Prevalence and Characterization of Heterogeneous Variable-Number Tandem-Repeat Clusters Comprising Drug-Susceptible and/or Variable Resistant Mycobacterium tuberculosis Complex Isolates in the Netherlands from 2004 to 2016

Abstract

The variable-number tandem-repeat (VNTR) typing method is used to study tuberculosis (TB) transmission. Clustering of isolates with identical VNTR patterns is assumed to reflect recent transmission. Hence, clusters are thought to be homogeneous regarding antibiotic resistance. In practice, however, heterogeneous clusters are also identified. This study investigates the prevalence and characteristics of heterogeneous VNTR clusters and assesses whether isolates in these clusters remain clustered when subjected to whole-genome sequencing (WGS). In the period from 2004 to 2016, 9,072 isolates were included. Demographic and epidemiological linkage data were obtained from the Netherlands Tuberculosis Register. VNTR clusters were defined as homogeneous when isolates shared identical resistance profiles or as heterogeneous if both susceptible and (variable) resistant isolates were found. Multivariate logistic regression analysis was performed to identify factors associated with heterogeneous clustering. Isolates from 2016 were subjected to WGS, and a genetic distance of 12 single nucleotide polymorphisms (SNPs) was used as the cutoff for WGS clustering. In total, 4,661/9,072 (51%) isolates were clustered into 985 different VNTR clusters, of which 217 (22%) were heterogeneous. Patient characteristics associated with heterogeneous clustering were non-Dutch ethnicity (odds ratio [OR], 1.46 [95% confidence interval {CI}, 1.22 to 1.75]), asylum seeker (OR, 1.51 [95% CI, 1.24 to 1.85]), extrapulmonary TB (OR, 1.26 [95% CI, 1.09 to 1.46]), previous TB diagnosis (OR, 1.38 [95% CI, 1.04 to 1.82]), and not being a contact of a TB patient (OR, 1.35 [95% CI, 1.08 to 1.69]). With WGS, 34% of heterogeneous and 78% of homogeneous isolates from 2016 remained clustered. Heterogeneous VNTR clusters are common but seem to be explained by a substantial degree of false clustering by VNTR typing compared to WGS.

Whole Genome Sequencing for Determining the Source of Mycobacterium bovis Infections in Livestock Herds and Wildlife in New Zealand

“…For example, although most VNTR types tended to cluster into only one sub-group in the Otago branch, type VNTR27 isolates cluster in several different groups (see the phylogenetic tree in Figure 3b ). This clustering of unrelated types has been described in other comparisons of WGS to VNTR typing ( 23 , 46 , 47 ). There were also several instances where types tended to switch back and forth within a subgroup, (see REA types 11 and 12 and REA types 1 and 6 in the tree in Supplementary Figure 5 ), as was observed by Trewby et al ( 18 ).…”

High Incidence of Active Tuberculosis in Asylum Seekers from Eritrea and Somalia in the First 5 Years after Arrival in the Netherlands

“…Third, transmission within ethnic groups in the new country of residence can also contribute to the higher TB rates found in asylum seekers. Occasional outbreaks have been reported in ethnic groups, including recently arrived asylum seekers (18). Finally, the WHO figures could be an underestimation of actual TB rates (18)(19)(20).…”

Genetic patterns, sublineages and dynamics of tuberculosis transmission in Cuba, a low burden country

“…[20] It is lower than that found in Germany, Finland and the Netherlands, all countries with low TB incidence and effective control programs. [21–23]…”

“…[20] It is lower than that found in Germany, Finland and the Netherlands, all countries with low TB incidence and effective control programs. [21][22][23] Rapid identification of the most discriminative loci saves time and resources during monitoring of isolates with particular characteristics, in field investigation of past or potential outbreaks, and tracking imported isolates. In comparison with a review and analysis study of 56 articles, published between 2002 and 2019, that evaluated the discriminatory power of each locus, it is observed that five of the six highly discriminative loci found in these studies correspond to those of this research.…”