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Bogiel T, Dura A, Woźniak M, Mikucka A, Kanarek P. Usefulness of Capillary Gel Electrophoresis-Based PCR for Detection of Clostridioides difficile Strains with Hypervirulent Ribotypes. Gels 2024; 10:343. [PMID: 38786259 PMCID: PMC11121280 DOI: 10.3390/gels10050343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/10/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024] Open
Abstract
Clostridioides difficile is a complex of anaerobic bacteria responsible for the epidemics of post-antibiotic diarrhea as one of the examples of CDI (Clostridioides difficile infection). As many as 70% of cases concern hospitalized patients, particularly those in intensive care units. Ribotyping is one of the most common methods for differentiating bacterial strains. The purpose of this work was to show the effectiveness of the gel electrophoresis-based PCR ribotyping method and the Webribo database for typing C. difficile isolates, including the hypervirulent 027 ribotype. DNA samples extracted from 69 C. difficile strains with previously marked genotypes were included in this study. PCR was performed using 16S-23S primers, and capillary gel electrophoresis was performed on the Applied Biosystem 3130xl Genetic Analyzer. The Webribo database was applied for ribotype assignment. Out of 69 samples, 48 belonged to already known ribotypes, 13 represented new ribotypes and 8 was indicated as similar to the existing ones, having some differences. Capillary gel electrophoresis-based PCR is an effective method for the differentiation of C. difficile ribotypes and can be recognized as a very useful tool in epidemiological studies, while the Webribo database is a useful and an accessible database for a quick analysis of C. difficile ribotypes.
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Affiliation(s)
- Tomasz Bogiel
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-094 Bydgoszcz, Poland;
- Department of Clinical Microbiology, Antoni Jurasz University Hospital No. 1, 85-094 Bydgoszcz, Poland
| | - Alicja Dura
- Department of Forensic Medicine, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Toruń, Poland; (A.D.)
| | - Marcin Woźniak
- Department of Forensic Medicine, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Toruń, Poland; (A.D.)
| | - Agnieszka Mikucka
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-094 Bydgoszcz, Poland;
- Department of Clinical Microbiology, Antoni Jurasz University Hospital No. 1, 85-094 Bydgoszcz, Poland
| | - Piotr Kanarek
- Department of Microbiology and Food Technology, Faculty of Agriculture and Biotechnology, Bydgoszcz University of Science and Technology, 85-029 Bydgoszcz, Poland
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Smith AM, Erasmus LK, Tau NP, Smouse SL, Ngomane HM, Disenyeng B, Whitelaw A, Lawrence CA, Sekwadi P, Thomas J. Enteric fever cluster identification in South Africa using genomic surveillance of Salmonella enterica serovar Typhi. Microb Genom 2023; 9. [PMID: 37339282 DOI: 10.1099/mgen.0.001044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023] Open
Abstract
The National Institute for Communicable Diseases in South Africa participates in national laboratory-based surveillance for human isolates of Salmonella species. Laboratory analysis includes whole-genome sequencing (WGS) of isolates. We report on WGS-based surveillance of Salmonella enterica serovar Typhi (Salmonella Typhi) in South Africa from 2020 through 2021. We describe how WGS analysis identified clusters of enteric fever in the Western Cape Province of South Africa and describe the epidemiological investigations associated with these clusters. A total of 206 Salmonella Typhi isolates were received for analysis. Genomic DNA was isolated from bacteria and WGS was performed using Illumina NextSeq technology. WGS data were investigated using multiple bioinformatics tools, including those available at the Centre for Genomic Epidemiology, EnteroBase and Pathogenwatch. Core-genome multilocus sequence typing was used to investigate the phylogeny of isolates and identify clusters. Three major clusters of enteric fever were identified in the Western Cape Province; cluster one (n=11 isolates), cluster two (n=13 isolates), and cluster three (n=14 isolates). To date, no likely source has been identified for any of the clusters. All isolates associated with the clusters, showed the same genotype (4.3.1.1.EA1) and resistome (antimicrobial resistance genes: bla TEM-1B, catA1, sul1, sul2, dfrA7). The implementation of genomic surveillance of Salmonella Typhi in South Africa has enabled rapid detection of clusters indicative of possible outbreaks. Cluster identification allows for targeted epidemiological investigations and a timely, coordinated public health response.
