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Duodu S, Ayiku ANA, Adelani AA, Daah DA, Amoako EK, Jansen MD, Cudjoe KS. Serotype distribution, virulence and antibiotic resistance of Streptococcus agalactiae isolated from cultured tilapia Oreochromis niloticus in Lake Volta, Ghana. Dis Aquat Organ 2024; 158:27-36. [PMID: 38661135 DOI: 10.3354/dao03780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Streptococcus agalactiae infection is one of the major factors limiting the expansion of tilapia farming globally. In this study, we investigated the serotype distribution, virulence and antimicrobial resistance of S. agalactiae isolates from tilapia farmed in Lake Volta, Ghana. Isolates from 300 moribund fish were characterised by Gram staining, MALDI-TOF/MS and 16S rRNA sequencing. Serotype identification was based on multiplex polymerase chain reaction (PCR) amplification of the capsular polysaccharide genes. Detection of virulence genes (cfb, fbsA and cspA) and histopathology were used to infer the pathogenicity of the isolates. The susceptibility of isolates to antibiotics was tested using the Kirby-Bauer disk diffusion assay. All 32 isolates identified as S. agalactiae were of serotype Ia. This was notably different from isolates previously collected from the farms in 2017, which belonged to serotype Ib, suggesting a possible serotype replacement. The prevalence of the pathogen was related to the scale of farm operation, with large-scale farms showing higher S. agalactiae positivity. Data from histopathological analysis and PCR amplification of targeted virulence genes confirmed the virulence potential and ability of the isolates to cause systemic infection in tilapia. Except for gentamicin, the majority of the isolates were less resistant to the tested antibiotics. All isolates were fully sensitive to oxytetracycline, erythromycin, florfenicol, enrofloxacin, ampicillin and amoxicillin. This study has improved our understanding of the specific S. agalactiae serotypes circulating in Lake Volta and demonstrates the need for continuous monitoring to guide the use of antimicrobials and vaccines against streptococcal infections in Ghanaian aquaculture systems.
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Affiliation(s)
- Samuel Duodu
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, LG54 Volta Rd, Legon-Accra, Ghana
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, LG54 Volta Rd, Legon-Accra, Ghana
| | - Angela N A Ayiku
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, LG54 Volta Rd, Legon-Accra, Ghana
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, LG54 Volta Rd, Legon-Accra, Ghana
| | - Abigail A Adelani
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, LG54 Volta Rd, Legon-Accra, Ghana
| | - Derrick A Daah
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, LG54 Volta Rd, Legon-Accra, Ghana
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, LG54 Volta Rd, Legon-Accra, Ghana
| | - Enock K Amoako
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, LG54 Volta Rd, Legon-Accra, Ghana
| | - Mona D Jansen
- Norwegian Veterinary Institute, Elizabeth Stephansons vei 1, 1433 Ås, Norway
| | - Kofitsyo S Cudjoe
- Norwegian Veterinary Institute, Elizabeth Stephansons vei 1, 1433 Ås, Norway
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Bajanca-Lavado MP, Pinto M, Carvalho MD, Jantarada Domingos G, Melo-Cristino J. Rare serotype c Haemophilus influenzae invasive isolate: characterization of the first case in Portugal. Eur J Clin Microbiol Infect Dis 2024; 43:791-795. [PMID: 38332396 DOI: 10.1007/s10096-024-04774-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/02/2024] [Indexed: 02/10/2024]
Abstract
We report for the first time in Portugal a serotype c Haemophilus influenzae isolated from an adult, with HIV-1 infection. Whole-genome sequencing characterized the isolate as clonal complex ST-7, albeit with a novel MLST (ST2754) due to a unique atpG profile. Integration of this genome with other available H. influenzae serotype c genomes from PubMLST revealed its overall genetic distinctiveness, with the closest related isolate being identified in France in 2020. This surveillance study, involving collaboration among hospitals and reference laboratory, successfully contributed to the identification and characterization of this rare serotype.
