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Han SH, Kim JH, Na J, Yoo JG, Oh MH. Genotypic Classification of Staphylococcus aureus and Bacillus cereus from Korean Slaughterhouses Using Semiautomated Repetitive Sequence-Based Polymerase Chain Reaction. Foodborne Pathog Dis 2019; 16:769-777. [PMID: 31335181 DOI: 10.1089/fpd.2019.2619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A repetitive sequence-based polymerase chain reaction (rep-PCR) technique utilizing a semiautomated system, namely DiversiLab, was applied to determine the genotypes of Staphylococcus aureus and Bacillus cereus obtained from slaughterhouses. Twenty-four S. aureus and 16 B. cereus isolates from pigs and Hanwoo cattle from three slaughterhouses were used to create a DNA fingerprint library with the system software. Scatterplots demonstrated that rep-PCR groupings of S. aureus isolates were in good agreement with their origins. Specifically, linked rep-PCR profiles were observed for S. aureus isolates recovered from the same slaughterhouse, and higher genetic similarities were found among strains isolated from adjacent regions. All S. aureus isolates except one (ID: A-Hanwoo-9) from slaughterhouse "A" clustered with the three S. aureus reference strains, Korea Culture Center of Microorganisms (KCCM) 41291, KCCM 12214, and Culture Collection of Antimicrobial Resistant Microbes (CCARM) 3A007 (similarity values >95%). Moreover, most isolates obtained from slaughterhouse "B" clustered with S. aureus KCCM 11335 and KCCM 41331, and two isolates from slaughterhouse "C" clustered with CCARM 0027. Therefore, for this species, genotypic characteristics of regional isolates can be used to track the pathway of contamination. In contrast, B. cereus isolates showed high genetic diversity and could not be clustered with any specific group. Collectively, this system is useful for analyzing genetic diversity and is a rapid and reproducible typing method; however, there is a need to develop rep-PCR libraries for its use as a rapid identification method.
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Affiliation(s)
- Sang-Ha Han
- National Institute of Animal Science, Rural Development Administration, Wanju-gun, Korea.,Advanced Food Safety Research Group, BrainKorea21 Plus, Department of Food Science and Technology, Chung-Aug University, Seoul, Korea
| | - Jong-Hui Kim
- National Institute of Animal Science, Rural Development Administration, Wanju-gun, Korea
| | - Jeongkyeong Na
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, Korea
| | - Jae Gyu Yoo
- National Institute of Animal Science, Rural Development Administration, Wanju-gun, Korea
| | - Mi-Hwa Oh
- National Institute of Animal Science, Rural Development Administration, Wanju-gun, Korea
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Tang S, Orsi RH, Luo H, Ge C, Zhang G, Baker RC, Stevenson A, Wiedmann M. Assessment and Comparison of Molecular Subtyping and Characterization Methods for Salmonella. Front Microbiol 2019; 10:1591. [PMID: 31354679 PMCID: PMC6639432 DOI: 10.3389/fmicb.2019.01591] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/26/2019] [Indexed: 01/26/2023] Open
Abstract
The food industry is facing a major transition regarding methods for confirmation, characterization, and subtyping of Salmonella. Whole-genome sequencing (WGS) is rapidly becoming both the method of choice and the gold standard for Salmonella subtyping; however, routine use of WGS by the food industry is often not feasible due to cost constraints or the need for rapid results. To facilitate selection of subtyping methods by the food industry, we present: (i) a comparison between classical serotyping and selected widely used molecular-based subtyping methods including pulsed-field gel electrophoresis, multilocus sequence typing, and WGS (including WGS-based serovar prediction) and (ii) a scoring system to evaluate and compare Salmonella subtyping assays. This literature-based assessment supports the superior discriminatory power of WGS for source tracking and root cause elimination in food safety incident; however, circumstances in which use of other subtyping methods may be warranted were also identified. This review provides practical guidance for the food industry and presents a starting point for further comparative evaluation of Salmonella characterization and subtyping methods.