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Affiliation(s)
- Anthony Marius Smith
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Linda Kathleen Erasmus
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Nomsa Pauline Tau
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Shannon Lucrecia Smouse
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Hlengiwe Mimmy Ngomane
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Bolele Disenyeng
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Andrew Whitelaw
- Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Charlene Ann Lawrence
- Communicable Disease Control, Service Priorities Coordination, Department of Health, Cape Town, South Africa
| | - Phuti Sekwadi
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Juno Thomas
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
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Hassan WMM, Tawab AAAE, El-Shannat SM. Current advances in molecular subtyping using multilocus variable number of tandem repeat analysis of Salmonella Enteritidis and Salmonella Typhimurium in Egyptian chickens. Vet World 2020; 13:2252-2259. [PMID: 33281364 PMCID: PMC7704301 DOI: 10.14202/vetworld.2020.2252-2259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/21/2020] [Indexed: 11/23/2022] Open
Abstract
Aim: This study aimed to characterize the genetic diversity, evolutionary level, and prevalence of genotypes of common isolates of Salmonella (Salmonella Enteritidis and Salmonella Typhimurium). Using one of the most advanced molecular recognition techniques, multilocus variable number of tandem repeat analysis (MLVA), we characterized the genotype and prevalence of S. Enteritidis and S. Typhimurium. Materials and Methods: One hundred and twenty-five internal organ samples were collected from the major chicken slaughterhouses in Egypt, and Salmonella species were isolated. PCR was utilized to amplify the IE-1 and Flic-C genes to identify S. Enteritidis and S. Typhimurium DNA, respectively, from Salmonella isolates. MLVA was applied on nine samples of S. Enteritidis DNA and three samples of S. Typhimurium DNA. Six variable number tandem repeat (VNTR) loci (Sal02, Sal04, Sal06, Sal10, Sal20, and Sal23) were amplified. Results: Of the examined samples (n=125), a total of 12 isolates (9.6%) were either identified as Enteritidis or Typhimurium. PCR-mediated amplification of IE-1 and Flic-C revealed that 75% (n=9) of the 12 Salmonella isolates were S. Enteritidis and 25% (n=3) were S. Typhimurium. The six loci amplified through MLVA had allelic diversity. The most discriminatory heterogenic locus for S. Enteritidis was Sal20. Sal04 and Sal23 were the most discriminatory heterogenic loci for S. Typhimurium. VNTR allelic profile analysis revealed nine unique genotypes for S. Enteritidis and three for S. Typhimurium. Conclusion: This study was the first to use MLVA analysis to identify S. Enteritidis and S. Typhimurium strains isolated from chickens in Egypt. The molecular typing data reported herein allowed us to characterize the genotypes of S. Enteritidis and S. Typhimurium that are most prevalent in Egyptian chickens. Moreover, this epidemiological information provides valuable insight on how to prevent disease transmission. Moreover, our methods provide an alternative to traditional serotyping techniques that may produce inaccurate strain identifications for organisms with rough lipopolysaccharide structures.