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Affiliation(s)
- Maria Paula Bajanca-Lavado
- Haemophilus Influenzae Reference Laboratory, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal.
| | - Miguel Pinto
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Maria Dinah Carvalho
- Laboratório de Microbiologia, Serviço de Patologia Clínica, Centro Hospitalar Universitário Lisboa Norte, Lisbon, Portugal
| | - Gonçalo Jantarada Domingos
- Infectious Diseases Department, Santa Maria Hospital-Centro Hospitalar Universitário Lisboa Norte, Lisbon, Portugal
| | - José Melo-Cristino
- Laboratório de Microbiologia, Serviço de Patologia Clínica, Centro Hospitalar Universitário Lisboa Norte, Lisbon, Portugal
- Instituto de Microbiologia, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
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Wu CF, Hsu CY, Chou CC, Wang CM, Huang SW, Kuo HC. Serotypes, virulence factors and multilocus sequence typing of Glaesserella parasuis from diseased pigs in Taiwan. PeerJ 2023; 11:e15823. [PMID: 37790626 PMCID: PMC10544350 DOI: 10.7717/peerj.15823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 07/10/2023] [Indexed: 10/05/2023] Open
Abstract
Background Glaesserella parasuis (G. parasuis) belongs to the normal microbiota of the upper respiratory tract in the swine, but virulent strains can cause systemic infections commonly known as Glässer's disease that leads to significant economic loss in the swine industry. Fifteen serotypes of G. parasuis have been classified by gel immunodiffusion test while the molecular serotyping based on variation within the capsule loci have further improved the serotype determination of unidentified field strains. Serovar has been commonly used as an indicator of virulence; however, virulence can be significantly differ in the field isolates with the same serotype. To date, investigations of G. parasuis isolated in Taiwan regarding antimicrobial resistance, serotypes, genotypes and virulence factors remain unclear. Methods A total of 276 G.parasuis field isolates were collected from 263 diseased pigs at the Animal Disease Diagnostic Center of National Chiayi University in Taiwan from January 2013 to July 2021. Putative virulence factors and serotypes of the isolates were identified by polymerase chain reaction (PCR) and antimicrobial susceptibility testing was performed by microbroth dilution assay. Additionally, the epidemiology of G. parasuis was characterized by multilocus sequence typing (MLST). Results Serotype 4 (33.3%) and 5 (21.4%) were the most prevalent, followed by nontypable isolates (15.9%), serotype 13 (9.4%), 12 (6.5%), 14 (6.2%), 7 (3.3%), 1 (1.8%), 9 (1.1%), 11 (0.7%) and 6 (0.4%). Nine out of 10 putative virulence factors showed high positive rates, including group 1 vtaA (100%), fhuA (80.4%), hhdA (98.6%), hhdB (96.0%), sclB7 (99.6%), sclB11 (94.9%), nhaC (98.2%), HAPS_0254 (85.9%), and cirA (99.3%). According to the results of antimicrobial susceptibility testing, ceftiofur and florfenicol were highly susceptible (>90%). Notably, 68.8% isolates showed multidrug resistance. MLST revealed 16 new alleles and 67 new sequence types (STs). STs of these isolated G. parasuis strains were classified into three clonal complexes and 45 singletons by Based Upon Related Sequence Types (BURST) analysis. All the G. parasuis strains in PubMLST database, including strains from the diseased pigs in the study, were defined into two main clusters by Unweighted Pair Group Method with Arithmetic Mean (UPGMA). Most isolates in this study and virulent isolates from the database were mainly located in cluster 2, while cluster 1 included a high percentage of nasal isolates from asymptomatic carriers. In conclusion, this study provides current prevalence and antimicrobial susceptibility of G. parasuis in Taiwan, which can be used in clinical diagnosis and treatment of Glässer's disease.