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Affiliation(s)
- Silin Tang
- Mars Global Food Safety Center, Beijing, China
| | - Renato H. Orsi
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States
| | - Hao Luo
- Mars Global Food Safety Center, Beijing, China
| | - Chongtao Ge
- Mars Global Food Safety Center, Beijing, China
| | | | | | | | - Martin Wiedmann
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States
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Kashiwaya K, Saga T, Ishii Y, Sakata R, Iwata M, Yoshizawa S, Chang B, Ohnishi M, Tateda K. Worldwide Lineages of Clinical Pneumococci in a Japanese Teaching Hospital Identified by DiversiLab System. J Infect Chemother 2016; 22:407-13. [PMID: 27107736 DOI: 10.1016/j.jiac.2016.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/11/2016] [Accepted: 03/16/2016] [Indexed: 11/19/2022]
Abstract
Pneumococcal Molecular Epidemiology Network (PMEN) clones are representatives of worldwide-spreading pathogens. DiversiLab system, a repetitive PCR system, has been proposed as a less labor-and time-intensive genotyping platform alternative to conventional methods. However, the utility and analysis parameters of DiversiLab for identifying worldwide lineages was not established. To evaluate and optimize the performance of DiversiLab for identifying worldwide pneumococcal lineages, we examined 245 consecutive isolates of clinical Streptococcus pneumoniae from all age-group patients at a teaching hospital in Japan. The capsular swelling reaction of all isolates yielded 24 different serotypes. Intensive visual observation (VO) of DiversiLab band pattern difference divided all isolates into 73 clusters. Multilocus sequence typing (MLST) of representative 73 isolates from each VO cluster yielded 51 different STs. Among them, PMEN-related lineages accounted for 63% (46/73). Although the serotype of PMEN-related isolates was identical to that of the original PMEN clone in 70% (32/46), CC156-related PMEN lineages, namely Greece(6B)-22 and Colombia(23F)-26, harbored various capsular types discordant to the original PMEN clones. Regarding automated analysis, genotyping by extended Jaccard (XJ) with a 75% similarity index cutoff (SIC) showed the highest correlation with serotyping (adjusted Rand's coefficient, 0.528). Elevating the SIC for XJ to 85% increased the discriminatory power sufficient for distinguishing two major PMEN-related isolates of Taiwan(19F)-14 and Netherlands(3)-31. These results demonstrated a potential utility of DiversiLab for identifying worldwide lineage of pneumococcus. An optimized parameters of automated analysis should be useful especially for comparison for reference strains by "identification" function of DiversiLab.
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Affiliation(s)
- Kiyoshi Kashiwaya
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan; Department of Clinical Laboratory, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Tomoo Saga
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan; Central Laboratory Division, Akita University Hospital, Akita, Japan.
| | - Yoshikazu Ishii
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Ryuji Sakata
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Morihiro Iwata
- Clinical Laboratory Department, Toho University Omori Medical Center, Tokyo, Japan
| | - Sadako Yoshizawa
- Division of Infection Control, Toho University Omori Medical Center, Tokyo, Japan
| | - Bin Chang
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazuhiro Tateda
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan; Clinical Laboratory Department, Toho University Omori Medical Center, Tokyo, Japan; Division of Infection Control, Toho University Omori Medical Center, Tokyo, Japan
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Development and Evaluation of a Loop-Mediated Isothermal Amplification Method for Rapid Detection of Aspergillus fumigatus. J Clin Microbiol 2016; 54:950-5. [PMID: 26791368 DOI: 10.1128/jcm.01751-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 01/03/2016] [Indexed: 01/04/2023] Open
Abstract
Aspergillus fumigatusis a conditional pathogen and the major cause of life-threatening invasive aspergillosis (IA) in immunocompromised patients. The early and rapid detection ofA. fumigatusinfection is still a major challenge. In this study, the new member of the fungal annexin family, annexin C4, was chosen as the target to design a loop-mediated isothermal amplification (LAMP) assay for the rapid, specific, and sensitive detection ofA. fumigatus The evaluation of the specificity of the LAMP assay that was developed showed that no false-positive results were observed for the 22 non-A. fumigatusstrains, including 5 species of theAspergillusgenus. Its detection limit was approximately 10 copies per reaction in reference plasmids, with higher sensitivity than that of real-time quantitative PCR (qPCR) at 10(2)copies for the same target. Clinical samples from a total of 69 patients with probable IA (n =14) and possible IA (n= 55) were subjected to the LAMP assay, and positive results were found for the 14 patients with probable IA (100%) and 34 patients with possible IA (61.82%). When detection using the LAMP assay was compared with that using qPCR in the 69 clinical samples, the LAMP assay demonstrated a sensitivity of 89.19% and the concordance rate for the two methods was 72.46%. Accordingly, we report that a valuable LAMP assay for the rapid, specific, and simple detection ofA. fumigatusin clinical testing has been developed.
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Momeni SS, Whiddon J, Cheon K, Moser SA, Childers NK. Assessment of clonality and serotypes of Streptococcus mutans among children by multilocus sequence typing. Eur J Oral Sci 2015; 123:416-24. [PMID: 26443288 DOI: 10.1111/eos.12221] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2015] [Indexed: 11/29/2022]
Abstract
Studies using multilocus sequence typing (MLST) have demonstrated that Streptococcus mutans isolates are genetically diverse. Our laboratory previously demonstrated clonality of S. mutans using MLST but could not discount the possibility of sampling bias. In this study, the clonality of randomly selected S. mutans plaque isolates from African-American children was examined using MLST. Serotype and the presence of collagen-binding proteins (CBPs) encoded by cnm/cbm were also assessed. One-hundred S. mutans isolates were randomly selected for MLST analysis. Sequence analysis was performed and phylogenetic trees were generated using start2 and mega. Thirty-four sequence types were identified, of which 27 were unique to this population. Seventy-five per cent of the isolates clustered into 16 clonal groups. The serotypes observed were c (n = 84), e (n = 3), and k (n = 11). The prevalence of S. mutans isolates of serotype k was notably high, at 17.5%. All isolates were cnm/cbm negative. The clonality of S. mutans demonstrated in this study illustrates the importance of localized population studies and are consistent with transmission. The prevalence of serotype k, a recently proposed systemic pathogen, observed in this study, is higher than reported in most populations and is the first report of S. mutans serotype k in a United States population.