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Affiliation(s)
- Wafaa M M Hassan
- Reference Laboratory for Quality Control on Poultry Production, Animal Health Research Institute, Dokki, Giza, Egypt
| | - Ashraf A Abd El Tawab
- Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Benha University, Benha, Egypt
| | - Sara M El-Shannat
- Department of Microbiology, Animal Health Research Institute, Marsa Matruh, Egypt
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Samajpati S, Das S, Jain P, Ray U, Mandal S, Samanta S, Das S, Dutta S. Changes in antimicrobial resistance and molecular attributes of Salmonellae causing enteric fever in Kolkata, India, 2014-2018. INFECTION GENETICS AND EVOLUTION 2020; 84:104478. [PMID: 32736039 DOI: 10.1016/j.meegid.2020.104478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 11/18/2022]
Abstract
Globally, enteric fever caused by Salmonella Typhi (S. Typhi, ST) and S. Paratyphi A (SPA) remain one of the major diseases of public health importance. In this study, a total of 457 (380 ST, 77 SPA) blood isolates were collected from three tertiary care hospitals in Kolkata during 2014-18. Additionally, 66 (3.4%) ST and 5 (0.25%) SPA were recovered from blood culture of 1962 patients attending OPD of one pediatric hospital during 2016-18. The study isolates were tested for antimicrobial resistance (AMR) profiles; AMR genes; molecular sub-types by PFGE, MLVA and CRISPR. Among the total 446 ST and 82 SPA isolates, fluoroquinolone (FQ) resistance was very common in both serovars. Ciprofloxacin resistance of 24.9% and 9.8% & ofloxacin resistance of 20.9% and 87.8% were found in ST and SPA respectively. Majority (>70%) of the isolates showed decreased susceptibility to ciprofloxacin (DCS). A single point mutation in gyrA gene (S83F) was responsible for causing DCS in 37.5% (n = 42/112) ST and 63% (n = 46/73) SPA isolates. Multidrug resistance (MDR) was found only in 3.4% ST isolates and encoded the genes blaTEM-1, catA, sul, strA-strB, class 1 integron with dfrA7. All MDR ST (n = 15) possessed non-conjugative non-IncHI1 (180 kb) plasmid except one having conjugative IncHI1 (230 kb) plasmid and one without plasmid. The MDR genes were integrated near chromosomal cyaA gene site in ST with/without the presence of plasmid (nonIncH1). Almost 65.7% resistant ST belonged to H58 haplotype. PFGE showed clonally related isolates with 81% similarity in ST and 87% in SPA. Similarly, CRISPR typing showed less diversity among the isolates. However, the isolates (ST and SPA) were found to be more diverse by MLVA typing (D value 0.987 and 0.938). The study reports decrease in MDR and increase in FQ resistance among typhoidal Salmonella isolates over the years giving interesting information for enteric fever treatment.
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Affiliation(s)
- Sriparna Samajpati
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, P-33 C.I.T Road, Kolkata, West Bengal 700010, India
| | - Surojit Das
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, P-33 C.I.T Road, Kolkata, West Bengal 700010, India
| | - Priyanka Jain
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, P-33 C.I.T Road, Kolkata, West Bengal 700010, India
| | - Ujjwayini Ray
- Microbiology Division, Apollo Gleneagles Hospitals, 58 Canal Circular Road, Kolkata, West Bengal 700054, India
| | - Subhranshu Mandal
- Microbiology Division, Calcutta Medical Research Institute, 7/2 Diamond Harbour Road, Kolkata, West Bengal 700027, India
| | - Sandip Samanta
- Department of Pediatrics, Dr. B. C. Roy Post Graduate Institute of Pediatric Sciences, Kolkata, West Bengal 700054, India
| | - Santasabuj Das
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, P-33 C.I.T Road, Kolkata, West Bengal 700010, India
| | - Shanta Dutta
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, P-33 C.I.T Road, Kolkata, West Bengal 700010, India.
