Descriptions
Outline
Click the species name for a description of the organismF11
We have completed the sequencing of a representative isolate of the F11 strain, which is found in large clusters around the world, particularly in South Africa.
Dr. Tommie Victor of Stellenbosch University, South Africa, provided the F11 genomic DNA for sequencing.
C
The C strain has been highly transmitted in New York City. In one study this strain was found to be more common among injection drug users and resistant to reactive nitrogen intermediates. (Friedman et al. J Infect Dis. 1997 Aug;176(2):478-84.)
Dr. Barry Kreiswirth of the Public Health Research Institute, Newark, NJ, provided the genomic DNA for the C strain sequencing.
Haarlem
Members of the Haarlem family of M. tuberculosis strains have been found in many parts of the world. The first representative of the family was discovered in Haarlem, The Netherlands.
The strain was provided by Barry Kreisworth, Public Health Research Institute.
KZN
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
98-R604 INH-RIF-EM
Isolated from a single host during the course of a chronic infection.
W-148
Highly multi-drug resistant; variant of the Beijing family; found in large cluster of identical or highly similar isolates.