Abstract
Actinobacillus pleuropneumoniae is the etiological agent of porcine pleuropneumonia, a disease of major impact on pig health, welfare, and productivity globally. Serovar 8 (APP) is the predominant clinical serovar in Norway and the United Kingdom (UK), and has been isolated from clinical cases in Denmark. The primary objective of this study was to characterize the genetic variability of isolates of A. pleuropneumoniae APP8 in the Norwegian population. The secondary objectives were to determine the within-host variability of APP8; to compare the APP8 bacterial populations in Norway, Denmark, and the UK, including antimicrobial resistance (AMR) gene profiles and to assess the effect of national differences in antimicrobial drug use and restricted animal movement on the occurrence of resistance. Isolates of APP8 from the UK (n=67), Denmark (n=22), and Norway (n=123) collected between 1983 and 2020 were compared using whole genome sequencing. To investigate genetic variability within individual hosts, an additional 104 APP8 isolates from the lungs of six Norwegian pigs were compared. Very low within-host variation was observed (≤ 2 single nucleotide polymorphisms). The phylogeny of 123 Norwegian APP8 isolates from 76 herds revealed some within-herd genetic variation, but substantial geographical clustering. When inferring the relatedness of the three international APP8 collections, the topology highlighted the existence of two distinct monophyletic branches characterized by the Norwegian and UK isolates, respectively. Three Danish isolates were scattered across the UK branch, whereas the remaining 19 Danish isolates clustered in two monophyletic groups nested in the Norwegian branch. Coalescence analysis, performed to estimate the divergences from a common ancestor, indicated a last common ancestor several centuries ago. The phylogenetic analyses also revealed striking differences in occurrence of AMR genes, as these were 23-times more prevalent among the UK isolates than among the Norwegian isolates. An increased understanding of the effects of population strategies is helpful in surveillance and control of infectious diseases.
Highlights
Comparing genome sequence data provides information on molecular and epidemiologic relationships
Samples from different years were scattered across the phylogeny, with few SNPs between isolates sampled up to 13 years apart, suggesting that APP8 is diversifying at a slow rate in the population
Isolates sampled within-host were nearly identical, and there was little genetic variability between isolates from pigs in a herd during an outbreak, supporting that one sample per animal and only a few samples per herd should suffice for diagnostic sampling
Summary
Comparing genome sequence data provides information on molecular and epidemiologic relationships. Genetic variability can be compared at many levels within and between species populations and is influenced both by inherent biologic characteristics that affect the transmission of the pathogen, as well as by host population structures and events (i.e., host population dynamics). The Norwegian pig production system has a pyramidal structure, with a unidirectional flow of animals from a low number of genetic nucleus breeding herds at the top, to a larger number of commercial producers at the bottom (Norwegian Veterinary Institute, 2021a). In most modern pig producing countries, herds are endemically infected with A. pleuropneumoniae, with healthy carrier pigs harboring the bacterium in their tonsils (Gottschalk, 2015; Sassu et al, 2017). To what extent bacteria involved in lung infections are genetically heterogeneous or are solely monoclonal has not been elucidated
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