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Martin C. J. Maiden - One of the best experts on this subject based on the ideXlab platform.
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using Multilocus Sequence Typing to study bacterial variation prospects in the genomic era
Future Microbiology, 2014Co-Authors: Keith A. Jolley, Martin C. J. MaidenAbstract:Multilocus Sequence Typing (MLST) indexes the Sequence variation present in a small number (usually seven) of housekeeping gene fragments located around the bacterial genome. Unique alleles at these loci are assigned arbitrary integer identifiers, which effectively summarizes the variation present in several thousand base pairs of genome Sequence information as a series of numbers. Comparing bacterial isolates using allele-based methods efficiently corrects for the effects of lateral gene transfer present in many bacterial populations and is computationally efficient. This 'gene-by-gene' approach can be applied to larger collections of loci, such as the ribosomal protein genes used in ribosomal MLST (rMLST), up to and including the complete set of coding Sequences present in a genome, whole-genome MLST (wgMLST), providing scalable, efficient and readily interpreted genome analysis.
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strain Typing and determination of population structure of candida krusei by Multilocus Sequence Typing
Journal of Clinical Microbiology, 2007Co-Authors: Mette D. Jacobsen, Martin C. J. Maiden, Neil A. R. Gow, Duncan James Shaw, Frank C. OddsAbstract:A Multilocus Sequence Typing (MLST) scheme for Candida krusei was devised, based on sequencing of six gene fragments of the species. The existence of heterozygous results for each of the six fragments Sequenced confirms that C. krusei is diploid for at least part of its genome. The C. krusei MLST scheme had a discriminatory index of 0.998, making this system ideal for strain Typing of C. krusei clinical isolates. MLST data for 122 independent C. krusei isolates from a range of geographical sources were analyzed by eBURST, structure, and the unweighted-pair group method using average linkages to derive a population structure comprising four subtype strain clusters. There was no evidence of geographical associations with particular subtypes. Data for pairs of isolates from seven patients showed that each patient was colonized and/or infected with strain types that were indistinguishable by MLST. The C. krusei MLST database can be accessed online at http://pubmlst.org/ckrusei/.
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Multilocus Sequence Typing for global surveillance of meningococcal disease
Fems Microbiology Reviews, 2007Co-Authors: Carina Brehony, Keith A. Jolley, Martin C. J. MaidenAbstract:The global surveillance of bacterial pathogens is particularly important for bacteria with diverse and dynamic populations that cause periodic epidemics or pandemics. The isolate characterization methods employed for surveillance should: (1) generate unambiguous data; (2) be readily implemented in a variety of scenarios and be reproducible among laboratories; (3) be scalable and preferably available in a high throughput format; and (4) be cost effective. Multilocus Sequence Typing (MLST) was designed to meet these criteria and has been implemented effectively for a wide range of microorganisms. The ‘Impact of meningococcal epidemiology and population biology on public health in Europe (EU-MenNet)’ project had amongst its objectives: (1) to disseminate meningococcal MLST and Sequence-based Typing throughout Europe by establishing a centre for training and data generation, and (2) to produce a comprehensive Europe-wide picture of meningococcal disease epidemiology for the first time. Data produced from the project have shown the distribution of a relatively small number of STs, clonal complexes and PorA types that account for a large proportion of the disease-associated isolates in Europe. The project demonstrates how molecular Typing can be combined with epidemiological data via the Internet for global disease surveillance.
