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Chatterjee R, Chowdhury AR, Mukherjee D, Chakravortty D. From Eberthella typhi to Salmonella Typhi: The Fascinating Journey of the Virulence and Pathogenicity of Salmonella Typhi. ACS OMEGA 2023; 8:25674-25697. [PMID: 37521659 PMCID: PMC10373206 DOI: 10.1021/acsomega.3c02386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 06/30/2023] [Indexed: 08/01/2023]
Abstract
Salmonella Typhi (S. Typhi), the invasive typhoidal serovar of Salmonella enterica that causes typhoid fever in humans, is a severe threat to global health. It is one of the major causes of high morbidity and mortality in developing countries. According to recent WHO estimates, approximately 11-21 million typhoid fever illnesses occur annually worldwide, accounting for 0.12-0.16 million deaths. Salmonella infection can spread to healthy individuals by the consumption of contaminated food and water. Typhoid fever in humans sometimes is accompanied by several other critical extraintestinal complications related to the central nervous system, cardiovascular system, pulmonary system, and hepatobiliary system. Salmonella Pathogenicity Island-1 and Salmonella Pathogenicity Island-2 are the two genomic segments containing genes encoding virulent factors that regulate its invasion and systemic pathogenesis. This Review aims to shed light on a comparative analysis of the virulence and pathogenesis of the typhoidal and nontyphoidal serovars of S. enterica.
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Affiliation(s)
- Ritika Chatterjee
- Department
of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Atish Roy Chowdhury
- Department
of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Debapriya Mukherjee
- Department
of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Dipshikha Chakravortty
- Department
of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bangalore, Karnataka 560012, India
- Centre
for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, Karnataka 560012, India
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Esteban-Cuesta I, Labrador M, Hunt K, Reese S, Fischer J, Schwaiger K, Gareis M. Phenotypic and Genetic Comparison of a Plant-Internalized and an Animal-Isolated Salmonella Choleraesuis Strain. Microorganisms 2021; 9:microorganisms9081554. [PMID: 34442630 PMCID: PMC8398053 DOI: 10.3390/microorganisms9081554] [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: 06/22/2021] [Revised: 07/05/2021] [Accepted: 07/16/2021] [Indexed: 11/16/2022] Open
Abstract
Contamination of fresh produce with human pathogens poses an important risk for consumers, especially after raw consumption. Moreover, if microorganisms are internalized, no removal by means of further hygienic measures would be possible. Human pathogenic bacteria identified in these food items are mostly of human or animal origin and an adaptation to this new niche and particularly for internalization would be presumed. This study compares a plant-internalized and an animal-borne Salmonella enterica subsp. enterica serovar Choleraesuis aiming at the identification of adaptation of the plant-internalized strain to its original environment. For this purpose, a phenotypical characterization by means of growth curves under conditions resembling the indigenous environment from the plant-internalized strain and further analyses using Pulsed-field gel electrophoresis and Matrix-assisted laser desorption ionization time of flight spectrometry were assessed. Furthermore, comparative genomic analyses by means of single nucleotide polymorphisms and identification of present/absent genes were performed. Although some phenotypical and genetic differences could be found, no signs of a specific adaptation for colonization and internalization in plants could be clearly identified. This could suggest that any Salmonella strain could directly settle in this niche without any evolutionary process being necessary. Further comparative analysis including internalized strains would be necessary to assess this question. However, these kinds of strains are not easily available.
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Affiliation(s)
- Irene Esteban-Cuesta
- Chair of Food Safety, Veterinary Faculty, LMU Munich, 85764 Oberschleissheim, Germany; (K.H.); (K.S.); (M.G.)
- Correspondence:
| | - Mirian Labrador
- Departamento de Producción Animal y Ciencia de los Alimentos, Veterinary Faculty, Instituto Agroalimentario de Aragon-IA2, University of Zaragoza-CITA, 50013 Zaragoza, Spain;
| | - Katharina Hunt
- Chair of Food Safety, Veterinary Faculty, LMU Munich, 85764 Oberschleissheim, Germany; (K.H.); (K.S.); (M.G.)
| | - Sven Reese
- Chair of Anatomy, Histology and Embryology, Department of Veterinary Sciences, Faculty of Veterinary Medicine, LMU Munich, 80539 Munich, Germany;
| | - Jennie Fischer
- National Salmonella Reference Laboratory, Unit Food Microbiology, Host-Pathogen-Interactions, Department of Biological Safety, German Federal Institute for Risk Assessment (Bundesinstitut für Risikobewertung—BfR), 12277 Berlin, Germany;
| | - Karin Schwaiger
- Chair of Food Safety, Veterinary Faculty, LMU Munich, 85764 Oberschleissheim, Germany; (K.H.); (K.S.); (M.G.)
- Unit of Food Hygiene and Technology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, 1220 Vienna, Austria
| | - Manfred Gareis
- Chair of Food Safety, Veterinary Faculty, LMU Munich, 85764 Oberschleissheim, Germany; (K.H.); (K.S.); (M.G.)
