601
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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.
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Affiliation(s)
- Georgina Manning
- Veterinary Laboratories Agency (Weybridge), New Haw, Addlestone, Surrey KT15 3NB, United Kingdom
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602
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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.
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Affiliation(s)
- Evelyne Guévremont
- Faculté de Médecine Vétérinaire, Université de Montréal, C.P. 5000, St-Hyacinthe, Quebec, Canada J2S 7C6
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603
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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.
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Affiliation(s)
- Gerardo Manfreda
- Department of Food Science, Alma Mater Studiorum, University of Bologna, Via S. Giacomo 9, 40126 Bologna, Italy.
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604
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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.
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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.
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605
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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.
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Affiliation(s)
- Rachel Urwin
- Peter Medawar Building for Pathogen Research and Department of Zoology, University of Oxford, South Parks Road, OX1 3SY, Oxford, UK
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606
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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.
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Affiliation(s)
- B M Pearson
- BBSRC Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
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607
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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.
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Affiliation(s)
- F M Colles
- Departments of Zoology, University of Oxford, Oxford OX1 3SY, United Kingdom
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608
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Wilson DL, Bell JA, Young VB, Wilder SR, Mansfield LS, Linz JE. Variation of the natural transformation frequency of Campylobacter jejuni in liquid shake culture. Microbiology (Reading) 2003; 149:3603-3615. [PMID: 14663092 DOI: 10.1099/mic.0.26531-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Natural transformation, a mechanism that generates genetic diversity in Campylobacter jejuni, was studied in a novel liquid shake culturing system that allowed an approximately 10 000-fold increase in cell density. C. jejuni transformation frequency was analysed in this system under 10 %, 5·0 % and 0·7 % CO2 atmospheres. At 5·0 % and 10 % CO2 concentrations, when purified isogenic chromosomal DNA was used to assess competence, transformation frequency ranged from 10−3 to 10−4 at low cell concentrations and declined as cell density increased. Transformation frequency under a 0·7 % CO2 atmosphere was more stable, maintaining 10−3 levels at high cell densities, and was 10- to 100-fold higher than that under a 10 % CO2 atmosphere. Three of four C. jejuni strains tested under a 5·0 % CO2 atmosphere were naturally competent for isogenic DNA; competent strains demonstrated a lack of barriers to intraspecies genetic exchange by taking up and incorporating chromosomal DNA from multiple C. jejuni donors. C. jejuni showed a preference for its own DNA at the species level, and co-cultivation demonstrated that DNA transfer via natural transformation occurred between isogenic populations during short periods of exposure in liquid medium when cell density and presumably DNA concentrations were low. Transformation frequency during co-cultivation of isogenic populations was also influenced by CO2 concentration. Under a 0·7 % CO2 atmosphere, co-cultivation transformation frequency increased approximately 500-fold in a linear fashion with regard to cell density, and was 1000- to 10 000-fold higher during late-exponential-phase growth when compared to cultures grown under a 10 % CO2 atmosphere.
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Affiliation(s)
- David L Wilson
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, Michigan, USA
- National Food Safety and Toxicology Center, Michigan State University, East Lansing, Michigan, USA
| | - Julia A Bell
- National Food Safety and Toxicology Center, Michigan State University, East Lansing, Michigan, USA
| | - Vincent B Young
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
- National Food Safety and Toxicology Center, Michigan State University, East Lansing, Michigan, USA
| | - Stacey R Wilder
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
- National Food Safety and Toxicology Center, Michigan State University, East Lansing, Michigan, USA
| | - Linda S Mansfield
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
- National Food Safety and Toxicology Center, Michigan State University, East Lansing, Michigan, USA
| | - John E Linz
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, Michigan, USA
- National Food Safety and Toxicology Center, Michigan State University, East Lansing, Michigan, USA
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609
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Ko KS, Hong SK, Lee HK, Park MY, Kook YH. Molecular evolution of the dotA gene in Legionella pneumophila. J Bacteriol 2003; 185:6269-77. [PMID: 14563861 PMCID: PMC219400 DOI: 10.1128/jb.185.21.6269-6277.2003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The molecular evolution of dotA, which is related to the virulence of Legionella pneumophila, was investigated by comparing the sequences of 15 reference strains (serogroups 1 to 15). It was found that dotA has a complex mosaic structure. The whole dotA gene of Legionella pneumophila subsp. pneumophila serogroups 2, 6, and 12 has been transferred from Legionella pneumophila subsp. fraseri. A discrepancy was found between the trees inferred from the nucleotide and deduced amino acid sequences of dotA, which suggests that multiple hits, resulting in synonymous substitutions, have occurred. Gene phylogenies inferred from three different segments (the 5'-end region, the central, large periplasmic domain, and the 3'-end region) showed impressively dissimilar topologies. This was concordant with the sequence polymorphisms, indicating that each region has experienced an independent evolutionary history, and was evident even within the same domain of each strain. For example, the PP2 domain was found to have a heterogeneous structure, which led us hypothesize that the dotA gene of L. pneumophila may have originated from two or more different sources. Comparisons of synonymous and nonsynonymous substitutions demonstrated that the PP2 domain has been under strong selective pressure with respect to amino acid change. Split decomposition analysis also supported the intragenic recombination of dotA. Multiple recombinational exchange within the dotA gene, encoding an integral cytoplasmic membrane protein that is secreted, probably provided increased fitness in certain environmental niches, such as within a particular biofilm community or species of amoebae.
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Affiliation(s)
- Kwan Soo Ko
- Department of Microbiology and Cancer Research Institute, Institute of Endemic Diseases, SNUMRC, Seoul National University College of Medicine, and Clinical Research Institute, Seoul National University Hospital, Seoul 110-799, Korea
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610
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Wang XM, Noble L, Kreiswirth BN, Eisner W, McClements W, Jansen KU, Anderson AS. Evaluation of a multilocus sequence typing system for Staphylococcus epidermidis. J Med Microbiol 2003; 52:989-998. [PMID: 14532344 DOI: 10.1099/jmm.0.05360-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Staphylococcus epidermidis is a significant cause of nosocomial disease. However, the taxonomy of this pathogen, particularly at subspecies level, is unclear. A multilocus sequence typing (MLST) scheme has therefore been investigated as a tool to elucidate taxonomic relationships within this group, based on genetic relatedness. DNA sequences for internal fragments of seven housekeeping genes were compared in 47 geographically and temporally diverse S. epidermidis isolates that were obtained from clinical infections. Twenty-three different allelic profiles were detected; 17 of these were represented by single strains and the largest profile group contained 17 isolates. Diversity of the same collection of isolates was investigated by using PFGE of SmaI-digested genomic DNA to test the discrimination and validity of the MLST approach. Isolates within the largest profile group were resolved into four distinct PFGE clusters on the basis of their SmaI digest patterns. Isolates within other profile groups that contained multiple isolates had matching PFGE SmaI patterns within each group. It appears that MLST is an effective method for grouping S. epidermidis strains at the subspecies level; however, it is not as discriminatory as it has been for other species for which MLST schemes have been established and, used alone, would not be a useful method for epidemiological studies. In addition, it was demonstrated that this method was effective for confirming the identity of S. epidermidis CoNS (coagulase-negative) isolates.
