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Zhuang L, Gong J, Zhang P, Zhang D, Zhao Y, Yang J, Liu G, Zhang Y, Shen Q. Research progress of loop-mediated isothermal amplification in the detection of Salmonella for food safety applications. DISCOVER NANO 2024; 19:124. [PMID: 39105889 PMCID: PMC11303641 DOI: 10.1186/s11671-024-04075-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 07/29/2024] [Indexed: 08/07/2024]
Abstract
Salmonella, the prevailing zoonotic pathogen within the Enterobacteriaceae family, holds the foremost position in global bacterial poisoning incidents, thereby signifying its paramount importance in public health. Consequently, the imperative for expeditious and uncomplicated detection techniques for Salmonella in food is underscored. After more than two decades of development, loop-mediated isothermal amplification (LAMP) has emerged as a potent adjunct to the polymerase chain reaction, demonstrating significant advantages in the realm of isothermal amplification. Its growing prominence is evident in the increasing number of reports on its application in the rapid detection of Salmonella. This paper provides a systematic exposition of the technical principles and characteristics of LAMP, along with an overview of the research progress made in the rapid detection of Salmonella using LAMP and its derivatives. Additionally, the target genes reported in various levels, including Salmonella genus, species, serogroup, and serotype, are summarized, aiming to offer a valuable reference for the advancement of LAMP application in Salmonella detection. Finally, we look forward to the development direction of LAMP and expect more competitive methods to provide strong support for food safety applications.
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Affiliation(s)
- Linlin Zhuang
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong, 212400, People's Republic of China
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering and Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing, 211102, People's Republic of China
| | - Jiansen Gong
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, 225125, People's Republic of China
| | - Ping Zhang
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, 225125, People's Republic of China
| | - Di Zhang
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, 225125, People's Republic of China
| | - Ying Zhao
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering and Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing, 211102, People's Republic of China
| | - Jianbo Yang
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong, 212400, People's Republic of China
| | - Guofang Liu
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong, 212400, People's Republic of China
| | - Yu Zhang
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering and Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing, 211102, People's Republic of China.
| | - Qiuping Shen
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong, 212400, People's Republic of China.
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Petrin S, Tiengo A, Longo A, Furlan M, Marafin E, Zavagnin P, Orsini M, Losasso C, Barco L. Uncommon Salmonella Infantis Variants with Incomplete Antigenic Formula in the Poultry Food Chain, Italy. Emerg Infect Dis 2024; 30:795-799. [PMID: 38526241 PMCID: PMC10977818 DOI: 10.3201/eid3004.231074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024] Open
Abstract
Uncommon Salmonella Infantis variants displaying only flagellar antigens phenotypically showed identical incomplete antigenic formula but differed by molecular serotyping. Although most formed rough colonies, all shared antimicrobial resistances and the presence of usg gene with wild-type Salmonella Infantis. Moreover, they were undistinguishable wild-type Salmonella Infantis by whole-genome sequencing.
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Affiliation(s)
| | | | - Alessandra Longo
- National and World Organisation for Animal Health Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Maddalena Furlan
- National and World Organisation for Animal Health Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Elisa Marafin
- National and World Organisation for Animal Health Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Paola Zavagnin
- National and World Organisation for Animal Health Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Massimiliano Orsini
- National and World Organisation for Animal Health Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
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Konganti K, Reed E, Mammel M, Kayikcioglu T, Binet R, Jarvis K, Ferreira CM, Bell RL, Zheng J, Windsor AM, Ottesen A, Grim CJ, Ramachandran P. bettercallsal: better calling of Salmonella serotypes from enrichment cultures using shotgun metagenomic profiling and its application in an outbreak setting. Front Microbiol 2023; 14:1200983. [PMID: 37601366 PMCID: PMC10434220 DOI: 10.3389/fmicb.2023.1200983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/28/2023] [Indexed: 08/22/2023] Open
Abstract
Most current Salmonella subtyping analyses rely on whole genome sequencing (WGS), which focuses on the high-resolution analysis of single genomes or multiple single genomes from the isolated colonies on microbiological agar plates. In this study, we introduce bioinformatics innovations for a metagenomic outbreak response workflow that accurately identifies multiple Salmonella serovars at the same time. bettercallsal is one of the first analysis tools to identify multiple Salmonella enterica serotypes from metagenomic or quasi-metagenomic datasets with high accuracy, allowing these isolate-independent methods to be incorporated into surveillance and root cause investigations. It was tested on an in silico benchmark dataset comprising 29 unique Salmonella serovars, 46 non-Salmonella bacterial genomes, and 10 viral genomes at varying read depths and on previously well-characterized and sequenced non-selective primary and selective enrichments of papaya and peach samples from separate outbreak investigations that resulted in the identification of multiple Salmonella serovars using traditional isolate culturing and WGS as well as nucleic acid assays. Analyses were also conducted on these datasets using a custom-built k-mer tool, SeqSero2, and Kallisto to compare serotype calling to bettercallsal. The in silico dataset analyzed with bettercallsal achieved the maximum precision, recall, and accuracy of 100, 83, and 94%, respectively. In the papaya outbreak samples, bettercallsal identified the presence of multiple serovars in agreement with the Luminex® xMAP assay results and also identified more serovars per sample, as evidenced by NCBI SNP clustering. In peach outbreak samples, bettercallsal identified two serovars in concordance with k-mer analysis and the Luminex xMAP assay. The genome hit reported by bettercallsal clustered with the chicken isolate genome, as reported by the FDA peach outbreak investigation from sequenced isolates (WGS). Overall, bettercallsal outperformed k-mer, Seqsero2, and Kallisto in identifying multiple serovars from enrichment cultures using shotgun metagenomic sequencing.
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Affiliation(s)
- Kranti Konganti
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
| | - Elizabeth Reed
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
| | - Mark Mammel
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
| | - Tunc Kayikcioglu
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
| | - Rachel Binet
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
| | - Karen Jarvis
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
| | - Christina M. Ferreira
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
| | - Rebecca L. Bell
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
| | - Jie Zheng
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
| | - Amanda M. Windsor
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
| | - Andrea Ottesen
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, United States
| | - Christopher J. Grim
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
| | - Padmini Ramachandran
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
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4
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Pavon RDN, Mendoza PDG, Flores CAR, Calayag AMB, Rivera WL. Genotypic virulence profiles and associations in Salmonella isolated from meat samples in wet markets and abattoirs of Metro Manila, Philippines. BMC Microbiol 2022; 22:292. [PMID: 36474155 PMCID: PMC9724337 DOI: 10.1186/s12866-022-02697-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 11/08/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Salmonella are pathogenic foodborne bacteria with complex pathogenicity from numerous virulence genes housed in Salmonella pathogenicity islands (SPIs), plasmids, and other gene cassettes. However, Salmonella virulence gene distributions and mechanisms remain unestablished. In the Philippines, studies mainly report Salmonella incidences and antimicrobial resistance, but little to none on virulence profiles, their associations to animal sources, collection sites and Salmonella serogroups. Hence, a total of 799 Salmonella isolates, previously obtained from pig, cow, and chicken meat samples in wet markets and abattoirs (wet markets: 124 chicken, 151 cow, and 352 pig meat isolates; abattoirs: 172 pig tonsil and jejunum isolates) in Metro Manila, Philippines, were revived and confirmed as Salmonella through invA gene polymerase chain reaction (PCR). Isolates were then screened for eight virulence genes, namely avrA, hilA, sseC, mgtC, spi4R, pipB, spvC and spvR, by optimized multiplex PCR and significant pair associations between virulence genes were determined through Fisher's exact test. Gene frequency patterns were also determined. Salmonella serogroups in addition to animal sources and location types were also used to predict virulence genes prevalence using binary logistic regression. RESULTS High frequencies (64 to 98%) of SPI virulence genes were detected among 799 Salmonella isolates namely mgtC, pipB, avrA, hilA, spi4R and sseC, from most to least. However, only one isolate was positive for plasmid-borne virulence genes, spvC and spvR. Diversity in virulence genes across Salmonella serogroups for 587 Salmonella isolates (O:3 = 250, O:4 = 133, O:6,7 = 99, O:8 = 93, O:9 = 12) was also demonstrated through statistical predictions, particularly for avrA, hilA, sseC, and mgtC. mgtC, the most frequent virulence gene, was predicted by serogroup O:9, while sseC, the least frequent, was predicted by serogroup O:4 and chicken animal source. The highest virulence gene pattern involved SPIs 1-5 genes which suggests the wide distribution and high pathogenic potential of Salmonella. Statistical analyses showed five virulence gene pair associations, namely avrA and hilA, avrA and spi4R, hilA and spi4R, sseC and spi4R, and mgtC and pipB. The animal sources predicted the presence of virulence genes, sseC and pipB, whereas location type for hilA and spi4R, suggesting that these factors may contribute to the type and pathogenicity of Salmonella present. CONCLUSION The high prevalence of virulence genes among Salmonella in the study suggests the high pathogenic potential of Salmonella from abattoirs and wet markets of Metro Manila, Philippines which poses food safety and public health concerns and threatens the Philippine food animal industry. Statistical associations between virulence genes and prediction analyses across Salmonella serogroups and external factors such as animal source and location type and presence of virulence genes suggest the diversity of Salmonella virulence and illustrate determining factors to Salmonella pathogenicity. This study recommends relevant agencies in the Philippines to improve standards in food animal industries and increase efforts in monitoring of foodborne pathogens.
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Affiliation(s)
- Rance Derrick N. Pavon
- grid.11134.360000 0004 0636 6193Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, 1101 Philippines
| | - Paolo D. G. Mendoza
- grid.11134.360000 0004 0636 6193Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, 1101 Philippines
| | - Camille Andrea R. Flores
- grid.11134.360000 0004 0636 6193Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, 1101 Philippines
| | - Alyzza Marie B. Calayag
- grid.11134.360000 0004 0636 6193Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, 1101 Philippines
| | - Windell L. Rivera
- grid.11134.360000 0004 0636 6193Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, 1101 Philippines
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Davies CP, Jurkiw T, Haendiges J, Reed E, Anderson N, Grasso-Kelley E, Hoffmann M, Zheng J. Changes in the genomes and methylomes of three Salmonella enterica serovars after long-term storage in ground black pepper. Front Microbiol 2022; 13:970135. [PMID: 36160197 PMCID: PMC9507087 DOI: 10.3389/fmicb.2022.970135] [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] [Received: 06/15/2022] [Accepted: 08/16/2022] [Indexed: 11/28/2022] Open
Abstract
Low moisture foods (LMFs) have traditionally been recognized as safe for consumption, as most bacteria require higher water content to grow. However, outbreaks due to LMF foods are increasing, and the microbial pathogen Salmonella enterica is frequently implicated. S. enterica can survive in LMFs for years, but few serovars have been studied, and the mechanisms which underlie this longevity are not well understood. Here, we determine that S. enterica serovars S. Tennessee, S. Anatum, and S. Reading but not S. Oranienburg can survive in the ground black pepper for 6 years. S. Reading was not previously associated with any LMF. Using both Illumina and Pacific Biosciences sequencing technologies, we also document changes in the genomes and methylomes of the surviving serovars over this 6-year period. The three serovars acquired a small number of single nucleotide polymorphisms (SNPs) including seven substitutions (four synonymous, two non-synonymous, and one substitution in a non-coding region), and two insertion-deletions. Nine distinct N6-methyladenine (m6A) methylated motifs across the three serovars were identified including five which were previously known, Gm6ATC, CAGm6AG, BATGCm6AT, CRTm6AYN6CTC, and CCm6AN7TGAG, and four novel serovar-specific motifs, GRTm6AN8TTYG, GAm6ACN7GTA, GAA m6ACY, and CAAm6ANCC. Interestingly, the BATGCAT motif was incompletely methylated (35–64% sites across the genome methylated), suggesting a possible role in gene regulation. Furthermore, the number of methylated BATGCm6AT motifs increased after storage in ground black pepper for 6 years from 475 to 657 (S. Tennessee), 366 to 608 (S. Anatum), and 525 to 570 (S. Reading), thus warranting further study as an adaptive mechanism. This is the first long-term assessment of genomic changes in S. enterica in a low moisture environment, and the first study to examine the methylome of any bacteria over a period of years, to our knowledge. These data contribute to our understanding of S. enterica survival in LMFs, and coupled with further studies, will provide the information necessary to design effective interventions which reduce S. enterica in LMFs and maintain a healthy, safe food supply.