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Affiliation(s)
- Stephanie S Momeni
- Department of Biology, College of Arts and Sciences, University of Alabama at Birmingham, Birmingham, AL, USA.,Department of Pediatric Dentistry, School of Dentistry, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jennifer Whiddon
- Department of Pathology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kyounga Cheon
- Department of Pediatric Dentistry, School of Dentistry, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Stephen A Moser
- Department of Pathology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Noel K Childers
- Department of Pediatric Dentistry, School of Dentistry, University of Alabama at Birmingham, Birmingham, AL, USA
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Anderson KM, Abbott J, Zhao S, Liu E, Himathongkham S. Molecular Subtyping of Shiga Toxin-Producing Escherichia coli Using a Commercial Repetitive Sequence-Based PCR Assay. J Food Prot 2015; 78:902-11. [PMID: 25951383 DOI: 10.4315/0362-028x.jfp-14-430] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
PCR-based typing methods, such as repetitive sequence-based PCR (rep-PCR), may facilitate the identification of Shiga toxin-producing Escherichia coli (STEC) by serving as screening methods to reduce the number of isolates to be processed for further confirmation. In this study, we used a commercial rep-PCR typing system to generate DNA fingerprint profiles for STEC O157 (n = 60) and non-O157 (n = 91) isolates from human, food, and animal samples and then compared the results with those obtained from pulsed-field gel electrophoresis (PFGE). Fifteen serogroups were analyzed using the Kullback Leibler or extended Jaccard statistical method, and the unweighted pair group method of averages algorithm was used to create dendrograms. Among the 151 STEC isolates tested, all were typeable by rep-PCR. Among the non-O157 isolates, rep-PCR clustered 79 (88.8%) of 89 isolates according to serogroup status, with peak differences ranging from 1 (96.4% similarity) to 12 (58.7% similarity). The genetic relatedness of the non-O157 serogroups mirrored the branching of distinct clonal groups elucidated by other investigators. Although the discriminatory power of rep-PCR (Simpson's index of diversity [SID] = 0.954) for the O157 isolates was less than that of PFGE (SID = 0.993), rep-PCR was able to identify 29 pattern types, suggesting that this method can be used for strain typing, although not to the same level as PFGE. Similar results were obtained from analysis of the non-O157 isolates. With rep-PCR, we assigned non-O157 isolates to 46 pattern types with a SID of 0.977. By PFGE, non-O157 STEC strains were divided into 77 pattern types with a SID of 0.996. Together, these results indicate the ability of the rep-PCR typing system to distinguish between and within O157 and non-O157 STEC groups. Rapid PCR-based typing methods could be invaluable tools for use in outbreak investigations by excluding unrelated STEC isolates within 24 h.
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Affiliation(s)
- Kimberly M Anderson
- U.S. Food and Drug Administration, Office of Regulatory Affairs, San Francisco District Laboratory, Alameda, California 94502, USA.
| | - Jason Abbott
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Laurel, Maryland 20708, USA
| | - Shaohua Zhao
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Laurel, Maryland 20708, USA
| | - Eileen Liu
- U.S. Food and Drug Administration, Office of Regulatory Affairs, San Francisco District Laboratory, Alameda, California 94502, USA
| | - Sunee Himathongkham
- U.S. Food and Drug Administration, Office of Regulatory Affairs, Office of Regulatory Science, Rockville, Maryland 20857, USA
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Charnock C, Nordlie AL, Hjeltnes B. Toxin production and antibiotic resistances in Escherichia coli isolated from bathing areas along the coastline of the Oslo fjord. Curr Microbiol 2014; 69:317-28. [PMID: 24801333 DOI: 10.1007/s00284-014-0587-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 03/01/2014] [Indexed: 01/24/2023]
Abstract
The presence of enterovirulent and/or antibiotic resistant strains of Escherichia coli in recreational bathing waters would represent a clear health issue. In total, 144 E. coli isolated from 26 beaches along the inner Oslo fjord were examined for virulence determinants and resistance to clinically important antibiotics. No isolates possessed the genetic determinants associated with enterotoxigenic strains and none showed the prototypic sorbitol negative, O157:H7 phenotype. A small number (∼1 %) produced alpha-hemolysin. Occurrences and patterns of antibiotic resistances were similar to those of E. coli isolated previously from environmental samples. In total, 6 % of the strains showed one or more clinically relevant resistances and 1.4 % were multi-drug resistant. Microarray analyses suggested that the resistance determinants were generally associated with mobile genetic elements. Resistant strains were not clonally related, and were, furthermore not concentrated at one or a few beach sites. This suggests that these strains are entering the waters at a low rate but in a widespread manner. The study demonstrates that resistant E. coli are present in coastal bathing waters where they can come into contact with bathers, and that the resistance determinants are potentially transferable. Some of the resistances registered in the study are to important antibiotics used in human medicine such as fluoroquinolones. The spread of antibiotic resistant genes, from the clinical setting to the environment, has clear implications with respect to the current management of bacterial infections and the long term value of antimicrobial therapy. The present study is the first of its kind in Norway.
