Whole Genome Sequencing Analysis of Intrapatient Microevolution in Mycobacterium tuberculosis: Potential Impact on the Inference of Tuberculosis Transmission

Pérez‐Lago, Laura; Comas, Iñaki; Navarro, Yurena; Gónzález-Candelas, Fernando; Herránz, Marta; Bouza, Emilio; Viedma, Darío García de

doi:10.1093/infdis/jit439

Cited by 116 publications

(121 citation statements)

References 37 publications

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“…SNP calling was performed as indicated elsewhere (15). In summary, after mapping to a reference strain, we extracted all variable positions in the strain of interest.…”

Section: Microbiological Proceduresmentioning

confidence: 99%

Urgent Implementation in a Hospital Setting of a Strategy To Rule Out Secondary Cases Caused by Imported Extensively Drug-Resistant Mycobacterium tuberculosis Strains at Diagnosis

et al. 2016

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h Current migratory movements require new strategies for rapidly tracking the transmission of high-risk imported Mycobacterium tuberculosis strains. Whole-genome sequencing (WGS) enables us to identify single-nucleotide polymorphisms (SNPs) and therefore design PCRs to track specific relevant strains. However, fast implementation of these strategies in the hospital setting is difficult because professionals working in diagnostics, molecular epidemiology, and genomics are generally at separate institutions. In this study, we describe the urgent implementation of a system that integrates genomics and molecular tools in a genuine high-risk epidemiological alert involving 2 independent importations of extensively drug resistant (XDR) and pre-XDR Beijing M. tuberculosis strains from Russia into Spain. Both cases involved commercial sex workers with long-standing tuberculosis (TB). The system was based on strain-specific PCRs tailored from WGS data that were transferred to the local node that was managing the epidemiological alert. The optimized tests were available for prospective implementation in the local node 33 working days after receiving the primary cultures of the XDR strains and were applied to all 42 new incident cases. An interpretable result was obtained in each case (directly from sputum for 27 stain-positive cases) and corresponded to the amplification profiles for strains other than the targeted pre-XDR and XDR strains, which made it possible to prospectively rule out transmission of these high-risk strains at diagnosis. C urrent massive migratory movements in Europe and elsewhere will likely affect the international distribution of Mycobacterium tuberculosis strains. Multidrug-resistant, extensively resistant, and highly transmissible M. tuberculosis strains, which are restricted mostly to high-prevalence settings, can now cross frontiers more easily and be imported into countries where they are not yet a major problem. In this new scenario, strategies for rapid tracking of the importation and subsequent transmission of these high-risk strains in the host population must be implemented.Surveillance of the importation/distribution of M. tuberculosis strains is supported mainly by universal genotyping of the isolates and systematic comparison of genotypic profiles in databases comprising whole populations (1, 2). This approach allows us to identify when a strain is imported into a population for the first time and to track subsequent transmission clusters caused by it. An alternative approach involves strain-specific PCRs designed to track specific outbreak strains in specific circumstances (3-5). The development of a strain-specific PCR is possible only when the strain harbors a specific genetic feature (e.g., large deletions [regions of difference] or insertions [mostly IS6110 insertions]) that enables it to be targeted. Consequently, robust strain-specific genetic data could not be obtained until recently, as knowledge of genetic composition was not always sufficient, and the specificity of the selec...

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“…SNP calling was performed as indicated elsewhere (15). In summary, after mapping to a reference strain, we extracted all variable positions in the strain of interest.…”

Section: Microbiological Proceduresmentioning

confidence: 99%

Urgent Implementation in a Hospital Setting of a Strategy To Rule Out Secondary Cases Caused by Imported Extensively Drug-Resistant Mycobacterium tuberculosis Strains at Diagnosis

et al. 2016

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“…lonal Mycobacterium tuberculosis variants appear along the sequential infections of hosts involved in the same transmission cluster (1). IS6110 in M. tuberculosis has been one of the most widely used elements in molecular epidemiology and has a transposition rate estimated at ϳ18% over a period of 5 to 6 years (2).…”

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In Vivo IS 6110 Profile Changes in a Mycobacterium tuberculosis Strain as Determined by Tracking over 14 Years

