About the KZN TB Strains
Three strains of M. tuberculosis isolated from patients in KwaZulu-Natal, South Africa have been sequenced using both Solexa and Sanger sequencing technology. The raw sequence data for the unassembled Solexa sequence runs are now available from the Broad Institute web site (see below) and NCBI. Draft genome assemblies for these 3 strains can be downloaded from here. We used both sequencing methods so the TB community can benefit from the speed of the Solexa technology and the whole genome contiguity that Sanger sequence delivers.
These three strains were selected because they represent a range of important drug resistance phenotypes spanning fully drug-sensitive (DS) to multiply drug resistant (MDR), to extensively drug resistant (XDR). XDR TB is extremely difficult to treat because it is resistant to the first line anti-TB drugs INH and rifampin, and it is resistant to at least one fluoroquinolone plus at least one second line injectable drug (capreomycin, kanamycin, or amikacin.). Recently, a high mortality rate for patients infected with XDR TB was reported in the KwaZulu-Natal region (Gandhi et al 2006, Lancet (368):1575-1580). The XDR (KZN 605), MDR (KZN 1435), and DS (KZN 4207) strains were selected for sequencing from among other strains in the KZN region. The three strains represent three levels of drug resistance:
- KZN 4207: drug sensitive
- KZN 1435: multiple drug resistant
- KZN 605: extensively drug resistant
NOTE: The latest sequence data is available here. For the older versions, please refer to the table below.
For each strain, two files of sequence and two corresponding files of quality scores are available.
The data files are available for anonymous ftp at:
ftp://ftp.broad.mit.edu/pub/annotation/mtuberculosis/kzn
You may also follow the links to individual files found below.
| Strain | Sequence file | Quality file |
|---|---|---|
| KZN 4207 - DS | KZN_4207_DS_1.fasta.gz | KZN_4207_DS_1.qual.gz |
| KZN_4207_DS_2.fasta.gz | KZN_4207_DS_2.qual.gz | |
| KZN 1435 - MDR | KZN_1435_MDR_1.fasta.gz | KZN_1435_MDR_1.qual.gz |
| KZN_1435_MDR_2.fasta.gz | KZN_1435_MDR_2.qual.gz | |
| KZN 605 - XDR | KZN_605_XDR_1.fasta.gz | KZN_605_XDR_1.qual.gz |
| KZN_605_XDR_2.fasta.gz | KZN_605_XDR_2.qual.gz |