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Choi O, Kim S, Kang B, Lee Y, Bae J, Kim J. Genetic Diversity and Distribution of Korean Isolates of Burkholderia glumae. PLANT DISEASE 2021; 105:1398-1407. [PMID: 33325743 DOI: 10.1094/pdis-08-20-1795-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Burkholderia glumae causes panicle blight of rice (grain rot in Japan and Korea), and the severity of damage is increasing worldwide. During 2017 and 2018, 137 isolates of B. glumae were isolated from symptomatic grain rot of rice cultivated in paddy fields throughout South Korea. Genetic diversity of the isolates was determined using transposase-based PCR (Tnp-PCR) genomic fingerprinting. All 138 isolates, including the B. glumae BGR1 strain, produced toxoflavin in various amounts, and 17 isolates produced an unidentified purple or orange pigment on Luria-Bertani medium and casamino acid-peptone-glucose medium, respectively, at 28°C. Transposase-based PCR genomic fingerprinting was performed using a novel primer designed based on transposase (tnp) gene sequences located at the ends of the toxoflavin efflux transporter operon; this method provided reliable and reproducible results. Through Tnp-PCR genomic fingerprinting, the genetic groups of Korean B. glumae isolates were divided into 11 clusters and three divisions. The Korean B. glumae isolates were mainly grouped in division I (73%). Interestingly, most of the pigment-producing isolates were grouped in divisions II and III; of these, 10 were grouped in cluster VIII, which comprised 67% of this cluster. Results of a phylogenetic analysis based on tofI and hrpB gene sequences were consistent with classification by Tnp-PCR genomic fingerprinting. The BGR1 strain did not belong to any of the clusters, indicating that this strain does not exhibit the typical genetic representation of B. glumae. B. glumae isolates showed diversity in the use of carbon and nitrogen sources, but no correlation with genetic classification by PCR fingerprinting was found. This is the first study to analyze the geographical distribution and genetic diversity of Korean B. glumae isolates.
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Affiliation(s)
- Okhee Choi
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Seunghoe Kim
- Department of Plant Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Byeongsam Kang
- Division of Applied Life Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Yeyeong Lee
- Department of Plant Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Juyoung Bae
- Department of Plant Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jinwoo Kim
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
- Department of Plant Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
- Division of Applied Life Science, Gyeongsang National University, Jinju, Republic of Korea
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BOX-PCR fingerprinting for molecular typing of Salmonella enterica subsp. enterica serovar Enteritidis strains originated from humans, dairy cattle, and broiler chickens. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/s00580-019-02897-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Assessing Transmission of Antimicrobial-Resistant Escherichia coli in Wild Giraffe Contact Networks. Appl Environ Microbiol 2018; 85:AEM.02136-18. [PMID: 30413480 DOI: 10.1128/aem.02136-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/11/2018] [Indexed: 12/13/2022] Open
Abstract
There is growing evidence that anthropogenic sources of antibiotics and antimicrobial-resistant bacteria can spill over into natural ecosystems, raising questions about the role wild animals play in the emergence, maintenance, and dispersal of antibiotic resistance genes. In particular, we lack an understanding of how resistance genes circulate within wild animal populations, including whether specific host characteristics, such as social associations, promote interhost transmission of these genes. In this study, we used social network analysis to explore the forces shaping population-level patterns of resistant Escherichia coli in wild giraffe (Giraffa camelopardalis) and assess the relative importance of social contact for the dissemination of resistant E. coli between giraffe. Of 195 giraffe sampled, only 5.1% harbored E. coli isolates resistant to one or more tested antibiotics. Whole-genome sequencing on a subset of resistant isolates revealed a number of acquired resistance genes with linkages to mobile genetic elements. However, we found no evidence that the spread of resistance genes among giraffe was facilitated by interhost associations. Giraffe with lower social degree were more likely to harbor resistant E. coli, but this relationship was likely driven by a correlation between an individual's social connectedness and age. Indeed, resistant E. coli was most frequently detected in socially isolated neonates, indicating that resistant E. coli may have a selective advantage in the gastrointestinal tracts of neonates compared to other age classes. Taken together, these results suggest that the maintenance of antimicrobial-resistant bacteria in wild populations may, in part, be determined by host traits and microbial competition dynamics within the host.IMPORTANCE Antimicrobial resistance represents a significant threat to human health, food security, and the global economy. To fully understand the evolution and dissemination of resistance genes, a complete picture of antimicrobial resistance in all biological compartments, including natural ecosystems, is required. The environment and wild animals may act as reservoirs for anthropogenically derived resistance genes that could be transferrable to clinically relevant bacteria of humans and domestic animals. Our study investigated the possible transmission mechanisms for antimicrobial-resistant bacteria within a wild animal population and, more broadly, contributes to our understanding of how resistance genes are spread and maintained in natural ecosystems.
