The colonization of Ireland by mammals has been the subject of extensive study using genetic meth... more The colonization of Ireland by mammals has been the subject of extensive study using genetic methods and forms a central problem in understanding the phylogeography of European mammals after the Last Glacial Maximum. Ireland exhibits a depauperate mammal fauna relative to Great Britain and continental Europe, and a range of natural and anthropogenic processes have given rise to its modern fauna. Previous Europe-wide surveys of the European badger ( Meles meles ) have found conflicting microsatellite and mitochondrial DNA evidence in Irish populations, suggesting Irish badgers have arisen from admixture between human imported British and Scandinavian animals. The extent and history of contact between British and Irish badger populations remains unclear. We use comprehensive genetic data from Great Britain and Ireland to demonstrate that badgers in Ireland's northeastern and southeastern counties are genetically similar to contemporary British populations. Simulation analyses sugg...
Figure S1. Patches and Divisional Veterinary Offices (DVOs) within NI. Table S1. Summary statisti... more Figure S1. Patches and Divisional Veterinary Offices (DVOs) within NI. Table S1. Summary statistics for herd level variables. Table S2. Summary statistics for patch level variables. Table S3. AIC values for each of the models, compared to null models containing only the â total reactorsâ variable. Table S4. Final full model for the breakdown level analysis constructed using all data. Table S5. Final full model for the breakdown level analysis constructed using only data from herds with milk licences. Table S6. Final full model for the breakdown level analysis constructed using only data from herds without milk licences. Table S7. Final full model for the herd level analysis constructed using all data. Table S8. Final full model for the herd level analysis constructed using data from herds with milk licences. Table S9. Final full model for the herd level analysis constructed using data from herds without milk licences. Table S10. Final full model for the patch level analysis construc...
Various genetic markers have been exploited for fingerprinting the Mycobacterium tuberculosis com... more Various genetic markers have been exploited for fingerprinting the Mycobacterium tuberculosis complex (MTBC) in molecular epidemiological studies, mainly through identifying restriction fragment length polymorphisms (RFLP). In large-scale studies, RFLP typing has practical processing and analysis limitations; therefore, attempts have been made to move towards PCR-based typing techniques. Spoligotyping (spacer oligotyping) and, more recently, variable-number tandem repeat (VNTR) typing have provided PCR-derived typing techniques. This study describes the identification and characterization of novel VNTR loci, consisting of tandem repeats in the size range of 53 to 59 bp in the MTBC, and their assessment as typing tools in 47 Mycobacterium bovis field isolates and nine MTBC strains. Spoligotyping and the previously described set of exact tandem repeats (ETRs) (R. Frothingham and W. A. Meeker-O'Connell, Microbiology 144: 1189-1196, 1998) were also applied to the same panel of isola...
Introduction Genetic selection of resistant individuals may offer a complementary control strateg... more Introduction Genetic selection of resistant individuals may offer a complementary control strategy for bovine tuberculosis. Hypothesising underlying non-additive genetic variation, we present an approach to identify loci displaying heterozygote (dis)advantage associated with resistance to Mycobacterium bovis and compare with results from standard genome scans.
Surveillance genotyping (variable number tandem repeat profiling and spoligotyping) of Mycobacter... more Surveillance genotyping (variable number tandem repeat profiling and spoligotyping) of Mycobacterium bovis isolates from culture-confirmed bovine tuberculosis (TB)-affected herds in Northern Ireland is presented for the years 2003 to 2008 inclusive. A total of 175 M bovis genotypes were identified in 8630 isolates from 6609 herds. On average, 73 genotypes were identified each year, with 29 genotypes present in all six years. Highly significant differences (P<0.0001) were observed between the relative frequency of some genotypes in the years 2003 to 2008. The spatial distribution of M bovis genotypes was not random (P<0.0001). Significant geographical localisation of M bovis genotypes was evident, suggesting that sources tended to be local. Despite regions being dominated by geographically localised genotypes, substantial and exploitable local diversity was still evident. Genotypes were also translocated significant distances from their normal geographical location.
The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease, 2003
To determine whether multidrug-resistant (MDR) strains of Mycobacterium bovis isolated from patie... more To determine whether multidrug-resistant (MDR) strains of Mycobacterium bovis isolated from patients in Scotland were genotypically related. Genotypes of MDR strains were determined using three molecular fingerprinting techniques: pulsed-field gel electrophoresis (PFGE), spoligotyping and restriction fragment length polymorphism (RFLP). PFGE profiles were also obtained for all medical and veterinary isolates occurring in Scotland in 1997-1998. MDR strains showed individual Dra I PFGE profiles. Case III/98 had a profile represented in both veterinary and medical populations, Case I/94 had a profile observed in medical but not veterinary isolates, and Case II/98 had a profile unique to this study. Afl II PFGE discriminated the resistant strains. Spoligotyping grouped Cases I/94 and II/98 (ST-134). Case III/98 had a spoligotype ST-140, which is commonly observed in veterinary isolates. Similarly, DRr-RFLP analysis grouped cases I/94 and II/98, whereas Case III/98 had a common veterinar...