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Sahibzada S, Pang S, Hernández-Jover M, Jordan D, Abraham S, O'Dea M, Heller J. Prevalence and antimicrobial resistance of MRSA across different pig age groups in an intensive pig production system in Australia. Zoonoses Public Health 2020; 67:576-586. [PMID: 32458580 DOI: 10.1111/zph.12721] [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: 04/03/2019] [Revised: 11/21/2019] [Accepted: 04/14/2020] [Indexed: 01/22/2023]
Abstract
This observational study aimed to determine MRSA prevalence using strain-specific real-time PCR at the pig level, stratified by age groupings, within a pig enterprise. A total of 658 samples were collected from individual pigs (n = 618) and the piggery environment (n = 40), distributed amongst five different pig age groups. Presumptive MRSA isolates were confirmed by the presence of mecA, and MALDI-TOF was performed for species verification. All isolates were tested against 18 different antimicrobials. MRSA was isolated from 75.2% (95% CI 71.8-78.6) of samples collected from pigs, and 71% of the MRSA isolates from this source were identified as community-associated (CA)-MRSA ST93, while the remainder were livestock-associated (LA)-MRSA ST398. Amongst environmental isolates, 80% (CI 64.3-95.7) were ST93 and the remainder ST398. All MRSA isolates from pigs and the environment were susceptible to ciprofloxacin, gentamicin, linezolid, mupirocin, rifampicin, sulfamethoxazole-trimethoprim, teicoplanin and vancomycin. Phenotypic rates of resistance were penicillin (100%), clindamycin (97.6%), erythromycin (96.3%), ceftiofur (93.7%), chloramphenicol (81.2%), tetracycline (63.1%) and amoxicillin-clavulanate (63.9%). A low prevalence of resistance (9.2%) was observed against neomycin and quinupristin-dalfopristin. The probability of MRSA carriage in dry sows (42.2%) was found to be significantly lower (p < .001) when compared to other age groups: farrowing sows (76.8%, RR1.82), weaners (97.8%, RR 2.32), growers (94.2%, RR 2.23) and finishers (98.3%, RR 2.33). Amongst different production age groups, a significant difference was also found in antimicrobial resistance for amoxicillin-clavulanate, neomycin, chloramphenicol and tetracycline. Using the RT-PCR assay adopted in this study, filtering of highly prevalent ST93 and non-ST93 isolates was performed at high throughput and low cost. In conclusion, this study found that weaner pigs presented a higher risk for CA-MRSA and antimicrobial resistance compared to other age groups. These findings have major implications for how investigations of MRSA outbreaks should be approached under the One-Health context.
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Affiliation(s)
- Shafi Sahibzada
- Antimicrobial Resistance and Infectious Diseases Laboratory, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia.,School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia.,Graham Centre for Agricultural Innovation, Wagga Wagga, NSW, Australia
| | - Stanley Pang
- Antimicrobial Resistance and Infectious Diseases Laboratory, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia.,PathWest Laboratory Medicine - WA, Fiona Stanley Hospital, Murdoch, Australia
| | - Marta Hernández-Jover
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia.,Graham Centre for Agricultural Innovation, Wagga Wagga, NSW, Australia
| | - David Jordan
- New South Wales Department of Primary Industries, Wollongbar, NSW, Australia
| | - Sam Abraham
- Antimicrobial Resistance and Infectious Diseases Laboratory, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Mark O'Dea
- Antimicrobial Resistance and Infectious Diseases Laboratory, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Jane Heller
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia.,Graham Centre for Agricultural Innovation, Wagga Wagga, NSW, Australia
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Mellor KC, Petrovska L, Thomson NR, Harris K, Reid SWJ, Mather AE. Antimicrobial Resistance Diversity Suggestive of Distinct Salmonella Typhimurium Sources or Selective Pressures in Food-Production Animals. Front Microbiol 2019; 10:708. [PMID: 31031720 PMCID: PMC6473194 DOI: 10.3389/fmicb.2019.00708] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 03/21/2019] [Indexed: 11/13/2022] Open
Abstract
Salmonella enterica subsp. enterica serovar Typhimurium is a common cause of enterocolitis in humans globally, with multidrug resistant (MDR) strains posing an enhanced threat. S. Typhimurium is also a pathogen in food-production animals, and these populations can act as reservoirs of the bacterium. Therefore, surveillance and control measures within food-production animal populations are of importance both to animal and human health and have the potential to be enhanced though improved understanding of the epidemiology of S. Typhimurium within and between food-production animal populations. Here, data from Scotland and national surveillance England and Wales data for isolates from cattle (n = 1115), chickens (n = 248) and pigs (n = 2174) collected between 2003 and 2014 were analyzed. Ecological diversity analyses and rarefaction curves were used to compare the diversity of observed antimicrobial resistance (AMR) profiles between the host species, and within host species populations. Higher AMR profile diversity was observed in isolates from pigs compared to chickens across diversity measures and isolates from cattle for three of four diversity measures. Variation in AMR profile diversity between production sectors was noted, with higher AMR diversity of isolates from broiler compared to layer chickens, breeder compared to rearer and finisher pigs and beef compared to dairy cattle. Findings indicate variation in AMR profile diversity both within and between food-production animal host species. These observations suggest alternate sources of AMR bacteria and/or variation in selective evolutionary pressures within and between food-production animal host species populations.