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Affiliation(s)
- Xin-Min Wang
- Merck and Co. Inc., PO Box 4 WP 26-265, Sumneytown Pike, West Point, PA 19486, USA 2Merck and Co. Inc., PO Box 2000 RY80Y 230, 126 E. Lincoln Ave., Rahway, NJ 07065, USA 3PHRI TB Center, Public Health Research Institute, 225 Warren Street, Newark, NJ 07103, USA
| | - Liliane Noble
- Merck and Co. Inc., PO Box 4 WP 26-265, Sumneytown Pike, West Point, PA 19486, USA 2Merck and Co. Inc., PO Box 2000 RY80Y 230, 126 E. Lincoln Ave., Rahway, NJ 07065, USA 3PHRI TB Center, Public Health Research Institute, 225 Warren Street, Newark, NJ 07103, USA
| | - Barry N Kreiswirth
- Merck and Co. Inc., PO Box 4 WP 26-265, Sumneytown Pike, West Point, PA 19486, USA 2Merck and Co. Inc., PO Box 2000 RY80Y 230, 126 E. Lincoln Ave., Rahway, NJ 07065, USA 3PHRI TB Center, Public Health Research Institute, 225 Warren Street, Newark, NJ 07103, USA
| | - William Eisner
- Merck and Co. Inc., PO Box 4 WP 26-265, Sumneytown Pike, West Point, PA 19486, USA 2Merck and Co. Inc., PO Box 2000 RY80Y 230, 126 E. Lincoln Ave., Rahway, NJ 07065, USA 3PHRI TB Center, Public Health Research Institute, 225 Warren Street, Newark, NJ 07103, USA
| | - William McClements
- Merck and Co. Inc., PO Box 4 WP 26-265, Sumneytown Pike, West Point, PA 19486, USA 2Merck and Co. Inc., PO Box 2000 RY80Y 230, 126 E. Lincoln Ave., Rahway, NJ 07065, USA 3PHRI TB Center, Public Health Research Institute, 225 Warren Street, Newark, NJ 07103, USA
| | - Kathrin U Jansen
- Merck and Co. Inc., PO Box 4 WP 26-265, Sumneytown Pike, West Point, PA 19486, USA 2Merck and Co. Inc., PO Box 2000 RY80Y 230, 126 E. Lincoln Ave., Rahway, NJ 07065, USA 3PHRI TB Center, Public Health Research Institute, 225 Warren Street, Newark, NJ 07103, USA
| | - Annaliesa S Anderson
- Merck and Co. Inc., PO Box 4 WP 26-265, Sumneytown Pike, West Point, PA 19486, USA 2Merck and Co. Inc., PO Box 2000 RY80Y 230, 126 E. Lincoln Ave., Rahway, NJ 07065, USA 3PHRI TB Center, Public Health Research Institute, 225 Warren Street, Newark, NJ 07103, USA
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611
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Sadowy E, Zhou J, Meats E, Gniadkowski M, Spratt BG, Hryniewicz W. Identification of multidrug-resistant Streptococcus pneumoniae strains isolated in Poland by multilocus sequence typing. Microb Drug Resist 2003; 9:81-6. [PMID: 12705686 DOI: 10.1089/107662903764736373] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Multilocus sequence typing (MLST) of 35 isolates of multidrug-resistant Streptococcus pneumoniae recovered in Poland during 1995-1996 distinguished 10 different sequence types (ST). The majority of the isolates were assigned to two Polish clones of serotypes 6B and 23F, although the international clones, Spain23F-1 and Spain9V-3, were also identified. Similar results were obtained using pulsed-field gel electrophoresis (PFGE), providing a direct comparison of these two typing methods.
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Affiliation(s)
- Ewa Sadowy
- Sera & Vaccines Central Research Laboratory, 00-725 Warsaw, Poland.
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612
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Abstract
AIM This is a review of the natural Campylobacter colonization and transmission among ruminant livestock in the dairy farm environment. METHODS AND RESULTS Using cultural detection methods and enumeration techniques the distribution of Campylobacter in ruminant animals at birth, on the farm, at slaughter and in the farm environment have been examined. Colonization and shedding rates are higher among young animals while patterns of shedding in adult animals may be seasonal. Stored and land-dispersed slurries provide a reservoir for scavenging birds and flies and a source for runoff. CONCLUSIONS The dairy farm plays a significant role in the dissemination of Campylobacter subtypes that can cause disease in the human community. SIGNIFICANCE AND IMPACT OF STUDY An understanding of the role of the dairy farm in the environmental cycle of Campylobacter is required in order to devise intervention strategies.
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Affiliation(s)
- K Stanley
- Rowett Research Institute, Bucksburn, Aberdeen, UK.
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613
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Sails AD, Swaminathan B, Fields PI. Clonal complexes of Campylobacter jejuni identified by multilocus sequence typing correlate with strain associations identified by multilocus enzyme electrophoresis. J Clin Microbiol 2003; 41:4058-67. [PMID: 12958226 PMCID: PMC193858 DOI: 10.1128/jcm.41.9.4058-4067.2003] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) with SmaI were used to subtype 55 isolates of Campylobacter jejuni from a diverse range of human and animal sources previously characterized by multilocus enzyme electrophoresis (MEE). MEE and MLST targeted 11 and 7 loci, respectively, and all loci were unique to each method. MEE, MLST, and PFGE identified 40, 37, and 48 discrete subtypes, respectively, with many of the subtypes occurring only once within the data set. Simpson's indices of diversity were calculated to be 0.979, 0.966, and 0.994 for MEE, MLST, and PFGE, respectively, demonstrating that MEE and MLST had similar discriminatory powers but that PFGE was more discriminatory. Allele diversity was higher in the MLST loci; individual single-locus diversities for the 11 MEE loci and the 7 MLST loci were 0.491 and 0.854, respectively. The clonal complexes recognized by MLST correlated with the strain associations previously recognized by MEE and contained some isolates indistinguishable by PFGE. Many clusters contained isolates from diverse geographical regions and from both humans and animals. These results demonstrate the usefulness of MLST for investigation of the global epidemiology of this important pathogen and illustrate its potential to identify indistinguishable strains or clones in geographically distinct regions.
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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.
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614
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Wiesner RS, Hendrixson DR, DiRita VJ. Natural transformation of Campylobacter jejuni requires components of a type II secretion system. J Bacteriol 2003; 185:5408-18. [PMID: 12949093 PMCID: PMC193740 DOI: 10.1128/jb.185.18.5408-5418.2003] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The human pathogen Campylobacter jejuni is one of more than 40 naturally competent bacterial species able to import macromolecular DNA from the environment and incorporate it into their genomes. However, in C. jejuni little is known about the genes involved in this process. We used random transposon mutagenesis to identify genes that are required for the transformation of this organism. We isolated mutants with insertions in 11 different genes; most of the mutants are affected in the DNA uptake stage of transformation, whereas two mutants are affected in steps subsequent to DNA uptake, such as recombination into the chromosome or in DNA transport across the inner membrane. Several of these genes encode proteins homologous to those involved in type II secretion systems, biogenesis of type IV pili, and competence for natural transformation in gram-positive and gram-negative species. Other genes identified in our screen encode proteins unique to C. jejuni or are homologous to proteins that have not been shown to play a role in the transformation in other bacteria.
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Affiliation(s)
- Rebecca S Wiesner
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109-0620, USA
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615
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Tavanti A, Gow NAR, Senesi S, Maiden MCJ, Odds FC. Optimization and validation of multilocus sequence typing for Candida albicans. J Clin Microbiol 2003; 41:3765-76. [PMID: 12904388 PMCID: PMC179823 DOI: 10.1128/jcm.41.8.3765-3776.2003] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multilocus sequence typing (MLST) was applied to 75 Candida albicans isolates, including 2 that were expected to be identical, 48 that came from diverse geographical and clinical sources, and 15 that were sequential isolates from two patients. DNA fragments ( approximately 500 bp) of eight genes encoding housekeeping functions were sequenced, including four that have been described before for C. albicans MLST, and four new gene fragments, AAT1a, AAT1b, MPI, and ZWF1. In total, 87 polymorphic sites were found among 50 notionally different isolates, giving 46 unique sequence types, underlining the power of MLST to differentiate isolates for epidemiological studies. Additional typing information was obtained by detecting variations in size at the transcribed spacer region of the 25S rRNA gene and tests for homozygosity at the mating type-like (MTL) locus. The stability of MLST was confirmed in two sets of consecutive isolates from two patients. In each set the isolates were identical or varied by a single nucleotide. Reference strain SC5314 and a derived mutant, CAF2, gave identical MLST types. Heterozygous polymorphisms were found in at least one isolate for all but 16 (18.4%) of the variable nucleotides, and 35 (41%) of the 87 individual sequence changes generated nonsynonymous amino acids. Cloning and restriction digestion of a gene fragment containing heterozygous polymorphisms indicated that the heterozygosity was genuine and not the result of sequencing errors. Our data validate and extend previous MLST results for C. albicans, and we propose an optimized system based on sequencing eight gene fragments for routine MLST with this species.
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Affiliation(s)
- Arianna Tavanti
- Department of Molecular & Cell Biology, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, United Kingdom
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616
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La Scola B, Boyadjiev I, Greub G, Khamis A, Martin C, Raoult D. Amoeba-resisting bacteria and ventilator-associated pneumonia. Emerg Infect Dis 2003; 9:815-21. [PMID: 12890321 PMCID: PMC3023432 DOI: 10.3201/eid0907.020760] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
To evaluate the role of amoeba-associated bacteria as agents of ventilator-associated pneumonia (VAP), we tested the water from an intensive care unit (ICU) every week for 6 months for such bacteria isolates; serum samples and bronchoalveolar lavage samples (BAL) were also obtained from 30 ICU patients. BAL samples were examined for amoeba-associated bacteria DNA by suicide-polymerase chain reaction, and serum samples were tested against ICU amoeba-associated bacteria. A total of 310 amoeba-associated bacteria from 10 species were isolated. Twelve of 30 serum samples seroconverted to one amoeba-associated bacterium isolated in the ICU, mainly Legionella anisa and Bosea massiliensis, the most common isolates from water (p=0.021). Amoeba-associated bacteria DNA was detected in BAL samples from two patients whose samples later seroconverted. Seroconversion was significantly associated with VAP and systemic inflammatory response syndrome, especially in patients for whom no etiologic agent was found by usual microbiologic investigations. Amoeba-associated bacteria might be a cause of VAP in ICUs, especially when microbiologic investigations are negative.