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Affiliation(s)
- Cary P. Davies
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, NEA, U.S. Department of Agriculture, Beltsville, MD, United States
- *Correspondence: Cary P. Davies,
| | - Thomas Jurkiw
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Julie Haendiges
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Elizabeth Reed
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Nathan Anderson
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, Bedford Park, IL, United States
| | - Elizabeth Grasso-Kelley
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, Bedford Park, IL, United States
| | - Maria Hoffmann
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Jie Zheng
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
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Haendiges J, Davidson GR, Pettengill JB, Reed E, Ramachandran P, Blessington T, Miller JD, Anderson N, Myoda S, Brown EW, Zheng J, Tikekar R, Hoffmann M. Genomic evidence of environmental and resident Salmonella Senftenberg and Montevideo contamination in the pistachio supply-chain. PLoS One 2021; 16:e0259471. [PMID: 34735518 PMCID: PMC8568146 DOI: 10.1371/journal.pone.0259471] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/19/2021] [Indexed: 12/04/2022] Open
Abstract
Pistachios have been implicated in two salmonellosis outbreaks and multiple recalls in the U.S. This study performed an in-depth retrospective data analysis of Salmonella associated with pistachios as well as a storage study to evaluate the survivability of Salmonella on inoculated inshell pistachios to further understand the genetics and microbiological dynamics of this commodity-pathogen pair. The retrospective data analysis on isolates associated with pistachios was performed utilizing short-read and long-read sequencing technologies. The sequence data were analyzed using two methods: the FDA's Center for Food Safety and Applied Nutrition Single Nucleotide Polymorphism (SNP) analysis and Whole Genome Multilocus Sequence Typing (wgMLST). The year-long storage study evaluated the survival of five strains of Salmonella on pistachios stored at 25 °C at 35% and 54% relative humidity (RH). Our results demonstrate: i) evidence of persistent Salmonella Senftenberg and Salmonella Montevideo strains in pistachio environments, some of which may be due to clonal resident strains and some of which may be due to preharvest contamination; ii) presence of the Copper Homeostasis and Silver Resistance Island (CHASRI) in Salmonella Senftenberg and Montevideo strains in the pistachio supply chain; and iii) the use of metagenomic analysis is a novel tool for determining the composition of serovar survival in a cocktail inoculated storage study.
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Affiliation(s)
- Julie Haendiges
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, United States of America
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, United States of America
| | - Gordon R Davidson
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, United States of America
| | - James B Pettengill
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, United States of America
| | - Elizabeth Reed
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, United States of America
| | - Padmini Ramachandran
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, United States of America
| | - Tyann Blessington
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, United States of America
| | - Jesse D Miller
- Neogen Corporation, Lansing, Michigan, United States of America
| | - Nathan Anderson
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, Bedford Park, Illinois, United States of America
| | - Sam Myoda
- IEH Incorporated, Seattle, Washington, United States of America
| | - Eric W Brown
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, United States of America
| | - Jie Zheng
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, United States of America
| | - Rohan Tikekar
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, United States of America
| | - Maria Hoffmann
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, United States of America
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Development of a Genoserotyping Method for Salmonella Infantis Detection on the Basis of Pangenome Analysis. Microorganisms 2020; 9:microorganisms9010067. [PMID: 33383801 PMCID: PMC7824266 DOI: 10.3390/microorganisms9010067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 12/24/2020] [Accepted: 12/25/2020] [Indexed: 11/29/2022] Open
Abstract
In recent years, Salmonella Infantis has become a predominant serovariant in clinical and poultry isolates, thereby imposing a substantial economic burden on both public health and the livestock industry. With the aim of coping with the steep increase in serovar Infantis prevalence, a polymerase chain reaction (PCR)-based rapid and accurate diagnostic assay was developed in this study through pangenome profiling of 60 Salmonella serovars. A gene marker, SIN_02055, was identified, which is present in the S. Infantis genome but not in the pangenome of the other serovars. Primers specific to SIN_02055 were used to accurately detect serovar Infantis, and to successfully differentiate Infantis from the other 59 serovars in real-time PCR with a R2 of 0.999 and an efficiency of 95.76%. The developed method was applied to 54 Salmonella strains belonging to eight dominant serovars, and distinguished Infantis from the other seven serovars with an accuracy of 100%. The diagnostic primer set also did not show false positive amplification with 32 strains from eight non-Salmonella bacterial species. This cost-effective and rapid method can be considered an alternative to the classic serotyping using antisera.
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Luo Y, Huang C, Ye J, Octavia S, Wang H, Dunbar SA, Jin D, Tang YW, Lan R. Comparison of xMAP Salmonella Serotyping Assay With Traditional Serotyping and Discordance Resolution by Whole Genome Sequencing. Front Cell Infect Microbiol 2020; 10:452. [PMID: 33014887 PMCID: PMC7504902 DOI: 10.3389/fcimb.2020.00452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 07/23/2020] [Indexed: 11/14/2022] Open
Abstract
Salmonella spp. are a major cause of foodborne illness throughout the world. Traditional serotyping by antisera agglutination has been used as a standard identification method for many years but newer nucleic acid-based tests have become available that may provide advantages in workflow and test turnaround time. In this study, we evaluated the Luminex® xMAP® Salmonella Serotyping Assay (SSA), a multiplex nucleic acid test capable of identifying 85% of the most common Salmonella serotypes, in comparison to the traditional serum agglutination test (SAT) on 4 standard strains and 255 isolates from human (224), environmental, and food (31) samples. Of the total of 259 isolates, 256 could be typed by the SSA. Of these, 197 (77.0%) were fully typed and 59 (23.0%) were partially typed. By SAT, 246 of the 259 isolates (95%) were successfully typed. Sixty isolates had discrepant results between SAT and SSA and were resolved using whole genome sequencing (WGS). By SAT, 80.0% (48/60) of the isolates were consistent with WGS while by SSA 91.7% (55/60) were partially consistent with WGS. By serovar, all 30 serovars except one tested were fully or partially typable. The workflow comparison showed that SSA provided advantages over SAT with a hands-on time (HOT) of 3.5 min and total turnaround time (TAT) of 6 h, as compared to 1 h HOT and 2–6 days TAT for SAT. Overall, this study showed that molecular serotyping is promising as a rapid method for Salmonella serotyping with good accuracy for typing most common Salmonella serovars circulating in China.
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Affiliation(s)
- Yun Luo
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.,Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Chen Huang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Julian Ye
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Sophie Octavia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Huanying Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, China
| | | | - Dazhi Jin
- Centre of Laboratory Medicine, Zhejiang Provincial People Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China.,School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, China
| | - Yi-Wei Tang
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States.,Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY, United States.,Cepheid, Danaher Diagnostic Platform, Shanghai, China
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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Xu F, Ge C, Luo H, Li S, Wiedmann M, Deng X, Zhang G, Stevenson A, Baker RC, Tang S. Evaluation of real-time nanopore sequencing for Salmonella serotype prediction. Food Microbiol 2020; 89:103452. [DOI: 10.1016/j.fm.2020.103452] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 02/02/2020] [Accepted: 02/03/2020] [Indexed: 12/21/2022]
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10
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Gu G, Strawn LK, Zheng J, Reed EA, Rideout SL. Diversity and Dynamics of Salmonella enterica in Water Sources, Poultry Litters, and Field Soils Amended With Poultry Litter in a Major Agricultural Area of Virginia. Front Microbiol 2019; 10:2868. [PMID: 31956319 PMCID: PMC6951424 DOI: 10.3389/fmicb.2019.02868] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/27/2019] [Indexed: 11/13/2022] Open
Abstract
The Eastern Shore of Virginia (ESV) is a major agricultural region in Virginia and in the past has been linked to some tomato-associated outbreaks of salmonellosis. In this study, water samples were collected weekly from irrigation ponds and wells in four representative vegetable farms (Farms A–D, each farm paired with one pond and one well) and a creek as well. In addition, water samples from two sites in the Chesapeake Bay on the ESV were collected monthly. Poultry litter was sampled monthly from three commercial broiler farms. Soil samples were collected monthly after fertilization with poultry litter from 10 farms in 2014 and another 14 farms in 2015. A most probable number method was used to detect Salmonella enterica presence and concentration in collected samples. Presumptive Salmonella colonies were confirmed by the cross-streaking method. Molecular serotyping was carried out to determine the Salmonella serovars. The average prevalence of Salmonella in pond, well, creek, and bay water samples was 19.3, 3.3, 24.2, and 29.2%, respectively. There were significant spatial and temporal differences for Salmonella incidence in various water sources. The prevalence of S. enterica in four tested ponds from farms A, B, C, and D were 16, 12, 22, and 27%, respectively. While the prevalence of S. enterica in irrigation wells was significantly lower, some well water samples tested positive during the study. Salmonella Newport was found to be the predominant serovar isolated from water samples. All poultry houses of the three tested broiler farms were Salmonella-positive at certain sampling points during the study with prevalence ranging from 14.3 to 35.4%. Salmonella was found to be able to survive up to 4 months in poultry litter amended soils from the tested farms in 2014, and up to 6 months in 2015. This research examined the dynamics of S. enterica in relationship to water source, poultry litter, and amended soil in a major agricultural area, and provides useful information for food safety risk assessments.
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Affiliation(s)
- Ganyu Gu
- Eastern Shore Agricultural Research and Extension Center, Virginia Tech, Blacksburg, VA, United States
| | - Laura K Strawn
- Eastern Shore Agricultural Research and Extension Center, Virginia Tech, Blacksburg, VA, United States
| | - Jie Zheng
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, United States
| | - Elizabeth A Reed
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, United States
| | - Steven L Rideout
- Eastern Shore Agricultural Research and Extension Center, Virginia Tech, Blacksburg, VA, United States
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11
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Gand M, Mattheus W, Roosens NHC, Dierick K, Marchal K, De Keersmaecker SCJ, Bertrand S. A multiplex oligonucleotide ligation-PCR method for the genoserotyping of common Salmonella using a liquid bead suspension assay. Food Microbiol 2019; 87:103394. [PMID: 31948635 DOI: 10.1016/j.fm.2019.103394] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/21/2019] [Accepted: 11/20/2019] [Indexed: 01/14/2023]
Abstract
Salmonella is a major pathogen having a public health and economic impact in both humans and animals. Six serotypes of the Salmonella genus are mentioned in the Belgian and European regulation as to be rapidly excluded from the food chain (EU regulation N°2160/2003, Belgian royal decree 27/04/2017). The reference method for Salmonella serotyping, including slide-agglutination and biochemical tests, is time-consuming, expensive, not always objective, and therefore does not match the fast identification criteria required by the legislation. In this study, a molecular method, using genetic markers detected by Multiplex Oligonucleotide Ligation - PCR and Luminex technology, was developed for the identification of the 6 Salmonella serotypes and their variants subjected to an official control. The resulting method was validated with the analysis of 971 Salmonella isolated from different matrixes (human, animal, food or environment) and 33 non-Salmonella strains. The results were compared with the reference identifications, achieving an accuracy of 99.7%. The cost-effective high-throughput genoserotyping assay is performed in 1 day and generates objective results, thanks to the automatic interpretation of raw data using a barcode system. In conclusion, it is fully adapted to the implementation in first line laboratories and meets the requirements of the regulation.