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Smith AM, Tau NP, Smouse SL, Allam M, Ismail A, Ramalwa NR, Disenyeng B, Ngomane M, Thomas J. Outbreak of Listeria monocytogenes in South Africa, 2017-2018: Laboratory Activities and Experiences Associated with Whole-Genome Sequencing Analysis of Isolates. Foodborne Pathog Dis 2019; 16:524-530. [PMID: 31062992 PMCID: PMC6653791 DOI: 10.1089/fpd.2018.2586] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In South Africa, a progressive increase in listeriosis cases was noted from mid-June 2017, heralding what was to become the world's largest listeriosis outbreak. A total of 1060 cases were reported for the period January 1, 2017 to July 17, 2018. We describe laboratory activities, experiences, and results of whole-genome sequencing (WGS) analysis of Listeria monocytogenes isolates associated with this outbreak. Bacteria were identified using the VITEK-2 COMPACT 15 microbial identification system. WGS was performed using Illumina MiSeq technology. WGS data were analyzed using CLC Genomics Workbench Software and free-to-use on-line analysis tools/pipelines. Multilocus sequence typing (MLST) showed that 91% of clinical isolates were sequence type 6 (ST6), determining that the outbreak was largely associated with L. monocytogenes ST6. Epidemiological and laboratory findings led to investigation of a large ready-to-eat processed meat production facility in South Africa, named Enterprise Foods. L. monocytogenes ST6 was found in environmental sampling swabs of the production facility and in ready-to-eat processed meat products (including polony, a product similar to bologna sausage) manufactured at the facility. ST6 isolates, sourced at the Enterprise Foods production facility and from Enterprise food products, were shown by single nucleotide polymorphism (SNP) analysis to be highly related to clinical isolates; these nonclinical ST6 isolates showed <10 SNP differences when compared to clinical ST6 isolates. Core-genome MLST showed that clinical ST6 isolates and Enterprise-related ST6 isolates had no more than 4 allele differences between each other, suggestive of a high probability of epidemiological relatedness. WGS data interpreted together with epidemiological data concluded that the source of the listeriosis outbreak was ready-to-eat processed meat products manufactured by Enterprise Foods. Listeriosis has now been added to the South African list of mandatory notifiable medical conditions. Surveillance systems have been strengthened to facilitate prevention and early detection of listeriosis outbreaks.
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Affiliation(s)
- Anthony M Smith
- 1 Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa.,2 Department of Clinical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nomsa P Tau
- 1 Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Shannon L Smouse
- 1 Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Mushal Allam
- 3 Sequencing Core Facility, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- 3 Sequencing Core Facility, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Ntsieni R Ramalwa
- 1 Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Bolele Disenyeng
- 1 Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Mimmy Ngomane
- 1 Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Juno Thomas
- 1 Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa.,2 Department of Clinical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Smith AM. Review of molecular subtyping methodologies used to investigate outbreaks due to multidrug-resistant enteric bacterial pathogens in sub-Saharan Africa. Afr J Lab Med 2019; 8:760. [PMID: 31205868 PMCID: PMC6556818 DOI: 10.4102/ajlm.v8i1.760] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 09/25/2018] [Indexed: 01/05/2023] Open
Abstract
Background In sub-Saharan Africa, molecular epidemiological investigation of outbreaks caused by antimicrobial-resistant enteric bacterial pathogens have mostly been described for Salmonella species, Vibrio cholerae, Shigella species and Escherichia coli. For these organisms, I reviewed all publications describing the use of molecular subtyping methodologies to investigate outbreaks caused by multidrug-resistant (MDR) enteric bacterial infections. Objectives To describe the use of molecular subtyping methodologies to investigate outbreaks caused by MDR enteric bacterial pathogens in sub-Saharan Africa and to describe the current status of molecular subtyping capabilities in the region. Methods A PubMed database literature search (English language only) was performed using the search strings: ‘Africa outbreak MDR’, ‘Africa outbreak multi’, ‘Africa outbreak multidrug’, ‘Africa outbreak multi drug’, ‘Africa outbreak resistance’, ‘Africa outbreak resistant’, ‘Africa outbreak drug’, ‘Africa outbreak antibiotic’, ‘Africa outbreak antimicrobial’. These search strings were used in combination with genus and species names of the organisms listed above. All results were included in the review. Results The year 1991 saw one of the first reports describing the use of molecular subtyping methodologies in sub-Saharan Africa; this included the use of plasmid profiling to characterise Salmonella Enteritidis. To date, several methodologies have been used; pulsed-field gel electrophoresis analysis and multilocus sequence typing have been the most commonly used methodologies. Investigations have particularly highlighted the emergence and spread of MDR clones; these include Salmonella Typhi H58 and Salmonella Typhimurium ST313 clones. In recent times, whole-genome sequencing (WGS) analysis approaches have increasingly been used. Conclusion Traditional molecular subtyping methodologies are still commonly used and still have their place in investigations; however, WGS approaches have increasingly been used and are slowly gaining a stronghold. African laboratories need to start adapting their molecular surveillance methodologies to include WGS, as it is foreseen that WGS analysis will eventually replace all traditional methodologies.