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Affiliation(s)
- Colin Charnock
- Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, St. Olavs Plass, Oslo, Norway,
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Morimoto N, Takeuchi H, Nishida Y, Morisawa M, Yoshikawa T, Morita T, Morimoto M, Sugimoto C, Matsumura Y, Sugiura T. Clinical Application of the DiversiLab Microbial Typing System Using Repetitive Sequence-Based PCR for Characterization of Helicobacter pylori in Japan. J Clin Lab Anal 2014; 29:250-3. [PMID: 24796534 DOI: 10.1002/jcla.21758] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Accepted: 03/03/2014] [Indexed: 12/15/2022] Open
Abstract
We evaluated the DiversiLab (DL) system with universal primers, a semiautomated repetitive extragenic palindromic sequence-based polymerase chain reaction (PCR) (rep-PCR) system, for the characterization of Helicobacter pylori in Japan. All 135 isolates from Japanese patients with gastric cancer (GC, n = 55) or non-GC (n = 80) were used and subjected to the drug susceptibility examinations (amoxicillin, AMPC; metronidazole, MNZ; and clarithromycin, CAM) by E-test. There were 28 MNZ-resistant (20.7%), 35 CAM-resistant (25.9%), and 16 MNZ/CAM-resistant (11.9%) isolates. DL rep-PCR fingerprinting analysis at the level of 95% similarity revealed five major groups (A-E) and the other including 45 isolates. The occupation rates of GC-derived isolates in groups B (54.2%) and E (58.8%) were higher than in the other groups: A (26.7%), C (28.6%), D (30.0%), and the other (40.0%). Relative higher occupation rates of drug resistants, such as MNZ-, CAM- and double MNZ/CAM-resistant isolates, were observed in groups B (45.8%), C (42.6%), and D (40%). Five of eight GC-derived isolates with MNZ/CAM resistance were significantly assigned to group B (P = 0.0312, χ(2) -test). These results suggest that the isolates classified in group B have a potential to contribute to the development of severe gastric disorders. The DL system, rapid and high sensitive technology, would be widely available in clinical laboratory for pathological and epidemiological analyses even in H. pylori.
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Affiliation(s)
- Norihito Morimoto
- Department of Clinical Laboratory, Kochi Medical School Hospital, Kochi University, Kohasu, Oko-cho, Nankoku, Kochi, Japan
| | - Hiroaki Takeuchi
- Clinical Laboratory Medicine, Kochi University School of Medicine, Kochi, Japan
| | - Yoshie Nishida
- Department of Clinical Laboratory, Kochi Medical School Hospital, Kochi University, Kohasu, Oko-cho, Nankoku, Kochi, Japan.,Clinical Laboratory Medicine, Kochi University School of Medicine, Kochi, Japan
| | - Mie Morisawa
- Department of Clinical Laboratory, Kochi Medical School Hospital, Kochi University, Kohasu, Oko-cho, Nankoku, Kochi, Japan
| | - Tomoe Yoshikawa
- Department of Clinical Laboratory, Kochi Medical School Hospital, Kochi University, Kohasu, Oko-cho, Nankoku, Kochi, Japan
| | - Tamae Morita
- Department of Clinical Laboratory, Kochi Medical School Hospital, Kochi University, Kohasu, Oko-cho, Nankoku, Kochi, Japan
| | - Miyuki Morimoto
- Department of Clinical Laboratory, Kochi Medical School Hospital, Kochi University, Kohasu, Oko-cho, Nankoku, Kochi, Japan
| | - Chizuko Sugimoto
- Clinical Laboratory Medicine, Kochi University School of Medicine, Kochi, Japan
| | - Yoshihisa Matsumura
- Clinical Laboratory Medicine, Kochi University School of Medicine, Kochi, Japan
| | - Tetsuro Sugiura
- Department of Clinical Laboratory, Kochi Medical School Hospital, Kochi University, Kohasu, Oko-cho, Nankoku, Kochi, Japan.,Clinical Laboratory Medicine, Kochi University School of Medicine, Kochi, Japan
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Zając M, Hoszowski A, Wasyl D. Identification of common, non-typable and autoagglutinating Salmonella strains with Premi®Test Salmonella assay. Acta Vet Hung 2013; 61:425-31. [PMID: 23974934 DOI: 10.1556/avet.2013.028] [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: 11/19/2022]
Abstract
Since Salmonella serotyping according to the White-Kauffmann-Le Minor scheme fails to identify rough and atypical serological variants, this study aimed at improving serovar identification with the commercially available Premi®Test Salmonella Assay. The array was validated against a set of Salmonella reference strains (n = 27) and field isolates of known serological structure (n = 112) showing up to 97.8% congruent results. Its diagnostic suitability was further verified with random field isolates (n = 52; 100% congruence). For 'rough' isolates (n = 54) and those with antigen expression failure (n = 19) the assay showed, respectively, 98.1% and 73.7% of serovar recognition. It considerably improved diagnostic capacity while typing troublesome isolates such as those failing to express flagellar antigens or showing autoagglutination. The method offers lower labour time compared to the traditional serotyping and does not require a broad range of diagnostic sera.