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Affiliation(s)
- Mathieu Gand
- Sciensano, Infectious Diseases in Humans, Bacterial Diseases, B-1180 Brussels, Belgium; Department of Information Technology, IDLab, Imec, Ghent University, B-9052 Ghent, Belgium
| | - Wesley Mattheus
- Sciensano, Infectious Diseases in Humans, Bacterial Diseases, B-1180 Brussels, Belgium.
| | - Nancy H C Roosens
- Sciensano, Transversal Activities in Applied Genomics, B-1050 Brussels, Belgium
| | - Katelijne Dierick
- Sciensano, Infectious Diseases in Humans, Food Pathogen, B-1050 Brussels, Belgium
| | - Kathleen Marchal
- Department of Information Technology, IDLab, Imec, Ghent University, B-9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
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12
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SeqSero2: Rapid and Improved Salmonella Serotype Determination Using Whole-Genome Sequencing Data. Appl Environ Microbiol 2019; 85:AEM.01746-19. [PMID: 31540993 DOI: 10.1128/aem.01746-19] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 09/17/2019] [Indexed: 11/20/2022] Open
Abstract
SeqSero, launched in 2015, is a software tool for Salmonella serotype determination from whole-genome sequencing (WGS) data. Despite its routine use in public health and food safety laboratories in the United States and other countries, the original SeqSero pipeline is relatively slow (minutes per genome using sequencing reads), is not optimized for draft genome assemblies, and may assign multiple serotypes for a strain. Here, we present SeqSero2 (github.com/denglab/SeqSero2; denglab.info/SeqSero2), an algorithmic transformation and functional update of the original SeqSero. Major improvements include (i) additional sequence markers for identification of Salmonella species and subspecies and certain serotypes, (ii) a k-mer based algorithm for rapid serotype prediction from raw reads (seconds per genome) and improved serotype prediction from assemblies, and (iii) a targeted assembly approach for specific retrieval of serotype determinants from WGS for serotype prediction, new allele discovery, and prediction troubleshooting. Evaluated using 5,794 genomes representing 364 common U.S. serotypes, including 2,280 human isolates of 117 serotypes from the National Antimicrobial Resistance Monitoring System, SeqSero2 is up to 50 times faster than the original SeqSero while maintaining equivalent accuracy for raw reads and substantially improving accuracy for assemblies. SeqSero2 further suggested that 3% of the tested genomes contained reads from multiple serotypes, indicating a use for contamination detection. In addition to short reads, SeqSero2 demonstrated potential for accurate and rapid serotype prediction directly from long nanopore reads despite base call errors. Testing of 40 nanopore-sequenced genomes of 17 serotypes yielded a single H antigen misidentification.IMPORTANCE Serotyping is the basis of public health surveillance of Salmonella It remains a first-line subtyping method even as surveillance continues to be transformed by whole-genome sequencing. SeqSero allows the integration of Salmonella serotyping into a whole-genome-sequencing-based laboratory workflow while maintaining continuity with the classic serotyping scheme. SeqSero2, informed by extensive testing and application of SeqSero in the United States and other countries, incorporates important improvements and updates that further strengthen its application in routine and large-scale surveillance of Salmonella by whole-genome sequencing.
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13
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Kasturi KN. A real-time PCR for rapid identification of Salmonella enterica Gaminara serovar. J Microbiol Methods 2019; 169:105729. [PMID: 31711901 DOI: 10.1016/j.mimet.2019.105729] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/13/2019] [Accepted: 09/21/2019] [Indexed: 12/17/2022]
Abstract
Salmonella is one of the leading causes of foodborne illnesses in the USA. When a Salmonella outbreak occurs, rapid identification of the causative serovar is important for tracing the source of contamination and for preventing the further spread of the illness. Each serovar is characterized by the presence of a group-specific somatic O-antigen(s) and an assortment of flagellar phase-1 and phase-2 antigens. As the traditional serotyping protocol is time consuming, labor intensive, and expensive, faster and less expensive molecular diagnostic methods are needed. This report outlines the development of a rapid multiplex real-time PCR procedure that facilitates the identification of Salmonella serogroup I and the serovars of the group. Using Salmonella Gaminara serovar (O16:d:1,7) as an example, first the gene(s) responsible for expression of the somatic O antigen, O16, and the nucleotide sequence of the variable-region of genes encoding the flagellar phase-1 (d) and phase-2 (1,7) antigens were identified. Then, a multiplex real-time PCR was designed that incorporated primers and probes specific for the three target genes and confirmed the specificity. The assay had 100% inclusivity for all three gene targets, detecting 2 genomic DNA copies of O16 and 1,7 gene targets and 10 copies of d gene target. Importance: Rapid molecular methods to identify Salmonella serovars should increase the precision of routine surveillance of clinically important serovars and promote public health.
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Affiliation(s)
- Kuppuswamy N Kasturi
- U. S. Food and Drug Administration, Office of Regulatory Affairs, Office of Regulatory Science, Northeast Food and Feed Laboratory, Jamaica, New York 11433, USA.
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14
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Moore MM, Nucci MJ, Madson SM, Wagley GS, Keys CE, Brown EW, McQUISTON JR, Fields PI. Evaluation of a Bead-Based Salmonella Molecular Serotyping Method for Salmonella Isolated from Food and Environmental Samples. J Food Prot 2019; 82:1973-1987. [PMID: 31644335 DOI: 10.4315/0362-028x.jfp-18-600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Salmonella is a leading cause of foodborne illness worldwide, and foods containing Salmonella (except raw meat and poultry products) are considered adulterated. Serotyping of Salmonella is an essential part of surveillance and investigation of outbreaks. This study evaluated a bead-based Salmonella molecular serotyping (SMS) method, which included the O-group 1, H-antigen, alternate target, and O-group 2 assays, compared with traditional serotyping. Salmonella was isolated from food, pet food, and environmental samples or were reference strains. A total of 572 isolates were analyzed by using two formats of the SMS method in comparison with traditional methods: 485 were analyzed by using Radix SMS (a custom user-mixed format), 218 were analyzed by using Luminex SMS (a commercial kit format), and 131 of the total isolates were analyzed by both formats for comparison. The SMS method was evaluated on the basis of the successful identification of antigens by the probes included in the method. The method identified 550 (96.2%) isolates as expected, 6 (1.0%) isolates were not identified as initially expected but were shown to be correctly identified by SMS after reanalysis by traditional serotyping, and 16 (2.8%) isolates not identified as expected possessed an antigen that should have been detected by the method but was not. Among the isolates considered correctly identified, 255 (44.6%) were identified to a single serovar, 44 (7.7%) required additional biochemical testing to differentiate variants or subspecies, and 251 (43.9%) were partially serotyped because probes for some antigens were not in the assay or had allelic variation for known serovars. Whole genome sequencing, SeqSero, and the Salmonella In Silico Typing Resource gave added confirmation for three isolates. Addition of the O-group 2 assay enabled the identification of 55 (9.6%) of 572 isolates. The SMS method could fully or partially serotype most isolates within a day. The SMS method should be a valuable tool when faster screening methods are needed, such as outbreaks and screening large numbers of environmental isolates.
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Affiliation(s)
- M M Moore
- U.S. Food and Drug Administration, Office of Regulatory Affairs, Pacific Northwest Laboratory, Applied Technology Center, Bothell, Washington 98021
| | - M J Nucci
- U.S. Food and Drug Administration, Office of Regulatory Affairs, Denver Laboratory, Lakewood, Colorado 80225
| | - S M Madson
- U.S. Food and Drug Administration, Office of Regulatory Affairs, Arkansas Laboratory, Jefferson, Arkansas 72079
| | - G S Wagley
- U.S. Food and Drug Administration, Office of Regulatory Affairs, Southeast Food and Feed Laboratory, Atlanta, Georgia 30309
| | - C E Keys
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Regulatory Science, College Park, Maryland 20740
| | - E W Brown
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Regulatory Science, College Park, Maryland 20740
| | - J R McQUISTON
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, Enteric Diseases Laboratory Branch, Atlanta, Georgia 30333, USA
| | - P I Fields
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne and Environmental Diseases, Enteric Diseases Laboratory Branch, Atlanta, Georgia 30333, USA
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15
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Longo A, Losasso C, Vitulano F, Mastrorilli E, Turchetto S, Petrin S, Mantovani C, Dalla Pozza MC, Ramon E, Conedera G, Citterio CV, Ricci A, Barco L, Lettini AA. Insight into an outbreak of Salmonella Choleraesuis var. Kunzendorf in wild boars. Vet Microbiol 2019; 238:108423. [PMID: 31648730 DOI: 10.1016/j.vetmic.2019.108423] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/19/2019] [Accepted: 09/19/2019] [Indexed: 10/26/2022]
Abstract
An unusual mortality of wild boars occurred in Italy from 2012 to 2015 due to Salmonella Choleraesuis infection. In order to confirm the occurrence of an outbreak of S. Choleraesuis in wild boars and to epidemically characterise the unique S. Choleraesuis biovar, a collection of isolates belonging to wild boars was investigated from the phenotypic, molecular and genomic points of view (PFGE and WGS). Moreover, the possibility of transmission to domestic pigs and humans, temporally and geographically close to the wild boar epidemic, was tested by also including in the panel isolates from infected domestic pigs and from one human case of infection. Wild boar isolates displayed a high genetic correlation, thus suggesting they are part of the same outbreak, with a common invasiveness potential. Conversely, no correlation between pig isolates and those from the other sources (wild boars and human) was found. However, the phylogenetic and PFGE analyses suggest a high degree of similarity between the human and the investigated wild boar outbreak isolates, implying the potential for the spread of Salmonella Choleraesuis among these species.
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Affiliation(s)
- Alessandra Longo
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, PD, Italy
| | - Carmen Losasso
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, PD, Italy.
| | - Federica Vitulano
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, PD, Italy
| | - Eleonora Mastrorilli
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, PD, Italy
| | - Sara Turchetto
- SCT2 - Treviso, Belluno and Venezia - O.U. Eco-pathology, Istituto Zooprofilattico Sperimentale delle Venezie, Belluno, Italy
| | - Sara Petrin
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, PD, Italy
| | - Claudio Mantovani
- Science Communication Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro PD, Italy
| | - Maria Cristina Dalla Pozza
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, PD, Italy
| | - Elena Ramon
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, PD, Italy
| | - Gabriella Conedera
- SCT4 - Friuli Venezia Giulia - Istituto Zooprofilattico Sperimentale delle Venezie, Pordenone, Italy
| | - Carlo V Citterio
- SCT2 - Treviso, Belluno and Venezia - O.U. Eco-pathology, Istituto Zooprofilattico Sperimentale delle Venezie, Belluno, Italy
| | - Antonia Ricci
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, PD, Italy
| | - Lisa Barco
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, PD, Italy
| | - Antonia Anna Lettini
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, PD, Italy
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16
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Longo A, Petrin S, Mastrorilli E, Tiengo A, Lettini AA, Barco L, Ricci A, Losasso C, Cibin V. Characterizing Salmonella enterica Serovar Choleraesuis, var. Kunzendorf: A Comparative Case Study. Front Vet Sci 2019; 6:316. [PMID: 31620457 PMCID: PMC6763558 DOI: 10.3389/fvets.2019.00316] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/04/2019] [Indexed: 11/15/2022] Open
Abstract
Different Salmonella serovars generally display different antigenic formulae, but there are some exceptions. For instance, the same antigenic formula, 6,7:c:1,5, is shared by Salmonella enterica serovar, Paratyphi C, Typhisuis, and Choleraesuis. Moreover, three biotypes have been described within the S. Choleraesuis serovar. A distinction among such biotypes can only be based on biochemical behaviors (biotyping) posing serious concerns when rapid characterization is required. The study of an outbreak of severe epizootic salmonellosis in wild boars occurred in Italy between 2012 and 2014 and the typing of the isolates recovered from the outbreak were used to test different approaches for serovar identification. A number of 30 S. Choleraesuis var. Kunzendorf isolates from the outbreak were typed by means of four different methods to derive serovar and biotype: (i) slide agglutination method followed by biochemical tests, (ii) suspension array xMAP® Salmonella Serotyping Assay (SSA), (iii) whole genome sequencing (WGS) and data analysis using SeqSero tool, and (iv) WGS and data analysis using Salmonella TypeFinder tool. Slide agglutination, xMAP® SSA and WGS, followed by SeqSero analysis, are methods that infer the serovars according to the White-Kauffmann-Le Minor (WKL) scheme, based exclusively on antigens. Using these methods, isolates with incomplete antigenic formulae could be misleadingly excluded from an outbreak. On the contrary, WGS followed by Salmonella TypeFinder data analysis, which predicts the serotype on the basis of Multilocus sequence typing (MLST), might be able to cluster together isolates belonging to the same outbreak irrespective of the antigenic formula. Results suggest the benefit of routine use of a combination of in silico MLST and antigenic formula analysis to solve specific ambiguous case studies for outbreak investigation purposes.