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Affiliation(s)
- Anthony M Smith
- Centre for Enteric Diseases, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.,Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Kumar Y, Mani KR, Tahlan AK. Analysis of Salmonella enterica Serovar Typhi by Outer Membrane Protein (OMP) Profiling, Random Amplification of Polymorphic DNA (RAPD) and Pulsed Field Gel Electrophoresis (PFGE). Trop Life Sci Res 2019; 30:57-71. [PMID: 30847033 PMCID: PMC6396889 DOI: 10.21315/tlsr2019.30.1.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A number of countries, including developed countries, still have typhoid fever as a major problem resulting in frequent outbreaks. The importance of controlling spread of typhoid fever is well known and necessitates periodic studies to delineate epidemiological relationships. Although phage typing remains to be the preferred conventional method for characterisation of typhoid bacilli, it is of limited use due to prevalence of few predominant phage types in the country like India. Therefore, an effort has been made to assess three molecular methods [Outer Membrane Protein (OMP) Profiling, Random Amplification of Polymorphic DNA (RAPD) and Pulsed Field Gel Electrophoresis (PFGE)] for typing of Salmonella enterica serovar Typhi. 128 Salmonella enterica serovar Typhi isolates were identified using biotyping and serotyping followed by antimicrobial susceptibility testing. These isolates were further subjected to OMP analysis, RAPD and PFGE. PFGE (114 unique clusters) was found to be the most discriminatory method followed by RAPD (94 unique clusters) and OMP profiling (50 unique clusters). Multidrug resistant strains were well discriminated by all three methods used in the study. PFGE still remains the most preferred method for detailed epidemiological investigations. However, random amplification of polymorphic DNA and outer membrane protein profiling can also be considered for molecular discrimination of the isolates in the laboratories lacking high-end facilities.
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Affiliation(s)
- Yashwant Kumar
- National Salmonella and Escherichia Centre, Central Research Institute, Kasauli-173204, Himachal Pradesh, India
| | - Kavaratty Raju Mani
- National Salmonella and Escherichia Centre, Central Research Institute, Kasauli-173204, Himachal Pradesh, India
| | - Ajay Kumar Tahlan
- National Salmonella and Escherichia Centre, Central Research Institute, Kasauli-173204, Himachal Pradesh, India
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Shekhawat SS, Gaurav A, Joseph B, Kumar H, Kumar N. Random amplified polymorphic DNA-based molecular heterogeneity analysis of Salmonella enterica isolates from foods of animal origin. Vet World 2019; 12:146-154. [PMID: 30936669 PMCID: PMC6431806 DOI: 10.14202/vetworld.2019.146-154] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 12/03/2018] [Indexed: 12/31/2022] Open
Abstract
Aim: This study aims to study the significance of random amplified polymorphic DNA (RAPD) typing in heterogeneity analysis of Salmonella serovars, isolated from foods of animal origin. Materials and Methods: Salmonella serovars isolated and identified from different foods of animal origin such as meat, milk, and egg by standard bacteriological methods. DNA isolated from all 10 isolates which are confirmed by biochemical and serotyping methods and then RAPD was performed using the primers OPB 10, primer 1290, NSC I, NSC II, and primer 3. Then, RAPD data were analyzed using the BioNumerics software, Belgium, Germany. Results: RAPD polymerase chain reaction (PCR) using five primers, namely OPB 10, primer 1290, NSC I, NSC II, and primer 3, classified the 10 isolates into 9, 10, 10, 7, and 10 RAPD-PCR types with discriminating powers of 0.1987, 0.423, 0.50889, 0.1842, and 0.2582, respectively. The phylogram constructed with NSC I profile classified isolates based on geographical origin. Primer 1290, NSC II, and primer 3 produced some uniform bands in all isolates indicating their binding ability in conserved genomic region. This study revealed that RAPD profile can be best used for finding out the heterogeneity at molecular level of Salmonella isolates in combination with other molecular and phenotypic typing techniques. Thus, our results support earlier observation of its significance by different workers on different Salmonella serotypes. Conclusion: Repeatability of RAPD-PCR is insufficient to distinguish genetic differences among Salmonella serovars.
