Genomic characterization of Bordetella pertussis in South Africa, 2015-2019

Abstract

Pertussis remains a public health concern in South Africa, with an increase in reported cases and outbreaks in recent years. Whole genome sequencing was performed on 32 Bordetella pertussis isolates sourced from three different surveillance programmes in South Africa between 2015 and 2019. Genome sequences were characterized using multilocus sequence typing, vaccine antigen genes (ptxP, ptxA, ptxB, prn and fimH) and overall genome structure. All isolates were sequence type 2 and harboured the pertussis toxin promoter allele ptxP3. The dominant genotype was ptxP3-ptxA1-ptxB2-prn2-fimH2 (31/32, 96.9 %), with no pertactin-deficient or other mutations in vaccine antigen genes identified. Amongst 21 isolates yielding closed genome assemblies, eight distinct genome structures were detected, with 61.9 % (13/21) of the isolates exhibiting three predominant structures. Increases in case numbers are probably not due to evolutionary changes in the genome but possibly due to other factors such as the cyclical nature of B. pertussis disease, waning immunity due to the use of acellular vaccines and/or population immunity gaps.

Keywords: B. pertussis; Illumina sequencing; PacBio sequencing; genome structural characterization; vaccine antigen genes; whole genome sequencing.

Fig. 1.

Maximum-likelihood phylogenetic tree for South African B. pertussis isolates and isolates from other geographical locations (2012–2019) based on the concatenated alignment of SNPs of the whole genome. The tree was rooted using the B. pertussis E476 reference (vaccine strain: Tohama I). The inner ring of the figure indicates the genome rearrangement type for South African isolates, the middle ring indicates the ptxP lineage and the outer ring indicates the country of isolation.

Fig. 2.

Genome organization and re-arrangement patterns amongst South African B. pertussis isolates collected in 2015–2019 in relation to reference E476 (n=13). Each coloured block represents a region of the genome called a localized co-linear block. A localized co-linear block below the central black line indicates an inversion event.