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Affiliation(s)
| | | | | | | | | | | | | | - Carmen Losasso
- World Organisation for Animal Health (OIE), National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'Università, Legnaro, Italy
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17
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Charlermroj R, Makornwattana M, Phuengwas S, Meerak J, Pichpol D, Karoonuthaisiri N. DNA-based bead array technology for simultaneous identification of eleven foodborne pathogens in chicken meat. Food Control 2019. [DOI: 10.1016/j.foodcont.2019.02.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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18
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19
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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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20
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Ibrahim GM, Morin PM. Salmonella Serotyping Using Whole Genome Sequencing. Front Microbiol 2018; 9:2993. [PMID: 30619114 PMCID: PMC6300517 DOI: 10.3389/fmicb.2018.02993] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 11/20/2018] [Indexed: 11/24/2022] Open
Abstract
Until recently, traditional serology and the Kauffmann White Scheme (KWS) have been the gold standard for Salmonella serotyping. Whole Genome Sequencing (WGS) has now emerged as an alternative in this field. Serotype information remains a cornerstone in food safety and public health activities to reduce the burden of salmonellosis. At the same time, recent advances in WGS have improved the ability to perform advanced pathogen characterization while improving trace back investigations to determine the source of foodborne illness during outbreaks. Serovar prediction based on WGS can be performed using in silico data analysis tools. Three such tools have been developed: (a). Salmonella in silico Typing Resource (SISTR), (b). SeqSero, and (c). in silico 7-gene MLST ST (Multilocus Sequence Typing Sub-Typing) which was generated using the SISTR platform. Public health officials around the world are diligently working to validate these tools for replacing traditional surveillance methods to provide a more powerful approach for molecular epidemiology in support of public health investigations. In this study, we report a retrospective analysis of our laboratory inventory of 1,041 Salmonella isolates collected between 1999 and 2017. These isolates are of public health significance since they all came from either food, feed or environmental swabs. They were all serotyped by both traditional serology and WGS using an in silico SeqSero tool for serovar prediction. Both predicted identical Salmonella serotypes in 899 isolates (86.4% of the 1,041 Salmonella isolates). SeqSero assignments differed from traditional serological testing in 80 isolates (7.7%) and no serotype prediction was ascertained from 62 isolates (5.9%). This retrospective study is an excellent example of using WGS and SeqSero as a data analysis tool to predict Salmonella serotypes that can provide numerous advantages including molecular and genetic details regarding the characteristics of the Salmonella isolates compared to traditional KWS serotyping. In conclusion, it is evident that using WGS and in silico tools for Salmonella serotyping might someday replace traditional serotyping.
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Affiliation(s)
- George M Ibrahim
- Microbiological Sciences Branch, Northeast Food and Feed Laboratory, United States Food & Drug Administration, Jamaica, NY, United States
| | - Paul M Morin
- Microbiological Sciences Branch, Northeast Food and Feed Laboratory, United States Food & Drug Administration, Jamaica, NY, United States
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21
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Schneider A, Niemeyer CM. DNA Surface Technology: From Gene Sensors to Integrated Systems for Life and Materials Sciences. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201811713] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ann‐Kathrin Schneider
- Institute for Biological Interfaces (IBG 1) Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldshafen Germany
| | - Christof M. Niemeyer
- Institute for Biological Interfaces (IBG 1) Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldshafen Germany
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22
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Schneider A, Niemeyer CM. DNA Surface Technology: From Gene Sensors to Integrated Systems for Life and Materials Sciences. Angew Chem Int Ed Engl 2018; 57:16959-16967. [DOI: 10.1002/anie.201811713] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/15/2018] [Indexed: 01/21/2023]
Affiliation(s)
- Ann‐Kathrin Schneider
- Institute for Biological Interfaces (IBG 1) Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldshafen Germany
| | - Christof M. Niemeyer
- Institute for Biological Interfaces (IBG 1) Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldshafen Germany
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23
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Zhang P, Zhuang L, Zhang D, Xu J, Dou X, Wang C, Gong J. Serovar-Specific Polymerase Chain Reaction for Detection of Salmonella enterica Serovar Indiana. Foodborne Pathog Dis 2018; 15:776-781. [PMID: 30183348 DOI: 10.1089/fpd.2018.2492] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Salmonella enterica serovar Indiana (S. Indiana) is a newly emerging pathogen with high levels of drug resistance. It has become one of the most common Salmonella serovars in China with a worldwide distribution, posing significant public health concerns. Detection of S. Indiana by traditional bacteriological methods is time-consuming and laborious, which prevents timely surveillance and effective control of the pathogen. In this study, comparative genomics was used to identify an A7P63_13850 gene that is uniquely present in S. Indiana, but not in other Salmonella serovars or any non-Salmonella bacteria. Then, a polymerase chain reaction (PCR) assay targeting this serovar-specific gene was established for specific detection of S. Indiana. The detection limit of this method is 10 pg per reaction for bacterial genomic DNA, being equivalent to 100 colony-forming units (CFU) per reaction. The established PCR amplifies all S. Indiana strains (n = 56), but none of other Salmonella serovars (n = 146) and non-Salmonella species (n = 14). The assay established in this study was also used to detect clinical samples from poultry, showed a positivity of 14.7% (23/156) for S. Indiana, which were verified by bacteriological methods. The highly sensitive and serovar-specific PCR for S. Indiana established in this study is suitable and convenient for detection of S. Indiana which aids in surveillance and control of the pathogen.
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Affiliation(s)
- Ping Zhang
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, China
| | - Linlin Zhuang
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Di Zhang
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, China
| | - Jingxiao Xu
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, China
| | - Xinhong Dou
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, China
| | - Chengming Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, Alabama
| | - Jiansen Gong
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, China
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24
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Aydin M, Carter-Conger J, Gao N, Gilmore DF, Ricke SC, Ahn S. Molecular identification of common Salmonella serovars using multiplex DNA sensor-based suspension array. Anal Bioanal Chem 2018; 410:2637-2646. [DOI: 10.1007/s00216-018-0938-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/25/2018] [Accepted: 02/02/2018] [Indexed: 12/15/2022]
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25
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Rho J, Jang W, Hwang I, Lee D, Lee CH, Chung TD. Multiplex immunoassays using virus-tethered gold microspheres by DC impedance-based flow cytometry. Biosens Bioelectron 2017; 102:121-128. [PMID: 29128714 DOI: 10.1016/j.bios.2017.11.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/31/2017] [Accepted: 11/06/2017] [Indexed: 11/17/2022]
Abstract
Bead-based multiplex immunoassays for common use require enhanced sensitivity and effective prevention of non-specific adsorption, as well as miniaturization of the detection device. In this work, we have implemented virus-tethered gold microspheres for multiplex immunoassay applications, employing a DC impedance-based flow cytometer as a detection element. The advantages of virus-tethered gold microspheres, including excellent prevention of non-specific adsorption, are extended to signal enhancement arising from the large quantity of antibody loading on each virion, and to flexible movement of filamentous virus. Individual virus-tethered beads generate their own DC impedance and fluorescence signals, which are simultaneously detected by a chip-based microfluidic flow cytometer. This system successfully realized multiplex immunoassays involving four biomarkers: cardiac troponin I (cTnI), prostate specific antigen (PSA), creatine kinase MB (CK-MB), and myoglobin in undiluted human sera, elevating sensitivity by up to 5.7-fold compared to the beads without virus. Constructive integration between filamentous virus-tethered Au-layered microspheres and use of a microfluidic cytometer suggests a promising strategy for competitive multiplex immunoassay development based on suspension arrays.
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Affiliation(s)
- Jihun Rho
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Woohyuk Jang
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Inseong Hwang
- InSol Co., Ltd., Yangjae-daero 85-gil, Gangdong-gu, Seoul 05408, Republic of Korea
| | - Dahye Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Chang Heon Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Taek Dong Chung
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea; Program in Nano Science and Technology, Graduate School of Convergence Science and Technology, Seoul National University, Suwon-Si, Gyeonggi-do 16229, Republic of Korea; Advanced Institutes of Convergence Technology, Suwon-Si, Gyeonggi-do 16229, Republic of Korea.
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Kumar Y, Bansal S, Jaiswal P. Loop-Mediated Isothermal Amplification (LAMP): A Rapid and Sensitive Tool for Quality Assessment of Meat Products. Compr Rev Food Sci Food Saf 2017; 16:1359-1378. [DOI: 10.1111/1541-4337.12309] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 08/16/2017] [Accepted: 08/16/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Yogesh Kumar
- ICAR-Central Inst. of Post-Harvest Engineering and Technology (CIPHET); Ludhiana India
| | - Sangita Bansal
- ICAR-Central Inst. of Post-Harvest Engineering and Technology (CIPHET); Ludhiana India
| | - Pranita Jaiswal
- ICAR-Central Inst. of Post-Harvest Engineering and Technology (CIPHET); Ludhiana India
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Jean-Gilles Beaubrun J, Ewing L, Dudley K, Benhamed F, Wang H, Hanes DE. Evaluation of a multiplex PCR method to serotype Salmonella in animal feeds pre-enrichment broth cultures. MethodsX 2017; 4:335-345. [PMID: 29872638 PMCID: PMC5986982 DOI: 10.1016/j.mex.2017.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 07/29/2017] [Accepted: 09/08/2017] [Indexed: 11/26/2022] Open
Abstract
The identification of Salmonella enterica serotypes remains a highly important public health concern for microbiological analysis of foods, feeds, and clinical samples. Outbreaks of human salmonellosis are sometimes linked to contact with infected animals and animal feeds. To possibly reduce the number of outbreaks, it is important to rapidly, efficiently detect Salmonella enterica in animal feeds and food products. A multiplex PCR for molecular serotyping of Salmonella enterica previously used in a single lab validation study for serotyping in multiple human food matrices was used in this investigation to evaluate the effectiveness of the multiplex PCR assay as serotyping method and screening tool for Salmonella in animal feeds. This approach is unique in that: •The multiplex PCR serotyping assay may be used for rapid screening and serotyping of Salmonella enterica from contaminated animal feed at the non-selective pre-enrichment step.•The assay may provide the serotype or identification of Salmonella in positive samples at concentration as low as 10 CFU/25 g after a 24 h non-selective pre-enrichment step.•In addition to the ability to serotype, this assay contains invA as an internal control for Salmonella positive identification. The invA shows positive indication for Salmonella outside of the 30 serotypic banding patterns.
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Affiliation(s)
- Junia Jean-Gilles Beaubrun
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Laurel, MD 207081, United States
| | - Laura Ewing
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Laurel, MD 207081, United States
| | - Kim Dudley
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Laurel, MD 207081, United States
| | - Faiza Benhamed
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Laurel, MD 20708, United States
| | - Hua Wang
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, MD 20740, United States
| | - Darcy E. Hanes
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Laurel, MD 207081, United States
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Zheng Z, Zheng W, Wang H, Pan J, Pu X. Serotype determination of Salmonella by xTAG assay. J Microbiol Methods 2017; 141:101-107. [PMID: 28818598 DOI: 10.1016/j.mimet.2017.08.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 08/12/2017] [Accepted: 08/12/2017] [Indexed: 12/24/2022]
Abstract
Currently, no protocols or commercial kits are available to determine the serotypes of Salmonella by using Luminex MAGPIX®. In this study, an xTAG assay for serotype determination of Salmonella suitable for Luminex MAGPIX® is described and 228 Salmonella isolates were serotype determined by this xTAG assay. The xTAG assay consists of two steps: 1) Multiplex PCR to amplify simultaneously O, H and Vi antigen genes of Salmonella, and 2) Magplex-TAG™ microsphere hybridization to identify accurately the specific PCR products of different antigens. Compared with the serotyping results of traditional serum agglutination test, the sensitivity and specificity of the xTAG assay were 95.1% and 100%, respectively. The agreement rate of these two assays was 95.2%. Compared with Luminex xMAP® Salmonella Serotyping Assay (SSA) kit, the advantages of this xTAG assay are: First, the magnetic beads make it applicable to both the Luminex®100/200™ and MAGPIX® systems. Second, only primers rather than both primers and probes are needed in the xTAG assay, and the process of coupling antigen-specific oligonucleotide probes to beads is circumvented, which make the xTAG assay convenient to be utilized by other laboratories. The xTAG assay may serve as a rapid alternative or complementary method for traditional Salmonella serotyping tests, especially for laboratories that utilize the MAGPIX® systems.
