Table 1. Pairwise identity and indels in the mclx genes in a panel of 150 Mtb complex strains/clinical isolates 1 .
| Organism | Lineage | mclx 1 | mclx 2 | mclx 3 |
|---|---|---|---|---|
| Maf GM041182 | WA-2 | 99.97%—del -1406 (T) | 99.90% | 99.90% |
| Maf K85 | WA-2 | 99.90%—del -1406 (T); del—2481 C) | 99.90% | 99.97% |
| Mbv 04–303 | - | 99.97% | 99.90% | 100.00% |
| Mbv AF2122/97 | - | 99.90% | 99.90% | 100.00% |
| Mbv AN5 | - | 100.00% | 99.90% | 100.00% |
| Mbv BCG ATCC 35733 | - | 100.00% | 99.90% | 99.97% |
| Mbv BCG ATCC 35740 | - | 99.90% | 99.90% | 99.97% |
| Mbv BCG China | - | 100.00% | 99.90% | 99.80%—ins—2198–2202 (GGCGG) |
| Mbv BCG Frappier | - | 100.00% | 99.90% | 99.97% |
| Mbv BCG Korea 1168P | - | 100.00% | 99.90% | 99.97% |
| Mbv BCG Mexico | - | 100.00% | 99.90% | 99.97% |
| Mbv BCG Moreau | - | 100.00% | 99.90% | 99.97% |
| Mbv BCG Pasteur 1173P2 | - | 100.00% | 99.90% | 99.90% |
| Mbv BCG Tokyo 172 | - | 100.00% | 99.90% | 99.97% |
| Mcn CIPT 140010059 | - | 99.90% | 99.90% | 93.40%—ins—2519–2521 (CCA) |
| Mcn CIPT 140060008 | - | 99.80% | 99.60% | 93.50%—ins—2521–2523 (ACC) |
| Mcn CIPT 140070002 | - | 99.90% | 99.90% | 98.90% |
| Mcn CIPT 140070005 | - | 99.70% | 99.60% | 98.60% |
| Mcn CIPT 140070007 | - | 99.30% | 99.50% | 99.00% |
| Mcn CIPT 140070008 | - | 99.70% | 99.90% | 99.10% |
| Mcn CIPT 140070013 | - | 99.30% | 98.50% | 98.80% |
| Mcn CIPT 140070017 | - | 99.00% | 99.20% | 97.00%—ins—2531–2533 (GCC) |
| Mtb '98-R604 INH-RIF-EM' | EAm | 100.00% | 99.90%—ins—840 (T) | 99.97%—del—2716 (A) |
| Mtb 02_1987 | EAs | 99.90% | 99.97% | 100.00% |
| Mtb 1034 | EAs | 99.97% | 99.97% | 100.00% |
| Mtb 210 | EAs | 99.97% | 99.97% | 99.97% |
| Mtb 43–16836 | IO | 100.00% | 99.97% | 99.90%—ins—1393–1394 (TA) |
| Mtb 7199–99 | EAm | 100.00% | 99.90% | 100.00% |
| Mtb BT1 | EAs | 99.97% | 99.97% | 99.97% |
| Mtb BT2 | EAs | 99.97% | 99.97% | 99.97% |
| Mtb BTB05-552 | EAm | 100.00% | 99.97% | 100.00% |
| Mtb BTB05-559 | EAm | 100.00% | 99.97% | 100.00% |
| Mtb C | EAm | 99.50%—ins—3195 (T); ins—3211 (G); ins—3218 (G) | 99.90% | 99.90%—ins—2919 (G); ins—2992 (G) |
| Mtb CAS/NITR204 | EAI | 98.90%- 15 del/ 1 ins | 99.20%- 13 del | 98.70%- 19 del/ 2 ins |
| Mtb CCDC5079 | EAs | 99.97% | 99.90%—del—2523–2525 (CGA) | 99.97% |
| Mtb CCDC5180 | EAs | 99.97% | 99.97% | 99.97% |
| Mtb CDC1551 | EAm | 100.00% | 99.96% | 100.00% |
| Mtb CDC1551A | 100.00% | 99.97% | 100.00% | |
| Mtb CTRI-2 | EAm | 100.00% | 99.90%—ins—840 (T) | 100.00% |
| Mtb EAI5 | 100.00% | 99.90% | 99.90%—del—1388–1392 (TTGCG) | |