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Affiliation(s)
| | - Ioanna Boyadjiev
- Unité des Rickettsies, Marseille, France
- Hôpital Nord, Marseille, France
| | | | | | | | - Didier Raoult
- Unité des Rickettsies, Marseille, France
- Hôpital Nord, Marseille, France
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617
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Jones N, Bohnsack JF, Takahashi S, Oliver KA, Chan MS, Kunst F, Glaser P, Rusniok C, Crook DWM, Harding RM, Bisharat N, Spratt BG. Multilocus sequence typing system for group B streptococcus. J Clin Microbiol 2003; 41:2530-6. [PMID: 12791877 PMCID: PMC156480 DOI: 10.1128/jcm.41.6.2530-2536.2003] [Citation(s) in RCA: 448] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A multilocus sequence typing (MLST) system was developed for group B streptococcus (GBS). The system was used to characterize a collection (n = 152) of globally and ecologically diverse human strains of GBS that included representatives of capsular serotypes Ia, Ib, II, III, V, VI, and VIII. Fragments (459 to 519 bp) of seven housekeeping genes were amplified by PCR for each strain and sequenced. The combination of alleles at the seven loci provided an allelic profile or sequence type (ST) for each strain. A subset of the strains were characterized by restriction digest patterning, and these results were highly congruent with those obtained with MLST. There were 29 STs, but 66% of isolates were assigned to four major STs. ST-1 and ST-19 were significantly associated with asymptomatic carriage, whereas ST-23 included both carried and invasive strains. All 44 isolates of ST-17 were serotype III clones, and this ST appeared to define a homogeneous clone that was strongly associated with neonatal invasive infections. The finding that isolates with different capsular serotypes had the same ST suggests that recombination occurs at the capsular locus. A web site for GBS MLST was set up and can be accessed at http://sagalactiae.mlst.net. The GBS MLST system offers investigators a valuable typing tool that will promote further investigation of the population biology of this organism.
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Affiliation(s)
- Nicola Jones
- Nuffield Department of Clinical Laboratory Sciences, Institute for Molecular Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
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618
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Meats E, Feil EJ, Stringer S, Cody AJ, Goldstein R, Kroll JS, Popovic T, Spratt BG. Characterization of encapsulated and noncapsulated Haemophilus influenzae and determination of phylogenetic relationships by multilocus sequence typing. J Clin Microbiol 2003; 41:1623-36. [PMID: 12682154 PMCID: PMC153921 DOI: 10.1128/jcm.41.4.1623-1636.2003] [Citation(s) in RCA: 293] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A multilocus sequence typing (MLST) scheme has been developed for the unambiguous characterization of encapsulated and noncapsulated Haemophilus influenzae isolates. The sequences of internal fragments of seven housekeeping genes were determined for 131 isolates, comprising a diverse set of 104 serotype a, b, c, d, e, and f isolates and 27 noncapsulated isolates. Many of the encapsulated isolates had previously been characterized by multilocus enzyme electrophoresis (MLEE), and the validity of the MLST scheme was established by the very similar clustering of isolates obtained by these methods. Isolates of serotypes c, d, e, and f formed monophyletic groups on a dendrogram constructed from the differences in the allelic profiles of the isolates, whereas there were highly divergent lineages of both serotype a and b isolates. Noncapsulated isolates were distinct from encapsulated isolates and, with one exception, were within two highly divergent clusters. The relationships between the major lineages of encapsulated H. influenzae inferred from MLEE data could not be discerned on a dendrogram constructed from differences in the allelic profiles, but were apparent on a tree reconstructed from the concatenated nucleotide sequences. Recombination has not therefore completely eliminated phylogenetic signal, and in support of this, for encapsulated isolates, there was significant congruence between many of the trees reconstructed from the sequences of the seven individual loci. Congruence was less apparent for noncapsulated isolates, suggesting that the impact of recombination is greater among noncapsulated than encapsulated isolates. The H. influenzae MLST scheme is available at www.mlst.net, it allows any isolate to be compared with those in the MLST database, and (for encapsulated isolates) it assigns isolates to their phylogenetic lineage, via the Internet.
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Affiliation(s)
- Emma Meats
- Department of Infectious Disease Epidemiology, Imperial College London, St. Mary's Hospital, London W2 1PG, United Kingdom
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619
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Wareing DRA, Ure R, Colles FM, Bolton FJ, Fox AJ, Maiden MCJ, Dingle KE. Reference isolates for the clonal complexes of Campylobacter jejuni. Lett Appl Microbiol 2003; 36:106-10. [PMID: 12535131 DOI: 10.1046/j.1472-765x.2003.01270.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS To identify and make available through the National Collection of Type Cultures (NCTC) a set of reference isolates for the clonal complexes of Campylobacter jejuni. METHODS AND RESULTS The development of a multilocus sequence typing scheme for C. jejuni enabled the genetic characterization of a large number of isolates (n = 814) from cases of human disease, animals, birds and their food products. The nucleotide sequence data were used to assign each isolate an allelic profile or sequence type (ST) and examine the C. jejuni population structure in terms of clonal complexes. The clonal complexes consisted of an abundant central or founder genotype (ST), after which the complex was named, together with very closely related, generally less abundant genotypes differing from the founder at one, two or three loci. The clonal complex is an informative unit for the study C. jejuni epidemiology. It provides data which enabled the choice of 13 C. jejuni founder isolates for submission to the NCTC as a representative cross-section of the C. jejuni population. CONCLUSIONS These 13 isolates provide a defined resource for further research into aspects of C. jejuni biology such as genomic diversity, virulence and adaptation to particular hosts or environmental survival. SIGNIFICANCE AND IMPACT OF STUDY This isolate collection is available through the NCTC and provides a resource for further research.
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Affiliation(s)
- D R A Wareing
- The Public Health Laboratory, Royal Preston Hospital, P.O. Box 202, Preston PR2 9HG, UK.
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620
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Abstract
Mapping, and ultimately preventing, the dissemination of infectious agents is an important topic in public health. Newly developed molecular-microbiological methods have contributed significantly to recent advances in the efficient tracking of the nosocomial and environmental spread of microbial pathogens. Not only has the application of novel technologies led to improved understanding of microbial epidemiology, but the concepts of population structure and dynamics of many of the medically significant microorganisms have advanced significantly also. Currently, genetic identification of microbes is also within the reach of clinical microbiology laboratory professionals including those without specialized technology research interests. This review summarizes the possibilities for high-throughput molecular-microbiological typing in adequately equipped medical microbiology laboratories from both clinical and fundamental research perspectives. First, the development and application of methods for large-scale comparative typing of serially isolated microbial strains are discussed. The outcome of studies employing these methods allows for long-term epidemiologic surveillance of infectious diseases. Second, recent methods enable an almost nucleotide-by-nucleotide genetic comparison of smaller numbers of strains, thereby facilitating the identification of the genetic basis of, for instance, medically relevant microbiological traits. Whereas the first approach provides insights into the dynamic spread of infectious agents, the second provides insights into intragenomic dynamics and genetic functionality. The current state of technology is summarized, and future perspectives are sketched.
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Affiliation(s)
- A van Belkum
- Erasmus MC, Department of Medical Microbiology & Infectious Diseases, Rotterdam, The Netherlands.
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621
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Salcedo C, Arreaza L, Alcalá B, de la Fuente L, Vázquez JA. Development of a multilocus sequence typing method for analysis of Listeria monocytogenes clones. J Clin Microbiol 2003; 41:757-62. [PMID: 12574278 PMCID: PMC149676 DOI: 10.1128/jcm.41.2.757-762.2003] [Citation(s) in RCA: 135] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study is a first step in the development of multilocus sequence typing (MLST) method for Listeria monocytogenes. Nine housekeeping genes were analyzed in a set of 62 strains isolated from different sources and geographic locations in Spain. These strains were previously characterized by pulsed-field gel electrophoresis (PFGE). Because of low diversity, two loci were discarded from the study. The sequence analysis of the seven remaining genes showed 29 different allelic combinations, with 22 of them represented by only one strain. The results of this sequence analysis were generally consistent with those of PFGE. Because MLST allows the easy comparison and exchange of results obtained in different laboratories, the future application of this new molecular method could be a useful tool for the listeriosis surveillance systems that will allow the identification and distribution of analysis of L. monocytogenes clones in the environment.