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Affiliation(s)
- Magdalena Zając
- 1 National Veterinary Research Institute Department of Microbiology, National Reference Laboratory for Salmonellosis Partyzantów 57 24-100 Puławy Poland
| | - Andrzej Hoszowski
- 1 National Veterinary Research Institute Department of Microbiology, National Reference Laboratory for Salmonellosis Partyzantów 57 24-100 Puławy Poland
| | - Dariusz Wasyl
- 1 National Veterinary Research Institute Department of Microbiology, National Reference Laboratory for Salmonellosis Partyzantów 57 24-100 Puławy Poland
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Hyeon JY, Chon JW, Park JH, Kim MS, Oh YH, Choi IS, Seo KH. A Comparison of Subtyping Methods for Differentiating Salmonella enterica Serovar Enteritidis Isolates Obtained from Food and Human Sources. Osong Public Health Res Perspect 2013; 4:27-33. [PMID: 24159526 PMCID: PMC3747678 DOI: 10.1016/j.phrp.2012.12.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 12/15/2012] [Accepted: 12/19/2012] [Indexed: 11/14/2022] Open
Abstract
Purpose: To evaluate the abilities of these subtyping methods, we distinguished Salmonella Enteritidis (S. Enteritidis) isolated from food products and human clinical samples between 2009 and 2010 in Seoul using five subtyping methods. Methods: We determined the subtypes of 20 S. Enteritidis isolates from food and human sources using phage typing, antimicrobial susceptibility, pulsed-field gel electrophoresis (PFGE), repetitive sequence-based PCR (rep-PCR), and multi-locus sequence typing (MLST). Results: A total of 20 tested isolates were differentiated into six antimicrobial susceptibility patterns, three different phage types, four different PFGE profiles, seven rep-PCR patterns, and one MLST type. Food isolates were considerably more susceptible to antibiotics than human isolates. We were best able to discriminate among S. Enteritidis isolates using rep-PCR, and obtained the highest Simpson’s diversity index of 0.82, whereas other methods produced indices that were less than 0.71. PFGE pattern appeared to be more related to antimicrobial resistance and phage types of S. Enteritidis isolates than rep-PCR. MLST revealed identical alleles in all isolates at all seven loci examined, indicating no resolution. Conclusion: The results of this study suggest that rep-PCR provided the best discriminatory power for phenotypically similar S. Enteritidis isolates of food and human origins, whereas the discriminatory ability of MLST may be problematic because of the high sequence conservation of the targeted genes.
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Affiliation(s)
- Ji-Yeon Hyeon
- College of Veterinary Medicine, Konkuk University, Seoul, Korea . ; Division of Vaccine Research, Korea National Institute of Health, Osong, Korea
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Denis M, Houard E, Fablet A, Rouxel S, Salvat G. Distribution of serotypes and genotypes of Salmonella enterica species in French pig production. Vet Rec 2013; 173:370. [PMID: 24106251 DOI: 10.1136/vr.101901] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
The population of Salmonella found at various stages of pig production in France was characterised to analyse the distribution and spread of Salmonella in the pig production chain. We serotyped and genotyped by PFGE 174 isolates collected from breeding pigs from breeding farms, 163 collected from breeding pigs from production farms, and 325 collected from fattening pigs. Forty-seven serovars and 110 genotypes were identified. The major serovars were S Derby (263 isolates) and S Typhimurium (162 isolates). The percentage of S Derby isolates decreased slightly through the production system (44.3, 41.1 per cent and 36.5 per cent) and 79.1 per cent of the S Derby isolates were distributed in the five genotypes common to all three stages. The percentage of S Typhimurium isolates was high for slaughter pigs (40.8 per cent) and 43 of the 46 S Typhimurium genotypes were only identified at this stage. Distributions of S Derby and S Typhimurium between breeding and fattening pigs were different. S Derby was found throughout the pig production pyramid, suggesting that this serotype may be transmitted by the transfer of animals between herds. The presence of multiple S Typhimurium genotypes in fattening pigs suggests that there were many sources of contamination at this stage, with fattening pigs having higher levels of exposure and/or sensitivity to this serotype.