| Mtb EAI5/NITR206 | IO | 99.90% | 99.97% | 100.00% |
| Mtb EAS054 | IO | 99.97% | 99.97% | 99.80%—del—1388–1392 (TTGCG) |
| Mtb F11 | EAm | 99.97% | 99.90%—ins—840 (T) | 100.00% |
| Mtb FJ05194 | EAs | 100.00% | 99.90% | 100.00% |
| Mtb GuangZ0019 | EAm | 100.00% | 99.97% | 100.00% |
| Mtb H37Ra | EAm | 100.00% | 100.00% | 100.00% |
| Mtb H37RvCO | EAm | 100.00% | 100.00% | 100.00% |
| Mtb HKBS1 | EAs | 99.97% | 99.97% | 99.97% |
| Mtb HM | EAm* | 99.97% | 99.90%—ins—840 (T) | 99.00%—ins—1921–1953 (TG. . .TG) |
| Mtb HN878 | EAs | 99.97% | 99.97% | 99.97% |
| Mtb INS_MDR | EAm | 100.00% | 99.97% | 100.00% |
| Mtb INS_SEN | EAm | 100.00% | 99.97% | 100.00% |
| Mtb INS_XDR | EAm | 100.00% | 99.97% | 100.00% |
| Mtb KZN 1435 | EAm | 100.00% | 99.90%—ins—840 (T) | 99.97% |
| Mtb KZN 4207 | EAm | 100.00% | 99.90%—ins—840 (T) | 99.97% |
| Mtb KZN 605 | EAm | 100.00% | 99.90%—ins—840 (T) | 99.97% |
| Mtb KZN R506 | EAm | 100.00% | 99.90%—ins—840 (T) | 99.97% |
| Mtb KZN V2475 | EAm | 100.00% | 99.90%—ins—840 (T) | 99.97% |
| Mtb MTB-489 | ? | 99.97% | 100.00% | 99.97% |
| Mtb NA-A0008 | ? | 99.97%—del—871 (C) | 99.90% | 99.80%—del—1388–1392 (TTGCG); del—2044 (C) |
| Mtb NA-A0009 | ? | 99.90%—del—871 (C); ins—2308–2310 (AG); del—2901 (C) | 99.97% | 99.80%—del—1388–1392 (TTGCG); del—2104 (G) |
| Mtb NCGM2209 | EAs | 99.97% | 99.97% | 100.00% |
| Mtb OSDD071 | EAI | 100.00% | 99.97% | 99.90% |
| Mtb OSDD105 | EAm | 100.00% | 99.90% | 99.97%—del—900 (C) |
| Mtb OSDD493 | EAm | 99.97%—del—352 (C) | 99.97% | 100.00% |
| Mtb PanR0201 | EAm | 100.00% | 99.90%—ins—840 (T) | 100.00% |
| Mtb PanR0202 | EAm | 100.00% | 99.97% | 100.00% |
| Mtb PanR0205 | EAm | 100.00% | 99.90%—ins—840 (T) | 99.97% |
| Mtb PanR0206 | EAm | 100.00% | 99.90% | 100.00% |
| Mtb PanR0207 | EAm | 100.00% | 99.90%—ins—840 (T) | 99.97% |
| Mtb PanR0208 | EAm | 100.00% | 99.97% | 100.00% |
| Mtb PanR0209 | EAm | 100.00% | 99.90%—ins—840 (T) | 99.97% |
| Mtb PanR0304 | EAm | 100.00% | 99.90%—ins—840 (T) | 100.00% |
| Mtb PanR0305 | EAm | 100.00% | 99.97% | 100.00% |
| Mtb PanR0306 | EAm | 100.00% | 99.90%—ins—840 (T) | 99.97% |
| Mtb PanR0307 | EAm | 100.00% | 99.90%—ins—840 (T) | 99.97% |
| Mtb PanR0308 | EAm | 100.00% | 99.90%—ins—840 (T) | 100.00% |
| Mtb PanR0309 | EAm | 100.00% | 99.97% | 100.00% |
| Mtb PanR0313 | EAm | 100.00% | 99.90%—ins—840 (T) | 100.00% |
| Mtb PanR0314 | EAm | 100.00% | 99.90%—ins—840 (T) | 99.97% |
| Mtb PanR0315 | EAm | 100.00% | 99.90% | 100.00% |
| Mtb PanR0316 | EAm | 100.00% | 99.97% | 99.97% |
