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Ubeyratne KH, Madalagama RP, Liu X, Pathirage S, Ariyawansa S, Wong MKL, Tun HM. Phenotypic and genotypic characterization of antibiotic-resistant Salmonella isolated from humans, aquaculture, and poultry in Sri Lanka: A retrospective study. J Infect Public Health 2023; 16 Suppl 1:203-209. [PMID: 37935606 DOI: 10.1016/j.jiph.2023.10.028] [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: 09/09/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND In Sri Lanka, foodborne diseases caused by nontyphoidal Salmonella are of increasing concern. We therefore aimed to characterize the dominant Salmonella serovars in humans, poultry, and aquaculture through a One Health approach. METHODS We collected isolates from different sectors, confirmed their identities using PCR, screened their antibiotic resistance profiles, and determined their antibiotic resistance genes based on whole-genome sequencing. RESULTS Of the 75 Salmonella isolates identified, the majority of serotypes were unidentified. Both Salmonella enterica serovar Enteritidis (S. Enteritidis) and Salmonella enterica serovar Typhimurium (S. Typhimurium) could be isolated from human sources and were also found prevalent in the poultry sector. ST36, ST11 and ST1541 were the dominant serotypes of S. Typhimurium and S. Enteritidis, respectively. Alarmingly, 4% (1/25) of poultry Salmonella isolates were resistant to ciprofloxacin, suggesting an emergence of this phenotype. Moreover, virulence genes were very diverse among S. Enteritidis and S. Typhimurium isolates. CONCLUSIONS With the diversity of unidentified serotypes found and the detection of emerging resistances, our study highlights the importance of a One Health approach to monitoring antibiotic resistance. For public health initiatives in Sri Lanka to be successful in mitigating salmonellosis, all three sectors - humans, aquaculture, and poultry - must be tackled concomitantly in a coordinated manner under the One Health approach because antibiotic resistance genes, and even specific sequence types, may be able to spread across the aforementioned sectors. We anticipate that our results will inform public health policies in Sri Lanka to tackle foodborne illnesses.
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Affiliation(s)
- Kamalika H Ubeyratne
- Central Veterinary Investigation Center, Veterinary Research Institute, Gannoruwa, Peradeniya 20400, Sri Lanka
| | - Roshan P Madalagama
- Bacteriology Division, Veterinary Research Institute, Gannoruwa, Peradeniya 20400, Sri Lanka
| | - Xin Liu
- Microbiota I-Center (MagIC), The Chinese University of Hong Kong, Hong Kong SAR, China; System Microbiology and Antimicrobial Resistance (SMART) Lab, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Sujatha Pathirage
- Enteric Laboratory, Medical Research Institute, Colombo 08, Sri Lanka
| | - Sujeewa Ariyawansa
- National Aquatic Resources Research & Development Agency, Crow Island, Colombo 15, Sri Lanka
| | - Matthew K L Wong
- Microbiota I-Center (MagIC), The Chinese University of Hong Kong, Hong Kong SAR, China; System Microbiology and Antimicrobial Resistance (SMART) Lab, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hein M Tun
- Microbiota I-Center (MagIC), The Chinese University of Hong Kong, Hong Kong SAR, China; System Microbiology and Antimicrobial Resistance (SMART) Lab, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China; The Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
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Smith S, Marquardt T, Jennison AV, D'Addona A, Stewart J, Yarwood T, Ho J, Binotto E, Harris J, Fahmy M, Esmonde J, Richardson M, Graham RMA, Gair R, Ariotti L, Preston-Thomas A, Rubenach S, O'Sullivan S, Allen D, Ragh T, Grayson S, Manoy S, Warner JM, Meumann EM, Robson JM, Hanson J. Clinical Manifestations and Genomic Evaluation of Melioidosis Outbreak among Children after Sporting Event, Australia. Emerg Infect Dis 2023; 29:2218-2228. [PMID: 37877500 PMCID: PMC10617349 DOI: 10.3201/eid2911.230951] [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] [Indexed: 10/26/2023] Open
Abstract
Melioidosis, caused by the environmental gram-negative bacterium Burkholderia pseudomallei, usually develops in adults with predisposing conditions and in Australia more commonly occurs during the monsoonal wet season. We report an outbreak of 7 cases of melioidosis in immunocompetent children in Australia. All the children had participated in a single-day sporting event during the dry season in a tropical region of Australia, and all had limited cutaneous disease. All case-patients had an adverse reaction to oral trimethoprim/sulfamethoxazole treatment, necessitating its discontinuation. We describe the clinical features, environmental sampling, genomic epidemiologic investigation, and public health response to the outbreak. Management of this outbreak shows the potential benefits of making melioidosis a notifiable disease. The approach used could also be used as a framework for similar outbreaks in the future.
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Rathnayake IU, Graham RMA, Bayliss J, Staples M, Micalizzi G, Ariotti L, Cover L, Heron B, Graham T, Stafford R, Rubenach S, D'Addona A, Jennison AV. Implementation of routine genomic surveillance provided insights into a locally acquired outbreak caused by a rare clade of Salmonella enterica serovar Enteritidis in Queensland, Australia. Microb Genom 2023; 9:mgen001059. [PMID: 37459172 PMCID: PMC10438802 DOI: 10.1099/mgen.0.001059] [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: 02/17/2023] [Accepted: 06/08/2023] [Indexed: 07/20/2023] Open
Abstract
Salmonellosis is a significant public health problem globally. In Australia, Salmonella enterica serovar Enteritidis is one of the main causes of salmonellosis. This study reports how the implementation of routine genetic surveillance of isolates from human S. Enteritidis cases enabled identification of the likely source of an outbreak that occurred in a remote town in Far North Queensland, Australia. This study included patient, food and water samples collected during an outbreak investigation. S. Enteritidis of the novel sequence type 5438 was isolated from all seven patient samples and one bore water sample but not any of the food samples. Both whole-genome single nucleotide polymorphism (SNP) and core-genome multilocus sequence typing analysis revealed that S. Enteritidis isolated from outbreak-related patient samples and the bore water isolates clustered together with fewer than five SNP differences and ten allelic differences. This genetic relatedness informed the outbreak response team around public health interventions and no further cases were identified post-treatment of the bore water. This disease cluster was identified through the routine sequencing of S. Enteritidis performed by the state public health laboratory in an actionable time frame. Additionally, genomic surveillance captured a case with unknown epidemiological links to the affected community, ruled out a simultaneous outbreak in an adjacent state as the source and provided evidence for the likely source preventing further transmission. Therefore, this report provides compelling support for the implementation of whole-genome sequencing based genotyping methods in public health microbiology laboratories for better outbreak detection and management.