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Affiliation(s)
- C Salcedo
- Servicio de Bacteriología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain
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622
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Viscidi RP, Demma JC. Genetic diversity of Neisseria gonorrhoeae housekeeping genes. J Clin Microbiol 2003; 41:197-204. [PMID: 12517848 PMCID: PMC149597 DOI: 10.1128/jcm.41.1.197-204.2003] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2002] [Revised: 07/26/2002] [Accepted: 10/16/2002] [Indexed: 11/20/2022] Open
Abstract
Molecular typing of Neisseria gonorrhoeae strains is an important tool for epidemiological studies of gonococcal infection and transmission. The recently developed multilocus sequence typing (MLST) method is based on the genetic variation among housekeeping genes. As a preliminary investigation for the development of such a method, we characterized the genetic diversity at 18 gonococcal housekeeping gene loci. Approximately 17,500 nucleotides, spanning 18 loci, were sequenced from 24 isolates. Including strain FA 1090, which has been fully sequenced, and three unique glnA sequences from GenBank, the number of alleles identified for the 18 loci ranged from 2 to 18, with a mean of 8.3 alleles per locus. The majority of polymorphic sites were distributed randomly along the genes, consistent with evolution of DNA sequences by point mutation. In addition, several examples of clustered mutations and insertions or deletions were detected, which most likely occurred by recombinational events. While purifying selection is the dominant force driving the evolution of these housekeeping genes, positive selection also appeared to operate on the abcZ and gpdh loci. The 25 completely characterized strains each had a unique allelic profile with as few as three loci (pilA, abcZ, and pip or pgi2). Molecular typing based on the allelic profile of housekeeping genes resolved the isolates better than either porB nucleotide sequencing or typing of the opa gene. The allelic profiles for the pilA, abcZ, and serC loci of paired strains from 16 sexual contacts were identical. A potential MLST for N. gonorrhoeae, based on approximately 500- to 600-bp gene fragments of seven housekeeping gene loci, would include the pilA, abcZ, serC, glnA, gdh, gnd, and pip loci.
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Affiliation(s)
- Raphael P Viscidi
- Stanley Division of Developmental Neurovirology, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.
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623
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Schouls LM, Reulen S, Duim B, Wagenaar JA, Willems RJL, Dingle KE, Colles FM, Van Embden JDA. Comparative genotyping of Campylobacter jejuni by amplified fragment length polymorphism, multilocus sequence typing, and short repeat sequencing: strain diversity, host range, and recombination. J Clin Microbiol 2003; 41:15-26. [PMID: 12517820 PMCID: PMC149617 DOI: 10.1128/jcm.41.1.15-26.2003] [Citation(s) in RCA: 198] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Three molecular typing methods were used to study the relationships among 184 Campylobacter strains isolated from humans, cattle, and chickens. All strains were genotyped by amplified fragment length polymorphism (AFLP) analysis, multilocus sequence typing (MLST), and sequence analysis of a genomic region with short tandem repeats designated clustered regularly interspaced short palindromic repeats (CRISPRs). MLST and AFLP analysis yielded more than 100 different profiles and patterns, respectively. These multiple-locus typing methods resulted in similar genetic clustering, indicating that both are useful in disclosing genetic relationships between Campylobacter jejuni isolates. Group separation analysis of the AFLP analysis and MLST data revealed an unexpected association between cattle and human strains, suggesting a common source of infection. Analysis of the polymorphic CRISPR region carrying short repeats allowed about two-thirds of the typeable strains to be distinguished, similar to AFLP analysis and MLST. The three methods proved to be equally powerful in identifying strains from outbreaks of human campylobacteriosis. Analysis of the MLST data showed that intra- and interspecies recombination occurs frequently and that the role of recombination in sequence variation is 50 times greater than that of mutation. Examination of strains cultured from cecum swabs revealed that individual chickens harbored multiple Campylobacter strain types and that some genotypes were found in more than one chicken. We conclude that typing of Campylobacter strains is useful for identification of outbreaks but is probably not useful for source tracing and global epidemiology because of carriage of strains of multiple types and an extremely high diversity of strains in animals.
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Affiliation(s)
- Leo M Schouls
- Research Laboratory for Infectious Diseases, National Institute of Public Health and the Environment, Bilthoven, The Netherlands.
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624
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Dingle KE, Colles FM, Ure R, Wagenaar JA, Duim B, Bolton FJ, Fox AJ, Wareing DRA, Maiden MCJ. Molecular characterization of Campylobacter jejuni clones: a basis for epidemiologic investigation. Emerg Infect Dis 2002. [PMID: 12194772 PMCID: PMC2732546 DOI: 10.3201/eid0809.02-0122] [Citation(s) in RCA: 164] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
A total of 814 isolates of the foodborne pathogen Campylobacter jejuni were characterized by multilocus sequence typing (MLST) and analysis of the variation of two cell-surface components: the heat-stable (HS) serotyping antigen and the flagella protein FlaA short variable region (SVR). We identified 379 combinations of the MLST loci (sequence types) and 215 combinations of the cell-surface components among these isolates, which had been obtained from human disease, animals, food, and the environment. Despite this diversity, 748 (92%) of the isolates belonged to one of 17 clonal complexes, 6 of which contained many (318, 63%) of the human disease isolates. Several clonal complexes exhibited associations with isolation source or particular cell-surface components; however, the latter were poorly predictive of clonal complex. These data demonstrate that the clonal complex, as defined by MLST, is an epidemiologically relevant unit for both long and short-term investigations of C. jejuni epidemiology.
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Affiliation(s)
- Kate E Dingle
- Department of Zoology, University of Oxford, United Kingdom
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625
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King SJ, Leigh JA, Heath PJ, Luque I, Tarradas C, Dowson CG, Whatmore AM. Development of a multilocus sequence typing scheme for the pig pathogen Streptococcus suis: identification of virulent clones and potential capsular serotype exchange. J Clin Microbiol 2002; 40:3671-80. [PMID: 12354864 PMCID: PMC130843 DOI: 10.1128/jcm.40.10.3671-3680.2002] [Citation(s) in RCA: 210] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptococcus suis is an important pathogen of pigs and occasionally causes serious human disease. However, little is known about the S. suis population structure, the clonal relationships between strains, the potential of particular clones to cause disease, and the relevance of serotype as a marker for epidemiology. Here we describe a multilocus sequence typing (MLST) scheme for S. suis developed in order to begin to address these issues. Seven housekeeping gene fragments from each of 294 S. suis isolates obtained from various S. suis diseases and from asymptomatic carriage representing 28 serotypes and nine distinct countries of origin were sequenced. Between 32 and 46 alleles per locus were identified, giving the ability to distinguish >1.6 x 10(11) sequence types (STs). However only 92 STs were identified in this study. Of the 92 STs 18 contained multiple isolates, the most common of which, ST1, was identified on 141 occasions from six countries. Assignment of the STs to lineages resulted in 37 being identified as unique and unrelated STs while the remaining 55 were assigned to 10 complexes. ST complexes ST1, ST27, and ST87 dominate the population; while the ST1 complex was strongly associated with isolates from septicemia, meningitis, and arthritis, the ST87 and ST27 complexes were found to contain significantly higher numbers of lung isolates. In agreement with the observed distribution of disease-causing isolates of S. suis, most isolates previously characterized as of high virulence in porcine infection models belong to ST1, while isolates belonging to other STs appear to be less virulent in general. Finally nine STs were found to contain isolates of multiple serotypes, and many isolates belonging to the same serotypes were found to have very disparate genetic backgrounds. As well as highlighting that the serotype can often be a poor indicator of genetic relatedness between S. suis isolates, these findings suggest that capsular genes may be moving horizontally through the S. suis population.
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Affiliation(s)
- Samantha J King
- Infectious Disease Research Group, Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
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626
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Dingle KE, Colles FM, Ure R, Wagenaar JA, Duim B, Bolton FJ, Fox AJ, Wareing DR, Maiden MC. Molecular characterization of Campylobacter jejuni clones: a basis for epidemiologic investigation. Emerg Infect Dis 2002; 8:949-55. [PMID: 12194772 PMCID: PMC2732546 DOI: 10.3201/eid0809.020122] [Citation(s) in RCA: 149] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A total of 814 isolates of the foodborne pathogen Campylobacter jejuni were characterized by multilocus sequence typing (MLST) and analysis of the variation of two cell-surface components: the heat-stable (HS) serotyping antigen and the flagella protein FlaA short variable region. We identified 379 combinations of the MLST loci (sequence types) and 215 combinations of the cell-surface components among these isolates, which had been obtained from human disease, animals, food, and the environment. Despite this diversity, 748 (92%) of the isolates belonged to one of 17 clonal complexes, 6 of which contained many (318, 63%) of the human disease isolates. Several clonal complexes exhibited associations with isolation source or particular cell-surface components; however, the latter were poorly predictive of clonal complex. These data demonstrate that the clonal complex, as defined by MLST, is an epidemiologically relevant unit for both long and short-term investigations of C. jejuni epidemiology.