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Borewicz KA, Kim HB, Singer RS, Gebhart CJ, Sreevatsan S, Johnson T, Isaacson RE. Changes in the Porcine Intestinal Microbiome in Response to Infection with Salmonella enterica and Lawsonia intracellularis. PLoS One 2015; 10:e0139106. [PMID: 26461107 PMCID: PMC4604083 DOI: 10.1371/journal.pone.0139106] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 09/08/2015] [Indexed: 12/23/2022] Open
Abstract
Salmonella enterica is a leading cause of food borne illness. Recent studies have shown that S. enterica is a pathogen capable of causing alterations to the composition of the intestinal microbiome. A recent prospective study of French pork production farms found a statistically significant association between Lawsonia intracellularis and carriage of S. enterica. In the current study the composition of the gut microbiome was determined in pigs challenged with S. enterica serovar Typhimurium and or L. intracellularis and compared to non-challenged control pigs. Principal coordinate analysis demonstrated that there was a disruption in the composition of the gut microbiome in the colon and cecum of pigs challenged with either pathogen. The compositions of the microbiomes of challenged pigs were similar to each other but differed from the non-challenged controls. There also were statistically significant increases in Anaerobacter, Barnesiella, Pediococcus, Sporacetigenium, Turicibacter, Catenibacterium, Prevotella, Pseudobutyrivibrio, and Xylanibacter in the challenged pigs. To determine if these changes were specific to experimentally challenged pigs, we determined the compositions of the fecal microbiomes of naturally infected pigs that were carriers of S. enterica. Pigs that were frequent shedders of S. enterica were shown to have similar fecal microbiomes compared to non-shedders or pigs that shed S. enterica infrequently. In a comparison of the differentially abundant bacteria in the naturally infected pigs compared to experimentally challenged pigs, 9 genera were differentially abundant and each exhibited the same increase or decrease in abundance between the two groups. Thus, there were similar changes in the GI microbiome associated with carriage of S. enterica regardless of whether the pigs were experimentally challenged with S. enterica or acquired it naturally.
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Affiliation(s)
- Klaudyna A. Borewicz
- Department of Veterinary and Biomedical Sciences, University of Minnesota, 1971 Commonwealth Ave., St. Paul, MN, 55108, United States of America
| | - Hyeun Bum Kim
- Department of Veterinary and Biomedical Sciences, University of Minnesota, 1971 Commonwealth Ave., St. Paul, MN, 55108, United States of America
| | - Randall S. Singer
- Department of Veterinary and Biomedical Sciences, University of Minnesota, 1971 Commonwealth Ave., St. Paul, MN, 55108, United States of America
| | - Connie J. Gebhart
- Department of Veterinary and Biomedical Sciences, University of Minnesota, 1971 Commonwealth Ave., St. Paul, MN, 55108, United States of America
| | - Srinand Sreevatsan
- Department of Veterinary and Biomedical Sciences, University of Minnesota, 1971 Commonwealth Ave., St. Paul, MN, 55108, United States of America
| | - Timothy Johnson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, 1971 Commonwealth Ave., St. Paul, MN, 55108, United States of America
| | - Richard E. Isaacson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, 1971 Commonwealth Ave., St. Paul, MN, 55108, United States of America
- * E-mail:
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Comparative Genomics Provides Insight into the Diversity of the Attaching and Effacing Escherichia coli Virulence Plasmids. Infect Immun 2015; 83:4103-17. [PMID: 26238712 DOI: 10.1128/iai.00769-15] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 07/26/2015] [Indexed: 12/22/2022] Open
Abstract
Attaching and effacing Escherichia coli (AEEC) strains are a genomically diverse group of diarrheagenic E. coli strains that are characterized by the presence of the locus of enterocyte effacement (LEE) genomic island, which encodes a type III secretion system that is essential to virulence. AEEC strains can be further classified as either enterohemorrhagic E. coli (EHEC), typical enteropathogenic E. coli (EPEC), or atypical EPEC, depending on the presence or absence of the Shiga toxin genes or bundle-forming pilus (BFP) genes. Recent AEEC genomic studies have focused on the diversity of the core genome, and less is known regarding the genetic diversity and relatedness of AEEC plasmids. Comparative genomic analyses in this study demonstrated genetic similarity among AEEC plasmid genes involved in plasmid replication conjugative transfer and maintenance, while the remainder of the plasmids had sequence variability. Investigation of the EPEC adherence factor (EAF) plasmids, which carry the BFP genes, demonstrated significant plasmid diversity even among isolates within the same phylogenomic lineage, suggesting that these EAF-like plasmids have undergone genetic modifications or have been lost and acquired multiple times. Global transcriptional analyses of the EPEC prototype isolate E2348/69 and two EAF plasmid mutants of this isolate demonstrated that the plasmid genes influence the expression of a number of chromosomal genes in addition to the LEE. This suggests that the genetic diversity of the EAF plasmids could contribute to differences in the global virulence regulons of EPEC isolates.