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Multilocus Sequence Typing system for the endosymbiont wolbachia pipientis
Applied and Environmental Microbiology, 2006Co-Authors: Laura Baldo, Martin C. J. Maiden, Keith A. Jolley, Julie Dunning C Hotopp, Seth R Bordenstein, Sarah Biber, Rhitoban Ray Choudhury, Cheryl Y Hayashi, Herve Tettelin, John H WerrenAbstract:The eubacterial genus Wolbachia comprises one of the most abundant groups of obligate intracellular bacteria, and it has a host range that spans the phyla Arthropoda and Nematoda. Here we developed a Multilocus Sequence Typing (MLST) scheme as a universal genoTyping tool for Wolbachia. Internal fragments of five ubiquitous genes (gatB, coxA, hcpA, fbpA, and ftsZ) were chosen, and primers that amplified across the major Wolbachia supergroups found in arthropods, as well as other divergent lineages, were designed. A supplemental Typing system using the hypervariable regions of the Wolbachia surface protein (WSP) was also developed. Thirty-seven strains belonging to supergroups A, B, D, and F obtained from singly infected hosts were characterized by using MLST and WSP. The number of alleles per MLST locus ranged from 25 to 31, and the average levels of genetic diversity among alleles were 6.5% to 9.2%. A total of 35 unique allelic profiles were found. The results confirmed that there is a high level of recombination in chromosomal genes. MLST was shown to be effective for detecting diversity among strains within a single host species, as well as for identifying closely related strains found in different arthropod hosts. Identical or similar allelic profiles were obtained for strains harbored by different insect species and causing distinct reproductive phenotypes. Strains with similar WSP Sequences can have very different MLST allelic profiles and vice versa, indicating the importance of the MLST approach for strain identification. The MLST system provides a universal and unambiguous tool for strain Typing, population genetics, and molecular evolutionary studies. The central database for storing and organizing Wolbachia bacterial and host information can be accessed at http://pubmlst.org/wolbachia/.
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candida albicans strain maintenance replacement and microvariation demonstrated by Multilocus Sequence Typing
Journal of Clinical Microbiology, 2006Co-Authors: Frank C. Odds, Martin C. J. Maiden, Mette D. Jacobsen, Arianna Tavanti, Amanda Denise Davidson, Duncan James Shaw, Julie A Whyte, Christopher C Kibbler, David Ellis, Neil A. R. GowAbstract:We typed 165 Candida albicans isolates from 44 different sources by Multilocus Sequence Typing (MLST) and ABC Typing of rRNA genes and determined their homozygosity or heterozygosity at the mating-type-like locus (MTL). The isolates represented pairs or larger sets from individual sources, which allowed the determination of strain diversity within patients. A comparison of replicate Sequence data determined a reproducibility threshold for regarding isolates as MLST indistinguishable. For 36 isolate sets, MLST and ABC Typing showed indistinguishable or highly related strain types among isolates from different sites or from the same site at different times from each patient. This observation included 11 sets with at least one isolate from a blood culture and a nonsterile site from the same patient. For one patient, strain replacement was evidenced in the form of two sets of isolates from different hospital admissions where the strain types within each set were nearly identical but where the two sets differed both by MLST and ABC Typing. MLST therefore confirms the existing view of C. albicans strain carriage. Microvariation, evidenced as small differences between MLST types, resulted in most instances from a loss of heterozygosity at one or more of the Sequenced loci. Among isolate sets that showed major strain type differences, some isolates could be excluded as likely examples of handling errors during storage. However, for a minority of isolates, intermittent differences in ABC type for tightly clustered MLST types and intermittent appearances of MTL homozygosity lead us to propose that some C. albicans isolates, or all isolates under yet-to-be-determined conditions, maintain a high level of genetic diversity by mechanisms such as recombination, gene conversion, or chromosomal ploidy change.
Brian G. Spratt - One of the best experts on this subject based on the ideXlab platform.
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The Multilocus Sequence Typing network: mlst.net.
Nucleic acids research, 2005Co-Authors: David M. Aanensen, Brian G. SprattAbstract:The unambiguous characterization of strains of a pathogen is crucial for addressing questions relating to its epidemiology, population and evolutionary biology. Multilocus Sequence Typing (MLST), which defines strains from the Sequences at seven house-keeping loci, has become the method of choice for molecular Typing of many bacterial and fungal pathogens (and non-pathogens), and MLST schemes and strain databases are available for a growing number of prokaryotic and eukaryotic organisms. Sequence data are ideal for strain characterization as they are unambiguous, meaning strains can readily be compared between laboratories via the Internet. Laboratories undertaking MLST can quickly progress from sequencing the seven gene fragments to characterizing their strains and relating them to those submitted by others and to the population as a whole. We provide the gateway to a number of MLST schemes, each of which contain a set of tools for the initial characterization of strains, and methods for relating query strains to other strains of the species, including clustering based on differences in allelic profiles, phylogenetic trees based on concatenated Sequences, and a recently developed method (eBURST) for identifying clonal complexes within a species and displaying the overall structure of the population. This network of MLST websites is available at http://www.mlst.net.