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Affiliation(s)
- Irani U. Rathnayake
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Coopers Plains, Queensland, Australia
| | - Rikki M. A. Graham
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Coopers Plains, Queensland, Australia
| | - Jo Bayliss
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Coopers Plains, Queensland, Australia
| | - Megan Staples
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Coopers Plains, Queensland, Australia
| | - Gino Micalizzi
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Coopers Plains, Queensland, Australia
| | - Lawrence Ariotti
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Coopers Plains, Queensland, Australia
| | - Leonie Cover
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Coopers Plains, Queensland, Australia
| | - Brett Heron
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Coopers Plains, Queensland, Australia
| | - Trudy Graham
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Coopers Plains, Queensland, Australia
| | - Russell Stafford
- OzFoodNet, Communicable Diseases Branch, Queensland Public Health and Scientific Services, Queensland Department of Health, Butterfield Street, Herston, Brisbane, Queensland, Australia
| | - Sally Rubenach
- Health Surveillance, Tropical Public Health Services Cairns, Cairns and Hinterland Hospital and Health Service, Queensland Department of Health, Cairns, Queensland, Australia
| | - Andrew D'Addona
- Environmental Health, Tropical Public Health Services Cairns, Cairns and Hinterland Hospital and Health Service, Queensland Department of Health, Cairns, Queensland, Australia
| | - Amy V. Jennison
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Coopers Plains, Queensland, Australia
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Svahn AJ, Suster CJE, Chang SL, Rockett RJ, Sim EM, Cliff OM, Wang Q, Arnott A, Ramsperger M, Sorrell TC, Sintchenko V, Prokopenko M. Pangenome Analysis of a Salmonella Enteritidis Population Links a Major Outbreak to a Gifsy-1-Like Prophage Containing Anti-Inflammatory Gene gogB. Microbiol Spectr 2023; 11:e0279122. [PMID: 36916949 PMCID: PMC10100743 DOI: 10.1128/spectrum.02791-22] [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: 07/20/2022] [Accepted: 02/26/2023] [Indexed: 03/15/2023] Open
Abstract
A major outbreak of the globally significant Salmonella Enteritidis foodborne pathogen was identified within a large clinical data set by a program of routine WGS of clinical presentations of salmonellosis in New South Wales, Australia. Pangenome analysis helped to quantify and isolate prophage content within the accessory partition of the pangenome. A prophage similar to Gifsy-1 (henceforth GF-1L) was found to occur in all isolates of the outbreak core SNP cluster, and in three other isolates. Further analysis revealed that the GF-1L prophage carried the gogB virulence factor. These observations suggest that GF-1L may be an important marker of virulence for S. Enteritidis population screening and, that anti-inflammatory, gogB-mediated virulence currently associated with Salmonella Typhimurium may also be displayed by S. Enteritidis. IMPORTANCE We examined 5 years of genomic and epidemiological data for the significant global foodborne pathogen, Salmonella enterica. Although Salmonella enterica subspecies enterica serovar Enteritidis (S. Enteritidis) is the leading cause of salmonellosis in the USA and Europe, prior to 2018 it was not endemic in the southern states of Australia. However, in 2018 a large outbreak led to the endemicity of S. Enteritidis in New South Wales, Australia, and a unique opportunity to study this phenomenon. Using pangenome analysis we uncovered that this clone contained a Gifsy-1-like prophage harboring the known virulence factor gogB. The prophage reported has not previously been described in S. Enteritidis isolates.
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Affiliation(s)
- Adam J. Svahn
- Centre for Complex Systems, Faculty of Engineering, The University of Sydney, Sydney, NSW, Australia
- Sydney Infectious Diseases Institute, The University of Sydney, Westmead, NSW, Australia
| | - Carl J. E. Suster
- Sydney Infectious Diseases Institute, The University of Sydney, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Westmead, New South Wales, Australia
| | - Sheryl L. Chang
- Centre for Complex Systems, Faculty of Engineering, The University of Sydney, Sydney, NSW, Australia
| | - Rebecca J. Rockett
- Sydney Infectious Diseases Institute, The University of Sydney, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Westmead, New South Wales, Australia
| | - Eby M. Sim
- Sydney Infectious Diseases Institute, The University of Sydney, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Westmead, New South Wales, Australia
| | - Oliver M. Cliff
- Centre for Complex Systems, Faculty of Engineering, The University of Sydney, Sydney, NSW, Australia
- School of Physics, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Qinning Wang
- Centre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Westmead, New South Wales, Australia
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Alicia Arnott
- Sydney Infectious Diseases Institute, The University of Sydney, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Westmead, New South Wales, Australia
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Marc Ramsperger
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Tania C. Sorrell
- Sydney Infectious Diseases Institute, The University of Sydney, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Westmead, New South Wales, Australia
| | - Vitali Sintchenko
- Sydney Infectious Diseases Institute, The University of Sydney, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Westmead, New South Wales, Australia
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Mikhail Prokopenko
- Centre for Complex Systems, Faculty of Engineering, The University of Sydney, Sydney, NSW, Australia
- Sydney Infectious Diseases Institute, The University of Sydney, Westmead, NSW, Australia
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Genomic Epidemiology and Multilevel Genome Typing of Australian Salmonella enterica Serovar Enteritidis. Microbiol Spectr 2023; 11:e0301422. [PMID: 36625638 PMCID: PMC9927265 DOI: 10.1128/spectrum.03014-22] [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: 01/11/2023] Open
Abstract