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Affiliation(s)
- Zhibei Zheng
- Hangzhou Center for Disease Control and Prevention, Hangzhou, Zhejiang, China.
| | - Wei Zheng
- Hangzhou Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
| | - Haoqiu Wang
- Hangzhou Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
| | - Jincao Pan
- Hangzhou Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
| | - Xiaoying Pu
- Hangzhou Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
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Felten A, Guillier L, Radomski N, Mistou MY, Lailler R, Cadel-Six S. Genome Target Evaluator (GTEvaluator): A workflow exploiting genome dataset to measure the sensitivity and specificity of genetic markers. PLoS One 2017; 12:e0182082. [PMID: 28750049 PMCID: PMC5531552 DOI: 10.1371/journal.pone.0182082] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 07/12/2017] [Indexed: 11/30/2022] Open
Abstract
Most of the bacterial typing methods used to discriminate isolates in medical or food safety microbiology are based on genetic markers used as targets in PCR or hybridization experiments. These DNA typing methods are important tools for studying prevalence and epidemiology, for conducting surveillance, investigations and control of biological hazard sources. In that perspective, it is crucial to insure that the chosen genetic markers have the greatest specificity and sensitivity. The wealth of whole-genome sequences available for many bacterial species offers the opportunity to evaluate the performance of these genetic markers. In the present study, we have developed GTEvaluator, a bioinformatics workflow which ranks genetic markers depending on their sensitivity and specificity towards groups of well-defined genomes. GTEvaluator identifies the most performant genetic markers to target individuals among a population. The individuals (i.e. a group of genomes within a collection) are defined by any kind of particular phenotypic or biological properties inside a related population (i.e. collection of genomes). The performance of the genetic markers is computed by a distance value which takes into account both sensitivity and specificity. In this study we report two examples of GTEvaluator application. In the first example Bacillus phenotypic markers were evaluated for their capacity to distinguish B. cereus from B. thuringiensis. In the second experiment, GTEvaluator measured the performance of genetic markers dedicated to the molecular serotyping of Salmonella enterica. In one in silico experiment it was possible to test 64 markers onto 134 genomes corresponding to 14 different serotypes.
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Affiliation(s)
- Arnaud Felten
- Université PARIS-EST, ANSES, Laboratory for Food Safety, Maisons-Alfort, France
| | - Laurent Guillier
- Université PARIS-EST, ANSES, Laboratory for Food Safety, Maisons-Alfort, France
| | - Nicolas Radomski
- Université PARIS-EST, ANSES, Laboratory for Food Safety, Maisons-Alfort, France
| | - Michel-Yves Mistou
- Université PARIS-EST, ANSES, Laboratory for Food Safety, Maisons-Alfort, France
| | - Renaud Lailler
- Université PARIS-EST, ANSES, Laboratory for Food Safety, Maisons-Alfort, France
| | - Sabrina Cadel-Six
- Université PARIS-EST, ANSES, Laboratory for Food Safety, Maisons-Alfort, France
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Real-Time PCR Method for Detection of Salmonella spp. in Environmental Samples. Appl Environ Microbiol 2017; 83:AEM.00644-17. [PMID: 28500041 DOI: 10.1128/aem.00644-17] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 05/02/2017] [Indexed: 01/01/2023] Open
Abstract
The methods currently used for detecting Salmonella in environmental samples require 2 days to produce results and have limited sensitivity. Here, we describe the development and validation of a real-time PCR Salmonella screening method that produces results in 18 to 24 h. Primers and probes specific to the gene invA, group D, and Salmonella enterica serovar Enteritidis organisms were designed and evaluated for inclusivity and exclusivity using a panel of 329 Salmonella isolates representing 126 serovars and 22 non-Salmonella organisms. The invA- and group D-specific sets identified all the isolates accurately. The PCR method had 100% inclusivity and detected 1 to 2 copies of Salmonella DNA per reaction. Primers specific for Salmonella-differentiating fragment 1 (Sdf-1) in conjunction with the group D set had 100% inclusivity for 32 S Enteritidis isolates and 100% exclusivity for the 297 non-Enteritidis Salmonella isolates. Single-laboratory validation performed on 1,741 environmental samples demonstrated that the PCR method detected 55% more positives than the Vitek immunodiagnostic assay system (VIDAS) method. The PCR results correlated well with the culture results, and the method did not report any false-negative results. The receiver operating characteristic (ROC) analysis documented excellent agreement between the results from the culture and PCR methods (area under the curve, 0.90; 95% confidence interval of 0.76 to 1.0) confirming the validity of the PCR method.IMPORTANCE This validated PCR method detects 55% more positives for Salmonella in half the time required for the reference method, VIDAS. The validated PCR method will help to strengthen public health efforts through rapid screening of Salmonella spp. in environmental samples.
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Ogunremi D, Nadin-Davis S, Dupras AA, Márquez IG, Omidi K, Pope L, Devenish J, Burke T, Allain R, Leclair D. Evaluation of a Multiplex PCR Assay for the Identification of Salmonella Serovars Enteritidis and Typhimurium Using Retail and Abattoir Samples. J Food Prot 2017; 80:295-301. [PMID: 28221989 DOI: 10.4315/0362-028x.jfp-16-167] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A multiplex PCR was developed to identify the two most common serovars of Salmonella causing foodborne illness in Canada, namely, serovars Enteritidis and Typhimurium. The PCR was designed to amplify DNA fragments from four Salmonella genes, namely, invA gene (211-bp fragment), iroB gene (309-bp fragment), Typhimurium STM 4497 (523-bp fragment), and Enteritidis SE147228 (612-bp fragment). In addition, a 1,026-bp ribosomal DNA (rDNA) fragment universally present in bacterial species was included in the assay as an internal control fragment. The detection rate of the PCR was 100% among Salmonella Enteritidis (n = 92) and Salmonella Typhimurium (n = 33) isolates. All tested Salmonella isolates (n = 194) were successfully identified based on the amplification of at least one Salmonella -specific DNA fragment. None of the four Salmonella DNA amplicons were detected in any of the non- Salmonella isolates (n = 126), indicating an exclusivity rate of 100%. When applied to crude extracts of 2,001 field isolates of Salmonella obtained during the course of a national microbiological baseline study in broiler chickens and chicken products sampled from abattoir and retail outlets, 163 isolates, or 8.1%, tested positive for Salmonella Enteritidis and another 80 isolates, or 4.0%, tested as Salmonella Typhimurium. All isolates identified by serological testing as Salmonella Enteritidis in the microbiological study were also identified by using the multiplex PCR. The new test can be used to identify or confirm pure isolates of the two serovars and is also amenable for integration into existing culture procedures for accurate detection of Salmonella colonies.
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Affiliation(s)
- Dele Ogunremi
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, Ontario, Canada K2H 8P9
| | - Susan Nadin-Davis
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, Ontario, Canada K2H 8P9
| | - Andrée Ann Dupras
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, Ontario, Canada K2H 8P9
| | - Imelda Gálvan Márquez
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, Ontario, Canada K2H 8P9
| | - Katayoun Omidi
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, Ontario, Canada K2H 8P9
| | - Louise Pope
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, Ontario, Canada K2H 8P9
| | - John Devenish
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, Ontario, Canada K2H 8P9
| | - Teresa Burke
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, Ontario, Canada K2H 8P9
| | - Ray Allain
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, Ontario, Canada K2H 8P9
| | - Daniel Leclair
- Food Safety Science Division, Floor 5, 1400 Merivale Road, Tower 2, Ottawa, Ontario, Canada K1A 0Y9
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Reslova N, Michna V, Kasny M, Mikel P, Kralik P. xMAP Technology: Applications in Detection of Pathogens. Front Microbiol 2017; 8:55. [PMID: 28179899 PMCID: PMC5263158 DOI: 10.3389/fmicb.2017.00055] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 01/09/2017] [Indexed: 12/14/2022] Open
Abstract
xMAP technology is applicable for high-throughput, multiplex and simultaneous detection of different analytes within a single complex sample. xMAP multiplex assays are currently available in various nucleic acid and immunoassay formats, enabling simultaneous detection and typing of pathogenic viruses, bacteria, parasites and fungi and also antigen or antibody interception. As an open architecture platform, the xMAP technology is beneficial to end users and therefore it is used in various pharmaceutical, clinical and research laboratories. The main aim of this review is to summarize the latest findings and applications in the field of pathogen detection using microsphere-based multiplex assays.
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Affiliation(s)
- Nikol Reslova
- Department of Food and Feed Safety, Veterinary Research InstituteBrno, Czechia; Department of Botany and Zoology, Faculty of Science, Masaryk UniversityBrno, Czechia
| | - Veronika Michna
- Department of Food and Feed Safety, Veterinary Research InstituteBrno, Czechia; Department of Experimental Biology, Faculty of Science, Masaryk UniversityBrno, Czechia
| | - Martin Kasny
- Department of Botany and Zoology, Faculty of Science, Masaryk University Brno, Czechia
| | - Pavel Mikel
- Department of Food and Feed Safety, Veterinary Research InstituteBrno, Czechia; Department of Experimental Biology, Faculty of Science, Masaryk UniversityBrno, Czechia
| | - Petr Kralik
- Department of Food and Feed Safety, Veterinary Research Institute Brno, Czechia
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Molecular detection assay of five Salmonella serotypes of public interest: Typhimurium, Enteritidis, Newport, Heidelberg, and Hadar. J Microbiol Methods 2016; 134:14-20. [PMID: 27993596 DOI: 10.1016/j.mimet.2016.12.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 12/12/2016] [Accepted: 12/12/2016] [Indexed: 01/14/2023]
Abstract
Foodborne illnesses due to Salmonella represent an important public-health concern worldwide. In the United States, a majority of Salmonella infections are associated with a small number of serotypes. Furthermore, some serotypes that are overrepresented among human disease are also associated with multi-drug resistance phenotypes. Rapid detection of serotypes of public-health concern might help reduce the burden of salmonellosis cases and limit exposure to multi-drug resistant Salmonella. We developed a two-step real-time PCR-based rapid method for the identification and detection of five Salmonella serotypes that are either overrepresented in human disease or frequently associated with multi-drug resistance, including serotypes Enteritidis, Typhimurium, Newport, Hadar, and Heidelberg. Two sets of four markers were developed to detect and differentiate the five serotypes. The first set of markers was developed as a screening step to detect the five serotypes; whereas, the second set was used to further distinguish serotypes Heidelberg, Newport and Hadar. The utilization of these markers on a two-step investigation strategy provides a diagnostic specificity of 97% for the detection of Typhimurium, Enteritidis, Heidelberg, Infantis, Newport and Hadar. The diagnostic sensitivity of the detection makers is >96%. The availability of this two-step rapid method will facilitate specific detection of Salmonella serotypes that contribute to a significant proportion of human disease and carry antimicrobial resistance.
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Molecular Surveillance Identifies Multiple Transmissions of Typhoid in West Africa. PLoS Negl Trop Dis 2016; 10:e0004781. [PMID: 27657909 PMCID: PMC5033494 DOI: 10.1371/journal.pntd.0004781] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 05/25/2016] [Indexed: 11/19/2022] Open
Abstract
Background The burden of typhoid in sub-Saharan African (SSA) countries has been difficult to estimate, in part, due to suboptimal laboratory diagnostics. However, surveillance blood cultures at two sites in Nigeria have identified typhoid associated with Salmonella enterica serovar Typhi (S. Typhi) as an important cause of bacteremia in children. Methods A total of 128 S. Typhi isolates from these studies in Nigeria were whole-genome sequenced, and the resulting data was used to place these Nigerian isolates into a worldwide context based on their phylogeny and carriage of molecular determinants of antibiotic resistance. Results Several distinct S. Typhi genotypes were identified in Nigeria that were related to other clusters of S. Typhi isolates from north, west and central regions of Africa. The rapidly expanding S. Typhi clade 4.3.1 (H58) previously associated with multiple antimicrobial resistances in Asia and in east, central and southern Africa, was not detected in this study. However, antimicrobial resistance was common amongst the Nigerian isolates and was associated with several plasmids, including the IncHI1 plasmid commonly associated with S. Typhi. Conclusions These data indicate that typhoid in Nigeria was established through multiple independent introductions into the country, with evidence of regional spread. MDR typhoid appears to be evolving independently of the haplotype H58 found in other typhoid endemic countries. This study highlights an urgent need for routine surveillance to monitor the epidemiology of typhoid and evolution of antimicrobial resistance within the bacterial population as a means to facilitate public health interventions to reduce the substantial morbidity and mortality of typhoid. Typhoid fever, a serious bloodstream infection caused by the bacterium Salmonella Typhi, is a major cause of disease and death around the world. There have been limited data on the epidemiology of typhoid in many countries in sub-Saharan African, including Nigeria. Recent evidence, however, showed that typhoid was an important cause of bacteraemia in children residing in two regions of Nigeria. Here, we analyzed the whole genome sequences of 128 S. Typhi isolates from two studies in order to elucidate the population structure and characterize the genetic components of antimicrobial resistance. We found that the multiple S. Typhi genotypes identified were closely related to other S. Typhi from neighboring regions of Africa and that multidrug resistance (MDR) was common among these isolates, and in many cases was associated with the IncHI1 plasmid known to cause MDR typhoid. These results provide evidence that typhoid was established in Nigeria as a result of several independent introductions into the country and that there has been extensive exchange of S. Typhi in and around the region of West Africa. This study emphasizes the importance of surveillance to improve our understanding of the epidemiology of typhoid, which is needed to underpin public health measures to reduce the spread of disease and facilitate patient management.