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Affiliation(s)
- M Denis
- Hygiene and Quality of Poultry and Pig Products Unit, ANSES, BP53, site des Croix, Ploufragan 22440, France
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Lukinmaa-Åberg S, Horsma J, Pasanen T, Mero S, Aulu L, Vaara M, Siitonen A, Antikainen J. Applicability of DiversiLab repetitive sequence-based PCR method in epidemiological typing of enterohemorrhagic Escherichia coli (EHEC). Foodborne Pathog Dis 2013; 10:632-8. [PMID: 23692078 DOI: 10.1089/fpd.2012.1411] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) causes diarrhea, often with severe complications. Rapid and discriminatory typing of EHEC using advanced molecular methods is needed for determination of the genetic relatedness of clones responsible for foodborne outbreaks and for finding out the transmission sources of the outbreaks. This study evaluated the potential of DiversiLab, a semiautomated repetitive sequence-based polymerase chain reaction method for the genotyping of EHEC strains. A set of 52 EHEC strains belonging to 15 O:H serotypes was clustered into 10 DiversiLab groups. All of the O157 strains and one O55 strain were classified into the same group based on a 90% similarity threshold. The other serotypes were classified to their own DiversiLab group, with the exception of one R:H(-) strain that was grouped with O5:H(-) strains. In addition, O26 and O111 strains were grouped together but ultimately subdivided according to their O-serotypes based on a 95% similarity threshold. The O104 strain, which was associated with a major outbreak of hemolytic uremic syndrome in Germany in May 2011, was also classified independently. The DiversiLab performed well in identifying isolates, but the discriminatory power of the repetitive sequence-based polymerase chain reaction method was lower than that of pulsed-field gel electrophoresis. Analysis of 15 enteropathogenic E. coli (EPEC) strains revealed that some EPEC strains clustered together with EHEC strains. Therefore, the DiversiLab system cannot be used to discriminate between these pathogroups. In conclusion, DiversiLab is a rapid and easy system for the primary exclusion of unrelated EHEC strains based on their serotypes, but more discriminatory methods, such as pulsed-field gel electrophoresis, are needed for accurate typing of the EHEC strains.
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Affiliation(s)
- Susanna Lukinmaa-Åberg
- Bacteriology Unit, Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare THL, Helsinki, Finland
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Momeni SS, Whiddon J, Moser SA, Cheon K, Ruby JD, Childers NK. Comparative genotyping of Streptococcus mutans by repetitive extragenic palindromic polymerase chain reaction and multilocus sequence typing. Mol Oral Microbiol 2012. [PMID: 23194334 DOI: 10.1111/omi.12002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The genetic diversity of Streptococcus mutans has been extensively studied using a variety of genotyping methods. Repetitive extragenic palindromic-polymerase chain reaction (rep-PCR) is a genotyping approach used for screening large numbers of bacterial isolates. This two-part study used multilocus sequence typing (MLST) analysis to evaluate genotypes previously identified as unique using rep-PCR. In part one, an isolate was selected from each of the 22 S. mutans rep-PCR genotype groups representing 8000 clinical isolates. For part two, four additional isolates were selected from the six most commonly occurring genotype groups (GG) for further analysis. Real-time PCR was performed using eight housekeeping S. mutans gene loci and the amplicons were sequenced. Sequence data analysis was performed using CLC DNA Workbench and alleles were compared with the PubMLST database for Oral Streptococcus using the Nakano scheme. Concatenated sequences were evaluated with MEGA using a minimum evolution method with bootstrap. All 22 rep-PCR genotypes were unique by MLST analysis. Within rep-PCR GGs, MLST matched rep-PCR in three groups demonstrating clonality; three groups exhibited more diversity with MLST. The discovery of three clonal groups is unique to this study and suggests that S. mutans genotypes are shared between unrelated subjects. Furthermore, MLST defined 19 new alleles and 26 new sequence types that have been confirmed and registered with PubMLST. Methods for processing were streamlined and a process for using MLST with rep-PCR is suggested. In conclusion, MLST verified that rep-PCR is a reliable and cost-effective method for screening large numbers of S. mutans strains for epidemiological study.
