapse
|
3
|
Response to Questions Posed by the Food Safety and Inspection Service: Enhancing Salmonella Control in Poultry Products. J Food Prot 2024; 87:100168. [PMID: 37939849 DOI: 10.1016/j.jfp.2023.100168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 11/10/2023]
|
4
|
Muzyukina P, Soutourina O. CRISPR genotyping methods: Tracing the evolution from spoligotyping to machine learning. Biochimie 2024; 217:66-73. [PMID: 37506757 DOI: 10.1016/j.biochi.2023.07.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/16/2023] [Accepted: 07/24/2023] [Indexed: 07/30/2023]
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems provide prokaryotes with adaptive immunity defenses against foreign genetic invaders. The identification of CRISPR-Cas function is among the most impactful discoveries of recent decades that have shaped the development of genome editing in various organisms paving the way for a plethora of promising applications in biotechnology and health. Even before the discovery of CRISPR-Cas biological role, the particular structure of CRISPR loci has been explored for epidemiological genotyping of bacterial pathogens. CRISPR-Cas loci are arranged in CRISPR arrays of mostly identical direct repeats intercalated with invader-derived spacers and an operon of cas genes encoding the Cas protein components. Each small CRISPR RNA (crRNA) encoded within the CRISPR array constitutes a key functional unit of this RNA-based CRISPR-Cas defense system guiding the Cas effector proteins toward the foreign nucleic acids for their destruction. The information acquired from prior invader encounters and stored within CRISPR arrays turns out to be extremely valuable in tracing the microevolution and epidemiology of major bacterial pathogens. We review here the history of CRISPR-based typing strategies highlighting the first PCR-based methods that have set the stage for recent developments of high-throughput sequencing and machine learning-based approaches. A great amount of whole genome sequencing and metagenomic data accumulated in recent years opens up new avenues for combining experimental and computational approaches of high-resolution CRISPR-based typing.
Collapse
Affiliation(s)
- P Muzyukina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - O Soutourina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France; Institut Universitaire de France (IUF), Paris, France.
| |
Collapse
|
5
|
Sanderson H, White AP. Methods for Genomic Epidemiology of Bacterial Pathogens: Example Salmonella. Methods Mol Biol 2024; 2813:19-37. [PMID: 38888768 DOI: 10.1007/978-1-0716-3890-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Genomics has revolutionized how we characterize and monitor infectious diseases for public health. The surveillance and characterization of Salmonella has improved drastically within the past decade. In this chapter, we discuss the prerequisites for good bacterial genomics studies and make note of advantages and disadvantages of this research approach. We discuss methods for outbreak detection and the evolutionary and epidemiological characterization of Salmonella spp. We provide an outline for determining the sequence type and serotype of isolates, building a core genome phylogenetic tree, and detecting antimicrobial resistance genes, virulence factors, and mobile genetic elements. These methods can be used to study other pathogenic bacterial species.
Collapse
Affiliation(s)
- Haley Sanderson
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
- Biological Informatics Center of Excellence, Agriculture and Agri-Food Canada, Saskatoon, Canada
| | - Aaron P White
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada.
| |
Collapse
|
6
|
Richards AK, Kue S, Norris CG, Shariat NW. Genomic and phenotypic characterization of Salmonella enterica serovar Kentucky. Microb Genom 2023; 9:001089. [PMID: 37750759 PMCID: PMC10569734 DOI: 10.1099/mgen.0.001089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 07/27/2023] [Indexed: 09/27/2023] Open
Abstract
Non-typhoidal Salmonella are extremely diverse and different serovars can exhibit varied phenotypes, including host adaptation and the ability to cause clinical illness in animals and humans. In the USA, Salmonella enterica serovar Kentucky is infrequently found to cause human illness, despite being the top serovar isolated from broiler chickens. Conversely, in Europe, this serovar falls in the top 10 serovars linked to human salmonellosis. Serovar Kentucky is polyphyletic and has two lineages, Kentucky-I and Kentucky-II; isolates belonging to Kentucky-I are frequently isolated from poultry in the USA, while Kentucky-II isolates tend to be associated with human illness. In this study, we analysed whole-genome sequences and associated metadata deposited in public databases between 2017 and 2021 by federal agencies to determine serovar Kentucky incidence across different animal and human sources. Of 5151 genomes, 90.3 % were from isolates that came from broilers, while 5.9 % were from humans and 3.0 % were from cattle. Kentucky-I isolates were associated with broilers, while isolates belonging to Kentucky-II and a new lineage, Kentucky-III, were more commonly associated with cattle and humans. Very few serovar Kentucky isolates were associated with turkey and swine sources. Phylogenetic analyses showed that Kentucky-III genomes were more closely related to Kentucky-I, and this was confirmed by CRISPR-typing and multilocus sequence typing (MLST). In a macrophage assay, serovar Kentucky-II isolates were able to replicate over eight times better than Kentucky-I isolates. Analysis of virulence factors showed unique patterns across these three groups, and these differences may be linked to their association with different hosts.
Collapse
Affiliation(s)
- Amber K. Richards
- Department of Population Health, University of Georgia, Athens, GA, USA
| | - Song Kue
- Department of Population Health, University of Georgia, Athens, GA, USA
| | - Connor G. Norris
- Department of Population Health, University of Georgia, Athens, GA, USA
| | - Nikki W. Shariat
- Department of Population Health, University of Georgia, Athens, GA, USA
- Center for Food Safety, University of Georgia, Griffin, GA, USA
| |
Collapse
|
7
|
Sánchez-Serrano A, Mejía L, Camaró ML, Ortolá-Malvar S, Llácer-Luna M, García-González N, González-Candelas F. Genomic Surveillance of Salmonella from the Comunitat Valenciana (Spain). Antibiotics (Basel) 2023; 12:antibiotics12050883. [PMID: 37237786 DOI: 10.3390/antibiotics12050883] [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: 04/08/2023] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
Salmonella enterica subspecies enterica is one of the most important foodborne pathogens and the causative agent of salmonellosis, which affects both humans and animals producing numerous infections every year. The study and understanding of its epidemiology are key to monitoring and controlling these bacteria. With the development of whole-genome sequencing (WGS) technologies, surveillance based on traditional serotyping and phenotypic tests of resistance is being replaced by genomic surveillance. To introduce WGS as a routine methodology for the surveillance of food-borne Salmonella in the region, we applied this technology to analyze a set of 141 S. enterica isolates obtained from various food sources between 2010 and 2017 in the Comunitat Valenciana (Spain). For this, we performed an evaluation of the most relevant Salmonella typing methods, serotyping and sequence typing, using both traditional and in silico approaches. We extended the use of WGS to detect antimicrobial resistance determinants and predicted minimum inhibitory concentrations (MICs). Finally, to understand possible contaminant sources in this region and their relationship to antimicrobial resistance (AMR), we performed cluster detection combining single-nucleotide polymorphism (SNP) pairwise distances and phylogenetic and epidemiological data. The results of in silico serotyping with WGS data were highly congruent with those of serological analyses (98.5% concordance). Multi-locus sequence typing (MLST) profiles obtained with WGS information were also highly congruent with the sequence type (ST) assignment based on Sanger sequencing (91.9% coincidence). In silico identification of antimicrobial resistance determinants and minimum inhibitory concentrations revealed a high number of resistance genes and possible resistant isolates. A combined phylogenetic and epidemiological analysis with complete genome sequences revealed relationships among isolates indicative of possible common sources for isolates with separate sampling in time and space that had not been detected from epidemiological information. As a result, we demonstrate the usefulness of WGS and in silico methods to obtain an improved characterization of S. enterica enterica isolates, allowing better surveillance of the pathogen in food products and in potential environmental and clinical samples of related interest.
Collapse
Affiliation(s)
- Andrea Sánchez-Serrano
- Joint Research Unit "Infection and Public Health", FISABIO-University of Valencia, 46020 Valencia, Spain
| | - Lorena Mejía
- Joint Research Unit "Infection and Public Health", FISABIO-University of Valencia, 46020 Valencia, Spain
- Institute for Integrative Systems Biology (I2SysBio), CSIC-University of Valencia, 46980 Valencia, Spain
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | | | | | | | - Neris García-González
- Joint Research Unit "Infection and Public Health", FISABIO-University of Valencia, 46020 Valencia, Spain
- Institute for Integrative Systems Biology (I2SysBio), CSIC-University of Valencia, 46980 Valencia, Spain
| | - Fernando González-Candelas
- Joint Research Unit "Infection and Public Health", FISABIO-University of Valencia, 46020 Valencia, Spain
- Institute for Integrative Systems Biology (I2SysBio), CSIC-University of Valencia, 46980 Valencia, Spain
- CIBER in Epidemiology and Public Health, 28029 Madrid, Spain
| |
Collapse
|
8
|
Kumar Panda R, Darshana Patra S, Kumar Mohakud N, Ranjan Sahu B, Ghosh M, Misra N, Suar M. Draft genome of clinical isolate Salmonella enterica Typhimurium ms204 from Odisha, India, reveals multi drug resistance and decreased virulent gene expression. Gene 2023; 863:147248. [PMID: 36738898 DOI: 10.1016/j.gene.2023.147248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 01/16/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023]
Abstract
Salmonellosis, a food-borne illnesses caused by enteropathogenic bacterium Salmonella spp., is a continuous concern in both developed and developing countries. This study was carried out to perform an in-depth examination of an MDR Salmonella strain isolated from gastroenteritis patients in Odisha, India, in order to understand the genomic architecture, distribution of pathogenic island regions, and virulence factor diversity. Fecal samples were obtained from individuals with acute gastroenteritis and further subjected to panel of biochemical tests. The IlluminaHiSeq X sequencer system was used to generate whole-genome sequencing. The draft genome was submitted to gene prediction and annotation using RAST annotation system. Pathogenicity Island database and bioinformatics pipeline were used to find Salmonella pathogenicity islands (SPI) from the built scaffold. The gene expression in SPI1 and SPI2 encoded regions was investigated using qRT-PCR. The taxonomic position of Salmonella enterica subsp. enterica serovar Typhimurium was validated by serotype analysis and 16S rRNA based phylogenetic analysis. The de-novo genome assembly showed total length of 5,034,110 bp and produced 37 contigs. There are nine prophage areas, comprising of 12 regions and scaffold 8 contained a single plasmid, IncFIB. The isolate contains six known SPI genes content which was shown to be largely conserved from SPI1 to SPI2. We identified the sit ABCD cluster regulatory cascade and acquired antibiotic resistance genes in S. enterica Typhimurium ms204. Further research may aid in the correct diagnosis and monitoring of MDR Salmonella strains with a variety of physiological activities.
Collapse
Affiliation(s)
| | | | - Nirmal Kumar Mohakud
- Kalinga Institute of Medical Sciences (KIMS), KIIT University, Bhubaneswar 751024, India
| | - Bikash Ranjan Sahu
- Department of Zoology, Centurion University of Technology and Management, India
| | - Mrinmoy Ghosh
- KIIT-Technology Business Incubator (KIIT-TBI), KIIT University, Bhubaneswar 751024, India
| | - Namrata Misra
- KIIT-Technology Business Incubator (KIIT-TBI), KIIT University, Bhubaneswar 751024, India
| | - Mrutyunjay Suar
- School of Biotechnology, KIIT University, Bhubaneswar 751024, India; KIIT-Technology Business Incubator (KIIT-TBI), KIIT University, Bhubaneswar 751024, India.
| |
Collapse
|
9
|
Kushwaha SK, Kumar AA, Gupta H, Marathe SA. The Phylogenetic Study of the CRISPR-Cas System in Enterobacteriaceae. Curr Microbiol 2023; 80:196. [PMID: 37118221 DOI: 10.1007/s00284-023-03298-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 04/07/2023] [Indexed: 04/30/2023]
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated (Cas) system is a bacterial and archaeal adaptive immune system undergoing rapid multifaceted evolution. This evolution plausibly occurs due to the genetic exchanges of complete loci or individual entities. Here, we systematically investigate the evolutionary framework of the CRISPR-Cas system in six Enterobacteriaceae species and its evolutionary association with housekeeping genes as determined by the gyrB phenogram. The strains show high variability in the cas3 gene and the CRISPR1 locus among the closely related Enterobacteriaceae species, hinting at a series of genetic exchanges. The CRISPR leader is conserved, especially toward the distal end, and could be a core region of the leader. The spacers are conserved within the strains of most species, while some strains show unique sets of spacers. However, inter-species spacer conservation was rarely observed. For a considerable proportion of these spacers, protospacer sources were not detected. These results advance our understanding of the dynamics of the CRISPR-Cas system; however, the biological functions are yet to be characterised.