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Affiliation(s)
- Kate C. Mellor
- Royal Veterinary College, Hatfield, United Kingdom
- London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | - Nicholas R. Thomson
- London School of Hygiene & Tropical Medicine, London, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Kate Harris
- Animal and Plant Health Agency, Weybridge, United Kingdom
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Gal-Mor O. Persistent Infection and Long-Term Carriage of Typhoidal and Nontyphoidal Salmonellae. Clin Microbiol Rev 2019; 32:e00088-18. [PMID: 30487167 PMCID: PMC6302356 DOI: 10.1128/cmr.00088-18] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The ability of pathogenic bacteria to affect higher organisms and cause disease is one of the most dramatic properties of microorganisms. Some pathogens can establish transient colonization only, but others are capable of infecting their host for many years or even for a lifetime. Long-term infection is called persistence, and this phenotype is fundamental for the biology of important human pathogens, including Helicobacter pylori, Mycobacterium tuberculosis, and Salmonella enterica Both typhoidal and nontyphoidal serovars of the species Salmonella enterica can cause persistent infection in humans; however, as these two Salmonella groups cause clinically distinct diseases, the characteristics of their persistent infections in humans differ significantly. Here, following a general summary of Salmonella pathogenicity, host specificity, epidemiology, and laboratory diagnosis, I review the current knowledge about Salmonella persistence and discuss the relevant epidemiology of persistence (including carrier rate, duration of shedding, and host and pathogen risk factors), the host response to Salmonella persistence, Salmonella genes involved in this lifestyle, as well as genetic and phenotypic changes acquired during prolonged infection within the host. Additionally, I highlight differences between the persistence of typhoidal and nontyphoidal Salmonella strains in humans and summarize the current gaps and limitations in our understanding, diagnosis, and curing of persistent Salmonella infections.
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Affiliation(s)
- Ohad Gal-Mor
- Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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Fu S, Hiley L, Octavia S, Tanaka MM, Sintchenko V, Lan R. Comparative genomics of Australian and international isolates of Salmonella Typhimurium: correlation of core genome evolution with CRISPR and prophage profiles. Sci Rep 2017; 7:9733. [PMID: 28851865 PMCID: PMC5575072 DOI: 10.1038/s41598-017-06079-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 06/07/2017] [Indexed: 12/16/2022] Open
Abstract
Salmonella enterica subsp enterica serovar Typhimurium (S. Typhimurium) is a serovar with broad host range. To determine the genomic diversity of S. Typhimurium, we sequenced 39 isolates (37 Australian and 2 UK isolates) representing 14 Repeats Groups (RGs) determined primarily by clustered regularly interspaced short palindromic repeats (CRISPR). Analysis of single nucleotide polymorphisms (SNPs) among the 39 isolates yielded an average of 1,232 SNPs per isolate, ranging from 128 SNPs to 11,339 SNPs relative to the reference strain LT2. Phylogenetic analysis of the 39 isolates together with 66 publicly available genomes divided the 105 isolates into five clades and 19 lineages, with the majority of the isolates belonging to clades I and II. The composition of CRISPR profiles correlated well with the lineages, showing progressive deletion and occasional duplication of spacers. Prophage genes contributed nearly a quarter of the S. Typhimurium accessory genome. Prophage profiles were found to be correlated with lineages and CRISPR profiles. Three new variants of HP2-like P2 prophage, several new variants of P22 prophage and a plasmid-like genomic island StmGI_0323 were found. This study presents evidence of horizontal transfer from other serovars or species and provides a broader understanding of the global genomic diversity of S. Typhimurium.
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Affiliation(s)
- Songzhe Fu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Lester Hiley
- Public Health Microbiology Laboratory, Forensic and Scientific Services, Queensland Department of Health, Brisbane, Queensland, Australia
| | - Sophie Octavia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Mark M Tanaka
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Vitali Sintchenko
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Sydney, New South Wales, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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PGAdb-builder: A web service tool for creating pan-genome allele database for molecular fine typing. Sci Rep 2016; 6:36213. [PMID: 27824078 PMCID: PMC5099940 DOI: 10.1038/srep36213] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/12/2016] [Indexed: 01/07/2023] Open
Abstract
With the advance of next generation sequencing techniques, whole genome sequencing (WGS) is expected to become the optimal method for molecular subtyping of bacterial isolates. To use WGS as a general subtyping method for disease outbreak investigation and surveillance, the layout of WGS-based typing must be comparable among laboratories. Whole genome multilocus sequence typing (wgMLST) is an approach that achieves this requirement. To apply wgMLST as a standard subtyping approach, a pan-genome allele database (PGAdb) for the population of a bacterial organism must first be established. We present a free web service tool, PGAdb-builder (http://wgmlstdb.imst.nsysu.edu.tw), for the construction of bacterial PGAdb. The effectiveness of PGAdb-builder was tested by constructing a pan-genome allele database for Salmonella enterica serovar Typhimurium, with the database being applied to create a wgMLST tree for a panel of epidemiologically well-characterized S. Typhimurium isolates. The performance of the wgMLST-based approach was as high as that of the SNP-based approach in Leekitcharoenphon’s study used for discerning among epidemiologically related and non-related isolates.
