1
|
Borah P, Porwollik S, Desai P, Nayak P, Borah PP, Cheng P, McClelland M. A simplified multiplex PCR-based typing method for common Salmonella enterica serovars supported by online server-based detection system. Indian J Med Res 2017; 146:272-280. [PMID: 29265030 PMCID: PMC5761039 DOI: 10.4103/ijmr.ijmr_1258_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Background & objectives: A rapid and simple alternative method is needed to replace the laborious, time-consuming Salmonella serotyping. The objective of the present study was to improve and simplify a previously reported multiplex polymerase chain reaction (PCR)-based method and to create an online server to enable rapid determination of serovars. Methods: A method of multiplex PCR-based genome typing (MPGT) was standardized using 59 Salmonella isolates of 31 serovars. Several previously reported primers were modified to obtain a more accurate performance. The screen was separated into four different multiplex reactions distinguishable on standard electrophoresis. A blind study was subsequently performed with 81 isolates of 10 serovars most prevalent in India. Whole genome information from 440 Salmonella isolates was used to confirm the usefulness of this method and concurrence of in silico predictions and PCR results were investigated. A public server (http://www.mpgt-salmonella.res.in) was established for data storage and determination of closest previously observed Salmonella isolates based on obtained MPGT patterns. Results: The 16 target genes amplified showed variability in their presence in strains from different serotypes. Hence, identical amplification patterns suggested genetic relatedness of strains and usually identical serological behaviour. The observed absence/presence patterns of genes were converted to an MPGT code. Altogether, 83 different codes were predicted in silico based on the whole genome information of 440 strains. Results confirmed that major serovars usually displayed unique MPGT codes. Interpretation & conclusions: The multiplex PCR assay resulted in specific binary codes for isolates from each of the 31 Salmonella serovars tested. The online server allowed the user to compare obtained PCR results with stored previous patterns. Simplicity, speed and cost-effectiveness make this tool useful for quick outbreak management.
Collapse
Affiliation(s)
- Probodh Borah
- Department of Microbiology, College of Veterinary Science, Assam Agricultural University, Guwahati, India
| | - Steffen Porwollik
- Deparment of Microbiology & Molecular Genetics, University of California, Irvine, USA
| | - Prerak Desai
- Deparment of Microbiology & Molecular Genetics, University of California, Irvine, USA
| | - Prakash Nayak
- Department of Bioinformatics Centre, College of Veterinary Science, Assam Agricultural University, Guwahati, India
| | - Partha Pratim Borah
- Department of Animal Biotechnology, College of Veterinary Science, Assam Agricultural University, Guwahati, India
| | - Pui Cheng
- Deparment of Microbiology & Molecular Genetics, University of California, Irvine, USA
| | - Michael McClelland
- Deparment of Microbiology & Molecular Genetics, University of California, Irvine, USA
| |
Collapse
|
2
|
Nishat S, Hamim I, Khalil MI, Ali MA, Hossain MA, Meah MB, Islam MR. Genetic diversity of the bacterial wilt pathogen Ralstonia solanacearum using a RAPD marker. C R Biol 2015; 338:757-67. [PMID: 26302834 DOI: 10.1016/j.crvi.2015.06.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 06/06/2015] [Accepted: 06/09/2015] [Indexed: 11/27/2022]
Abstract
Bacterial wilt caused by Ralstonia solanacearum is a destructive disease of many economically important crop species. A significant variation in wilt incidence and severity in eggplant and potato was observed among the growing areas surveyed. R. solanacearum isolates obtained both from eggplant and potato belong to biovar III, while isolates from eggplant belong to race 1 and isolates obtained from potato belong to race 3. Random amplified polymorphic DNA (RAPD) technique was used as a tool for assessing genetic variation and relationship among seven isolate groups of R. solanacearum viz., RsB-1, RsB-2, RsB-3, RsP-1, RsP-2, RsP-3 and RsP-4, consisting in a total of 28 isolates. Out of the RAPD markers used, amplification with four decamer primers produced 70 bands with sizes ranging from 100 to 1400 bp. Out of 70 bands, 68 bands (97.06%) were polymorphic and two bands (2.94%) were monomorphic amongst the seven R. solanacearum isolates group. The Unweighted Pair Group Method of Arithmetic Means (UPGMA) dendrogram constructed from Nei's genetic distance produced two main clusters of the seven isolates of R. solanacearum. The isolates RsB-1, RsB-2, RsB-3 and R-4 grouped in cluster І, while RsP-2, RsP-3 and RsP-4 grouped in cluster ІІ. The highest intra-variety similarity index (Si) was found in RsB-1 isolate (86.35%) and the lowest one in RsP-2 (56.59%). The results indicated that relatively higher and lower levels of genetic variation were found in RsP-3 and RsB-3, respectively. The coefficient of gene differentiation (G(st)) was 0.5487, reflecting the existence of a high level of genetic variations among seven isolates of R. solanacearum. Comparatively higher genetic distance (0.4293) and lower genetic identity (0.6510) were observed between RsB-2 and RsP-4 combinations. The lowest genetic distance (0.0357) and highest genetic identity (0.9650) were found in RsB-1 vs. RsB-2 pair. Thus, RAPD offers a potentially simple, rapid and reliable method to evaluate genetic diversity analysis in R. solanacearum.
