Comparative genomic profiling of Dutch clinical Bordetella pertussis isolates using DNA microarrays: Identification of genes absent from epidemic strains

Audrey J King,Qiushui He,Kees Heuvelman,Frits R Mooi,Han Gj Van Der Heide,Dimitri Diavatopoulos,Karin Van Leeuwen,Marjolein Van Gent,Tamara Van Gorkom,Jeroen La Pennings

doi:10.1186/1471-2164-9-311

Abstract

BackgroundWhooping cough caused by Bordetella pertussis in humans, is re-emerging in many countries despite vaccination. Several studies have shown that significant shifts have occurred in the B. pertussis population resulting in antigenic divergence between vaccine strains and circulating strains and suggesting pathogen adaptation. In the Netherlands, the resurgence of pertussis is associated with the rise of B. pertussis strains with an altered promoter region for pertussis toxin (ptxP3).ResultsWe used Multi-Locus Sequence Typing (MLST), Multiple-Locus Variable Number of Tandem Repeat Analysis (MLVA) and microarray-based comparative genomic hybridization (CGH) to characterize the ptxP3 strains associated with the Dutch epidemic. For CGH analysis, we developed an oligonucleotide (70-mers) microarray consisting of 3,581 oligonucleotides representing 94% of the gene repertoire of the B. pertussis strain Tohama I. Nine different MLST profiles and 38 different MLVA types were found in the period 1993 to 2004. Forty-three Dutch clinical isolates were analyzed with CGH, 98 genes were found to be absent in at least one of the B. pertussis strains tested, these genes were clustered in 8 distinct regions of difference.ConclusionThe presented MLST, MLVA and CGH-analysis identified distinctive characteristics of ptxP3 B. pertussis strains -the most prominent of which was a genomic deletion removing about 23,000 bp. We propose a model for the emergence of ptxP3 strains.

Highlights

Whooping cough caused by Bordetella pertussis in humans, is re-emerging in many countries despite vaccination
Based on the combined results of the three typing methods, we present a model for the evolution of the ptxP1 and ptxP3 lineages (Fig. 6)
The tree is mainly based on two point mutations found in ptx promoter (ptxP) and fim3 resulting in three lineages, ptxP1-fim3-1, ptxP3-fim3-1 and ptxP3-fim3-2

Summary

Introduction

Whooping cough caused by Bordetella pertussis in humans, is re-emerging in many countries despite vaccination. Bordetella bronchiseptica, Bordetella parapertussis and Bordetella pertussis are closely related respiratory pathogens that infect mammalian species.B. bronchiseptica causes chronic respiratory tract infections in a wide variety of mammals but has only been sporadically isolated from humans [1,2]. B. pertussisis is a human pathogen that causes pertussis, known as whooping cough, a disease that is severe in infants. World-wide, whooping cough causes up to 300,000 deaths every year, mostly among unvaccinated infants [4]. Even in countries with a high vaccination coverage, a significant increase in the pertussis incidence has been observed since the 1990s [57]. In the Netherlands, such an increase in pertussis has been observed since 1996 [8]

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