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Dingman DW. Comparative analysis of Paenibacillus larvae genotypes isolated in Connecticut. Arch Microbiol 2015; 197:789-95. [PMID: 25929327 DOI: 10.1007/s00203-015-1113-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 02/26/2015] [Accepted: 04/23/2015] [Indexed: 10/23/2022]
Abstract
Ninety-six strains of Paenibacillus larvae, causative agent of American foulbrood in honey bee (Apis mellifera) larvae, collected from Connecticut, USA (CT), honey bees, and 12 P. larvae strains not from CT, were genotyped via ERIC-PCR and XbaI-RFLP analysis. All CT-isolates, five strains isolated in South America, three strains from North America (not CT), and one strain isolated in Australia grouped into the ERIC I genotype. Three P. larvae formerly subsp. pulvifaciens strains grouped into ERIC III and IV genotypes. XbaI-RFLP genotyping showed three genotypes within the CT-isolates, and two were identified as XbaI-RFLP Type I and III. The third XbaI-RFLP genotype (Type Ib) represented one of four new XbaI-RFLP genotypes identified. Comparison of genotype results for the P. larvae strains tested was used to develop a correlation between ERIC-PCR genotyping and XbaI-RFLP genotyping. Sixteen CT-isolates were tetracycline-resistant and demonstrated PCR amplification using oligonucleotide primers for tetL. All 16 isolates grouped within XbaI-RFLP Type Ib, suggesting limited introduction of a tetracycline-resistant strain into CT.
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Affiliation(s)
- Douglas W Dingman
- Department of Entomology, The Connecticut Agricultural Experiment Station, 123 Huntington Street, P. O. Box 1106, New Haven, CT, 06504, USA,
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Doan NTL, Van Hoorde K, Cnockaert M, De Brandt E, Aerts M, Le Thanh B, Vandamme P. Validation of MALDI-TOF MS for rapid classification and identification of lactic acid bacteria, with a focus on isolates from traditional fermented foods in Northern Vietnam. Lett Appl Microbiol 2012; 55:265-73. [PMID: 22774847 DOI: 10.1111/j.1472-765x.2012.03287.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS To evaluate the potential use of MALDI-TOF MS for fast and reliable classification and identification of lactic acid bacteria (LAB) from traditional fermented foods. METHODS AND RESULTS A total of 119 strains of LAB from fermented meat (nem chua) were analysed with both (GTG)(5)-PCR fingerprinting and MALDI-TOF MS. Cluster analysis of the profiles revealed five species represented by a single isolate both in (GTG)(5)-PCR and in MALDI-TOF MS; five species grouped alike for (GTG)(5)-PCR and for MALDI-TOF MS; however, differences in minimal similarity between the delineated (GTG)(5)-PCR and MALDI-TOF MS clusters could be observed; three species showed more heterogeneity in their MALDI-TOF MS profiles compared to their (GTG)(5)-PCR profiles; two species, each represented by a single MALDI-TOF cluster, were subdivided in the corresponding (GTG)(5)-PCR dendrogram. As proof of the identification potential of MALDI-TOF MS, LAB diversity from one fermented mustard sample was analysed using MALDI-TOF MS. PheS gene sequencing was used for validation. CONCLUSIONS MALDI-TOF MS is a powerful, fast, reliable and cost-effective technique for the identification of LAB associated with the production of fermented foods. SIGNIFICANCE AND IMPACT OF THE STUDY Food LAB can be identified using MALDI-TOF MS, and its application could possibly be extended to other food matrices and/or other food-derived micro-organisms.
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Affiliation(s)
- N T L Doan
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
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Anderson P, Hume M, Byrd J, Hernandez C, Stevens S, Stringfellow K, Caldwell D. Evaluation of repetitive extragenic palindromic-polymerase chain reaction and denatured gradient gel electrophoresis in identifying Salmonella serotypes isolated from processed turkeys. Poult Sci 2010; 89:1293-300. [DOI: 10.3382/ps.2009-00390] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Isaeva A, Kulikov E, Tarasyan K, Letarov A. A Novel High-Resolving Method for Genomic PCR-Fingerprinting of Enterobacteria. Acta Naturae 2010; 2:82-8. [PMID: 22649631 PMCID: PMC3347548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
We developed a novel PCR-fingerprinting system for differentiation of enterobacterial strains using a single oligonucleotide primer IS1tr that matches the inverted terminal repeats of the IS1 insertion element. Compared to widely used BOX-PCR and ribotyping methods, our system features higher resolution allowing differentiation of closely related isolates that appear identical in BOX-PCR and ribotyping but differ in their phage sensitivity. The IS1-profiling system is less sensitive to the quality of the material and equipment used. At the same time, BOX-PCR is more universal and suitable for bacterial strain grouping and reconstruction of the low-distance phylogeny. Thus, our system represents an important supplement to the existing set of tools for bacterial strain differentiation; it is particularly valuable for a detailed investigation of highly divergent and rapidly evolving natural bacterial populations and for studies on coliphage ecology. However, some isolates could not be reliably differentiated by IS1-PCR, because of the low number of bands in their patterns. For improvement of IS1-fingerprinting characteristics, we offer to modify the system by introducing the second primer TR8834 hybridizing to the sequence of a transposase gene that is widely spread in enterobacterial genomes.
