Characteristics of MT27 isolates. Among the 237 B. pertussis MT27 isolates tested, 208 (88%) carried the allele profile of ptxP3/ptxA1/prn2/fim3A, and were the most predominant subtype. The remaining 29 isolates carried the minor allele profiles, ptxP3/ptxA1/prn2/fim3B (n = 19, 8%), ptxP3/ptxA1/prn9/fim3A (n = 5, 2%), ptxP3/ptxA1/prn9/fim3B (n = 2, 0.8%) ptxP3/ptxA1/prn3/fim3A (n = 1, 0.4%), ptxP3/ptxA1/prn14/fim3A (n = 1, 0.4%), and ptxP1/ptxA1/prn15/fim3A (n = 1, 0.4%). The B. pertussis MT27 isolate carrying ptxP1 allele was identified for the first time in Japan.
Discriminatory power and reliability of the SNP genotyping. A total of 237 MT27 isolates were divided into 10 SNP genotypes (SGs) with a Simpson’s DI of 0.79 (95% CI, 0.76–0.82) (Fig. 1). Four SGs, SG1, SG2, SG7, and SG10 were the prevalent genotypes, representing 35%, 11%, 22% and 13% of the isolates, respectively. Other SGs, SG3–SG6, SG8, and SG9 were minor genotypes (representing 0.4–7.2% of the isolates). SG2 had a unique 20-position SNP profile because six SNPs (SNP2, SNP8, SNP11, SNP19, SNP20, and SNP34) were specifically associated with SG2. In contrast, five SGs (SG6–SG10) formed a phylogenetic cluster on the maximum parsimony tree (Fig. 1). The reference strain Tohama I (MLVA type, MT83) belonged to SG1.
In reference to the 51 sequenced isolates, all 20-position SNP profiles identified by the SNP genotyping were identical to those obtained from WGS data. The SBE-based SNP genotyping showed high reliability.
Comparison with whole-genome SNP genotyping. Fig. 2 shows the phylogenetic tree of the 51 MT27 isolates based on whole-genome SNPs. The tree was constructed based on 254 SNPs that were identified among the genome-sequenced isolates using CSI Phylogeny 1.4 (Supplementary Table S3), and it was compared with SBE-based SNP genotyping with 20 SNP targets. Almost all isolates (49/51) were distinguished by the whole-genome SNP genotyping. SG1 isolates did not cluster closely, but other isolates (SG2, SG5–SG8, and SG10) clustered into each group of the SBE-based SNP genotypes. Whole-genome SNP genotyping illustrated that SG1 is a genetically diverse strain. Except for SG1 isolates, there was good agreement between the SBE-SNP genotyping and the whole-genome SNP genotyping.
Temporal changes in SNP genotypes and genotypic diversity. Fig. 3 shows the temporal trend of the frequency of SGs during four time periods. The MT27 isolates from 1999–2004 (n = 39) belonged to only SG1, whereas the isolates from 2005–2009 (n = 24) belonged to SG1, SG2, and SG7, but SG1 was most predominant. Further, the isolates from 2010–2014 (n = 115) belonged to 9 SGs (SG1, SG2, and SG4–SG10), and those from 2015–2018 (n = 59) to 6 SGs (SG1, SG3, SG5, SG7, SG8, and SG10). The frequency of the SG1 strain markedly decreased in the 2010s: 100% in 1999–2004, 92% in 2005–2009, 17% in 2010–2014, and 7% in 2015–2018. In contrast, the frequency of SG7 strain increased: 0% in 1999–2004, 4% in 2005–2009, 25% in 2010–2014, and 39% in 2015–2018. Simpson’s DI for the SGs was zero in 1999–2004, 0.16 in 2005–2009, 0.83 in 2010–2014, and 0.76 in 2015–2018. Taken together, the genotypic diversity of MT27 isolates was extremely low in the 2000s, but increased markedly in the 2010s.
Relationship between SNP genotypes and virulence-associated allelic genes. Seven allele profiles were identified in the MT27 isolates tested. The isolate carrying ptxP3/ptxA1/prn2/fim3A was found to be predominant in all SGs (Table 4). The isolates carrying other allele profiles were in SG1, SG7, and SG10, but the numbers of isolates were much smaller compared with isolates carrying the predominant allele profile. There were no SGs predominantly related to the minor allele profiles.
Application of SNP genotyping to outbreak-associated isolates. MT27 isolates from pertussis outbreaks were genotyped (Table 5). Fifteen outbreak-associated isolates were collected in Miyazaki prefecture 36, and all exhibited the same genotype of SG2. Similarly, all isolates from Toyama and Niigata prefectures (n = 4 each) belonged to the same SG10. Of the 12 isolates from Nagano prefecture, 1 and 11 were SG5 and SG7, respectively. The SG5 strain was not closely related to the SG7 strain since the SG5 strain had eight different SNPs in the 20-position SNP profile as compared with the SG7 strain. Together, all except one isolate were classified into the same SNP genotypes for each outbreak.
SNP genotyping for non-MT27 isolates. A total of 104 non-MT27 isolates were classified into 4 SGs (SG1, SG3, SG7, and SG10) with a Simpson’s DI of 0.21 (95% CI, 0.11–0.31) (Supplementary Table S4). Ninety-two isolates (89%) belonged to SG1 and the remainder (11%) to SG3, SG7, and SG10. The isolates belonging to SG3, SG7, and SG10 were recent isolates collected in the 2010s. Overall, the genotypic diversity was much lower than that of MT27 isolates.
SNP genotyping for Taiwanese isolates. We genotyped B. pertussis isolates collected in Taiwan during 2010–2019. Of 48 isolates, 30 (62.5%) were MT27 and 18 (37.5%) were non-MT27 (Supplementary Table S5). The MT27 isolates were subdivided into 5 SGs (SG1, SG3, SG5, SG7, and SG11) with a Simpson’s DI of 0.69 (95% CI, 0.56–0.82). Fifteen MT27 isolates belonged to SG1 and the remainder to SG3 (n = 4), SG5 (n = 1), SG7 (n = 3), and SG11 (n = 7). Similarly, the non-MT27 isolates were classified into 4 SGs (SG1, SG3, SG7, and SG11) with a Simpson’s DI of 0.73 (95% CI, 0.61–0.85). The SG11 was not found in the Japanese isolates tested including non-MT27 isolates, and its 20-position SNP profile was CGAAATTGTCCGGCCTGTTG.
SNP genotypes of US isolates. We determined 20-position SNP profiles of MT27 isolates collected in the US during 2000–2013, based on their complete genome sequences available in the GenBank database 16. One hundred twenty-two MT27 isolates were classified into the 6 SGs, i.e., SG1 (n = 89), SG3 (n = 5), SG4 (n = 6), SG7 (n = 20), SG11 (n = 1), and SG12 (n = 1). The minor SG12 was novel and its 20-position SNP profiles was CGAAATCGCCCAGCATGTTG. Simpson’s DI for the SGs was zero in 2000–2004, zero in 2005–2009, and 0.64 in 2010–2013 (Supplementary Fig. S1). The genotypic diversity of the US isolates markedly increased in the 2010s, similar to that of Japanese MT27 isolates.