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Affiliation(s)
- Ching-Fen Wu
- Department of Veterinary Medicine, National Chiayi University, Chiayi City, Taiwan
| | - Chia-Yu Hsu
- Department of Veterinary Medicine, National Chiayi University, Chiayi City, Taiwan
| | - Chi-Chung Chou
- Department of Veterinary Medicine, National Chung Hsing University, Taichung, Taichung, Taiwan
| | - Chao-Min Wang
- Department of Veterinary Medicine, National Chiayi University, Chiayi City, Taiwan
| | - Szu-Wei Huang
- Department of Veterinary Medicine, National Chiayi University, Chiayi City, Taiwan
| | - Hung-Chih Kuo
- Department of Veterinary Medicine, National Chiayi University, Chiayi City, Taiwan
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Mohanapriya K, Agri H, Anbazhagan S, Khawaskar D, Jayakumar V, Lalrinzuala MV, Himani KM, Sophia I, Mariappan AK, Nagaleekar VK, Sinha DK, Chaudhuri P, Chaturvedi VK, Singh BR, Thomas P. Development and validation of multiplex PCR based molecular serotyping of Salmonella serovars associated with poultry in India. J Microbiol Methods 2023; 207:106710. [PMID: 37003300 DOI: 10.1016/j.mimet.2023.106710] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 03/26/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023]
Abstract
Salmonella species are Gram-negative bacteria with more than 2600 serovars. Among these serovars, many are associated with various diseases in livestock and humans. White Kauffman Le-Minor (WKL) serotyping scheme applies specific serum to determine the serovars of Salmonella. Recent studies have applied molecular methods for serovar predictions. These methods include PCR, hybridization and sequence data to detect/predict serovar-specific genetic elements. Among these, PCR is a robust method if the unique genetic element is already known. Within this context, also involving novel primers, two multiplex PCR assays were standardized to detect six important Salmonella serovars viz. Typhimurium, Enteritidis, Kentucky, Infantis, Virchow and Gallinarum associated with poultry in India. The developed PCR assays showed targeted serovar specificity. Serial dilution experiments of both kit-based and crude lysate DNA preparations indicated similar applicability of both methods for testing from pure cultures. Further the developed assays were validated with 25 recent field isolates to confirm the applicability in routine diagnosis. The PCR assay could predict all the targeted serovars (17/25) with 100% specificity (CI-95%; 0.63-1). Molecular serotyping can reduce the number of serum used incomparison to the conventional serotyping which involves more random application of serum.
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Affiliation(s)
- K Mohanapriya
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Himani Agri
- Division of Veterinary Public Health and Epidemiology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Subbaiyan Anbazhagan
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India; ICMR-National Animal Resource Facility for Biomedical Research, Hyderabad, Telangana, India
| | - Damini Khawaskar
- Division of Veterinary Public Health and Epidemiology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Varsha Jayakumar
- Division of Veterinary Public Health and Epidemiology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Michael V Lalrinzuala
- Division of Veterinary Public Health and Epidemiology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
| | - K M Himani
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
| | - I Sophia
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Asok K Mariappan
- Avian Disease Section, Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Viswas Konasagara Nagaleekar
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Dharmendra K Sinha
- Division of Veterinary Public Health and Epidemiology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Pallab Chaudhuri
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Vinod K Chaturvedi
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Bhoj R Singh
- Division of Veterinary Public Health and Epidemiology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
| | - Prasad Thomas
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India.
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Cui Y, Guo F, Cai X, Cao X, Guo J, Wang H, Yang B, Zhou H, Su X, Blackall PJ, Xu F. Ct value-based real time PCR serotyping of Glaesserella parasuis. Vet Microbiol 2021; 254:109011. [PMID: 33610013 DOI: 10.1016/j.vetmic.2021.109011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/03/2021] [Indexed: 11/24/2022]
Abstract
Glaesserella parasuis is the causative agent of Glässer's disease in swine. Serotyping plays an essential role in prevalence investigations and in the development of vaccination strategies for the prevention of this disease. Molecular serotyping based on variation within the capsule loci of the 15 serovars is more accurate and efficient than traditional serological serotyping. To reduce the running time and facilitate ease of data interpretation, we developed a simple and rapid cycle threshold (Ct) value-based real time PCR (qPCR) method for the identification and serotyping of G. parasuis. The qPCR method distinguished between all 15 serovar reference strains of G. parasuis with efficiency values ranging between 85.5 % and 110.4 % and, R2 values > 0.98. The qPCR serotyping was evaluated using 83 clinical isolates with 43 of the isolates having been previously assigned to a serovar by the gel immuno-diffusion (GID) assay and 40 non-typeable isolates. The qPCR results of 41/43 (95.3 %) isolates were concordant with the GID assay except two isolates of serovar 12 were assigned to serovar 5. In addition, the qPCR serotyping assigned a serovar to each of the 40 non-typeable isolates. Of the 83 isolates tested to assign a serovar, a concordance rate of 98.8 % (82/83) was determined between the qPCR and the previously reported multiplex PCR of Howell et al. (2015) (including those that were either serovars 5 or 12). Despite the inability to differentiate between serovars 5 and 12, the Ct value-based qPCR serotyping represents an attractive alternative to current molecular serotyping method for G. parasuis and could be used for both epidemiological monitoring and the guidance of vaccination programs.