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Affiliation(s)
- A.S. Isaeva
- Winogradsky Institute of Microbiology, Russian Academy of Sciences
| | - E.E. Kulikov
- Winogradsky Institute of Microbiology, Russian Academy of Sciences
| | - K.K. Tarasyan
- Winogradsky Institute of Microbiology, Russian Academy of Sciences
| | - A.V. Letarov
- Winogradsky Institute of Microbiology, Russian Academy of Sciences
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11
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Duan H, Chai T, Liu J, Zhang X, Qi C, Gao J, Wang Y, Cai Y, Miao Z, Yao M, Schlenker G. Source identification of airborne Escherichia coli of swine house surroundings using ERIC-PCR and REP-PCR. ENVIRONMENTAL RESEARCH 2009; 109:511-7. [PMID: 19349045 PMCID: PMC7126843 DOI: 10.1016/j.envres.2009.02.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Revised: 02/19/2009] [Accepted: 02/24/2009] [Indexed: 05/19/2023]
Abstract
Evidence is mounting that microorganisms originating from livestock impact the air quality of the animal houses themselves and the public in the surrounding neighborhoods. The aim of this study was to develop efficient bacterial source tracking capabilities to identify sources of Escherichia coli aerosol pollution caused by pigs. Airborne E. coli were isolated from indoor air, upwind air (10 and 50 m away) and downwind air samples (10, 50, 100, 200 and 400 m away) for five swine houses using six-stage Andersen microbial samplers and Reuter-Centrifugal samplers (RCS). E. coli strains from pig fecal samples were also collected simultaneously. The enterobacterial repetitive intergenic consensus polymerize chain reaction (ERIC-PCR) and the repetitive extragenic palindromic (REP-PCR) approaches were used to study the genetic variability and to determine the strain relationships among E. coli isolated from different sites in each swine house. Results showed that 35.1% (20/57) of the bacterial DNA fingerprints from the fecal isolates matched with the corresponding strains isolated from indoor and downwind air samples (similarity > or = 90%). E. coli strains from the indoor and downwind air samples were closely related to the E. coli strains isolated from feces, while those isolated from upwind air samples (swine house C) had low similarity (61-69%). Our results suggest that some strains isolated from downwind and indoor air originated in the swine feces. Effective hygienic measures should be taken in animal farms to prevent or minimize the downwind spread of microorganism aerosol.
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Affiliation(s)
- Huiyong Duan
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Research Center for Animal Disease Control Engineering Shandong Province, Tai’an 271018, China
- College of Animal Husbandry and Veterinary Medicine, Jining Agricultural School, 272100 Jining, Shandong, China
| | - Tongjie Chai
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Research Center for Animal Disease Control Engineering Shandong Province, Tai’an 271018, China
- Corresponding author. Fax: +86 538 8241503.
| | - Jianzhu Liu
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Research Center for Animal Disease Control Engineering Shandong Province, Tai’an 271018, China
| | - Xingxiao Zhang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Research Center for Animal Disease Control Engineering Shandong Province, Tai’an 271018, China
| | - Chunhua Qi
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Research Center for Animal Disease Control Engineering Shandong Province, Tai’an 271018, China
| | - Jing Gao
- Central Hospital of Taian City, Shandong, China
| | - Yaling Wang
- College of Life Science, Dalian Nationalities University, China
| | - Yumei Cai
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Research Center for Animal Disease Control Engineering Shandong Province, Tai’an 271018, China
| | - Zengmin Miao
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Research Center for Animal Disease Control Engineering Shandong Province, Tai’an 271018, China
| | - Meiling Yao
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Research Center for Animal Disease Control Engineering Shandong Province, Tai’an 271018, China
| | - Gerd Schlenker
- Institute of Animal and Environmental Hygiene, Free University Berlin, Germany
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Albufera U, Bhugaloo-Vial P, Issack MI, Jaufeerally-Fakim Y. Molecular characterization of Salmonella isolates by REP-PCR and RAPD analysis. INFECTION GENETICS AND EVOLUTION 2007; 9:322-7. [PMID: 18243815 DOI: 10.1016/j.meegid.2007.12.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2007] [Revised: 12/10/2007] [Accepted: 12/12/2007] [Indexed: 11/17/2022]
Abstract
Eighteen Salmonella isolates from both human and food (non-human) sources (fish, meat, and poultry) were characterized using conventional culture methods, biochemical, serological, and molecular analyses. REP-PCR and RAPD produced DNA profiles for differentiation purposes. Enterobacterial repetitive intergenic consensus (ERIC), repetitive extragenic palindronic (REP) and BOXAIR primers were selected for REP-PCR and two arbitrary primers, namely OPP-16 and OPS-11 were used for RAPD to generate DNA fingerprints from the Salmonella isolates. REP-PCR method showed greater discriminatory power in differentiating closely related strains of the related strains of Salmonella and produced more complex banding patterns as compared with RAPD. A dendogram was constructed with both sets of profiles using SPSS Version 13.0 computer software and showed that most human isolates were separately clustered from the non-human isolates. Two of the human isolates were closely related to some of the non-human isolates. A good correlation was also observed between the serogrouping of the O antigen and the molecular profiles obtained from REP-PCR and RAPD data of the Salmonella isolates. The results of a principal coordinate analysis (PCA) corresponded to the clustering in the dendrogram.