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Affiliation(s)
- S S Momeni
- Department of Pediatric Dentistry, University of Alabama School of Dentistry, Birmingham, AL, USA
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Tewari D, Sandt CH, Miller DM, Jayarao BM, M'ikanatha NM. Prevalence of Salmonella Cerro in Laboratory-Based Submissions of Cattle and Comparison with Human Infections in Pennsylvania, 2005–2010. Foodborne Pathog Dis 2012; 9:928-33. [DOI: 10.1089/fpd.2012.1142] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Deepanker Tewari
- Pennsylvania Veterinary Laboratory, Pennsylvania Department of Agriculture, Harrisburg, Pennsylvania
| | - Carol H. Sandt
- Bureau of Laboratories, Pennsylvania Department of Health, Exton, Pennsylvania
| | - Dawn M. Miller
- Pennsylvania Veterinary Laboratory, Pennsylvania Department of Agriculture, Harrisburg, Pennsylvania
| | - Bhushan M. Jayarao
- Department of Veterinary Biomedical Sciences, Penn State, University Park, Pennsylvania
| | - Nkuchia M. M'ikanatha
- Division of Infectious Disease Epidemiology, Pennsylvania Department of Health, Harrisburg, Pennsylvania
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Molecular epidemiology of Acinetobacter baumannii bloodstream isolates obtained in the United States from 1995 to 2004 using rep-PCR and multilocus sequence typing. J Clin Microbiol 2012; 50:3493-500. [PMID: 22895032 DOI: 10.1128/jcm.01759-12] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Using a repetitive-sequence-based (rep)-PCR (DiversiLab), we have molecularly typed Acinetobacter nosocomial bloodstream isolates (Acinetobacter baumannii [n = 187], Acinetobacter pittii [n = 23], and Acinetobacter nosocomialis [n = 61]) obtained from patients hospitalized in U.S. hospitals over a 10-year period (1995-2004) during a nationwide surveillance study (Surveillance and Control of Pathogens of Epidemiological Importance [SCOPE]). Patterns of A. baumannii rep-PCR were compared to those of previously identified international clonal lineages (ICs) and were further investigated by multilocus sequence typing (MLST) to compare the two typing methods. Forty-seven of the A. baumannii isolates clustered with the previously defined IC 2. ICs 1, 3, 6, and 7 were also detected. The remaining 81 isolates were unrelated to the described ICs. In contrast, A. pittii and A. nosocomialis isolates were more heterogeneous, as determined by rep-PCR. Our MLST results were in good correlation with the rep-PCR clusters. Our study confirms previous data indicating the predominance of a few major clonal A. baumannii lineages in the United States, particularly IC 2. The presence in the United States of A. baumannii ICs 1, 2, and 3 from as early as 1995 suggests that global dissemination of these lineages was an early event.
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Lankau EW, Cruz Bedon L, Mackie RI. Salmonella strains isolated from Galápagos iguanas show spatial structuring of serovar and genomic diversity. PLoS One 2012; 7:e37302. [PMID: 22615968 PMCID: PMC3353930 DOI: 10.1371/journal.pone.0037302] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Accepted: 04/19/2012] [Indexed: 01/31/2023] Open
Abstract
It is thought that dispersal limitation primarily structures host-associated bacterial populations because host distributions inherently limit transmission opportunities. However, enteric bacteria may disperse great distances during food-borne outbreaks. It is unclear if such rapid long-distance dispersal events happen regularly in natural systems or if these events represent an anthropogenic exception. We characterized Salmonella enterica isolates from the feces of free-living Galápagos land and marine iguanas from five sites on four islands using serotyping and genomic fingerprinting. Each site hosted unique and nearly exclusive serovar assemblages. Genomic fingerprint analysis offered a more complex model of S. enterica biogeography, with evidence of both unique strain pools and of spatial population structuring along a geographic gradient. These findings suggest that even relatively generalist enteric bacteria may be strongly dispersal limited in a natural system with strong barriers, such as oceanic divides. Yet, these differing results seen on two typing methods also suggests that genomic variation is less dispersal limited, allowing for different ecological processes to shape biogeographical patterns of the core and flexible portions of this bacterial species' genome.
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Affiliation(s)
- Emily W. Lankau
- Department of Animal Sciences and College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Lenin Cruz Bedon
- Armador del Pirata, Puerto Ayora, Isla Santa Cruz, Galápagos Islands, Ecuador
| | - Roderick I. Mackie
- Department of Animal Sciences and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
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Chenu JW, Cox JM, Pavic A. Classification of Salmonella enterica serotypes from Australian poultry using repetitive sequence-based PCR. J Appl Microbiol 2011; 112:185-96. [PMID: 21981579 DOI: 10.1111/j.1365-2672.2011.05172.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS To evaluate a semi-automated repetitive extragenic palindromic sequence-based PCR (rep-PCR) system for the classification of Salmonella serotypes from Australian poultry. METHODS AND RESULTS Using a DNA fingerprint library within the DiversiLab(®) System, four separate databases were constructed (serogroup B, C, E and Other). These databases contained 483 serologically confirmed (reference laboratory) Salmonella isolates. A blinded set of Salmonella cultures (n = 155) were typed by rep-PCR, matched against the internal library and compared with traditional serotyping. The predicted (Kullback-Leibler) serotype of 143 (92·3%) isolates matched traditional typing (P < 0·05). Of the 12 (7·7%) remaining isolates, ten (6·5%) resulted in 'No Match', one (0·65%) was incorrectly matched to the library (Salm. subsp 1 ser 4,12:-:-), and the other (0·65%) was referenced as Salm. ser. Sofia, whereas rep-PCR and in-house serotyping concurred as Salmonella serovar Typhimurium. Financial analysis showed higher material cost (215%) and a lower labour component (47·5%) for rep-PCR compared with serotyping. CONCLUSION The DiversiLab(®) System, with serogroup databases, was successfully implemented as an adjunct for reference serotyping of Salmonella enterica. SIGNIFICANCE AND IMPACT OF THE STUDY The DiversiLab(®) System platform is a cost-effective and easy-to-use system, which can putatively determine Salmonella enterica serotypes within a few hours.