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Rehman A, Sarwar Y, Raza ZA, Hussain SZ, Mustafa T, Khan WS, Ghauri MA, Haque A, Hussain I. Metal nanoparticle assisted polymerase chain reaction for strain typing of Salmonella Typhi. Analyst 2016; 140:7366-72. [PMID: 26381602 DOI: 10.1039/c5an01286d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Salmonella enterica serotype Typhi (S. Typhi) is the causative agent of typhoid fever and remains a major health threat in most of the developing countries. The prompt diagnosis of typhoid directly from the patient's blood requires high level of sensitivity and specificity. Some of us were the first to report PCR based diagnosis of typhoid. This approach has since then been reported by many scientists using different genomic targets. Since the number of bacteria circulating in the blood of a patient can be as low as 0.3 cfu ml(-1), there is always a room for improvement in diagnostic PCR. In the present study, the role of different types of nanoparticles was investigated to improve the existing PCR based methods for diagnosis and strain typing of S. Typhi (targeting Variable Number of Tandem Repeats [VNTR]) by using optimized PCR systems. Three different types of nanoparticles were used i.e., citrate stabilized gold nanoparticles, rhamnolipid stabilized gold and silver nanoparticles, and magnetic iron oxide nanoparticles. The non-specific amplification was significantly reduced in VNTR typing when gold and silver nanoparticles were used in an appropriate concentration. More importantly, the addition of nanoparticles decreased the non-specificity to a significant level in the case of multiplex PCR thus further validating the reliability of PCR for the diagnosis of typhoid.
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Affiliation(s)
- Asma Rehman
- Nanobiotech Group, National Institute for Biotechnology & Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Pakistan
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Mohammed M, Cormican M. Whole genome sequencing provides possible explanations for the difference in phage susceptibility among two Salmonella Typhimurium phage types (DT8 and DT30) associated with a single foodborne outbreak. BMC Res Notes 2015; 8:728. [PMID: 26613761 PMCID: PMC4661946 DOI: 10.1186/s13104-015-1687-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 11/10/2015] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Phage typing has been used for decades as a rapid, low cost approach for the epidemiological surveillance of Salmonella enterica subsp. enterica serovar Typhimurium. Although molecular methods are replacing phage typing the system is still in use and provides a valuable model for study of phage-host interaction. Phage typing depends on the pattern of bacterial resistance or sensitivity to a panel of specific bacteriophages. In the phage typing scheme, S. Typhimurium definitive phage types (DT) 8 and 30 differ greatly in their susceptibility to the 30 typing phages of S. Typhimurium; DT8 is susceptible to 11 phages whereas DT30 is resistant to all typing phages except one phage although both DT8 and DT30 were reported to be associated with a single foodborne salmonellosis outbreak in Ireland between 2009 and 2011. We wished to study the genomic correlates of the DT8 and DT30 difference in phage susceptibility using the whole genome sequence (WGS) of S. Typhimurium DT8 and DT30 representatives. RESULTS Comparative genome analysis revealed that both S. Typhimurium DT8 and DT30 are lysogenic for three prophages including two S. Typhimurium associated prophages (Gifsy-2 and ST64B) and one S. Enteritidis associated prophage (Enteritidis lysogenic phage S) which has not been detected previously in S. Typhimurium. Furthermore, DT8 and DT30 contain identical clustered regularly interspaced short palindromic repeats (CRISPRs). Interestingly, S. Typhimurium DT8 harbours an accessory genome represented by a virulence plasmid that is highly related to the pSLT plasmid of S. Typhimurium strain LT2 (phage typed as DT4) and codes a unique methyltransferase (MTase); M.EcoGIX related MTase. This plasmid is not detected in DT30. On the other hand, DT30 carries a unique genomic island similar to the integrative and conjugative element (ICE) of Enterotoxigenic Escherichia coli (ETEC) and encodes type IV secretion pathway system (T4SS) and several hypothetical proteins. This genomic island is not detected in DT8. CONCLUSIONS We suggest that differences in phage susceptibility between DT8 and DT30 may be related to acquisition of ICE in DT30 and loss of pSLT like plasmid that might be associated with DT30 resistance to almost all phages used in the typing scheme. Additional studies are required to determine the significance of the differences among DT8 and DT30 in relation to the difference in phage susceptibility. This study represents an initial step toward understanding the molecular basis of this host-phage relationship.
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Affiliation(s)
- Manal Mohammed
- School of Medicine, National University of Ireland Galway, Galway, Ireland.
| | - Martin Cormican
- School of Medicine, National University of Ireland Galway, Galway, Ireland.