Salmonella enterica serovar Enteritidis is one of the leading causes of salmonellosis in Australia. In this study, a total of 568 S. Enteritidis isolates from two Australian states across two consecutive years were analyzed and compared to international strains, using the S. Enteritidis multilevel genome typing (MGT) database, which contained 40,390 publicly available genomes from 99 countries. The Australian S. Enteritidis isolates were divided into three phylogenetic clades (A, B, and C). Clades A and C represented 16.4% and 3.5% of the total isolates, respectively, and were of local origin. Clade B accounted for 80.1% of the isolates which belonged to seven previously defined lineages but was dominated by the global epidemic lineage. At the MGT5 level, three out of five top sequence types (STs) in Australia were also top STs in Asia, suggesting that a fair proportion of Australian S. Enteritidis cases may be epidemiologically linked with Asian strains. In 2018, a large egg-associated local outbreak was caused by a recently defined clade B lineage prevalent in Europe and was closely related, but not directly linked, to three European isolates. Additionally, over half (54.8%) of predicted multidrug resistance (MDR) isolates belonged to 10 MDR-associated MGT-STs, which were also frequent in Asian S. Enteritidis . Overall, this study investigated the genomic epidemiology of S. Enteritidis in Australia, including the first large local outbreak, using MGT. The open MGT platform enables a standardized and sharable nomenclature that can be effectively applied to public health for unified surveillance of S. Enteritidis nationally and globally. IMPORTANCE Salmonella enterica serovar Enteritidis is a leading cause of foodborne infections. We previously developed a genomic typing database (MGTdb) for S. Enteritidis to facilitate global surveillance of this pathogen. In this study, we examined the genomic features of Australian S. Enteritidis using the MGTdb and found that Australian S. Enteritidis is mainly epidemiologically linked with Asian strains (especially strains carrying antimicrobial resistance genes), followed by European strains. The first large-scale egg-associated local outbreak in Australia was caused by a recently defined lineage prevalent in Europe, and three European isolates in the MGTdb were closely related but not directly linked to this outbreak. In summary, the S. Enteritidis MGTdb open platform is shown to be a potentially powerful tool for national and global public health surveillance of this pathogen.
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Characterisation of Salmonella Enteritidis ST11 and ST1925 Associated with Human Intestinal and Extra-Intestinal Infections in Singapore. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19095671. [PMID: 35565065 PMCID: PMC9104914 DOI: 10.3390/ijerph19095671] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/01/2022] [Accepted: 05/03/2022] [Indexed: 12/04/2022]
Abstract
Salmonella Enteritidis is a major foodborne pathogen worldwide. In this study, a total of 276 S. enteritidis isolates, collected between 2016 and 2017 from human, food and farm/slaughterhouse samples, were studied to enhance the understanding of the epidemiology of human salmonellosis in Singapore. Results showed all 276 isolates belonged either to ST1925 (70.3%) or ST11 (29.7%), with ST11 being significantly more frequent in extra-intestinal isolates and chicken isolates. Food isolates, most of which were from poultry, showed the highest prevalence of resistance (33–37%) against beta-lactams or beta-lactams/beta-lactamase inhibitor combination (ampicillin, piperacillin and ampicillin/sulbactam). The analysis showed the detection of genes associated with resistance to aminoglycoside genes (99.6%), tetracycline (55.1%), and beta-lactams (14.9%) of all isolates. Nine types of plasmids were found in 266 isolates; the most common incompatibility group profiles were IncFIB(S)-IncFII(S)-IncX1 (72.2%) and IncFIB(S)-IncFII(S) (15.8%). Most plasmid harbouring isolates from chicken (63.6%, 14/22) and from human (73.8%, 175/237) shared the same plasmid profile (IncFIB(S)-IncFII(S)-IncX1). SNP analysis showed clustering of several isolates from poultry food products and human isolates, suggesting phylogenetic relatedness among these isolates. Lastly, this study provides important epidemiological insights on the application of phenotypic and next-generation sequencing (NGS) tools for improved food safety and public health surveillance and outbreak investigation of S.enteritidis.
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Zakaria Z, Hassan L, Sharif Z, Ahmad N, Mohd Ali R, Amir Husin S, Mohamed Sohaimi N, Abu Bakar S, Garba B. Virulence Gene Profile, Antimicrobial Resistance and Multilocus Sequence Typing of Salmonella enterica Subsp. enterica Serovar Enteritidis from Chickens and Chicken Products. Animals (Basel) 2022; 12:ani12010097. [PMID: 35011203 PMCID: PMC8749576 DOI: 10.3390/ani12010097] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 11/01/2021] [Accepted: 11/04/2021] [Indexed: 01/19/2023] Open
Abstract
This study was undertaken to determine the virulence, antimicrobial resistance and molecular subtypes of Salmonella in the Central Region of Peninsular Malaysia. A total of 45 Salmonella Enteritidis were detected from live chicken (cloacal swab), and chicken products (fresh and ready-to-eat meat) samples upon cultural isolation and serotyping. Similarly, an antimicrobial susceptibility test based on the Kirby Bauer disk diffusion method as well as antimicrobial resistance AMR genes, virulence determinants and multilocus sequence typing (MLST) typing were conducted after the Whole Genome Sequencing and analysis of the isolates. The results indicate that sequence types ST1925 (63.7%), and ST11 (26.5%) were the predominant out of the seven sequence types identified (ST292, ST329, ST365, ST423 and ST2132). The phenotypic antimicrobial profile corresponds to the genotypic characterization in that the majority of the isolates that exhibited tetracycline, gentamycin and aminoglycoside resistance; they also possessed the tetC and blaTEM β-Lactam resistance genes. However, isolates from cloacal swabs showed the highest number of resistance genes compared to the chicken products (fresh and ready-to-eat meat) samples. Furthermore, most of the virulence genes were found to cluster in the Salmonella pathogenicity island (SPI). In this study, all the isolates were found to possess SPI-1, which codes for the type III secretion system, which functions as actin-binding proteins (SptP and SopE). The virulence plasmid (VP) genes (spvB, spvC) were present in all genotypes except ST365. The findings of this study, particularly with regard to the molecular subtypes and AMR profiles of the Salmonella Enteritidis serotype shows multidrug-resistance features as well as genetic characteristics indicative of high pathogenicity.
