Lalor, MK; Casali, N; Walker, TM; Anderson, LF; Davidson, JA; Ratna, N; Mullarkey, C; ... Abubakar, I; + view all Lalor, MK; Casali, N; Walker, TM; Anderson, LF; Davidson, JA; Ratna, N; Mullarkey, C; Gent, M; Foster, K; Brown, T; Magee, J; Barrett, A; Crook, DW; Drobniewski, F; Thomas, HL; Abubakar, I; - view fewer (2018) The use of whole-genome sequencing in cluster investigation of an MDR-TB outbreak. European Respiratory Journal , 51 (6) , Article 1702313. 10.1183/13993003.02313-2017.

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Abstract

We used whole-genome sequencing to delineate transmission networks and investigate the benefits of whole-genome sequencing during cluster investigation. We included clustered cases of M/XDR-TB linked by MIRU-VNTR, or epidemiological information in the national cluster B1006, notified between 2007-2013 in the UK. We excluded cases whose isolates differed by >12 SNPs from further investigation. Data relating to patients’ social networks were collected. Twenty-seven cases were investigated, 22 had whole-genome sequencing; 8 (36%) of which were excluded as their isolates differed by >12 SNPs to other cases. Eighteen cases were ruled into the transmission network based on genomic and epidemiological information. Evidence of transmission was inconclusive in 39% (7/18) of cases in the transmission network following whole-genome sequencing and epidemiological investigation. This investigation of a drug resistant TB cluster illustrates the opportunities and limitations of wholegenome sequencing in understanding transmission in a setting with a high proportion of migrant cases. The use of WGS should be combined with classical epidemiological methods. However not every cluster will be solvable, regardless of the quality of genomic data.

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