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Obaro SK, Hassan-Hanga F, Olateju EK, Umoru D, Lawson L, Olanipekun G, Ibrahim S, Munir H, Ihesiolor G, Maduekwe A, Ohiaeri C, Adetola A, Shetima D, Jibir BW, Nakaura H, Kocmich N, Ajose T, Idiong D, Masokano K, Ifabiyi A, Ihebuzor N, Chen B, Meza J, Akindele A, Rezac-Elgohary A, Olaosebikan R, Suwaid S, Gambo M, Alter R, Davies HD, Fey PD. Salmonella Bacteremia Among Children in Central and Northwest Nigeria, 2008-2015. Clin Infect Dis 2016; 61 Suppl 4:S325-31. [PMID: 26449948 DOI: 10.1093/cid/civ745] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Etiologic agents of childhood bacteremia remain poorly defined in Nigeria. The absence of such data promotes indiscriminate use of antibiotics and delays implementation of appropriate preventive strategies. METHODS We established diagnostic laboratories for bacteremia surveillance at regional sites in central and northwest Nigeria. Acutely ill children aged <5 years with clinically suspected bacteremia were evaluated at rural and urban clinical facilities in the Federal Capital Territory, central region and in Kano, northwest Nigeria. Blood was cultured using the automated Bactec incubator system. RESULTS Between September 2008 and April 2015, we screened 10,133 children. Clinically significant bacteremia was detected in 609 of 4051 (15%) in the northwest and 457 of 6082 (7.5%) in the central region. Across both regions, Salmonella species account for 24%-59.8% of bacteremias and are the commonest cause of childhood bacteremia, with a predominance of Salmonella enterica serovar Typhi. The prevalence of resistance to ampicillin, chloramphenicol, and cotrimoxazole was 38.11%, with regional differences in susceptibility to different antibiotics but high prevalence of resistance to readily available oral antibiotics. CONCLUSIONS Salmonella Typhi is the leading cause of childhood bacteremia in central Nigeria. Expanded surveillance is planned to define the dynamics of transmission. The high prevalence of multidrug-resistant strains calls for improvement in environmental sanitation in the long term and vaccination in the short term.
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Affiliation(s)
- Stephen K Obaro
- Division of Pediatric Infectious Diseases Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha International Foundation Against Infectious Diseases in Nigeria, Abuja Department of Pediatrics Department of Pediatrics, University of Abuja Teaching Hospital, Gwagwalada
| | | | - Eyinade K Olateju
- Department of Pediatrics, University of Abuja Teaching Hospital, Gwagwalada
| | | | | | - Grace Olanipekun
- International Foundation Against Infectious Diseases in Nigeria, Abuja
| | - Sadeeq Ibrahim
- Department of Pediatrics Department of Medical Microbiology, Aminu Kano Teaching Hospital
| | - Huda Munir
- Department of Medical Microbiology, Aminu Kano Teaching Hospital
| | | | - Augustine Maduekwe
- Department of Pediatrics, Wuse General Hospital, Abuja, Federal Capital Territory
| | - Chinatu Ohiaeri
- Department of Pediatrics, Federal Medical Center, Keffi, Nassarawa State
| | | | - Denis Shetima
- Department of Pediatrics, National Hospital, Central Business Area, Abuja, Federal Capital Territory
| | - Binta W Jibir
- Department of Pediatrics, Murtala Specialist Hospital
| | | | | | - Therasa Ajose
- International Foundation Against Infectious Diseases in Nigeria, Abuja
| | - David Idiong
- International Foundation Against Infectious Diseases in Nigeria, Abuja Department of Microbiology, Bingham University, Karu, Nassarawa State
| | | | - Adeyemi Ifabiyi
- International Foundation Against Infectious Diseases in Nigeria, Abuja
| | - Nnenna Ihebuzor
- National Primary Health Care Development Agency, Abuja, Federal Capital Territory, Nigeria
| | - Baojiang Chen
- Department of Biostatistics, College of Public Health
| | - Jane Meza
- Department of Biostatistics, College of Public Health
| | - Adebayo Akindele
- International Foundation Against Infectious Diseases in Nigeria, Abuja
| | | | | | - Salman Suwaid
- Department of Pediatrics, Murtala Specialist Hospital
| | | | - Roxanne Alter
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha
| | - Herbert D Davies
- Division of Pediatric Infectious Diseases Department of Biostatistics, College of Public Health Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha
| | - Paul D Fey
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha
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Draft Genome Sequences of Salmonella enterica subsp. enterica Serovars Typhimurium and Nottingham Isolated from Food Products. GENOME ANNOUNCEMENTS 2016; 4:4/4/e00699-16. [PMID: 27445384 PMCID: PMC4956457 DOI: 10.1128/genomea.00699-16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
A quantitative real-time PCR (qPCR) designed to detect Salmonella enterica subsp. enterica serovar Enteritidis, targeting the sdf gene, generated positive results for S. enterica subsp. enterica serovar Typhimurium (CFSAN033950) and S. enterica subsp. enterica serovar Nottingham (CFSAN006803) isolated from food samples. Both strains show pulsed-field gel electrophoresis (PFGE) patterns distinct from those of S. Enteritidis. Here, we report the genome sequences of these two strains.
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37
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Cabral-Castro MJ, Peralta RHS, Cavalcanti MG, Puccioni-Sohler M, Carvalho VL, da Costa Vasconcelos PF, Peralta JM. A Luminex-based single DNA fragment amplification assay as a practical tool for detecting and serotyping dengue virus. J Virol Methods 2016; 236:18-24. [PMID: 27393681 DOI: 10.1016/j.jviromet.2016.07.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 06/07/2016] [Accepted: 07/04/2016] [Indexed: 10/21/2022]
Abstract
Dengue is a mosquito-borne viral infection that can evolve from subclinical to severe forms of disease. Early recognition during initial primary and secondary infections correlates with a reduced case-fatality rate in susceptible groups. The aim of this study was to standardize a DNA hybridization assay based on the Luminex technology for detecting and serotyping dengue virus (DENV). Reference DENVs representing the four different serotypes were used as controls to standardize the test. For validation, 16 DENV isolates obtained from a reference laboratory were analyzed in a double-blind manner to validate the test. Sixty blood samples from patients suspected of having dengue fever were used to evaluate the methodology after the validation step, and the results were compared with the reference semi-nested RT-PCR. Additionally, five human samples of each Zika and Chikungunya confirmed patients were used for specificity analysis. The Luminex-based assay correctly identified all 16 DENV isolates. In the evaluation step, the results of the RT-PCR/Luminex assay showed a concordance of 86.7% with those of the semi-nested RT-PCR. None of other virus infection samples was amplified. This is the first description of a hybridization assay that can discriminate the four DENV serotypes using probes against a single DENV sequence. The results indicated that the RT-PCR/Luminex DENV assay designed and evaluated in this study is a valuable additional tool for the early and rapid detection and serotyping of DENV, which could, in the future, be applied to new targets such as the Zika and Chikungunya viruses.
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Affiliation(s)
- Mauro Jorge Cabral-Castro
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | | | - Marta Guimarães Cavalcanti
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil; Departamento de Doenças Infecciosas e Parasitárias, Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Marzia Puccioni-Sohler
- Laboratório de Líquido Cefalorraqueano, Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Valéria Lima Carvalho
- Instituto Evandro Chagas, Seção de Arbovirologia e Febres Hemorrágicas, Ananindeua, Pará, Brazil
| | | | - José Mauro Peralta
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
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Evaluation of Molecular Methods for Identification of Salmonella Serovars. J Clin Microbiol 2016; 54:1992-8. [PMID: 27194688 DOI: 10.1128/jcm.00262-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/10/2016] [Indexed: 11/20/2022] Open
Abstract
Classification by serotyping is the essential first step in the characterization of Salmonella isolates and is important for surveillance, source tracking, and outbreak detection. To improve detection and reduce the burden of salmonellosis, several rapid and high-throughput molecular Salmonella serotyping methods have been developed.The aim of this study was to compare three commercial kits, Salm SeroGen (Salm Sero-Genotyping AS-1 kit), Check&Trace (Check-Points), and xMAP (xMAP Salmonella serotyping assay), to the Salmonella genoserotyping array (SGSA) developed by our laboratory. They were assessed using a panel of 321 isolates that represent commonly reported serovars from human and nonhuman sources globally. The four methods correctly identified 73.8% to 94.7% of the isolates tested. The methods correctly identified 85% and 98% of the clinically important Salmonella serovars Enteritidis and Typhimurium, respectively. The methods correctly identified 75% to 100% of the nontyphoidal, broad host range Salmonella serovars, including Heidelberg, Hadar, Infantis, Kentucky, Montevideo, Newport, and Virchow. The sensitivity and specificity of Salmonella serovars Typhimurium and Enteritidis ranged from 85% to 100% and 99% to 100%, respectively.It is anticipated that whole-genome sequencing will replace serotyping in public health laboratories in the future. However, at present, it is approximately three times more expensive than molecular methods. Until consistent standards and methodologies are deployed for whole-genome sequencing, data analysis and interlaboratory comparability remain a challenge. The use of molecular serotyping will provide a valuable high-throughput alternative to traditional serotyping. This comprehensive analysis provides a detailed comparison of commercial kits available for the molecular serotyping of Salmonella.
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Liang D, Lu J, Wu Q, Ke B, Jiang C, Long J, Fang Y, Lin L, Zeng N, Fu L, Jiang L. Comparing the ability of luminex xMAP®
salmonella serotyping assay and traditional serotyping method for serotyping salmonella isolated from southern Chinese population. J Appl Microbiol 2016; 120:1668-76. [PMID: 26914944 DOI: 10.1111/jam.13106] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 01/27/2016] [Accepted: 02/17/2016] [Indexed: 11/26/2022]
Affiliation(s)
- D.W. Liang
- Center of Clinical Laboratory; Zhujiang Hospital; Southern Medical University; Guangzhou China
| | - J.H. Lu
- Department of Laboratory Medicine; The First People's Hospital of Shunde District; Foshan China
| | - Q. Wu
- Haizhu district Center for Disease Control and Prevention; Guangzhou China
| | - B.X. Ke
- Institute of Microbiology; Guangdong Provincial Center for Disease Control and Prevention; Guangzhou China
| | - C.H. Jiang
- Center of Clinical Laboratory; Zhujiang Hospital; Southern Medical University; Guangzhou China
| | - J. Long
- Center of Clinical Laboratory; Zhujiang Hospital; Southern Medical University; Guangzhou China
| | - Y.P. Fang
- Center of Clinical Laboratory; Zhujiang Hospital; Southern Medical University; Guangzhou China
| | - L.J. Lin
- Center of Clinical Laboratory; Zhujiang Hospital; Southern Medical University; Guangzhou China
| | - N.Y. Zeng
- Center of Clinical Laboratory; Zhujiang Hospital; Southern Medical University; Guangzhou China
| | - L. Fu
- Center of Clinical Laboratory; Zhujiang Hospital; Southern Medical University; Guangzhou China
| | - L.X. Jiang
- Center of Clinical Laboratory; Zhujiang Hospital; Southern Medical University; Guangzhou China
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Lettini AA, Vo Than T, Marafin E, Longo A, Antonello K, Zavagnin P, Barco L, Mancin M, Cibin V, Morini M, Dang Thi Sao M, Nguyen Thi T, Pham Trung H, Le L, Nguyen Duc T, Ricci A. Distribution of Salmonella Serovars and Antimicrobial Susceptibility from Poultry and Swine Farms in Central Vietnam. Zoonoses Public Health 2016; 63:569-576. [PMID: 26952244 DOI: 10.1111/zph.12265] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Indexed: 11/29/2022]
Abstract
This study was conducted to estimate the prevalence of Salmonella spp. and their antimicrobial susceptibilities on poultry and swine farms, sampled in 2 regions in Central Vietnam. A total of 67 poultry farms and 46 swine farms were sampled in a period of 5 months (from September 2012 to January 2013). Salmonella spp. was prevalent in 46.3% and 71.7% of poultry and swine farms, respectively. Altogether, 99 non-typhoidal Salmonella were isolated and the most common serovars were Salmonella Weltevreden (19%), followed by Salmonella Typhimurium (12%) and Salmonella 4,[5],12:i:- (11%). Overall, 71 of 99 (72%) Salmonella isolates were resistant to at least one of the 14 antimicrobial agents tested. Both in poultry and swine farms, high levels of resistance were observed for ampicillin, chloramphenicol, ciprofloxacin, sulphamethoxazole and tetracycline. The presence of Salmonella isolates from poultry and swine farms which were resistant to different classes of antimicrobials suggests that alternative control measures to antimicrobials should be implemented. Moreover, an effective policy should be promoted to encourage a prudent use of these agents in animal farming in Vietnam.
