551
|
Fitch BR, Sachen KL, Wilder SR, Burg MA, Lacher DW, Khalife WT, Whittam TS, Young VB. Genetic diversity of Campylobacter sp. isolates from retail chicken products and humans with gastroenteritis in Central Michigan. J Clin Microbiol 2005; 43:4221-4. [PMID: 16081984 PMCID: PMC1233928 DOI: 10.1128/jcm.43.8.4221-4224.2005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multilocus sequencing was used to compare Campylobacter sp. strains isolated from retail chicken products and humans with gastroenteritis in central Michigan. Sequence comparisons demonstrated overlapping diversity between chicken and human isolates. Campylobacter jejuni isolates from clinical sources had a greater diversity of flagellin alleles and a higher rate of quinolone resistance than isolates from retail chicken products.
Collapse
Affiliation(s)
- Brooke R. Fitch
- Department of Microbiology and Molecular Genetics, Medical Technology Program, Infectious Diseases Unit, Department of Internal Medicine, National Food Safety and Toxicology Center, Michigan State University, East Lansing, Michigan 48824, Microbiology Laboratory, Sparrow Hospital, Lansing, Michigan 48912
| | - Kacey L. Sachen
- Department of Microbiology and Molecular Genetics, Medical Technology Program, Infectious Diseases Unit, Department of Internal Medicine, National Food Safety and Toxicology Center, Michigan State University, East Lansing, Michigan 48824, Microbiology Laboratory, Sparrow Hospital, Lansing, Michigan 48912
| | - Stacey R. Wilder
- Department of Microbiology and Molecular Genetics, Medical Technology Program, Infectious Diseases Unit, Department of Internal Medicine, National Food Safety and Toxicology Center, Michigan State University, East Lansing, Michigan 48824, Microbiology Laboratory, Sparrow Hospital, Lansing, Michigan 48912
| | - Matthew A. Burg
- Department of Microbiology and Molecular Genetics, Medical Technology Program, Infectious Diseases Unit, Department of Internal Medicine, National Food Safety and Toxicology Center, Michigan State University, East Lansing, Michigan 48824, Microbiology Laboratory, Sparrow Hospital, Lansing, Michigan 48912
| | - David W. Lacher
- Department of Microbiology and Molecular Genetics, Medical Technology Program, Infectious Diseases Unit, Department of Internal Medicine, National Food Safety and Toxicology Center, Michigan State University, East Lansing, Michigan 48824, Microbiology Laboratory, Sparrow Hospital, Lansing, Michigan 48912
| | - Walid T. Khalife
- Department of Microbiology and Molecular Genetics, Medical Technology Program, Infectious Diseases Unit, Department of Internal Medicine, National Food Safety and Toxicology Center, Michigan State University, East Lansing, Michigan 48824, Microbiology Laboratory, Sparrow Hospital, Lansing, Michigan 48912
| | - Thomas S. Whittam
- Department of Microbiology and Molecular Genetics, Medical Technology Program, Infectious Diseases Unit, Department of Internal Medicine, National Food Safety and Toxicology Center, Michigan State University, East Lansing, Michigan 48824, Microbiology Laboratory, Sparrow Hospital, Lansing, Michigan 48912
| | - Vincent B. Young
- Department of Microbiology and Molecular Genetics, Medical Technology Program, Infectious Diseases Unit, Department of Internal Medicine, National Food Safety and Toxicology Center, Michigan State University, East Lansing, Michigan 48824, Microbiology Laboratory, Sparrow Hospital, Lansing, Michigan 48912
- Corresponding author. Mailing address: Room B42, Food Safety and Toxicology Building, Michigan State University, East Lansing, MI 48824. Phone: (517) 432-3100. Fax: (517) 432-2310. E-mail:
| |
Collapse
|
552
|
Sukhnanand S, Alcaine S, Warnick LD, Su WL, Hof J, Craver MPJ, McDonough P, Boor KJ, Wiedmann M. DNA sequence-based subtyping and evolutionary analysis of selected Salmonella enterica serotypes. J Clin Microbiol 2005; 43:3688-98. [PMID: 16081897 PMCID: PMC1233967 DOI: 10.1128/jcm.43.8.3688-3698.2005] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
While serotyping and phage typing have been used widely to characterize Salmonella isolates, sensitive subtyping methods that allow for evolutionary analyses are essential for examining Salmonella transmission, ecology, and evolution. A set of 25 Salmonella enterica isolates, representing five clinically relevant serotypes (serotypes Agona, Heidelberg, Schwarzengrund, Typhimurium, and Typhimurium var. Copenhagen) was initially used to develop a multilocus sequence typing (MLST) scheme for Salmonella targeting seven housekeeping and virulence genes (panB, fimA, aceK, mdh, icdA, manB, and spaN). A total of eight MLST types were found among the 25 isolates sequenced. A good correlation between MLST types and Salmonella serotypes was observed; only one serotype Typhimurium var. Copenhagen isolate displayed an MLST type otherwise typical for serotype Typhimurium isolates. Since manB, fimA, and mdh allowed for the highest subtype discrimination among the initial 25 isolates, we chose these three genes to perform DNA sequencing of an additional 41 Salmonella isolates representing a larger diversity of serotypes. This "three-gene sequence typing scheme" allowed discrimination of 25 sequence types (STs) among a total of 66 isolates; STs correlated well with serotypes and allowed within-serotype differentiation for 9 of the 12 serotypes characterized. Phylogenetic analyses showed that serotypes Kentucky and Newport could each be separated into two distinct, statistically well supported evolutionary lineages. Our results show that a three-gene sequence typing scheme allows for accurate serotype prediction and for limited subtype discrimination among clinically relevant serotypes of Salmonella. Three-gene sequence typing also supports the notion that Salmonella serotypes represent both monophyletic and polyphyletic lineages.
Collapse
Affiliation(s)
- Sharinne Sukhnanand
- Department of Food Science, Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York 14853
| | - Sam Alcaine
- Department of Food Science, Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York 14853
| | - Lorin D. Warnick
- Department of Food Science, Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York 14853
| | - Wan-Lin Su
- Department of Food Science, Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York 14853
| | - Jessica Hof
- Department of Food Science, Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York 14853
| | - Mary Pat J. Craver
- Department of Food Science, Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York 14853
| | - Patrick McDonough
- Department of Food Science, Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York 14853
| | - Kathryn J. Boor
- Department of Food Science, Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York 14853
| | - Martin Wiedmann
- Department of Food Science, Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York 14853
- Corresponding author. Mailing address: Department of Food Science, 412 Stocking Hall, Cornell University, Ithaca, NY 14853. Phone: (607) 254-2838. Fax: (607) 254-4868. E-mail:
| |
Collapse
|
553
|
Diggle MA, Clarke SC. Truncated xpt gene present in invasive Streptococcus pneumoniae may have implications for MLST schemes. J Med Microbiol 2005; 54:909-912. [PMID: 16157542 DOI: 10.1099/jmm.0.46106-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A serotype 1 disease-causing pneumococcus possessing a truncated xanthine phosphoribosyltransferase (xpt) housekeeping gene is described. The deletion is within the gene region used for multi-locus sequence typing (MLST) and may have occurred through genetic transformation or capsule switch between clones. The identification of this deletion in a clinical isolate therefore warrants highlighting due to potential errors that may ensue in isolate characterization and due to the fact that deletions may occur in other genes in this or other species characterized by MLST.
Collapse
Affiliation(s)
- M A Diggle
- Scottish Meningococcus and Pneumococcus Reference Laboratory, House on the Hill, Stobhill Hospital, Balornock Road, Glasgow G21 3UW, UK 2Division of Infection and Immunity, Institute of Biomedical and Life Sciences, Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK
| | - S C Clarke
- Scottish Meningococcus and Pneumococcus Reference Laboratory, House on the Hill, Stobhill Hospital, Balornock Road, Glasgow G21 3UW, UK 2Division of Infection and Immunity, Institute of Biomedical and Life Sciences, Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK
| |
Collapse
|
554
|
Sacchi CT, Alber D, Dull P, Mothershed EA, Whitney AM, Barnett GA, Popovic T, Mayer LW. High level of sequence diversity in the 16S rRNA genes of Haemophilus influenzae isolates is useful for molecular subtyping. J Clin Microbiol 2005; 43:3734-42. [PMID: 16081903 PMCID: PMC1233939 DOI: 10.1128/jcm.43.8.3734-3742.2005] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A molecular typing method based on the 16S rRNA sequence diversity was developed for Haemophilus influenzae isolates. A total of 330 H. influenzae isolates were analyzed, representing a diverse collection of U.S. isolates. We found a high level of 16S rRNA sequence heterogeneity (up to 2.73%) and observed an exclusive correlation between 16S types and serotypes (a to f); no 16S type was found in more than one serotype. Similarly, no multilocus sequence typing (MLST) sequence type (ST) was found in more than one serotype. Our 16S typing and MLST results are in agreement with those of previous studies showing that serotypable H. influenzae isolates behave as highly clonal populations and emphasize the lack of clonality of nontypable (NT) H. influenzae isolates. There was not a 1:1 correlation between 16S types and STs, but all H. influenzae serotypable isolates clustered similarly. This correlation was not observed for NT H. influenzae; the two methods clustered NT H. influenzae isolates differently. 16S rRNA gene sequencing alone provides a level of discrimination similar to that obtained with the analysis of seven genes for MLST. We demonstrated that 16S typing is an additional and complementary approach to MLST, particularly for NT H. influenzae isolates, and is potentially useful for outbreak investigation.
Collapse
Affiliation(s)
- Claudio T Sacchi
- Meningitis and Special Pathogens Branch, Division of Bacterial and Mycotic Diseases, National Center for Infectious Diseases, CDC, MS D-11, 1600 Clifton Road, NE, Atlanta, GA 30333, USA.
| | | | | | | | | | | | | | | |
Collapse
|
555
|
French N, Barrigas M, Brown P, Ribiero P, Williams N, Leatherbarrow H, Birtles R, Bolton E, Fearnhead P, Fox A. Spatial epidemiology and natural population structure of Campylobacter jejuni colonizing a farmland ecosystem. Environ Microbiol 2005; 7:1116-26. [PMID: 16011749 DOI: 10.1111/j.1462-2920.2005.00782.x] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent progress in determining the population structure of Campylobacter jejuni, and discerning associations between genotypes and specific niches, has emphasized the shortfall in our understanding of the ecology and epidemiology of this bacterium. We examined the natural structure of the C. jejuni community associated with cattle farmland in the UK by structured spatiotemporal sampling of habitats, including livestock and wild animal faeces, environmental water and soil, over a 10-week period within a 100 km2 area. A total of 172 isolates were characterized using multilocus sequence typing into 65 sequence types (STs). Isolates from cattle faeces were significantly over-represented in the ST-61 complex, whereas isolates from wildlife faeces and water were more likely to belong to the ST-45 complex and a number of unusual STs, many of which were first encountered during this study. Sampling within a narrow spatiotemporal window permitted the application of novel statistical methods exploring the relationship between the genetic relatedness and spatial separation of isolates. This approach showed that isolates from the same sampling squares and squares separated by <1.0 km were genetically more similar than isolates separated by greater distances. Our study demonstrates the potential of multilocus sequence typing combined with spatial modelling in exploring natural transmission pathways for C. jejuni.
