Genomic dissection of Australian Bordetella pertussis isolates from the 2008–2012 epidemic - 09/03/16

Doi : 10.1016/j.jinf.2016.01.005

Azadeh Safarchi ^a, Sophie Octavia ^a, Sunny Z. Wu ^a, Sandeep Kaur ^a, Vitali Sintchenko ^b,^c, Gwendolyn L. Gilbert ^b,^c, Nicholas Wood ^d,^e,^f, Peter McIntyre ^d,^e,^f, Helen Marshall ^g, Anthony D. Keil ^h, Ruiting Lan ^a,^⁎
^a School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
^b Centre for Infectious Diseases and Microbiology – Public Health, Institute of Clinical Pathology and Medical Research, Pathology West, Westmead Hospital, New South Wales, Australia
^c Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, New South Wales, Australia
^d National Centre for Immunisation Research and Surveillance of Vaccine Preventable Diseases (NCIRS), The Children’s Hospital at Westmead, Westmead, New South Wales 2145, Australia
^e Discipline of Paediatrics and Child Health, University of Sydney, The Children’s Hospital at Westmead, Westmead, New South Wales 2145, Australia
^f Department of Microbiology and Infectious Diseases, The Children’s Hospital at Westmead, New South Wales, Australia
^g Vaccinology and Immunology Research Trials Unit, Women's and Children's Hospital and School of Medicine and Robinson Research Institute, University of Adelaide, South Australia, Australia
^h Department of Microbiology, PathWest Laboratory Medicine WA, Princess Margaret Hospital for Children, Perth, Australia

^∗Corresponding author. Tel.: +61 2 9385 2095; fax: +61 2 9385 1483.

Summary

Objectives

Despite high pertussis vaccination coverage, Australia experienced a prolonged epidemic in 2008–2012. The predominant Bordetella pertussis genotype harboured pertussis toxin promoter allele, ptxP3, and pertactin gene allele, prn2. The emergence and expansion of prn non-expressing isolates (Prn negative), were also observed. We aimed to investigate the microevolution and genomic diversity of epidemic B. pertussis isolates.

Methods

We sequenced 22 B. pertussis isolates collected in 2008–2012 from two states of Australia which are geographically widely separated. Ten of the 22 were Prn negative isolates with three different modes of silencing of prn (prn::IS481F, prn::IS481R and prn::IS1002). Five pre-epidemic isolates were also sequenced for comparison.

Results

Five single nucleotide polymorphisms were common in the epidemic isolates and differentiated them from pre-epidemic isolates. The Australian epidemic isolates can be divided into five lineages (EL1–EL5) with EL1 containing only Prn negative isolates. Comparison with global isolates showed that three lineages remained geographically and temporally distinct whereas two lineages mixed with isolates from 2012 UK outbreak.

Conclusion

Our results suggest significant diversification and the microevolution of B. pertussis within the 2008–2012 Australian epidemic.

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Highlights

•	Single nucleotide polymorphisms play an important role in the microevolution of the Australian 2008–2012 epidemic B. pertussis.
•	The Australian 2008–2012 epidemic B. pertussis isolates can be divided into five lineages with spatial and temporal clustering of isolates.
•	The same mechanism of inactivation of the prn gene can occur independently.

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Keywords : Bordetella pertussis, Molecular epidemiology, Whole genome sequencing, Microevolution, Single nucleotide polymorphism

Plan

Introduction

Materials and methods

Bacterial strains

DNA sequencing and assembly

SNP identification

Insertion sequence elements analysis

Phylogenetic analysis

Results and discussion

Selection and sequencing of epidemic isolates

Significant polymorphisms in SP13 strains

Phylogenetic relationships of the Australian SP13 isolates

The relationship of Australian SP13 isolates with contemporary global isolates

Potential role of adaptive SNPs in epidemic SP13 B. pertussis isolates

No specific small indels are associated with epidemic lineages

Insertion sequence elements

Micro-evolution of B. pertussis by gene loss

Conclusion

Conflicts of interest

Statement of funding

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Vol 72 - N° 4

P. 468-477 - avril 2016 Retour au numéro

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Genomic dissection of Australian Bordetella pertussis isolates from the 2008–2012 epidemic - 09/03/16

Summary

Objectives

Methods

Results

Conclusion

Highlights

Plan

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