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Affiliation(s)
- Zunita Zakaria
- Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang 43400, Malaysia;
- Correspondence:
| | - Latiffah Hassan
- Department of Veterinary Laboratory Diagnostics, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang 43400, Malaysia; (L.H.); (N.M.S.)
| | - Zawiyah Sharif
- Food Safety and Quality Division, Ministry of Health, Putrajaya 62675, Malaysia; (Z.S.); (S.A.B.)
| | - Norazah Ahmad
- Veterinary Public Health Division, Department of Veterinary Services Malaysia, Putrajaya 62630, Malaysia; (N.A.); (R.M.A.)
| | - Rohaya Mohd Ali
- Veterinary Public Health Division, Department of Veterinary Services Malaysia, Putrajaya 62630, Malaysia; (N.A.); (R.M.A.)
| | - Suraya Amir Husin
- Medical Development Division, Ministry of Health, Putrajaya 62590, Malaysia;
| | - Norfitriah Mohamed Sohaimi
- Department of Veterinary Laboratory Diagnostics, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang 43400, Malaysia; (L.H.); (N.M.S.)
| | - Shafini Abu Bakar
- Food Safety and Quality Division, Ministry of Health, Putrajaya 62675, Malaysia; (Z.S.); (S.A.B.)
| | - Bashiru Garba
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang 43400, Malaysia;
- Faculty of Veterinary Medicine, Usmanu Danfodiyo University, Sultan Abubakar Road, City Campus Complex, Sokoto 840212, Nigeria
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Ksibi B, Ktari S, Ghedira K, Othman H, Maalej S, Mnif B, Fabre L, Rhimi F, Hello SL, Hammami A. Antimicrobial resistance genes, virulence markers and prophage sequences in Salmonella enterica serovar Enteritidis isolated in Tunisia using whole genome sequencing. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100151. [PMID: 35909609 PMCID: PMC9325895 DOI: 10.1016/j.crmicr.2022.100151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Antimcrobial resistance genes, virulence factors and prophage sequences were studied in WGS of 45 Salmonella Enteritidis from different sources. WGS is most powerful tool for determining genomic variation in S. Enteritidis. Two major lineages of S. Enteritidis were detected in Tunisia. Missense mutations identified in virulence genes were mostly detected in lineage B. Salmon118970_sal3 and RE_2010 phages were detected in lineage A and lineage B, respectively.
Salmonella Enteritidis causes a major public health problem in the world. Whole genome sequencing can give us a lot of information not only about the phylogenetic relatedness of these bacteria but also in antimicrobial resistance and virulence gene predictions. In this study, we analyzed the whole genome data of 45 S. Enteritidis isolates recovered in Tunisia from different origins, human, animal, and foodborne samples. Two major lineages (A and B) were detected based on 802 SNPs differences. Among these SNPs, 493 missense SNPs were identified. A total of 349 orthologue genes mutated by one or two missense SNPs were classified in 22 functional groups with the prevalence of carbohydrate transport and metabolism group. A good correlation between genotypic antibiotic resistance profiles and phenotypic analysis were observed. Only resistant isolates carried the respective molecular resistant determinants. The investigation of virulence markers showed the distribution of 11 Salmonella pathogenicity islands (SPI) out of 23 previously described. The SPI-1 and SPI-2 genes encoding type III secretion systems were highly conserved in all isolates except one. In addition, the virulence plasmid genes were present in all isolates except two. We showed the presence of two fimbrial operons sef and ste previously considered to be specific for typhoidal Salmonella. Our collection of S. Enteritidis reveal a diversity among prophage profiles. SNPs analysis showed that missense mutations identified in fimbriae and in SPI-1 and SPI-2 genes were mostly detected in lineage B. In conclusion, WGS is a powerful application to study functional genomic determinants of S. Enteritidis such as antimicrobial resistance genes, virulence markers and prophage sequences. Further studies are needed to predict the impact of the missenses SNPs that can affect the protein functions associated with pathogenicity.
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Sia CM, Baines SL, Valcanis M, Lee DYJ, Gonçalves da Silva A, Ballard SA, Easton M, Seemann T, Howden BP, Ingle DJ, Williamson DA. Genomic diversity of antimicrobial resistance in non-typhoidal Salmonella in Victoria, Australia. Microb Genom 2021; 7:000725. [PMID: 34907895 PMCID: PMC8767345 DOI: 10.1099/mgen.0.000725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 10/21/2021] [Indexed: 01/18/2023] Open
Abstract
Non-typhoidal Salmonella (NTS) is the second most common cause of foodborne bacterial gastroenteritis in Australia with antimicrobial resistance (AMR) increasing in recent years. Whole-genome sequencing (WGS) provides opportunities for in silico detection of AMR determinants. The objectives of this study were two-fold: (1) establish the utility of WGS analyses for inferring phenotypic resistance in NTS, and (2) explore clinically relevant genotypic AMR profiles to third generation cephalosporins (3GC) in NTS lineages. The concordance of 2490 NTS isolates with matched WGS and phenotypic susceptibility data against 13 clinically relevant antimicrobials was explored. In silico serovar prediction and typing was performed on assembled reads and interrogated for known AMR determinants. The surrounding genomic context, plasmid determinants and co-occurring AMR patterns were further investigated for multidrug resistant serovars harbouring bla CMY-2, bla CTX-M-55 or bla CTX-M-65. Our data demonstrated a high correlation between WGS and phenotypic susceptibility testing. Phenotypic-genotypic concordance was observed between 2440/2490 (98.0 %) isolates, with overall sensitivity and specificity rates >98 % and positive and negative predictive values >97 %. The most common AMR determinants were bla TEM-1, sul2 , tet (A), strA-strB and floR . Phenotypic resistance to cefotaxime and azithromycin was low and observed in 6.2 % (151/2486) and 0.9 % (16/1834) of the isolates, respectively. Several multi-drug resistant NTS lineages were resistant to 3GC due to different genetic mechanisms including bla CMY-2, bla CTX-M-55 or bla CTX-M-65. This study shows WGS can enhance existing AMR surveillance in NTS datasets routinely produced in public health laboratories to identify emerging AMR in NTS. These approaches will be critical for developing capacity to detect emerging public health threats such as resistance to 3GC.