Collapse
Affiliation(s)
- Nigel French
- Defra Epidemiology Fellowship Unit, Department of Veterinary Clinical Science, Faculty of Veterinary Science, Leahurst, Wirral, UK.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
556
|
Inglis GD, McAllister TA, Busz HW, Yanke LJ, Morck DW, Olson ME, Read RR. Effects of subtherapeutic administration of antimicrobial agents to beef cattle on the prevalence of antimicrobial resistance in Campylobacter jejuni and Campylobacter hyointestinalis. Appl Environ Microbiol 2005; 71:3872-81. [PMID: 16000800 PMCID: PMC1169002 DOI: 10.1128/aem.71.7.3872-3881.2005] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The influence of antimicrobial agents on the development of antimicrobial resistance (AMR) in Campylobacter isolates recovered from 300 beef cattle maintained in an experimental feedlot was monitored over a 315-day period (11 sample times). Groups of calves were assigned to one of the following antimicrobial treatments: chlortetracycline and sulfamethazine (CS), chlortetracycline alone (Ct), virginiamycin, monensin, tylosin phosphate, and no antimicrobial agent (i.e., control treatment). In total, 3,283 fecal samples were processed for campylobacters over the course of the experiment. Of the 2,052 bacterial isolates recovered, 92% were Campylobacter (1,518 were Campylobacter hyointestinalis and 380 were C. jejuni). None of the antimicrobial treatments decreased the isolation frequency of C. jejuni relative to the control treatment. In contrast, C. hyointestinalis was isolated less frequently from animals treated with CS and to a lesser extent from animals treated with Ct. The majority (> or =94%) of C. jejuni isolates were sensitive to ampicillin, erythromycin, and ciprofloxacin, but more isolates with resistance to tetracycline were recovered from animals fed Ct. All of the 1,500 isolates of C. hyointestinalis examined were sensitive to ciprofloxacin. In contrast, 11%, 10%, and 1% of these isolates were resistant to tetracycline, erythromycin, and ampicillin, respectively. The number of animals from which C. hyointestinalis isolates with resistance to erythromycin and tetracycline were recovered differed among the antimicrobial treatments. Only Ct administration increased the carriage rates of erythromycin-resistant isolates of C. hyointestinalis, and the inclusion of CS in the diet increased the number of animals from which tetracycline-resistant isolates were recovered. The majority of C. hyointestinalis isolates with resistance to tetracycline were obtained from cohorts within a single pen, and most of these isolates were recovered from cattle during feeding of a forage-based diet as opposed to a grain-based diet. The findings of this study show that the subtherapeutic administration of tetracycline, alone and in combination with sulfamethazine, to feedlot cattle can select for the carriage of resistant strains of Campylobacter species. Considering the widespread use of in-feed antimicrobial agents and the high frequency of beef cattle that shed campylobacters, the development of AMR should be monitored as part of an on-going surveillance program.
Collapse
Affiliation(s)
- G D Inglis
- Agriculture & Agri-Food Canada Research Centre, 5403 1st Avenue S, Lethbridge, AB T1J 4B1, Canada.
| | | | | | | | | | | | | |
Collapse
|
557
|
Sung K, Hiett KL, Stern NJ. Heat-treated Campylobacter spp. and mRNA stability as determined by reverse transcriptase-polymerase chain reaction. Foodborne Pathog Dis 2005; 2:130-7. [PMID: 15992307 DOI: 10.1089/fpd.2005.2.130] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The detection method of reverse transcriptase-polymerase chain reaction (RT-PCR), which specifically targets mRNA, was developed and tested for detection of cultivable Campylobacter spp. The expression of four DNA targets- flaA, tkt, porA, and a putative haem-copper oxidase domain-were assayed in heat-inactivated Campylobacter spp. to determine an optimum target for RT-PCR amplification. A diversity of Campylobacter spp. was tested; however, the presented RT-PCR technique was specific for C. jejuni, C. coli, and C. lari. The durability of mRNA species detected by our RT-PCR technique was dependent upon the individual Campylobacter spp. examined, the condition of heat treatment and post-treatment holding time, as well as the transcript targeted. The putative oxidase was determined to be the most stable mRNA species for this assay. The mRNA of the putative oxidase gene was detectable even after Campylobacter spp. had been treated at temperatures of 95-99 degrees C. Using DNA-based PCR, the four DNA targets could be amplified after heat inactivation followed by a 48 h holding time, indicating that the chromosomal DNA was not substantially degraded by the heat treatment. PCR products from the putative oxidase gene were detected at 10(2) to 10(3) C. jejuni CFU per mL, exhibiting the highest level of sensitivity among the genes tested. The results in the present study indicate that mRNA from Campylobacter spp. may persist in a form that is detectable by RT-PCR amplification for an extended period after heat treatment, demonstrating a poor correlation between mRNA detection and cell cultivability. With these results in mind, further investigations are necessary to determine the correlation between RT-PCR amplification and viability.
Collapse
Affiliation(s)
- Kidon Sung
- Department of Food Science and Technology, University of Georgia, Athens, GA, USA
| | | | | |
Collapse
|
558
|
Huang S, Luangtongkum T, Morishita TY, Zhang Q. Molecular typing of Campylobacter strains using the cmp gene encoding the major outer membrane protein. Foodborne Pathog Dis 2005; 2:12-23. [PMID: 15992295 DOI: 10.1089/fpd.2005.2.12] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Thermophilic Campylobacter, particularly Campylobacter jejuni, is one of the major foodborne human pathogens of animal origin. Reliable and sensitive typing tools are required for understanding the epidemiology and ecology of this zoonotic bacteria agent. Currently, several molecular typing methods are available for differentiating Campylobacter strains, but each of them has limitations. Our previous study revealed that considerable sequence polymorphism exists in the cmp gene encoding the major outer membrane protein of Campylobacter and suggested that sequence variation of cmp may be utilized for discrimination of Campylobacter strains. In this study, we evaluated the feasibility of the cmp-based typing tool, using pulsed-field gel electrophoresis (PFGE) as the "gold" standard for comparison. The cmp alleles were sequenced from multiple Campylobacter strains, grouped, and compared with the PFGE profiles of these strains using Bionumerics. Results showed that 43 cmp sequence types and 43 PFGE types existed among the 60 Campylobacter isolates. Typeability of these strains is 100% using either the cmp-based method or PFGE. The discrimination indices are 0.973 for the cmp-based method and 0.969 for PFGE, respectively. The cmp sequence types are 77.6% congruent with the PFGE types. These results indicate that the cmp-based typing is a simple, yet highly discriminatory approach for molecular differentiation of C. jejuni strains.
Collapse
Affiliation(s)
- Shouxiong Huang
- Food Animal Health Research Program, Ohio Agriculture Research and Development Center, The Ohio State University, Wooster, Ohio, USA
| | | | | | | |
Collapse
|
559
|
Schouls LM, van der Ende A, van de Pol I, Schot C, Spanjaard L, Vauterin P, Wilderbeek D, Witteveen S. Increase in genetic diversity of Haemophilus influenzae serotype b (Hib) strains after introduction of Hib vaccination in The Netherlands. J Clin Microbiol 2005; 43:2741-9. [PMID: 15956392 PMCID: PMC1151946 DOI: 10.1128/jcm.43.6.2741-2749.2005] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recently, there has been an increase in The Netherlands in the number of cases of invasive disease caused by Haemophilus influenzae serotype b (Hib). To study a possible change in the Hib population that could explain the rise in incidence, a multiple-locus variable number tandem repeats analysis (MLVA) was developed to genotype H. influenzae isolates. The MLVA enabled the differentiation of H. influenzae serotype b strains with higher discriminatory power than multilocus sequence typing (MLST). MLVA profiles of noncapsulated H. influenzae and H. influenzae serotype f strains were more heterogeneous than serotype b strains and were distinct from Hib, although some overlap occurred. The MLVA was used to genotype a collection of 520 H. influenzae serotype b strains isolated from patients in The Netherlands with invasive disease. The strains were collected from 1983 from 2002, covering a time period of 10 years before and 9 years after the introduction of the Hib vaccine in the Dutch national vaccination program. MLVA revealed a sharp increase in genetic diversity of Hib strains isolated from neonates to 4-year-old patients after 1993, when the Hib vaccine was introduced. Hib strains isolated from patients older than 4 years in age were genetically diverse, and no significant change in diversity was seen after the introduction of the vaccine. These observations suggest that after the introduction of the Hib vaccine young children no longer constitute the reservoir for Hib and that they are infected by adults carrying genetically diverse Hib strains.
Collapse
Affiliation(s)
- Leo M Schouls
- Laboratory for Vaccine-Preventable Diseases, National Institute of Public Health and the Environment, P.O. Box 1, 3720 BA Bilthoven, The Netherlands.
| | | | | | | | | | | | | | | |
Collapse
|
560
|
Clark CG, Bryden L, Cuff WR, Johnson PL, Jamieson F, Ciebin B, Wang G. Use of the oxford multilocus sequence typing protocol and sequencing of the flagellin short variable region to characterize isolates from a large outbreak of waterborne Campylobacter sp. strains in Walkerton, Ontario, Canada. J Clin Microbiol 2005; 43:2080-91. [PMID: 15872226 PMCID: PMC1153734 DOI: 10.1128/jcm.43.5.2080-2091.2005] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Walkerton (Ontario, Canada) outbreak of waterborne Escherichia coli O157:H7 and Campylobacter jejuni was quite limited in both space and time, making it a good model for exploring the utility of different typing and subtyping methods for the characterization of relationships among isolates of these organisms. We have extended previous work with these organisms through analysis by the Oxford multilocus sequence typing (MLST) and the flagellin short variable region (fla-SVR) sequencing methods. Additional isolates not epidemiologically related to the Walkerton outbreak have also been included. Both sequencing methods identified and differentiated between Walkerton outbreak strains 1 and 2. When these strains were compared with isolates that were not part of the outbreak, the information produced by the fla-SVR method more often correlated with epidemiological findings than that produced by MLST, though both methods were required for optimal discrimination. The MLST data were more relevant in terms of the overall population structure of the organisms. Both mutation and recombination appeared to be responsible for generating diversity among the isolates tested.
Collapse
Affiliation(s)
- Clifford G Clark
- Bacteriology and Enteric Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada.
| | | | | | | | | | | | | |
Collapse
|
561
|
Miller WG, On SLW, Wang G, Fontanoz S, Lastovica AJ, Mandrell RE. Extended multilocus sequence typing system for Campylobacter coli, C. lari, C. upsaliensis, and C. helveticus. J Clin Microbiol 2005; 43:2315-29. [PMID: 15872261 PMCID: PMC1153752 DOI: 10.1128/jcm.43.5.2315-2329.2005] [Citation(s) in RCA: 172] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
A multilocus sequence typing (MLST) system has been reported previously for Campylobacter jejuni to both differentiate strains and identify clonal lineages. However, sequence variation at the MLST loci prevents its use for closely related Campylobacter species. We describe herein an expanded MLST method to include three clinically relevant Campylobacter species, C. coli, C. lari, and C. upsaliensis, and a fourth Campylobacter species, C. helveticus. The C. coli and C. helveticus methods use the same seven C. jejuni loci (aspA, atpA, glnA, gltA, glyA, pgm, and tkt); however, adk and pgi were substituted for aspA and gltA in C. lari and for gltA and pgm in C. upsaliensis. Multiple C. coli (n = 57), C. lari (n = 20), C. upsaliensis (n = 78), and C. helveticus (n = 9) isolates, representing both clinical and environmental sources, were typed. All four species were genetically diverse: the majority (> 80%) of the isolates had unique sequence types (STs). Using this method, mixed C. lari, C. upsaliensis, and C. helveticus isolates were identified; upon separation, each isolate was shown to contain two strains of the same species with distinct STs. Additionally, the expanded MLST method was able to detect potential lateral transfer events between C. jejuni and either C. coli or C. lari and between C. upsaliensis and C. helveticus. Thus, the expanded MLST method will prove useful in differentiating strains of five Campylobacter species, identifying mixed Campylobacter cultures, and detecting genetic exchange within the genus.