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Affiliation(s)
- Yifang Cui
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Fangfang Guo
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xuwang Cai
- State Key Laboratory of Agricultural Microbiology, Division of Animal Infectious Disease, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Xiaoya Cao
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Jie Guo
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Hongjun Wang
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Bing Yang
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Hongzhuan Zhou
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xia Su
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Patrick J Blackall
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Fuzhou Xu
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Benahmed F, Wang H, Beaubrun JJG, Gopinath GR, Cheng CM, Hanes DE, Hammack TS, Rasmussen M, Davidson MK. Detection of Salmonella enterica subsp. enterica Serovar Cubana from Naturally Contaminated Chick Feed. J Food Prot 2017; 80:1815-1820. [PMID: 28981377 DOI: 10.4315/0362-028x.jfp-16-344] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Because some significant outbreaks of human salmonellosis have been traced to contaminated animal feed, the rapid and efficient detection of Salmonella in feed is essential. However, the current U.S. Food and Drug Administration Bacteriological Analytical Manual (BAM) culture method that uses lactose broth as a preenrichment medium has not reliably supported the results of real-time PCR assays for certain foods. We evaluated the BAM culture method and a quantitative real-time PCR (qPCR) assay using two preenrichment media, modified buffered peptone water and lactose broth, to detect Salmonella enterica subsp. enterica serovar Cubana in naturally contaminated chick feed. After 24 h of incubation, the qPCR method was as sensitive as the culture method when modified buffered peptone water was used as the preenrichment medium but less sensitive than culture when lactose broth was used. After 48 h of incubation, detection of Salmonella Cubana by qPCR and by culture in either preenrichment medium was equivalent. We also compared the performance of the traditional serotyping method, which uses pure cultures of Salmonella grown on blood agar, to two molecular serotyping methods. The serotyping method based on whole genome sequencing also requires pure cultures, but the PCR-based molecular serotyping method can be done directly with the enriched culture medium. The PCR-based molecular serotyping method provided simple and rapid detection and identification of Salmonella Cubana. However, whole genome sequencing allows accurate identification of many Salmonella serotypes and highlights variations in the genomes, even in tight genomic clusters. We also compared the genome of the chick feed isolate with 58 Salmonella Cubana strains in GenBank and found that the chick feed isolate was very closely related to an isolate from a foodborne outbreak involving alfalfa sprouts.
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Affiliation(s)
- Faiza Benahmed
- 1 U.S. Food and Drug Administration, Center for Veterinary Medicine, Division of Animal and Food Microbiology, Laurel, Maryland 20708
| | - Hua Wang
- 2 U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Division of Microbiology, College Park, Maryland 20740
| | - Junia Jean-Gilles Beaubrun
- 3 U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Division of Virulence Assessment, Laurel, Maryland 20708; and
| | - Gopal R Gopinath
- 3 U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Division of Virulence Assessment, Laurel, Maryland 20708; and
| | - Chorng-Ming Cheng
- 4 U.S. Food and Drug Administration, Pacific Regional Laboratory Southwest, Irvine, California 92612, USA (retired)
| | - Darcy E Hanes
- 3 U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Division of Virulence Assessment, Laurel, Maryland 20708; and
| | - Thomas S Hammack
- 2 U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Division of Microbiology, College Park, Maryland 20740
| | - Mark Rasmussen
- 1 U.S. Food and Drug Administration, Center for Veterinary Medicine, Division of Animal and Food Microbiology, Laurel, Maryland 20708
| | - Maureen K Davidson
- 1 U.S. Food and Drug Administration, Center for Veterinary Medicine, Division of Animal and Food Microbiology, Laurel, Maryland 20708
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Nagaraj G, Ganaie F, Govindan V, Ravikumar KL. Development of PCRSeqTyping-a novel molecular assay for typing of Streptococcus pneumoniae. Pneumonia (Nathan) 2017; 9:8. [PMID: 28702310 PMCID: PMC5471960 DOI: 10.1186/s41479-017-0032-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 05/01/2017] [Indexed: 11/25/2022] Open
Abstract
Background Precise serotyping of pneumococci is essential for vaccine development, to better understand the pathogenicity and trends of drug resistance. Currently used conventional and molecular methods of serotyping are expensive and time-consuming, with limited coverage of serotypes. An accurate and rapid serotyping method with complete coverage of serotypes is an urgent necessity. This study describes the development and application of a novel technology that addresses this need. Methods Polymerase chain reaction (PCR) was performed, targeting 1061 bp cpsB region, and the amplicon was subjected to sequencing. The sequence data was analyzed using the National Centre for Biotechnology Information database. For homologous strains, a second round of PCR, sequencing, and data analysis was performed targeting 10 group-specific genes located in the capsular polysaccharide region. Ninety-one pneumococcal reference strains were analyzed with PCRSeqTyping and compared with Quellung reaction using Pneumotest Kit (SSI, Denmark). Results A 100% correlation of PCRSeqTyping results was observed with Pneumotest results. Fifty-nine reference strains were uniquely identified in the first step of PCRSeqTyping. The remaining 32 homologous strains out of 91 were also uniquely identified in the second step. Conclusion This study describes a PCRSeqTyping assay that is accurate and rapid, with high reproducibility. This assay is amenable for clinical testing and does not require culturing of the samples. It is a significant improvement over other methods because it covers all pneumococcal serotypes, and it has the potential for use in diagnostic laboratories and surveillance studies.