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Multilocus Sequence Typing of streptococcus pyogenes and the relationships between emm type and clone
Infection and Immunity, 2001Co-Authors: Mark C Enright, Brian G. Spratt, Awdhesh Kalia, John H Cross, Debra E BessenAbstract:Multilocus Sequence Typing (MLST) is a tool that can be used to study the molecular epidemiology and population genetic structure of microorganisms. A MLST scheme was developed for Streptococcus pyogenes and the nucleotide Sequences of internal fragments of seven selected housekeeping loci were obtained for 212 isolates. A total of 100 unique combinations of housekeeping alleles (allelic profiles) were identified. The MLST scheme was highly concordant with several other Typing methods. The emm type, corresponding to a locus that is subject to host immune selection, was determined for each isolate; of the >150 distinct emm types identified to date, 78 are represented in this report. For a given emm type, the majority of isolates shared five or more of the seven housekeeping alleles. Stable associations between emm type and MLST were documented by comparing isolates obtained decades apart and/or from different continents. For the 33 emm types for which more than one isolate was examined, only five emm types were present on widely divergent backgrounds, differing at four or more of the housekeeping loci. The findings indicate that the majority of emm types examined define clones or clonal complexes. In addition, an MLST database is made accessible to investigators who seek to characterize other isolates of this species via the internet (http://www.mlst.net).
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estimating recombinational parameters in streptococcus pneumoniae from Multilocus Sequence Typing data
Genetics, 2000Co-Authors: Edward J. Feil, Mark C Enright, John Maynard Smith, Brian G. SprattAbstract:Multilocus Sequence Typing (MLST) is a highly discriminatory molecular Typing method that defines isolates of bacterial pathogens using the Sequences of ~450-bp internal fragments of seven housekeeping genes. This technique has been applied to 575 isolates of Streptococcus pneumoniae and identifies a number of discrete clonal complexes. These clonal complexes are typically represented by a single group of isolates sharing identical alleles at all seven loci, plus single-locus variants that differ from this group at only one out of the seven loci. As MLST is highly discriminatory, the members of each clonal complex can be assumed to have a recent common ancestor, and the molecular events that give rise to the single-locus variants can be used to estimate the relative contributions of recombination and mutation to clonal divergence. By comparing the Sequences of the variant alleles within each clonal complex with the allele typically found within that clonal complex, we estimate that recombination has generated new alleles at a frequency ~10-fold higher than mutation, and that a single nucleotide site is ~50 times more likely to change through recombination than mutation. We also demonstrate how to estimate the average length of recombinational replacements from MLST data.
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estimating recombinational parameters in streptococcus pneumoniae from Multilocus Sequence Typing data
Genetics, 2000Co-Authors: Edward J. Feil, Mark C Enright, John Maynard Smith, Brian G. SprattAbstract:Multilocus Sequence Typing (MLST) is a highly discriminatory molecular Typing method that defines isolates of bacterial pathogens using the Sequences of approximately 450-bp internal fragments of seven housekeeping genes. This technique has been applied to 575 isolates of Streptococcus pneumoniae and identifies a number of discrete clonal complexes. These clonal complexes are typically represented by a single group of isolates sharing identical alleles at all seven loci, plus single-locus variants that differ from this group at only one out of the seven loci. As MLST is highly discriminatory, the members of each clonal complex can be assumed to have a recent common ancestor, and the molecular events that give rise to the single-locus variants can be used to estimate the relative contributions of recombination and mutation to clonal divergence. By comparing the Sequences of the variant alleles within each clonal complex with the allele typically found within that clonal complex, we estimate that recombination has generated new alleles at a frequency approximately 10-fold higher than mutation, and that a single nucleotide site is approximately 50 times more likely to change through recombination than mutation. We also demonstrate how to estimate the average length of recombinational replacements from MLST data.