Collapse
Affiliation(s)
- Simran Krishnakant Kushwaha
- Department of Biological Sciences, Faculty Division-III, Birla Institute of Technology & Science, 3277-B, Pilani Campus, Pilani, Rajasthan, 333031, India
| | - Aryahi A Kumar
- Department of Biological Sciences, Faculty Division-III, Birla Institute of Technology & Science, 3277-B, Pilani Campus, Pilani, Rajasthan, 333031, India
| | - Hardik Gupta
- Department of Biological Sciences, Faculty Division-III, Birla Institute of Technology & Science, 3277-B, Pilani Campus, Pilani, Rajasthan, 333031, India
| | - Sandhya Amol Marathe
- Department of Biological Sciences, Faculty Division-III, Birla Institute of Technology & Science, 3277-B, Pilani Campus, Pilani, Rajasthan, 333031, India.
| |
Collapse
|
10
|
Liu CC, Hsiao WWL. Large-scale comparative genomics to refine the organization of the global Salmonella enterica population structure. Microb Genom 2022; 8:mgen000906. [PMID: 36748524 PMCID: PMC9837569 DOI: 10.1099/mgen.0.000906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The White-Kauffmann-Le Minor (WKL) scheme is the most widely used Salmonella typing scheme for reporting the disease prevalence of the enteric pathogen. With the advent of whole-genome sequencing (WGS), in silico methods have increasingly replaced traditional serotyping due to reproducibility, speed and coverage. However, despite integrating genomic-based typing by in silico serotyping tools such as SISTR, in silico serotyping in certain contexts remains ambiguous and insufficiently informative. Specifically, in silico serotyping does not attempt to resolve polyphyly. Furthermore, in spite of the widespread acknowledgement of polyphyly from genomic studies, the prevalence of polyphyletic serovars is not well characterized. Here, we applied a genomics approach to acquire the necessary resolution to classify genetically discordant serovars and propose an alternative typing scheme that consistently reflect natural Salmonella populations. By accessing the unprecedented volume of bacterial genomic data publicly available in GenomeTrakr and PubMLST databases (>180 000 genomes representing 723 serovars), we characterized the global Salmonella population structure and systematically identified putative non-monophyletic serovars. The proportion of putative non-monophyletic serovars was estimated higher than previous reports, reinforcing the inability of antigenic determinants to depict the complexity of Salmonella evolutionary history. We explored the extent of genetic diversity masked by serotyping labels and found significant intra-serovar molecular differences across many clinically important serovars. To avoid false discovery due to incorrect in silico serotyping calls, we cross-referenced reported serovar labels and concluded a low error rate in in silico serotyping. The combined application of clustering statistics and genome-wide association methods demonstrated effective characterization of stable bacterial populations and explained functional differences. The collective methods adopted in our study have practical values in establishing genomic-based typing nomenclatures for an entire microbial species or closely related subpopulations. Ultimately, we foresee an improved typing scheme to be a hybrid that integrates both genomic and antigenic information such that the resolution from WGS is leveraged to improve the precision of subpopulation classification while preserving the common names defined by the WKL scheme.
Collapse
Affiliation(s)
- Chao Chun Liu
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - William W. L. Hsiao
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada,Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada,*Correspondence: William W. L. Hsiao,
| |
Collapse
|
11
|
Achtman M, Zhou Z, Charlesworth J, Baxter L. EnteroBase: hierarchical clustering of 100 000s of bacterial genomes into species/subspecies and populations. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210240. [PMID: 35989609 PMCID: PMC9393565 DOI: 10.1098/rstb.2021.0240] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 03/07/2022] [Indexed: 12/14/2022] Open
Abstract
The definition of bacterial species is traditionally a taxonomic issue while bacterial populations are identified by population genetics. These assignments are species specific, and depend on the practitioner. Legacy multilocus sequence typing is commonly used to identify sequence types (STs) and clusters (ST Complexes). However, these approaches are not adequate for the millions of genomic sequences from bacterial pathogens that have been generated since 2012. EnteroBase (http://enterobase.warwick.ac.uk) automatically clusters core genome MLST allelic profiles into hierarchical clusters (HierCC) after assembling annotated draft genomes from short-read sequences. HierCC clusters span core sequence diversity from the species level down to individual transmission chains. Here we evaluate HierCC's ability to correctly assign 100 000s of genomes to the species/subspecies and population levels for Salmonella, Escherichia, Clostridoides, Yersinia, Vibrio and Streptococcus. HierCC assignments were more consistent with maximum-likelihood super-trees of core SNPs or presence/absence of accessory genes than classical taxonomic assignments or 95% ANI. However, neither HierCC nor ANI were uniformly consistent with classical taxonomy of Streptococcus. HierCC was also consistent with legacy eBGs/ST Complexes in Salmonella or Escherichia and with O serogroups in Salmonella. Thus, EnteroBase HierCC supports the automated identification of and assignment to species/subspecies and populations for multiple genera. This article is part of a discussion meeting issue 'Genomic population structures of microbial pathogens'.
Collapse
|
12
|
Cherchame E, Ilango G, Noël V, Cadel-Six S. Polyphyly in widespread Salmonella enterica serovars and using genomic proximity to choose the best reference genome for bioinformatics analyses. Front Public Health 2022; 10:963188. [PMID: 36159272 PMCID: PMC9493441 DOI: 10.3389/fpubh.2022.963188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 08/02/2022] [Indexed: 01/24/2023] Open
Abstract
Salmonella is the most common cause of gastroenteritis in the world. Over the past 5 years, whole-genome analysis has led to the high-resolution characterization of clinical and foodborne Salmonella responsible for typhoid fever, foodborne illness or contamination of the agro-food chain. Whole-genome analyses are simplified by the availability of high-quality, complete genomes for mapping analysis and for calculating the pairwise distance between genomes, but unfortunately some difficulties may still remain. For some serovars, the complete genome is not available, or some serovars are polyphyletic and knowing the serovar alone is not sufficient for choosing the most appropriate reference genome. For these serovars, it is essential to identify the genetically closest complete genome to be able to carry out precise genome analyses. In this study, we explored the genomic proximity of 650 genomes of the 58 Salmonella enterica subsp. enterica serovars most frequently isolated in humans and from the food chain in the United States (US) and in Europe (EU), with a special focus on France. For each serovar, to take into account their genomic diversity, we included all the multilocus sequence type (MLST) profiles represented in EnteroBase with 10 or more genomes (on 19 July 2021). A phylogenetic analysis using both core- and pan-genome approaches was carried out to identify the genomic proximity of all the Salmonella studied and 20 polyphyletic serovars that have not yet been described in the literature. This study determined the genetic proximity between all 58 serovars studied and revealed polyphyletic serovars, their genomic lineages and MLST profiles. Finally, we enhanced the open-access databases with 73 new genomes and produced a list of high-quality complete reference genomes for 48 S. enterica subsp. enterica serovars among the most isolated in the US, EU, and France.
Collapse
|
13
|
Multilayered Networks of SalmoNet2 Enable Strain Comparisons of the Salmonella Genus on a Molecular Level. mSystems 2022; 7:e0149321. [PMID: 35913188 PMCID: PMC9426430 DOI: 10.1128/msystems.01493-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Serovars of the genus Salmonella primarily evolved as gastrointestinal pathogens in a wide range of hosts. Some serotypes later evolved further, adopting a more invasive lifestyle in a narrower host range associated with systemic infections. A system-level knowledge of these pathogens could identify the complex adaptations associated with the evolution of serovars with distinct pathogenicity, host range, and risk to human health. This promises to aid the design of interventions and serve as a knowledge base in the Salmonella research community. Here, we present SalmoNet2, a major update to SalmoNet1, the first multilayered interaction resource for Salmonella strains, containing protein-protein, transcriptional regulatory, and enzyme-enzyme interactions. The new version extends the number of Salmonella networks from 11 to 20. We now include a strain from the second species in the Salmonella genus, a strain from the Salmonella enterica subspecies arizonae and additional strains of importance from the subspecies enterica, including S. Typhimurium strain D23580, an epidemic multidrug-resistant strain associated with invasive nontyphoidal salmonellosis (iNTS). The database now uses strain specific metabolic models instead of a generalized model to highlight differences between strains. The update has increased the coverage of high-quality protein-protein interactions, and enhanced interoperability with other computational resources by adopting standardized formats. The resource website has been updated with tutorials to help researchers analyze their Salmonella data using molecular interaction networks from SalmoNet2. SalmoNet2 is accessible at http://salmonet.org/. IMPORTANCE Multilayered network databases collate interaction information from multiple sources, and are powerful both as a knowledge base and subject of analysis. Here, we present SalmoNet2, an integrated network resource containing protein-protein, transcriptional regulatory, and metabolic interactions for 20 Salmonella strains. Key improvements to the update include expanding the number of strains, strain-specific metabolic networks, an increase in high-quality protein-protein interactions, community standard computational formats to help interoperability, and online tutorials to help users analyze their data using SalmoNet2.
Collapse
|
14
|
Tate H, Hsu CH, Chen JC, Han J, Foley SL, Folster JP, Francois Watkins LK, Reynolds J, Tillman GE, Nyirabahizi E, Zhao S. Genomic Diversity, Antimicrobial Resistance, and Virulence Gene Profiles of Salmonella Serovar Kentucky Isolated from Humans, Food, and Animal Ceca Content Sources in the United States. Foodborne Pathog Dis 2022; 19:509-521. [PMID: 35960531 DOI: 10.1089/fpd.2022.0005] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Salmonella serovar Kentucky is frequently isolated from chickens and dairy cattle, but recovery from humans is comparatively low based on the U.S. National Antimicrobial Resistance Monitoring System (NARMS) reports. We aimed to better describe the genetic diversity, antimicrobial resistance, and virulence determinants of Salmonella Kentucky isolates from humans, food animal ceca, retail meat and poultry products, imported foods and food products, and other samples. We analyzed the genomes of 774 Salmonella Kentucky isolates and found that 63% (54/86) of human isolates were sequence type (ST)198, 33% (29/86) were ST152, and 3.5% (3/86) were ST314. Ninety-one percent (570/629) of cecal isolates and retail meat and poultry isolates were ST152 or ST152-like (one allele difference), and 9.2% (58/629) were ST198. Isolates from imported food were mostly ST198 (60%, 22/37) and ST314 (29.7%, 11/37). ST198 isolates clustered into two main lineages. Clade ST198.2 comprised almost entirely isolates from humans and imported foods, all containing triple mutations in the quinolone resistance-determining region (QRDR) that confer resistance to fluoroquinolones. Clade ST198.1 contained isolates from humans, ceca, retail meat and poultry products, and imported foods that largely lacked QRDR mutations. ST152 isolates from cattle had a lineage (Clade 2) distinct from ST152 isolates from chicken (Clade 4), and half of ST152 human isolates clustered within two other clades (Clades 1 and 3), largely distinct from Clades 2 and 4. Although clinical illness associated with Salmonella Kentucky is low, ST198 appears to account for most human infections in the Unites States but is uncommon among ceca of domestic food animals and retail meat and poultry products. These findings, combined with human exposure data, suggest that fluoroquinolone-resistant ST198 infections may be linked to the consumption of food products that are imported or consumed while traveling. We also found unique differences in the composition of virulence genes and antimicrobial resistance genes among the clades, which may provide clues to the host specificity and pathogenicity of Salmonella Kentucky lineages.
Collapse
Affiliation(s)
- Heather Tate
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Chih-Hao Hsu
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Jessica C Chen
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jing Han
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Steven L Foley
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Jason P Folster
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Louise K Francois Watkins
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jared Reynolds
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Glenn E Tillman
- Food Safety and Inspection Service, U.S. Department of Agriculture, Athens, Georgia, USA
| | - Epiphanie Nyirabahizi
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Shaohua Zhao
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
| |
Collapse
|
15
|
Pightling AW, Rand H, Pettengill J. Using Evolutionary Analyses to Refine Whole-Genome Sequence Match Criteria. Front Microbiol 2022; 13:797997. [PMID: 35875579 PMCID: PMC9301902 DOI: 10.3389/fmicb.2022.797997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Whole-genome sequence databases continue to grow. Collection times between samples are also growing, providing both a challenge for comparing recently collected sequence data to historical samples and an opportunity for evolutionary analyses that can be used to refine match criteria. We measured evolutionary rates for 22 Salmonella enterica serotypes. Based upon these measurements, we propose using an evolutionary rate of 1.97 single-nucleotide polymorphisms (SNPs) per year when determining whether genome sequences match.