Collapse
Affiliation(s)
- Sayeda Nishat
- Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Islam Hamim
- Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - M Ibrahim Khalil
- Plant Pathology Division, Bangladesh Institute of Nuclear Agriculture, Mymensingh, Bangladesh
| | - Md Ayub Ali
- Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Muhammed Ali Hossain
- Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - M Bahadur Meah
- Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Md Rashidul Islam
- Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh.
| |
Collapse
|
3
|
Taban BM, Aytac SA, Akkoc N, Akcelik M. Characterization of antibiotic resistance in Salmonella enterica isolates determined from ready-to-eat (RTE) salad vegetables. Braz J Microbiol 2013; 44:385-91. [PMID: 24294226 PMCID: PMC3833132 DOI: 10.1590/s1517-83822013005000047] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Accepted: 06/05/2012] [Indexed: 11/22/2022] Open
Abstract
In the last decade, ready-to-eat (RTE) salad vegetables are gaining increasing importance in human diet. However, since they are consumed fresh, inadequate washing during processing can bring on some foodborne illnesses, like salmonellosis, since these food items have natural contamination from soil and water. During 2009-2010, a total of 81 samples were purchased arbitrarily from local markets in Ankara, and were examined for Salmonella contamination. Salmonella screening was performed by using anti-Salmonella magnetic beads system and polymerase chain reaction (PCR) identification of the suspected colonies. Then, the antibiotic resistance profiles of four Salmonella strains identified (strains RTE-1, RTE-2, RTE-3, and RTE-4) were also investigated, since the mechanism by which Salmonella spp. have accumulated antibiotic resistance genes is of interest. All strains showed resistance against sulfonamides (MIC > 128 mg/L). Further results suggested that associated sulfonamide resistance genes were encoded by the 55.0 kb plasmid of strain RTE-1 that involves no integrons. As a result of using two primers (P1254 and P1283) in randomly amplified polymorphic DNA-PCR (RAPD-PCR) analysis, two common amplicons (364 bp and 1065 bp) were determined. The findings of this study provide support to the adoption of guidelines for the prudent use of antibiotics in order to reduce the number of pathogens present on vegetable and fruit farms. Besides, since it is shown that these bacteria started to gain resistance to antibiotics, it is necessary to further investigate the prevalence of them in foods.