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Multilocus Sequence Typing
Trends in Microbiology, 1999Co-Authors: Mark C Enright, Brian G. SprattAbstract:Multilocus Sequence Typing (MLST) provides a new approach to molecular epidemiology that can identify and track the global spread of virulent or antibiotic-resistant isolates of bacterial pathogens using the Internet. MLST databases, together with interrogation software, are available for Neisseria meningitidis and Streptococcus pneumoniae and databases for Streptococcus pyogenes and Staphylococcus aureus will be released shortly.
Mark C Enright - One of the best experts on this subject based on the ideXlab platform.
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inferring a population structure for staphylococcus epidermidis from Multilocus Sequence Typing data
Journal of Bacteriology, 2007Co-Authors: Maria Miragaia, Herminia De Lencastre, Jonathan C Thomas, Isabel Couto, Mark C EnrightAbstract:Despite its importance as a human pathogen, information on population structure and global epidemiology of Staphylococcus epidermidis is scarce and the relative importance of the mechanisms contributing to clonal diversification is unknown. In this study, we addressed these issues by analyzing a representative collection of S. epidermidis isolates from diverse geographic and clinical origins using Multilocus Sequence Typing (MLST). Additionally, we characterized the mobile element (SCCmec) carrying the genetic determinant of methicillin resistance. The 217 S. epidermidis isolates from our collection were split by MLST into 74 types, suggesting a high level of genetic diversity. Analysis of MLST data using the eBURST algorithm revealed the existence of nine epidemic clonal lineages that were disseminated worldwide. One single clonal lineage (clonal complex 2) comprised 74% of the isolates, whereas the remaining isolates were clustered into 8 minor clonal lineages and 13 singletons. According to our evolutionary model, SCCmec was acquired at least 56 times by S. epidermidis. Although geographic dissemination of S. epidermidis strains and the value of the index of association between the alleles, 0.2898 (P < 0.05), support the clonality of S. epidermidis species, examination of the Sequence changes at MLST loci during clonal diversification showed that recombination gives rise to new alleles approximately twice as frequently as point mutations. We suggest that S. epidermidis has a population with an epidemic structure, in which nine clones have emerged upon a recombining background and evolved quickly through frequent transfer of genetic mobile elements, including SCCmec.
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improved Multilocus Sequence Typing scheme for staphylococcus epidermidis
Journal of Clinical Microbiology, 2007Co-Authors: Jonathan C Thomas, Miguel R Vargas, Maria Miragaia, Gordon L Archer, Sharon J. Peacock, Mark C EnrightAbstract:We evaluated three Multilocus Sequence Typing (MLST) schemes for Staphylococcus epidermidis and selected the seven most discriminatory loci for the formation of a new, more powerful MLST scheme. This improved scheme gave 31 Sequence types (STs) and 5 clonal complexes (CCs), whereas the other schemes delineate 16 to 24 STs and 1 to 3 CCs.
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Multilocus Sequence Typing and the evolution of methicillin resistant staphylococcus aureus
Clinical Microbiology and Infection, 2004Co-Authors: D A Robinson, Mark C EnrightAbstract:The prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in many countries is increasing and, in hospitals in some areas, more than half of all S. aureus disease isolates are MRSA. MRSA strains are becoming increasingly multiresistant, and have recently developed resistance to vancomycin, used successfully to treat MRSA for more than 30 years. This review summarises recent studies that have elucidated the evolutionary history of MRSA. The first MRSA isolate evolved from a sensitive, epidemic strain prevalent in Europe, and its progeny-the first MRSA clone-quickly spread to other continents. Analyses of epidemic MRSA isolates from hospitals in different countries by molecular methods, including Multilocus Sequence Typing (MLST) and DNA microarray analysis, reveal that MRSA strains have evolved separately within five distinct epidemic, sensitive lineages. However, resistance has been transferred to S. aureus on many more than five occasions, as some lineages have acquired different structural types of the element carrying the methicillin resistance gene. The emergence of MRSA as a community pathogen has been noted in several countries, and MLST and SCCmec Typing have been used to demonstrate that community-acquired MRSA strains are typically related only distantly to hospital MRSA strains, and thus represent novel acquisitions of SCCmec.