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Affiliation(s)
- Kate E. Dingle
- University of Oxford, Oxford, United Kingdom; †Public Health Laboratory, Royal Preston Hospital, Preston, United Kingdom
| | - Frances M. Colles
- University of Oxford, Oxford, United Kingdom; †Public Health Laboratory, Royal Preston Hospital, Preston, United Kingdom
| | - Roisin Ure
- University of Oxford, Oxford, United Kingdom; †Public Health Laboratory, Royal Preston Hospital, Preston, United Kingdom
- Institute for Animal Science and Health, Lelystad, the Netherlands
- Public Health Laboratory, Withington Hospital, Manchester, United Kingdom
| | - Jaap A. Wagenaar
- Institute for Animal Science and Health, Lelystad, the Netherlands
| | - Birgitta Duim
- Institute for Animal Science and Health, Lelystad, the Netherlands
| | - Frederick J. Bolton
- University of Oxford, Oxford, United Kingdom; †Public Health Laboratory, Royal Preston Hospital, Preston, United Kingdom
- Institute for Animal Science and Health, Lelystad, the Netherlands
- Public Health Laboratory, Withington Hospital, Manchester, United Kingdom
| | - Andrew J. Fox
- Public Health Laboratory, Withington Hospital, Manchester, United Kingdom
| | - David R.A. Wareing
- University of Oxford, Oxford, United Kingdom; †Public Health Laboratory, Royal Preston Hospital, Preston, United Kingdom
- Institute for Animal Science and Health, Lelystad, the Netherlands
- Public Health Laboratory, Withington Hospital, Manchester, United Kingdom
| | - Martin C.J. Maiden
- University of Oxford, Oxford, United Kingdom; †Public Health Laboratory, Royal Preston Hospital, Preston, United Kingdom
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627
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Cai S, Kabuki DY, Kuaye AY, Cargioli TG, Chung MS, Nielsen R, Wiedmann M. Rational design of DNA sequence-based strategies for subtyping Listeria monocytogenes. J Clin Microbiol 2002; 40:3319-25. [PMID: 12202573 PMCID: PMC130781 DOI: 10.1128/jcm.40.9.3319-3325.2002] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2002] [Revised: 05/29/2002] [Accepted: 07/01/2002] [Indexed: 11/20/2022] Open
Abstract
The ability to differentiate bacteria beyond the species level is essential for identifying and tracking infectious disease outbreaks and to improve our knowledge of the population genetics, epidemiology, and ecology of bacterial pathogens. Commonly used subtyping methods, such as serotyping, phage typing, ribotyping, and pulsed-field gel electrophoresis, can yield ambiguous results that are difficult to standardize and share among laboratories. DNA sequence-based subtyping strategies can reduce interpretation ambiguity. We report the development of a rational approach for designing sequence-based subtyping methods. Listeria monocytogenes was selected as the model organism for testing the efficacy of this approach. Two housekeeping genes (recA and prs), one stress response gene (sigB), two virulence genes (actA and inlA), and two intergenic regions (hly-mpl and plcA-hly) were sequenced for 15 L. monocytogenes isolates. Isolates were chosen from a representative collection of more than 1,000 L. monocytogenes isolates to reflect the genetic diversity of this species. DNA sequences were aligned, and sliding window analyses were performed for each gene to define 600-bp-long regions that were (i) most polymorphic (using ProSeq) or (ii) most discriminatory (using a new algorithm implemented in WINDOWMIN). Complete gene sequences for actA (1,929 bp) and inlA (2,235 bp) provided the highest discrimination (identifying 15 and 14 allelic types, respectively). WINDOWMIN allowed identification of 600-bp regions within these genes that provided similar discriminatory power (yielding 15 and 13 allelic types, respectively). The most discriminatory 600-bp fragments identified in the housekeeping and stress response genes differentiated the isolates into 8 to 10 subtypes; intergenic region sequences yielded 8 and 12 allelic types based on 335- and 242-bp sequences for hly-mpl and plcA-hly, respectively. Regions identified as most polymorphic were not necessarily most discriminatory; therefore, application of the WINDOWMIN algorithm provided a powerful tool for determining the best target regions for DNA sequence-based subtyping. Our specific results also show that inclusion of virulence gene target sequences in a DNA sequence-based subtyping scheme for L. monocytogenes is necessary to achieve maximum subtype differentiation.
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Affiliation(s)
- Steven Cai
- Department of Food Science, Cornell University, Ithaca, New York 14853, USA
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628
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Wareing DRA, Bolton FJ, Fox AJ, Wright PA, Greenway DLA. Phenotypic diversity of Campylobacter isolates from sporadic cases of human enteritis in the UK. J Appl Microbiol 2002; 92:502-9. [PMID: 11872126 DOI: 10.1046/j.1365-2672.2002.01552.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS The aim of this study was to identify and subtype a large collection of isolates of Campylobacter spp. to quantify diversity among strains causing human disease from geographically diverse sources in the United Kingdom. METHODS AND RESULTS Isolates were characterized by the Penner serotyping scheme, Preston phage typing and biotyping methods. The diversity index calculated from the combined results of all three methods was 0.997 and indicated that isolates from sporadic cases of infection are very diverse. Strong associations between common phagetypes (PG52, PG121 and PG55) and the three most common serotypes (HS1, HS2 and HS4) found in the study were evident. CONCLUSIONS Strains of C. jejuni causing human infections in the United Kingdom are very phenotypically diverse. Individual strains characterized by serotype, phagetype and biotype were detected throughout the 7-month study period and from geographically distinct sources, indicating an unrecognized outbreak or other epidemiologically significant source of human infection. SIGNIFICANCE AND IMPACT OF THE STUDY The low frequency incidence of most C. jejuni strains should enable easy recognition of outbreaks by strain type surveillance at local, regional and national level in the United Kingdom. The characterization of common strain profiles in this study by simple phenotypic methods could provide the basis for strain specific epidemiological studies for reservoirs of infection and transmission routes for human infection.
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Affiliation(s)
- D R A Wareing
- Public Health Laboratory, Royal Preston Hospital, PO Box 202, Preston PR2 9HG, UK.
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629
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van Loo IHM, Heuvelman KJ, King AJ, Mooi FR. Multilocus sequence typing of Bordetella pertussis based on surface protein genes. J Clin Microbiol 2002; 40:1994-2001. [PMID: 12037054 PMCID: PMC130760 DOI: 10.1128/jcm.40.6.1994-2001.2002] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2001] [Revised: 01/01/2002] [Accepted: 03/19/2002] [Indexed: 01/16/2023] Open
Abstract
Despite more than 50 years of vaccination, Bordetella pertussis has remained endemic in The Netherlands, causing epidemic outbreaks every 3 to 5 years. Strain variation may play a role in the persistence of B. pertussis and was studied by sequencing 15 genes coding for surface proteins, including genes for all five components of acellular pertussis vaccines: pertussis toxin (Ptx), pertactin (Prn), filamentous hemagglutinin, and fimbriae (Fim2 and Fim3). A low level of allelic variation was observed, confirming a recent evolutionary origin of B. pertussis. In modern isolates, polymorphism was observed only in prn, ptxS1, ptxS3, and tcfA. Polymorphism in ptxS1, ptxS3, and tcfA was used to categorize isolates in multilocus sequence types (MLSTs). Analysis of Dutch isolates from 1949 to 1999 revealed five MLSTs, which showed a highly dynamic temporal behavior. We observed significant changes in the MLSTs after the introduction of pertussis vaccination in The Netherlands. Epidemic years were found to be associated with the expansion of MLST-4 or MLST-5. MLST-5 showed a remarkable expansion from 10% in 1997 to 80% in 1999. The MLST analysis was extended to a number of widely separated geographic regions: Finland, Italy, Japan, and the United States. MLST-4 and MLST-5 were found to dominate in Italy and the United States. In Finland and Japan, MLST-3 and MLST-2, respectively, were predominant. Thus, although each region showed distinctive MLST frequencies, in three of the five regions MLST-4 and MLST-5 were predominant. These types may represent newly emerged, successful clones. The identification of highly successful clones may shed light on the question of how B. pertussis is able to maintain itself in vaccinated populations.
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Affiliation(s)
- Inge H M van Loo
- Laboratory for Infectious Diseases Research, National Institute of Public Health and the Environment, Bilthoven, The Netherlands
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630
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Homan WL, Tribe D, Poznanski S, Li M, Hogg G, Spalburg E, Van Embden JDA, Willems RJL. Multilocus sequence typing scheme for Enterococcus faecium. J Clin Microbiol 2002; 40:1963-71. [PMID: 12037049 PMCID: PMC130786 DOI: 10.1128/jcm.40.6.1963-1971.2002] [Citation(s) in RCA: 406] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2001] [Revised: 02/18/2002] [Accepted: 03/21/2002] [Indexed: 11/20/2022] Open
Abstract
A multilocus sequence typing (MLST) scheme has been developed for Enterococcus faecium. Internal fragments from seven housekeeping genes of 123 epidemiologically unlinked isolates from humans and livestock and 16 human-derived isolates from several outbreaks in the United States, the United Kingdom, Australia, and The Netherlands were analyzed. A total of 62 sequence types were detected in vancomycin-sensitive E. faecium (VSEF) and vancomycin-resistant E. faecium (VREF) isolates. VSEF isolates were genetically more diverse than VREF isolates. Both VSEF and VREF isolates clustered in host-specific lineages that were similar to the host-specific clustering obtained by amplified fragment length polymorphism analysis. Outbreak isolates from hospitalized humans clustered in a subgroup that was defined by the presence of a unique allele from the housekeeping gene purK and the surface protein gene esp. The MLST results suggest that epidemic lineages of E. faecium emerged recently worldwide, while genetic variation in both VREF and VSEF was created by longer-term recombination. The results show that MLST of E. faecium provides an excellent tool for isolate characterization and long-term epidemiologic analysis.