Collapse
Affiliation(s)
- William G Miller
- USDA, ARS, WRRC, Produce Safety and Microbiology Research Unit, 800 Buchanan St., Albany, CA 94710, USA.
| | | | | | | | | | | |
Collapse
|
562
|
Nemoy LL, Kotetishvili M, Tigno J, Keefer-Norris A, Harris AD, Perencevich EN, Johnson JA, Torpey D, Sulakvelidze A, Morris JG, Stine OC. Multilocus sequence typing versus pulsed-field gel electrophoresis for characterization of extended-spectrum beta-lactamase-producing Escherichia coli isolates. J Clin Microbiol 2005; 43:1776-81. [PMID: 15814998 PMCID: PMC1081380 DOI: 10.1128/jcm.43.4.1776-1781.2005] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli strains are emerging pathogens. Molecular typing of ESBL-producing E. coli is useful for surveillance purposes, to monitor outbreaks and track nosocomial spread. Although pulsed-field gel electrophoresis (PFGE) is the current "gold standard" for bacterial molecular typing, multilocus sequence typing (MLST) may offer advantages. Forty ESBL-producing E. coli isolates were selected at random from a cohort of intensive care unit patients who had active surveillance perirectal cultures done. PFGE identified 19 unique PFGE types (PT) among the 40 isolates; MLST identified 22 unique sequence types. MLST had greater discriminatory ability than PFGE for ESBL-producing E. coli. Simpson's indices of diversity for PFGE and MLST were 0.895 and 0.956, respectively. There were five clonal complexes (CCs) (isolates with differences of no more than two loci) that each contained multiple PT, but each PT was found in only one CC, indicating genetic consistency within a CC. MLST has clear utility in studies of ESBL-producing E. coli, based on a greater discriminatory ability and reproducibility than PFGE and the ability to a priori define genetically related bacterial strains.
Collapse
Affiliation(s)
- Lucia L Nemoy
- Department of Epidemiology and Preventive Medicine, University of Maryland School of Medicine, MSTF Building, Room 9-34, 10 South Pine Street, Baltimore, MD 21201, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
563
|
Dingle KE, Clarke L, Bowler ICJW. Ciprofloxacin resistance among human Campylobacter isolates 1991–2004: an update. J Antimicrob Chemother 2005; 56:435-7. [PMID: 15956098 DOI: 10.1093/jac/dki192] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
564
|
Pérez-Losada M, Viscidi RP, Demma JC, Zenilman J, Crandall KA. Population genetics of Neisseria gonorrhoeae in a high-prevalence community using a hypervariable outer membrane porB and 13 slowly evolving housekeeping genes. Mol Biol Evol 2005; 22:1887-902. [PMID: 15944444 DOI: 10.1093/molbev/msi184] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Baltimore, Md., is an urban community with a high prevalence of Neisseria gonorrhoeae. Due to partially protective immune responses, introduction of new strains from other host populations, and exposure of N. gonorrhoeae to antibiotics, the phenotypic and genotypic characteristics of the circulating strains can fluctuate over time. Understanding the overall genetic diversity and population structure of N. gonorrhoeae is essential for informing public health interventions to eliminate this pathogen. We studied gonococci population genetics in Baltimore by analyzing a hypervariable and strongly selected outer membrane porB gene and 13 slowly evolving and presumably neutral housekeeping genes (abcZ, adk, aroE, fumC, gdh, glnA, gnd, pdhC, pgm, pilA, ppk, pyrD, and serC) in 204 isolates collected in 1991, 1996, and 2001 from male and female patients of two public sexually transmitted diseases clinics. Genetic diversity (), recombination (C), growth (g), population structure, and adaptive selection under codon-substitution and amino acid property models were estimated and compared between these two gene classes. Estimates of the F(ST) fixation index and the chi(2) test of sequence absolute frequencies revealed significant temporal substructuring for both gene types. Baltimore's N. gonorrhoeae populations have increased since 1991 as indicated by consistent positive values of g. Female patients showed similar or lower levels of and C than male patients. Within the MLST housekeeping genes, levels of and C ranged from 0.001-0.013 and 0.000-0.018, respectively. Overall recombination seems to be the dominant force driving evolution in these populations. All loci showed amino acid sites and physicochemical properties under adaptive (or positive-destabilizing) selection, rejecting the generally assumed hypothesis of stabilizing selection for these MLST genes. Within the porB gene, protein I B showed higher and C values than protein I A. Directional positive selection possibly mediated by the immune system operates to a significant extent in the protein I sequences, as indicated by the distribution of the positively selected sites in the surface-exposed loops. Thirteen amino acid physicochemical properties seem to drive protein evolution of the PI porins in N. gonorrhoeae.
Collapse
|
565
|
Price LB, Johnson E, Vailes R, Silbergeld E. Fluoroquinolone-resistant Campylobacter isolates from conventional and antibiotic-free chicken products. ENVIRONMENTAL HEALTH PERSPECTIVES 2005; 113:557-60. [PMID: 15866763 PMCID: PMC1257547 DOI: 10.1289/ehp.7647] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The use of fluoroquinolones (FQs) in poultry production is an important issue in public health today. In February 2002, two prominent U.S. poultry companies pledged to stop using FQs for flock-wide treatment. One year later, we began a survey of Campylobacter isolates on chicken products from these two companies and from two producers claiming total abstention from antibiotic use. Using both standard isolation methods and new methods modified to enhance detection of FQ-resistant Campylobacter, we compared rates of FQ-resistant Campylobacter among these products. Four major findings were drawn from this study: a) antibiotic-free brands were not more likely to be contaminated with Campylobacter; b) a high percentage of products from the two conventional brands were contaminated with FQ-resistant Campylobacter (43 and 96%); c) these conventional brands had significantly higher odds of carrying resistant strains compared with antibiotic-free products; and d) supplementing media with FQs increased the sensitivity of detecting FQ-resistant strains among mixed populations of Campylobacter, thus reducing a bias toward underestimating the prevalence of FQ-resistant Campylobacter on samples. These results suggest that FQ resistance may persist in the commercial poultry environment in the absence of FQ-selective pressure and that these strains contaminate a larger proportion of foods than reported previously.
Collapse
Affiliation(s)
- Lance B Price
- Johns Hopkins University, Bloomberg School of Public Health, 615 N. Wolfe Street, Suite W6114, Baltimore, MD 21205, USA.
| | | | | | | |
Collapse
|
566
|
Spratt BG, Hanage WP, Li B, Aanensen DM, Feil EJ. Displaying the relatedness among isolates of bacterial species -- the eBURST approach. FEMS Microbiol Lett 2005; 241:129-34. [PMID: 15598523 DOI: 10.1016/j.femsle.2004.11.015] [Citation(s) in RCA: 158] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2004] [Revised: 11/05/2004] [Accepted: 11/05/2004] [Indexed: 11/18/2022] Open
Abstract
Determining the most appropriate way to represent the relationships between bacterial isolates is complicated by the differing rates of recombination within species. In many cases, a bifurcating tree can be positively misleading. The recently described program eBURST can be used with multilocus data to define groups or clonal complexes of related isolates derived from a common ancestor, the patterns of descent linking them together, and the ancestral genotype. eBURST has recently been extensively updated to include additional tools for exploring the relationships between isolates. We discuss the advantages of this approach and describe its use to explore patterns of descent within clonal complexes identified using multilocus sequence typing.
Collapse
Affiliation(s)
- Brian G Spratt
- Department of Infectious Disease Epidemiology, Faculty of Medicine, Imperial College London, St. Mary's Hospital, Old Medical School Building, London W2 1PG, UK.
| | | | | | | | | |
Collapse
|
567
|
Dingle KE, Colles FM, Falush D, Maiden MCJ. Sequence typing and comparison of population biology of Campylobacter coli and Campylobacter jejuni. J Clin Microbiol 2005; 43:340-7. [PMID: 15634992 PMCID: PMC540151 DOI: 10.1128/jcm.43.1.340-347.2005] [Citation(s) in RCA: 162] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A multilocus sequence typing (MLST) scheme that uses the same loci as a previously described system for Campylobacter jejuni was developed for Campylobacter coli. The C. coli-specific primers were validated with 53 isolates from humans, chickens, and pigs, together with 15 Penner serotype reference isolates. The nucleotide sequence of the flaA short variable region (SVR) was determined for each isolate. These sequence data were compared to equivalent information for 17 C. jejuni isolates representing the known genetic diversity of this species. C. coli and C. jejuni share approximately 86.5% identity at the nucleotide sequence level within the MLST loci. There is evidence of genetic exchange of the housekeeping genes between the two species, but at a very low rate; only one sequence type from each species showed evidence of imported DNA. The flaA gene was more variable and has been exchanged many times between the two species, making it an unreliable marker for species identification but useful for distinguishing closely related strains. All but 3 of 21 human C. coli clinical isolates were distinct, according to the combined MLST and SVR sequences. The use of a common MLST scheme allows direct comparisons of the population biology and molecular epidemiology of these two closely related human pathogens.
Collapse
Affiliation(s)
- Kate E Dingle
- Nuffield Department of Clinical Sciences, Oxford University, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
| | | | | | | |
Collapse
|
568
|
de Las Rivas B, Marcobal A, Muñoz R. Allelic diversity and population structure in Oenococcus oeni as determined from sequence analysis of housekeeping genes. Appl Environ Microbiol 2005; 70:7210-9. [PMID: 15574919 PMCID: PMC535203 DOI: 10.1128/aem.70.12.7210-7219.2004] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Oenococcus oeni is the organism of choice for promoting malolactic fermentation in wine. The population biology of O. oeni is poorly understood and remains unclear. For a better understanding of the mode of genetic variation within this species, we investigated by using multilocus sequence typing (MLST) with the gyrB, pgm, ddl, recP, and mleA genes the genetic diversity and genetic relationships among 18 O. oeni strains isolated in various years from wines of the United States, France, Germany, Spain, and Italy. These strains have also been characterized by ribotyping and restriction fragment length polymorphism (RFLP) analysis of the PCR-amplified 16S-23S rRNA gene intergenic spacer region (ISR). Ribotyping grouped the strains into two groups; however, the RFLP analysis of the ISRs showed no differences in the strains analyzed. In contrast, MLST in oenococci had a good discriminatory ability, and we have found a higher genetic diversity than indicated by ribotyping analysis. All sequence types were represented by a single strain, and all the strains could be distinguished from each other because they had unique combinations of alleles. Strains assumed to be identical showed the same sequence type. Phylogenetic analyses indicated a panmictic population structure in O. oeni. Sequences were analyzed for evidence of recombination by split decomposition analysis and analysis of clustered polymorphisms. All results indicated that recombination plays a major role in creating the genetic heterogeneity of O. oeni. A low standardized index of association value indicated that the O. oeni genes analyzed are close to linkage equilibrium. This study constitutes the first step in the development of an MLST method for O. oeni and the first example of the application of MLST to a nonpathogenic food production bacteria.