Collapse
Affiliation(s)
- Arthur W Pightling
- Biostatistics and Bioinformatics Staff, Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
| | - Hugh Rand
- Biostatistics and Bioinformatics Staff, Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
| | - James Pettengill
- Biostatistics and Bioinformatics Staff, Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
| |
Collapse
|
16
|
Mohakud NK, Panda RK, Patra SD, Sahu BR, Ghosh M, Kushwaha GS, Misra N, Suar M. Genome analysis and virulence gene expression profile of a multi drug resistant Salmonella enterica serovar Typhimurium ms202. Gut Pathog 2022; 14:28. [PMID: 35765034 PMCID: PMC9237969 DOI: 10.1186/s13099-022-00498-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 05/19/2022] [Indexed: 12/01/2022] Open
Abstract
Background In India, multi-drug resistance in Salmonella enterica serovar Typhimurium poses a significant health threat. Indeed, S. Typhimurium has remained unknown for a large portion of its genome associated with various physiological functions including mechanism of drug resistance and virulence. The whole-genome sequence of a Salmonella strain obtained from feces of a patient with gastroenteritis in Odisha, India, was analyzed for understanding the disease association and underlying virulence mechanisms. Results The de novo assembly yielded 17 contigs and showed 99.9% similarity to S. enterica sub sp enterica strain LT2 and S. enteric subsp salamae strain DSM 9220. S. Typhimurium ms202 strain constitutes six known Salmonella pathogenicity islands and nine different phages. The comparative interpretation of pathogenic islands displayed the genes contained in SPI-1 and SPI-2 to be highly conserved. We identified sit ABCD cluster regulatory cascade in SPI-1. Multiple antimicrobial resistance genes were identified that directly implies antibiotic-resistant phenotype. Notably, seven unique genes were identified as "acquired antibiotic resistance". These data suggest that virulence in S. enterica Typhimurium ms202 is associated with SPI-1 and SPI-2. Further, we found several virulent genes encoding SPI regions belonging to type III secretion systems (T3SS) of bacteria were significantly upregulated in ms202 compared to control LT2. Moreover, all these genes were significantly downregulated in S. enterica Typhimurium ms202 as compared to control LT2 on adding Mn2+ exogenously. Conclusions Our study raises a vital concern about the potential diffusion of a novel multi-drug resistant S. enterica Typhimurium ms202. It justifies this clinical pathogen to demonstrate a higher degree survival due to higher expression of virulent genes and enhanced ability of metallic ion acquisition. Supplementary Information The online version contains supplementary material available at 10.1186/s13099-022-00498-w.
Collapse
Affiliation(s)
- Nirmal Kumar Mohakud
- School of Biotechnology, KIIT University, Bhubaneswar, 751024, India.,Kalinga Institute of Medical Sciences (KIMS), KIIT University, Bhubaneswar, 751024, India
| | | | | | | | - Mrinmoy Ghosh
- KIIT-Technology Business Incubator (KIIT-TBI), KIIT University, Bhubaneswar, 751024, India.
| | - Gajraj Singh Kushwaha
- KIIT-Technology Business Incubator (KIIT-TBI), KIIT University, Bhubaneswar, 751024, India
| | - Namrata Misra
- KIIT-Technology Business Incubator (KIIT-TBI), KIIT University, Bhubaneswar, 751024, India
| | - Mrutyunjay Suar
- School of Biotechnology, KIIT University, Bhubaneswar, 751024, India. .,KIIT-Technology Business Incubator (KIIT-TBI), KIIT University, Bhubaneswar, 751024, India.
| |
Collapse
|
17
|
Gopinath GR, Jang H, Beaubrun JJG, Gangiredla J, Mammel MK, Müller A, Tamber S, Patel IR, Ewing L, Weinstein LM, Wang CZ, Finkelstein S, Negrete F, Muruvanda T, Allard M, Sockett DC, Pagotto F, Tall BD, Stephan R. Phylogenomic Analysis of Salmonella enterica subsp. enterica Serovar Bovismorbificans from Clinical and Food Samples Using Whole Genome Wide Core Genes and kmer Binning Methods to Identify Two Distinct Polyphyletic Genome Pathotypes. Microorganisms 2022; 10:microorganisms10061199. [PMID: 35744717 PMCID: PMC9228720 DOI: 10.3390/microorganisms10061199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 12/04/2022] Open
Abstract
Salmonella enterica subsp. enterica serovar Bovismorbificans has caused multiple outbreaks involving the consumption of produce, hummus, and processed meat products worldwide. To elucidate the intra-serovar genomic structure of S. Bovismorbificans, a core-genome analysis with 2690 loci (based on 150 complete genomes representing Salmonella enterica serovars developed as part of this study) and a k-mer-binning based strategy were carried out on 95 whole genome sequencing (WGS) assemblies from Swiss, Canadian, and USA collections of S. Bovismorbificans strains from foodborne infections. Data mining of a digital DNA tiling array of legacy SARA and SARB strains was conducted to identify near-neighbors of S. Bovismorbificans. The core genome analysis and the k-mer-binning methods identified two polyphyletic clusters, each with emerging evolutionary properties. Four STs (2640, 142, 1499, and 377), which constituted the majority of the publicly available WGS datasets from >260 strains analyzed by k-mer-binning based strategy, contained a conserved core genome backbone with a different evolutionary lineage as compared to strains comprising the other cluster (ST150). In addition, the assortment of genotypic features contributing to pathogenesis and persistence, such as antimicrobial resistance, prophage, plasmid, and virulence factor genes, were assessed to understand the emerging characteristics of this serovar that are relevant clinically and for food safety concerns. The phylogenomic profiling of polyphyletic S. Bovismorbificans in this study corresponds to intra-serovar variations observed in S. Napoli and S. Newport serovars using similar high-resolution genomic profiling approaches and contributes to the understanding of the evolution and sequence divergence of foodborne Salmonellae. These intra-serovar differences may have to be thoroughly understood for the accurate classification of foodborne Salmonella strains needed for the uniform development of future food safety mitigation strategies.
Collapse
Affiliation(s)
- Gopal R. Gopinath
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
- Correspondence: ; Tel.: +1-240-402-3612
| | - Hyein Jang
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
| | - Junia Jean-Gilles Beaubrun
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
- Biological Analysis Division, Public Health Command Europe Laboratory Sciences, Room 102, Bldg 3810, Kirchberg Kaserne, RP 66849 Landstuhl, Germany
| | - Jayanthi Gangiredla
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
| | - Mark K. Mammel
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
| | - Andrea Müller
- Institute for Food Safety and Hygiene, University of Zurich, CH-8057 Zurich, Switzerland; (A.M.); (R.S.)
| | - Sandeep Tamber
- Food Directorate, Bureau of Microbial Hazards/Health Canada, Ottawa, ON K1A 0K9, Canada; (S.T.); (F.P.)
| | - Isha R. Patel
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
| | - Laura Ewing
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
| | - Leah M. Weinstein
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
| | - Caroline Z. Wang
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
| | - Samantha Finkelstein
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
| | - Flavia Negrete
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
| | - Tim Muruvanda
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD 20740, USA; (T.M.); (M.A.)
| | - Marc Allard
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD 20740, USA; (T.M.); (M.A.)
| | - Donald C. Sockett
- Wisconsin Veterinary Diagnostic Laboratory, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Franco Pagotto
- Food Directorate, Bureau of Microbial Hazards/Health Canada, Ottawa, ON K1A 0K9, Canada; (S.T.); (F.P.)
| | - Ben D. Tall
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
| | - Roger Stephan
- Institute for Food Safety and Hygiene, University of Zurich, CH-8057 Zurich, Switzerland; (A.M.); (R.S.)
| |
Collapse
|
18
|
Tanui CK, Karanth S, Njage PM, Meng J, Pradhan AK. Machine learning-based predictive modeling to identify genotypic traits associated with Salmonella enterica disease endpoints in isolates from ground chicken. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112701] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
19
|
Brown EW, Bell R, Zhang G, Timme R, Zheng J, Hammack TS, Allard MW. Salmonella Genomics in Public Health and Food Safety. EcoSal Plus 2021; 9:eESP00082020. [PMID: 34125583 PMCID: PMC11163839 DOI: 10.1128/ecosalplus.esp-0008-2020] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/16/2021] [Indexed: 12/26/2022]
Abstract
The species Salmonella enterica comprises over 2,600 serovars, many of which are known to be intracellular pathogens of mammals, birds, and reptiles. It is now apparent that Salmonella is a highly adapted environmental microbe and can readily persist in a number of environmental niches, including water, soil, and various plant (including produce) species. Much of what is known about the evolution and diversity of nontyphoidal Salmonella serovars (NTS) in the environment is the result of the rise of the genomics era in enteric microbiology. There are over 340,000 Salmonella genomes available in public databases. This extraordinary breadth of genomic diversity now available for the species, coupled with widespread availability and affordability of whole-genome sequencing (WGS) instrumentation, has transformed the way in which we detect, differentiate, and characterize Salmonella enterica strains in a timely way. Not only have WGS data afforded a detailed and global examination of the molecular epidemiological movement of Salmonella from diverse environmental reservoirs into human and animal hosts, but they have also allowed considerable consolidation of the diagnostic effort required to test for various phenotypes important to the characterization of Salmonella. For example, drug resistance, serovar, virulence determinants, and other genome-based attributes can all be discerned using a genome sequence. Finally, genomic analysis, in conjunction with functional and phenotypic approaches, is beginning to provide new insights into the precise adaptive changes that permit persistence of NTS in so many diverse and challenging environmental niches.
Collapse
Affiliation(s)
- Eric W. Brown
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Rebecca Bell
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Guodong Zhang
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Ruth Timme
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Jie Zheng
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Thomas S. Hammack
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Marc W. Allard
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| |
Collapse
|
20
|
Li C, Wang Y, Gao Y, Li C, Ma B, Wang H. Antimicrobial Resistance and CRISPR Typing Among Salmonella Isolates From Poultry Farms in China. Front Microbiol 2021; 12:730046. [PMID: 34603259 PMCID: PMC8481896 DOI: 10.3389/fmicb.2021.730046] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/18/2021] [Indexed: 11/13/2022] Open
Abstract
Although knowledge of the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas system has been applied in many research areas, comprehensive studies of this system in Salmonella, particularly in analysis of antibiotic resistance, have not been reported. In this work, 75 Salmonella isolates obtained from broilers or broilers products were characterized to determine their antimicrobial susceptibilities, antibiotic resistance gene profiles, and CRISPR array diversities, and genotyping was explored. In total, 80.00% (60/75) of the strains were multidrug resistant, and the main pattern observed in the isolates was CN-AZM-AMP-AMC-CAZ-CIP-ATM-TE-SXT-FOS-C. The resistance genes of streptomycin (aadA), phenicol (floR-like and catB3-like), β-lactams (bla TEM, bla OXA, and bla CTX), tetracycline [tet(A)-like], and sulfonamides (sul1 and sul2) appeared at higher frequencies among the corresponding resistant isolates. Subsequently, we analyzed the CRISPR arrays and found 517 unique spacer sequences and 31 unique direct repeat sequences. Based on the CRISPR spacer sequences, we developed a novel typing method, CRISPR locus three spacer sequences typing (CLTSST), to help identify sources of Salmonella outbreaks especially correlated with epidemiological data. Compared with multi-locus sequence typing (MLST), conventional CRISPR typing (CCT), and CRISPR locus spacer pair typing (CLSPT), discrimination using CLTSST was weaker than that using CCT but stronger than that using MLST and CLSPT. In addition, we also found that there were no close correlations between CRISPR loci and antibiotics but had close correlations between CRISPR loci and antibiotic resistance genes in Salmonella isolates.
Collapse
Affiliation(s)
- Cui Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yulong Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yufeng Gao
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Chao Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Boheng Ma
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Hongning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| |
Collapse
|
21
|
Zaworski J, Dagva O, Kingston AW, Fomenkov A, Morgan RD, Bossi L, Raleigh EA. Genome archaeology of two laboratory Salmonella enterica enterica sv Typhimurium. G3 (BETHESDA, MD.) 2021; 11:jkab226. [PMID: 34544129 PMCID: PMC8496262 DOI: 10.1093/g3journal/jkab226] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/29/2021] [Indexed: 11/25/2022]
Abstract
The Salmonella research community has used strains and bacteriophages over decades, exchanging useful new isolates among laboratories for the study of cell surface antigens, metabolic pathways and restriction-modification (RM) studies. Here we present the sequences of two laboratory Salmonella strains (STK005, an isolate of LB5000; and its descendant ER3625). In the ancestry of LB5000, segments of ∼15 and ∼42 kb were introduced from Salmonella enterica sv Abony 803 into S. enterica sv Typhimurium LT2, forming strain SD14; this strain is thus a hybrid of S. enterica isolates. Strains in the SD14 lineage were used to define flagellar antigens from the 1950s to the 1970s, and to define three RM systems from the 1960s to the 1980s. LB5000 was also used as a host in phage typing systems used by epidemiologists. In the age of cheaper and easier sequencing, this resource will provide access to the sequence that underlies the extensive literature.