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Affiliation(s)
- Wieger L Homan
- Research Laboratory for Infectious Diseases, National Institute of Public Health and the Environment, Bilthoven, The Netherlands.
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631
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Kotetishvili M, Stine OC, Kreger A, Morris JG, Sulakvelidze A. Multilocus sequence typing for characterization of clinical and environmental salmonella strains. J Clin Microbiol 2002; 40:1626-35. [PMID: 11980932 PMCID: PMC130929 DOI: 10.1128/jcm.40.5.1626-1635.2002] [Citation(s) in RCA: 136] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multilocus sequence typing (MLST) based on the 16S RNA, pduF, glnA, and manB genes was developed for Salmonella, and its discriminatory ability was compared to those of pulsed-field gel electrophoresis (PFGE) and serotyping. PFGE differentiated several strains undifferentiable by serotyping, and 78 distinct PFGE types were identified among 231 Salmonella isolates grouped into 22 serotypes and 12 strains of undetermined serotype. The strains of several PFGE types were further differentiated by MLST, which suggests that the discriminatory ability of MLST for the typing of Salmonella is better than that of serotyping and/or PFGE typing. manB-based sequence typing identified two distinct genetic clusters containing 32 of 54 (59%) clinical isolates whose manB gene sequences were analyzed. The G+C contents and Splitstree analysis of the manB, glnA, and pduF genes of Salmonella indicated that the genes differ in their evolutionary origins and that recombination played a significant role in their evolution.
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Affiliation(s)
- Mamuka Kotetishvili
- Division of Molecular Epidemiology, Department of Epidemiology and Preventive Medicine, University of Maryland School of Medicine, 10 South Pine Street, Baltimore, MD 21201, USA
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632
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de Boer P, Wagenaar JA, Achterberg RP, van Putten JPM, Schouls LM, Duim B. Generation of Campylobacter jejuni genetic diversity in vivo. Mol Microbiol 2002; 44:351-9. [PMID: 11972775 DOI: 10.1046/j.1365-2958.2002.02930.x] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Molecular epidemiology studies suggest that horizontal genetic exchange is a major cause of pathogen biodiversity. We tested this concept for the bacterial enteropathogen Campylobacter jejuni by seeking direct in vivo evidence for the exchange of genetic material among Campylobacter strains. For this purpose, two antibiotic resistance markers were inserted into the hipO or htrA gene of genetically distinct and naturally transformable C. jejuni strains. Genetic exchange of the resistance markers was analysed after co-cultivation of homologous and heterologous strains in vitro and in vivo during experimental infection of chickens. Double-resistant recombinants were obtained both in vitro and from the chicken intestine for all combinations of strains tested. Bidirectional genetic exchange of DNA between homologous and heterologous strains was confirmed by Southern blotting in combination with flaA polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), amplified fragment length polymorphism (AFLP) and pulsed field gel electrophoresis (PFGE). Extensive PFGE analyses of isolated recombinants indicated the frequent occurrence of genetic rearrangements during the experimental infection, in addition to the homologous recombination of the antibiotic resistance genes. Together, the data indicate unequivocally that interstrain genetic exchange as well as intragenomic alterations do occur in vivo during C. jejuni infection. These events probably explain the genome plasticity observed for this pathogen.
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MESH Headings
- Animals
- Base Sequence
- Campylobacter Infections/drug therapy
- Campylobacter jejuni/genetics
- Chickens
- Conjugation, Genetic
- DNA Primers
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- Directed Molecular Evolution/methods
- Drug Resistance, Microbial/genetics
- Electrophoresis, Gel, Pulsed-Field
- Genetic Markers
- Genetic Variation
- Genotype
- Polymerase Chain Reaction
- Polymorphism, Restriction Fragment Length
- Recombination, Genetic
- Salmonella Infections, Animal/drug therapy
- Transformation, Genetic
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Affiliation(s)
- Paulo de Boer
- Institute for Animal Science and Health, Division of Infectious Diseases and Food Chain Quality, PO Box 65, 8200 AB Lelystad, The Netherlands.
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633
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Ahmed IH, Manning G, Wassenaar TM, Cawthraw S, Newell DG. Identification of genetic differences between two Campylobacter jejuni strains with different colonization potentials. MICROBIOLOGY (READING, ENGLAND) 2002; 148:1203-1212. [PMID: 11932464 DOI: 10.1099/00221287-148-4-1203] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The consumption of poultry meat contaminated with Campylobacter jejuni is considered to be a risk factor for human campylobacteriosis. The development of targeted strategies to control campylobacters in broilers would benefit from knowledge of those bacterial factors important in colonization of the avian gut. During preliminary studies it was noted that C. jejuni NCTC 11168 was a poorer colonizer of chickens than strain 81116. This poor colonization could not be fully restored by in vivo passage, suggesting that it was a genetically endowed property of strain 11168. As the genome sequence is available for this strain, the technique of subtractive hybridization was used to identify gene fragments of strain 81116 not present in strain 11168. After two screening cycles, 24 out of 42 clones were identified as having DNA inserts specific for strain 81116. Six of these 24 clones contained gene fragment inserts with similarities to restriction-modification enzymes found in other bacteria. Two inserts had similarity to arsenic-resistance genes, whereas four others had similarities to cytochrome c oxidase III, dTDP-glucose 4,6-dehydratase, gamma-glutamyl transpeptidase and an abortive phage-resistance protein. At least some of these genes may be involved with colonization. A further six inserts had weak similarities to hypothetical proteins or to proteins with assigned functions from strain 11168. The remaining six clones had gene-fragment inserts with no database matches. Southern-blot analysis confirmed that strain-dependent variation existed for each of these DNA inserts. These results indicate that subtractive hybridization can successfully identify genes that are absent from the only C. jejuni strain for which the genome sequence is currently available.
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Affiliation(s)
- If H Ahmed
- Veterinary Laboratories Agency (Weybridge), New Haw, Addlestone, Surrey KT15 3NB, UK1
| | - Georgina Manning
- Veterinary Laboratories Agency (Weybridge), New Haw, Addlestone, Surrey KT15 3NB, UK1
| | - Trudy M Wassenaar
- Molecular Microbiology and Genomics Consultants, Zotzenheim, Germany2
- Veterinary Laboratories Agency (Weybridge), New Haw, Addlestone, Surrey KT15 3NB, UK1
| | - Shaun Cawthraw
- Veterinary Laboratories Agency (Weybridge), New Haw, Addlestone, Surrey KT15 3NB, UK1
| | - Diane G Newell
- Veterinary Laboratories Agency (Weybridge), New Haw, Addlestone, Surrey KT15 3NB, UK1
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634
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Eriksson A, Haubold B, Mehlig B. Statistics of selectively neutral genetic variation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2002; 65:040901. [PMID: 12005797 DOI: 10.1103/physreve.65.040901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2001] [Revised: 11/29/2001] [Indexed: 05/23/2023]
Abstract
Random models of evolution are instrumental in extracting rates of microscopic evolutionary mechanisms from empirical observations on genetic variation in genome sequences. In this context it is necessary to know the statistical properties of empirical observables (such as the local homozygosity, for instance). Previous work relies on numerical results or assumes Gaussian approximations for the corresponding distributions. In this paper we give an analytical derivation of the statistical properties of the local homozygosity and other empirical observables assuming selective neutrality. We find that such distributions can be very non-Gaussian.
