Mutations Associated with Rifampicin Resistance in Mycobacterium tuberculosis Isolates from Moroccan Patients: Systematic Review

Table 2

Phenotypic and genotypic drug susceptibility results.

		Conventional drug susceptibility testing (DST)				Genotypic drug susceptibility method			Comparison of phenotypic and genotypic resistance (INH^R/RIF^R)
Studies included in the review	Isolates (n)	Susceptible for all first-line drugs	INH^R	RIF^R	MDR	Molecular assay	Sample processing and DNA extraction	Isolates (n)
Oudghiri et al. 2018 [26]	703	221	194	198	90	PCR and DNA sequencing (performed only for MDR: 90)	DNA was prepared from scraped colonies suspended in distilled water, followed by heat inactivation	84	6 MDR isolates contained no mutations in the sequenced region (157 bp)
							DNA was immediately used or stored at −20°C until use
Karimi et al. 2018 [27]	70	19	13	12	26	GenoType® MTBDRplus V2.0 (performed for all resistant strains: 51)	The assay was applied on direct sputum specimens and on culture isolates	47	4 (1 INH^R and 3 RIF^R) phenotypically resistant strains did not exhibit any mutation using GenoType® MTBDRplus assay
Ennassiri et al. 2017 [28]	319	172	31	9	107	GenoType® MTBDRplus V2.0 (performed for RIF^R and MDR: 116)	The assay was performed on isolates after solid culture or directly on decontaminated sputum specimens	98	18 RIF^R samples were missing wild-type probes with no gain in mutation probes
Bentaleb et al. 2017 [29]	67	22	—	45	—	qPCR-HRM (120 pb) (performed for RIF^R strains: 45)	DNA was extracted and purified using QIAamp DNA mini kit according to the manufacturer’s protocol	40	5 RIF^R strains contained no mutation in the rpoB amplified region and were classified as phenotypically RIF-resistant isolates
							DNA was stored at −20°C until use
Chaoui et al. 2014 [24]	500	346	—	154	—	RIFO (performed for RIF^R strains: 154)	DNA was prepared from scraped colonies suspended in 1x TE buffer, followed by heat inactivation	140	14 RIF^R isolates that were phenotypically resistant did not exhibit any point mutation in the hot-spot region of the rpoB gene
							DNA was stored at −20°C until use
Zakham et al. 2013 [25]	133	94	10	18	11	PCR and DNA sequencing (performed for all resistant strains: 39)	Specimens decontaminated by N-acetyl-l-cysteine were first thawed and centrifuged. For each specimen, the pellet was treated by heat shock	33	6 (3 INH^R, 1 RIF^R, and 2 MDR) strains did not exhibit any point mutation in the amplified regions (rpoB and katG genes and inhA promoter region)
							DNA was immediately used or stored at −20°C until use
Total	1792	874	248	436	234	—	—	442	53 (4 INH^R, 8 MDR, and 41 RIF^R)

n: number; INH^R: isoniazid resistant; RIF^R: rifampicin resistant; RIFO: rifoligotyping; qPCR-HRM: quantitative polymerase chain reaction-high-resolution melting; MDR: multidrug resistant.