et al. 2015

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f Transposition and homologous recombination of IS6110 appear in Mycobacterium tuberculosis along in vivo sequential infections. These events were checked in different clones of a successful strain, M. tuberculosis Zaragoza, with the focus on a variant in which integration of a copy of IS6110 in the origin of replication (oriC) region occurred. Clonal Mycobacterium tuberculosis variants appear along the sequential infections of hosts involved in the same transmission cluster (1). IS6110 in M. tuberculosis has been one of the most widely used elements in molecular epidemiology and has a transposition rate estimated at ϳ18% over a period of 5 to 6 years (2). The IS6110 element itself modulates expression of neighboring genes and, depending on its location, could confer both transmission ability and virulence (3-5). Microevolution events due to the transposition of IS6110 are usually reflected in variations of restriction fragment length polymorphism (RFLP) patterns (6, 7). Minor variations in IS6110 fingerprints, spoligotypes, or mycobacterial interspersed repetitive-unit (MIRU)-variable-number tandem-repeat (VNTR) loci reveal microevolution in clonal infections (6,8). These changes could have effects on the molecular structure of the mycobacterial genome and the biology of the bacillus (7).Molecular epidemiological studies carried out for more than a decade have provided accuracy in the study of the transmission (9). The usefulness of the approach has been proven, even in countries with low incidences of tuberculosis (10). The M. tuberculosis Zaragoza strain spread in Zaragoza, Spain, and reached 18.7% of all isolates of M. tuberculosis in 2001 to 2004 (11). This strain was classified in principal genetic group 3 and in singlenucleotide polymorphism (SNP) cluster group 6a (12), it demonstrated the rare spoligotype SIT773, and it carried 12 localized copies of IS6110 (13). In addition, in the context of a highthroughput survey of in vivo IS6110 transposition in multiple M. tuberculosis genomes, an additional IS6110 copy was detected in the oriC region in one isolate (14). The purpose of this study was to review the in vivo genomic changes of the M. tuberculosis Zaragoza strain, focusing on this variant.Among the 2,348 isolates collected between 2000 and 2013, 246 were identified as M. tuberculosis Zaragoza by IS6110 RFLP typing (15) and spoligotyping (16) in the context of tuberculosis surveillance in our region. By tracking the strain changes throughout time, we found 7 different variants, i.e., variants 1 to 7 (Fig. 1). An additional copy of IS6110 was detected in six evolved clones, namely, variants 1 to 6. Variant 7 lost one copy in the RFLP pattern and was the only variant that revealed a change in its spoligotyping pattern. Clones 1, 2, 4, 5, 6, and 7 were isolated from only one patient, whereas variant 3 was isolated from 12 patients, as described below.In variant 7, 10 of the 12 IS6110 insertion sites known for M. tuberculosis Zaragoza were confirmed by PCR (13). However, the two nonamplified copies were l...

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“…In the present case, the strain always remained pansusceptible despite a long history of treatment interruptions and poor adherence. Acquisition of variability in M. tuberculosis can also prove to be advantageous in contexts other than resistance (16,22), since it can aid in escape from the immune system and in the acquisition of more infective phenotypes (23) and can lead to the emergence of more infective variants. The finding of a potential hypermutator phenotype for Beijing strains (7) could point to a high tendency to accumulate diversity.…”

Section: Discussionmentioning

confidence: 99%

“…Four sequential isolates were used to identify SNPs as detailed elsewhere (16). We extracted the DNA from pooled colonies.…”

Section: Microbiological Methodsmentioning

confidence: 99%

Persistent Infection by a Mycobacterium tuberculosis Strain That Was Theorized To Have Advantageous Properties, as It Was Responsible for a Massive Outbreak

et al. 2015

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The strains involved in tuberculosis outbreaks are considered highly virulent and transmissible. We analyzed the case of a patient in Madrid, Spain, who was persistently infected over an 8-year period by the same Beijing Mycobacterium tuberculosis strain. The strain was responsible for a severe outbreak on Gran Canaria Island. The case provides us with a unique opportunity to challenge our assumptions about M. tuberculosis Beijing strains. No clinical/radiological findings consistent with a virulent strain were documented, and the in vitro growth rate of the strain in macrophages was only moderate. No secondary cases stemming from this prolonged active case were detected in the host population. The strain did not acquire resistance mutations, despite constant treatment interruptions, and it remained extremely stable, as demonstrated by the lack of single-nucleotide-polymorphism (SNP)-based differences between the sequential isolates. Our data suggest that the general assumption about M. tuberculosis Beijing strains having advantageous properties (in terms of virulence, transmissibility, and the tendency to acquire mutations and resistance) is not always accurate.

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Whole Genome Sequencing Analysis of Intrapatient Microevolution in Mycobacterium tuberculosis: Potential Impact on the Inference of Tuberculosis Transmission

Abstract: Our study adds new data to the understanding of variability in M. tuberculosis in a wide clinical scenario and alerts about the difficulties of establishing thresholds to differentiate relatedness in M. tuberculosis with epidemiological purposes.

Cited by 116 publications

References 37 publications

Urgent Implementation in a Hospital Setting of a Strategy To Rule Out Secondary Cases Caused by Imported Extensively Drug-Resistant Mycobacterium tuberculosis Strains at Diagnosis

Urgent Implementation in a Hospital Setting of a Strategy To Rule Out Secondary Cases Caused by Imported Extensively Drug-Resistant Mycobacterium tuberculosis Strains at Diagnosis

In Vivo IS 6110 Profile Changes in a Mycobacterium tuberculosis Strain as Determined by Tracking over 14 Years

Persistent Infection by a Mycobacterium tuberculosis Strain That Was Theorized To Have Advantageous Properties, as It Was Responsible for a Massive Outbreak

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