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Affiliation(s)
- A Eriksson
- Physics and Engineering Physics, Chalmers/GU, Gothenburg, Sweden
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635
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Bougnoux ME, Morand S, d'Enfert C. Usefulness of multilocus sequence typing for characterization of clinical isolates of Candida albicans. J Clin Microbiol 2002; 40:1290-7. [PMID: 11923347 PMCID: PMC140389 DOI: 10.1128/jcm.40.4.1290-1297.2002] [Citation(s) in RCA: 152] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Molecular characterization of Candida albicans isolates is essential for understanding the epidemiology of nosocomial infections caused by this yeast. Here, we investigated the potential value of multilocus sequence typing (MLST) for characterizing epidemiologically related or unrelated C. albicans strains of various clinical origins. Accordingly, we sequenced the internal regions (loci) of six selected housekeeping genes of 40 C. albicans clinical isolates and 2 reference strains. In all, 68 polymorphic nucleotide sites were identified, of which 65 were found to be heterozygous in at least one isolate. Ten to 24 different genotypes were observed at the different loci, resulting, when combined, in 39 unique genotype combinations or diploid sequence types (DSTs). When MLST was applied to 26 epidemiologically unrelated isolates and the 2 reference strains, it allowed the identification of 27 independent DSTs, thus demonstrating a discriminatory power of 99.7. Using multidimensional scaling together with the minimum spanning tree method to analyze interstrain relationships, we identified six groups of genetically related isolates on the basis of bootstrap values of greater than 900. Application of MLST to 14 epidemiologically related isolates showed that those recovered from patients in the same hospital ward during the same 3 months had specific DSTs, although 73% of these isolates were genetically very close. This suggests that MLST can trace minute variations in the sequences of related isolates. Overall, MLST proved to be a highly discriminatory and stable method for unambiguous characterization of C. albicans.
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Affiliation(s)
- M-E Bougnoux
- Unité Microbiologie et Environnement, Institut Pasteur, Paris, France.
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636
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Oza AN, Thwaites RT, Wareing DRA, Bolton FJ, Frost JA. Detection of heat-stable antigens of Campylobacter jejuni and C. coli by direct agglutination and passive hemagglutination. J Clin Microbiol 2002; 40:996-1000. [PMID: 11880429 PMCID: PMC120255 DOI: 10.1128/jcm.40.3.996-1000.2002] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The two serotyping schemes for the detection of heat-stable antigens of Campylobacter jejuni and Campylobacter coli use the same strains for antiserum production but differ in the detection systems used for identifying agglutination. The Penner method uses passive hemagglutination (PHA) while the Laboratory of Enteric Pathogens method uses the same antisera but in a whole-bacterial-cell direct agglutination (DA) protocol. C. jejuni produces a polysaccharide capsule, which is antigenic, and is the main component detected by the PHA method. The DA method will detect both capsule antigens and lipopolysaccharide (LPS) or lipooligosaccharide (LOS) surface antigens. Comparison of both methods by using a selection of isolates from human infection has shown a range of variation in agglutination specificity, reflecting the differences in antigens detected by the two methods. While 27.4% of the 416 C. jejuni isolates reacted with the antisera raised against the same type strains by either method, the majority showed a range of more complex relationships. None of the 37 C. coli isolates reacted with the same antiserum by both methods. Together the two schemes gave a total of 102 distinct combined serogroups for C. jejuni and 16 for C. coli. Thus, while some clonally related isolates share the same capsule and LOS or LPS antigens, other strains appear to have a common capsule antigen but differ in their LPS or LOS structures or vice versa.
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Affiliation(s)
- A N Oza
- Campylobacter Reference Laboratory, Laboratory of Enteric Pathogens, Central Public Health Laboratory, London NW9 5HT, England
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637
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Nallapareddy SR, Duh RW, Singh KV, Murray BE. Molecular typing of selected Enterococcus faecalis isolates: pilot study using multilocus sequence typing and pulsed-field gel electrophoresis. J Clin Microbiol 2002; 40:868-76. [PMID: 11880407 PMCID: PMC120268 DOI: 10.1128/jcm.40.3.868-876.2002] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The present study compared the recently developed multilocus sequence typing (MLST) approach with a well-established molecular typing technique, pulsed-field gel electrophoresis (PFGE), for subspecies differentiation of Enterococcus faecalis isolates. We sequenced intragenic regions of three E. faecalis antigen-encoding genes (ace, encoding a collagen and laminin adhesin; efaA, encoding an endocarditis antigen; and salA, encoding a cell wall associated antigen) and one housekeeping gene (pyrC) of 22 E. faecalis isolates chosen largely for their temporal and geographical diversity, but also including some outbreak isolates. MLST analysis of polymorphic regions of these four genes identified 13 distinct sequence types (STs) with different allelic profiles; the composite sequences generated from the four sequenced gene fragments of individual isolates showed 98.3 to 100% identity among the 22 isolates. We also found that the allelic profiles from two sequences, ace and salA, were sufficient to distinguish all 13 STs of this study. The 13 STs corresponded to 12 different PFGE types, with one previously designated PFGE clone (a widespread U.S. clone of beta-lactamase-producing isolates) being classified into two highly related STs which differed at 2 of 2,894 bases, both in the same allele. MLST also confirmed the clonal relationships among the isolates of two other PFGE clonal groups, including vancomycin resistant isolates. Thus, this pilot study with representative E. faecalis isolates suggests that, similar to PFGE, the sequence-based typing method may be useful for differentiating isolates of E. faecalis to the subspecies level in addition to identifying outbreak isolates.
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Affiliation(s)
- Sreedhar R Nallapareddy
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical School, Houston, Texas 77030, USA
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638
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Krawczyk B, Lewandowski K, Kur J. Comparative studies of the Acinetobacter genus and the species identification method based on the recA sequences. Mol Cell Probes 2002; 16:1-11. [PMID: 12005442 DOI: 10.1006/mcpr.2001.0388] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The recA gene is indispensable for a maintaining and diversification of the bacterial genetic material. Given its important role in ensuring cell viability, it is not surprising that the RecA protein is both ubiquitous and well conserved among a range of prokaryotes. Previously, we reported Acinetobacter genomic species identification method based on PCR amplification of an internal fragment of the recA gene with subsequent restriction analysis (RFLP) with HinfI and MboI enzymes. In present study, the PCR products containing the internal fragment of the recA gene, for 25 Acinetobacter strains belonging to all genomic species, were sequenced. Based on the nucleotide sequences the restriction maps and phylogenetic tree were prepared. The restriction maps revealed that Tsp509I restriction enzyme is the most discriminating for RFLP. To verify the computer analysis, the amplified DNAs from all reference genomic species available (43 strains) and 34 clinical strains were digested with each of the three restriction endonucleases mentioned. The results of digestion confirmed the computer analysis. The reconstructed phylogenetic tree showed linkages between genomic species 1 (Acinetobacter calcoaceticus), 2 (Acinetobacter baumannii), 3, 'between 1 and 3', TU13 and 'close to TU13'; genomic species 4, 6, BJ13, BJ14, BJ15, BJ16 and BJ17; genomic species 7 (Acinetobacter johnsonii) and TU14; genomic species 10 and 11; genomic species 8 (Acinetobacter Iwoffii), 9, 12 (Acinetobacter radioresistens) and TU15; and genomic species 5 (Acinetobacter junii). It is interesting that one branch in the phylogenetic tree contains haemolytic species-genomic species 4 (A. haemolyticus), BJ13, BJ14, BJ15, BJ16 and BJ17. The proposed genotypic method clearly revealed that the RFLP profiles obtained with Tsp509I enzyme might be useful for species identification of Acinetobacter strains. In this context, recA/RFLP genotypic method should be seen as an ideal preliminary screening method for large numbers of isolates, with the ultimate confirmatory role reserved for DNA hybridization analysis.
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Affiliation(s)
- B Krawczyk
- Department of Microbiology, Technical University of Gdańsk, Poland.
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639
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Gilbert M, Karwaski MF, Bernatchez S, Young NM, Taboada E, Michniewicz J, Cunningham AM, Wakarchuk WW. The genetic bases for the variation in the lipo-oligosaccharide of the mucosal pathogen, Campylobacter jejuni. Biosynthesis of sialylated ganglioside mimics in the core oligosaccharide. J Biol Chem 2002; 277:327-37. [PMID: 11689567 DOI: 10.1074/jbc.m108452200] [Citation(s) in RCA: 202] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have compared the lipo-oligosaccharide (LOS) biosynthesis loci from 11 Campylobacter jejuni strains expressing a total of 8 different ganglioside mimics in their LOS outer cores. Based on the organization of the genes, the 11 corresponding loci could be classified into three classes, with one of them being clearly an intermediate evolutionary step between the other two. Comparative genomics and expression of specific glycosyltransferases combined with in vitro activity assays allowed us to identify at least five distinct mechanisms that allow C. jejuni to vary the structure of the LOS outer core as follows: 1) different gene complements; 2) phase variation because of homopolymeric tracts; 3) gene inactivation by the deletion or insertion of a single base (without phase variation); 4) single mutation leading to the inactivation of a glycosyltransferase; and 5) single or multiple mutations leading to "allelic" glycosyltransferases with different acceptor specificities. The differences in the LOS outer core structures expressed by the 11 C. jejuni strains examined can be explained by one or more of the five mechanisms described in this work.