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Affiliation(s)
- Geetha Nagaraj
- Central Research Laboratory, KIMS Hospital and Research Centre, KR Road, VV Purum, Bangalore, Karnataka 560 004 India
| | - Feroze Ganaie
- Central Research Laboratory, KIMS Hospital and Research Centre, KR Road, VV Purum, Bangalore, Karnataka 560 004 India
| | - Vandana Govindan
- Central Research Laboratory, KIMS Hospital and Research Centre, KR Road, VV Purum, Bangalore, Karnataka 560 004 India
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Zhao L, Xiong Y, Meng D, Guo J, Li Y, Liang L, Han R, Wang Y, Guo X, Wang R, Zhang L, Gao L, Wang J. An 11-year study of shigellosis and Shigella species in Taiyuan, China: Active surveillance, epidemic characteristics, and molecular serotyping. J Infect Public Health 2017; 10:794-798. [PMID: 28188118 DOI: 10.1016/j.jiph.2017.01.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 12/15/2016] [Accepted: 01/07/2017] [Indexed: 10/20/2022] Open
Abstract
A hospital-based surveillance of shigellosis was conducted in Taiyuan from 2005 to 2015. A total of 2655 stool cultures were collected from patients with diarrhea, 115 were identified as S. flexneri and 107 were S. sonnei. The highest infection rates were found among children under 5 years of age (34.2 %), and during the summer (61.0 %). Six serotypes were identified among S. flexneriisolates:1a, 2a, 2b, Xv, X and Y. Serotype 2a and Xv were the dominant serotypes in two periods, 2012-2015 and 2005-2008, respectively. High shigellosis rates over the past decade highlight shigellosis is still a major public health problem in Taiyuan.
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Affiliation(s)
- Lifeng Zhao
- Laboratory of Microbiology, Taiyuan Center for Disease Control and Prevention, Taiyuan, Shanxi Province 030012, China.
| | - Yanwen Xiong
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing 102206, China.
| | - Dequan Meng
- Laboratory of Microbiology, Taiyuan Center for Disease Control and Prevention, Taiyuan, Shanxi Province 030012, China.
| | - Jiane Guo
- Laboratory of Microbiology, Taiyuan Center for Disease Control and Prevention, Taiyuan, Shanxi Province 030012, China.
| | - Yiping Li
- Laboratory of Microbiology, Taiyuan Center for Disease Control and Prevention, Taiyuan, Shanxi Province 030012, China.
| | - Lirong Liang
- Laboratory of Microbiology, Taiyuan Center for Disease Control and Prevention, Taiyuan, Shanxi Province 030012, China.
| | - Rui Han
- Laboratory of Microbiology, Taiyuan Center for Disease Control and Prevention, Taiyuan, Shanxi Province 030012, China.
| | - Yanqin Wang
- Laboratory of Microbiology, Taiyuan Center for Disease Control and Prevention, Taiyuan, Shanxi Province 030012, China.
| | - Xiaofang Guo
- Laboratory of Microbiology, Taiyuan Center for Disease Control and Prevention, Taiyuan, Shanxi Province 030012, China.
| | - Rui Wang
- Laboratory of Microbiology, Taiyuan Center for Disease Control and Prevention, Taiyuan, Shanxi Province 030012, China.
| | - Ladi Zhang
- Laboratory of Microbiology, Taiyuan Center for Disease Control and Prevention, Taiyuan, Shanxi Province 030012, China.
| | - Li Gao
- Laboratory of Microbiology, Taiyuan Center for Disease Control and Prevention, Taiyuan, Shanxi Province 030012, China.
| | - Jitao Wang
- Laboratory of Microbiology, Taiyuan Center for Disease Control and Prevention, Taiyuan, Shanxi Province 030012, China.