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Affiliation(s)
- Cheryll M. Sia
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Sarah L. Baines
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Darren Y. J. Lee
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Susan A. Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | | | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Danielle J. Ingle
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australia
| | - Deborah A. Williamson
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Microbiology, Royal Melbourne Hospital, Melbourne, Australia
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10
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Zakaria Z, Hassan L, Ahmad N, Husin SA, Ali RM, Sharif Z, Sohaimi NM, Garba B. Discerning the Antimicrobial Resistance, Virulence, and Phylogenetic Relatedness of Salmonella Isolates Across the Human, Poultry, and Food Materials Sources in Malaysia. Front Microbiol 2021; 12:652642. [PMID: 34531832 PMCID: PMC8438298 DOI: 10.3389/fmicb.2021.652642] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 08/09/2021] [Indexed: 12/15/2022] Open
Abstract
Salmonella enterica subspecies enterica serovar Enteritidis is one of the major foodborne zoonotic pathogens globally. It has significantly impacted human health and global trade. In this investigation, whole-genome sequencing was employed to determine the antimicrobial resistance (AMR) pattern of a collection of Salmonella Enteritidis isolated from humans, poultry, and food sources. The study also investigated the virulence genes profile of the isolates as well as the phylogenetic relationships among strains. Illumina NextSeq technology was used to sequence the genome of 82 Salmonella Enteritidis strains isolated over 3 years (2016-2018) in Peninsular Malaysia. The pattern of resistance showed that tetracycline had the highest frequency (37/82, 45.12%), and isolates from food samples showed the highest rate of 9/18 (50.00%), followed by human 17/35 (48.57%) and then poultry 11/29 (37.93%). The second drug with the highest resistance rate is ampicillin with 5/29 (17.24%) for poultry, 4/35 (11.43%) for human, and 0/18 (0.00%) for food isolates respectively. Similarly, a total of 19 antimicrobial resistance (AMR) genes corresponding to the nine drugs used in the disc diffusion assay were evaluated from the whole genome sequence data. The aminoglycoside resistance gene aac(6')-ly was detected in 79 of the 82 isolates (96.34%). While the phylogenetic analysis revealed distinct lineages isolated, the three sources indicating possible cross-contamination. In conclusion, the results showed that the genomic profile of Salmonella Enteritidis isolated from humans, poultry, and food samples share genetic traits, hence the need to institute measures at controlling the continuous spread of these resistant pathogens.
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Affiliation(s)
- Zunita Zakaria
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia.,Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Malaysia
| | - Latiffah Hassan
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Malaysia.,Department of Veterinary Laboratory Diagnostics, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Malaysia
| | - Norazah Ahmad
- Infectious Diseases Research Centre, Institute for Medical Research, National Institutes of Health, Selangor, Malaysia
| | - Suraya Amir Husin
- Medical Development Division, Ministry of Health, Putrajaya, Malaysia
| | - Rohaya Mohd Ali
- Diagnostic and Quality Assurance Division, Department of Veterinary Services, Ministry of Agriculture and Agro-Based Industry, Putrajaya, Malaysia
| | - Zawiyah Sharif
- Food Safety and Quality Division, Ministry of Health, Selangor, Malaysia
| | - Norfitriah Mohamed Sohaimi
- Department of Veterinary Laboratory Diagnostics, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Malaysia
| | - Bashiru Garba
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Malaysia.,Department of Veterinary Public Health and Preventive Medicine, Faculty of Veterinary Medicine, Usmanu Danfodiyo University, Sokoto, Nigeria
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11
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Luo L, Payne M, Kaur S, Hu D, Cheney L, Octavia S, Wang Q, Tanaka MM, Sintchenko V, Lan R. Elucidation of global and national genomic epidemiology of Salmonella enterica serovar Enteritidis through multilevel genome typing. Microb Genom 2021; 7. [PMID: 34292145 PMCID: PMC8477392 DOI: 10.1099/mgen.0.000605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Salmonella enterica serovar Enteritidis is a major cause of foodborne Salmonella infections and outbreaks in humans. Effective surveillance and timely outbreak detection are essential for public health control. Multilevel genome typing (MGT) with multiple levels of resolution has been previously demonstrated as a promising tool for this purpose. In this study, we developed MGT with nine levels for S. Enteritidis and characterised the genomic epidemiology of S. Enteritidis in detail. We examined 26 670 publicly available S. Enteritidis genome sequences from isolates spanning 101 years from 86 countries to reveal their spatial and temporal distributions. Using the lower resolution MGT levels, globally prevalent and regionally restricted sequence types (STs) were identified; avian associated MGT4-STs were found that were common in human cases in the USA; temporal trends were observed in the UK with MGT5-STs from 2014 to 2018 revealing both long lived endemic STs and the rapid expansion of new STs. Using MGT3 to MGT6, we identified multidrug resistance (MDR) associated STs at various MGT levels, which improves precision of detection and global tracking of MDR clones. We also found that the majority of the global S. Enteritidis population fell within two predominant lineages, which had significantly different propensity of causing large scale outbreaks. An online open MGT database has been established for unified international surveillance of S. Enteritidis. We demonstrated that MGT provides a flexible and high-resolution genome typing tool for S. Enteritidis surveillance and outbreak detection.
