Whole-Genome Analysis of Bordetella pertussis MT27 Isolates from School-Associated Outbreaks: Single-Nucleotide Polymorphism Diversity and Threshold of the Outbreak Strains

Abstract

Bordetella pertussis is a highly infectious bacterium that easily causes pertussis outbreaks in humans, especially in school-aged children. In detection and investigation of outbreaks, excluding non-outbreak isolates is important for understanding the bacterial transmission routes.

Whole-genome comparison of two same-genotype macrolide-resistant Bordetella pertussis isolates collected in Japan

“…However, the whole-genome analysis revealed 11 SNP differences on CDS and variations in genome structures between the MRBP genomes. In a previous study, we proposed a threshold of three or less SNPs per genome for considering strains as the same in pertussis outbreaks [ 30 ]. According to this criterion, BP616 and BP625 were determined to be different strains.…”

Identifying SNP threshold from P2 sequences for investigating norovirus transmission

“…Whether to interpret a phylogenetic cluster or several adjacent clusters as closely related strains shared by all the cases in single outbreak usually relies on some criteria, such as single nucleotide polymorphism (SNP) in the viral population or genetic distances among sequences below a certain threshold - SNP threshold. A single variable sequence at a consensus level from the infected case is usually used for the tracking of outbreaks, among which SNP threshold has been considered as an effective tool to identify relationships among strains ( Hatherell et al, 2016 ; Sukhrie et al, 2013 ; Kamachi et al, 2023 ; Walker et al, 2013 ). Nucleotide variations among samples collected from outbreaks may offer insights into cluster detection and separation of patients without linkages, having been adopted in the identifications of outbreaks caused by many other pathogens, such as Salmonella enterica ( Octavia et al, 2015 ), tuberculosis ( Hatherell et al, 2016 ), Bordetella pertussis ( Kamachi et al, 2023 ), SARS-CoV-2 ( Smith et al, 2021 ), influenza virus ( Xue and Bloom, 2020 ), HIV ( Lorenzo-Redondo et al, 2021 ), among others.…”

“…A single variable sequence at a consensus level from the infected case is usually used for the tracking of outbreaks, among which SNP threshold has been considered as an effective tool to identify relationships among strains ( Hatherell et al, 2016 ; Sukhrie et al, 2013 ; Kamachi et al, 2023 ; Walker et al, 2013 ). Nucleotide variations among samples collected from outbreaks may offer insights into cluster detection and separation of patients without linkages, having been adopted in the identifications of outbreaks caused by many other pathogens, such as Salmonella enterica ( Octavia et al, 2015 ), tuberculosis ( Hatherell et al, 2016 ), Bordetella pertussis ( Kamachi et al, 2023 ), SARS-CoV-2 ( Smith et al, 2021 ), influenza virus ( Xue and Bloom, 2020 ), HIV ( Lorenzo-Redondo et al, 2021 ), among others. For example, a threshold of 5 was commonly adopted in delineating epidemiologically linked tuberculosis patients ( Walker et al, 2013 ; Bryant et al, 2013 ).…”