Collapse
|
569
|
Klena JD, Parker CT, Knibb K, Ibbitt JC, Devane PML, Horn ST, Miller WG, Konkel ME. Differentiation of Campylobacter coli, Campylobacter jejuni, Campylobacter lari, and Campylobacter upsaliensis by a multiplex PCR developed from the nucleotide sequence of the lipid A gene lpxA. J Clin Microbiol 2005; 42:5549-57. [PMID: 15583280 PMCID: PMC535264 DOI: 10.1128/jcm.42.12.5549-5557.2004] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We describe a multiplex PCR assay to identify and discriminate between isolates of Campylobacter coli, Campylobacter jejuni, Campylobacter lari, and Campylobacter upsaliensis. The C. jejuni isolate F38011 lpxA gene, encoding a UDP-N-acetylglucosamine acyltransferase, was identified by sequence analysis of an expression plasmid that restored wild-type lipopolysaccharide levels in Escherichia coli strain SM105 [lpxA(Ts)]. With oligonucleotide primers developed to the C. jejuni lpxA gene, nearly full-length lpxA amplicons were amplified from an additional 11 isolates of C. jejuni, 20 isolates of C. coli, 16 isolates of C. lari, and five isolates of C. upsaliensis. The nucleotide sequence of each amplicon was determined, and sequence alignment revealed a high level of species discrimination. Oligonucleotide primers were constructed to exploit species differences, and a multiplex PCR assay was developed to positively identify isolates of C. coli, C. jejuni, C. lari, and C. upsaliensis. We characterized an additional set of 41 thermotolerant isolates by partial nucleotide sequence analysis to further demonstrate the uniqueness of each species-specific region. The multiplex PCR assay was validated with 105 genetically defined isolates of C. coli, C. jejuni, C. lari, and C. upsaliensis, 34 strains representing 12 additional Campylobacter species, and 24 strains representing 19 non-Campylobacter species. Application of the multiplex PCR method to whole-cell lysates obtained from 108 clinical and environmental thermotolerant Campylobacter isolates resulted in 100% correlation with biochemical typing methods.
Collapse
Affiliation(s)
- John D Klena
- Department of Plant and Microbial Sciences, University of Canterbury, Christchurch, New Zealand.
| | | | | | | | | | | | | | | |
Collapse
|
570
|
Fouts DE, Mongodin EF, Mandrell RE, Miller WG, Rasko DA, Ravel J, Brinkac LM, DeBoy RT, Parker CT, Daugherty SC, Dodson RJ, Durkin AS, Madupu R, Sullivan SA, Shetty JU, Ayodeji MA, Shvartsbeyn A, Schatz MC, Badger JH, Fraser CM, Nelson KE. Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species. PLoS Biol 2005; 3:e15. [PMID: 15660156 PMCID: PMC539331 DOI: 10.1371/journal.pbio.0030015] [Citation(s) in RCA: 398] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2004] [Accepted: 11/11/2004] [Indexed: 12/19/2022] Open
Abstract
Sequencing and comparative genome analysis of four strains of Campylobacter including C. lari RM2100, C. upsaliensis RM3195, and C. coli RM2228 has revealed major structural differences that are associated with the insertion of phage- and plasmid-like genomic islands, as well as major variations in the lipooligosaccharide complex. Poly G tracts are longer, are greater in number, and show greater variability in C. upsaliensis than in the other species. Many genes involved in host colonization, including racR/S, cadF, cdt, ciaB, and flagellin genes, are conserved across the species, but variations that appear to be species specific are evident for a lipooligosaccharide locus, a capsular (extracellular) polysaccharide locus, and a novel Campylobacter putative licABCD virulence locus. The strains also vary in their metabolic profiles, as well as their resistance profiles to a range of antibiotics. It is evident that the newly identified hypothetical and conserved hypothetical proteins, as well as uncharacterized two-component regulatory systems and membrane proteins, may hold additional significant information on the major differences in virulence among the species, as well as the specificity of the strains for particular hosts.
Collapse
Affiliation(s)
- Derrick E Fouts
- The Institute for Genomic Research, Rockville, Maryland, United States of America.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
571
|
Taboada EN, Acedillo RR, Carrillo CD, Findlay WA, Medeiros DT, Mykytczuk OL, Roberts MJ, Valencia CA, Farber JM, Nash JHE. Large-scale comparative genomics meta-analysis of Campylobacter jejuni isolates reveals low level of genome plasticity. J Clin Microbiol 2004; 42:4566-76. [PMID: 15472310 PMCID: PMC522315 DOI: 10.1128/jcm.42.10.4566-4576.2004] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have used comparative genomic hybridization (CGH) on a full-genome Campylobacter jejuni microarray to examine genome-wide gene conservation patterns among 51 strains isolated from food and clinical sources. These data have been integrated with data from three previous C. jejuni CGH studies to perform a meta-analysis that included 97 strains from the four separate data sets. Although many genes were found to be divergent across multiple strains (n = 350), many genes (n = 249) were uniquely variable in single strains. Thus, the strains in each data set comprise strains with a unique genetic diversity not found in the strains in the other data sets. Despite the large increase in the collective number of variable C. jejuni genes (n = 599) found in the meta-analysis data set, nearly half of these (n = 276) mapped to previously defined variable loci, and it therefore appears that large regions of the C. jejuni genome are genetically stable. A detailed analysis of the microarray data revealed that divergent genes could be differentiated on the basis of the amplitudes of their differential microarray signals. Of 599 variable genes, 122 could be classified as highly divergent on the basis of CGH data. Nearly all highly divergent genes (117 of 122) had divergent neighbors and showed high levels of intraspecies variability. The approach outlined here has enabled us to distinguish global trends of gene conservation in C. jejuni and has enabled us to define this group of genes as a robust set of variable markers that can become the cornerstone of a new generation of genotyping methods that use genome-wide C. jejuni gene variability data.
Collapse
Affiliation(s)
- Eduardo N Taboada
- Pathogen Genomics Group, Institute for Biological Sciences, National Research Council of Canada, Ottawa, Ontario, Canada
| | | | | | | | | | | | | | | | | | | |
Collapse
|
572
|
Mellmann A, Mosters J, Bartelt E, Roggentin P, Ammon A, Friedrich AW, Karch H, Harmsen D. Sequence-based typing of flaB is a more stable screening tool than typing of flaA for monitoring of Campylobacter populations. J Clin Microbiol 2004; 42:4840-2. [PMID: 15472357 PMCID: PMC522316 DOI: 10.1128/jcm.42.10.4840-4842.2004] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Different typing schemes for Campylobacter spp. were evaluated with 70 outbreak and sporadic isolates. The discriminatory indexes were 0.944 (by pulsed-field gel electrophoresis), 0.920 (by genotyping of the flagellin A gene), 0.902 (by genotyping of flaB), and 0.886 (by multilocus sequence typing). Cross-classification gave 94.77 or 95.82% (PFGE-flaA or PFGE-flaB) concordance. flaA was overdiscriminatory in three cases, most probably due to intragenomic recombination.
Collapse
|
573
|
Abstract
AIMS To determine the prevalence of chronic shedding of Campylobacter species by beef cattle, a longitudinal study of shedding patterns was conducted in a cohort of 60 beef steers over a 4-month period. METHODS AND RESULTS Steers were maintained in a simulated feedlot setting but individually in pens to minimize transmission among animals. At each collection time, campylobacters in faeces were detected using conventional PCR. In addition, quantities of Campylobacter jejuni and C. lanienae in faeces were measured using real-time quantitative (RTQ) PCR. All of the steers tested shed Campylobacter species during the course of the study, and overall, 90% of the 299 samples tested were positive for Campylobacter DNA. The majority of the animals (86%) shed campylobacters at >/=4 sample times. The most prevalent taxon detected in bovine faeces was C. lanienae (56% of samples) followed by C. jejuni (13%), C. hyointestinalis (8%), and C. fetus (2%). No C. coli was detected, and 13% of the faecal samples contained two or more of the above species. Seven (12%) and 34 (57%) animals shed C. jejuni and C. lanienae at >/=3 sample times, respectively. For both C. lanienae and C. jejuni, a substantial number of cells were detected in faeces using RTQ-PCR; 27% of the samples positive for C. jejuni contained populations >10(4) cells g(-1) (maximum of 5 x 10(5) cells g(-1)), and 44% of samples positive for C. lanienae possessed populations >10(6) cells g(-1) (maximum of 4 x 10(8) cells g(-1)). A significant correlation was observed between shedding of C. lanienae and the severity of liver abscesses. In 27% of the samples, an amplicon was obtained for genus-specific but not for the species-specific primers. Sequencing of the partial 16S rRNA gene suggested the presence of at least two undescribed Campylobacter species but this has yet to be confirmed. CONCLUSIONS A high percentage of feedlot cattle shed large quantities of Campylobacter species in their faeces over a protracted period of time (ca 112 days). SIGNIFICANCE AND IMPACT OF THE STUDY This is the first study of longitudinal shedding patterns of campylobacters in beef cattle using PCR-detection methods. In addition, this is the first use of RTQ-PCR to directly quantify C. jejuni or C. lanienae in faeces. The results of the study show that a large number of cattle (>85%) chronically shed campylobacters in feedlots.
Collapse
Affiliation(s)
- G D Inglis
- Agriculture and Agri-Food Canada Research Centre, Lethbridge, Canada.
| | | | | |
Collapse
|
574
|
Brown PE, Christensen OF, Clough HE, Diggle PJ, Hart CA, Hazel S, Kemp R, Leatherbarrow AJH, Moore A, Sutherst J, Turner J, Williams NJ, Wright EJ, French NP. Frequency and spatial distribution of environmental Campylobacter spp. Appl Environ Microbiol 2004; 70:6501-11. [PMID: 15528512 PMCID: PMC525266 DOI: 10.1128/aem.70.11.6501-6511.2004] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2003] [Accepted: 05/31/2004] [Indexed: 11/20/2022] Open
Abstract
Humans are exposed to Campylobacter spp. in a range of sources via both food and environmental pathways. For this study, we explored the frequency and distribution of thermophilic Campylobacter spp. in a 10- by 10-km square rural area of Cheshire, United Kingdom. The area contains approximately 70, mainly dairy, farms and is used extensively for outdoor recreational activities. Campylobacter spp. were isolated from a range of environmental samples by use of a systematic sampling grid. Livestock (mainly cattle) and wildlife feces and environmental water and soil samples were cultured, and isolates were presumptively identified by standard techniques. These isolates were further characterized by PCR. Campylobacter jejuni was the most prevalent species in all animal samples, ranging from 11% in samples from nonavian wildlife to 36% in cattle feces, and was isolated from 15% of water samples. Campylobacter coli was commonly found in water (17%) and sheep (21%) samples, but rarely in other samples. Campylobacter lari was recovered from all sample types, with the exception of sheep feces, and was found in moderate numbers in birds (7%) and water (5%). Campylobacter hyointestinalis was only recovered from cattle (7%) and birds (1%). The spatial distribution and determinants of C. jejuni in cattle feces were examined by the use of model-based spatial statistics. The distribution was consistent with very localized within-farm or within-field transmission and showed little evidence of any larger-scale spatial dependence. We concluded that there is a potentially high risk of human exposure to Campylobacter spp., particularly C. jejuni, in the environment of our study area. The prevalence and likely risk posed by C. jejuni-positive cattle feces in the environment diminished as the fecal material aged. After we took into account the age of the fecal material, the absence or presence of rain, and the presence of bird feces, there was evidence of significant variation in the prevalence of C. jejuni-positive cattle feces between grazing fields but no evidence of spatial clustering beyond this resolution. The spatial pattern of C. jejuni is therefore consistent with that for an organism that is ubiquitous in areas contaminated with cattle feces, with a short-scale variation in infection intensity that cannot be explained solely by variations in the age of the fecal material. The observed pattern is not consistent with large-scale transmission attributable to watercourses, wildlife territories, or other geographical features that transcend field and farm boundaries.
