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Resolution of phylogenetic typing in Mycobacterium tuberculosis: a comparison between WGS and tNGS

M de Diego Fuertes(1) E Costa Conceição(2) F Wells(2) V Rennie(1) T H Heupink(1) R M Warren(2) A Van Rie(1) A Dippenaar(1)

1:University of Antwerp; 2:Stellenbosch University

Strain typing is crucial for public health interventions. For 60 patients, we processed a sputum sediment by Deeplex® Myc-TB (Deeplex) and DNA from the corresponding primary liquid culture by Illumina whole genome sequencing (WGS) with MAGMA pipeline analysis. Of the 60 samples, Deeplex was unsuccessful for 7 (11.7%), reported “Other than lineage 4.9” (undefined) for 20 (33.3%), a lineage for 35 (58.3%), and sub-lineage for only 11 (18.3%) samples. MAGMA reported lineage plus sub-lineage for 59 (98%) samples. Mixed infection (minority strain ≥3% for Deeplex, any level for MAGMA) occurred in 4 samples. One sample was reported as 91% Mtb 2.2.1 + 8% Mtb by MAGMA, and 87% M. bovis + 39% undefined Mtb lineage by Deeplex. One sample was 99% NTM + 1% Mtb by MAGMA but 100% Mtb 4.3 by Deeplex. Another sample contained 5 Mtb lineages, animal strains and M. canettii (4%) + undefined Mtb lineage (96%) in Deeplex and 100% Mtb in MAGMA. The fourth sample contained two undefined lineages at 11% and 89% in Deeplex but 100% Mtb 2.2.1 in MAGMA. Discordances between spoligotype and lineage assignment in Deeplex were observed. Most (62%) samples shared an identical spoligotype (7 groups of size 2-19). In contrast, only 3.4% samples were part of a WGS cluster when using a 12 SNP cut-off. Only 1 of 7 spoligotype groups had a SNP distance <12.  Our results suggest that the tNGS Deeplex assay has poor phylogenetic resolution, limiting its ability to inform public health interventions.

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