Tracking a tuberculosis outbreak over 21 years: strain-specific single nucleotide polymorphism-typing combined with targeted whole genome sequencing.


Autoria(s): Stucki, David; Ballif, Marie; Bodmer, Thomas; Coscolla, Mireia; Maurer, Anne-Marie; Droz, Sara Christine; Butz, Christa; Borrell, Sonia; Längle, Christel; Feldmann, Julia; Furrer, Hansjakob; Mordasini, Carlo; Helbling, Peter; Rieder, Hans L; Egger, Matthias; Gagneux, Sébastien; Fenner, Lukas
Data(s)

01/04/2015

Resumo

BACKGROUND  Whole genome sequencing (WGS) is increasingly used in molecular-epidemiological investigations of bacterial pathogens, despite cost- and time-intensive analyses. We combined strain-specific single nucleotide polymorphism (SNP)-typing and targeted WGS to investigate a tuberculosis cluster spanning 21 years in Bern, Switzerland. METHODS  Based on genome sequences of three historical outbreak Mycobacterium tuberculosis isolates, we developed a strain-specific SNP-typing assay to identify further cases. We screened 1,642 patient isolates, and performed WGS on all identified cluster isolates. We extracted SNPs to construct genomic networks. Clinical and social data were retrospectively collected. RESULTS  We identified 68 patients associated with the outbreak strain. Most were diagnosed in 1991-1995, but cases were observed until 2011. Two thirds belonged to the homeless and substance abuser milieu. Targeted WGS revealed 133 variable SNP positions among outbreak isolates. Genomic network analyses suggested a single origin of the outbreak, with subsequent division into three sub-clusters. Isolates from patients with confirmed epidemiological links differed by 0-11 SNPs. CONCLUSIONS  Strain-specific SNP-genotyping allowed rapid and inexpensive identification of M. tuberculosis outbreak isolates in a population-based strain collection. Subsequent targeted WGS provided detailed insights into transmission dynamics. This combined approach could be applied to track bacterial pathogens in real-time and at high resolution.

Formato

application/pdf

application/pdf

Identificador

http://boris.unibe.ch/59939/1/infdis.jiu601.full.pdf

http://boris.unibe.ch/59939/15/Stucki%20JInfectDis%202015.pdf

Stucki, David; Ballif, Marie; Bodmer, Thomas; Coscolla, Mireia; Maurer, Anne-Marie; Droz, Sara Christine; Butz, Christa; Borrell, Sonia; Längle, Christel; Feldmann, Julia; Furrer, Hansjakob; Mordasini, Carlo; Helbling, Peter; Rieder, Hans L; Egger, Matthias; Gagneux, Sébastien; Fenner, Lukas (2015). Tracking a tuberculosis outbreak over 21 years: strain-specific single nucleotide polymorphism-typing combined with targeted whole genome sequencing. Journal of infectious diseases, 211(8), pp. 1306-1316. Oxford University Press 10.1093/infdis/jiu601 <http://dx.doi.org/10.1093/infdis/jiu601>

doi:10.7892/boris.59939

info:doi:10.1093/infdis/jiu601

info:pmid:25362193

urn:issn:0022-1899

Idioma(s)

eng

Publicador

Oxford University Press

Relação

http://boris.unibe.ch/59939/

Direitos

info:eu-repo/semantics/openAccess

info:eu-repo/semantics/restrictedAccess

Fonte

Stucki, David; Ballif, Marie; Bodmer, Thomas; Coscolla, Mireia; Maurer, Anne-Marie; Droz, Sara Christine; Butz, Christa; Borrell, Sonia; Längle, Christel; Feldmann, Julia; Furrer, Hansjakob; Mordasini, Carlo; Helbling, Peter; Rieder, Hans L; Egger, Matthias; Gagneux, Sébastien; Fenner, Lukas (2015). Tracking a tuberculosis outbreak over 21 years: strain-specific single nucleotide polymorphism-typing combined with targeted whole genome sequencing. Journal of infectious diseases, 211(8), pp. 1306-1316. Oxford University Press 10.1093/infdis/jiu601 <http://dx.doi.org/10.1093/infdis/jiu601>

Palavras-Chave #610 Medicine & health #360 Social problems & social services #570 Life sciences; biology
Tipo

info:eu-repo/semantics/article

info:eu-repo/semantics/publishedVersion

PeerReviewed