Collapse
Affiliation(s)
- P E Brown
- Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
575
|
Connerton PL, Loc Carrillo CM, Swift C, Dillon E, Scott A, Rees CED, Dodd CER, Frost J, Connerton IF. Longitudinal study of Campylobacter jejuni bacteriophages and their hosts from broiler chickens. Appl Environ Microbiol 2004; 70:3877-83. [PMID: 15240258 PMCID: PMC444807 DOI: 10.1128/aem.70.7.3877-3883.2004] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A longitudinal study of bacteriophages and their hosts was carried out at a broiler house that had been identified as having a population of Campylobacter-specific bacteriophages. Cloacal and excreta samples were collected from three successive broiler flocks reared in the same barn. Campylobacter jejuni was isolated from each flock, whereas bacteriophages could be isolated from flocks 1 and 2 but were not isolated from flock 3. The bacteriophages isolated from flocks 1 and 2 were closely related to each other in terms of host range, morphology, genome size, and genetic content. All Campylobacter isolates from flock 1 were genotypically indistinguishable by pulsed-field gel electrophoresis (PFGE). PFGE and multilocus sequence typing indicated that this C. jejuni type was maintained from flock 1 to flock 2 but was largely superseded by three genetically distinct C. jejuni types insensitive to the resident bacteriophages. All isolates from the third batch of birds were insensitive to bacteriophages and genotypically distinct. These results are significant because this is the first study of an environmental population of C. jejuni bacteriophages and their influence on the Campylobacter populations of broiler house chickens. The role of developing bacteriophage resistance was investigated as this is a possible obstacle to the use of bacteriophage therapy to reduce the numbers of campylobacters in chickens. In this broiler house succession was largely due to incursion of new genotypes rather than to de novo development of resistance.
Collapse
Affiliation(s)
- P L Connerton
- Division of Food Sciences, School of Biosciences, Sutton Bonington Campus, University of Nottingham, Loughborough LE12 5RD, United Kingdom
| | | | | | | | | | | | | | | | | |
Collapse
|
576
|
Sung KD, Stern NJ, Hiett KL. Relationship of messenger RNA reverse transcriptase-polymerase chain reaction signal to Campylobacter spp. viability. Avian Dis 2004; 48:254-62. [PMID: 15283412 DOI: 10.1637/7062] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
SUMMARY. Discriminating viable from dead cells is of importance in the development of bacterial detection methods. A positive reverse transcriptase-polymerase chain reaction (RT-PCR) amplification signal was tested as a potential predictor of chick colonization. Some researchers have suggested that the presence of messenger RNA (mRNA) may not correlate with cell viability. Chicken colonization by cells that have positive mRNA signal but that are noncultivable would provide a correlation in cell viability and persistence of mRNA. The role of a viable but noncultivable (VBNC) form of Campylobacter spp. for colonization of poultry could be verified by such an mRNA signal. The levels of four strains of Campylobacter spp., previously isolated from poultry feces, declined progressively over time, and loss of cultivability occurred after 6 to 7 wk incubation in phosphate-buffered saline (PBS) at 4 C. Cold-stored, noncultivable and heat-inactivated (60 C for 10 min) Campylobacter spp. produced inconsistent amplified products from RT-PCR assay, depending on the target transcripts and strains used, although all fresh cultures showed mRNA signals. For the most part, signals of mRNA species from VBNC and heat-killed Campylobacter spp. AH-1, AH-2, and CH-3 persisted. RT-PCR amplification of transcripts originating from the tkt and cmp genes and a 256-base pair amplicon (from a previously described putative haem-copper oxidase) provided consistent signals, whereas transcripts from the flaA gene did not. Presumed VBNC and heat-inactivated Campylobacter spp., which produced positive mRNA signal but was not cultivable by conventional culture-based methods, did not establish colonization in the intestine of chicks 7 days after challenge. These results lead us to question the correlation between mRNA durability with cell viability as well as the significance of the VBNC cells in environmental transmission of Campylobacter spp.
Collapse
Affiliation(s)
- K D Sung
- Department of Food Science and Technology, University of Georgia, Athens, GA 30606, USA
| | | | | |
Collapse
|
577
|
Schouls LM, van der Heide HGJ, Vauterin L, Vauterin P, Mooi FR. Multiple-locus variable-number tandem repeat analysis of Dutch Bordetella pertussis strains reveals rapid genetic changes with clonal expansion during the late 1990s. J Bacteriol 2004; 186:5496-505. [PMID: 15292152 PMCID: PMC490882 DOI: 10.1128/jb.186.16.5496-5505.2004] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bordetella pertussis, the causative agent of whooping cough, has remained endemic in The Netherlands despite extensive nationwide vaccination since 1953. In the 1990s, several epidemic periods have resulted in many cases of pertussis. We have proposed that strain variation has played a major role in the upsurges of this disease in The Netherlands. Therefore, molecular characterization of strains is important in identifying the causes of pertussis epidemiology. For this reason, we have developed a multiple-locus variable-number tandem repeat analysis (MLVA) typing system for B. pertussis. By combining the MLVA profile with the allelic profile based on multiple-antigen sequence typing, we were able to further differentiate strains. The relationships between the various genotypes were visualized by constructing a minimum spanning tree. MLVA of Dutch strains of B. pertussis revealed that the genotypes of the strains isolated in the prevaccination period were diverse and clearly distinct from the strains isolated in the 1990s. Furthermore, there was a decrease in diversity in the strains from the late 1990s, with a remarkable clonal expansion that coincided with the epidemic periods. Using this genotyping, we have been able to show that B. pertussis is much more dynamic than expected.
Collapse
Affiliation(s)
- Leo M Schouls
- Laboratory for Vaccine-Preventable Diseases, National Institute of Public Health and the Environment, Bilthoven, The Netherlands.
| | | | | | | | | |
Collapse
|
578
|
Cladera AM, Bennasar A, Barceló M, Lalucat J, García-Valdés E. Comparative genetic diversity of Pseudomonas stutzeri genomovars, clonal structure, and phylogeny of the species. J Bacteriol 2004; 186:5239-48. [PMID: 15292125 PMCID: PMC490930 DOI: 10.1128/jb.186.16.5239-5248.2004] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A combined phylogenetic and multilocus DNA sequence analysis of 26 Pseudomonas stutzeri strains distributed within the 9 genomovars of the species has been performed. Type strains of the two most closely related species (P. balearica, former genomovar 6, and P. mendocina), together with P. aeruginosa, as the type species of the genus, have been included in the study. The extremely high genetic diversity and the clonal structure of the species were confirmed by the sequence analysis. Clustering of strains in the consensus phylogeny inferred from the analysis of seven nucleotide sequences (16S ribosomal DNA, internally transcribed spacer region 1, gyrB, rpoD, nosZ, catA, and nahH) confirmed the monophyletic origin of the genomovars within the Pseudomonas branch and is in good agreement with earlier DNA-DNA similarity analysis, indicating that the selected genes are representative of the whole genome in members of the species.
Collapse
Affiliation(s)
- Aina Maria Cladera
- Departament de Biologia, Microbiologia, Universitat de les Illes Balears, and Institut Mediterrani d'Estudis Avançats (CSIC-UIB), Palma de Mallorca, Spain
| | | | | | | | | |
Collapse
|
579
|
Best EL, Fox AJ, Frost JA, Bolton FJ. Identification of Campylobacter jejuni multilocus sequence type ST-21 clonal complex by single-nucleotide polymorphism analysis. J Clin Microbiol 2004; 42:2836-9. [PMID: 15184486 PMCID: PMC427879 DOI: 10.1128/jcm.42.6.2836-2839.2004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Conserved single-nucleotide polymorphisms (SNPs) which characterize the allelic profile of the major epidemiological lineage ST-21 were identified from the alleles within the current Campylobacter jejuni multilocus sequence typing (MLST) database. Allelic discrimination assays were designed for the detection of SNPs, enabling rapid strain profiling for clonal complex ST-21. This method is suitable for epidemiological investigations and is complementary to full MLST.
Collapse
Affiliation(s)
- E L Best
- Campylobacter Reference Unit, Laboratory of Enteric Pathogens, Specialist and Reference Microbiology Division, Health Protection Agency, 61 Colindale Ave., London NW9 5HT, United Kingdom.
| | | | | | | |
Collapse
|
580
|
Tavanti A, Gow NAR, Maiden MCJ, Odds FC, Shaw DJ. Genetic evidence for recombination in Candida albicans based on haplotype analysis. Fungal Genet Biol 2004; 41:553-62. [PMID: 15050544 DOI: 10.1016/j.fgb.2003.12.008] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2003] [Accepted: 12/24/2003] [Indexed: 10/26/2022]
Abstract
The possibility of sexual reproduction in the human pathogenic fungus Candida albicans is a question of great interest in medical mycology. Not only is it a fundamental biological issue, but it is also a potential mechanism for contributing to the phenotypic plasticity (and hence the virulence) of the organism. Molecular genotyping methods such as multi-locus sequence typing (MLST) are generating data that can shed light on this question. In the present study we have used MLST information to generate haplotypes that identify many different homologues of a chromosome within a collection of strains. Particular combinations of these haplotypes provide evidence for chromosomal segregation and intra-chromosome recombination. All of our observations of haplotype diversity could also be explained by other mechanisms, such as gene conversion or mitotic recombination, and the resolution of these issues will require a denser map of accurately localised markers. A common event observed in strain evolution is loss of heterozygosity at a particular marker. Our results contribute to the emerging picture of C. albicans as an organism whose primary means of reproduction is clonal, but with a small but important contribution from sexual reproduction, occurring in nature but not under commonly used laboratory conditions.
Collapse
Affiliation(s)
- Arianna Tavanti
- Department of Molecular and Cell Biology, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | | | | | | | | |
Collapse
|
581
|
Jolley KA, Chan MS, Maiden MCJ. mlstdbNet - distributed multi-locus sequence typing (MLST) databases. BMC Bioinformatics 2004; 5:86. [PMID: 15230973 PMCID: PMC459212 DOI: 10.1186/1471-2105-5-86] [Citation(s) in RCA: 408] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2004] [Accepted: 07/01/2004] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Multi-locus sequence typing (MLST) is a method of typing that facilitates the discrimination of microbial isolates by comparing the sequences of housekeeping gene fragments. The mlstdbNet software enables the implementation of distributed web-accessible MLST databases that can be linked widely over the Internet. RESULTS The software enables multiple isolate databases to query a single profiles database that contains allelic profile and sequence definitions. This separation enables isolate databases to be established by individual laboratories, each customized to the needs of the particular project and with appropriate access restrictions, while maintaining the benefits of a single definitive source of profile and sequence information. Databases are described by an XML file that is parsed by a Perl CGI script. The software offers a large number of ways to query the databases and to further break down and export the results generated. Additional features can be enabled by installing third-party (freely available) tools. CONCLUSION Development of a distributed structure for MLST databases offers scalability and flexibility, allowing participating centres to maintain ownership of their own data, without introducing duplication and data integrity issues.