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Hayford AE, Brown EW, Zhao S, Mammel MK, Gangiredla J, Abbott JW, Friedman SL, Ayers SL, Lewis JL, Lacher DW, McDermott P, Elkins CA. Genetic and resistance phenotypic subtyping of Salmonella Saintpaul isolates from various food sources and humans: Phylogenetic concordance in combinatory analyses. INFECTION GENETICS AND EVOLUTION 2015; 36:92-107. [PMID: 26299886 DOI: 10.1016/j.meegid.2015.08.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 08/10/2015] [Accepted: 08/18/2015] [Indexed: 10/23/2022]
Abstract
Bacterial pathogen subtyping for public health traceback of foodborne outbreaks has increasingly produced a number of disparate molecular techniques of varying resolution. Here, we bridge the molecular divide across three methodologies, transform data types for cross-comparison, and test phylogenetic concordance. Single nucleotide polymorphism (SNP) discovery was combined with pulsed-field gel electrophoresis (PFGE) and antimicrobial susceptibility profiles for identifying and differentiating 183 strains of closely related Salmonella enterica serovar Saintpaul isolates from retail meats, produce-associated outbreaks, and clinical sources. Fifty-six SNPs across 30 different genes were identified by comparative genomic analysis. These SNPs stratified general, monophyletic S. Saintpaul serovar specific signatures down to informative strain-specific markers. This SNP panel resulted in 17 distinct genotypes that, in concert with standard PFGE profiling, generated additional discriminatory power among clonal swarms of isolates when the data were transformed into a cross-comparable binary format. In a limited number of cases, antimicrobial susceptibility profiles (ASP) provided additional attributes for some strains when combined similarly. However, as expected from presumably acquired elements, resistant and susceptible populations produced some conflicting signals in most clonal complexes but they remained largely undisruptive to the general concordance. Taken in concert together, the three datasets (SNPs, PFGE,ASP) yielded a matrix of 156 independent phylogenetic characters that were statistically evaluated and found to be largely congruent, resulting in a consistently structured, non-homoplastic, phylogenetic signal and tree topology.
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Affiliation(s)
- Alice E Hayford
- Division of Molecular Biology, Center for Food Safety Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA.
| | - Eric W Brown
- Division of Microbiology, Center for Food Safety and Applied Nutrition, U S Food and Drug Administration, College Park, MD 20740, USA
| | - Shaohua Zhao
- Division of Animal and Food Microbiology, Center for Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA
| | - Mark K Mammel
- Division of Molecular Biology, Center for Food Safety Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA
| | - Jayanthi Gangiredla
- Division of Molecular Biology, Center for Food Safety Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA
| | - Jason W Abbott
- Division of Animal and Food Microbiology, Center for Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA
| | - Sharon L Friedman
- Division of Animal and Food Microbiology, Center for Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA
| | - Sherry L Ayers
- Division of Animal and Food Microbiology, Center for Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA
| | - Jada L Lewis
- Division of Molecular Biology, Center for Food Safety Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA
| | - David W Lacher
- Division of Molecular Biology, Center for Food Safety Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA
| | - Patrick McDermott
- National Antimicrobial Resistance Monitoring System,Center for Veterinary Medicine, U. S. Food Drug Administration, Laurel, MD 20708, USA
| | - Christopher A Elkins
- Division of Molecular Biology, Center for Food Safety Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA
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Wuyts V, Mattheus W, Roosens NHC, Marchal K, Bertrand S, De Keersmaecker SCJ. A multiplex oligonucleotide ligation-PCR as a complementary tool for subtyping of Salmonella Typhimurium. Appl Microbiol Biotechnol 2015. [PMID: 26205523 PMCID: PMC4561068 DOI: 10.1007/s00253-015-6831-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Subtyping below the serovar level is essential for surveillance and outbreak detection and investigation of Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) and its monophasic variant 1,4,[5],12:i:- (S. 1,4,[5],12:i:-), frequent causes of foodborne infections. In an attempt to overcome the intrinsic shortcomings of currently used subtyping techniques, a multiplex oligonucleotide ligation-PCR (MOL-PCR) assay was developed which combines different types of molecular markers in a high-throughput microsphere suspension array. The 52 molecular markers include prophage genes, amplified fragment length polymorphism (AFLP) elements, Salmonella genomic island 1 (SGI1), allantoinase gene allB, MLVA locus STTR10, antibiotic resistance genes, single nucleotide polymorphisms (SNPs) and phase 2 flagellar gene fljB. The in vitro stability of these markers was confirmed in a serial passage experiment. The validation of the MOL-PCR assay for subtyping of S. Typhimurium and S. 1,4,[5],12:i:- on 519 isolates shows that the method is rapid, reproducible, flexible, accessible, easy to use and relatively inexpensive. Additionally, a 100 % typeability and a discriminatory power equivalent to that of phage typing were observed, and epidemiological concordance was assessed on isolates of 2 different outbreaks. Furthermore, a data analysis method is provided so that the MOL-PCR assay allows for objective, computerised data analysis and data interpretation of which the results can be easily exchanged between different laboratories in an international surveillance network.
