Whole Genome Sequence (WGS) of Bordetella pertussis Strains in Amhara Regional State, Ethiopia

Abstract Background Pertussis or whooping cough is an acute respiratory tract disease caused by Bordetella pertussis . In 2014, globally, there were an estimated 24.1 million pertussis cases and 160,700 deaths from pertussis in children under five years old. Due to vaccine pressure, there have been genotype changes in the circulating Bordetella pertussis strains. This study aimed to determine the genotype distribution of Bordetella pertussis strains in Amhara Regional State, Ethiopia. Methods A cross-sectional study design was employed on clinically suspected pertussis patients. Sixteen DNA samples positive for IS 481 (Ct ≤ 28 cycles), were sequenced using next-generation Illumina whole genome sequencing. The sequenced data was analyzed using software’s (Bowtie2 v2.2.9, Samtools v1.8, Bedtools v2.27.1). Sequenced data was compared with reference strains using Basic Local Alignment Search Tool (BLAST) and phylogenetic tree. Results The ptxP1, fim4 and prn1 alleles were found in 11/15 (73%) of sequenced samples. The remaining four samples carried the ptxP3, fim2 and prn2 alleles. None of the samples carrying the ptxP1 allele was found to carry the fim2 or prn2 allele and none of the samples carrying the ptxP3 allele was found to carry the fim4 or prn1 allele. Conclusions The ptxP1 allele carrying Bordetella pertussis was the commonest strain circulating in Amhara Regional State, Ethiopia. An increased number of ptxP3 strains in Ethiopia indicates the shift of Bordetella pertussis from ptxP1 to ptxP3 strains. This ptxP allele shift needs further investigation whether it is associated with the type of vaccine used or not.