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Affiliation(s)
- A A Lettini
- Istituto Zooprofilattico Sperimentale delle Venezie, National Reference Laboratory for Salmonellosis, Legnaro (PD), Italy
| | - T Vo Than
- Central of Vietnam Veterinary Institute, Nha Trang, Vietnam
| | - E Marafin
- Istituto Zooprofilattico Sperimentale delle Venezie, National Reference Laboratory for Salmonellosis, Legnaro (PD), Italy
| | - A Longo
- Istituto Zooprofilattico Sperimentale delle Venezie, National Reference Laboratory for Salmonellosis, Legnaro (PD), Italy
| | - K Antonello
- Istituto Zooprofilattico Sperimentale delle Venezie, National Reference Laboratory for Salmonellosis, Legnaro (PD), Italy
| | - P Zavagnin
- Istituto Zooprofilattico Sperimentale delle Venezie, National Reference Laboratory for Salmonellosis, Legnaro (PD), Italy
| | - L Barco
- Istituto Zooprofilattico Sperimentale delle Venezie, National Reference Laboratory for Salmonellosis, Legnaro (PD), Italy
| | - M Mancin
- Istituto Zooprofilattico Sperimentale delle Venezie, National Reference Laboratory for Salmonellosis, Legnaro (PD), Italy
| | - V Cibin
- Istituto Zooprofilattico Sperimentale delle Venezie, National Reference Laboratory for Salmonellosis, Legnaro (PD), Italy
| | - M Morini
- International Cooperation Office, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro (PD), Italy
| | - M Dang Thi Sao
- Central of Vietnam Veterinary Institute, Nha Trang, Vietnam
| | - T Nguyen Thi
- Central of Vietnam Veterinary Institute, Nha Trang, Vietnam
| | - H Pham Trung
- Central of Vietnam Veterinary Institute, Nha Trang, Vietnam
| | - L Le
- Central of Vietnam Veterinary Institute, Nha Trang, Vietnam
| | - T Nguyen Duc
- Central of Vietnam Veterinary Institute, Nha Trang, Vietnam
| | - A Ricci
- Istituto Zooprofilattico Sperimentale delle Venezie, National Reference Laboratory for Salmonellosis, Legnaro (PD), Italy.
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Yoshida CE, Kruczkiewicz P, Laing CR, Lingohr EJ, Gannon VPJ, Nash JHE, Taboada EN. The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies. PLoS One 2016; 11:e0147101. [PMID: 26800248 PMCID: PMC4723315 DOI: 10.1371/journal.pone.0147101] [Citation(s) in RCA: 335] [Impact Index Per Article: 41.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 12/29/2015] [Indexed: 11/28/2022] Open
Abstract
For nearly 100 years serotyping has been the gold standard for the identification of Salmonella serovars. Despite the increasing adoption of DNA-based subtyping approaches, serotype information remains a cornerstone in food safety and public health activities aimed at reducing the burden of salmonellosis. At the same time, recent advances in whole-genome sequencing (WGS) promise to revolutionize our ability to perform advanced pathogen characterization in support of improved source attribution and outbreak analysis. We present the Salmonella In Silico Typing Resource (SISTR), a bioinformatics platform for rapidly performing simultaneous in silico analyses for several leading subtyping methods on draft Salmonella genome assemblies. In addition to performing serovar prediction by genoserotyping, this resource integrates sequence-based typing analyses for: Multi-Locus Sequence Typing (MLST), ribosomal MLST (rMLST), and core genome MLST (cgMLST). We show how phylogenetic context from cgMLST analysis can supplement the genoserotyping analysis and increase the accuracy of in silico serovar prediction to over 94.6% on a dataset comprised of 4,188 finished genomes and WGS draft assemblies. In addition to allowing analysis of user-uploaded whole-genome assemblies, the SISTR platform incorporates a database comprising over 4,000 publicly available genomes, allowing users to place their isolates in a broader phylogenetic and epidemiological context. The resource incorporates several metadata driven visualizations to examine the phylogenetic, geospatial and temporal distribution of genome-sequenced isolates. As sequencing of Salmonella isolates at public health laboratories around the world becomes increasingly common, rapid in silico analysis of minimally processed draft genome assemblies provides a powerful approach for molecular epidemiology in support of public health investigations. Moreover, this type of integrated analysis using multiple sequence-based methods of sub-typing allows for continuity with historical serotyping data as we transition towards the increasing adoption of genomic analyses in epidemiology. The SISTR platform is freely available on the web at https://lfz.corefacility.ca/sistr-app/.
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Affiliation(s)
- Catherine E. Yoshida
- National Microbiology Laboratory at Guelph, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Peter Kruczkiewicz
- National Microbiology Laboratory at Lethbridge, Public Health Agency of Canada, Lethbridge, Alberta, Canada.
| | - Chad R. Laing
- National Microbiology Laboratory at Lethbridge, Public Health Agency of Canada, Lethbridge, Alberta, Canada.
| | - Erika J. Lingohr
- National Microbiology Laboratory at Guelph, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Victor P. J. Gannon
- National Microbiology Laboratory at Lethbridge, Public Health Agency of Canada, Lethbridge, Alberta, Canada.
| | - John H. E. Nash
- National Microbiology Laboratory at Guelph, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Eduardo N. Taboada
- National Microbiology Laboratory at Lethbridge, Public Health Agency of Canada, Lethbridge, Alberta, Canada.
- * E-mail:
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42
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Doerscher DR, Lutz TL, Whisenant SJ, Smith KR, Morris CA, Schroeder CM. Microbiological Testing Results of Boneless and Ground Beef Purchased for the National School Lunch Program, 2011 to 2014. J Food Prot 2015; 78:1656-63. [PMID: 26319719 DOI: 10.4315/0362-028x.jfp-15-101] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The Agricultural Marketing Service (AMS) purchases boneless and ground beef for distribution to recipients through federal nutrition assistance programs, including the National School Lunch Program, which represents 93% of the overall volume. Approximately every 2,000 lb (ca. 907 kg) of boneless beef and 10,000 lb (ca. 4,535 kg) of ground beef are designated a "lot" and tested for Escherichia coli O157:H7, Salmonella, standard plate count organisms (SPCs), E. coli, and coliforms. Any lot of beef positive for E. coli O157:H7 or for Salmonella, or any beef with concentrations of organisms exceeding critical limits for SPCs (100,000 CFU g(-1)), E. coli (500 CFU g(-1)), or coliforms (1,000 CFU g(-1)) is rejected for purchase by AMS and must be diverted from federal nutrition assistance programs. From July 2011 through June 2014, 537,478,212 lb (ca. 243,795,996 kg) of boneless beef and 428,130,984 lb (ca. 194,196,932 kg) of ground beef were produced for federal nutrition assistance programs. Of the 230,359 boneless beef samples collected over this period, 82 (0.04%) were positive for E. coli O157:H7, 924 (0.40%) were positive for Salmonella, 222 (0.10%) exceeded the critical limit for SPCs, 69 (0.03%) exceeded the critical limit for E. coli, and 123 (0.05%) exceeded the critical limit for coliforms. Of the 46,527 ground beef samples collected over this period, 30 (0.06%) were positive for E. coli O157:H7, 360 (0.77%) were positive for Salmonella, 20 (0.04%) exceeded the critical limit for SPCs, 22 (0.05%) exceeded the critical limit for E. coli, and 17 (0.04%) exceeded the critical limit for coliforms. Cumulatively, these data suggest beef produced for the AMS National School Lunch Program is done so under an adequate food safety system, as indicated by the low percentage of lots that were pathogen positive or exceeded critical limits for indicator organisms.
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Affiliation(s)
- Darin R Doerscher
- Livestock, Poultry, and Seed Program, Agricultural Marketing Service, U.S. Department of Agriculture, 1400 Independence Avenue, Washington, D.C. 20250, USA
| | - Terry L Lutz
- Livestock, Poultry, and Seed Program, Agricultural Marketing Service, U.S. Department of Agriculture, 1400 Independence Avenue, Washington, D.C. 20250, USA
| | - Stephen J Whisenant
- Livestock, Poultry, and Seed Program, Agricultural Marketing Service, U.S. Department of Agriculture, 1400 Independence Avenue, Washington, D.C. 20250, USA
| | - Kerry R Smith
- Livestock, Poultry, and Seed Program, Agricultural Marketing Service, U.S. Department of Agriculture, 1400 Independence Avenue, Washington, D.C. 20250, USA
| | - Craig A Morris
- Livestock, Poultry, and Seed Program, Agricultural Marketing Service, U.S. Department of Agriculture, 1400 Independence Avenue, Washington, D.C. 20250, USA
| | - Carl M Schroeder
- Livestock, Poultry, and Seed Program, Agricultural Marketing Service, U.S. Department of Agriculture, 1400 Independence Avenue, Washington, D.C. 20250, USA.
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Deng X, Desai PT, den Bakker HC, Mikoleit M, Tolar B, Trees E, Hendriksen RS, Frye JG, Porwollik S, Weimer BC, Wiedmann M, Weinstock GM, Fields PI, McClelland M. Genomic epidemiology of Salmonella enterica serotype Enteritidis based on population structure of prevalent lineages. Emerg Infect Dis 2015; 20:1481-9. [PMID: 25147968 PMCID: PMC4178404 DOI: 10.3201/eid2009.131095] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Major lineages emerged during the 17th–18th centuries and diversified during the 1920s and 1950s. Salmonella enterica serotype Enteritidis is one of the most commonly reported causes of human salmonellosis. Its low genetic diversity, measured by fingerprinting methods, has made subtyping a challenge. We used whole-genome sequencing to characterize 125 S. enterica Enteritidis and 3 S. enterica serotype Nitra strains. Single-nucleotide polymorphisms were filtered to identify 4,887 reliable loci that distinguished all isolates from each other. Our whole-genome single-nucleotide polymorphism typing approach was robust for S. enterica Enteritidis subtyping with combined data for different strains from 2 different sequencing platforms. Five major genetic lineages were recognized, which revealed possible patterns of geographic and epidemiologic distribution. Analyses on the population dynamics and evolutionary history estimated that major lineages emerged during the 17th–18th centuries and diversified during the 1920s and 1950s.
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44
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Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Give, Isolated from an Imported Chili Powder Product. GENOME ANNOUNCEMENTS 2015; 3:3/4/e00726-15. [PMID: 26139723 PMCID: PMC4490851 DOI: 10.1128/genomea.00726-15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We report the genome sequence of Salmonella enterica subsp. enterica serovar Give (CFSAN012622), isolated from imported chili powder in 2014. This genome contains genes previously reported to be specific only to S. enterica serovar Enteritidis. This strain shows a unique pulsed-field gel electrophoresis (PFGE) pattern clustering with serovar Enteritidis (JEG X01.0005).