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Affiliation(s)
- U Albufera
- Agricultural and Food Sciences Department, University of Mauritius, Reduit, Mauritius
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13
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Pounder JI, Shutt CK, Schaecher BJ, Woods GL. Clinical evaluation of repetitive sequence-based polymerase chain reaction using the Diversi-Lab System for strain typing of vancomycin-resistant enterococci. Diagn Microbiol Infect Dis 2006; 54:183-7. [PMID: 16423495 DOI: 10.1016/j.diagmicrobio.2005.08.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2005] [Accepted: 08/15/2005] [Indexed: 10/25/2022]
Abstract
The reliability of the Diversi-Lab System, an automated method of microbial strain typing using repetitive sequence-based polymerase chain reaction (rep-PCR), was evaluated by comparing results with those obtained by pulsed-field gel electrophoresis (PFGE). Ninety-five clinical isolates of vancomycin-resistant enterococci (VRE; 13 groups, 2-17 isolates per group) sent to Associated Regional and University Pathologists (ARUP) Laboratories for typing were tested by both methods. Rep-PCR and PFGE results were concordant for 83 isolates: all 32 isolates in 6 of the groups and 51 of the 63 isolates in the other 7 groups. Clustering of the remaining 12 isolates differed. With the Diversi-Lab System, analysis is objective, and results are available in 4 h, compared with a more subjective analysis and a 2- to 3-day turnaround time for PFGE. The Diversi-Lab System may be a viable alternative to PFGE for typing VRE in clinical reference laboratories.
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Affiliation(s)
- June I Pounder
- Associated Regional and University Pathologists Institute for Clinical and Experimental Pathology, Salt Lake City, UT 84108, USA.
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Rasschaert G, Houf K, Imberechts H, Grijspeerdt K, De Zutter L, Heyndrickx M. Comparison of five repetitive-sequence-based PCR typing methods for molecular discrimination of Salmonella enterica isolates. J Clin Microbiol 2005; 43:3615-23. [PMID: 16081887 PMCID: PMC1234001 DOI: 10.1128/jcm.43.8.3615-3623.2005] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2004] [Revised: 01/19/2005] [Accepted: 04/12/2005] [Indexed: 11/20/2022] Open
Abstract
Five repetitive-element PCR (rep-PCR) techniques [primer sets ERIC1R-ERIC2 and REP1R-REP2I and primers ERIC2, BOXA1R, and (GTG)5] were evaluated for the discrimination of Salmonella enterica isolates at the serotype level. On the basis of number, even distribution over the whole fingerprint, and clarity of bands in the fingerprints, the enterobacterial repetitive intergenic consensus (ERIC) primer set and the (GTG)5 primer were chosen for use in the following experiments. For these two primer sets, reproducibility was tested on different lysates of five selected serotypes of Salmonella in the same PCR by using three different PCR runs. Reproducibility was poor between different PCR runs but high within the same PCR run. Furthermore, 80 different serotypes and five isolates which were not typeable by serotyping were fingerprinted. All strains were typeable by the ERIC primer set and the (GTG)5 primer and generated unique fingerprints, except for some strains with incomplete antigenic codes. Finally, 55 genetically different strains belonging to 10 serotypes were fingerprinted to examine the genetic diversity of the rep-PCR within serotypes. This experiment showed that one serotype did not always correlate to only one ERIC or (GTG)5 fingerprint but that the fingerprint heterogeneity within a serotype was limited. In epidemiological studies, ERIC- and/or (GTG)5-PCR can be used to limit the number of strains that have to be serotyped. The reproducibility of isolates in one PCR run, the discriminatory power, and the genetic diversity (stability) of the fingerprint were similar for the Eric primer set and the (GTG)5 primer, so both are equally able to discriminate Salmonella serotypes.