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Multilocus Sequence Typing of streptococcus pyogenes and the relationships between emm type and clone
Infection and Immunity, 2001Co-Authors: Mark C Enright, Brian G. Spratt, Awdhesh Kalia, John H Cross, Debra E BessenAbstract:Multilocus Sequence Typing (MLST) is a tool that can be used to study the molecular epidemiology and population genetic structure of microorganisms. A MLST scheme was developed for Streptococcus pyogenes and the nucleotide Sequences of internal fragments of seven selected housekeeping loci were obtained for 212 isolates. A total of 100 unique combinations of housekeeping alleles (allelic profiles) were identified. The MLST scheme was highly concordant with several other Typing methods. The emm type, corresponding to a locus that is subject to host immune selection, was determined for each isolate; of the >150 distinct emm types identified to date, 78 are represented in this report. For a given emm type, the majority of isolates shared five or more of the seven housekeeping alleles. Stable associations between emm type and MLST were documented by comparing isolates obtained decades apart and/or from different continents. For the 33 emm types for which more than one isolate was examined, only five emm types were present on widely divergent backgrounds, differing at four or more of the housekeeping loci. The findings indicate that the majority of emm types examined define clones or clonal complexes. In addition, an MLST database is made accessible to investigators who seek to characterize other isolates of this species via the internet (http://www.mlst.net).
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estimating recombinational parameters in streptococcus pneumoniae from Multilocus Sequence Typing data
Genetics, 2000Co-Authors: Edward J. Feil, Mark C Enright, John Maynard Smith, Brian G. SprattAbstract:Multilocus Sequence Typing (MLST) is a highly discriminatory molecular Typing method that defines isolates of bacterial pathogens using the Sequences of ~450-bp internal fragments of seven housekeeping genes. This technique has been applied to 575 isolates of Streptococcus pneumoniae and identifies a number of discrete clonal complexes. These clonal complexes are typically represented by a single group of isolates sharing identical alleles at all seven loci, plus single-locus variants that differ from this group at only one out of the seven loci. As MLST is highly discriminatory, the members of each clonal complex can be assumed to have a recent common ancestor, and the molecular events that give rise to the single-locus variants can be used to estimate the relative contributions of recombination and mutation to clonal divergence. By comparing the Sequences of the variant alleles within each clonal complex with the allele typically found within that clonal complex, we estimate that recombination has generated new alleles at a frequency ~10-fold higher than mutation, and that a single nucleotide site is ~50 times more likely to change through recombination than mutation. We also demonstrate how to estimate the average length of recombinational replacements from MLST data.
Derrick W. Crook - One of the best experts on this subject based on the ideXlab platform.
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hash based core genome Multilocus Sequence Typing for clostridium difficile
Journal of Clinical Microbiology, 2019Co-Authors: Derrick W. Crook, David W Eyre, T E A Peto, Sarah A WalkerAbstract:Pathogen whole-genome sequencing has huge potential as a tool to better understand infection transmission. However, rapidly identifying closely related genomes among a background of thousands of other genomes is challenging. Here, we describe a refinement to core genome Multilocus Sequence Typing (cgMLST) in which alleles at each gene are reproducibly converted to a unique hash, or short string of letters (hash-cgMLST). This avoids the resource-intensive need for a single centralized database of sequentially numbered alleles. We test the reproducibility and discriminatory power of cgMLST/hash-cgMLST compared to those of mapping-based approaches in Clostridium difficile, using repeated sequencing of the same isolates (replicates) and data from consecutive infection isolates from six English hospitals. Hash-cgMLST provided the same results as standard cgMLST, with minimal performance penalty. Comparing 272 replicate Sequence pairs using reference-based mapping, there were 0, 1, or 2 single-nucleotide polymorphisms (SNPs) between 262 (96%), 5 (2%), and 1 ( 2 differences, respectively. False gene differences were clustered in specific genes and associated with fragmented assemblies, but were reduced using the SKESA assembler. Considering 412 pairs of infections with ≤2 SNPS, i.e., consistent with recent transmission, 376 (91%) had ≤2 gene differences and 16 (4%) had ≥4. Comparing a genome to 100,000 others took <1 min using hash-cgMLST. Hash-cgMLST is an effective surveillance tool for rapidly identifying clusters of related genomes. However, cgMLST/hash-cgMLST generate more false variants than mapping-based approaches. Follow-up mapping-based analyses are likely required to precisely define close genetic relationships.
