Investigation of a rapidly spreading tuberculosis outbreak using whole-genome sequencing

Comín, Jéssica; Chaure, Armando; Cebollada, Alberto; Ibarz, Daniel; Viñuelas, Jesús; Vitoria, María Asunción; Iglesias, María José; Samper, Sofía

doi:10.1016/j.meegid.2020.104184

Cited by 17 publications

(19 citation statements)

References 20 publications

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“…Tracking the transmission chain in this outbreak was difficult, as multiple infectious foci co-existed at the same time, and it has been demonstrated that identical sequences could derive from different transmission events [10]. Different from another outbreak studied in our laboratory [22], which was contextualised in household and school environments, this outbreak had a high proportion of individuals with risk factors, such as ID users, alcoholics, prisoners, homelessness and prostitution.…”

Section: Discussionmentioning

confidence: 77%

A whole-genome sequencing study of an X-family tuberculosis outbreak focus on transmission chain along 25 years

et al. 2021

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Lineage 4/X-family of Mycobacterium tuberculosis is not very notorious, except for the CDC1551 strain. One strain of this family, named Ara50, caused one of the largest tuberculosis outbreaks of the Aragon region, Spain, during the 1990s and remained until 2018. These X-strains are characterised by high transmissibility and by carrying a low copy number of IS6110 in their genomes. Epidemiological data of the 61 patients consisted of inmates, HIV seropositives, intravenous drug users and the homeless. The application of whole-genome sequencing (WGS) to 36 out of 61 isolates, selected by IS6110-RFLP, allowed to confirm 32 as recent transmissions. We

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Section: Discussionmentioning

confidence: 77%

A whole-genome sequencing study of an X-family tuberculosis outbreak focus on transmission chain along 25 years

et al. 2021

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“…Afterwards, MIRU-VNTR was recommended, whose discrimination power and use in molecular epidemiology had been previously demonstrated 5,[12][13][14] . In the last years, WGS has been applied to investigate outbreaks, and to analyse phylogeny and resistance [15][16][17] . In 2018, pilot studies carried out in Europe showed the added value of WGS for diagnosing TB as well as for detecting www.nature.com/scientificreports/ and tracing TB transmission events 2 .…”

Section: Discussionmentioning

confidence: 99%

The value of the continuous genotyping of multi-drug resistant tuberculosis over 20 years in Spain

Iglesias

Ibarz

Cebollada

et al. 2020

Sci Rep

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Molecular epidemiology of circulating clinical isolates is crucial to improve prevention strategies. The Spanish Working Group on multidrug resistant tuberculosis (MDR-TB) is a network that monitors the MDR-TB isolates in Spain since 1998. The aim of this study was to present the study of the MDR-TB and extensively drug-resistant tuberculosis (XDR-TB) patterns in Spain using the different recommended genotyping methods over time by a national coordinated system. Based on the proposed genotyping methods in the European Union until 2018, the preservation of one method, MIRU-VNTR, applied to selected clustered strains permitted to maintain our study open for 20 years. The distribution of demographic, clinical and epidemiological characteristics of clustered and non-clustered cases of MDR/XDR tuberculosis with proportion differences as assessed by Pearson’s chi-squared or Fisher’s exact test was compared. The differences in the quantitative variables using the Student's-t test and the Mann–Whitney U test were evaluated. The results obtained showed a total of 48.4% of the cases grouped in 77 clusters. Younger age groups, having a known TB case contact (10.2% vs 4.7%) and XDR-TB (16.5% vs 1.8%) were significantly associated with clustering. The largest cluster corresponded to a Mycobacterium bovis strain mainly spread during the nineties. A total of 68.4% of the clusters detected were distributed among the different Spanish regions and six clusters involving 104 cases were grouped in 17 and 18 years. Comparison of the genotypes obtained with those European genotypes included in The European Surveillance System (TESSy) showed that 87 cases had become part of 20 European clusters. The continuity of MDR strain genotyping in time has offered a widespread picture of the situation that allows better management of this public health problem. It also shows the advantage of maintaining one genotyping method over time, which allowed the comparison between ancient, present and future samples.

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“…The field of molecular epidemiology for investigating recent TB transmission is rapidly evolving, with WGS increasingly being used in public health practice to detect clusters and identify and characterize recent transmission (13)(14)(15)(16). However, analysis and use of WGS, such as SNP cutoffs, is still not standardized (17,18).…”

Section: Discussionmentioning

confidence: 99%

Logically Inferred Tuberculosis Transmission (LITT): A Data Integration Algorithm to Rank Potential Source Cases

Winglee

McDaniel

Linde

et al. 2021

Front. Public Health

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Understanding tuberculosis (TB) transmission chains can help public health staff target their resources to prevent further transmission, but currently there are few tools to automate this process. We have developed the Logically Inferred Tuberculosis Transmission (LITT) algorithm to systematize the integration and analysis of whole-genome sequencing, clinical, and epidemiological data. Based on the work typically performed by hand during a cluster investigation, LITT identifies and ranks potential source cases for each case in a TB cluster. We evaluated LITT using a diverse dataset of 534 cases in 56 clusters (size range: 2–69 cases), which were investigated locally in three different U.S. jurisdictions. Investigators and LITT agreed on the most likely source case for 145 (80%) of 181 cases. By reviewing discrepancies, we found that many of the remaining differences resulted from errors in the dataset used for the LITT algorithm. In addition, we developed a graphical user interface, user's manual, and training resources to improve LITT accessibility for frontline staff. While LITT cannot replace thorough field investigation, the algorithm can help investigators systematically analyze and interpret complex data over the course of a TB cluster investigation.Code available at:https://github.com/CDCgov/TB_molecular_epidemiology/tree/1.0; https://zenodo.org/badge/latestdoi/166261171.

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Investigation of a rapidly spreading tuberculosis outbreak using whole-genome sequencing

Cited by 17 publications

References 20 publications

A whole-genome sequencing study of an X-family tuberculosis outbreak focus on transmission chain along 25 years

A whole-genome sequencing study of an X-family tuberculosis outbreak focus on transmission chain along 25 years

The value of the continuous genotyping of multi-drug resistant tuberculosis over 20 years in Spain

Logically Inferred Tuberculosis Transmission (LITT): A Data Integration Algorithm to Rank Potential Source Cases

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