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Affiliation(s)
- Véronique Wuyts
- Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 20 bus 2460, 3001, Leuven, Belgium
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Defining the Core Genome of Salmonella enterica Serovar Typhimurium for Genomic Surveillance and Epidemiological Typing. J Clin Microbiol 2015; 53:2530-8. [PMID: 26019201 DOI: 10.1128/jcm.03407-14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 05/25/2015] [Indexed: 11/20/2022] Open
Abstract
Salmonella enterica serovar Typhimurium is the most common Salmonella serovar causing foodborne infections in Australia and many other countries. Twenty-one S. Typhimurium strains from Salmonella reference collection A (SARA) were analyzed using Illumina high-throughput genome sequencing. Single nucleotide polymorphisms (SNPs) in 21 SARA strains ranged from 46 to 11,916 SNPs, with an average of 1,577 SNPs per strain. Together with 47 strains selected from publicly available S. Typhimurium genomes, the S. Typhimurium core genes (STCG) were determined. The STCG consist of 3,846 genes, a set that is much larger than that of the 2,882 Salmonella core genes (SCG) found previously. The STCG together with 1,576 core intergenic regions (IGRs) were defined as the S. Typhimurium core genome. Using 93 S. Typhimurium genomes from 13 epidemiologically confirmed community outbreaks, we demonstrated that typing based on the S. Typhimurium core genome (STCG plus core IGRs) provides superior resolution and higher discriminatory power than that based on SCG for outbreak investigation and molecular epidemiology of S. Typhimurium. STCG and STCG plus core IGR typing achieved 100% separation of all outbreaks compared to that of SCG typing, which failed to separate isolates from two outbreaks from background isolates. Defining the S. Typhimurium core genome allows standardization of genes/regions to be used for high-resolution epidemiological typing and genomic surveillance of S. Typhimurium.
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Octavia S, Sara J, Lan R. Characterization of a large novel phage-like plasmid in Salmonella enterica serovar Typhimurium. FEMS Microbiol Lett 2015; 362:fnv044. [PMID: 25795590 DOI: 10.1093/femsle/fnv044] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/16/2015] [Indexed: 11/14/2022] Open
Abstract
Salmonella enterica serovar Typhimurium is a food-borne pathogen and a leading cause of gastroenteritis in humans. Recently, we sequenced a phage-type DT108 strain (L945) and found reads with high similarity to both Salmonella typhi strain CT18 plasmid pHCM2 and bacteriophage SSU5. In this study, we completely sequenced the novel phage-like plasmid which was designated as pSTM_Φ. The presence of this phage-like plasmid was examined in a collection of 284 Salmonella Typhimurium isolates using PCR of the parB gene and only one other isolate (L946) was found to carry the phage-like plasmid suggesting that it is infrequently present amongst Salmonella Typhimurium isolates. pSTM_Φ is a circular phage-like plasmid of 107.7 kb encoding 132 coding regions (ORFs) with the majority of the ORFs encoding hypothetical proteins. Comparative analysis with other closely related phage-like plasmids and the SSU5 phage revealed that there were four divergent lineages of phage-like plasmids found in the family of Enterobacteriaceae. In conclusion, pSTM_Φ is a new member of an emerging family of phage-like plasmids.
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Affiliation(s)
- Sophie Octavia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Josephine Sara
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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Bachmann NL, Petty NK, Ben Zakour NL, Szubert JM, Savill J, Beatson SA. Genome analysis and CRISPR typing of Salmonella enterica serovar Virchow. BMC Genomics 2014; 15:389. [PMID: 24885207 PMCID: PMC4042001 DOI: 10.1186/1471-2164-15-389] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 05/02/2014] [Indexed: 12/11/2022] Open
Abstract
Background Salmonella enterica subsp. enterica serovar Virchow has been recognized as a significant health burden in Asia, Australia and Europe. In addition to its global distribution, S. Virchow is clinically significant due to the frequency at which it causes invasive infections and its association with outbreaks arising from food-borne transmission. Here, we examine the genome of an invasive isolate of S. Virchow SVQ1 (phage type 8) from an outbreak in southeast Queensland, Australia. In addition to identifying new potential genotyping targets that could be used for discriminating between S. Virchow strains in outbreak scenarios, we also aimed to carry out a comprehensive comparative analysis of the S. Virchow genomes. Results Genome comparisons between S. Virchow SVQ1 and S. Virchow SL491, a previously published strain, identified a high degree of genomic similarity between the two strains with fewer than 200 single nucleotide differences. Clustered Regularly Interspaced Palindromic Repeats (CRISPR) regions were identified as a highly variable region that could be used to discriminate between S. Virchow isolates. We amplified and sequenced the CRISPR regions of fifteen S. Virchow isolates collected from seven different outbreaks across Australia. We observed three allelic types of the CRISPR region from these isolates based on the presence/absence of the spacers and were able to discriminate S. Virchow phage type 8 isolates originating from different outbreaks. A comparison with 27 published Salmonella genomes found that the S. Virchow SVQ1 genome encodes 11 previously described Salmonella Pathogenicity Islands (SPI), as well as additional genomic islands including a remnant integrative conjugative element that is distinct from SPI-7. In addition, the S. Virchow genome possesses a novel prophage that encodes the Type III secretion system effector protein SopE, a key Salmonella virulence factor. The prophage shares very little similarity to the SopE prophages found in other Salmonella serovars suggesting an independent acquisition of sopE. Conclusions The availability of this genome will serve as a genome template and facilitate further studies on understanding the virulence and global distribution of the S. Virchow serovar, as well as the development of genotyping methods for outbreak investigations. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-389) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | - John Savill
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