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Affiliation(s)
- G. Rasschaert
- Ghent University, Faculty of Veterinary Medicine, Department of Veterinary
Public Health and Food Safety, Merelbeke, Veterinary and Agrochemical Research Centre, Brussels, Ministry of the Flemish Community, Center for Agricultural Research, Department for
Animal Product Quality and Transformation Technology, Melle, Belgium
| | - K. Houf
- Ghent University, Faculty of Veterinary Medicine, Department of Veterinary
Public Health and Food Safety, Merelbeke, Veterinary and Agrochemical Research Centre, Brussels, Ministry of the Flemish Community, Center for Agricultural Research, Department for
Animal Product Quality and Transformation Technology, Melle, Belgium
| | - H. Imberechts
- Ghent University, Faculty of Veterinary Medicine, Department of Veterinary
Public Health and Food Safety, Merelbeke, Veterinary and Agrochemical Research Centre, Brussels, Ministry of the Flemish Community, Center for Agricultural Research, Department for
Animal Product Quality and Transformation Technology, Melle, Belgium
| | - K. Grijspeerdt
- Ghent University, Faculty of Veterinary Medicine, Department of Veterinary
Public Health and Food Safety, Merelbeke, Veterinary and Agrochemical Research Centre, Brussels, Ministry of the Flemish Community, Center for Agricultural Research, Department for
Animal Product Quality and Transformation Technology, Melle, Belgium
| | - L. De Zutter
- Ghent University, Faculty of Veterinary Medicine, Department of Veterinary
Public Health and Food Safety, Merelbeke, Veterinary and Agrochemical Research Centre, Brussels, Ministry of the Flemish Community, Center for Agricultural Research, Department for
Animal Product Quality and Transformation Technology, Melle, Belgium
| | - M. Heyndrickx
- Ghent University, Faculty of Veterinary Medicine, Department of Veterinary
Public Health and Food Safety, Merelbeke, Veterinary and Agrochemical Research Centre, Brussels, Ministry of the Flemish Community, Center for Agricultural Research, Department for
Animal Product Quality and Transformation Technology, Melle, Belgium
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Healy M, Huong J, Bittner T, Lising M, Frye S, Raza S, Schrock R, Manry J, Renwick A, Nieto R, Woods C, Versalovic J, Lupski JR. Microbial DNA typing by automated repetitive-sequence-based PCR. J Clin Microbiol 2005; 43:199-207. [PMID: 15634972 PMCID: PMC540112 DOI: 10.1128/jcm.43.1.199-207.2005] [Citation(s) in RCA: 259] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Repetitive sequence-based PCR (rep-PCR) has been recognized as an effective method for bacterial strain typing. Recently, rep-PCR has been commercially adapted to an automated format known as the DiversiLab system to provide a reliable PCR-based typing system for clinical laboratories. We describe the adaptations made to automate rep-PCR and explore the performance and reproducibility of the system as a molecular genotyping tool for bacterial strain typing. The modifications for automation included changes in rep-PCR chemistry and thermal cycling parameters, incorporation of microfluidics-based DNA amplicon fractionation and detection, and Internet-based computer-assisted analysis, reporting, and data storage. The performance and reproducibility of the automated rep-PCR were examined by performing DNA typing and replicate testing with multiple laboratories, personnel, instruments, DNA template concentrations, and culture conditions prior to DNA isolation. Finally, we demonstrated the use of automated rep-PCR for clinical laboratory applications by using isolates from an outbreak of Neisseria meningitidis infections. N. meningitidis outbreak-related strains were distinguished from other isolates. The DiversiLab system is a highly integrated, convenient, and rapid testing platform that may allow clinical laboratories to realize the potential of microbial DNA typing.
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Affiliation(s)
- Mimi Healy
- Spectral Genomics, Inc., 8080 North Stadium Dr., Suite 1200, Houston, TX 77054, USA.
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Healy M, Reece K, Walton D, Huong J, Shah K, Kontoyiannis DP. Identification to the species level and differentiation between strains of Aspergillus clinical isolates by automated repetitive-sequence-based PCR. J Clin Microbiol 2004; 42:4016-24. [PMID: 15364984 PMCID: PMC516350 DOI: 10.1128/jcm.42.9.4016-4024.2004] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A commercially available repetitive-sequence-based PCR (rep-PCR) DNA fingerprinting assay adapted to an automated format, the DiversiLab system, enables rapid microbial identification and strain typing. We explored the performance of the DiversiLab system as a molecular typing tool for 69 Aspergillus isolates (38 A. fumigatus, 15 A. flavus, and 16 A. terreus isolates) had been previously characterized by morphological analysis. Initially, 27 Aspergillus isolates (10 A. fumigatus, 9 A. flavus, and 8 A. terreus isolates) were used as controls to create a rep-PCR-based DNA fingerprint library with the DiversiLab software. Then, 42 blinded Aspergillus isolates were typed using the system. The rep-PCR-based profile revealed 98% concordance with morphology-based identification. rep-PCR-based DNA fingerprints were reproducible and were consistent for DNA from both hyphae and conidia. DiversiLab dendrogram reports correctly identified all A. fumigatus (n = 28), A. terreus (n = 8), and A. flavus (n = 6) isolates in the 42 blinded Aspergillus isolates. rep-PCR-based identification of all isolates was 100% in agreement with the contiguous internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2) sequence-based identification of the respective isolates. Additionally, the DiversiLab system could demonstrate strain-level differentiation of A. flavus and A. terreus. Automated rep-PCR may be a time-efficient, effective, easy-to-use, novel genotyping tool for identifying and determining the strain relatedness of fungi. This system may be useful for epidemiological studies, molecular typing, and surveillance of Aspergillus species.