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Affiliation(s)
- Surendra Singh Shekhawat
- Department of Veterinary Public Health and Epidemiology, College of Veterinary and Animal Science, Navania, Vallabhnagar, Udaipur, Rajasthan, India
| | - Abhishek Gaurav
- Department of Veterinary Public Health and Epidemiology, College of Veterinary and Animal Science, Navania, Vallabhnagar, Udaipur, Rajasthan, India
| | - Bincy Joseph
- Department of Veterinary Microbiology, College of Veterinary and Animal Science, Navania, Vallabhnagar, Udaipur, Rajasthan, India
| | - Hitesh Kumar
- Department of Veterinary Public Health and Epidemiology, College of Veterinary and Animal Science, Navania, Vallabhnagar, Udaipur, Rajasthan, India
| | - Nirmal Kumar
- Department of Veterinary Public Health and Epidemiology, College of Veterinary and Animal Science, Navania, Vallabhnagar, Udaipur, Rajasthan, India
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Keddy KH, Smith AM, Sooka A, Tau NP, Ngomane HMP, Radhakrishnan A, Als D, Benson FG. The Burden of Typhoid Fever in South Africa: The Potential Impact of Selected Interventions. Am J Trop Med Hyg 2018; 99:55-63. [PMID: 30047360 PMCID: PMC6128358 DOI: 10.4269/ajtmh.18-0182] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Typhoid fever is notifiable in South Africa but clinical notification is notoriously poor. South Africa has an estimated annual incidence rate of 0.1 cases per 100,000 population of culture-confirmed typhoid fever, decreased from 17 cases per 100,000 population in the 1980s. This work was undertaken to identify the reasons for this decrease and identify potential weaknesses that may result in an increase of observed cases. Culture-confirmed cases, with additional demographic and clinical data have been collected from selected sentinel sites since 2003. Data on contextual factors (gross domestic product [GDP], sanitation, female education, and childhood diarrhea mortality) were collected. National incidence rates of culture-confirmed typhoid fever have remained constant for the past 13 years, with the exception of an outbreak in 2005: incidence was 0.4 per 100,000 population. Paratyphoid fever remains a rare disease. Antimicrobial susceptibility data suggest resistance to ciprofloxacin and azithromycin is emerging. The South African population increased from 27.5 million in 1980 to 55.0 million in 2015: urbanization increased from 50% to 65%, GDP increased from United States Dollar (USD) $2,910 to USD $6,167, access to sanitation improved from 64.4% to 70.0% in the urban population and 26.4% to 60.5% in rural areas. Female literacy levels improved from 74.8% to 92.6% over the period. Improved socioeconomic circumstances in South Africa have been temporally associated with decreasing incidence rates of typhoid fever over a 35-year period. Ongoing challenges remain including potential for large outbreaks, a large immigrant population, and emerging antimicrobial resistance. Continued active surveillance is mandatory.
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Affiliation(s)
- Karen H Keddy
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Centre for Enteric Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Anthony M Smith
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Centre for Enteric Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Arvinda Sooka
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Nomsa P Tau
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Hlengiwe M P Ngomane
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa
| | | | - Daina Als
- Centre for Global Child Health, The Hospital for Sick Children, Toronto, Canada
| | - Frew G Benson
- Gauteng Provincial Health Department, Johannesburg, South Africa
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