Tracking a Tuberculosis Outbreak Over 21 Years: Strain-Specific Single-Nucleotide Polymorphism Typing Combined With Targeted Whole-Genome Sequencing

Stucki, David; Ballif, Marie; Bodmer, Thomas; Coscollá, Mireia; Maurer, Anne-Marie; Droz, Sara; Butz, Christa; Borrell, Sònia; Längle, Christel; Feldmann, Julia; Furrer, Hansjakob; Mordasini, Carlo; Helbling, Peter; Rieder, Hans L.; Egger, Matthias; Gagneux, Sébastien; Fenner, Lukas

doi:10.1093/infdis/jiu601

Cited by 84 publications

(89 citation statements)

References 29 publications

(47 reference statements)

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“…SNP=single-nucleotide polymorphism. [74][75][76][77][78] Comprehensive analysis of the genome of the pathogen Requires culture (or specimen enrichment); more expensive; might be computationally demanding or complex Identification of transmission chains, mutations conferring resistance, heteroresistance (low resolution), mixed infections, specimen heterogeneity, and intrapatient evolution 82,85,90 ahpC, 93 and 16S rRNA. 94 Highly transmissible MDR outbreak clones with specific combinations of low-cost resistance and compensatory mutations have already emerged in several areas of the world.…”

Section: Clustermentioning

confidence: 99%

The epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant, extensively drug-resistant, and incurable tuberculosis

Dheda

Gumbo

Maartens

et al. 2017

The Lancet Respiratory Medicine

506

474

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Section: Clustermentioning

confidence: 99%

The epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant, extensively drug-resistant, and incurable tuberculosis

Dheda

Gumbo

Maartens

et al. 2017

The Lancet Respiratory Medicine

506

474

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“…Similarly, in Bern, Switzerland, a genotype detected by RFLP profiling caused a large number of tuberculosis cases during the 1990's (Stucki et al, 2015). The cases were associated to the typical risk factors in local populations found in European cities such as HIV infection or alcoholism.…”

Section: Outbreak Investigation In Mycobacterium Tuberculosis: the Gementioning

confidence: 94%

“…The cases were associated to the typical risk factors in local populations found in European cities such as HIV infection or alcoholism. Stucki et al (2015) sequenced the complete genome of strains belonging to the original outbreak along with local control strains. By comparing outbreak and control strains they designed a realtime SNP typing assay based on the detection of genome position with a polymorphism specific to the outbreak strains.…”

Section: Outbreak Investigation In Mycobacterium Tuberculosis: the Gementioning

confidence: 99%

“…Furthermore, the analysis of the transmission network together with the epidemiological information revealed two different sub-outbreaks initiated by two different "super-spreaders". Therefore, next generation sequencing of the Hamburg (Roetzer et al, 2013), the Bern outbreak (Stucki et al, 2015) and others (Török and Peacock, 2012;Smit et al, 2015;Lee et al, 2015) have revealed the complexity of tuberculosis outbreaks. Given that tuberculosis is not an acute disease and that a tuberculosis case can be latent, asymptomatic for years, the true extent of tuberculosis outbreaks can only be revealed by a sustained genotyping efforts over years.…”

Section: Outbreak Investigation In Mycobacterium Tuberculosis: the Gementioning

confidence: 99%

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Genomic Analysis of Bacterial Outbreaks

Sánchez-Busó

Comas

Beamud

et al. 2016

Evolutionary Biology

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“…Wholegenome sequencing (WGS) has simplified the identification of genotypic peculiarities (based on specific single nucleotide polymorphisms [SNPs]) from which we can design strain-specific PCRs (4,5).…”

mentioning

confidence: 99%

Ultrafast Assessment of the Presence of a High-Risk Mycobacterium tuberculosis Strain in a Population

et al. 2016

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A persistent 8-year infection by a Beijing Mycobacterium tuberculosis strain from a previous outbreak after importation from West Africa obliged us to investigate secondary cases. We developed a multiplex PCR method based on whole-genome sequencing to target strain-specific single nucleotide polymorphisms (SNPs). In 1 week, we analyzed 868 isolates stored over 6 years. Only 2 cases (immigrants from Guinea Conakry) harbored the strain, which ruled out transmission-despite opportunitiesand challenged some of the advantages associated with Beijing strains. Extensive application of genotyping strategies to characterize Mycobacterium tuberculosis has enabled us to identify strains that are advantageous because of their virulence, ability to acquire resistance, or efficiency in causing severe outbreaks.Once such strains are identified, their fingerprints can be used as a reference to closely monitor their emergence in populations where they remain undetected (1). However, this approach requires universal population-based systematic fingerprinting programs.Alternatively, strain-specific PCRs can be used to track the emergence of theoretically advantageous strains (2, 3). Wholegenome sequencing (WGS) has simplified the identification of genotypic peculiarities (based on specific single nucleotide polymorphisms [SNPs]) from which we can design strain-specific PCRs (4, 5).We developed an allele-specific oligonucleotide (ASO)-multiplex PCR method based on WGS data to track the presence of a susceptible Beijing strain in Madrid, Spain. This strain was responsible for a severe outbreak on Gran Canaria Island (GCI) in the 1990s, and it was eventually shown to be the cause of around one-quarter of the total number of cases on the island (6). The GCI strain was still found in 2007 and 2008 as shown after the application of a specific PCR (7). In Madrid, we identified a nonadherent case with persistently active infectious tuberculosis (8 years) caused by the Gran Canaria strain (8), which obliged us to fast track potential secondary cases.(The results of this study were partially presented at the 2015 ESM Meeting, Riga, Latvia, 28 June to 1 July 2015.)The persistent case was diagnosed in our institution in 2006. The mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) pattern of this isolate coincided with the pattern described for the GCI strain (7). Using fingerprinting data from 2006 to 2008, we only detected 3 patients, all of whom were linked to the GCI outbreak. Given that the population-based genotyping program running in our area was discontinued at the end of 2008, we were unable to identify potential secondary cases that occurred from 2009 to 2014, when previously exposed cases were more likely to develop the disease. To update the 2009 to 2014 gap, we developed an ASO-PCR method to retrospectively fast track the GCI strain by directly analyzing stored isolates.WGS of 4 isolates from our case was performed as indicated elsewhere (4). We followed standard library preparation protocols. Us...

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Tracking a Tuberculosis Outbreak Over 21 Years: Strain-Specific Single-Nucleotide Polymorphism Typing Combined With Targeted Whole-Genome Sequencing

Cited by 84 publications

References 29 publications

The epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant, extensively drug-resistant, and incurable tuberculosis

The epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant, extensively drug-resistant, and incurable tuberculosis

Genomic Analysis of Bacterial Outbreaks

Ultrafast Assessment of the Presence of a High-Risk Mycobacterium tuberculosis Strain in a Population

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