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Affiliation(s)
- Michel Gilbert
- Institute for Biological Sciences, National Research Council of Canada, 100 Sussex Dr., Ottawa, Ontario K1A 0R6, Canada
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640
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Desai M, Logan JM, Frost JA, Stanley J. Genome sequence-based fluorescent amplified fragment length polymorphism of Campylobacter jejuni, its relationship to serotyping, and its implications for epidemiological analysis. J Clin Microbiol 2001; 39:3823-9. [PMID: 11682493 PMCID: PMC88450 DOI: 10.1128/jcm.39.11.3823-3829.2001] [Citation(s) in RCA: 33] [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
The published genome sequence of Campylobacter jejuni strain NCTC 11168 was used to model an accurate and highly reproducible fluorescent amplified fragment length polymorphism (FAFLP) analysis. Predicted and experimentally observed amplified fragments (AFs) generated with the primer pair HindIII+A and HhaI+A were compared. All but one of the 61 predicted AFs were reproducibly detected, and no unpredicted fragments were amplified. This FAFLP analysis was used to genotype 74 C. jejuni strains belonging to the nine heat-stable (HS) serotypes most prevalent in human disease in England and Wales. The 74 C. jejuni strains exhibited 60 FAFLP profiles, and cluster analysis of them yielded a radial tree showing genetic relationships between and within 13 major clusters. Some clusters were related, and others were unrelated, to a single HS serotype. For example, all strains belonging to serotypes HS6 and HS19 grouped into corresponding single genotypic clusters, while strains of serotypes HS11 and HS18 each grouped into two genotypic clusters. Strains of HS50, the most prevalent serotype infecting humans, were found both in one large (multiserotype) cluster complex and dispersed throughout the tree. The strain genotypes within each FAFLP cluster were characterized by a particular combination of AFs, and among the cluster there were additional differential AFs. Identification of such AFs could act as a search tool to look for potential associations with disease or animal hosts, when applied to large number of human isolates. Genome-sequence based FAFLP, thus, has the potential to establish a genetic database for epidemiological investigations of Campylobacter.
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Affiliation(s)
- M Desai
- Molecular Biology Unit, Virus Reference Division, Central Public Health Laboratory, London NW9 5HT, United Kingdom.
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641
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Dorrell N, Mangan JA, Laing KG, Hinds J, Linton D, Al-Ghusein H, Barrell BG, Parkhill J, Stoker NG, Karlyshev AV, Butcher PD, Wren BW. Whole genome comparison of Campylobacter jejuni human isolates using a low-cost microarray reveals extensive genetic diversity. Genome Res 2001; 11:1706-15. [PMID: 11591647 PMCID: PMC311159 DOI: 10.1101/gr.185801] [Citation(s) in RCA: 253] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Campylobacter jejuni is the leading cause of bacterial food-borne diarrhoeal disease throughout the world, and yet is still a poorly understood pathogen. Whole genome microarray comparisons of 11 C. jejuni strains of diverse origin identified genes in up to 30 NCTC 11168 loci ranging from 0.7 to 18.7 kb that are either absent or highly divergent in these isolates. Many of these regions are associated with the biosynthesis of surface structures including flagella, lipo-oligosaccharide, and the newly identified capsule. Other strain-variable genes of known function include those responsible for iron acquisition, DNA restriction/modification, and sialylation. In fact, at least 21% of genes in the sequenced strain appear dispensable as they are absent or highly divergent in one or more of the isolates tested, thus defining 1300 C. jejuni core genes. Such core genes contribute mainly to metabolic, biosynthetic, cellular, and regulatory processes, but many virulence determinants are also conserved. Comparison of the capsule biosynthesis locus revealed conservation of all the genes in this region in strains with the same Penner serotype as strain NCTC 11168. By contrast, between 5 and 17 NCTC 11168 genes in this region are either absent or highly divergent in strains of a different serotype from the sequenced strain, providing further evidence that the capsule accounts for Penner serotype specificity. These studies reveal extensive genetic diversity among C. jejuni strains and pave the way toward identifying correlates of pathogenicity and developing improved epidemiological tools for this problematic pathogen.
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Affiliation(s)
- N Dorrell
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
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642
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Dingle KE, Van Den Braak N, Colles FM, Price LJ, Woodward DL, Rodgers FG, Endtz HP, Van Belkum A, Maiden MC. Sequence typing confirms that Campylobacter jejuni strains associated with Guillain-Barré and Miller-Fisher syndromes are of diverse genetic lineage, serotype, and flagella type. J Clin Microbiol 2001; 39:3346-9. [PMID: 11526174 PMCID: PMC88342 DOI: 10.1128/jcm.39.9.3346-3349.2001] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2001] [Accepted: 06/28/2001] [Indexed: 11/20/2022] Open
Abstract
Guillain-Barré syndrome (GBS) and Miller-Fisher syndrome (MFS) are correlated with prior infection by Campylobacter jejuni in up to 40% of cases. Nucleotide sequence-based typing of 25 C. jejuni isolates associated with neuropathy permitted robust comparisons with equivalent data from approximately 800 C. jejuni isolates not associated with neuropathy. A total of 13 genetic lineages and 20 flaA short variable region nucleotide sequences were present among the 25 isolates. A minority of isolates (4 of 25) had the flaA short variable region nucleotide sequences that were previously proposed as a marker for GBS-associated isolates. These 4 isolates probably represented the Penner serotype 19 lineage, which has been proposed to have an association with GBS.
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Affiliation(s)
- K E Dingle
- Wellcome Trust Centre for the Epidemiology of Infectious Disease, Department of Zoology, University of Oxford, Oxford, OX1 3FY, United Kingdom
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643
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Fitzgerald C, Helsel LO, Nicholson MA, Olsen SJ, Swerdlow DL, Flahart R, Sexton J, Fields PI. Evaluation of methods for subtyping Campylobacter jejuni during an outbreak involving a food handler. J Clin Microbiol 2001; 39:2386-90. [PMID: 11427543 PMCID: PMC88159 DOI: 10.1128/jcm.39.7.2386-2390.2001] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In October 1998, the Centers for Disease Control and Prevention (CDC) assisted in an investigation of an outbreak of campylobacteriosis at a school in Salina, Kansas. Twenty-two isolates were submitted from the Kansas state public health laboratory to CDC, 9 associated with the outbreak and 13 epidemiologically unrelated sporadic isolates. Pulsed-field gel electrophoresis (PFGE) using SmaI and SalI was initially used to validate the epidemiologic data. We then tested the ability of other subtyping techniques to distinguish the outbreak-associated isolates from unrelated sporadic isolates. The methods employed were somatic O serotyping, PCR-restriction fragment length polymorphism (RFLP) analysis of flaA, DNA sequence analysis of 582 bp of flaA that included the short variable region (SVR), and sequencing of the entire flaA gene. PFGE was the most discriminatory technique, yielding 11 SmaI and 10 SalI restriction profiles. All outbreak isolates were indistinguishable by PFGE, somatic O serotyping, and sequencing of the 582-bp region of the flaA gene. fla typing by PCR-RFLP grouped one sporadic isolate with the outbreak strain. Analysis of the DNA sequence of a 582-bp segment of flaA produced strain groupings similar to that generated by PCR-RFLP but further differentiated two flaA PCR-RFLP types (with a 1-bp difference in the 582-bp region). Two sporadic strains were distinct by flaA PCR-RFLP but differed only by a single base substitution in the 582-bp region. The entire flaA gene was sequenced from strains differing by a single base pair in the 582-bp region, and the data revealed that additional discrimination may in some cases be obtained by sequencing outside the SVR. PFGE was superior to all other typing methods tested for strain discrimination; it was crucial for understanding the Kansas outbreak and, when SmaI was used, provided adequate discrimination between unrelated isolates.
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Affiliation(s)
- C Fitzgerald
- Foodborne and Diarrheal Diseases Branch, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
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644
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Suerbaum S, Lohrengel M, Sonnevend A, Ruberg F, Kist M. Allelic diversity and recombination in Campylobacter jejuni. J Bacteriol 2001; 183:2553-9. [PMID: 11274115 PMCID: PMC95172 DOI: 10.1128/jb.183.8.2553-2559.2001] [Citation(s) in RCA: 110] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The allelic diversity and population structure of Campylobacter jejuni were studied by multilocus nucleotide sequence analysis. Sequences from seven housekeeping genes were obtained from 32 C. jejuni isolates isolated from enteritis patients in Germany, Hungary, Thailand, and the United States. Also included was strain NCTC 11168, the complete genomic sequence of which has recently been published. For all loci analyzed, multiple strains carried identical alleles. The frequency of synonymous and nonsynonymous sequence polymorphisms was low. The number of unique alleles per locus ranged from 9 to 15. These alleles occurred in 31 different combinations (sequence types), so that all but two pairs of strains could be distinguished from each other. Sequences were analyzed for evidence of recombination by the homoplasy test and split decomposition. These analyses showed that intraspecific recombination is frequent in C. jejuni and has generated extensive diversity of allelic profiles from a small number of polymorphic nucleotides.
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Affiliation(s)
- S Suerbaum
- Institut für Hygiene und Mikrobiologie der Universität Würzburg, D-97080 Würzburg, Germany.
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