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10
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Bugarel M, Tudor A, Loneragan GH, Nightingale KK. Molecular detection assay of five Salmonella serotypes of public interest: Typhimurium, Enteritidis, Newport, Heidelberg, and Hadar. J Microbiol Methods 2017; 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] [What about the content of this article? (0)] [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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11
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Elder JR, Bugarel M, den Bakker HC, Loneragan GH, Nightingale KK. Interrogation of single nucleotide polymorphisms in gnd provides a novel method for molecular serogrouping of clinically important Shiga toxin producing Escherichia coli (STEC) targeted by regulation in the United States, including the "big six" non-O157 STEC and STEC O157. J Microbiol Methods 2016; 129:85-93. [PMID: 27432340 DOI: 10.1016/j.mimet.2016.07.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/06/2016] [Accepted: 07/07/2016] [Indexed: 12/22/2022]
Abstract
Escherichia coli O157:H7 has frequently been associated with foodborne infections and is considered an adulterant in raw non-intact beef in the U.S. Shiga toxin-producing E. coli (STEC) belonging to serogroups O26, O45, O103, O111, O121, and O145 (known as the "big six" non-O157) were estimated to cause >70% of foodborne infections attributed to non-O157 serogroups in the U.S., as a result, these six serogroups have also been targeted by regulation in the U.S. The purpose of this study was to develop a rapid and high-throughput molecular method to group STEC isolates into seven clinically important serogroups (i.e., O157 and the "big six" non-O157 serogroups) targeted by regulation in the U.S. by interrogating single nucleotide polymorphisms (SNPs) in gnd. A collection of 195 STEC isolates, including isolates belonging to O157:H7 (n=18), O26 (n=21), O45 (n=19), O103 (n=24), O111 (n=24), O121 (n=23), O145 (n=21), and ten other STEC serogroups (n=45), was assembled and characterized by full gnd sequencing to identify informative SNPs for molecular serogrouping. A multiplex SNP typing assay was developed to interrogate twelve informative gnd SNPs by single base pair extension chemistry and used to characterize the STEC isolate collection assembled here. SNP types were assigned to each isolate by the assay and polymorphisms were confirmed with gnd sequence data. O-serogroup-specific SNP types were identified for each of the seven clinically important STEC serogroups, which allowed the differentiation of these seven STEC serogroups from other non-O157 STEC serogroups. Although serogroups of the "big six" non-O157 STEC and O157:H7 contained multiple SNP types per O-serogroup, there were no overlapping SNP types between serogroups. Our results demonstrate that molecular serogrouping of STEC isolates by interrogation of informative SNPs in gnd represents an alternative to traditional serogrouping by agglutination for rapid and high-throughput identification of clinically important STEC serogroups targeted by regulation for surveillance and epidemiological investigations.
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Affiliation(s)
- J R Elder
- Department of Food and Animal Sciences, Texas Tech University, Lubbock, TX 79409, United States; Department of Animal Sciences, Colorado State University, Fort Collins, CO 80523, United States
| | - M Bugarel
- Department of Food and Animal Sciences, Texas Tech University, Lubbock, TX 79409, United States
| | - H C den Bakker
- Department of Food and Animal Sciences, Texas Tech University, Lubbock, TX 79409, United States; Department of Food Science and Technology, Cornell University, Ithaca, NY 14853, United States
| | - G H Loneragan
- Department of Food and Animal Sciences, Texas Tech University, Lubbock, TX 79409, United States
| | - K K Nightingale
- Department of Food and Animal Sciences, Texas Tech University, Lubbock, TX 79409, United States; Department of Animal Sciences, Colorado State University, Fort Collins, CO 80523, United States.
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12
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Jean-Gilles Beaubrun J, Flamer ML, Addy N, Ewing L, Gopinath G, Jarvis K, Grim C, Hanes DE. Evaluation of corn oil as an additive in the pre-enrichment step to increase recovery of Salmonella enterica from oregano. Food Microbiol 2016; 57:195-203. [PMID: 27052719 DOI: 10.1016/j.fm.2016.03.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 01/26/2016] [Accepted: 03/09/2016] [Indexed: 10/22/2022]
Abstract
Phenolic compounds associated with essential oils of spices and herbs possess a variety of antioxidant and antimicrobial properties that interfere with Salmonella detection from fresh and dried products. Finding a compound to neutralize the effect of these antimicrobial compounds, while allowing Salmonella growth during pre-enrichment, is a crucial step in both traditional pathogen isolation and molecular detection from these foods. This study evaluated the effectiveness of corn oil as a component of the pre-enrichment broth to counteract antimicrobial compounds properties and increase the recovery of Salmonella from spices. Oregano samples artificially contaminated with Salmonella enterica were pre-enriched in modified Buffered Peptone Water (mBPW) supplemented with and without 2% (vol/vol) corn oil respectively. Samples were incubated overnight at 37 °C. The results showed that recovery of Salmonella from oregano samples was increased by ≥50% when pre-enriched with corn oil. Serovars were confirmed using a PCR serotyping method. In addition, shot-gun metagenomics analyses demonstrated bacterial diversity and the effect of corn oil on the relative prevalence of Salmonella in the oregano samples. Modifying pre-enrichment broths with corn oil improved the detection and isolation of Salmonella from oregano, and may provide an alternative method for pathogen detection in dried food matrices such as spices.