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Affiliation(s)
- Lijuan Luo
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Michael Payne
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sandeep Kaur
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Dalong Hu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Liam Cheney
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sophie Octavia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Qinning Wang
- Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research - NSW Health Pathology, Westmead Hospital, 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
- Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research - NSW Health Pathology, Westmead Hospital, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, University of 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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12
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Achtman M, Zhou Z, Alikhan NF, Tyne W, Parkhill J, Cormican M, Chiou CS, Torpdahl M, Litrup E, Prendergast DM, Moore JE, Strain S, Kornschober C, Meinersmann R, Uesbeck A, Weill FX, Coffey A, Andrews-Polymenis H, Curtiss 3rd R, Fanning S. Genomic diversity of Salmonella enterica -The UoWUCC 10K genomes project. Wellcome Open Res 2021; 5:223. [PMID: 33614977 PMCID: PMC7869069 DOI: 10.12688/wellcomeopenres.16291.2] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2021] [Indexed: 12/31/2022] Open
Abstract
Background: Most publicly available genomes of Salmonella enterica are from human disease in the US and the UK, or from domesticated animals in the US. Methods: Here we describe a historical collection of 10,000 strains isolated between 1891-2010 in 73 different countries. They encompass a broad range of sources, ranging from rivers through reptiles to the diversity of all S. enterica isolated on the island of Ireland between 2000 and 2005. Genomic DNA was isolated, and sequenced by Illumina short read sequencing. Results: The short reads are publicly available in the Short Reads Archive. They were also uploaded to EnteroBase, which assembled and annotated draft genomes. 9769 draft genomes which passed quality control were genotyped with multiple levels of multilocus sequence typing, and used to predict serovars. Genomes were assigned to hierarchical clusters on the basis of numbers of pair-wise allelic differences in core genes, which were mapped to genetic Lineages within phylogenetic trees. Conclusions: The University of Warwick/University College Cork (UoWUCC) project greatly extends the geographic sources, dates and core genomic diversity of publicly available S. enterica genomes. We illustrate these features by an overview of core genomic Lineages within 33,000 publicly available Salmonella genomes whose strains were isolated before 2011. We also present detailed examinations of HC400, HC900 and HC2000 hierarchical clusters within exemplar Lineages, including serovars Typhimurium, Enteritidis and Mbandaka. These analyses confirm the polyphyletic nature of multiple serovars while showing that discrete clusters with geographical specificity can be reliably recognized by hierarchical clustering approaches. The results also demonstrate that the genomes sequenced here provide an important counterbalance to the sampling bias which is so dominant in current genomic sequencing.
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Affiliation(s)
- Mark Achtman
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Zhemin Zhou
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | | | - William Tyne
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Martin Cormican
- National Salmonella, Shigella and Listeria Reference Laboratory, Galway, H91 YR71, Ireland
| | - Chien-Shun Chiou
- Central Regional Laboratory, Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taichung, None, Taiwan
| | - Mia Torpdahl
- Statens Serum Institut, Copenhagen S, DK-2300, Denmark
| | - Eva Litrup
- Statens Serum Institut, Copenhagen S, DK-2300, Denmark
| | - Deirdre M. Prendergast
- Backweston complex, Department of Agriculture, Food and the Marine (DAFM), Celbridge, Co. Kildare, W23 X3PH, Ireland
| | - John E. Moore
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast, BT9 7AD, UK
| | - Sam Strain
- Animal Health and Welfare NI, Dungannon, BT71 6JT, UK
| | - Christian Kornschober
- Institute for Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety (AGES), Graz, 8010, Austria
| | - Richard Meinersmann
- US National Poultry Research Center, USDA Agricultural Research Service, Athens, GA, 30605, USA
| | - Alexandra Uesbeck
- Institute for Medical Microbiology, Immunology, and Hygiene, University of Cologne, Cologne, 50935, Germany
| | - François-Xavier Weill
- Unité des bactéries pathogènes entériques, Institut Pasteur, Paris, cedex 15, France
| | - Aidan Coffey
- Cork Institute of Technology, Cork, T12P928, Ireland
| | - Helene Andrews-Polymenis
- Dept. of Microbial Pathogenesis and Immunology, College of Medicine Texas A&M University, Bryan, TX, 77807, USA
| | - Roy Curtiss 3rd
- Dept. of Infectious Diseases & Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, 32611, USA
| | - Séamus Fanning
- UCD-Centre for Food Safety, University College Dublin, Dublin, D04 N2E5, Ireland
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13
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Baines SL, da Silva AG, Carter GP, Jennison A, Rathnayake I, Graham RM, Sintchenko V, Wang Q, Rockett RJ, Timms VJ, Martinez E, Ballard S, Tomita T, Isles N, Horan KA, Pitchers W, Stinear TP, Williamson DA, Howden BP, Seemann T. Complete microbial genomes for public health in Australia and the Southwest Pacific. Microb Genom 2020; 6:mgen000471. [PMID: 33180013 PMCID: PMC8116684 DOI: 10.1099/mgen.0.000471] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/21/2020] [Indexed: 12/13/2022] Open
Abstract
Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health laboratory activities. Here, we announce a BioProject (PRJNA556438) dedicated to sharing complete genomes chosen to represent a range of pathogenic bacteria with regional importance to Australia and the Southwest Pacific; enriching the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health microbiology laboratories. In this first step, we present 26 complete high-quality bacterial genomes. Additionally, we describe here a framework for reconstructing complete microbial genomes and highlight some of the challenges and considerations for accurate and reproducible genome reconstruction.