Collapse
Affiliation(s)
- Keith A Jolley
- The Peter Medawar Building for Pathogen Research and Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3SY, UK
| | - Man-Suen Chan
- Department of Paediatrics, Institute for Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Martin CJ Maiden
- The Peter Medawar Building for Pathogen Research and Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3SY, UK
| |
Collapse
|
582
|
Siemer BL, Harrington CS, Nielsen EM, Borck B, Nielsen NL, Engberg J, On SLW. Genetic relatedness among Campylobacter jejuni serotyped isolates of diverse origin as determined by numerical analysis of amplified fragment length polymorphism (AFLP) profiles. J Appl Microbiol 2004; 96:795-802. [PMID: 15012818 DOI: 10.1111/j.1365-2672.2004.02205.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS To use amplified fragment length polymorphism (AFLP) analysis to evaluate the genetic relatedness among 254 Campylobacter jejuni reference and field strains of diverse origin representing all defined 'Penner' serotypes for this species. METHODS AND RESULTS Field strains (n = 207) from human diarrhoea and diverse animal and environmental sources were collected mainly through a National surveillance programme in Denmark and serotyped by use of the established 'Penner' scheme. Genetic relationships among these isolates, and the archetypal serotype reference strains, were assessed by numerical analysis of AFLP profiles derived from genomic DNA. Extensive genetic diversity was seen among the strains examined; however, 43 groups of isolates were identified at the 92% similarity (S-) level. Thirteen groups contained isolates from a single host, possibly representing genotypes of 'low risk' to human health. The remaining 30 groups contained isolates from humans, chickens and associated food products, cattle, sheep, turkeys, ostriches and/or dogs. Strains assigned to serotypes 2, 6/7, 11 and 12 formed major clusters at the 77.6% S-level. Most other serotypes did not form homogeneous clusters. CONCLUSIONS High-resolution genotyping applied to strains from a comprehensive range of sources provides evidence for multiple sources of sporadic C. jejuni infection. The results suggest that public health protection measures should be directed at all foods of animal origin. SIGNIFICANCE AND IMPACT OF THE STUDY The genetic relatedness among all 'Penner' serotypes of C. jejuni is assessed by AFLP analysis. In addition, further evidence of epidemic and host-specific clones of C. jejuni is provided.
Collapse
Affiliation(s)
- B L Siemer
- Danish Veterinary Institute, Departments of Bacteriology, Copenhagen, Denmark
| | | | | | | | | | | | | |
Collapse
|
583
|
Vázquez JA, Berrón S. [Multilocus sequence typing: the molecular marker of the Internet era]. Enferm Infecc Microbiol Clin 2004; 22:113-20. [PMID: 14756994 DOI: 10.1016/s0213-005x(04)73045-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Global or longer term epidemiology track the spread of clonal lineages, associated with hipervirulence or resistance or multi-resistance to antimicrobial agents. Therefore, the application of a molecular typing system for this purpose should produce data easily shared by different and geographically distant laboratories, as well as distinguish those clonal lineages even with low levels of variability accumulated in the genome.A marker based on the DNA sequence will produce objective results easily organized in data bases accessible by Internet. The application of a similar strategy that was used in the analysis of isoenzymes, by sequencing variable fragments of selected housekeeping genes, will allow obtaining a general view of the distribution of the clonal lineages and tracking their spread.
Collapse
Affiliation(s)
- Julio A Vázquez
- Laboratorio de Referencia de Neisserias, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, España.
| | | |
Collapse
|
584
|
Konkel ME, Klena JD, Rivera-Amill V, Monteville MR, Biswas D, Raphael B, Mickelson J. Secretion of virulence proteins from Campylobacter jejuni is dependent on a functional flagellar export apparatus. J Bacteriol 2004; 186:3296-303. [PMID: 15150214 PMCID: PMC415756 DOI: 10.1128/jb.186.11.3296-3303.2004] [Citation(s) in RCA: 233] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Campylobacter jejuni, a gram-negative motile bacterium, secretes a set of proteins termed the Campylobacter invasion antigens (Cia proteins). The purpose of this study was to determine whether the flagellar apparatus serves as the export apparatus for the Cia proteins. Mutations were generated in five genes encoding three structural components of the flagella, the flagellar basal body (flgB and flgC), hook (flgE2), and filament (flaA and flaB) genes, as well as in genes whose products are essential for flagellar protein export (flhB and fliI). While mutations that affected filament assembly were found to be nonmotile (Mot-) and did not secrete Cia proteins (S-), a flaA (flaB+) filament mutant was found to be nonmotile but Cia protein secretion competent (Mot-, S+). Complementation of a flaA flaB double mutant with a shuttle plasmid harboring either the flaA or flaB gene restored Cia protein secretion, suggesting that Cia export requires at least one of the two filament proteins. Infection of INT 407 human intestinal cells with the C. jejuni mutants revealed that maximal invasion of the epithelial cells required motile bacteria that are secretion competent. Collectively, these data suggest that the C. jejuni Cia proteins are secreted from the flagellar export apparatus.
Collapse
Affiliation(s)
- Michael E Konkel
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, USA.
| | | | | | | | | | | | | |
Collapse
|
585
|
Inglis GD, Kalischuk LD, Busz HW. A survey of Campylobacter species shed in faeces of beef cattle using polymerase chain reaction. Can J Microbiol 2004; 49:655-61. [PMID: 14735214 DOI: 10.1139/w03-087] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A polymerase chain reaction (PCR)-based survey of campylobacters associated with faeces collected from 382 beef cattle was undertaken. To ensure the removal of PCR inhibitors present in faeces and determine if adequate extraction was achieved, faeces were seeded with internal control DNA (i.e., DNA designed to amplify with the Campylobacter genus primer set, but provide a smaller amplicon) before the extraction procedure. In only two samples (0.5%) were the internal control or Campylobacter genus amplicons not detected. In the remaining 380 faecal samples, Campylobacter DNA was detected in 83% of the faecal samples (80% of the faecal samples were positive for Campylobacter genus DNA, and 3% of the samples were negative for Campylobacter genus DNA but positive for DNA of individual species). The most frequently detected species was Campylobacter lanienae (49%), a species only recently connected to livestock hosts. Campylobacter jejuni DNA was detected in 38% of the faecal samples, and Campylobacter hyointestinalis and Campylobacter coli DNA were detected in 8% and 0.5% of the samples, respectively. Campylobacter fetus DNA was not detected. Twenty-four percent of the faecal samples contained DNA of at least two species of Campylobacter. Of these samples, the majority (81%) contained DNA of C. jejuni and C. lanienae. The results of this study indicate that beef cattle commonly release a variety of Campylobacter species into the environment and may contribute to the high prevalence of campylobacteriosis in humans inhabiting areas of intensive cattle production, such as southern Alberta. Furthermore, this study demonstrates the utility of using PCR as a rapid and accurate method for simultaneously detecting the DNA of a diverse number of Campylobacter species associated with bovine faeces.
Collapse
Affiliation(s)
- G D Inglis
- Agriculture and Agri-Food Canada Research Centre, Lethbridge, AB, Canada.
| | | | | |
Collapse
|
586
|
Helgason E, Tourasse NJ, Meisal R, Caugant DA, Kolstø AB. Multilocus sequence typing scheme for bacteria of the Bacillus cereus group. Appl Environ Microbiol 2004; 70:191-201. [PMID: 14711642 PMCID: PMC321270 DOI: 10.1128/aem.70.1.191-201.2004] [Citation(s) in RCA: 222] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study we developed a multilocus sequence typing (MLST) scheme for bacteria of the Bacillus cereus group. This group, which includes the species B. cereus, B. thuringiensis, B. weihenstephanensis, and B. anthracis, is known to be genetically very diverse. It is also very important because it comprises pathogenic organisms as well as bacteria with industrial applications. The MLST system was established by using 77 strains having various origins, including humans, animals, food, and soil. A total of 67 of these strains had been analyzed previously by multilocus enzyme electrophoresis, and they were selected to represent the genetic diversity of this group of bacteria. Primers were designed for conserved regions of housekeeping genes, and 330- to 504-bp internal fragments of seven such genes, adk, ccpA, ftsA, glpT, pyrE, recF, and sucC, were sequenced for all strains. The number of alleles at individual loci ranged from 25 to 40, and a total of 53 allelic profiles or sequence types (STs) were distinguished. Analysis of the sequence data showed that the population structure of the B. cereus group is weakly clonal. In particular, all five B. anthracis isolates analyzed had the same ST. The MLST scheme which we developed has a high level of resolution and should be an excellent tool for studying the population structure and epidemiology of the B. cereus group.
Collapse
|
587
|
Davies RL, MacCorquodale R, Reilly S. Characterisation of bovine strains of Pasteurella multocida and comparison with isolates of avian, ovine and porcine origin. Vet Microbiol 2004; 99:145-58. [PMID: 15019106 DOI: 10.1016/j.vetmic.2003.11.013] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2003] [Revised: 11/07/2003] [Accepted: 11/07/2003] [Indexed: 11/19/2022]
Abstract
One hundred and fifty-three bovine Pasteurella multocida strains recovered primarily from cases of pneumonia and mastitis in England and Wales over an 11-year period were characterised by capsular PCR typing, comparison of outer membrane protein (OMP) profiles, and multilocus sequence analysis. All of the strains were of capsular type A with the exception of a single capsular type F isolate. Thirteen distinct OMP profiles (OMP-types) were identified based mainly on molecular mass heterogeneity of the heat-modifiable (OmpA) and porin (OmpH) proteins. However, 85% of the isolates were represented by just five OMP-types and 39% of the strains were of a single OMP-type. Multilocus sequence analysis revealed a limited degree of genetic diversity among bovine P. multocida isolates; strains of the same OMP-type have identical genetic backgrounds and represent distinct clones. Analysis of OMP variation was more discriminating than multilocus sequence analysis because strains of different OMP-types had the same, or similar, genetic backgrounds. The association of a small number of clones with the majority of cases of bovine pneumonia suggests that these clones have an increased capacity to cause disease compared to less frequently recovered clones. Molecular mass heterogeneity of OmpA and OmpH, in strains of the same or similar genetic background, suggests that these proteins are subject to diversifying selection within the host and might play important roles in host-pathogen interactions. Comparison of the OMP profiles of bovine isolates with those of avian, ovine and porcine strains showed that a high proportion of the respiratory tract infections in each of these species are caused by different strains of P. multocida. However, the presence of small numbers of closely related strains in more than one host species suggests that transmission of bacteria between different host species is also a factor in the population biology of P. multocida.