Collapse
Affiliation(s)
- Julie Zaworski
- Research Department, New England Biolabs, Ipswich, MA 01938-2723, USA
| | - Oyut Dagva
- Research Department, New England Biolabs, Ipswich, MA 01938-2723, USA
| | | | - Alexey Fomenkov
- Research Department, New England Biolabs, Ipswich, MA 01938-2723, USA
| | - Richard D Morgan
- Research Department, New England Biolabs, Ipswich, MA 01938-2723, USA
| | - Lionello Bossi
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), University Paris-Saclay, Gif-sur-Yvette 91198, France
| | | |
Collapse
|
22
|
Soltys RC, Sakomoto CK, Oltean HN, Guard J, Haley BJ, Shah DH. High-Resolution Comparative Genomics of Salmonella Kentucky Aids Source Tracing and Detection of ST198 and ST152 Lineage-Specific Mutations. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.695368] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Non-typhoidal Salmonella (NTS) is a major cause of foodborne illness globally. Salmonella Kentucky is a polyphyletic NTS serovar comprised of two predominant multilocus sequence types (STs): ST152 and ST198. Epidemiological studies have revealed that ST152 is most prevalent in US poultry whereas ST198 is more prevalent in international poultry. Interestingly, ST152 is sporadically associated with human illness, whereas ST198 is more commonly associated with human disease. The goal of this study was to develop a better understanding of the epidemiology of ST198 and ST152 in WA State. We compared the antimicrobial resistance phenotypes and genetic relationship, using pulsed-field gel electrophoresis, of 26 clinical strains of S. Kentucky isolated in Washington State between 2004 and 2014, and 140 poultry-associated strains of S. Kentucky mostly recovered from the northwestern USA between 2004 and 2014. We also sequenced whole genomes of representative human clinical and poultry isolates from the northwestern USA. Genome sequences of these isolates were compared with a global database of S. Kentucky genomes representing 400 ST198 and 50 ST152 strains. The results of the phenotypic, genotypic, and case report data on food consumption and travel show that human infections caused by fluoroquinolone-resistant (FluR) S. Kentucky ST198 in WA State originated from outside of North America. In contrast, fluoroquinolone-susceptible (FluS) S. Kentucky ST198 and S. Kentucky ST152 infection have a likely domestic origin, with domestic cattle and poultry being the potential sources. We also identified lineage-specific non-synonymous single nucleotide polymorphisms (SNPs) that distinguish ST198 and ST152. These SNPs may provide good targets for further investigations on lineage-specific traits such as variation in virulence, metabolic adaptation to different environments, and potential for the development of intervention strategies to improve the safety of food.
Collapse
|
23
|
Shariat NW, Timme RE, Walters AT. Phylogeny of Salmonella enterica subspecies arizonae by whole-genome sequencing reveals high incidence of polyphyly and low phase 1 H antigen variability. Microb Genom 2021; 7. [PMID: 33539276 PMCID: PMC8208698 DOI: 10.1099/mgen.0.000522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Salmonella enterica subspecies arizonae is frequently associated with animal reservoirs, particularly reptiles, and can cause illness in some mammals, including humans. Using whole-genome sequencing data, core genome phylogenetic analyses were performed using 112 S. enterica subsp. arizonae isolates, representing 46 of 102 described serovars. Nearly one-third of these are polyphyletic, including two serovars that appear in four and five distinct evolutionary lineages. Subspecies arizonae has a monophasic H antigen. Among the 46 serovars investigated, only 8 phase 1 H antigens were identified, demonstrating high conservation for this antigen. Prophages and plasmids were found throughout this subspecies, including five novel prophages. Polyphyly was also reflected in prophage content, although some clade-specific enrichment for some phages was observed. IncFII(S) was the most frequent plasmid replicon identified and was found in a quarter of S. enterica subsp. arizonae genomes. Salmonella pathogenicity islands (SPIs) 1 and 2 are present across all Salmonella, including this subspecies, although effectors sipA, sptP and arvA in SPI-1 and sseG and ssaI in SPI-2 appear to be lost in this lineage. SPI-20, encoding a type VI secretion system, is exclusive to this subspecies and is well maintained in all genomes sampled. A number of fimbral operons were identified, including the sas operon that appears to be a synapomorphy for this subspecies, while others exhibited more clade-specific patterns. This work reveals evolutionary patterns in S. enterica subsp. arizonae that make this subspecies a unique lineage within this very diverse species.
Collapse
Affiliation(s)
- Nikki W. Shariat
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
- *Correspondence: Nikki W. Shariat,
| | - Ruth E. Timme
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Abigail T. Walters
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| |
Collapse
|
24
|
Zhang G, Hu L, Luo Y, Santillana Farakos SM, Johnson R, Scott VN, Curry P, Melka D, Brown EW, Strain E, Bunning VK, Musser SM, Hammack TS. Survey of Salmonella in raw tree nuts at retail in the United States. J Food Sci 2021; 86:495-504. [PMID: 33438200 PMCID: PMC7898309 DOI: 10.1111/1750-3841.15569] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/17/2020] [Accepted: 11/19/2020] [Indexed: 12/01/2022]
Abstract
Abstract The objective of this survey was to estimate the prevalence, contamination level, and genetic diversity of Salmonella in selected raw, shelled tree nuts (Brazil nuts, cashews, hazelnuts, macadamia nuts, pecans, pine nuts, pistachios, and walnuts) at retail markets in the United States. A total of 3,374 samples of eight tree nuts were collected from different types of retail stores and markets nationwide between September 2015 and March 2017. These samples (375 g) were analyzed using a modified FDA's BAM Salmonella culture method. Of the 3,374 samples, 15 (0.44%) (95% confidence interval [CI] [0.25, 0.73]) were culturally confirmed as containing Salmonella; 17 isolates were obtained. Among these isolates, there were 11 serotypes. Salmonella was not detected in Brazil nuts (296), hazelnuts (487), pecans (510), pine nuts (500), and walnuts (498). Salmonella prevalence estimates in cashews (510), macadamia (278), and pistachios (295) were 0.20% (95% CI [<0.01, 1.09]), 2.52% (95% CI [1.02, 5.12]), and 2.37% (95% CI [0.96, 4.83]), respectively. The rates of Salmonella isolation from major/big‐chain supermarkets (1381), small‐chain supermarkets (328), discount/variety/drug stores (1329), and online (336) were 0.29% (95% CI [0.08, 0.74]), 0.30% (95% CI [0.01, 1.69]), 0.45% (95% CI [0.17, 0.98]), and 1.19% (95% CI [0.33, 3.02]), respectively. Salmonella prevalence in organic (530) and conventional (2,844) nuts was not different statistically (P = 0.0601). Of the enumerated samples (15), 80% had Salmonella levels ≤0.0092 most probable number (MPN)/g. The highest contamination level observed was 0.75 MPN/g. The prevalence and contamination levels of Salmonella in the tree nuts analyzed were generally comparable to previous reports. Pulsed‐field gel electrophoresis, serotype, and sequencing data all demonstrated that Salmonella population in nuts is very diverse genetically. Practical Application The prevalence, contamination level, and genetic diversity of Salmonella in eight types of tree nuts (3,374 samples collected nationwide) revealed in this survey could help the development of mitigation strategies to reduce public health risks associated with consumption of these nuts.
Collapse
Affiliation(s)
- Guodong Zhang
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, 5001 Campus Dr., College Park, MD, 20740, U.S.A
| | - Lijun Hu
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, 5001 Campus Dr., College Park, MD, 20740, U.S.A
| | - Yan Luo
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, 5001 Campus Dr., College Park, MD, 20740, U.S.A
| | - Sofia M Santillana Farakos
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, 5001 Campus Dr., College Park, MD, 20740, U.S.A
| | - Rhoma Johnson
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, 5001 Campus Dr., College Park, MD, 20740, U.S.A
| | - Virginia N Scott
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, 5001 Campus Dr., College Park, MD, 20740, U.S.A
| | - Phillip Curry
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, 5001 Campus Dr., College Park, MD, 20740, U.S.A
| | - David Melka
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, 5001 Campus Dr., College Park, MD, 20740, U.S.A
| | - Eric W Brown
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, 5001 Campus Dr., College Park, MD, 20740, U.S.A
| | - Errol Strain
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, 5001 Campus Dr., College Park, MD, 20740, U.S.A
| | - Vincent K Bunning
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, 5001 Campus Dr., College Park, MD, 20740, U.S.A
| | - Steven M Musser
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, 5001 Campus Dr., College Park, MD, 20740, U.S.A
| | - Thomas S Hammack
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, 5001 Campus Dr., College Park, MD, 20740, U.S.A
| |
Collapse
|
25
|
Kushwaha SK, Bhavesh NLS, Abdella B, Lahiri C, Marathe SA. The phylogenomics of CRISPR-Cas system and revelation of its features in Salmonella. Sci Rep 2020; 10:21156. [PMID: 33273523 PMCID: PMC7712790 DOI: 10.1038/s41598-020-77890-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 11/18/2020] [Indexed: 01/26/2023] Open
Abstract
Salmonellae display intricate evolutionary patterns comprising over 2500 serovars having diverse pathogenic profiles. The acquisition and/or exchange of various virulence factors influences the evolutionary framework. To gain insights into evolution of Salmonella in association with the CRISPR-Cas genes we performed phylogenetic surveillance across strains of 22 Salmonella serovars. The strains differed in their CRISPR1-leader and cas operon features assorting into two main clades, CRISPR1-STY/cas-STY and CRISPR1-STM/cas-STM, comprising majorly typhoidal and non-typhoidal Salmonella serovars respectively. Serovars of these two clades displayed better relatedness, concerning CRISPR1-leader and cas operon, across genera than between themselves. This signifies the acquisition of CRISPR1/Cas region could be through a horizontal gene transfer event owing to the presence of mobile genetic elements flanking CRISPR1 array. Comparison of CRISPR and cas phenograms with that of multilocus sequence typing (MLST) suggests differential evolution of CRISPR/Cas system. As opposed to broad-host-range, the host-specific serovars harbor fewer spacers. Mapping of protospacer sources suggested a partial correlation of spacer content with habitat diversity of the serovars. Some serovars like serovar Enteritidis and Typhimurium that inhabit similar environment/infect similar hosts hardly shared their protospacer sources.
Collapse
Affiliation(s)
- Simran Krishnakant Kushwaha
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India.
| | - Narra Lakshmi Sai Bhavesh
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Bahaa Abdella
- Department of Biological Sciences, Sunway University, Petaling Jaya, Selangor, Malaysia.,Faculty of Aquatic and Fisheries Sciences, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Chandrajit Lahiri
- Department of Biological Sciences, Sunway University, Petaling Jaya, Selangor, Malaysia
| | - Sandhya Amol Marathe
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India.
| |
Collapse
|
26
|
Hudson LK, Constantine-Renna L, Thomas L, Moore C, Qian X, Garman K, Dunn JR, Denes TG. Genomic characterization and phylogenetic analysis of Salmonella enterica serovar Javiana. PeerJ 2020; 8:e10256. [PMID: 33240617 PMCID: PMC7682435 DOI: 10.7717/peerj.10256] [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: 06/09/2020] [Accepted: 10/06/2020] [Indexed: 02/01/2023] Open
Abstract
Salmonella enterica serovar Javiana is the fourth most reported serovar of laboratory-confirmed human Salmonella infections in the U.S. and in Tennessee (TN). Although Salmonella ser. Javiana is a common cause of human infection, the majority of cases are sporadic in nature rather than outbreak-associated. To better understand Salmonella ser. Javiana microbial population structure in TN, we completed a phylogenetic analysis of 111 Salmonella ser. Javiana clinical isolates from TN collected from Jan. 2017 to Oct. 2018. We identified mobile genetic elements and genes known to confer antibiotic resistance present in the isolates, and performed a pan-genome-wide association study (pan-GWAS) to compare gene content between clades identified in this study. The population structure of TN Salmonella ser. Javiana clinical isolates consisted of three genetic clades: TN clade I (n = 54), TN clade II (n = 4), and TN clade III (n = 48). Using a 5, 10, and 25 hqSNP distance threshold for cluster identification, nine, 12, and 10 potential epidemiologically-relevant clusters were identified, respectively. The majority of genes that were found to be over-represented in specific clades were located in mobile genetic element (MGE) regions, including genes encoding integrases and phage structures (91.5%). Additionally, a large portion of the over-represented genes from TN clade II (44.9%) were located on an 87.5 kb plasmid containing genes encoding a toxin/antitoxin system (ccdAB). Additionally, we completed phylogenetic analyses of global Salmonella ser. Javiana datasets to gain a broader insight into the population structure of this serovar. We found that the global phylogeny consisted of three major clades (one of which all of the TN isolates belonged to) and two cgMLST eBurstGroups (ceBGs) and that the branch length between the two Salmonella ser. Javiana ceBGs (1,423 allelic differences) was comparable to those from other serovars that have been reported as polyphyletic (929–2,850 allelic differences). This study demonstrates the population structure of TN and global Salmonella ser. Javiana isolates, a clinically important Salmonella serovar and can provide guidance for phylogenetic cluster analyses for public health surveillance and response.