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Affiliation(s)
| | - Marie-Laure Flamer
- U.S. Food and Drug Administration, Laurel, MD, 20708, USA; UMCP JIFSAN Program, 5201 Paint Branch Pkwy Patapsco Building Suite 2134, University of Maryland, College Park, 20742, USA
| | - Nicole Addy
- U.S. Food and Drug Administration, Laurel, MD, 20708, USA; Oak Ridge Institute for Science and Technology, Oak Ridge, TN, USA
| | - Laura Ewing
- U.S. Food and Drug Administration, Laurel, MD, 20708, USA
| | - Gopal Gopinath
- U.S. Food and Drug Administration, Laurel, MD, 20708, USA
| | - Karen Jarvis
- U.S. Food and Drug Administration, Laurel, MD, 20708, USA
| | - Chris Grim
- U.S. Food and Drug Administration, Laurel, MD, 20708, USA; Oak Ridge Institute for Science and Technology, Oak Ridge, TN, USA
| | - Darcy E Hanes
- U.S. Food and Drug Administration, Laurel, MD, 20708, USA
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13
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Burns CC, Kilpatrick DR, Iber JC, Chen Q, Kew OM. Molecular Properties of Poliovirus Isolates: Nucleotide Sequence Analysis, Typing by PCR and Real-Time RT-PCR. Methods Mol Biol 2016; 1387:177-212. [PMID: 26983735 DOI: 10.1007/978-1-4939-3292-4_9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Virologic surveillance is essential to the success of the World Health Organization initiative to eradicate poliomyelitis. Molecular methods have been used to detect polioviruses in tissue culture isolates derived from stool samples obtained through surveillance for acute flaccid paralysis. This chapter describes the use of realtime PCR assays to identify and serotype polioviruses. In particular, a degenerate, inosine-containing, panpoliovirus (panPV) PCR primer set is used to distinguish polioviruses from NPEVs. The high degree of nucleotide sequence diversity among polioviruses presents a challenge to the systematic design of nucleic acid-based reagents. To accommodate the wide variability and rapid evolution of poliovirus genomes, degenerate codon positions on the template were matched to mixed-base or deoxyinosine residues on both the primers and the TaqMan™ probes. Additional assays distinguish between Sabin vaccine strains and non-Sabin strains. This chapter also describes the use of generic poliovirus specific primers, along with degenerate and inosine-containing primers, for routine VP1 sequencing of poliovirus isolates. These primers, along with nondegenerate serotype-specific Sabin primers, can also be used to sequence individual polioviruses in mixtures.
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Affiliation(s)
- Cara C Burns
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Disease, Centers for Disease Control and Prevention, 1600 Clifton Rd., NE MS G-10, Atlanta, GA, 30333, USA.
| | - David R Kilpatrick
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, National Center for Immunizationand Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jane C Iber
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, National Center for Immunizationand Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Qi Chen
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, National Center for Immunizationand Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Olen M Kew
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, National Center for Immunizationand Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA, USA
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14
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Chiou CS, Torpdahl M, Liao YS, Liao CH, Tsao CS, Liang SY, Wang YW, Kuo JC, Liu YY. Usefulness of pulsed-field gel electrophoresis profiles for the determination of Salmonella serovars. Int J Food Microbiol 2015. [PMID: 26208096 DOI: 10.1016/j.ijfoodmicro.2015.07.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We created a database consisting of a large number of Salmonella pulsed-field gel electrophoresis (PFGE) profiles covering a wide range of different serovars. This database was used for the prediction of the serovars based on the PFGE profiles for isolates from Taiwan and Denmark. The PFGE profiles proved very useful in the determination of a serovar although serovar prediction was more efficient for local isolates than those from a distant geographic area. To use a highly stringent band matching tolerance in the BioNumerics software is also important for the grouping of serovars.