| Mtb PanR0317 | EAm | 100.00% | 99.90%—ins—840 (T) | 99.97% |
| Mtb PanR0401 | EAm | 100.00% | 99.90%—ins—840 (T) | 99.97% |
| Mtb PanR0402 | EAm | 100.00% | 99.10%—ins—840 (T); del—3466 (G) | 99.97% |
| Mtb PanR0403 | EAm | 100.00% | 99.90%—ins—840 (T) | 100.00% |
| Mtb PanR0404 | EAm | 100.00% | 99.90%—ins—840 (T) | 100.00% |
| Mtb PanR0405 | EAm | 100.00% | 99.90%—ins—840 (T) | 99.97% |
| Mtb PanR0409 | EAm | 100.00% | 99.90%—ins—840 (T) | 100.00% |
| Mtb PanR0410 | EAm | 100.00% | 99.90%—ins—840 (T) | 99.97% |
| Mtb PanR0411 | EAm | 100.00% | 99.90%—ins—840 (T) | 99.97% |
| Mtb PanR0412 | EAm | 100.00% | 99.90%—ins—840 (T) | 99.97% |
| Mtb PanR0501 | EAm | 100.00% | 99.90%—ins—840 (T) | 99.97% |
| Mtb PanR0503 | EAm | 100.00% | 99.90%—ins—840 (T) | 100.00% |
| Mtb PanR0505 | EAm | 100.00% | 99.90%—ins—840 (T) | 99.97% |
| Mtb PanR0602 | EAm | 100.00% | 96.50%- 5 del/ 4 ins | 100.00% |
| Mtb PanR0603 | EAm | 100.00% | 99.90%-ins—840 (T) | 99.97% |
| Mtb PanR0604 | EAm | 100.00% | 99.90%-ins—840 (T) | 99.97% |
| Mtb PanR0605 | EAs | 99.97% | 99.97% | 99.97% |
| Mtb PanR0606 | EAs | 99.97% | 99.97% | 99.97% |
| Mtb PanR0607 | EAm | 100.00% | 99.90%—ins—840 (T) | 99.97% |
| Mtb PanR0609 | EAm | 100.00% | 99.90%—ins—840 (T) | 99.97% |
| Mtb PanR0610 | EAm | 100.00% | 99.90%—ins—840 (T) | 100.00% |
| Mtb PanR0611 | EAm | 99.97% | 99.90%—ins—840 (T) | 99.97% |
| Mtb PanR0702 | EAm | 100.00% | 99.90%—ins—840 (T) | 99.97% |
| Mtb PanR0703 | EAm | 99.97% | 99.90%—ins—840 (T) | 99.97% |
| Mtb PanR0704 | EAm | 99.97% | 99.90%—ins—840 (T) | 99.97% |
| Mtb PanR0707 | EAm | 100.00% | 99.90%—ins—840 (T) | 99.97% |
| Mtb PanR0708 | EAm | 99.97% | 99.90%—ins—840 (T) | 99.97% |
| Mtb PanR0801 | EAm | 100.00% | 99.90% | 100.00% |
| Mtb PanR0802 | EAm | 100.00% | 99.90%—ins—840 (T) | 99.97% |
| Mtb PanR0803 | EAm | 100.00% | 99.90%—ins—840 (T) | 99.97% |
| Mtb PanR0804 | EAm | 100.00% | 99.90%—ins—840 (T) | 99.97% |
| Mtb PanR0805 | EAm | 99.97% | 99.90%—ins—840 (T) | 99.97% |
| Mtb PanR0902 | EAm | 100.00% | 99.90% | 100.00% |
| Mtb PanR0903 | EAm | 100.00% | 99.90%—ins—840 (T) | 100.00% |
| Mtb PanR0904 | EAm | 100.00% | 99.90%—ins—840 (T) | 99.97% |
| Mtb PanR0906 | EAm | 99.97% | 99.90%—ins—840 (T) | 99.97% |
| Mtb PanR0907 | EAm | 100.00% | 99.90% | 100.00% |
| Mtb PanR0909 | EAm | 100.00% | 99.90%—ins—840 (T) | 99.97% |
| Mtb PanR1005 | EAm | 100.00% | 99.90%—ins—840 (T) | 99.97% |
| Mtb PanR1006 | EAm | 100.00% | 99.90%—ins—840 (T) | 99.97% |
| Mtb PanR1007 | EAm | 99.97% | 99.90%—ins—840 (T) | 99.97% |
| Mtb PanR1101 | EAm | 100.00% | 99.90%—ins—840 (T) | 100.00% |