Collapse
Affiliation(s)
| | - Sait Aykut Aytac
- Food Engineering Department, Faculty of Engineering, Hacettepe University, Beytepe, Ankara, Turkey
| | - Nefise Akkoc
- Biology Department, Faculty of Science, Ankara University, Tandogan, Ankara, Turkey
| | - Mustafa Akcelik
- Biology Department, Faculty of Science, Ankara University, Tandogan, Ankara, Turkey
| |
Collapse
|
4
|
Taşkale N, Akçelik M. Use of RAPD-PCR, plasmid profiling, class 1 integron analysis, and antimicrobial resistance for molecular characterisation of Salmonellastrains isolated from Turkey. ACTA ALIMENTARIA 2012. [DOI: 10.1556/aalim.2011.0008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
5
|
Grover A, Azmi W, Gadewar AV, Pattanayak D, Naik PS, Shekhawat GS, Chakrabarti SK. Genotypic diversity in a localized population of Ralstonia solanacearum as revealed by random amplified polymorphic DNA markers. J Appl Microbiol 2006; 101:798-806. [PMID: 16968291 DOI: 10.1111/j.1365-2672.2006.02974.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS To assess genotypic diversity within Ralstonia solanacearum isolates of a single field. METHODS AND RESULTS A total of 44 field isolates and 22 in vitro generated clones of R. solanacearum were studied for genotypic diversity by random amplified polymorphic DNA (RAPD) technique. Genomic DNA of these isolates and clones was extracted by proteinase-K-SDS lysis mini-prep method. RAPD analysis was done with 30 decamer primers. The data were analysed using NTSYSpc 2.02h software. Forty-two out of 44 field isolates and all the clonal isolates were identified as distinct genotypes at 70% similarity level. CONCLUSION Very high level of genome variability was observed within the field and clonal isolates of R. solanacearum. This might be a reason for the wide host range of this bacterium and for quick breakdown of wilt resistance in host plants. SIGNIFICANCE AND IMPACT OF THE STUDY The results suggest that it would be difficult to design specific diagnostic protocol for R. solanacearum even for a localized population and to breed cultivars with broad-spectrum resistance.
Collapse
Affiliation(s)
- A Grover
- Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | | | | | | | | | | | | |
Collapse
|
6
|
Heyndrickx M, Rijpens N, Herman L. Molecular Detection and Typing of Foodborne Bacterial Pathogens: A Review. Appl Microbiol 2005. [DOI: 10.1007/0-306-46888-3_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
7
|
de Souza Lopes AC, Falcão Rodrigues J, de Morais Júnior MA. Molecular typing of Klebsiella pneumoniae isolates from public hospitals in Recife, Brazil. Microbiol Res 2005; 160:37-46. [PMID: 15782936 DOI: 10.1016/j.micres.2004.09.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Thirty nosocomial isolates of Klebsiella pneumoniae, collected from three public hospitals in Recife, Brazil, between 1999 and 2000, were analysed in order to determine their epidemiological relatedness and genetic characteristics. The isolates were characterised by biotyping, antibiotyping, protein analysis, plasmid profile and random amplified polymorphic DNA (RAPD). The majority of the clinical isolates were resistant to multiple antibiotics, in particular to beta-lactams, and 30% were found to be ESBLs producers. RAPD proved to be the most effective technique in discriminating unrelated K. pneumoniae isolates. It was confirmed by the highly genetic similarity found among related isolates from an hospital outbreak. We conclude that K. pneumoniae infections in Recife has been caused by a variety of bacterial genotypes. This is the first report that revealed the subtypes of K. pneumoniae in Brazil by plasmid analysis and RAPD.
Collapse
|
8
|
Khoodoo MHR, Jaufeerally-Fakim Y. RAPD-PCR Fingerprinting and Southern Analysis of Xanthomonas axonopodis pv. dieffenbachiae Strains Isolated from Different Aroid Hosts and Locations. PLANT DISEASE 2004; 88:980-988. [PMID: 30812251 DOI: 10.1094/pdis.2004.88.9.980] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Anthurium blight, caused by Xanthomonas axonopodis pv. dieffenbachiae, is a systemic disease of Anthurium and other aroids. The aims of this work were to study the genetic diversity among X. axonopodis pv. dieffenbachiae strains and to identify, from the polymerase chain reaction (PCR) profiles, DNA probes that would be specific for the pathovar dieffenbachiae. Twenty-five X. axonopodis pv. dieffenbachiae strains, isolated from different hosts and geographical locations including Mauritius, were fingerprinted using the random amplified polymorphic DNA (RAPD)-PCR technique. The fingerprints were analyzed by the National Taxonomy System Software (NTSYS). The specificity of some of the RAPD fragments selected from PCR profiles was tested by Southern analyses of the PCR products. Ten arbitrary primers were chosen from an initial set of 111 decamers. Two hundred and nine RAPD markers were generated in eight individual DNA profiles. A correlation was found between the serotypes and the RAPD profiles for some groups of isolates. A possible link was also observed between the host range of the isolates tested and their RAPD profiles for strains isolated from Dieffenbachia and Philodendron. These results were confirmed by Southern analysis. Cluster analysis by the unweighted pair group method, arithmetic average (UPGMA) confirmed that the pathovar is genetically diverse with some strains that were clustered together showing similar host preferences. DNA probes with a potential use in molecular diagnostics of Anthurium blight were identified. This preliminary work could be used to develop PCR primers that will enable the sensitive detection of the pathogen in latently infected plants.