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Affiliation(s)
- Sarah L. Baines
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Glen P. Carter
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
| | - Amy Jennison
- Public Health Microbiology, Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Queensland Department of Health, Archerfield, Queensland 4108, Australia
| | - Irani Rathnayake
- Public Health Microbiology, Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Queensland Department of Health, Archerfield, Queensland 4108, Australia
| | - Rikki M. Graham
- Public Health Microbiology, Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Queensland Department of Health, Archerfield, Queensland 4108, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital and NSW Health Pathology, Sydney, New South Wales 2145, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Qinning Wang
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital and NSW Health Pathology, Sydney, New South Wales 2145, Australia
| | - Rebecca J. Rockett
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital and NSW Health Pathology, Sydney, New South Wales 2145, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Verlaine J. Timms
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital and NSW Health Pathology, Sydney, New South Wales 2145, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Elena Martinez
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital and NSW Health Pathology, Sydney, New South Wales 2145, Australia
| | - Susan Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Takehiro Tomita
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Nicole Isles
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Kristy A. Horan
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - William Pitchers
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
| | - Deborah A. Williamson
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Torsten Seemann
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Communicable Diseases Genomics Network (CDGN)
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
- Public Health Microbiology, Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Queensland Department of Health, Archerfield, Queensland 4108, Australia
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital and NSW Health Pathology, Sydney, New South Wales 2145, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales 2006, Australia
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14
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Achtman M, Zhou Z, Alikhan NF, Tyne W, Parkhill J, Cormican M, Chiou CS, Torpdahl M, Litrup E, Prendergast DM, Moore JE, Strain S, Kornschober C, Meinersmann R, Uesbeck A, Weill FX, Coffey A, Andrews-Polymenis H, Curtiss 3rd R, Fanning S. Genomic diversity of Salmonella enterica -The UoWUCC 10K genomes project. Wellcome Open Res 2020; 5:223. [PMID: 33614977 PMCID: PMC7869069 DOI: 10.12688/wellcomeopenres.16291.1] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2020] [Indexed: 01/25/2023] Open
Abstract
Background: Most publicly available genomes of Salmonella enterica are from human disease in the US and the UK, or from domesticated animals in the US. Methods: Here we describe a historical collection of 10,000 strains isolated between 1891-2010 in 73 different countries. They encompass a broad range of sources, ranging from rivers through reptiles to the diversity of all S. enterica isolated on the island of Ireland between 2000 and 2005. Genomic DNA was isolated, and sequenced by Illumina short read sequencing. Results: The short reads are publicly available in the Short Reads Archive. They were also uploaded to EnteroBase, which assembled and annotated draft genomes. 9769 draft genomes which passed quality control were genotyped with multiple levels of multilocus sequence typing, and used to predict serovars. Genomes were assigned to hierarchical clusters on the basis of numbers of pair-wise allelic differences in core genes, which were mapped to genetic Lineages within phylogenetic trees. Conclusions: The University of Warwick/University College Cork (UoWUCC) project greatly extends the geographic sources, dates and core genomic diversity of publicly available S. enterica genomes. We illustrate these features by an overview of core genomic Lineages within 33,000 publicly available Salmonella genomes whose strains were isolated before 2011. We also present detailed examinations of HC400, HC900 and HC2000 hierarchical clusters within exemplar Lineages, including serovars Typhimurium, Enteritidis and Mbandaka. These analyses confirm the polyphyletic nature of multiple serovars while showing that discrete clusters with geographical specificity can be reliably recognized by hierarchical clustering approaches. The results also demonstrate that the genomes sequenced here provide an important counterbalance to the sampling bias which is so dominant in current genomic sequencing.
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Affiliation(s)
- Mark Achtman
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Zhemin Zhou
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | | | - William Tyne
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Martin Cormican
- National Salmonella, Shigella and Listeria Reference Laboratory, Galway, H91 YR71, Ireland
| | - Chien-Shun Chiou
- Central Regional Laboratory, Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taichung, None, Taiwan
| | - Mia Torpdahl
- Statens Serum Institut, Copenhagen S, DK-2300, Denmark
| | - Eva Litrup
- Statens Serum Institut, Copenhagen S, DK-2300, Denmark
| | - Deirdre M. Prendergast
- Backweston complex, Department of Agriculture, Food and the Marine (DAFM), Celbridge, Co. Kildare, W23 X3PH, Ireland
| | - John E. Moore
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast, BT9 7AD, UK
| | - Sam Strain
- Animal Health and Welfare NI, Dungannon, BT71 6JT, UK
| | - Christian Kornschober
- Institute for Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety (AGES), Graz, 8010, Austria
| | - Richard Meinersmann
- US National Poultry Research Center, USDA Agricultural Research Service, Athens, GA, 30605, USA
| | - Alexandra Uesbeck
- Institute for Medical Microbiology, Immunology, and Hygiene, University of Cologne, Cologne, 50935, Germany
| | - François-Xavier Weill
- Unité des bactéries pathogènes entériques, Institut Pasteur, Paris, cedex 15, France
| | - Aidan Coffey
- Cork Institute of Technology, Cork, T12P928, Ireland
| | - Helene Andrews-Polymenis
- Dept. of Microbial Pathogenesis and Immunology, College of Medicine Texas A&M University, Bryan, TX, 77807, USA
| | - Roy Curtiss 3rd
- Dept. of Infectious Diseases & Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, 32611, USA
| | - Séamus Fanning
- UCD-Centre for Food Safety, University College Dublin, Dublin, D04 N2E5, Ireland
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15
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Fei X, Li Q, Olsen JE, Jiao X. A bioinformatic approach to identify core genome difference between Salmonella Pullorum and Salmonella Enteritidis. INFECTION GENETICS AND EVOLUTION 2020; 85:104446. [PMID: 32622081 DOI: 10.1016/j.meegid.2020.104446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/15/2020] [Accepted: 06/25/2020] [Indexed: 11/30/2022]
Abstract
S. Pullorum and S. Enteritidis are closely related in genetic terms, but they show very different pathogenicity and host range. S. Enteritidis infects many different hosts, usually causing acute gastroenteritis, while S. Pullorum is restricted to avian, where it causes systemic disease in young animals. The reason why they differ in host range and pathogenicity is unknown. The core-genome denotes those genes that are present in all strains within a clade, and in the present work, an automated bioinformatics workflow was developed and applied to identify core-genome differences between these two serovars with the aim to identify genome features associated with host specificity of S. Pullorum. Results showed that S. Pullorum unique coding sequences (CDS) were mainly concentrated in three regions not present in S. Enteritidis, suggesting that such CDS were taken up probably during the separation of the two types from their common ancestor. One of the unique regions encoded Pathogenicity Islands 19 (SPI-19), which encodes a type VI secretion system (T6SS). Single-nucleotide polymorphism (SNP) analysis identified 1791 conserved SNPs in coding sequences between the two serovars, including several SNPs located in a type IV secretion system (T4SS). Analyzing of 100 bp regions upstream of coding sequences identified 443 conserved SNPs between the two serovars, including SNP variations in type III secretion system effector (T3SE). In conclusion, this analysis has identified genetic features encoding putative factors controlling host-specificity in S. Pullorum. The novel bioinformatic workflow and associated scripts can directly be applied to other bacteria to uncover the genome difference between clades.