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Multilocus Sequence Typing of Clostridium difficile
Journal of Clinical Microbiology, 2009Co-Authors: David Griffiths, Warren N. Fawley, Melina Kachrimanidou, Rory Bowden, Derrick W. Crook, Rowena Fung, Tanya Golubchik, Rosalind M. Harding, Katie Jeffery, Keith A. JolleyAbstract:A robust high-throughput Multilocus Sequence Typing (MLST) scheme for Clostridium difficile was developed and validated using a diverse collection of 50 reference isolates representing 45 different PCR ribotypes and 102 isolates from recent clinical samples. A total of 49 PCR ribotypes were represented overall. All isolates were typed by MLST and yielded 40 Sequence types (STs). A web-accessible database was set up (http://pubmlst.org/cdifficile/) to facilitate the dissemination and comparison of C. difficile MLST genoTyping data among laboratories. MLST and PCR riboTyping were similar in discriminatory abilities, having indices of discrimination of 0.90 and 0.92, respectively. Some STs corresponded to a single PCR ribotype (32/40), other STs corresponded to multiple PCR ribotypes (8/40), and, conversely, the PCR ribotype was not always predictive of the ST. The total number of variable nucleotide sites in the concatenated MLST Sequences was 103/3,501 (2.9%). Concatenated MLST Sequences were used to construct a neighbor-joining tree which identified four phylogenetic groups of STs and one outlier (ST-11; PCR ribotype 078). These groups apparently correlate with clades identified previously by comparative genomics. The MLST scheme was sufficiently robust to allow direct genoTyping of C. difficile in total stool DNA extracts without isolate culture. The direct (nonculture) MLST approach may prove useful as a rapid genoTyping method, potentially benefiting individual patients and informing hospital infection control.
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Multilocus Sequence Typing system for group b streptococcus
Journal of Clinical Microbiology, 2003Co-Authors: Nicola Jones, Derrick W. Crook, John F Bohnsack, Shinji Takahashi, Karen A Oliver, Man Suen Chan, Frank Kunst, Philippe Glaser, Christophe Rusniok, Rosalind M. HardingAbstract: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.
Christopher G. Dowson - One of the best experts on this subject based on the ideXlab platform.
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Expanded Multilocus Sequence Typing for Burkholderia Species
Journal of Clinical Microbiology, 2009Co-Authors: Theodore Spilker, Adam Baldwin, Amy Bumford, Christopher G. Dowson, Eshwar Mahenthiralingam, John J. LipumaAbstract:PCR primers targeting loci in the current Burkholderia cepacia complex Multilocus Sequence Typing scheme were redesigned to (i) more reliably amplify these loci from B. cepacia complex species, (ii) amplify these same loci from additional Burkholderia species, and (iii) enable the use of a single primer set per locus for both amplification and DNA sequencing.