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Affiliation(s)
- Chien-Shun Chiou
- Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Taichung 40855, Taiwan.
| | - Mia Torpdahl
- Statens Serum Institut, DK-2300 Copenhagen S, Denmark.
| | - Ying-Shu Liao
- Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Taichung 40855, Taiwan.
| | - Chun-Hsing Liao
- Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Taichung 40855, Taiwan.
| | - Chi-Sen Tsao
- Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Taichung 40855, Taiwan.
| | - Shiu-Yun Liang
- Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Taichung 40855, Taiwan.
| | - You-Wun Wang
- Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Taichung 40855, Taiwan.
| | - Jung-Che Kuo
- Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Taichung 40855, Taiwan.
| | - Yen-Yi Liu
- Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Taichung 40855, Taiwan.
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15
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Yan Q, Jarvis KG, Chase HR, Hébert K, Trach LH, Lee C, Sadowski J, Lee B, Hwang S, Sathyamoorthy V, Mullane N, Pava-Ripoll M, Iversen C, Pagotto F, Fanning S, Tall BD. A proposed harmonized LPS molecular-subtyping scheme for Cronobacter species. Food Microbiol 2015; 50:38-43. [PMID: 25998813 DOI: 10.1016/j.fm.2015.03.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 03/06/2015] [Accepted: 03/09/2015] [Indexed: 11/23/2022]
Abstract
Cronobacter are opportunistic pathogens, which cause infections in all age groups. To aid the characterization of Cronobacter in foods and environments a harmonized LPS identification scheme for molecular serotyping is needed. To this end, we studied 409 Cronobacter isolates representing the seven Cronobacter species using two previously reported molecular serotyping schemes, described here as Mullane-Jarvis (M-J) and Sun schemes. PCR analysis revealed many overlapping results that were obtained when independently applying the two serotyping schemes. There were complete agreements between the two PCR schemes for Cronobacter sakazakii (Csak) O:1, Csak O:3, and Csak O:7 serotypes. However, only thirty-five of 41 Csak O:4 strains, identified using the M-J scheme, were PCR-positive with the Sun scheme primers. Also the Sun scheme Csak O:5 primers failed to identify this serotype in any of the C. sakazakii strains tested, but did recognize seven Cronobacter turicensis strains, which were identified as Ctur O:3 using the M-J scheme. Similarly, the Sun scheme Csak O:6 primers recognized 30 Cronobacter malonaticus O:2 strains identified with the M-J scheme, but failed to identify this serotype in any C. sakazakii strain investigated. In this report, these findings are summarized and a harmonized molecular-serotyping scheme is proposed which is predicated on the correct identification of Cronobacter species, prior to serotype determination. In summary, fourteen serotypes were identified using the combined protocol, which consists of Csak O:1-O:4, and Csak O:7; Cmal O:1-O:2; Cdub O:1-O:2, Cmuy O:1-O:2, Cuni O:1, as well as Ctur O:1 and Ctur O:3.
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16
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Abstract
Salmonella is a diverse foodborne pathogen, which has more than 2600 recognized serovars. Classification of Salmonella isolates into serovars is essential for surveillance and epidemiological investigations; however, determination of Salmonella serovars, by traditional serotyping, has some important limitations (e.g. labor intensive, time consuming). To overcome these limitations, multiple methods have been investigated to develop molecular serotyping schemes. Currently, molecular methods to predict Salmonella serovars include (i) molecular subtyping methods (e.g. PFGE, MLST), (ii) classification using serovar-specific genomic markers and (iii) direct methods, which identify genes encoding antigens or biosynthesis of antigens used for serotyping. Here, we reviewed reported methodologies for Salmonella molecular serotyping and determined the "serovar-prediction accuracy", as the percentage of isolates for which the serovar was correctly classified by a given method. Serovar-prediction accuracy ranged from 0 to 100%, 51 to 100% and 33 to 100% for molecular subtyping, serovar-specific genomic markers and direct methods, respectively. Major limitations of available schemes are errors in predicting closely related serovars (e.g. Typhimurium and 4,5,12:i:-), and polyphyletic serovars (e.g. Newport, Saintpaul). The high diversity of Salmonella serovars represents a considerable challenge for molecular serotyping approaches. With the recent improvement in sequencing technologies, full genome sequencing could be developed into a promising molecular approach to serotype Salmonella.
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Affiliation(s)
- Chunlei Shi
- Department of Food Science, Cornell University , Ithaca, NY , USA and
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