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Affiliation(s)
- M Healy
- Bacterial Barcodes, Inc., Houston, TX, USA
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Johnson JR, Stell AL, O'Bryan TT, Kuskowski M, Nowicki B, Johnson C, Maslow JN, Kaul A, Kavle J, Prats G. Global molecular epidemiology of the O15:K52:H1 extraintestinal pathogenic Escherichia coli clonal group: evidence of distribution beyond Europe. J Clin Microbiol 2002; 40:1913-23. [PMID: 12037043 PMCID: PMC130829 DOI: 10.1128/jcm.40.6.1913-1923.2002] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli O15:K52:H1 is a significant extraintestinal pathogen in Europe (G. Prats et al., J. Clin. Microbiol. 38:201-209, 2000). To search for evidence of this clonal group outside of Europe, 75 non-European E. coli isolates of serogroup O15 were compared with five members of the O15:K52:H1 clonal group from Barcelona, Spain, according to genomic background, virulence genotypes, and antimicrobial resistance profiles. Amplification phylotyping showed that 16 (21%) of the 75 non-European O15 isolates corresponded with the O15:K52:H1 clonal group. The 16 non-European O15:K52:H1 clonal group members represented diverse geographic locales. They were isolated almost exclusively from humans with extraintestinal infections and accounted for 50% of all O15 isolates from five human clinical collections studied. Most non-European clonal group members exhibited a consensus virulence factor profile that included the F16 or F7-2 papA alleles (P fimbrial structural subunit), papG allele II (P fimbrial adhesin), iha (putative adhesin siderophore), and iutA (aerobactin receptor). This resembles the virulence profiles of (i) European representatives of the O15:K52:H1 clonal group and (ii) phylogenetically related "clonal group A," a recently recognized significant contributor to trimethoprim-sulfamethoxazole resistance in the United States (A. R. Manges et al., N. Engl. J. Med. 345:1007-1013, 2001). Antimicrobial resistance profiles were variable, and resistance was inconsistently transferred by conjugation. These findings indicate that the O15:K52:H1 clonal group is broadly distributed beyond Europe, exhibits previously unrecognized phenotypic and genotypic diversity, and contributes significantly to extraintestinal infections in humans.
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Affiliation(s)
- James R Johnson
- Medical Service, Minneapolis VA Medical Center, MN 55417, USA.
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Kumao T, Ba-Thein W, Hayashi H. Molecular subtyping methods for detection of Salmonella enterica serovar Oranienburg outbreaks. J Clin Microbiol 2002; 40:2057-61. [PMID: 12037064 PMCID: PMC130768 DOI: 10.1128/jcm.40.6.2057-2061.2002] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study involved 82 Salmonella enterica serovar Oranienburg isolates from patients with gastroenteritis and/or focal infections, healthy carriers, and cuttlefish chips which were epidemiologically linked to a major outbreak that had affected 1,505 people in Japan between 1998 and 1999. We concurrently investigated four different molecular subtyping methods using human salmonellosis-associated Salmonella serovars and their applicability in detection of serovar Oranienburg in an outbreak. Pulsed-field gel electrophoresis (PFGE), enterobacterial repetitive intergenic sequence PCR (ERIC2-PCR), or 16S/23S rRNA ribotyping provided a high degree of interserovar discrimination for most of the serovars, with PFGE being the most discriminatory. For intraserovar typing of serovar Oranienburg, ERIC2-PCR was found to be the most sensitive. Native plasmid profiling, however, revealed nine different subgroups among epidemiologically and genetically related outbreak strains. Using these methods, a link was confirmed between food (cuttlefish chips) and patients in the serovar Oranienburg outbreak. This study underscores the limitations of chromosome-based and plasmid-based typing methods.
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Affiliation(s)
- Toshio Kumao
- Department of Infection Biology, Institute of Basic Medical Sciences, University of Tsukuba, Tsukuba 305-8575, Japan
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Rivas R, Velázquez E, Valverde A, Mateos PF, Martínez-Molina E. A two primers random amplified polymorphic DNA procedure to obtain polymerase chain reaction fingerprints of bacterial species. Electrophoresis 2001; 22:1086-9. [PMID: 11358129 DOI: 10.1002/1522-2683()22:6<1086::aid-elps1086>3.0.co;2-6] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Polymerase chain reation (PCR) fingerprints are used to characterize and recognize bacteria and are generally obtained using universal primers that generate an array of DNA amplicons, which can be separated by electrophoresis. Universal primers 8F and 1491 R have been used to amplify specifically 16S rDNA. We have used these primers at an annealing temperature of 50 degrees C. Agarose gel electrophoresis of PCR products revealed several bands. The band pattern of each bacterial species was different and the strains belonging to the same species shared an identical pattern. The patterns obtained did not show variations with plasmid DNA content or the growth stage of the bacteria. The peculiarity of the randomly amplified polymorphic DNA (RAPD) described in this work lies in the use of two large primers (proximately 20 nt) to obtain the pattern, since normally a only smaller primer is used, and in the new application for the primers used to amplify 16S rDNA. This new procedure, called two primers (TP)-RAPD fingerprinting, is thus rapid, sensitive, reliable, highly reproducible and suitable for experiments with a large number of microorganisms, and can be applied to bacterial taxonomy, ecological studies and for the detection of new bacterial species.