| Mtb PR05 | ? | 100.00% | 99.97% | 99.80%—del—1388–1392 (TTGCG) |
| Mtb R1207 | EAs | 99.90% | 99.97% | 100.00% |
| Mtb RGTB327 | EAm* | 99.90%—ins—454 (G); ins—684 (A) | 99.90%—ins—840 (T); ins—1331 (C) | 99.90%—ins—766 (G); ins—2844–2845 (GG) |
| Mtb RGTB423 | IO* | 99.97%—ins—2821 (C) | 99.90%—ins—390 (A) | 99.70%—ins—1121 (A); ins—2160–2162 (GCC); ins—3017 (G) |
| Mtb S96-129 | EAm | 100.00% | 99.97% | 100.00% |
| Mtb Beijing/NITR203 | EAs | 99.90% | 99.90% | 99.97% |
| Mtb Erdman = ATCC 35801 | EAm | 100.00% | 99.90% | 100.00% |
| Mtb Haarlem | EAm | 99.10%- 7 ins | 99.90% | 99.90%—del—2264 (G);del—2362 (G) |
| Mtb OSDD515 | EAm | 100.00% | 99.97% | 99.97%—del—938 (T) |
| Mtb SUMu001 | ? | 99.97%—del—952 (G) | 100.00% | 100.00% |
| Mtb SUMu002 | ? | 99.97%—del—952 (G) | 99.97% | 99.97%—ins—2487 (A) |
| Mtb SUMu003 | ? | 100.00% | 99.97% | 100.00% |
| Mtb SUMu004 | ? | 100.00% | 99.97% | 100.00% |
| Mtb SUMu005 | ? | 100.00% | 99.97% | 100.00% |
| Mtb SUMu006 | ? | 100.00% | 99.97% | 100.00% |
| Mtb SUMu008 | ? | 99.97%—del—952 (G) | 99.97% | 100.00% |
| Mtb SUMu010 | ? | 100.00% | 100.00% | 100.00% |
| Mtb SUMu011 | ? | 100.00% | 100.00% | 100.00% |
| Mtb SUMu012 | ? | 99.90%—del—2254 (G); del—2962 (G) | 100.00% | 100.00% |
| Mtb UM 1072388579 | ? | 100.00% | 99.90% | 100.00% |
| Mtb UT205 | EAm | 100.00% | 99.90%—ins—840 (T) | 100.00% |
| Mtb W-148 | EAs | 99.97% | 99.90%—del—2523–2525 (CGA) | 99.97% |
| Mtb WX3 | EAs | 99.97% | 99.97% | 99.97% |
| Mtb X122 | EAs | 99.97% | 99.90%—del—2523–2525 (CGA) | 99.97% |
| Mtb XDR1219 | EAs | 99.97% | 99.97% | 99.97% |
| Mtb XDR1221 | EAs | 99.90% | 99.97% | 100.00% |
1The pairwise identity refers to the % of conserved residues of each gene after aligning it with its orthologue from the reference strain M. tuberculosis H37Rv; the putative pseudogenes are highlighted in bold; indel ocurrences are described by their type (ins, insertion; del, deletion) and by their location (considering an alignment with the reference mclx genes from the Mtb H37Rv strain), except when the total number of isolated occurences exceeds 3, in which case only their frequency is indicated; Maf, Mycobacterium africanum; Mvb, Mycobacterium bovis; Mcn, Mycobacterium cannetti; Mtb, Mycobacterium tuberculosis; WA-2, West-African 2; EAm, Euro-American lineage; EAs, East-Asian lineage; IO, Indo-Oceanic; EAI, East-African Indian lineage
*, indicates that the information on the lineage was obtained by aligning the H37Rv RD with the genome/scaffolds of the respective organism.