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Affiliation(s)
- J W Chenu
- Birling Avian Laboratories, Bringelly, NSW, Australia
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Higgins PG, Hujer AM, Hujer KM, Bonomo RA, Seifert H. Interlaboratory reproducibility of DiversiLab rep-PCR typing and clustering of Acinetobacter baumannii isolates. J Med Microbiol 2011; 61:137-141. [PMID: 21903821 DOI: 10.1099/jmm.0.036046-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We have investigated the reproducibility of DiversiLab rep-PCR fingerprints between two laboratories with the aim of determining if the fingerprints and clustering are laboratory-specific or portable. One-hundred non-duplicate Acinetobacter baumannii isolates were used in this study. DNA isolation and rep-PCR were each performed separately in two laboratories and rep-PCR patterns generated in laboratory A were compared with those from laboratory B. Twelve A. baumannii isolates processed in laboratory A showed ≥98 % pattern similarity with the corresponding 12 isolates tested in laboratory B and were considered identical. Sixty-four isolates showed 95-97.9 % similarity with their corresponding isolates. Twenty-three isolates showed 90-94 % similarity with the corresponding isolates, while one isolate showed only 87.4 % similarity. However, intra-laboratory clustering was conserved: isolates that clustered in laboratory A also clustered in laboratory B. While clustering was conserved and reproducible at two different laboratories, demonstrating the robustness of rep-PCR, interlaboratory comparison of individual isolate fingerprints showed more variability. This comparison allows conclusions regarding clonality to be reached independent of the laboratory where the analysis is performed.
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Affiliation(s)
- Paul G Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Goldenfelsstrasse 19-21, 50935 Cologne, Germany
| | - Andrea M Hujer
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA.,Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Kristine M Hujer
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA.,Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Robert A Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA.,Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Harald Seifert
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Goldenfelsstrasse 19-21, 50935 Cologne, Germany
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Guo C, Liao Y, Li Y, Duan J, Guo Y, Wu Y, Cui Y, Sun H, Zhang J, Chen B, Zou Q, Guo G. Genotyping analysis of Helicobacter pylori using multiple-locus variable-number tandem-repeats analysis in five regions of China and Japan. BMC Microbiol 2011; 11:197. [PMID: 21888662 PMCID: PMC3178492 DOI: 10.1186/1471-2180-11-197] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2011] [Accepted: 09/03/2011] [Indexed: 01/03/2023] Open
Abstract
Background H. pylori (Helicobacter pylori) is the major causative agent of chronic active gastritis. The population of H. pylori shows a high genomic variability among isolates. And the polymorphism of repeat-units of genomics had participated the important process of evolution. Its long term colonization of the stomach caused different clinical outcomes, which may relate to the high degree of genetic variation of H. pylori. A variety of molecular typing tools have been developed to access genetic relatedness in H. pylori isolates. However, there is still no standard genotyping system of this bacterium. The MLVA (Multi-locus of variable number of tandem repeat analysis) method is useful for performing phylogenetic analysis and is widely used in bacteria genotyping; however, there's little application in H. pylori analysis. This article is the first application of the MLVA method to investigate H. pylori from different districts and ethnic groups of China. Results MLVA of 12 VNTR loci with high discrimination power based on 30 candidates were performed on a collection of 202 strains of H. pylori which originated from five regions of China and Japan. Phylogenetic tree was constructed using MLVA profiles. 12 VNTR loci presented with high various polymorphisms, and the results demonstrated very close relationships between genotypes and ethnic groups. Conclusions This study used MLVA methodology providing a new perspective on the ethnic groups and distribution characteristics of H. pylori.
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Affiliation(s)
- Chunliang Guo
- Department of Clinical Microbiology and Immunology, College of Medical Laboratory, Third Military Medical University, Chongqing, 400038, China
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Sha Q, Gunathilake A, Forstner MR, Hahn D. Temporal analyses of the distribution and diversity of Salmonella in natural biofilms. Syst Appl Microbiol 2011; 34:353-9. [DOI: 10.1016/j.syapm.2011.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Revised: 01/25/2011] [Accepted: 01/25/2011] [Indexed: 11/15/2022]
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Scientific Opinion on monitoring and assessment of the public health risk of “SalmonellaTyphimurium-like” strains. EFSA J 2010. [DOI: 10.2903/j.efsa.2010.1826] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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