Adrian R Allen1, Georgina Milne2, Kevin Drees3, Eleanor Presho2, Jordon Graham2, Paul McAdam4, Kerri Jones2, Lorraine Wright2, Robin Skuce2, Adrian M Whatmore5, Judith Graham6, Jeffrey T Foster3. 1. Agri Food and Biosciences Institute (AFBI), AFBI Stormont, Bacteriology Branch, Stoney Road, Belfast, United Kingdom.. Electronic address: Adrian.Allen@afbini.gov.uk. 2. Agri Food and Biosciences Institute (AFBI), AFBI Stormont, Bacteriology Branch, Stoney Road, Belfast, United Kingdom. 3. University of New Hampshire, Department of Molecular, Cellular and Biomedical Sciences, Rudman Hall, 46 College Road, Durham, NH, USA. 4. Fios Genomics, Nine Edinburgh Bioquarter, 9 Little France Road, Edinburgh, United Kingdom. 5. Department of Bacteriology, Animal and Plant Health Agency (APHA), New Haw, Addlestone, Surrey, United Kingdom. 6. Department of Agriculture, Environment and Rural Affairs, Veterinary Service, Belfast, Northern Ireland, United Kingdom.
Abstract
BACKGROUND: In the recent past (1997-2012), Northern Ireland in the United Kingdom suffered an outbreak of Brucella abortus, which at its height affected over 200 cattle herds. Initially, isolates were characterized using multi-locus variable number tandem repeats analysis (MLVA). While informative in this setting, hyper-variability in some loci limited the resolution necessary to infer fine-scale disease transmission networks. Consequently, we applied whole-genome sequencing to isolates from this outbreak to evaluate higher resolution markers for disease epizootiology. RESULTS: Phylogenetic analysis revealed that the B. abortus outbreak in Northern Ireland was caused by two distinct pathogen lineages. One contained isolates consistent with the 1997-2012 outbreak being linked to a previous endemic infection thought eradicated. The dominant second lineage exhibited little genetic diversity throughout the recrudescent outbreak, with limited population sub-structure evident. This finding was inconsistent with prior MLVA molecular characterizations that suggested the presence of seven clonal complexes. Spatio-temporal modeling revealed a significant association of pairwise SNP differences between isolates and geographic distances. However, effect sizes were very small due to reduced pathogen diversity. CONCLUSIONS: Genome sequence data suggested that hyper-variability in some MLVA loci contributed to an overestimate of pathogen diversity in the most recent outbreak. The low diversity observed in our genomic dataset made it inappropriate to apply phylodynamic methods to these data. We conclude that maintaining data repositories of genome sequence data will be invaluable for source attribution/epizootiological inference should recrudescence ever re-occur. However genomic epizootiological methods may have limited utility in some settings, such as when applied to recrudescent/re-emergent infections of slowly-evolving bacterial pathogens. Crown
BACKGROUND: In the recent past (1997-2012), Northern Ireland in the United Kingdom suffered an outbreak of Brucella abortus, which at its height affected over 200 cattle herds. Initially, isolates were characterized using multi-locus variable number tandem repeats analysis (MLVA). While informative in this setting, hyper-variability in some loci limited the resolution necessary to infer fine-scale disease transmission networks. Consequently, we applied whole-genome sequencing to isolates from this outbreak to evaluate higher resolution markers for disease epizootiology. RESULTS: Phylogenetic analysis revealed that the B. abortus outbreak in Northern Ireland was caused by two distinct pathogen lineages. One contained isolates consistent with the 1997-2012 outbreak being linked to a previous endemic infection thought eradicated. The dominant second lineage exhibited little genetic diversity throughout the recrudescent outbreak, with limited population sub-structure evident. This finding was inconsistent with prior MLVA molecular characterizations that suggested the presence of seven clonal complexes. Spatio-temporal modeling revealed a significant association of pairwise SNP differences between isolates and geographic distances. However, effect sizes were very small due to reduced pathogen diversity. CONCLUSIONS: Genome sequence data suggested that hyper-variability in some MLVA loci contributed to an overestimate of pathogen diversity in the most recent outbreak. The low diversity observed in our genomic dataset made it inappropriate to apply phylodynamic methods to these data. We conclude that maintaining data repositories of genome sequence data will be invaluable for source attribution/epizootiological inference should recrudescence ever re-occur. However genomic epizootiological methods may have limited utility in some settings, such as when applied to recrudescent/re-emergent infections of slowly-evolving bacterial pathogens. Crown
Authors: Mostafa Y Abdel-Glil; Prasad Thomas; Christian Brandt; Falk Melzer; Anbazhagan Subbaiyan; Pallab Chaudhuri; Dag Harmsen; Keith A Jolley; Anna Janowicz; Giuliano Garofolo; Heinrich Neubauer; Mathias W Pletz Journal: J Clin Microbiol Date: 2022-07-19 Impact factor: 11.677
Authors: Aman Ullah Khan; Falk Melzer; Ashraf E Sayour; Waleed S Shell; Jörg Linde; Mostafa Abdel-Glil; Sherif A G E El-Soally; Mandy C Elschner; Hossam E M Sayour; Eman Shawkat Ramadan; Shereen Aziz Mohamed; Ashraf Hendam; Rania I Ismail; Lubna F Farahat; Uwe Roesler; Heinrich Neubauer; Hosny El-Adawy Journal: Pathogens Date: 2021-06-16