| Literature DB >> 29769160 |
O Popovici1, Ph Monk2, D Chemtob3,4, D Chiotan5, P J Freidlin6,7, R Groenheit8, M Haanperä9, D Homorodean10, M Mansjö8, E Robinson11, E Rorman12, G Smith13, H Soini9, M J Van Der Werf14.
Abstract
Extensively drug-resistant (XDR) tuberculosis (TB) poses a threat to public health due to its complicated, expensive and often unsuccessful treatment. A cluster of three XDR TB cases was detected among foreign medical students of a Romanian university. The contact investigations included tuberculin skin testing or interferon gamma release assay, chest X-ray, sputum smear microscopy, culture, drug susceptibility testing, genotyping and whole-genome sequencing (WGS), and were addressed to students, personnel of the university, family members or other close contacts of the cases. These investigations increased the total number of cases to seven. All confirmed cases shared a very similar WGS profile. Two more cases were epidemiologically linked, but no laboratory confirmation exists. Despite all the efforts done, the source of the outbreak was not identified, but the transmission was controlled. The investigation was conducted by a team including epidemiologists and microbiologists from five countries (Finland, Israel, Romania, Sweden and the UK) and from the European Centre for Disease Prevention and Control. Our report shows how countries can collaborate to control the spread of XDR TB by exchanging information about cases and their contacts to enable identification of additional cases and transmission and to perform the source investigation.Entities:
Keywords: Contact tracing; extensively drug-resistant; tuberculosis; whole genome sequencing
Mesh:
Year: 2018 PMID: 29769160 PMCID: PMC9184956 DOI: 10.1017/S095026881800047X
Source DB: PubMed Journal: Epidemiol Infect ISSN: 0950-2688 Impact factor: 4.434
Whole-genome sequencing methodology used for sequencing of the strains in the extensive drug-resistant tuberculosis outbreak investigation
| Sequencing service, Organisation and country | Sequencing platform; manufacturer and model | Software for computational pipeline – peer-reviewed publication | Criteria for quality assessment/quality control of assembly | Genome assembly. Reference mapping or | Variant calling software | Relatedness | Validation | Quality assurance/control | In routine clinical use? | In clinical use for selected isolates | In use for research | Isolates sequenced/analysed for this investigation |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| National Institute for Health and Welfare, Finland | MiSeq | Mostly. RIDOM SeqSphere | Reference coverage (depth and %) mapped reads | Mapping and Burrows-Wheeler Aligner de novo (Velvet) | RIDOM Seqsphere | Implementation of methodology ongoing | No | MDR strains and isolates included in contact investigations | Yes | Case 6 | ||
| National Public Health Laboratory Tel Aviv, Israel | Illumina Hiseq 4000 | BioNumerics 7.6, Applied Maths | Reference coverage (depth and %) mapped reads | Mapping and de novo | BioNumerics 7.6 | Implementation of cgMLST in BioNumerics, still under evaluation and validation | In-house controls (Accred Qual Assur (2011)16 : 623–635) | No | Yes | Yes | Cases 1 and 5 | |
| Public Health Agency of Sweden, Sweden | Ion Torrent | No | Reference coverage (depth and %), amount of ambiguous calls | de novo (CLC Assembly Cell v 4.4.2) | CLC Assembly Cell v 4.4.2 | In house-script | Swedac (Sweden's national accreditation body). In progress | ERLTB-Net | Yes | Not applicable | Yes | Isolates from Romanian patients |
| Public Health England/Modernising Medical Microbiology Consortium, University of Oxford, UK | Illumina MiSeq | No | Reference coverage %, mapped reads | Reference mapping (Stampy-open source) | Custom | Elephant walk (custom) | United Kingdom Accreditation Service (UKAS) inspection against ISO15189 (2012) in progress | IQC and IQA Global Microbial Identifier proficiency testing; UK NEQAS for mycobacterial diagnostics | Yes | Not applicable | Yes | Cases 2, 3, 4 and 7 |
IQC, internal quality control; IQA, internal quality assurance.
Fig. 1.Illustration of a Minimum Spanning Tree with SNP differences indicated on the branches (core genome included in the analysis = 92.93%). Source: The WHO Supranational Reference Laboratory (SRL) for TB in Stockholm, Sweden.
Fig. 2.Epidemiological links between the seven confirmed extensively drug-resistant tuberculosis cases in the outbreak and two other epi-linked cases in UK contacts.
Onset of symptoms, and month and year of diagnosis and treatment initiation of extensively drug-resistant tuberculosis cases that are part of an outbreak linked to a university in Romania
| XDR TB case number and country of origin | Month and year of symptom onset | Month, year, and place of TB diagnosis | Month, year and place of XDR TB diagnosis | Month, year and place of XDR TB treatment initiation | Type of disease (pulmonary/extra-pulmonary) |
|---|---|---|---|---|---|
| 1 | February 2015 | July 2015 in Israel | September 2015 in Israel | October 2015 in Israel | Extra-pulmonary |
| 2 | NA (asymptomatic; detected through contact tracing) | October 2015 in Romania: chest X-ray with lesions; December 2015 in Romania: GeneXpert: | March 2016 in Romania; March 2016 in the UK | March 2016 in UK | Pulmonary |
| 3 | NA (asymptomatic; detected through contact tracing) | October 2015 in Romania: chest X-ray without lesions | October 2016 in the UK | October 2016 in the UK | Pulmonary |
| 4 | March 2016 | March 2016 in the UK | April 2016 in the UK | April 2016 in the UK | Pulmonary |
| 5 | NA (asymptomatic; detected through contact tracing) | October 2016 in Romania: chest X-ray with lesions; smear and culture negative | November 2016 in Israel | December 2016 in Israel | Pulmonary |
| 6 | June 2016 | August 2016 | September 2016 in Finland | August 2016 in Finland | Pulmonary |
| 7 | NA (asymptomatic; detected through contact tracing) | September 2016 | September 2016 in the UK | September 2016 in the UK | Pulmonary |
NA, not applicable; TB, tuberculosis; XDR TB, extensively drug-resistant TB.