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45
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Impact of Ciprofloxacin and Clindamycin Administration on Gram-Negative Bacteria Isolated from Healthy Volunteers and Characterization of the Resistance Genes They Harbor. Antimicrob Agents Chemother 2015; 59:4410-6. [PMID: 25987611 DOI: 10.1128/aac.00068-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 03/21/2015] [Indexed: 12/27/2022] Open
Abstract
The aim of this study was to assess the impact of ciprofloxacin, clindamycin, and placebo administration on culturable Gram-negative isolates and the antibiotic resistance genes they harbor. Saliva and fecal samples were collected from healthy human volunteers before and at intervals, up to 1 year after antibiotic administration. Samples were plated on selective and nonselective media to monitor changes in different colony types or bacterial species. Following ciprofloxacin administration, there was a decrease of Escherichia coli in feces and after clindamycin administration a decrease of Bacteroides in feces and Leptotrichia in saliva, which all returned to pretreatment levels within 1 to 4 months. Ciprofloxacin administration also resulted in an increase in ciprofloxacin-resistant Veillonella in saliva, which persisted for 12 months. Additionally, 949 aerobic and anaerobic isolates purified from ciprofloxacin- and clindamycin-containing plates were screened for the presence of resistance genes. Resistance gene carriage was widespread in isolates from all three treatment groups, and no association was observed between genes and antibiotic administration. Although the anaerobic component of the microbiota was not a major reservoir of aerobe-associated antimicrobial resistance (AMR) genes, we detected the sulfonamide resistance gene sul2 in anaerobic isolates. The longitudinal nature of the study allowed identification of distinct Escherichia coli clones harboring multiple resistance genes, including one carrying an extended-spectrum β-lactamase blaCTX-M group 9 gene, which persisted in the gut for up to 4 months. This study provided insight into the effects of antibiotic administration on healthy microbiota and the diversity of resistance genes harbored therein.
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Löfström C, Hintzmann AS, Sørensen G, Baggesen DL. Outbreak of Salmonella enterica serovar Typhimurium phage type DT41 in Danish poultry production. Vet Microbiol 2015; 178:167-72. [PMID: 25962983 DOI: 10.1016/j.vetmic.2015.04.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 04/17/2015] [Accepted: 04/20/2015] [Indexed: 02/06/2023]
Abstract
Salmonella enterica subspecies enterica serovar Typhimurium (S. Typhimurium) is one of the most prevalent serovars in Europe - where both poultry and poultry related products are common sources of human salmonellosis. Due to efficient control programs, the prevalence of S. Typhimurium in Danish poultry production is very low. Despite this, during the past decades there has been a reoccurring problem with infections with S. Typhimurium phage type DT41 in the Danish poultry production without identifying a clear source. In the end of 2013 and beginning of 2014 an increased isolation of S. Typhimurium DT41 was noted mainly in this production, but also in other samples. To investigate this is in more detail, 47 isolates from egg layers (n=5, 1 flock), broilers (n=33, 13 flocks), broiler breeding flocks and hatches (n=5; 2 flocks and 1 environmental hatchery sample), feed (n=1), poultry slaughter house (n=3, environmental sample and meat) were typed with multi locus variable number of tandem repeat analysis (MLVA) and pulsed-field gel electrophoresis (PFGE) to investigate the epidemiology of the outbreak. Based on PFGE results isolates were divided into four groups (Simpson's index of diversity (DI)=0.24±0.15). Due to the low DI, PFGE was not sufficient to provide information to unravel the outbreak. Based on MLVA typing the DT41 (42/47 isolates) and the RDNC isolates (5/47) were split into nine groups (DI=0.65±0.14). When a maximum divergence at one locus was permitted these could be gathered into four groups. Using this criterion, combined with epidemiological information, a spread of one type from broiler breeders to broilers and further to the poultry slaughter house was plausible. In conclusion, although it could be concluded that a spread within the broiler production pyramid had taken place the source of the sudden increase of S. Typhimurium DT41 remains unclear. To investigate this in more detail, further studies using whole genome sequencing to obtain a higher discriminatory strength and including isolates from a longer period of time and from various sources are in progress.
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Affiliation(s)
- Charlotta Löfström
- Division of Food Microbiology, National Food Institute, Technical University of Denmark, Mørkhøj Bygade 19, 2860 Søborg, Denmark.
| | - Ann-Sofie Hintzmann
- Division of Food Microbiology, National Food Institute, Technical University of Denmark, Mørkhøj Bygade 19, 2860 Søborg, Denmark
| | - Gitte Sørensen
- Division of Food Microbiology, National Food Institute, Technical University of Denmark, Mørkhøj Bygade 19, 2860 Søborg, Denmark
| | - Dorte Lau Baggesen
- Division of Food Microbiology, National Food Institute, Technical University of Denmark, Mørkhøj Bygade 19, 2860 Søborg, Denmark
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47
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Salmonella serotype determination utilizing high-throughput genome sequencing data. J Clin Microbiol 2015; 53:1685-92. [PMID: 25762776 DOI: 10.1128/jcm.00323-15] [Citation(s) in RCA: 288] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 03/08/2015] [Indexed: 11/20/2022] Open
Abstract
Serotyping forms the basis of national and international surveillance networks for Salmonella, one of the most prevalent foodborne pathogens worldwide (1-3). Public health microbiology is currently being transformed by whole-genome sequencing (WGS), which opens the door to serotype determination using WGS data. SeqSero (www.denglab.info/SeqSero) is a novel Web-based tool for determining Salmonella serotypes using high-throughput genome sequencing data. SeqSero is based on curated databases of Salmonella serotype determinants (rfb gene cluster, fliC and fljB alleles) and is predicted to determine serotype rapidly and accurately for nearly the full spectrum of Salmonella serotypes (more than 2,300 serotypes), from both raw sequencing reads and genome assemblies. The performance of SeqSero was evaluated by testing (i) raw reads from genomes of 308 Salmonella isolates of known serotype; (ii) raw reads from genomes of 3,306 Salmonella isolates sequenced and made publicly available by GenomeTrakr, a U.S. national monitoring network operated by the Food and Drug Administration; and (iii) 354 other publicly available draft or complete Salmonella genomes. We also demonstrated Salmonella serotype determination from raw sequencing reads of fecal metagenomes from mice orally infected with this pathogen. SeqSero can help to maintain the well-established utility of Salmonella serotyping when integrated into a platform of WGS-based pathogen subtyping and characterization.
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48
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Yun YS, Chae SJ, Na HY, Chung GT, Yoo CK, Lee DY. Modified Method of Multilocus Sequence Typing (MLST) for Serotyping inSalmonellaSpecies. ACTA ACUST UNITED AC 2015. [DOI: 10.4167/jbv.2015.45.4.314] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Young-Sun Yun
- Division of Enteric Diseases, Center for Infectious Diseases, Korea National Institute of Health, Osong, Korea
| | - Su-Jin Chae
- Division of Enteric Diseases, Center for Infectious Diseases, Korea National Institute of Health, Osong, Korea
| | - Hye-Young Na
- Division of Enteric Diseases, Center for Infectious Diseases, Korea National Institute of Health, Osong, Korea
| | - Gyung Tae Chung
- Division of Enteric Diseases, Center for Infectious Diseases, Korea National Institute of Health, Osong, Korea
| | - Cheon-Kwon Yoo
- Division of Enteric Diseases, Center for Infectious Diseases, Korea National Institute of Health, Osong, Korea
| | - Deog-Yong Lee
- Division of Enteric Diseases, Center for Infectious Diseases, Korea National Institute of Health, Osong, Korea
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49
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Diversity of Salmonella isolates from central Florida surface waters. Appl Environ Microbiol 2014; 80:6819-27. [PMID: 25172861 DOI: 10.1128/aem.02191-14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Identification of Salmonella serotypes is important for understanding the environmental diversity of the genus Salmonella. This study evaluates the diversity of Salmonella isolates recovered from 165 of 202 Central Florida surface water samples and investigates whether the serotype of the environmental Salmonella isolates can be predicted by a previously published multiplex PCR assay (S. Kim, J. G. Frye, J. Hu, P. J. Fedorka-Cray, R. Gautom, and D. S. Boyle, J. Clin. Microbiol. 44:3608-3615, 2006, http://dx.doi.org/10.1128/JCM.00701-06). Multiplex PCR was performed on 562 Salmonella isolates (as many as 36 isolates per water sample) to predict serotypes. Kauffmann-White serogrouping was used to confirm multiplex PCR pattern groupings before isolates were serotyped, analyzed by pulsed-field gel electrophoresis, and assayed for antimicrobial susceptibility. In 41.2% of the Salmonella-positive water samples, all Salmonella isolates had identical multiplex PCR patterns; in the remaining 58.8%, two or more multiplex PCR patterns were identified. Within each sample, isolates with matching multiplex PCR patterns had matching serogroups. The multiplex patterns of 495 isolates (88.1%) did not match any previously reported pattern. The remaining 68 isolates matched reported patterns but did not match the serotypes for those patterns. The use of the multiplex PCR allowed the number of isolates requiring further analysis to be reduced to 223. Thirty-three Salmonella enterica serotypes were identified; the most frequent included serotypes Muenchen, Rubislaw, Anatum, Gaminara, and IV_50:z4,z23:-. A majority (141/223) of Salmonella isolates clustered into one genotypic group. Salmonella isolates in Central Florida surface waters are serotypically, genotypically, and phenotypically (in terms of antimicrobial susceptibility) diverse. While isolates could be grouped as different or potentially the same using multiplex PCR, the multiplex PCR pattern did not predict the Salmonella serotype.
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Yoshida C, Lingohr EJ, Trognitz F, MacLaren N, Rosano A, Murphy SA, Villegas A, Polt M, Franklin K, Kostic T, Kropinski AM, Card RM. Multi-laboratory evaluation of the rapid genoserotyping array (SGSA) for the identification of Salmonella serovars. Diagn Microbiol Infect Dis 2014; 80:185-90. [PMID: 25219780 DOI: 10.1016/j.diagmicrobio.2014.08.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 07/31/2014] [Accepted: 08/21/2014] [Indexed: 10/24/2022]
Abstract
Salmonella serotyping is an essential first step for identification of isolates associated with disease outbreaks. The Salmonella genoserotyping array (SGSA) is a microarray-based alternative to standard serotyping designed to rapidly identify 57 of the most commonly reported serovars through detection of the genes encoding surface O and H antigens and reporting the corresponding serovar in accordance with the existing White-Kaufmann-Le Minor serotyping scheme. In this study, we evaluated the SGSA at 4 laboratories in 3 countries by testing 1874 isolates from human and non-human sources. The SGSA correctly identified 96.7% of isolates from the target 57 serovars. For the prevalent and clinically important Salmonella serovars Enteritidis and Typhimurium, test specificity and sensitivity were greater than 98% and 99%, respectively. Due to its high-throughput nature, the SGSA is a rapid and cost-effective alternative to standard serotyping for identifying the most prevalent serovars of Salmonella.
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Affiliation(s)
- Catherine Yoshida
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada (PHAC), Guelph, Ontario, Canada N1G 3W4.
| | - Erika J Lingohr
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada (PHAC), Guelph, Ontario, Canada N1G 3W4
| | | | - Nikki MacLaren
- Animal Health and Veterinary Laboratories Agency (AHVLA), New Haw, Addlestone, Surrey, United Kingdom KT15 3NB
| | - Andrea Rosano
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada (PHAC), Guelph, Ontario, Canada N1G 3W4
| | - Stephanie A Murphy
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada (PHAC), Guelph, Ontario, Canada N1G 3W4
| | - Andre Villegas
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada (PHAC), Guelph, Ontario, Canada N1G 3W4
| | - Marlies Polt
- Austrian Institute of Technology (AIT), 3430 Tulln an der Donau, Austria
| | - Kristyn Franklin
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada (PHAC), Guelph, Ontario, Canada N1G 3W4
| | - Tanja Kostic
- Austrian Institute of Technology (AIT), 3430 Tulln an der Donau, Austria
| | | | | | - Andrew M Kropinski
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada (PHAC), Guelph, Ontario, Canada N1G 3W4
| | - Roderick M Card
- Animal Health and Veterinary Laboratories Agency (AHVLA), New Haw, Addlestone, Surrey, United Kingdom KT15 3NB
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