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Transmission dynamics study of tuberculosis isolates with whole genome sequencing in southern Sweden

Alaridah, Nader LU ; Hallbäck, Erika Tång; Tångrot, Jeanette; Winqvist, Niclas LU ; Sturegård, Erik LU ; Florén-Johansson, Kerstin; Jönsson, Bodil; Tenland, Erik LU ; Welinder-Olsson, Christina and Medstrand, Patrik LU , et al. (2019) In Scientific Reports 9(1).
Abstract

Epidemiological contact tracing complemented with genotyping of clinical Mycobacterium tuberculosis isolates is important for understanding disease transmission. In Sweden, tuberculosis (TB) is mostly reported in migrant and homeless where epidemiologic contact tracing could pose a problem. This study compared epidemiologic linking with genotyping in a low burden country. Mycobacterium tuberculosis isolates (n = 93) collected at Scania University Hospital in Southern Sweden were analysed with the standard genotyping method mycobacterial interspersed repetitive units-variable number tandem repeats (MIRU-VNTR) and the results were compared with whole genome sequencing (WGS). Using a maximum of twelve single nucleotide polymorphisms (SNPs)... (More)

Epidemiological contact tracing complemented with genotyping of clinical Mycobacterium tuberculosis isolates is important for understanding disease transmission. In Sweden, tuberculosis (TB) is mostly reported in migrant and homeless where epidemiologic contact tracing could pose a problem. This study compared epidemiologic linking with genotyping in a low burden country. Mycobacterium tuberculosis isolates (n = 93) collected at Scania University Hospital in Southern Sweden were analysed with the standard genotyping method mycobacterial interspersed repetitive units-variable number tandem repeats (MIRU-VNTR) and the results were compared with whole genome sequencing (WGS). Using a maximum of twelve single nucleotide polymorphisms (SNPs) as the upper threshold of genomic relatedness noted among hosts, we identified 18 clusters with WGS comprising 52 patients with overall pairwise genetic maximum distances ranging from zero to nine SNPs. MIRU-VNTR and WGS clustered the same isolates, although the distribution differed depending on MIRU-VNTR limitations. Both genotyping techniques identified clusters where epidemiologic linking was insufficient, although WGS had higher correlation with epidemiologic data. To summarize, WGS provided better resolution of transmission than MIRU-VNTR in a setting with low TB incidence. WGS predicted epidemiologic links better which could consolidate and correct the epidemiologically linked cases, avoiding thus false clustering.

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Scientific Reports
volume
9
issue
1
publisher
Nature Publishing Group
external identifiers
  • scopus:85063276478
ISSN
2045-2322
DOI
10.1038/s41598-019-39971-z
language
English
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yes
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5ab3e7e6-6e22-421b-8dc9-3f358bced8c4
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2019-04-01 13:47:34
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2019-07-01 02:16:18
@article{5ab3e7e6-6e22-421b-8dc9-3f358bced8c4,
  abstract     = {<p>Epidemiological contact tracing complemented with genotyping of clinical Mycobacterium tuberculosis isolates is important for understanding disease transmission. In Sweden, tuberculosis (TB) is mostly reported in migrant and homeless where epidemiologic contact tracing could pose a problem. This study compared epidemiologic linking with genotyping in a low burden country. Mycobacterium tuberculosis isolates (n = 93) collected at Scania University Hospital in Southern Sweden were analysed with the standard genotyping method mycobacterial interspersed repetitive units-variable number tandem repeats (MIRU-VNTR) and the results were compared with whole genome sequencing (WGS). Using a maximum of twelve single nucleotide polymorphisms (SNPs) as the upper threshold of genomic relatedness noted among hosts, we identified 18 clusters with WGS comprising 52 patients with overall pairwise genetic maximum distances ranging from zero to nine SNPs. MIRU-VNTR and WGS clustered the same isolates, although the distribution differed depending on MIRU-VNTR limitations. Both genotyping techniques identified clusters where epidemiologic linking was insufficient, although WGS had higher correlation with epidemiologic data. To summarize, WGS provided better resolution of transmission than MIRU-VNTR in a setting with low TB incidence. WGS predicted epidemiologic links better which could consolidate and correct the epidemiologically linked cases, avoiding thus false clustering.</p>},
  articleno    = {4931},
  author       = {Alaridah, Nader and Hallbäck, Erika Tång and Tångrot, Jeanette and Winqvist, Niclas and Sturegård, Erik and Florén-Johansson, Kerstin and Jönsson, Bodil and Tenland, Erik and Welinder-Olsson, Christina and Medstrand, Patrik and Kaijser, Bertil and Godaly, Gabriela},
  issn         = {2045-2322},
  language     = {eng},
  month        = {03},
  number       = {1},
  publisher    = {Nature Publishing Group},
  series       = {Scientific Reports},
  title        = {Transmission dynamics study of tuberculosis isolates with whole genome sequencing in southern Sweden},
  url          = {http://dx.doi.org/10.1038/s41598-019-39971-z},
  volume       = {9},
  year         = {2019},
}