Whole genome sequencing–based analysis of tuberculosis (TB) in migrants: rapid tools for cross-border surveillance and to distinguish between recent transmission in the host country and new importations

Abstract

BackgroundThe analysis of transmission of tuberculosis (TB) is challenging in areas with a large migrant population. Standard genotyping may fail to differentiate transmission within the host country from new importations, which is key from an epidemiological perspective.AimTo propose a new strategy to simplify and optimise cross-border surveillance of tuberculosis and to distinguish between recent transmission in the host country and new importationsMethodsWe selected 10 clusters, defined by 24-locus mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR), from a population in Spain rich in migrants from eastern Europe, north Africa and west Africa and reanalysed 66 isolates by whole-genome sequencing (WGS). A multiplex-allele-specific PCR was designed to target strain-specific marker single nucleotide polymorphisms (SNPs), identified from WGS data, to optimise the surveillance of the most complex cluster.ResultsIn five of 10 clusters not all isolates showed the short genetic distances expected for recent transmission and revealed a higher number of SNPs, thus suggesting independent importations of prevalent strains in the country of origin. In the most complex cluster, rich in Moroccan cases, a multiplex allele-specific oligonucleotide-PCR (ASO-PCR) targeting the marker SNPs for the transmission subcluster enabled us to prospectively identify new secondary cases. The ASO-PCR-based strategy was transferred and applied in Morocco, demonstrating that the strain was prevalent in the country.ConclusionWe provide a new model for optimising the analysis of cross-border surveillance of TB transmission in the scenario of global migration.

Screening of inmates transferred to Spain reveals a Peruvian prison as a reservoir of persistent Mycobacterium tuberculosis MDR strains and mixed infections

“…We propose a shortcut based on tailoring strain-specific PCRs, targeting multiple marker SNPs for the strain to be surveyed taken from the WGS data. In previous studies, we demonstrated the efficiency and versatility of this novel approach for optimizing surveillance of actively transmitted strains 1,16 , fast-tracking secondary cases after importation of XDR-TB 17 , determining the presence and/or prevalence of an outbreak strain in a population by analyzing large collections in remarkable short periods of time [18][19][20] , and differentiating between recent transmission and importation in clusters involving migrants 4 . Additionally, this strategy has a potential clinical usefulness when tracking resistant strains, as it would allow us to assume the resistance profile of the tracked strain for a new case infected with it, without the need of characterizing specifically the resistance mutations 1,19 .…”

“…Cooperative multinational efforts provide an opportunity to offset local limitations. Joint studies revealed settings with active transmission of MDR-TB [1][2][3] and made it possible to evaluate the impact on host countries of the distribution of resistant strains introduced by migrant TB cases, which are circulating in their countries of origin 4,5 .…”

“…The SNP analysis was performed as described elsewhere 4 . Briefly, we mapped the reads for each strain against the most likely common ancestor of the M. tuberculosis complex, which was identical to H37Rv in terms of…”

“…SNPs for cluster Callao-1, we first filtered the SNPs of this strain with an in-house database, including 381 isolates that underwent high-quality sequencing in our laboratory, and in a second stage with a database which includes 4598 sequenced isolates and is representative of global MTBC diversity 4 . We then selected 3 specific SNPs that were common to all clustered members and 1 specific SNP from the "prison present branch", which was present in the transferred inmates PrC1 and PrC2 but absent in the other members.…”

Tuberculosis in migrants – screening, surveillance and ethics

“…WGS provides valuable information to assist individual patient management and public health responses, but widespread implementation in resource-limited settings remains unrealistic at present. Enhanced polymerase chain reaction (PCR) based methods may be more feasible in the interim, both for genetic drug resistance determination and transmission tracking [49]. In time, the establishment of global TB surveillance systems will complement epidemiological surveillance and could track cross-border transmission dynamics, but also pose risks to personal freedom that should be considered (see Ethics section).…”