Collapse
Affiliation(s)
- Lauren K Hudson
- Department of Food Science, University of Tennessee, Knoxville, TN, United States of America
| | | | - Linda Thomas
- Division of Laboratory Services, Tennessee Department of Health, Nashville, TN, United States of America
| | - Christina Moore
- Division of Laboratory Services, Tennessee Department of Health, Nashville, TN, United States of America
| | - Xiaorong Qian
- Division of Laboratory Services, Tennessee Department of Health, Nashville, TN, United States of America
| | - Katie Garman
- Tennessee Department of Health, Nashville, TN, United States of America
| | - John R Dunn
- Tennessee Department of Health, Nashville, TN, United States of America
| | - Thomas G Denes
- Department of Food Science, University of Tennessee, Knoxville, TN, United States of America
| |
Collapse
|
27
|
Wang H, Zeng X, Lin J. Enterobactin-specific antibodies inhibit in vitro growth of different gram-negative bacterial pathogens. Vaccine 2020; 38:7764-7773. [PMID: 33164800 DOI: 10.1016/j.vaccine.2020.10.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/26/2020] [Accepted: 10/12/2020] [Indexed: 01/17/2023]
Abstract
Enterobactin (Ent)-mediated high affinity iron acquisition is critically important for Gram-negative bacterial pathogens to survive and infect the host. Recently, we reported an efficient method to prepare novel Ent conjugate vaccines for inducing high level of Ent-specific antibodies, which displayed similar bacteriostatic feature as lipocalins, the host innate immune effectors with potent Ent-binding ability. The Ent-specific antibodies also showed a significant advantage over lipocalins by cross-reacting to various Ent derivatives including salmochelins, the glycosylated Ent that can help enteric pathogens evade the siderophore sequestration by host lipocalins. To demonstrate significant potential of the Ent conjugate vaccine for broader applications to prevent and control various Gram-negative infections in human and animal, in this study, we examined inhibitory effect of Ent-specific antibodies on the in vitro growth of three significant Gram-negative pathogens: Escherichia coli (n = 27), Salmonella enterica (n = 8), and Campylobacter spp. (n = 6). The tested strains were diverse with respect to hosts, geographical origins, serotypes, infection sites and siderophore productions. The Ent-specific antibodies significantly suppressed the growth of each tested strain under iron-restricted conditions. For example, the Ent-specific antibodies consistently exerted 2-5 log10 units of growth reduction on most tested avian pathogenic E. coli (9 of 10 strains) isolated in five countries. Despite various dynamic growth responses observed, notably, the Ent-specific antibodies displayed significantly higher magnitude of growth reduction than lipocalin-2 (up to 5 log10 units of difference) on majority of tested E. coli and S. enterica, which is likely due to sequestration of other siderophores (e.g., salmochelins) by the Ent-specific antibodies. Production of a variety of major siderophores by the tested E. coli and S. enterica strains was examined and confirmed by ultra high performance liquid chromatography-high resolution mass spectrometry analysis. Collectively, this study provides critical and compelling in vitro evidence supporting the feasibility of Ent-based immune interventions against several Gram-negative pathogens.
Collapse
Affiliation(s)
- Huiwen Wang
- Department of Animal Science, The University of Tennessee, Knoxville, TN, USA
| | - Ximin Zeng
- Department of Animal Science, The University of Tennessee, Knoxville, TN, USA
| | - Jun Lin
- Department of Animal Science, The University of Tennessee, Knoxville, TN, USA.
| |
Collapse
|
28
|
Elnekave E, Hong SL, Lim S, Johnson TJ, Perez A, Alvarez J. Comparing serotyping with whole-genome sequencing for subtyping of non-typhoidal Salmonella enterica: a large-scale analysis of 37 serotypes with a public health impact in the USA. Microb Genom 2020; 6:mgen000425. [PMID: 32845830 PMCID: PMC7643971 DOI: 10.1099/mgen.0.000425] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/03/2020] [Indexed: 01/21/2023] Open
Abstract
Serotyping has traditionally been used for subtyping of non-typhoidal Salmonella (NTS) isolates. However, its discriminatory power is limited, which impairs its use for epidemiological investigations of source attribution. Whole-genome sequencing (WGS) analysis allows more accurate subtyping of strains. However, because of the relative newness and cost of routine WGS, large-scale studies involving NTS WGS are still rare. We aimed to revisit the big picture of subtyping NTS with a public health impact by using traditional serotyping (i.e. reaction between antisera and surface antigens) and comparing the results with those obtained using WGS. For this purpose, we analysed 18 282 sequences of isolates belonging to 37 serotypes with a public health impact that were recovered in the USA between 2006 and 2017 from multiple sources, and were available at the National Center for Biotechnology Information (NCBI). Phylogenetic trees were reconstructed for each serotype using the core genome for the identification of genetic subpopulations. We demonstrated that WGS-based subtyping allows better identification of sources potentially linked with human infection and emerging subpopulations, along with providing information on the risk of dissemination of plasmids and acquired antimicrobial resistance genes (AARGs). In addition, by reconstructing a phylogenetic tree with representative isolates from all serotypes (n=370), we demonstrated genetic variability within and between serotypes, which formed monophyletic, polyphyletic and paraphyletic clades. Moreover, we found (in the entire data set) an increased detection rate for AARGs linked to key antimicrobials (such as quinolones and extended-spectrum cephalosporins) over time. The outputs of this large-scale analysis reveal new insights into the genetic diversity within and between serotypes; the polyphyly and paraphyly of certain serotypes may suggest that the subtyping of NTS to serotypes may not be sufficient. Moreover, the results and the methods presented here, leading to differentiation between genetic subpopulations based on their potential risk to public health, as well as narrowing down the possible sources of these infections, may be used as a baseline for subtyping of future NTS infections and help efforts to mitigate and prevent infections in the USA and globally.
Collapse
Affiliation(s)
- Ehud Elnekave
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Israel
| | - Samuel L. Hong
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, University of Leuven, Leuven, Belgium
| | - Seunghyun Lim
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
- Bioinformatics and Computational Biology Program, University of Minnesota, Rochester, Minnesota, USA
| | - Timothy J. Johnson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Andres Perez
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Julio Alvarez
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
- VISAVET Health Surveillance Center, Universidad Complutense, Madrid, Spain
- Department of Animal Health, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
| |
Collapse
|
29
|
Monte DFM, Nethery MA, Barrangou R, Landgraf M, Fedorka-Cray PJ. Whole-genome sequencing analysis and CRISPR genotyping of rare antibiotic-resistant Salmonella enterica serovars isolated from food and related sources. Food Microbiol 2020; 93:103601. [PMID: 32912589 DOI: 10.1016/j.fm.2020.103601] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 07/17/2020] [Accepted: 07/21/2020] [Indexed: 11/25/2022]
Abstract
For decades, Salmonella Typhimurium and Salmonella Enteritidis have prevailed in several countries as agents of salmonellosis outbreaks. In Brazil, the largest exporter of poultry meat, relatively little attention has been paid to infrequent serovars. Here, we report the emergence and characterization of rare serovars isolated from food and related sources collected between 2014 and 2016 in Brazil. Twenty-two Salmonella enterica isolates were analyzed through the use of whole-genome sequencing (WGS) and clustered regularly interspaced short palindromic repeats (CRISPR) genotyping. These isolates were classified into 10 infrequent serovars, including S. Abony, S. Isangi, S. Rochdale, S. Saphra, S. Orion, S. Ouakam, S. Grumpensis, S. Carrau, S. Abaetetuba, and S. Idikan. The presence of six antimicrobial resistance (AMR) genes, qnrB19, blaCMY-2, tetA, aac(6')-Iaa, sul2 and fosA7, which encode resistance to quinolones, third-generation cephalosporin, tetracycline, aminoglycoside, sulfonamide and fosfomycin, respectively, were confirmed by WGS. All S. Isangi harbored qnrB19 with conserved genomic context across strains, while S. Abony harbored blaCMY-2. Twelve (54.5%) strains displayed chromosomal mutations in parC (Thr57→Ser). Most serovars were classified as independent lineages, except S. Abony and S. Abaetetuba, which phylogenetically nested with Salmonella strains from different countries. CRISPR analysis revealed that the spacer content was strongly correlated with serovar and multi-locus sequence type for all strains, independently confirming the observed phylogenetic patterns, and highlighting the value of CRISPR-based genotyping for Salmonella. These findings add valuable information to the epidemiology of S. enterica in Brazil, where the emergency of antibiotic-resistant Salmonella continues to evolve.
Collapse
Affiliation(s)
- Daniel F M Monte
- Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, Food Research Center, University of São Paulo, Brazil; Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, NC, USA.
| | - Matthew A Nethery
- Genomic Sciences Graduate Program, North Carolina State University, Raleigh, NC, USA; Department of Food, Bioprocessing & Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Rodolphe Barrangou
- Genomic Sciences Graduate Program, North Carolina State University, Raleigh, NC, USA; Department of Food, Bioprocessing & Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Mariza Landgraf
- Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, Food Research Center, University of São Paulo, Brazil
| | - Paula J Fedorka-Cray
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, NC, USA.
| |
Collapse
|
30
|
Whole-Genome-Based Survey for Polyphyletic Serovars of Salmonella enterica subsp. enterica Provides New Insights into Public Health Surveillance. Int J Mol Sci 2020; 21:ijms21155226. [PMID: 32718035 PMCID: PMC7432358 DOI: 10.3390/ijms21155226] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/07/2020] [Accepted: 07/17/2020] [Indexed: 02/06/2023] Open
Abstract
Serotyping has traditionally been considered the basis for surveillance of Salmonella, but it cannot distinguish distinct lineages sharing the same serovar that vary in host range, pathogenicity and epidemiology. However, polyphyletic serovars have not been extensively investigated. Public health microbiology is currently being transformed by whole-genome sequencing (WGS) data, which promote the lineage determination using a more powerful and accurate technique than serotyping. The focus in this study is to survey and analyze putative polyphyletic serovars. The multi-locus sequence typing (MLST) phylogenetic analysis identified four putative polyphyletic serovars, namely, Montevideo, Bareilly, Saintpaul, and Muenchen. Whole-genome-based phylogeny and population structure highlighted the polyphyletic nature of Bareilly and Saintpaul and the multi-lineage nature of Montevideo and Muenchen. The population of these serovars was defined by extensive genetic diversity, the open pan genome and the small core genome. Source niche metadata revealed putative existence of lineage-specific niche adaptation (host-preference and environmental-preference), exhibited by lineage-specific genomic contents associated with metabolism and transport. Meanwhile, differences in genetic profiles relating to virulence and antimicrobial resistance within each lineage may contribute to pathogenicity and epidemiology. The results also showed that recombination events occurring at the H1-antigen loci may be an important reason for polyphyly. The results presented here provide the genomic basis of simple, rapid, and accurate identification of phylogenetic lineages of these serovars, which could have important implications for public health.
Collapse
|
31
|
Ramatla TA, Mphuthi N, Ramaili T, Taioe MO, Thekisoe OMM, Syakalima M. Molecular detection of virulence genes in Salmonella spp. isolated from chicken faeces in Mafikeng, South Africa. J S Afr Vet Assoc 2020; 91:e1-e7. [PMID: 32787420 PMCID: PMC7433231 DOI: 10.4102/jsava.v91i0.1994] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 02/21/2020] [Accepted: 03/16/2020] [Indexed: 11/29/2022] Open
Abstract
Chickens have been implicated in most Salmonella disease outbreaks because they act as carriers of the pathogen in their gut. There are over 2500 serotypes of Salmonella that have been reported worldwide and 2000 of these serovars can be found in chickens. The main objective of this study was to determine the Salmonella serotypes found in poultry farms around Mafikeng district, South Africa. Salmonella was identified according to the guidelines of the International Organization for Standardization (ISO) (ISO 6579:2002) standard techniques. Faecal samples were collected and analysed for Salmonella using conventional cultural methods and polymerase chain reaction targeting the 16S Ribosomal Deoxyribonucleic acid (rDNA) gene for Salmonella identification. Out of 130 presumptive Salmonella isolates determined by urease and triple sugar iron tests, only 46 isolates were identified as Salmonella serotypes of which S. Typhimurium was the most frequent with 18 (39.1%), followed by S. Heidelberg with 9 (19.6%), S. bongori with 7 (15.2%), S. Enteritidis with 6 (13.0%) and both S. Paratyphi B and S. Newport with 3 (6.5%) each. Seven virulence genes including invA 100%, spy 39%, hilA 9%, misL 30%, sdfI 13%, orfL 11% and spiC 9% were detected from these Salmonella isolates in this study. The presence of these virulence genes indicates high pathogenicity potential of these isolates which is a serious public health concern because of zoonotic potential of Salmonella.