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Zheng J, Pettengill J, Strain E, Allard MW, Ahmed R, Zhao S, Brown EW. Genetic diversity and evolution of Salmonella enterica serovar Enteritidis strains with different phage types. J Clin Microbiol 2014; 52:1490-500. [PMID: 24574287 PMCID: PMC3993623 DOI: 10.1128/jcm.00051-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 02/18/2014] [Indexed: 11/20/2022] Open
Abstract
Phage typing has been used for the epidemiological surveillance of Salmonella enterica serovar Enteritidis for over 2 decades. However, knowledge of the genetic and evolutionary relationships between phage types is very limited, making differences difficult to interpret. Here, single nucleotide polymorphisms (SNPs) identified from whole-genome comparisons were used to determine the relationships between some S. Enteritidis phage types (PTs) commonly associated with food-borne outbreaks in the United States. Emphasis was placed on the predominant phage types PT8, PT13a, and PT13 in North America. With >89,400 bp surveyed across 98 S. Enteritidis isolates representing 14 distinct phage types, 55 informative SNPs were discovered within 23 chromosomally anchored loci. To maximize the discriminatory and evolutionary partitioning of these highly homogeneous strains, sequences comprising informative SNPs were concatenated into a single combined data matrix and subjected to phylogenetic analysis. The resultant phylogeny allocated most S. Enteritidis isolates into two distinct clades (clades I and II) and four subclades. Synapomorphic (shared and derived) sets of SNPs capable of distinguishing individual clades/subclades were identified. However, individual phage types appeared to be evolutionarily disjunct when mapped to this phylogeny, suggesting that phage typing may not be valid for making phylogenetic inferences. Furthermore, the set of SNPs identified here represents useful genetic markers for strain differentiation of more clonal S. Enteritidis strains and provides core genotypic markers for future development of a SNP typing scheme with S. Enteritidis.
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Affiliation(s)
- Jie Zheng
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - James Pettengill
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Errol Strain
- 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
| | - Rafiq Ahmed
- National Microbiology Laboratory, Public Health Agency of Canada, Canadian Science Centre for Human and Animal Health, Winnipeg, MB, Canada
| | - Shaohua Zhao
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Eric W. Brown
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
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Foley SL, Johnson TJ, Ricke SC, Nayak R, Danzeisen J. Salmonella pathogenicity and host adaptation in chicken-associated serovars. Microbiol Mol Biol Rev 2013; 77:582-607. [PMID: 24296573 PMCID: PMC3973385 DOI: 10.1128/mmbr.00015-13] [Citation(s) in RCA: 185] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Enteric pathogens such as Salmonella enterica cause significant morbidity and mortality. S. enterica serovars are a diverse group of pathogens that have evolved to survive in a wide range of environments and across multiple hosts. S. enterica serovars such as S. Typhi, S. Dublin, and S. Gallinarum have a restricted host range, in which they are typically associated with one or a few host species, while S. Enteritidis and S. Typhimurium have broad host ranges. This review examines how S. enterica has evolved through adaptation to different host environments, especially as related to the chicken host, and continues to be an important human pathogen. Several factors impact host range, and these include the acquisition of genes via horizontal gene transfer with plasmids, transposons, and phages, which can potentially expand host range, and the loss of genes or their function, which would reduce the range of hosts that the organism can infect. S. Gallinarum, with a limited host range, has a large number of pseudogenes in its genome compared to broader-host-range serovars. S. enterica serovars such as S. Kentucky and S. Heidelberg also often have plasmids that may help them colonize poultry more efficiently. The ability to colonize different hosts also involves interactions with the host's immune system and commensal organisms that are present. Thus, the factors that impact the ability of Salmonella to colonize a particular host species, such as chickens, are complex and multifactorial, involving the host, the pathogen, and extrinsic pressures. It is the interplay of these factors which leads to the differences in host ranges that we observe today.
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Pang S, Octavia S, Feng L, Liu B, Reeves PR, Lan R, Wang L. Genomic diversity and adaptation of Salmonella enterica serovar Typhimurium from analysis of six genomes of different phage types. BMC Genomics 2013; 14:718. [PMID: 24138507 PMCID: PMC3853940 DOI: 10.1186/1471-2164-14-718] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 10/11/2013] [Indexed: 12/28/2022] Open
Abstract
Background Salmonella enterica serovar Typhimurium (or simply Typhimurium) is the most common serovar in both human infections and farm animals in Australia and many other countries. Typhimurium is a broad host range serovar but has also evolved into host-adapted variants (i.e. isolated from a particular host such as pigeons). Six Typhimurium strains of different phage types (defined by patterns of susceptibility to lysis by a set of bacteriophages) were analysed using Illumina high-throughput genome sequencing. Results Variations between strains were mainly due to single nucleotide polymorphisms (SNPs) with an average of 611 SNPs per strain, ranging from 391 SNPs to 922 SNPs. There were seven insertions/deletions (indels) involving whole or partial gene deletions, four inactivation events due to IS200 insertion and 15 pseudogenes due to early termination. Four of these inactivated or deleted genes may be virulence related. Nine prophage or prophage remnants were identified in the six strains. Gifsy-1, Gifsy-2 and the sopE2 and sspH2 phage remnants were present in all six genomes while Fels-1, Fels-2, ST64B, ST104 and CP4-57 were variably present. Four strains carried the 90-kb plasmid pSLT which contains several known virulence genes. However, two strains were found to lack the plasmid. In addition, one strain had a novel plasmid similar to Typhi strain CT18 plasmid pHCM2. Conclusion The genome data suggest that variations between strains were mainly due to accumulation of SNPs, some of which resulted in gene inactivation. Unique genetic elements that were common between host-adapted phage types were not found. This study advanced our understanding on the evolution and adaptation of Typhimurium at genomic level.