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Affiliation(s)
- R Rivas
- Departamento de Microbiología y Genética, Universidad de Salamanca, Spain
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Johnson JR, Clabots C, Azar M, Boxrud DJ, Besser JM, Thurn JR. Molecular analysis of a hospital cafeteria-associated salmonellosis outbreak using modified repetitive element PCR fingerprinting. J Clin Microbiol 2001; 39:3452-60. [PMID: 11574555 PMCID: PMC88371 DOI: 10.1128/jcm.39.10.3452-3460.2001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2000] [Accepted: 07/13/2001] [Indexed: 11/20/2022] Open
Abstract
A hospital cafeteria-associated outbreak of gastroenteritis due to Salmonella enterica serotype Infantis was retrospectively evaluated using modified repetitive element PCR (rep-PCR) fingerprinting with the ERIC2 and BOXA1R primers and computer-assisted gel analysis and dendrogram construction. Rep-PCR yielded objective between-cycler, same-strain similarity values of from 92% (composite fingerprints) to 96% (ERIC2 fingerprints). The 70 Salmonella isolates (which included 19 serotype Infantis isolates from the hospital outbreak, 10 other serotype Infantis isolates, and 41 isolates representing 14 other serotypes) were resolved well to the serotype level with each of the three fingerprint types (ERIC2, BOXA1R, and composite). Rep-PCR typing uncovered several historical serotyping errors and provided presumptive serotype assignments for other isolates with incomplete or undetermined serotypes. Analysis of replicate fingerprints for each isolate, as generated on two different thermal cyclers, indicated that most of the seeming subserotype discrimination noted in single-cycler dendrograms actually represented assay variability, since it was not reproducible in combined-cycler dendrograms. Rep-PCR typing, which would have been able to identify the presence of the hospital-associated serotype Infantis outbreak after the second outbreak isolate, could be used as a simple surrogate for serotyping by clinical microbiology laboratories that are equipped for diagnostic PCR.
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Affiliation(s)
- J R Johnson
- Medical Service, VA Medical Center, Minneapolis, Minnesota 55417, USA.
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Johnson JR, Stell AL, Delavari P. Canine feces as a reservoir of extraintestinal pathogenic Escherichia coli. Infect Immun 2001; 69:1306-14. [PMID: 11179292 PMCID: PMC98021 DOI: 10.1128/iai.69.3.1306-1314.2001] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2000] [Accepted: 11/20/2000] [Indexed: 11/20/2022] Open
Abstract
To test the canine reservoir hypothesis of extraintestinal pathogenic Escherichia coli (ExPEC), 63 environmental canine fecal deposits were evaluated for the presence of ExPEC by a combination of selective culturing, extended virulence genotyping, hemagglutination testing, O serotyping, and PCR-based phylotyping. Overall, 30% of canine fecal samples (56% of those that yielded viable E. coli) contained papG-positive E. coli, usually as the predominant E. coli strain and always possessing papG allele III (which encodes variant III of the P-fimbrial adhesin molecule PapG). Multiple other virulence-associated genes typical of human ExPEC were prevalent among the canine fecal isolates. According to serotyping, virulence genotyping, and random amplified polymorphic DNA analysis, over 50% of papG-positive fecal E. coli could be directly correlated with specific human clinical isolates from patients with cystitis, pyelonephritis, bacteremia, or meningitis, including archetypal human ExPEC strains 536, CP9, and RS218. Five canine fecal isolates and (clonally related) archetypal human pyelonephritis isolate 536 were found to share a novel allele of papA (which encodes the P-fimbrial structural subunit PapA). These data confirm that ExPEC representing known virulent clones are highly prevalent in canine feces, which consequently may provide a reservoir of ExPEC for acquisition by humans.
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Affiliation(s)
- J R Johnson
- VA Medical Center and Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55417, USA.
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Johnson JR, O'Bryan TT. Improved repetitive-element PCR fingerprinting for resolving pathogenic and nonpathogenic phylogenetic groups within Escherichia coli. CLINICAL AND DIAGNOSTIC LABORATORY IMMUNOLOGY 2000; 7:265-73. [PMID: 10702503 PMCID: PMC95859 DOI: 10.1128/cdli.7.2.265-273.2000] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/1999] [Accepted: 12/07/1999] [Indexed: 01/13/2023]
Abstract
Repetitive-element PCR (rep-PCR) fingerprinting is a promising molecular typing tool for Escherichia coli, including for discriminating between pathogenic and nonpathogenic clones, but is plagued by irreproducibility. Using the ERIC2 and BOXA1R primers and 15 E. coli strains from the ECOR reference collection (three from each phylogenetic group, as defined by multilocus enzyme electrophoresis [MLEE], including virulence-associated group B2), we rigorously assessed the effect of extremely elevated annealing temperatures on rep-PCR's reproducibility, discriminating power, and ability to reveal MLEE-defined phylogenetic relationships. Modified cycling conditions significantly improved assay reproducibility and discriminating power, allowing fingerprints from different cyclers to be analyzed together with minimal loss of resolution. The correspondence of rep-PCR with MLEE with respect to tree structure and regression analysis of distances was substantially better with modified than with standard cycling conditions. Nonetheless, rep-PCR was only a fair surrogate for MLEE, and when fingerprints from different days were compared, it failed to distinguish between different clones within all-important phylogenetic group B2. These findings indicate that although the performance and phylogenetic fidelity of rep-PCR fingerprinting can be improved substantially with modified assay conditions, even when so improved rep-PCR cannot fully substitute for MLEE as a phylogenetic typing method for pathogenic E. coli.
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Affiliation(s)
- J R Johnson
- VA Medical Center and Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA.
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