Collapse
Affiliation(s)
- Tsepo A Ramatla
- Department of Animal Health, Faculty of Natural and Agricultural Sciences, North-West University, Mafikeng.
| | | | | | | | | | | |
Collapse
|
32
|
Characterization of non-typhoid Salmonellae isolated from domestic animals and wildlife from selected areas of Zambia. SCIENTIFIC AFRICAN 2020. [DOI: 10.1016/j.sciaf.2020.e00345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
|
33
|
Pilar AVC, Petronella N, Dussault FM, Verster AJ, Bekal S, Levesque RC, Goodridge L, Tamber S. Similar yet different: phylogenomic analysis to delineate Salmonella and Citrobacter species boundaries. BMC Genomics 2020; 21:377. [PMID: 32471418 PMCID: PMC7257147 DOI: 10.1186/s12864-020-06780-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 05/13/2020] [Indexed: 12/14/2022] Open
Abstract
Background Salmonella enterica is a leading cause of foodborne illness worldwide resulting in considerable public health and economic costs. Testing for the presence of this pathogen in food is often hampered by the presence of background microflora that may present as Salmonella (false positives). False positive isolates belonging to the genus Citrobacter can be difficult to distinguish from Salmonella due to similarities in their genetics, cell surface antigens, and other phenotypes. In order to understand the genetic basis of these similarities, a comparative genomic approach was used to define the pan-, core, accessory, and unique coding sequences of a representative population of Salmonella and Citrobacter strains. Results Analysis of the genomic content of 58 S. enterica strains and 37 Citrobacter strains revealed the presence of 31,130 and 1540 coding sequences within the pan- and core genome of this population. Amino acid sequences unique to either Salmonella (n = 1112) or Citrobacter (n = 195) were identified and revealed potential niche-specific adaptations. Phylogenetic network analysis of the protein families encoded by the pan-genome indicated that genetic exchange between Salmonella and Citrobacter may have led to the acquisition of similar traits and also diversification within the genera. Conclusions Core genome analysis suggests that the Salmonella enterica and Citrobacter populations investigated here share a common evolutionary history. Comparative analysis of the core and pan-genomes was able to define the genetic features that distinguish Salmonella from Citrobacter and highlight niche specific adaptations.
Collapse
Affiliation(s)
| | - Nicholas Petronella
- Bureau of Food Surveillance and Science Integration, Health Canada, Ottawa, Ontario, Canada
| | - Forest M Dussault
- Bureau of Food Surveillance and Science Integration, Health Canada, Ottawa, Ontario, Canada
| | - Adrian J Verster
- Bureau of Food Surveillance and Science Integration, Health Canada, Ottawa, Ontario, Canada
| | - Sadjia Bekal
- Laboratoire de santé publique du Québec, Ste-Anne-de-Bellevue, Quebec, Canada
| | - Roger C Levesque
- Institute for Integrative and Systems Biology (IBIS), Université Laval, Quebec, Quebec, Canada
| | - Lawrence Goodridge
- Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, Quebec, Canada.,Food Science Department, University of Guelph, Guelph, Ontario, Canada
| | - Sandeep Tamber
- Bureau of Microbial Hazards, Health Canada, Ottawa, Ontario, Canada.
| |
Collapse
|
34
|
Chen Y, Chen Y, Pouillot R, Dennis S, Xian Z, Luchansky JB, Porto-Fett ACS, Lindsay JA, Hammack TS, Allard M, Van Doren JM, Brown EW. Genetic diversity and profiles of genes associated with virulence and stress resistance among isolates from the 2010-2013 interagency Listeria monocytogenes market basket survey. PLoS One 2020; 15:e0231393. [PMID: 32352974 PMCID: PMC7192433 DOI: 10.1371/journal.pone.0231393] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/23/2020] [Indexed: 12/15/2022] Open
Abstract
Whole genome sequencing (WGS) was performed on 201 Listeria monocytogenes isolates recovered from 102 of 27,389 refrigerated ready-to-eat (RTE) food samples purchased at retail in U.S. FoodNet sites as part of the 2010-2013 interagency L. monocytogenes Market Basket Survey (Lm MBS). Core genome multi-locus sequence typing (cgMLST) and in-silico analyses were conducted, and these data were analyzed with metadata for isolates from five food groups: produce, seafood, dairy, meat, and combination foods. Six of 201 isolates, from 3 samples, were subsequently confirmed as L. welshimeri. Three samples contained one isolate per sample; mmong the 96 samples that contained two isolates per sample, 3 samples each contained two different strains and 93 samples each contained duplicate isolates. After 93 duplicate isolates were removed, the remaining 102 isolates were delineated into 29 clonal complexes (CCs) or singletons based on their sequence type. The five most prevalent CCs were CC155, CC1, CC5, CC87, and CC321. The Shannon's diversity index for clones per food group ranged from 1.49 for dairy to 2.32 for produce isolates, which were not significantly different in pairwise comparisons. The most common molecular serogroup as determined by in-silico analysis was IIa (45.6%), followed by IIb (27.2%), IVb (20.4%), and IIc (4.9%). The proportions of isolates within lineages I, II, and III were 48.0%, 50.0% and 2.0%, respectively. Full-length inlA was present in 89.3% of isolates. Listeria pathogenicity island 3 (LIPI-3) and LIPI-4 were found in 51% and 30.6% of lineage I isolates, respectively. Stress survival islet 1 (SSI-1) was present in 34.7% of lineage I isolates, 80.4% of lineage II isolates and the 2 lineage III isolates; SSI-2 was present only in the CC121 isolate. Plasmids were found in 48% of isolates, including 24.5% of lineage I isolates and 72.5% of lineage II isolates. Among the plasmid-carrying isolates, 100% contained at least one cadmium resistance cassette and 89.8% contained bcrABC, involved in quaternary ammonium compound tolerance. Multiple clusters of isolates from different food samples were identified by cgMLST which, along with available metadata, could aid in the investigation of possible cross-contamination and persistence events.
Collapse
Affiliation(s)
- Yi Chen
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| | - Yuhuan Chen
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| | - Régis Pouillot
- Consultant, Buenos Aires, Argentina, United States of America
| | - Sherri Dennis
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| | - Zhihan Xian
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| | - John B. Luchansky
- USDA Agricultural Research Service, Wyndmoor, Pennsylvania, United States of America
| | - Anna C. S. Porto-Fett
- USDA Agricultural Research Service, Wyndmoor, Pennsylvania, United States of America
| | - James A. Lindsay
- USDA Agricultural Research Service, Beltsville, Maryland, United States of America
| | - Thomas S. Hammack
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| | - Marc Allard
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| | - Jane M. Van Doren
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| | - Eric W. Brown
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| |
Collapse
|
35
|
Mastrorilli E, Petrin S, Orsini M, Longo A, Cozza D, Luzzi I, Ricci A, Barco L, Losasso C. Comparative genomic analysis reveals high intra-serovar plasticity within Salmonella Napoli isolated in 2005-2017. BMC Genomics 2020; 21:202. [PMID: 32131727 PMCID: PMC7057659 DOI: 10.1186/s12864-020-6588-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 02/18/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Salmonella enterica subsp. enterica serovar Napoli (S. Napoli) is among the top serovars causing human infections in Italy, although it is relatively uncommon in other European countries; it is mainly isolated from humans and the environment, but neither the reservoir nor its route of infection are clearly defined. This serovar is characterized by high genomic diversity, and molecular evidences revealed important similarities with typhoidal serovars. RESULTS 179 S. Napoli genomes as well as 239 genomes of typhoidal and non-typhoidal serovars were analyzed in a comparative genomic study. Phylogenetic analysis and draft genome characterization in terms of Multi Locus Sequence Typing (MLST), plasmid replicons, Salmonella Pathogenicity Islands (SPIs), antimicrobial resistance genes (ARGs), phages, biocide and metal-tolerance genes confirm the high genetic variability of S. Napoli, also revealing a within-serovar phylogenetic structure more complex than previously known. Our work also confirms genomic similarity of S. Napoli to typhoidal serovars (S. Typhi and S. Paratyphi A), with S. Napoli samples clustering primarily according to ST, each being characterized by specific genomic traits. Moreover, two major subclades of S. Napoli can be clearly identified, with ST-474 being biphyletic. All STs span among isolation sources and years of isolation, highlighting the challenge this serovar poses to define its epidemiology and evolution. Altogether, S. Napoli strains carry less SPIs and less ARGs than other non-typhoidal serovars and seldom acquire plasmids. However, we here report the second case of an extended-spectrum β-lactamases (ESBLs) producing S. Napoli strain and the first cases of multidrug resistant (MDR) S. Napoli strains, all isolated from humans. CONCLUSIONS Our results provide evidence of genomic plasticity of S. Napoli, highlighting genomic similarity with typhoidal serovars and genomic features typical of non-typhoidal serovars, supporting the possibility of survival in different niches, both enteric and non-enteric. Presence of horizontally acquired ARGs and MDR profiles rises concerns regarding possible selective pressure exerted by human environment on this pathogen.
Collapse
Affiliation(s)
- Eleonora Mastrorilli
- Istituto Zooprofilattico Sperimentale delle Venezie, Microbial Ecology Unit, Legnaro, Italy
- Present address: European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Sara Petrin
- Istituto Zooprofilattico Sperimentale delle Venezie, Microbial Ecology Unit, Legnaro, Italy
| | - Massimiliano Orsini
- Istituto Zooprofilattico Sperimentale delle Venezie, Microbial Ecology Unit, Legnaro, Italy.
| | - Alessandra Longo
- Istituto Zooprofilattico Sperimentale delle Venezie, Microbial Ecology Unit, Legnaro, Italy
| | - Debora Cozza
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Ida Luzzi
- Istituto Superiore di Sanità, Rome, Italy
| | - Antonia Ricci
- Istituto Zooprofilattico Sperimentale delle Venezie, Food Safety Department, Legnaro, Italy
| | - Lisa Barco
- Istituto Zooprofilattico Sperimentale delle Venezie, Food Safety Department, Legnaro, Italy
| | - Carmen Losasso
- Istituto Zooprofilattico Sperimentale delle Venezie, Microbial Ecology Unit, Legnaro, Italy
| |
Collapse
|
36
|
Epidemiology of Salmonella enterica Serovar Dublin in Cattle and Humans in Denmark, 1996 to 2016: a Retrospective Whole-Genome-Based Study. Appl Environ Microbiol 2020; 86:AEM.01894-19. [PMID: 31732576 DOI: 10.1128/aem.01894-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/08/2019] [Indexed: 01/08/2023] Open
Abstract
Salmonella enterica serovar Dublin is a cattle-adapted S. enterica serovar causing both intestinal and systemic infection in its bovine host, and it is also a serious threat to human health. The present study aimed to determine the population structure of S Dublin isolates obtained from Danish cattle herds and to investigate how cattle isolates relate to Danish human isolates, as well as to non-Danish human and bovine isolates. Phylogenetic analysis of 197 Danish cattle isolates from 1996 to 2016 identified three major clades corresponding to distinct geographical regions of cattle herds. Persistence of closely related isolates within the same herd and their circulation between epidemiologically linked herds for a period of more than 20 years were demonstrated. These findings suggest that a lack of internal biosecurity and, to some extent, also a lack of external biosecurity in the herds have played an important role in the long-term persistence of S Dublin in Danish cattle herds in the period investigated. Global population analysis revealed that Danish cattle isolates clustered separately from bovine isolates from other countries, whereas human isolates were geographically spread. Resistance genes were not commonly demonstrated in Danish bovine isolates; only the isolates within one Danish clade were found to often harbor two plasmids of IncFII/IncFIB and IncN types, the latter plasmid carrying bla TEM-1, tetA, strA, and strB antibiotic resistance genes.IMPORTANCE S Dublin causes economic losses in cattle production, and the bacterium is a public health concern. A surveillance and control program has been in place in Denmark since 2002 with the ultimate goal to eradicate S Dublin from Danish cattle herds; however, a small proportion of herds have remained positive for many years. In this study, we demonstrate that herds with persistent infection often were infected with the same strain for many years, indicating that internal biosecurity has to be improved to curb the infection. Further, domestic cases of S Dublin infection in humans were found to be caused both by Danish cattle isolates and by isolates acquired abroad. This study shows the strength of whole-genome sequencing to obtain detailed information on epidemiology of S Dublin and allows us to suggest internal biosecurity as a main way to control this bacterium in Danish cattle herds.