Collapse
Affiliation(s)
- Robert L Davies
- Division of Infection and Immunity, Institute of Biomedical and Life Sciences, Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
| | | | | |
Collapse
|
588
|
Foley SL, Simjee S, Meng J, White DG, McDermott PF, Zhao S. Evaluation of molecular typing methods for Escherichia coli O157:H7 isolates from cattle, food, and humans. J Food Prot 2004; 67:651-7. [PMID: 15083714 DOI: 10.4315/0362-028x-67.4.651] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Escherichia coli O157:H7, a Shiga toxin-producing E. coli, has been the causative agent of many cases of severe, often life-threatening foodborne illness. Because of the importance of E. coli O157:H7 to public health, many molecular typing methods have been developed to determine its transmission routes and source of infection during epidemiological investigations. Pulsed-field gel electrophoresis (PFGE) is currently used by public health organizations to track infections of E. coli O157:H7 and other foodborne pathogens. In this study, we compared the ability of PFGE, multilocus sequence typing (MLST), and repetitive-element PCR (Rep-PCR) to distinguish among 92 E. coli O157:H7 isolates from cattle, food, and infected humans. Several virulence genes, including the intimin gene (eaeA), the hemolysin gene (hlyA), and the H7 fimbrial gene (fliC), and a housekeeping gene for beta-glucuronidase (uidA) were included in MLST. Rep-PCR reactions were performed using a commercially available typing kit (Bacterial Barcodes Inc., Houston, Tex.) with the provided Uprime-RI primer set. Results of the study indicated that PFGE provided the most discrimination among the techniques, identifying 72 distinct PFGE profiles for the isolates; Rep-PCR elucidated 14 different profiles, whereas MLST generated five profiles. Additionally, there did not appear to be any correlation among the typing methods examined in this study. Therefore, to date, PFGE remains the technique of choice for molecular subtyping of E. coli O157:H7.
Collapse
Affiliation(s)
- Steven L Foley
- Department of Biology, University of Central Arkansas, Conway, Arkansas 72035, USA
| | | | | | | | | | | |
Collapse
|
589
|
Feil EJ, Li BC, Aanensen DM, Hanage WP, Spratt BG. eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data. J Bacteriol 2004; 186:1518-30. [PMID: 14973027 PMCID: PMC344416 DOI: 10.1128/jb.186.5.1518-1530.2004] [Citation(s) in RCA: 1431] [Impact Index Per Article: 71.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The introduction of multilocus sequence typing (MLST) for the precise characterization of isolates of bacterial pathogens has had a marked impact on both routine epidemiological surveillance and microbial population biology. In both fields, a key prerequisite for exploiting this resource is the ability to discern the relatedness and patterns of evolutionary descent among isolates with similar genotypes. Traditional clustering techniques, such as dendrograms, provide a very poor representation of recent evolutionary events, as they attempt to reconstruct relationships in the absence of a realistic model of the way in which bacterial clones emerge and diversify to form clonal complexes. An increasingly popular approach, called BURST, has been used as an alternative, but present implementations are unable to cope with very large data sets and offer crude graphical outputs. Here we present a new implementation of this algorithm, eBURST, which divides an MLST data set of any size into groups of related isolates and clonal complexes, predicts the founding (ancestral) genotype of each clonal complex, and computes the bootstrap support for the assignment. The most parsimonious patterns of descent of all isolates in each clonal complex from the predicted founder(s) are then displayed. The advantages of eBURST for exploring patterns of evolutionary descent are demonstrated with a number of examples, including the simple Spain(23F)-1 clonal complex of Streptococcus pneumoniae, "population snapshots" of the entire S. pneumoniae and Staphylococcus aureus MLST databases, and the more complicated clonal complexes observed for Campylobacter jejuni and Neisseria meningitidis.
Collapse
Affiliation(s)
- Edward J Feil
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom.
| | | | | | | | | |
Collapse
|
590
|
Harrington CS, Moran L, Ridley AM, Newell DG, Madden RH. Inter-laboratory evaluation of three flagellin PCR/RFLP methods for typing Campylobacter jejuni and C. coli: the CAMPYNET experience. J Appl Microbiol 2004; 95:1321-33. [PMID: 14633007 DOI: 10.1046/j.1365-2672.2003.02101.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS To compare typeability, discriminatory ability, and inter-laboratory reproducibility of three flagellin PCR/RFLP (fla typing) methods previously described for Campylobacter. METHODS AND RESULTS The sample set (n = 100) was diverse, including both C. jejuni (n = 85) and C. coli (n = 15). Two of the three flaA typing methods amplified flaA alone, whereas one, a multiplex assay, amplified flaB in addition to flaA. DdeI restriction enzyme was employed for all methods, but HinfI was also investigated. 98-100% typeability was obtained for flaA-based methods, but only 93% for the multiplex assay, due to inconsistent amplification of a non-specific product. In addition, there appeared to be selective amplification of flaA over flaB. More DdeI types were generated using a longer flaA PCR amplicon, whilst additional use of HinfI increased the number of types by ca 25%. Inter-laboratory reproducibility for both flaA-based methods was defined at 100%. CONCLUSIONS Fla typing requires standardization with respect to PCR primers and restriction enzymes. This study identified an assay, employing the full flaA gene and DdeI digestion, as an appropriate method on which to standardize. 100% inter-laboratory reproducibility was demonstrated using that method. SIGNIFICANCE AND IMPACT OF THE STUDY This work should facilitate progress towards inter-laboratory standardization of fla typing.
Collapse
|
591
|
Hopkins KL, Desai M, Frost JA, Stanley J, Logan JMJ. Fluorescent amplified fragment length polymorphism genotyping of Campylobacter jejuni and Campylobacter coli strains and its relationship with host specificity, serotyping, and phage typing. J Clin Microbiol 2004; 42:229-35. [PMID: 14715757 PMCID: PMC321682 DOI: 10.1128/jcm.42.1.229-235.2004] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fluorescent amplified fragment length polymorphism (FAFLP) analysis was applied to 276 Campylobacter jejuni strains and 87 Campylobacter coli strains isolated from humans, pigs, cattle, poultry, and retail meats to investigate whether certain FAFLP genotypes of C. jejuni and C. coli are associated with a particular host and to determine the degree of association between FAFLP-defined genotypes and heat-stable serotypes and/or phage types. Within C. coli, the poultry strains clustered separately from those of porcine origin. In contrast, no evidence of host specificity was detected among C. jejuni strains. While C. coli strains show host specificity by FAFLP genotyping, C. jejuni strains that are genotypically similar appear to colonize a range of hosts, rather than being host adapted. Some serotypes and/or phage types (C. jejuni serotype HS18, phage type PT6, and serophage type HS19/PT2 and C. coli HS66, PT2, and HS56/PT2) were the most homogeneous by FAFLP genotyping, while others were more heterogeneous (C. jejuni HS5 and PT39, and C. coli HS24 and PT44) and therefore poor indicators of genetic relatedness between strains. The lack of host specificity in C. jejuni suggests that tracing the source of infection during epidemiological investigations will continue to be difficult. The lack of congruence between some serotypes and/or phage types and FAFLP genotype underlines the need for phenotypic testing to be supplemented by genotyping. This study also demonstrates how, in general, FAFLP generates "anonymous" genetic markers for strain characterization and epidemiological investigation of Campylobacter in the food chain.
Collapse
Affiliation(s)
- Katie L. Hopkins
- Specialist & Reference Microbiology Division, Health Protection Agency, London NW9 5HT, United Kingdom
| | - Meeta Desai
- Specialist & Reference Microbiology Division, Health Protection Agency, London NW9 5HT, United Kingdom
| | - Jennifer A. Frost
- Specialist & Reference Microbiology Division, Health Protection Agency, London NW9 5HT, United Kingdom
| | - John Stanley
- Specialist & Reference Microbiology Division, Health Protection Agency, London NW9 5HT, United Kingdom
| | - Julie M. J. Logan
- Specialist & Reference Microbiology Division, Health Protection Agency, London NW9 5HT, United Kingdom
- Corresponding author. Mailing address: Specialist & Reference Microbiology Division (GPBU), Health Protection Agency, 61 Colindale Ave., London, NW9 5HT, United Kingdom. Phone: 44 (0)20 8200 4400. Fax: 44 (0)20 8358 3138. E-mail:
| |
Collapse
|
592
|
Dodgson AR, Pujol C, Denning DW, Soll DR, Fox AJ. Multilocus sequence typing of Candida glabrata reveals geographically enriched clades. J Clin Microbiol 2004; 41:5709-17. [PMID: 14662965 PMCID: PMC309006 DOI: 10.1128/jcm.41.12.5709-5717.2003] [Citation(s) in RCA: 134] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The haploid pathogenic yeast Candida glabrata is the second most common Candida species isolated from cases of bloodstream infection. The clinical relevance of C. glabrata is enhanced by its reduced susceptibility to fluconazole. Despite this, little is known of the epidemiology or population structure of this species. We developed a multilocus sequence typing (MLST) scheme for C. glabrata and used it to fingerprint a geographically diverse collection of 107 clinical isolates and 2 reference strains. Appropriate loci were identified by amplifying and sequencing fragments of the coding regions of 11 C. glabrata genes in 10 unrelated isolates. The 6 most variable loci (FKS, LEU2, NMT1, TRP1, UGP1, and URA3) were sequenced in the collection of 109 isolates. From the 3,345 bp sequenced in each isolate, 81 nucleotide sites were found to be variable. These defined 30 STs among the 109 strains. The technique was validated by comparison with random amplified polymorphic DNA and the complex DNA fingerprinting probes Cg6 and Cg12. MLST identified 5 major clades among the isolates studied. Three of the clades exhibited significant geographical bias. Our data demonstrate for the first time, with such a large geographically diverse strain collection, that distinct genetic clades of C. glabrata prevail in different geographical regions.
Collapse
Affiliation(s)
- Andrew R Dodgson
- School of Medicine, University of Manchester, Manchester, United Kingdom
| | | | | | | | | |
Collapse
|
593
|
Duim B, Godschalk PCR, van den Braak N, Dingle KE, Dijkstra JR, Leyde E, van der Plas J, Colles FM, Endtz HP, Wagenaar JA, Maiden MCJ, van Belkum A. Molecular evidence for dissemination of unique Campylobacter jejuni clones in Curaçao, Netherlands Antilles. J Clin Microbiol 2004; 41:5593-7. [PMID: 14662946 PMCID: PMC309031 DOI: 10.1128/jcm.41.12.5593-5597.2003] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Campylobacter jejuni isolates (n = 234) associated with gastroenteritis and the Guillain-Barré syndrome (GBS) in the island of Curaçao, Netherlands Antilles, and collected from March 1999 to March 2000 were investigated by a range of molecular typing techniques. Data obtained by pulsed-field gel electrophoresis (PFGE), amplified fragment length polymorphism (AFLP) analysis, multilocus sequence typing (MLST), automated ribotyping, and sequence analysis of the short variable region of the flagellin gene (flaA) were analyzed separately and in combination. Similar groupings were obtained by all methods, with the data obtained by MLST and AFLP analysis exhibiting the highest degree of congruency. MLST identified 29 sequence types, which were assigned to 10 major clonal complexes. PFGE, AFLP analysis, and ribotyping identified 10, 9, and 8 of these clonal groups, respectively; however, these three techniques permitted subdivision of the clonal groups into more different types. Members of seven clonal groups comprising 107 isolates were obtained from November 1999 to February 2000, and no distinguishing characteristics were identified for two GBS-associated strains. The sequence type 41 (ST-41), ST-508, and ST-657 clonal complexes and their corresponding AFLP types have been rare or absent in the Campylobacter data sets described to date. We conclude that several clonal complexes of C. jejuni are associated with human disease in Curaçao, and some of these have not been reported elsewhere. Furthermore, given the observation that C. jejuni-associated diseases appear to be more severe from November to February, it can be speculated that this may be due to the presence of virulent clones with a limited span of circulation.