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Multilocus Sequence Typing of Intercontinental Bovine Staphylococcus aureus Isolates
Journal of Clinical Microbiology, 2005Co-Authors: Edward M. Smith, Laura E. Green, Graham F. Medley, H. E. Bird, Lawrence K. Fox, Ynte H. Schukken, J. V. Kruze, Andrew J. Bradley, Ruth N. Zadoks, Christopher G. DowsonAbstract:A total of 258 bovine-associated Staphylococcus aureus isolates from the United States, Chile, and the United Kingdom, plus the reference isolate S. aureus Newbould 305 (NCIMB 702892), were analyzed by Multilocus Sequence Typing (MLST). A collection of previously characterized United Kingdom isolates were also included in the analysis. The results demonstrated that MLST is suitable for the differentiation of bovine S. aureus isolates from various sites (milk, teat skin, milking machine unit liners, hands, and bedding) and countries. The theory of the host specificity of S. aureus is supported by the detection of a previously undescribed clonal complex that comprised 87.4% of the isolates studied, with representatives from all geographic locations investigated. This suggests that a single clonal group has achieved a widespread distribution and is responsible for the majority of infections. Some Sequence types (STs; ST25, ST115, ST124, and ST126) demonstrated site specificity, as they were significantly (P < 0.05) associated with milk or teat skin.
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Multilocus Sequence Typing scheme that provides both species and strain differentiation for the burkholderia cepacia complex
Journal of Clinical Microbiology, 2005Co-Authors: Adam Baldwin, Martin C. J. Maiden, Eshwar Mahenthiralingam, John J. Lipuma, Kathleen M Thickett, D Honeybourne, John R W Govan, David P Speert, Peter Vandamme, Christopher G. DowsonAbstract:A single Multilocus Sequence Typing (MLST) scheme was developed for precise characterization of the opportunistic pathogens of Burkholderia cepacia complex (BCC), a group composed of at least nine closely related species. Seven conserved housekeeping genes were selected after a comparison of five Burkholderia species, and a collection of strains was subjected to nucleotide Sequence analysis using a nested PCR amplification approach for each gene. MLST differentiated all nine current BCC species and identified 114 Sequence types within a collection of 119 strains. No differentiation was found between strains recovered from environmental or clinical sources. The improved resolution in strain identification offered by MLST was able to identify previously characterized epidemic strain lineages and also demonstrated the presence of four novel potential species groups within the complex. There was also evidence for recombination having an important role in the recent evolution of individual BCC species. This highly transferable, validated, MLST scheme provides a new means to assist in species identification as well as unambiguous strain discrimination of the BCC by a single approach. It is also the first MLST scheme designed at the outset to incorporate multiple species and should facilitate global epidemiological investigations of the BCC.
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development of a Multilocus Sequence Typing scheme for the opportunistic pathogen pseudomonas aeruginosa
Journal of Clinical Microbiology, 2004Co-Authors: Barry Curran, T L Pitt, D Jonas, Hajo Grundmann, Christopher G. DowsonAbstract:A Multilocus Sequence Typing (MLST) scheme has been developed for Pseudomonas aeruginosa which provides molecular Typing data that are highly discriminatory and electronically portable between laboratories. MLST data confirm the data from previous studies that suggest that P. aeruginosa is best described as nonclonal but as having an epidemic population. The index of association was 0.17, indicating a freely recombining population; however, there was evidence of clusters of closely related strains or clonal complexes among the members of this population. It is apparent that the Sequence types (STs) from single isolates, representing each of the present epidemic clones in the United Kingdom from Liverpool, Manchester, and the West Midlands, are not closely related to each other. This suggests distinct evolutionary origins for each of these epidemic clones in the United Kingdom. Furthermore, these clones are distinct from European clone C. Comparison of the results of MLST with those of toxA Typing and seroTyping revealed that strains with identical STs may possess different toxA types and diverse serotypes. Given that recombination is important in the population of P. aeruginosa, the lack of a linkage between toxA type and serotype is not surprising and reveals the strength of the MLST approach for obtaining a better understanding of the epidemiology of P. aeruginosa.
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Multilocus Sequence Typing for comparison of veterinary and human isolates of campylobacter jejuni
Applied and Environmental Microbiology, 2003Co-Authors: Georgina Manning, Christopher G. Dowson, Mary C Bagnall, I H Ahmed, Malcolm A West, D G NewellAbstract: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.