Collapse
Affiliation(s)
- M H R Khoodoo
- Biotechnology Unit, Faculty of Agriculture, University of Mauritius, Réduit, Mauritius
| | - Y Jaufeerally-Fakim
- Biotechnology Unit, Faculty of Agriculture, University of Mauritius, Réduit, Mauritius
| |
Collapse
|
9
|
Guard-Bouldin J, Gast RK, Humphrey TJ, Henzler DJ, Morales C, Coles K. Subpopulation characteristics of egg-contaminating Salmonella enterica serovar Enteritidis as defined by the lipopolysaccharide O chain. Appl Environ Microbiol 2004; 70:2756-63. [PMID: 15128529 PMCID: PMC404386 DOI: 10.1128/aem.70.5.2756-2763.2004] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Characterization of Salmonella enterica serovar Enteritidis was refined by incorporating new data from isolates obtained from avian sources, from the spleens of naturally infected mice, and from the United Kingdom into an existing lipopolysaccharide (LPS) O-chain compositional database. From least to greatest, the probability of avian isolates producing high-molecular-mass LPS O chain ranked as follows: pooled kidney, liver, and spleen; intestine; cecum; ovary and oviduct; albumen; yolk; and whole egg. Mouse isolates were most like avian intestinal samples, whereas United Kingdom isolates were most like those from the avian reproductive tract and egg. Non-reproductive tract organ isolates had significant loss of O chain. Isogenic isolates that varied in ability to make biofilm and to be orally invasive produced different O-chain structures at 25 degrees C but not at 37 degrees C. Hens infected at a 91:9 biofilm-positive/-negative colony phenotype ratio yielded only the negative phenotype from eggs. These results indicate that the environment within the hen applies stringent selection pressure on subpopulations of S. enterica serovar Enteritidis at certain points in the infection pathway that ends in egg contamination. The avian cecum, rather than the intestines, is the early interface between the environment and the host that supports emergence of subpopulation diversity. These results suggest that diet and other factors that alter cecal physiology should be investigated as a means to reduce egg contamination.
Collapse
Affiliation(s)
- Jean Guard-Bouldin
- Southeast Poultry Research Laboratory, Agricultural Research Service, U S Department of Agriculture, Athens, Georgia 30605, USA.
| | | | | | | | | | | |
Collapse
|
10
|
Szczuka E, Kaznowski A. Typing of clinical and environmental Aeromonas sp. strains by random amplified polymorphic DNA PCR, repetitive extragenic palindromic PCR, and enterobacterial repetitive intergenic consensus sequence PCR. J Clin Microbiol 2004; 42:220-8. [PMID: 14715756 PMCID: PMC321687 DOI: 10.1128/jcm.42.1.220-228.2004] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A collection of 120 strains isolated from stool specimens collected from humans suffering from gastroenteritis and from environmental samples were analyzed by random amplified polymorphic DNA PCR (RAPD), repetitive extragenic palindromic PCR (REP-PCR), and enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR). Species of Aeromonoas hydrophila, A. bestiarum, A. salmonicida, A. caviae, A. media, and A. veronii revealed clonal structure. There was no dominant clone causing gastroenteritis in humans. Moreover, there was no genetic similarity between clinical and environmental strains of Aeromonas sp. isolated from different geographical areas as well as from the same geographical area. Some clones colonized specific ecosystems, e.g., drinking water distribution systems. RAPD and ERIC-PCR methods had the same discriminatory power and proved to be useful for epidemiological investigation and population genetic analysis of Aeromonas spp., whereas REP-PCR was less effective for differentiating the isolates of Aeromonas spp.