Collapse
Affiliation(s)
- Birgitta Duim
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, The Netherlands.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
594
|
Manning G, Dowson CG, Bagnall MC, Ahmed IH, West M, Newell DG. Multilocus sequence typing for comparison of veterinary and human isolates of Campylobacter jejuni. Appl Environ Microbiol 2004; 69:6370-9. [PMID: 14602588 PMCID: PMC262249 DOI: 10.1128/aem.69.11.6370-6379.2003] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multilocus sequence typing (MLST) has been applied to 266 Campylobacter jejuni isolates, mainly from veterinary sources, including cattle, sheep, poultry, pigs, pets, and the environment, as well as isolates from human cases of campylobacteriosis. The populations of veterinary and human isolates overlap, suggesting that most veterinary sources should be considered reservoirs of pathogenic campylobacters. There were some associations between source and sequence type complex, indicating that host or source adaptation may exist. The pig isolates formed a distinct group by MLST and may well represent a potential pig-adapted clone of C. jejuni. A subset (n = 82) of isolates was reanalyzed with a second MLST scheme which provided a unique set of isolates that had been analyzed at a total of 12 loci. The distribution of isolates among the complexes in each of the two schemes was similar but not identical. In addition to isolates from human outbreaks, one group of isolates that were not epidemiologically linked was also identical at all 12 loci. This group of isolates is believed to represent another stable strain of C. jejuni.
Collapse
Affiliation(s)
- Georgina Manning
- Veterinary Laboratories Agency (Weybridge), New Haw, Addlestone, Surrey KT15 3NB, United Kingdom
| | | | | | | | | | | |
Collapse
|
595
|
Guévremont E, Higgins R, Quessy S. Characterization of Campylobacter isolates recovered from clinically healthy pigs and from sporadic cases of campylobacteriosis in humans. J Food Prot 2004; 67:228-34. [PMID: 14968951 DOI: 10.4315/0362-028x-67.2.228] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Campylobacter spp. were recovered from 660 (77.6%) of 850 swine cecal contents at the abattoir and from 24 (8.6%) of 278 specimens from sporadic cases of human diarrhea during the same period in the same geographical area. Campylobacter coli represented 95.7% of Campylobacter isolates recovered from pigs and 8.3% of those isolated from humans. Genetic profiles were determined by pulsed-field gel electrophoresis (PFGE) using KpnI enzyme to characterize the isolates in combination with phenotypic assays to detect production of cytotoxins, enterotoxins, and hemolysins. Among a subset of isolates (n = 10), up to five colonies from the same animal were characterized by PFGE. In 5 (50%) of 10 of the isolates, more than one genetic profile was observed per pig. Among the 100 isolates from pigs selected for further analysis, 81 different genetic profiles were observed, whereas 20 different genetic profiles were found among the 24 isolates of human origin. Cytotoxicity on Chinese hamster ovary cells was observed in 11 (11%) of 98 isolates from pigs and in 5 (21%) of 24 Campylobacter isolates from humans. No enterotoxin production was detected in Campylobacter isolates in this study, but 17 (71%) of 24 human and 61 (63%) of 97 pig isolates showed hemolytic activity. The study of genotypic and phenotypic profiles of swine and human isolates revealed no epidemiological relationship between isolates. The low genomic relatedness observed between groups of isolates and the weak toxicity level of swine isolates suggest that the hazard of contamination of humans by Campylobacter associated with swine production is low.
Collapse
Affiliation(s)
- Evelyne Guévremont
- Faculté de Médecine Vétérinaire, Université de Montréal, C.P. 5000, St-Hyacinthe, Quebec, Canada J2S 7C6
| | | | | |
Collapse
|
596
|
Manfreda G, De Cesare A, Bondioli V, Franchini A. Ribotyping characterisation of campylobacter isolates randomly collected from different sources in Italy. Diagn Microbiol Infect Dis 2004; 47:385-92. [PMID: 14522511 DOI: 10.1016/s0732-8893(03)00117-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In this study the potential for using the automated PstI ribotyping as a primary library typing method to survey Campylobacter and for identification of two thermophilic Campylobacter jejuni and Campylobacter coli species was evaluated. A total of 158 isolates randomly collected in Italy from different sources were analyzed. A large percentage of chicken (28%), turkey (27%) and turkey meat (25%) isolates shared their ribotyping profiles (ribotypes) with those of humans, whereas the swine isolates had unique profiles. The identification results obtained by ribotyping corresponded to those collected by using a multiplex PCR protocol specifically designed for C. jejuni and C. coli detection. The comparison of the PstI ribotyping profiles obtained in this research with those of the isolates collected over time will facilitate determining the ribotypes that are more frequently transmitted to humans in comparison to those that are normally harboured only in animals, foods and in the environment.
Collapse
Affiliation(s)
- Gerardo Manfreda
- Department of Food Science, Alma Mater Studiorum, University of Bologna, Via S. Giacomo 9, 40126 Bologna, Italy.
| | | | | | | |
Collapse
|
597
|
Sails AD, Swaminathan B, Fields PI. Utility of multilocus sequence typing as an epidemiological tool for investigation of outbreaks of gastroenteritis caused by Campylobacter jejuni. J Clin Microbiol 2004; 41:4733-9. [PMID: 14532212 PMCID: PMC254344 DOI: 10.1128/jcm.41.10.4733-4739.2003] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multilocus sequence typing (MLST) has been proven useful for the study of the global population structure of Campylobacter jejuni; however, its usefulness for the investigation of outbreaks of disease caused by C. jejuni has not been proven. In this study, MLST plus sequencing of the flaA short variable region (SVR) were applied to 47 isolates from 12 outbreaks of C. jejuni infection whose relatedness has been determined previously, and the results were compared to those of serotyping and pulsed-field gel electrophoresis (PFGE). Isolates implicated in an outbreak were indistinguishable by all four subtyping methods, with sporadic isolates being distinguished from outbreak isolates. Two sporadic isolates from one outbreak were resistant to SmaI digestion and therefore nontypeable by PFGE but were differentiated from the outbreak strain by the other methods. PFGE and flaA SVR typing were the most discriminatory methods, with discriminatory indices (DI) of 0.930 and 0.923, respectively. However, an epidemic strain from one outbreak was distinguished from the other outbreak isolates by flaA SVR typing; its flaA allele was different at five nucleotides, suggesting that this change was possibly mediated by recombination. MLST was less discriminatory than PFGE and flaA SVR typing (DI = 0.859), and many of the epidemic strains possessed common sequence types (STs) including ST-8, -21, -22, and -42. However, further discrimination within STs was achieved by flaA SVR typing or PFGE. The results from this study demonstrate that a combined approach of MLST plus flaA SVR typing provides a level of discrimination equivalent to PFGE for outbreak investigations.
Collapse
Affiliation(s)
- Andrew D Sails
- Foodborne and Diarrheal Diseases Branch, Division of Bacterial and Mycotic Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
| | | | | |
Collapse
|
598
|
Abstract
The characterization of pathogenic isolates plays a pivotal role in the epidemiology of infectious diseases, generating the information necessary for identifying, tracking, and intervening against disease outbreaks. In 1998 multi-locus sequence typing (MLST) was proposed as a nucleotide sequence-based approach that could be applied to many bacterial pathogens. It combined developments in high-throughput sequencing and bioinformatics with established population genetics techniques to provide a portable, reproducible, and scalable typing system that reflected the population and evolutionary biology of bacterial pathogens. MLST schemes have been developed for a variety of procaryotic and eucaryotic pathogens and the data generated have contributed to both epidemiological surveillance and fundamental studies of pathogen biology.
Collapse
Affiliation(s)
- Rachel Urwin
- Peter Medawar Building for Pathogen Research and Department of Zoology, University of Oxford, South Parks Road, OX1 3SY, Oxford, UK
| | | |
Collapse
|
599
|
Pearson BM, Pin C, Wright J, I'Anson K, Humphrey T, Wells JM. Comparative genome analysis of Campylobacter jejuni using whole genome DNA microarrays. FEBS Lett 2003; 554:224-30. [PMID: 14596944 DOI: 10.1016/s0014-5793(03)01164-5] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Whole genome DNA microarrays were constructed and used to investigate genomic diversity in 18 Campylobacter jejuni strains from diverse sources. New algorithms were developed that dynamically determine the boundary between the conserved and variable genes. Seven hypervariable plasticity regions (PR) were identified in the genome (PR1 to PR7) containing 136 genes (50%) of the variable gene pool. When comparisons were made with the sequenced strain NCTC11168, the number of absent or divergent genes ranged from 2.6% (40 genes) to 10.2% (163) and in total 16.3% (269) of the genes were variable. PR1 contains genes important in the utilisation of alternative electron acceptors for respiration and may confer a selective advantage to strains in restricted oxygen environments. PR2, 3 and 7 contain many outer membrane and periplasmic proteins and hypothetical proteins of unknown function that might be linked to phenotypic variation and adaptation to different ecological niches. PR4, 5 and 6 contain genes involved in the production and modification of antigenic surface structures.
Collapse
Affiliation(s)
- B M Pearson
- BBSRC Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
| | | | | | | | | | | |
Collapse
|
600
|
Colles FM, Jones K, Harding RM, Maiden MCJ. Genetic diversity of Campylobacter jejuni isolates from farm animals and the farm environment. Appl Environ Microbiol 2003; 69:7409-13. [PMID: 14660392 PMCID: PMC309911 DOI: 10.1128/aem.69.12.7409-7413.2003] [Citation(s) in RCA: 141] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2003] [Accepted: 09/08/2003] [Indexed: 11/20/2022] Open
Abstract
The genetic diversity of Campylobacter jejuni isolates from farm animals and their environment was investigated by multilocus sequence typing (MLST). A total of 30 genotypes, defined by allelic profiles (assigned to sequence types [STs]), were found in 112 C. jejuni isolates originating in poultry, cattle, sheep, starlings, and slurry. All but two of these genotypes belonged to one of nine C. jejuni clonal complexes previously identified in isolates from human disease and retail food samples and one clonal complex previously associated with an environmental source. There was some evidence for the association of certain clonal complexes with particular farm animals: isolates belonging to the ST-45 complex predominated among poultry isolates but were absent among sheep isolates, while isolates belonging to the ST-61 and ST-42 complexes were predominant among sheep isolates but were absent from the poultry isolates. In contrast, ST-21 complex isolates were distributed among the different isolation sources. Comparison with MLST data from 91 human disease isolates showed small but significant genetic differentiation between the farm and human isolates; however, representatives of six clonal complexes were found in both samples. These data demonstrate that MLST and the clonal complex model can be used to identify and compare the genotypes of C. jejuni isolates from farm animals and the environment with those from retail food and human disease.
Collapse
Affiliation(s)
- F M Colles
- Departments of Zoology, University of Oxford, Oxford OX1 3SY, United Kingdom
| | | | | | | |
Collapse
|