The colonization of Ireland by mammals has been the subject of extensive study using genetic meth... more The colonization of Ireland by mammals has been the subject of extensive study using genetic methods and forms a central problem in understanding the phylogeography of European mammals after the Last Glacial Maximum. Ireland exhibits a depauperate mammal fauna relative to Great Britain and continental Europe, and a range of natural and anthropogenic processes have given rise to its modern fauna. Previous Europe-wide surveys of the European badger ( Meles meles ) have found conflicting microsatellite and mitochondrial DNA evidence in Irish populations, suggesting Irish badgers have arisen from admixture between human imported British and Scandinavian animals. The extent and history of contact between British and Irish badger populations remains unclear. We use comprehensive genetic data from Great Britain and Ireland to demonstrate that badgers in Ireland's northeastern and southeastern counties are genetically similar to contemporary British populations. Simulation analyses sugg...
Figure S1. Patches and Divisional Veterinary Offices (DVOs) within NI. Table S1. Summary statisti... more Figure S1. Patches and Divisional Veterinary Offices (DVOs) within NI. Table S1. Summary statistics for herd level variables. Table S2. Summary statistics for patch level variables. Table S3. AIC values for each of the models, compared to null models containing only the â total reactorsâ variable. Table S4. Final full model for the breakdown level analysis constructed using all data. Table S5. Final full model for the breakdown level analysis constructed using only data from herds with milk licences. Table S6. Final full model for the breakdown level analysis constructed using only data from herds without milk licences. Table S7. Final full model for the herd level analysis constructed using all data. Table S8. Final full model for the herd level analysis constructed using data from herds with milk licences. Table S9. Final full model for the herd level analysis constructed using data from herds without milk licences. Table S10. Final full model for the patch level analysis construc...
Various genetic markers have been exploited for fingerprinting the Mycobacterium tuberculosis com... more Various genetic markers have been exploited for fingerprinting the Mycobacterium tuberculosis complex (MTBC) in molecular epidemiological studies, mainly through identifying restriction fragment length polymorphisms (RFLP). In large-scale studies, RFLP typing has practical processing and analysis limitations; therefore, attempts have been made to move towards PCR-based typing techniques. Spoligotyping (spacer oligotyping) and, more recently, variable-number tandem repeat (VNTR) typing have provided PCR-derived typing techniques. This study describes the identification and characterization of novel VNTR loci, consisting of tandem repeats in the size range of 53 to 59 bp in the MTBC, and their assessment as typing tools in 47 Mycobacterium bovis field isolates and nine MTBC strains. Spoligotyping and the previously described set of exact tandem repeats (ETRs) (R. Frothingham and W. A. Meeker-O'Connell, Microbiology 144: 1189-1196, 1998) were also applied to the same panel of isola...
Introduction Genetic selection of resistant individuals may offer a complementary control strateg... more Introduction Genetic selection of resistant individuals may offer a complementary control strategy for bovine tuberculosis. Hypothesising underlying non-additive genetic variation, we present an approach to identify loci displaying heterozygote (dis)advantage associated with resistance to Mycobacterium bovis and compare with results from standard genome scans.
Surveillance genotyping (variable number tandem repeat profiling and spoligotyping) of Mycobacter... more Surveillance genotyping (variable number tandem repeat profiling and spoligotyping) of Mycobacterium bovis isolates from culture-confirmed bovine tuberculosis (TB)-affected herds in Northern Ireland is presented for the years 2003 to 2008 inclusive. A total of 175 M bovis genotypes were identified in 8630 isolates from 6609 herds. On average, 73 genotypes were identified each year, with 29 genotypes present in all six years. Highly significant differences (P<0.0001) were observed between the relative frequency of some genotypes in the years 2003 to 2008. The spatial distribution of M bovis genotypes was not random (P<0.0001). Significant geographical localisation of M bovis genotypes was evident, suggesting that sources tended to be local. Despite regions being dominated by geographically localised genotypes, substantial and exploitable local diversity was still evident. Genotypes were also translocated significant distances from their normal geographical location.
The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease, 2003
To determine whether multidrug-resistant (MDR) strains of Mycobacterium bovis isolated from patie... more To determine whether multidrug-resistant (MDR) strains of Mycobacterium bovis isolated from patients in Scotland were genotypically related. Genotypes of MDR strains were determined using three molecular fingerprinting techniques: pulsed-field gel electrophoresis (PFGE), spoligotyping and restriction fragment length polymorphism (RFLP). PFGE profiles were also obtained for all medical and veterinary isolates occurring in Scotland in 1997-1998. MDR strains showed individual Dra I PFGE profiles. Case III/98 had a profile represented in both veterinary and medical populations, Case I/94 had a profile observed in medical but not veterinary isolates, and Case II/98 had a profile unique to this study. Afl II PFGE discriminated the resistant strains. Spoligotyping grouped Cases I/94 and II/98 (ST-134). Case III/98 had a spoligotype ST-140, which is commonly observed in veterinary isolates. Similarly, DRr-RFLP analysis grouped cases I/94 and II/98, whereas Case III/98 had a common veterinar...
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