Collapse
Affiliation(s)
- Ewa Szczuka
- Department of Microbiology, Institute of Experimental Biology, Adam Mickiewicz University, 61-701 Poznań, Poland
| | | |
Collapse
|
11
|
Bakeri SA, Yasin RM, Koh YT, Puthucheary SD, Thong KL. Genetic diversity of human isolates of Salmonella enterica serovar Enteritidis in Malaysia. J Appl Microbiol 2003; 95:773-80. [PMID: 12969291 DOI: 10.1046/j.1365-2672.2003.02033.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS The study was undertaken to determine clonal relationship and genetic diversity of the human strains of Salmonella enterica serovar Enteritidis isolated from 1995 to 2002 from different parts of Malaysia. METHODS AND RESULTS Antimicrobial susceptibility test, plasmid profiling and pulsed-field gel electrophoresis were applied to analyse 65 human isolates of S. Enteritidis obtained over an eight year period from different parts of Malaysia. Four nonhuman isolates were included for comparison. A total of 14 distinct XbaI-pulsed-field profiles (PFPs) were observed, although a single PFP X1 was predominant and this particular clone was found to be endemic in Malaysia. The incidence of drug resistant S. Enteritidis remained relatively low with only 37% of the strains analysed being resistant to one or more antimicrobial agents. All except one resistant strain carried at least one plasmid ranging in size from 3.7 to 62 MDa giving nine plasmid profiles. The three isolates from raw milk and one from well-water had similar PFPs to that of the human isolates. CONCLUSIONS Salmonella Enteritidis strains were more diverse than was previously thought. Fourteen subtypes were noted although one predominant clone persisted in Malaysia. The combination of pulsed-field gel electrophoresis, plasmid profiling and antibiograms provided additional discrimination to the highly clonal strains of S. Enteritidis. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first report to assess the genotypes of the predominant clinical S. Enteritidis in different parts of the country. As S. Enteritidis is highly endemic in Malaysia, the data generated would be useful for tracing the source during outbreaks of gastroenteritis in the study area.
Collapse
Affiliation(s)
- S A Bakeri
- Institute for Postgraduate Studies, University of Malaya, Kuala Lumpur, Malaysia
| | | | | | | | | |
Collapse
|
12
|
Khoodoo MHR, Issack MI, Jaufeerally-Fakim Y. Serotyping and RAPD profiles of Salmonella enterica isolates from Mauritius. Lett Appl Microbiol 2002; 35:146-52. [PMID: 12100591 DOI: 10.1046/j.1472-765x.2002.01151.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS The genus Salmonella is a common agent of gastroenteritis in Mauritius, generating more cases of the disease during summer than during winter. The aims of this study were to assess the genetic diversity of isolates of Salmonella enterica by RAPD fingerprinting, and to establish the relationship between human and chicken isolates. METHODS Twenty-six isolates were obtained from hospital laboratories and commercial poultry producers locally. RESULTS The RAPD profiles, biochemical and serological analyses showed that two of the chicken isolates were mistakenly identified as Salmonella. The genetic diversity of the remaining 24 isolates (five chicken and 19 human), confirmed as Salmonella, was analysed using four arbitrary primers, OPA-10, OPR-03, OPI-06 and OPJ-09, chosen from an initial set of 10 decamers. Seventy RAPD markers were generated in four individual DNA profiles. SIGNIFICANCE AND IMPACT OF THE STUDY Cluster analysis (UPGMA) performed using the NTSYS-pc V 1.8 computer software, confirmed that some strains of Salmonella isolated from chicken were genetically similar to those isolated from humans. Furthermore, a 1 kbp band amplified using primer OPA-10 was specific for the Salmonella genus as it was not amplified in any of the control bacteria.
