TY - JOUR
T1 - Comparative genomics of Bordetella pertussis isolates from New Zealand, a country with an uncommonly high incidence of whooping cough
AU - Ring, Natalie
AU - Davies, Heather
AU - Morgan, Julie
AU - Sundaresan, Maithreyi
AU - Tiong, Audrey
AU - Preston, Andrew
AU - Bagby, Stefan
N1 - Funding Information:
This work was funded by the University of Bath and Oxford Nanopore Technologies. The New Zealand isolates were originally collected, stored, prepared and shipped by the Institute of Environmental Science and Research, funded by the New Zealand Ministry of Health with the cooperation of the local diagnostic laboratories.
Funding Information:
This work was funded by the University of Bath and Oxford Nanopore Technologies. The New Zealand isolates were originally collected, stored, prepared and shipped by the Institute of Environmental Science and Research, funded by the New Zealand Ministry of Health with the cooperation of the local diagnostic laboratories. The authors are grateful to the Institute of Environmental Science and Research and the New Zealand Ministry of Health for providing the isolates investigated here, and to Oxford Nanopore Technologies for part-funding NR?s PhD studentship. We also continue to be thankful for the fantastic bioinformatics resource, CLIMB (developed by the MRC, grant number MR/L015080/1), without which the data analysis undertaken here would not have been possible.
Publisher Copyright:
© 2022 The Authors.
PY - 2022/1/27
Y1 - 2022/1/27
N2 - Whooping cough, the respiratory disease caused by Bordetella pertussis, has undergone a wide-spread resurgence over the last several decades. Previously, we developed a pipeline to assemble the repetitive B. pertussis genome into closed sequences using hybrid nanopore and Illumina sequencing. Here, this sequencing pipeline was used to conduct a more high-throughput, longitudinal screen of 66 strains isolated between 1982 and 2018 in New Zealand. New Zealand has a higher incidence of whooping cough than many other countries; usually at least twice as many cases per 100000 people as the USA and UK and often even higher, despite similar rates of vaccine uptake. To the best of our knowledge, these strains are the first New Zealand B. pertussis isolates to be sequenced. The analyses here show that, on the whole, genomic trends in New Zealand B. pertussis isolates, such as changing allelic profile in vaccine-related genes and increasing pertactin deficiency, have paralleled those seen elsewhere in the world. At the same time, phylogenetic comparisons of the New Zealand isolates with global isolates suggest that a number of strains are circulating in New Zealand, which cluster separately from other global strains, but which are closely related to each other. The results of this study add to a growing body of knowledge regarding recent changes to the B. pertussis genome, and are the first genetic investigation into B. pertussis isolates from New Zealand.
AB - Whooping cough, the respiratory disease caused by Bordetella pertussis, has undergone a wide-spread resurgence over the last several decades. Previously, we developed a pipeline to assemble the repetitive B. pertussis genome into closed sequences using hybrid nanopore and Illumina sequencing. Here, this sequencing pipeline was used to conduct a more high-throughput, longitudinal screen of 66 strains isolated between 1982 and 2018 in New Zealand. New Zealand has a higher incidence of whooping cough than many other countries; usually at least twice as many cases per 100000 people as the USA and UK and often even higher, despite similar rates of vaccine uptake. To the best of our knowledge, these strains are the first New Zealand B. pertussis isolates to be sequenced. The analyses here show that, on the whole, genomic trends in New Zealand B. pertussis isolates, such as changing allelic profile in vaccine-related genes and increasing pertactin deficiency, have paralleled those seen elsewhere in the world. At the same time, phylogenetic comparisons of the New Zealand isolates with global isolates suggest that a number of strains are circulating in New Zealand, which cluster separately from other global strains, but which are closely related to each other. The results of this study add to a growing body of knowledge regarding recent changes to the B. pertussis genome, and are the first genetic investigation into B. pertussis isolates from New Zealand.
U2 - 10.1099/mgen.0.000756
DO - 10.1099/mgen.0.000756
M3 - Article
SN - 2057-5858
VL - 8
JO - Microbial Genomics
JF - Microbial Genomics
IS - 1
M1 - MGEN000756
ER -