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Affiliation(s)
| | | | | | | | | | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia.
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18
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Draft Genome Sequences for Ten Salmonella enterica Serovar Typhimurium Phage Type 135 Variants. GENOME ANNOUNCEMENTS 2013; 1:1/3/e00293-13. [PMID: 23792739 PMCID: PMC3675509 DOI: 10.1128/genomea.00293-13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium) is a common cause of gastroenteritis in humans. Here, we report the draft genome sequences of 10 isolates of an S. Typhimurium phage type 135 variant that is linked to egg-associated outbreaks in Tasmania, Australia.
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Barco L, Barrucci F, Olsen JE, Ricci A. Salmonella source attribution based on microbial subtyping. Int J Food Microbiol 2013; 163:193-203. [PMID: 23562696 DOI: 10.1016/j.ijfoodmicro.2013.03.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Revised: 01/20/2013] [Accepted: 03/02/2013] [Indexed: 10/27/2022]
Abstract
Source attribution of cases of food-borne disease represents a valuable tool for identifying and prioritizing effective food-safety interventions. Microbial subtyping is one of the most common methods to infer potential sources of human food-borne infections. So far, Salmonella microbial subtyping source attribution models have been implemented by using serotyping and phage-typing data. Molecular-based methods may prove to be similarly valuable in the future, as already demonstrated for other food-borne pathogens like Campylobacter. This review assesses the state of the art concerning Salmonella source attribution through microbial subtyping approach. It summarizes the available microbial subtyping attribution models and discusses the use of conventional phenotypic typing methods, as well as of the most commonly applied molecular typing methods in the European Union (EU) laboratories in the context of their potential applicability for Salmonella source attribution studies.
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Affiliation(s)
- Lisa Barco
- OIE, National Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, Padova, 35020 Legnaro, Italy
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O antigen is the receptor of Vibrio cholerae serogroup O1 El Tor typing phage VP4. J Bacteriol 2012; 195:798-806. [PMID: 23222721 DOI: 10.1128/jb.01770-12] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Bacteriophage VP4 is a lytic phage of the Vibrio cholerae serogroup O1, and it is used in phage subtyping of V. cholerae biotype El Tor. Studies of phage infection mechanisms will promote the understanding of the basis of phage subtyping as well as the genetic differences between sensitive and resistant strains. In this study, we investigated the receptor that phage VP4 uses to bind to El Tor strains of V. cholerae and found that it infects strains through adsorbing the O antigen of V. cholerae O1. In some natural isolates that are resistant to VP4 infection, mutations were identified in the wb* cluster (O-antigen gene cluster), which is responsible for the biosynthesis of O antigen. Mutations in the manB, wbeE, and wbeU genes caused failure of adsorption of VP4 to these strains, whereas the observed amino acid residue mutations within wbeW and manC have no effect on VP4 infection. Additionally, although mutations in two resistant strains were found only in manB and wbeW, complementing both genes did not restore sensitivity to VP4 infection, suggesting that other resistance mechanisms may exist. Therefore, the mechanism of VP4 infection may provide a basis for subtyping the phage. Elaborate mutations of the O antigen may imbue V. cholerae strains with resistance to phage infection.
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Tankouo-Sandjong B, Kinde H, Wallace I. Development of a sequence typing scheme for differentiation of Salmonella Enteritidis strains. FEMS Microbiol Lett 2012; 331:165-75. [PMID: 22486191 DOI: 10.1111/j.1574-6968.2012.02568.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Revised: 04/03/2012] [Accepted: 04/04/2012] [Indexed: 11/30/2022] Open
Abstract
A DNA sequence typing scheme based on the caiC and SEN0629 loci was developed for differentiation of Salmonella Enteritidis strains and validated using a diverse collection of 102 isolates representing 38 phage types from different sources, year of isolation, geographical locations and epidemiological backgrounds. caiC encodes a probable crotonobetaine/carnitine-CoA ligase, and SEN0629 is a pseudogene. Our system allowed for discrimination of 16 sequence types (STs) among the 102 isolates analysed and intraphage type differentiation. Our findings also suggested that the stability of phage typing may be adversely affected by the occurrence of phage type conversion events. During a confirmatory phage typing analysis performed by a reference laboratory, 13 of 31 S. Enteritidis strains representing nine phage types were assigned phage types that differed from the ones originally determined by the same reference laboratory. It is possible that this phenomenon passes largely unrecognized in reference laboratories performing routine phage typing analyses. Our results demonstrate that phage typing is an unstable system displaying limited reproducibility and that the two-loci sequence typing scheme is highly discriminatory, stable, truly portable and has the potential to become the new gold standard for epidemiological typing of S . Enteritidis strains.
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Affiliation(s)
- Bertrand Tankouo-Sandjong
- California Animal Health and Food Safety Laboratory System, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
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