Collapse
Affiliation(s)
- M H R Khoodoo
- Faculty of Agriculture, University of Mauritius, Réduit, Mauritius.
| | | | | |
Collapse
|
13
|
Liebana E, Crowley CJ, Garcia-Migura L, Breslin MF, Corry JEL, Allen VM, Davies RH. Use of molecular fingerprinting to assist the understanding of the epidemiology of Salmonella contamination within broiler production. Br Poult Sci 2002; 43:38-46. [PMID: 12003336 DOI: 10.1080/00071660120109872] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
1. We analysed Salmonella isolates by conventional sero- and phage-typing, as well as by molecular techniques within the broiler production chain in two integrated companies. The most prevalent serovars were selected for genetic fingerprinting. 2. Isolates were first screened by plasmid profiling; subsequently, the most common plasmid types within the prevalent zoonotic serovars (enteritidis and typhimurium) and S. agama were further characterised by PstI-SphI ribotyping, and XbaI pulsed field gel electrophoresis (PFGE). 3. Salmonella binza, S. kedougou, and S. 4,12:d:- were endemic in the feed mills over long periods of time, and a variety of plasmid types for each of the serovars were found in the premises. 4. A similar situation was found with S. binza and S. senftenberg within the hatchery in company B. The Salmonella serovars which were resident in those locations were also the ones most widely distributed throughout the broiler flocks. 5. Plasmid profiling was useful to subdivide clusters of isolates within serovars, but for each serovar a high percentage (36 to 79%) of the isolates tested fall within a prevalent plasmid type. 6. A more detailed genetic analysis of the isolates by a multiple typing approach allowed for further strain differentiation, and allowed some epidemiological conclusions to be drawn.
Collapse
Affiliation(s)
- E Liebana
- Department of Bacterial Diseases, Veterinary Laboratories Agency-Weybridge, Addlestone, Surrey, England, UK.
| | | | | | | | | | | | | |
Collapse
|
14
|
Liebana E, Garcia-Migura L, Breslin MF, Davies RH, Woodward MJ. Diversity of strains of Salmonella enterica serotype enteritidis from English poultry farms assessed by multiple genetic fingerprinting. J Clin Microbiol 2001; 39:154-61. [PMID: 11136764 PMCID: PMC87695 DOI: 10.1128/jcm.39.1.154-161.2001] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Reliable and sufficiently discriminative methods are needed for differentiating individual strains of Salmonella enterica serotype Enteritidis beyond the phenotypic level; however, a consensus has not been reached as to which molecular method is best suited for this purpose. In addition, data are lacking on the molecular fingerprinting of serotype Enteritidis from poultry environments in the United Kingdom. This study evaluated the combined use of classical methods (phage typing) with three well-established molecular methods (ribotyping, macrorestriction analysis of genomic DNA, and plasmid profiling) in the assessment of diversity within 104 isolates of serotype Enteritidis from eight unaffiliated poultry farms in England. The most sensitive technique for identifying polymorphism was PstI-SphI ribotyping, distinguishing a total of 22 patterns, 10 of which were found among phage type 4 isolates. Pulsed-field gel electrophoresis of XbaI-digested genomic DNA segregated the isolates into only six types with minor differences between them. In addition, 14 plasmid profiles were found among this population. When all of the typing methods were combined, 54 types of strains were differentiated, and most of the poultry farms presented a variety of strains, which suggests that serotype Enteritidis organisms representing different genomic groups are circulating in England. In conclusion, geographical and animal origins of Salmonella serotype Enteritidis isolates may have a considerable influence on selecting the best typing strategy for individual programs, and a single method cannot be relied on for discriminating between strains.
Collapse
Affiliation(s)
- E Liebana
- Department of Bacterial Diseases, Veterinary Laboratories Agency-Weybridge, Addlestone, Surrey KT15 3NB, United Kingdom.
| | | | | | | | | |
Collapse
|
15
|
Millemann Y, Gaubert S, Remy D, Colmin C. Evaluation of IS200-PCR and comparison with other molecular markers To trace Salmonella enterica subsp. enterica serotype typhimurium bovine isolates from farm to meat. J Clin Microbiol 2000; 38:2204-9. [PMID: 10834977 PMCID: PMC86765 DOI: 10.1128/jcm.38.6.2204-2209.2000] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/1999] [Accepted: 03/25/2000] [Indexed: 11/20/2022] Open
Abstract
A procedure that uses an original molecular marker (IS200-PCR) and that is based on the amplification of DNA with outward-facing primers complementary to each end of IS200 has been evaluated with a collection of 85 Salmonella enterica subsp. enterica serotype Typhimurium isolates. These strains were isolated from a group of 10 cows at different stages: during transportation between the farm and the slaughterhouse, on the slaughter line, from the environment, and from the final product (ground beef). The 85 isolates were characterized by their antibiotic resistance patterns and were compared by IS200-PCR and by use of four other genotypic markers. Those markers included restriction profiles for 16S and 23S rRNA (ribotypes) and amplification profiles obtained by different approaches: random amplified polymorphic DNA analysis, enterobacterial repetitive intergenic consensus PCR, and PCR ribotyping. The results of the IS200-PCR were in accordance with those of other molecular typing methods for this collection of isolates. Five different genotypes were found, which made it possible to refine the hypotheses on transmission obtained from phenotypic results. The genotyping results indicated the massive contamination of the whole group of animals and of the environment by one clonal strain originally recovered from one cow that excreted the strain. On the other hand, a few animals and their environment appeared to be simultaneously contaminated with genetically different strains.