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Affiliation(s)
- Xiao Fei
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, China; Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, China; Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Qiuchun Li
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, China; Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, China
| | - John Elmerdahl Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Xinan Jiao
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, China; Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, China.
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16
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Kipper D, Hellfeldt RM, De Carli S, Lehmann FKM, Fonseca ASK, Ikuta N, Lunge VR. Salmonella serotype assignment by sequencing analysis of intergenic regions of ribosomal RNA operons. Poult Sci 2020; 98:5989-5998. [PMID: 31134273 DOI: 10.3382/ps/pez285] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 05/03/2019] [Indexed: 02/02/2023] Open
Abstract
Salmonella laboratorial detection is usually carried out by bacteriological culture and serological methods. Salmonella isolates are then classified into more than 2,650 serotypes with different somatic (O) and flagellar (H) antigenic combinations. More recently, DNA analysis methods were developed and applied for the identification of Salmonella serotypes, including intergenic spacer regions (ISRs) that separates DNA-encoding ribosomal subunits (rRNA gene) in Salmonella genomes. The present study aimed to evaluate the nucleotide diversity of the ISRs in 2 rRNA operons (rrnB and rrnH) for the assignment of Salmonella serotypes. A total of 63 Salmonella isolates (bacterial cultures) from 21 serotypes were obtained in the period of 2014 to 2017. DNA was extracted, and PCRs were used to detect the genus Salmonella and 4 important serotypes: Enteritidis, Gallinarum, Heidelberg, and Typhimurium. ISRs of the operons rrnB and rrnH were amplified by PCR and then sequenced. All sequence results were submitted to BLASTn search and were aligned in comparison to 72 Salmonella reference nucleotide sequences. The results demonstrated that 60 (95.2%) samples returned a sequence of the same serotype (determined by the traditional serological procedure) after searching in BLASTn and/or in the alignment with the reference sequences for both operons (rrnB and rrnH). These PCR-sequencing procedures had a general agreement index of 0.792 based on the Kappa analysis, 98.7% sensitivity value, 100% specificity, and 98.4% accuracy. Three different phylogenetic trees were generated from the alignments with the sequences of rrnH, rrnB, and rrnH plus rrnB and isolates clustered in specific branches according to the serotypes.
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Affiliation(s)
- Diéssy Kipper
- Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil (ULBRA), Canoas, Rio Grande do Sul, 92425-900, Brazil
| | - Rafaella Martins Hellfeldt
- Curso de Medicina Veterinária, Universidade Luterana do Brasil (ULBRA), Canoas, Rio Grande do Sul, 92425-900, Brazil
| | - Silvia De Carli
- Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil (ULBRA), Canoas, Rio Grande do Sul, 92425-900, Brazil.,Laboratório de Virologia Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 91501-970, Brazil
| | | | | | - Nilo Ikuta
- Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil (ULBRA), Canoas, Rio Grande do Sul, 92425-900, Brazil.,Curso de Medicina Veterinária, Universidade Luterana do Brasil (ULBRA), Canoas, Rio Grande do Sul, 92425-900, Brazil.,Simbios Biotecnologia, Cachoeirinha, Rio Grande do Sul, 94940-030, Brazil
| | - Vagner Ricardo Lunge
- Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil (ULBRA), Canoas, Rio Grande do Sul, 92425-900, Brazil.,Curso de Medicina Veterinária, Universidade Luterana do Brasil (ULBRA), Canoas, Rio Grande do Sul, 92425-900, Brazil.,Simbios Biotecnologia, Cachoeirinha, Rio Grande do Sul, 94940-030, Brazil
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Pulford CV, Perez-Sepulveda BM, Rodwell EV, Weill FX, Baker KS, Hinton JCD. Salmonella enterica Serovar Panama, an Understudied Serovar Responsible for Extraintestinal Salmonellosis Worldwide. Infect Immun 2019; 87:e00273-19. [PMID: 31262982 PMCID: PMC6704606 DOI: 10.1128/iai.00273-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In recent years nontyphoidal Salmonella has emerged as one of the pathogens most frequently isolated from the bloodstream in humans. Only a small group of Salmonella serovars cause this systemic infection, known as invasive nontyphoidal salmonellosis. Here, we present a focused minireview on Salmonella enterica serovar Panama, a serovar responsible for invasive salmonellosis worldwide. S Panama has been linked with infection of extraintestinal sites in humans, causing septicemia, meningitis, and osteomyelitis. The clinical picture is often complicated by antimicrobial resistance and has been associated with a large repertoire of transmission vehicles, including human feces and breast milk. Nonhuman sources of S Panama involve reptiles and environmental reservoirs, as well as food animals, such as pigs. The tendency of S Panama to cause invasive disease may be linked to certain serovar-specific genetic factors.
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Affiliation(s)
- Caisey V Pulford
- Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Blanca M Perez-Sepulveda
- Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Ella V Rodwell
- Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | | | - Kate S Baker
- Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Jay C D Hinton
- Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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18
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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.
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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
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