Collapse
|
37
|
Abstract
Lipopolysaccharides are a major component of the outer membrane in Gram-negative bacteria. They are composed of a conserved lipid structure that is embedded in the outer leaflet of the outer membrane and a polysaccharide known as the O-antigen. O-antigens are highly variable in structure across strains of a species and are crucial to a bacterium’s interactions with its environment. They constitute the first line of defense against both the immune system and bacteriophage infections and have been shown to mediate antimicrobial resistance. The significance of our research is in identifying the metabolic and genetic differences within and across O-antigen groups in Salmonella strains. Our effort constitutes a first step toward characterizing the O-antigen metabolic network across Gram-negative organisms and a comprehensive overview of genetic variations in Salmonella. O-antigens are glycopolymers in lipopolysaccharides expressed on the cell surface of Gram-negative bacteria. Variability in the O-antigen structure constitutes the basis for the establishment of the serotyping schema. We pursued a two-pronged approach to define the basis for O-antigen structural diversity. First, we developed a bottom-up systems biology approach to O-antigen metabolism by building a reconstruction of Salmonella O-antigen biosynthesis and used it to (i) update 410 existing Salmonella strain-specific metabolic models, (ii) predict a strain’s serogroup and its O-antigen glycan synthesis capability (yielding 98% agreement with experimental data), and (iii) extend our workflow to more than 1,400 Gram-negative strains. Second, we used a top-down pangenome analysis to elucidate the genetic basis for intraserogroup O-antigen structural variations. We assembled a database of O-antigen gene islands from over 11,000 sequenced Salmonella strains, revealing (i) that gene duplication, pseudogene formation, gene deletion, and bacteriophage insertion elements occur ubiquitously across serogroups; (ii) novel serotypes in the group O:4 B2 variant, as well as an additional genotype variant for group O:4, and (iii) two novel O-antigen gene islands in understudied subspecies. We thus comprehensively defined the genetic basis for O-antigen diversity.
Collapse
|
38
|
Identification of Primary Antimicrobial Resistance Drivers in Agricultural Nontyphoidal Salmonella enterica Serovars by Using Machine Learning. mSystems 2019; 4:4/4/e00211-19. [PMID: 31387929 PMCID: PMC6687941 DOI: 10.1128/msystems.00211-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Nontyphoidal Salmonella (NTS) is a leading global cause of bacterial foodborne morbidity and mortality. Our ability to treat severe NTS infections has been impaired by increasing antimicrobial resistance (AMR). To understand and mitigate the global health crisis AMR represents, we need to link the observed resistance phenotypes with their underlying genomic mechanisms. Broiler chickens represent a key reservoir and vector for NTS infections, but isolates from this setting have been characterized in only very low numbers relative to clinical isolates. In this study, we sequenced and assembled 97 genomes encompassing 7 serotypes isolated from broiler chicken in farms in British Columbia between 2005 and 2008. Through application of machine learning (ML) models to predict the observed AMR phenotype from this genomic data, we were able to generate highly (0.92 to 0.99) precise logistic regression models using known AMR gene annotations as features for 7 antibiotics (amoxicillin-clavulanic acid, ampicillin, cefoxitin, ceftiofur, ceftriaxone, streptomycin, and tetracycline). Similarly, we also trained "reference-free" k-mer-based set-covering machine phenotypic prediction models (0.91 to 1.0 precision) for these antibiotics. By combining the inferred k-mers and logistic regression weights, we identified the primary drivers of AMR for the 7 studied antibiotics in these isolates. With our research representing one of the largest studies of a diverse set of NTS isolates from broiler chicken, we can thus confirm that the AmpC-like CMY-2 β-lactamase is a primary driver of β-lactam resistance and that the phosphotransferases APH(6)-Id and APH(3″-Ib) are the principal drivers of streptomycin resistance in this important ecosystem.IMPORTANCE Antimicrobial resistance (AMR) represents an existential threat to the function of modern medicine. Genomics and machine learning methods are being increasingly used to analyze and predict AMR. This type of surveillance is very important to try to reduce the impact of AMR. Machine learning models are typically trained using genomic data, but the aspects of the genomes that they use to make predictions are rarely analyzed. In this work, we showed how, by using different types of machine learning models and performing this analysis, it is possible to identify the key genes underlying AMR in nontyphoidal Salmonella (NTS). NTS is among the leading cause of foodborne illness globally; however, AMR in NTS has not been heavily studied within the food chain itself. Therefore, in this work we performed a broad-scale analysis of the AMR in NTS isolates from commercial chicken farms and identified some priority AMR genes for surveillance.
Collapse
|
39
|
Monte DF, Lincopan N, Berman H, Cerdeira L, Keelara S, Thakur S, Fedorka-Cray PJ, Landgraf M. Genomic Features of High-Priority Salmonella enterica Serovars Circulating in the Food Production Chain, Brazil, 2000-2016. Sci Rep 2019; 9:11058. [PMID: 31363103 PMCID: PMC6667439 DOI: 10.1038/s41598-019-45838-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 06/11/2019] [Indexed: 11/09/2022] Open
Abstract
Multidrug-resistant (MDR) Salmonella enterica has been deemed a high-priority pathogen by the World Health Organization. Two hundred and sixty-four Salmonella enterica isolates recovered over a 16-year period (2000 to 2016) from the poultry and swine production chains, in Brazil, were investigated by whole-genome sequencing (WGS). Most international lineages belonging to 28 serovars, including, S. enterica serovars S. Schwarzengrund ST96, S. Typhimurium ST19, S. Minnesota ST548, S. Infantis ST32, S. Heidelberg ST15, S. Newport ST45, S. Brandenburg ST65 and S. Kentucky ST198 displayed MDR and virulent genetic backgrounds. In this regard, resistome analysis revealed presence of qnrE1 (identified for the first time in S. Typhimurium from food chain), qnrB19, qnrS1, blaCTX-M-8, blaCTX-M-2 and blaCMY-2 genes, as well as gyrA mutations; whereas ColpVC, IncHI2A, IncHI2, IncFIA, Incl1, IncA/C2, IncR, IncX1 and po111 plasmids were detected. In addition, phylogenetic analysis revealed multiple independent lineages such as S. enterica serovars S. Infantis, S. Schwarzengrund, S. Minnesota, S. Kentucky and S. Brandenburg. In brief, ocurrence and persistence of international lineages of S. enterica serovars in food production chain is supported by conserved genomes and wide virulome and resistome.
Collapse
Affiliation(s)
- Daniel F Monte
- Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, Food Research Center, University of São Paulo, São Paulo, Brazil. .,Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, USA.
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Hanna Berman
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, USA
| | - Louise Cerdeira
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Shivaramu Keelara
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, USA
| | - Siddhartha Thakur
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, USA
| | - Paula J Fedorka-Cray
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, USA
| | - Mariza Landgraf
- Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, Food Research Center, University of São Paulo, São Paulo, Brazil.
| |
Collapse
|
40
|
Cheng RA, Eade CR, Wiedmann M. Embracing Diversity: Differences in Virulence Mechanisms, Disease Severity, and Host Adaptations Contribute to the Success of Nontyphoidal Salmonella as a Foodborne Pathogen. Front Microbiol 2019; 10:1368. [PMID: 31316476 PMCID: PMC6611429 DOI: 10.3389/fmicb.2019.01368] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 05/31/2019] [Indexed: 12/19/2022] Open
Abstract
Not all Salmonella enterica serovars cause the same disease. S. enterica represents an incredibly diverse species comprising >2,600 unique serovars. While some S. enterica serovars are host-restricted, others infect a wide range of hosts. The diseases that nontyphoidal Salmonella (NTS) serovars cause vary considerably, with some serovars being significantly more likely to cause invasive disease in humans than others. Furthermore, while genomic analyses have advanced our understanding of the genetic diversity of these serovars, they have not been able to fully account for the observed clinical differences. One overarching challenge is that much of what is known about Salmonella's general biology and virulence strategies is concluded from studies examining a select few serovars, especially serovar Typhimurium. As targeted control strategies have been implemented to control select serovars, an increasing number of foodborne outbreaks involving serovars that are less frequently associated with human clinical illness are being detected. Harnessing what is known about the diversity of NTS serovars represents an important factor in achieving the ultimate goal of reducing salmonellosis-associated morbidity and mortality worldwide. In this review we summarize the current understanding of the differences and similarities among NTS serovars, highlighting the virulence mechanisms, genetic differences, and sources that characterize S. enterica diversity and contribute to its success as a foodborne pathogen.
Collapse
Affiliation(s)
- Rachel A. Cheng
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Colleen R. Eade
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY, United States
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY, United States
| |
Collapse
|
41
|
Harrand AS, Kovac J, Carroll LM, Guariglia-Oropeza V, Kent DJ, Wiedmann M. Assembly and Characterization of a Pathogen Strain Collection for Produce Safety Applications: Pre-growth Conditions Have a Larger Effect on Peroxyacetic Acid Tolerance Than Strain Diversity. Front Microbiol 2019; 10:1223. [PMID: 31231329 PMCID: PMC6558390 DOI: 10.3389/fmicb.2019.01223] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 05/16/2019] [Indexed: 12/21/2022] Open
Abstract
Effective control of foodborne pathogens on produce requires science-based validation of interventions and control strategies, which typically involves challenge studies with a set of bacterial strains representing the target pathogens or appropriate surrogates. In order to facilitate these types of studies, a produce-relevant strain collection was assembled to represent strains from produce outbreaks or pre-harvest environments, including Listeria monocytogenes (n = 11), Salmonella enterica (n = 23), shiga-toxin producing Escherichia coli (STEC) (n = 13), and possible surrogate organisms (n = 8); all strains were characterized by whole genome sequencing (WGS). Strain diversity was assured by including the 10 most common S. enterica serotypes, L. monocytogenes lineages I-IV, and E. coli O157 as well as selected "non-O157" STEC serotypes. As it has previously been shown that strains and genetic lineages of a pathogen may differ in their ability to survive different stress conditions, a subset of representative strains for each "pathogen group" (e.g., Salmonella, STEC) was selected and assessed for survival of exposure to peroxyacetic acid (PAA) using strains pre-grown under different conditions including (i) low pH, (ii) high salt, (iii) reduced water activity, (iv) different growth phases, (v) minimal medium, and (vi) different temperatures (21°C, 37°C). The results showed that across the three pathogen groups pre-growth conditions had a larger effect on bacterial reduction after PAA exposure as compared to strain diversity. Interestingly, bacteria exposed to salt stress (4.5% NaCl) consistently showed the least reduction after exposure to PAA; however, for STEC, strains pre-grown at 21°C were as tolerant to PAA exposure as strains pre-grown under salt stress. Overall, our data suggests that challenge studies conducted with multi-strain cocktails (pre-grown under a single specific condition) may not necessarily reflect the relevant phenotypic range needed to appropriately assess different intervention strategies.
Collapse
Affiliation(s)
| | - Jasna Kovac
- Department of Food Science, Pennsylvania State University, University Park, PA, United States
| | - Laura M. Carroll
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | | | - David J. Kent
- Department of Statistical Science, Cornell University, Ithaca, NY, United States
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY, United States
| |
Collapse
|
42
|
Feng Y, Lin E, Zou S, Chen CL, Chiu CH. Complete genome sequence of Salmonella enterica serovar Sendai shows H antigen convergence with S. Miami and recent divergence from S. Paratyphi A. BMC Genomics 2019; 20:398. [PMID: 31117944 PMCID: PMC6530103 DOI: 10.1186/s12864-019-5798-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/14/2019] [Indexed: 12/26/2022] Open
Abstract
Background Salmonella enterica consists of over 2500 serovars and displays dichotomy in disease manifestations and host range. Except for the enrichment of pseudogenes in genomes for human-restricted serovars, no hallmark has been identified to distinguish those with host-generalist serovars. The serovar Sendai is rare and human-restricted. Notably, it exhibits an O, H antigen formula as the host-generalist serovar Miami. Results We sequenced the complete genomes of the two serovars Sendai and Miami. Analysis at both nucleotide identity and gene content level demonstrates the same high degree of similarity between Sendai and Paratyphi A, but their distinct CRISPR spacers suggests a recent divergence history. A frameshift mutation occurred in rfbE for the entire lineage of Paratyphi A but not in Sendai, which may explain their distinct O antigens. The nucleotide sequence of Miami’s fliC is nearly identical to Sendai’s. The incongruent phylogeny of this gene with that of the adjacent genes suggests a recombination event responsible for Sendai and Miami possessing the same H antigen. Sendai’s even greater number of pseudogenes than that of Paratyphi A and Typhi indicates its undergoing continued genomic degradation. The phylogenetically distinct human-restricted serovars/strains share pseudogenes with the same inactivation mutations, therefore suggesting that recombination may have occurred and have been facilitated by their overlap in niches. Conclusions Analysis of Sendai’s genome and comparison with others reflect the finer evolutionary signatures of Salmonella in the process of niches changing from facultative to obligate parasite. Electronic supplementary material The online version of this article (10.1186/s12864-019-5798-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ye Feng
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China. .,Institute for Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China. .,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China.
| | - Enze Lin
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute for Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Shengmei Zou
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute for Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Chyi-Liang Chen
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan. .,Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan.
| |
Collapse
|
43
|
Ganji L, Alebouyeh M, Shirazi MH, Zali MR. Comparative transcriptional analysis for Toll-like receptors, inflammatory cytokines, and apoptotic genes in response to different cytolethal-encoding and noncoding isolates of Salmonella enterica and Campylobacter jejuni from food and human stool. Microb Pathog 2019; 133:103550. [PMID: 31112773 DOI: 10.1016/j.micpath.2019.103550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 05/16/2019] [Accepted: 05/17/2019] [Indexed: 12/24/2022]
Abstract
Diversity of Campylobacter and Salmonella strains in interaction with epithelial cells may explain distinct modes of the pathogenesis, varying from mild watery to severe inflammatory diarrhea. We analyzed impact of this diversity, in relation to carriage and expression of cytholethal distending toxin B (cdtB), on alteration of IL-8, TNF-α, TLR2, TLR4, TLR5, CASP3 mRNA and cytokine levels in HT-29 cell line. A diversity was observed for induction of genes among different strains. Great diversity in IL-8 induction was detected between cdtB+ and cdtB- strains. Early analysis showed down-regulation of TNF-α, mostly among cdtB+ strains. Any increase or decrease in expression of TLR2 in the cdtB-C. jejuni strains was orderly correlated with increase or decrease of TLR4 and TNF-α. Up-regulation of CASP3 was followed by upregulation of TLR2, -4 and/or TNF-α, regardless to the cdtB status. In conclusion, induction of inflammatory response could mediate by distinct C. jejuni and S. enterica strains by several ways.
