Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs

Table 3 The in-silico profiling results for isolates sequenced using MinION

Samples*	Method	RIF	INH	EMB	PYR	STR	ETH	AMK	CAP	FLQ	PAS
por5	DST	R	R	R	R	R	R	S	S	S	S
	TBProfiler	R	R	R	R	R	R	S	S	S	S
	Mykrobe**	R	R	R	82%R	R	–	S	S	S	–
por6	DST	R	R	R	R	R	R	R	R	R	S
	TBProfiler	R	R	R	R	R	R	R	R	R	S
	Mykrobe	R	R	R	R	R	–	82%R	82%R	R	–
por7	DST	R	R	R	R	R	R	R	R	R	S
	TBProfiler	R	R	R	R	R	R	S	S	R	S
	Mykrobe	R	92%R	S	R	83%R	–	S	S	91%R	–

DST drug susceptibility testing (R resistant, S sensitive); this table shows the percentage of replicates producing the correct result; − cannot be determined; bolded values indicate the % of replicates with DST phenotypes, where resistance mutations are not found in all replicates. Underlined values indicate where the variant is not present in software mutation library; RIF rifampicin, INH isoniazid, EMB ethambutol, PYR pyrazinamide, STR streptomycin, ETH ethionamide, AMK amikacin, CAP capreomycin, FLQ fluoroquinolones, PAS para-aminosalicylic acid. *All LAM4 strain-types or sub-lineage 4.3.4.2. **Mykrobe-Profiler TB (https://github.com/iqbal-lab/Mykrobe-predictor) implemented using its command-line version