Collapse
Affiliation(s)
- Y Millemann
- Epidémiologie et Analyse des Risques, Ecole Nationale Vétérinaire d'Alfort, F-94704 Maisons-Alfort Cedex, France.
| | | | | | | |
Collapse
|
16
|
Ahmed R, Soule G, Demczuk WH, Clark C, Khakhria R, Ratnam S, Marshall S, Ng LK, Woodward DL, Johnson WM, Rodgers FG. Epidemiologic typing of Salmonella enterica serotype enteritidis in a Canada-wide outbreak of gastroenteritis due to contaminated cheese. J Clin Microbiol 2000; 38:2403-6. [PMID: 10835016 PMCID: PMC86822 DOI: 10.1128/jcm.38.6.2403-2406.2000] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A major Canada-wide outbreak of gastroenteritis due to Salmonella enterica serotype Enteritidis phage type (PT) 8 occurred in 1998, and this was traced to contaminated cheese in a commercial lunch pack product. Phage typing and pulsed-field gel electrophoresis linked the clinical and cheese isolates of serotype Enteritidis but failed to differentiate outbreak from nonoutbreak PT 8 strains. Further differentiation was made by biotyping based on melibiose fermentation.
Collapse
Affiliation(s)
- R Ahmed
- National Laboratory for Enteric Pathogens, Bureau of Microbiology, Laboratory Centre for Disease Control, Winnipeg, Manitoba R3E 3R2, St. John's, Newfoundland, Canada. Rafiq_Ahmed@hc.,sc.gc.ca
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Rajashekara G, Haverly E, Halvorson DA, Ferris KE, Lauer DC, Nagaraja KV. Multidrug-resistant Salmonella Typhimurium DT104 in poultry. J Food Prot 2000; 63:155-61. [PMID: 10678417 DOI: 10.4315/0362-028x-63.2.155] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Salmonella Typhimurium isolates from feed ingredients or poultry sources isolated during 1995 to 1997 from different geographical locations within Minnesota were examined for the presence of Salmonella Typhimurium definitive type 104 (DT104). Antibiotic susceptibility studies indicated that 15 of 50 isolates of Salmonella Typhimurium had an antibiotic resistance pattern (ampicillin, chloramphenicol, streptomycin, sulfonamides, and tetracycline) that is usually observed with multidrug-resistant Salmonella Typhimurium DT104. Of the 15 isolates showing the antibiotic resistance pattern, 8 isolates were phage type 104, 3 isolates were typed as phage type 104 complex, and the remaining 4 isolates belonged to phage types 193, 81, and 126. DT104 was recovered from both feed ingredients and poultry samples. Of the seven feed ingredient-associated Salmonella Typhimurium isolates, four were DT104, whereas only 7 of 43 poultry-associated Salmonella Typhimurium isolates were DT104. A repetitive sequence-based polymerase chain reaction (rep-PCR) of 50 isolates of Salmonella Typhimurium representing 13 phage types identified seven distinct fingerprint profiles. No correlation between phage type and rep-PCR type was noticed. Eleven Salmonella Typhimurium isolates belonging to DT104 and its complex were grouped into two closely related rep-PCR types.
Collapse
Affiliation(s)
- G Rajashekara
- Department of Veterinary PathoBiology, College of Veterinary Medicine, University of Minnesota, St. Paul, USA
| | | | | | | | | | | |
Collapse
|