Collapse
Affiliation(s)
- Leila Ganji
- Department of Pathobiology, School of Public Health, University of Medical Sciences, Tehran, Iran; Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Research Center of Health Reference Laboratory, Ministry of Health and Medical Education, Tehran, Iran
| | - Masoud Alebouyeh
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad Hassan Shirazi
- Department of Pathobiology, School of Public Health, University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Science, Tehran, Iran
| |
Collapse
|
44
|
Zhang X, Payne M, Lan R. In silico Identification of Serovar-Specific Genes for Salmonella Serotyping. Front Microbiol 2019; 10:835. [PMID: 31068916 PMCID: PMC6491675 DOI: 10.3389/fmicb.2019.00835] [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: 12/26/2018] [Accepted: 04/01/2019] [Indexed: 11/23/2022] Open
Abstract
Salmonella enterica subspecies enterica is a highly diverse subspecies with more than 1500 serovars and the ability to distinguish serovars within this group is vital for surveillance. With the development of whole-genome sequencing technology, serovar prediction by traditional serotyping is being replaced by molecular serotyping. Existing in silico serovar prediction approaches utilize surface antigen encoding genes, core genome MLST and serovar-specific gene markers or DNA fragments for serotyping. However, these serovar-specific gene markers or DNA fragments only distinguished a small number of serovars. In this study, we compared 2258 Salmonella accessory genomes to identify 414 candidate serovar-specific or lineage-specific gene markers for 106 serovars which includes 24 polyphyletic serovars and the paraphyletic serovar Enteritidis. A combination of several lineage-specific gene markers can be used for the clear identification of the polyphyletic serovars and the paraphyletic serovar. We designed and evaluated an in silico serovar prediction approach by screening 1089 genomes representing 106 serovars against a set of 131 serovar-specific gene markers. The presence or absence of one or more serovar-specific gene markers was used to predict the serovar of an isolate from genomic data. We show that serovar-specific gene markers have comparable accuracy to other in silico serotyping methods with 84.8% of isolates assigned to the correct serovar with no false positives (FP) and false negatives (FN) and 10.5% of isolates assigned to a small subset of serovars containing the correct serovar with varied FP. Combined, 95.3% of genomes were correctly assigned to a serovar. This approach would be useful as diagnosis moves to culture-independent and metagenomic methods as well as providing a third alternative to confirm other genome-based analyses. The identification of a set of gene markers may also be useful in the development of more cost-effective molecular assays designed to detect specific gene markers of the all major serovars in a region. These assays would be useful in serotyping isolates where cultures are no longer obtained and traditional serotyping is therefore impossible.
Collapse
Affiliation(s)
- Xiaomei Zhang
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Michael Payne
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| |
Collapse
|
45
|
Understanding the multifaceted roles of the phosphoenolpyruvate: Phosphotransferase system in regulation of Salmonella virulence using a mutant defective in ptsI and crr expression. Microbiol Res 2019; 223-225:63-71. [PMID: 31178053 DOI: 10.1016/j.micres.2019.04.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 03/23/2019] [Accepted: 04/11/2019] [Indexed: 11/22/2022]
Abstract
The phosphoenolpyruvate (PEP):carbohydrate phosphotransferase system (PTS) catalyzes the translocation of sugar substrates with their concomitant phosphorylation in bacteria. In addition to its intrinsic role in sugar transport and metabolism, numerous recent studies report the versatility of the PTS to interconnect energy and signal transduction in response to sugar availability. In this study, the role of PTS in Salmonella virulence regulation was explored. To decipher the regulatory network coordinated by the PTS during Salmonella infection, a transcriptomic approach was applied to a transposon insertion mutant with defective expression of ptsI and crr, which encode enzyme I and enzyme IIAGlc of the PTS, respectively. There were 114 differentially expressed genes (DEGs) exhibiting two-fold or higher expression changes in the transposon mutant strain, with 13 up-regulated genes versus 101 down-regulated genes. One-third of the DEGs were associated with energy production and carbohydrate/amino acid metabolism pathways, implicating the prominent role of the PTS in carbohydrate transport. With regard to regulation of virulence, the tested mutant decreased the expression of genes associated with quorum sensing, Salmonella pathogenicity islands, flagella, and the PhoPQ regulon. We investigated the possibility of PTS-mediated regulation of virulence determinants identified in the transcriptomic analysis and proposed a regulatory circuit orchestrated by the PTS in Salmonella infection of host cells. These results suggest that Salmonella divergently controls virulence attributes in accordance with the availability of carbohydrates in the environment.
Collapse
|
46
|
Abstract
Pullorum disease, an acute poultry septicemia caused by Salmonella Gallinarum biovar Pullorum, is fatal for young chickens and is a heavy burden on poultry industry. The pathogen is rare in most developed countries but still extremely difficult to eliminate in China. Efficient epidemiological surveillance necessitates clarifying the origin of the isolates from different regions and their phylogenic relationships. Genomic epidemiological analysis of 97 S. Pullorum strains was carried out to reconstruct the phylogeny and transmission history of S. Pullorum. Further analysis demonstrated that functional gene loss and acquisition occurred simultaneously throughout the evolution of S. Pullorum, both of which reflected adaptation to the changing environment. The result of our study will be helpful in surveillance and prevention of pullorum disease. Salmonella enterica subspecies enterica serovar Gallinarum biovar Pullorum (S. Pullorum) is the etiological agent of pullorum disease, causing white diarrhea with high mortality in chickens. There are many unsolved issues surrounding the epidemiology of S. Pullorum, including its origin and transmission history as well as the discordance between its phenotypic heterogeneity and genetic monomorphism. In this paper, we report the results of whole-genome sequencing of a panel of 97 S. Pullorum strains isolated between 1962 and 2014 from four countries across three continents. We utilized 6,795 core genome single nucleotide polymorphisms (SNPs) to reconstruct a phylogenetic tree within a spatiotemporal Bayesian framework, estimating that the most recent common ancestor of S. Pullorum emerged in ∼914 CE (95% confidence interval [95%CI], 565 to 1273 CE). The extant S. Pullorum strains can be divided into four distinct lineages, each of which is significantly associated with geographical distribution. The intercontinental transmissions of lineages III and IV can be traced to the mid-19th century and are probably related to the “Hen Fever” prevalent at that time. Further genomic analysis indicated that the loss or pseudogenization of functional genes involved in metabolism and virulence in S. Pullorum has been ongoing since before and after divergence from the ancestor. In contrast, multiple prophages and plasmids have been acquired by S. Pullorum, and these have endowed it with new characteristics, especially the multidrug resistance conferred by two large plasmids in lineage I. The results of this study provide insight into the evolution of S. Pullorum and prove the efficiency of whole-genome sequencing in epidemiological surveillance of pullorum disease. IMPORTANCE Pullorum disease, an acute poultry septicemia caused by Salmonella Gallinarum biovar Pullorum, is fatal for young chickens and is a heavy burden on poultry industry. The pathogen is rare in most developed countries but still extremely difficult to eliminate in China. Efficient epidemiological surveillance necessitates clarifying the origin of the isolates from different regions and their phylogenic relationships. Genomic epidemiological analysis of 97 S. Pullorum strains was carried out to reconstruct the phylogeny and transmission history of S. Pullorum. Further analysis demonstrated that functional gene loss and acquisition occurred simultaneously throughout the evolution of S. Pullorum, both of which reflected adaptation to the changing environment. The result of our study will be helpful in surveillance and prevention of pullorum disease.
Collapse
|
47
|
Hu L, Stones R, Brown EW, Allard MW, Ma LM, Zhang G. DNA sequences and predicted protein structures of prot6E and sefA genes for Salmonella ser. Enteritidis detection. Food Control 2019. [DOI: 10.1016/j.foodcont.2018.09.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
48
|
Complete Genome Sequence of a Salmonella enterica subsp. enterica Serovar Fresno Isolate Recovered from a Bovine Lymph Node. Microbiol Resour Announc 2019; 8:MRA01338-18. [PMID: 30643877 PMCID: PMC6328650 DOI: 10.1128/mra.01338-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 12/11/2018] [Indexed: 11/21/2022] Open
Abstract
Salmonella enterica serovar Fresno is an infrequently isolated serovar whose ecology and genomic characteristics have not yet been described. To further understand the genomic characteristics of this serovar, we sequenced the complete genome of a single isolate recovered from a bovine lymph node at harvest. Salmonella enterica serovar Fresno is an infrequently isolated serovar whose ecology and genomic characteristics have not yet been described. To further understand the genomic characteristics of this serovar, we sequenced the complete genome of a single isolate recovered from a bovine lymph node at harvest.
Collapse
|
49
|
Antony L, Behr M, Sockett D, Miskimins D, Aulik N, Christopher-Hennings J, Nelson E, Allard MW, Scaria J. Genome divergence and increased virulence of outbreak associated Salmonella enterica subspecies enterica serovar Heidelberg. Gut Pathog 2018; 10:53. [PMID: 30603048 PMCID: PMC6304783 DOI: 10.1186/s13099-018-0279-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 12/15/2018] [Indexed: 11/20/2022] Open
Abstract
Salmonella enterica serotype Heidelberg is primarily a poultry adapted serotype of Salmonella that can also colonize other hosts and cause human disease. In this study, we compared the genomes of outbreak associated non-outbreak causing Salmonella ser. Heidelberg strains from diverse hosts and geographical regions. Human outbreak associated strains in this study were from a 2015 multistate outbreak of Salmonella ser. Heidelberg involving 15 states in the United States which originated from bull calves. Our clinicopathologic examination revealed that cases involving Salmonella ser. Heidelberg strains were predominantly young, less than weeks-old, dairy calves. Pre-existing or concurrent disease was found in the majority of the calves. Detection of Salmonella ser. Heidelberg correlated with markedly increased death losses clinically comparable to those seen in herds infected with S. Dublin, a known serious pathogen of cattle. Whole genome based single nucleotide polymorphism based analysis revealed that these calf isolates formed a distinct cluster along with outbreak associated human isolates. The defining feature of the outbreak associated strains, when compared to older isolates of S. Heidelberg, is that all isolates in this cluster contained Saf fimbrial genes which are generally absent in S. Heidelberg. The acquisition of several single nucleotide polymorphisms and the gain of Saf fimbrial genes may have contributed to the increased disease severity of these Salmonella ser. Heidelberg strains.
Collapse
Affiliation(s)
- Linto Antony
- 1Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD USA.,South Dakota Center for Biologics Research and Commercialization, Brookings, SD USA
| | - Melissa Behr
- 1Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD USA
| | - Donald Sockett
- 3Wisconsin Veterinary Diagnostic Laboratory, University of Wisconsin, Madison, WI USA
| | - Dale Miskimins
- 1Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD USA
| | - Nicole Aulik
- 3Wisconsin Veterinary Diagnostic Laboratory, University of Wisconsin, Madison, WI USA
| | - Jane Christopher-Hennings
- 1Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD USA.,South Dakota Center for Biologics Research and Commercialization, Brookings, SD USA
| | - Eric Nelson
- 1Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD USA.,South Dakota Center for Biologics Research and Commercialization, Brookings, SD USA
| | - Marc W Allard
- 4Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition, U.S. Food and Drug Administration, College Park, MD USA
| | - Joy Scaria
- 1Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD USA.,South Dakota Center for Biologics Research and Commercialization, Brookings, SD USA
| |
Collapse
|
50
|
Binet R, Pettengill EA, Hoffmann M, Hammack TS, Monday SR. Construction of stable fluorescent laboratory control strains for several food safety relevant Enterobacteriaceae. Food Microbiol 2018; 76:553-563. [DOI: 10.1016/j.fm.2017.10.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 10/26/2017] [Accepted: 10/27/2017] [Indexed: 02/06/2023]
|