In 2019, BCCM/ITM had the honor to welcome a new interesting subcollection into its public repository, known by mycobacteriologists as the “Mycobacterium tuberculosis complex (MTBC) clinical strains reference set” from the Borrell et al. (2019) publication.
This “MTBC clinical strains reference set” comprises 20 clinical strains covering 7 known human-adapted MTBC lineages (L1-L7) (Fig 1). Together with the newly described lineage 8 strain ITM 500961 (described by Ngabonziza et al. (2020) as the sole known viable L8 strain available so far) also available at BCCM/ITM, this reference set offers researchers the perfect opportunity to go beyond one single MTBC lineage and explore the phenotypic impact of MTBC diversity.
Why the need for such a reference set?
Members of the MTBC can cause tuberculosis (TB) in humans and various other mammals. The human-adapted strains comprise eight phylogenetic lineages that differ in their geographical distribution (Comas et al. 2013; Firdessa et al. 2013; Ngabonziza et al. 2020). There is growing evidence that this phylogeographic diversity modulates the outcome of TB infection and disease (Borrell et al. 2019).
As described by Borrell et al. (2019), for decades, TB research and development has mainly focused on the two canonical MTBC laboratory strains H37Rv and Erdman, together with the more recently used clinical strain CDC1551. These three strains all belong to MTBC Lineage 4 (Gagneux & Small 2007), and therefore do not represent the broader MTBC variability. Moreover, since their original isolation, these laboratory strains have been passaged countless times in various laboratories. This continuous passaging cycle can possibly lead to adaptation to laboratory conditions (Ioerger et al. 2010).
Borrell et al. (2019) emphasize that relying on only a few laboratory-adapted strains can thus be misleading as the study results might not paint the full picture and might not be directly transferrable to clinical settings where patients are infected with a diverse array of strains, including drug-resistant variants.
TB research and development would therefore benefit from validation in more genetic backgrounds, by incorporating the MTBC phylogenetic diversity. To facilitate this, Borrell et al. (2019) have assembled a set of 20 genetically well-characterized clinical strains representative of the known phylogenetic diversity of TB, comprising the first seven discovered human-adapted MTBC lineages.
What do you mean with well-characterized strains?
Borrell et al. (2019) used their global collection of MTBC clinical strains (and their associated phylogenomic data) to select a subset suitable as reference strains for future research.
This subset was characterized by performing whole-genome sequencing, spoligotyping and phenotypic drug-susceptibility testing for the main anti-TB drugs.
Moreover, the whole-genome sequencing (Illumina HiSeq 2500) data are freely available via the project accession number: PRJEB27802 on
ENA (https://www.ebi.ac.uk/ena/browser/view/PRJEB27802)
NCBI (https://www.ncbi.nlm.nih.gov/bioproject/PRJEB27802)
How can we avoid laboratory adaptation?
By having a joint agreement to avoid passaging these strains extensively between laboratories through repeated subculturing. This is why having a central “biobank” that assures the quality, purity and authenticity of the strains is of such great added value.
By ordering these strains from the Mycobacterial culture bank of the Belgian Coordinated Collections of Microorganisms (BCCM/ITM), you are ensured that the original properties of the strains are preserved.
Want to know more about the strain details?
Check the article of Borrell et al. 2019 or take a look at the strain info mentioned in our online catalogue on the BCCM website https://bccm.belspo.be/catalogues/catalogue-search?collection=ITM
You can use the strain numbers mentioned in Table 1 to facilitate your search through the online catalogue and/or to mention in your request letter.
|
BCCM/ITM Accession Nr (LIMS) |
BCCM/ITM Culture Nr |
Original ID |
Place of Birth |
Lineage |
|
ITM 500941 |
2018-00082 |
N0157 |
Philippines |
L1 |
|
ITM 500942 |
2018-00083 |
N0072 |
India |
L1 |
|
ITM 500944 |
2018-00085 |
N0145 |
China |
L2 |
|
ITM 500945 |
2018-00087 |
N0031 |
China |
L2 |
|
ITM 500946 |
2018-00088 |
N0155 |
China |
L2 |
|
ITM 500947 |
2018-00089 |
N0004 |
India |
L3 |
|
ITM 500948 |
2018-00090 |
N1274 |
Afghanistan |
L3 |
|
ITM 500949 |
2018-00091 |
N0054 |
Ethiopia |
L3 |
|
ITM 500950 |
2018-00092 |
N1216 |
Ghana |
L4 |
|
ITM 500951 |
2018-00093 |
N0136 |
USA |
L4 |
|
ITM 500952 |
2018-00094 |
N1283 |
Germany |
L4 |
|
ITM 500953 |
2018-00095 |
N1176 |
Ghana |
L5 |
|
ITM 500954 |
2018-00096 |
N1272 |
Ghana |
L5 |
|
ITM 500955 |
2018-00097 |
N1268 |
Sierra Leone |
L5 |
|
ITM 500956 |
2018-00098 |
N1201 |
Ghana |
L6 |
|
ITM 500957 |
2018-00099 |
N0091 |
Gambia |
L6 |
|
ITM 500958 |
2018-00100 |
N1202 |
Ghana |
L6 |
|
ITM 500959 |
2018-00101 |
N3913 |
Ethiopia |
L7 |
|
ITM 500960 |
2018-00102 |
N0069 |
China |
L1 |
|
ITM 500976 |
2018-03241 |
N0052 |
China |
L2 |
Table 1: Strain IDs from the MTBC Clinical strains reference set accompanied by their new BCCM/ITM accession numbers from the LIMS. Note: Strain N0052, mentioned in Borrell et al. 2019 as ITM-2018-02241 is now ITM-2018-03241 (ITM 500976).
How to order this MTBC clinical strains reference set?
Interested in using this MTBC clinical strains reference set for your research? Please send an e-mail to bccm.itm@itg.be and we will kindly help you further with the order procedure!
Fig 1 Maximum Likelihood topology of the 20 reference strains (open circles) plus 236 genomes representative of MTBC global diversity. © 2019 Borrell et al.
Branch lengths are proportional to nucleotide substitutions and the topology is rooted with Mycobacterium canettii. Bootstrap values for clades corresponding to main MTBC lineages are shown. Grey circles indicate the phylogenetic placement of laboratory M. tuberculosis strains commonly used. “A” stands for animal MTBC.
References:
Borrell, S., Trauner, A., Brites, D., Rigouts, L., Loiseau, C., Coscolla, M., Niemann, S., De Jong, B., Yeboah-Manu, D., Kato-Maeda, M., Feldmann, J., Reinhard, M., Beisel, C., & Gagneux, S. (2019). “Reference set of Mycobacterium tuberculosis clinical strains: A tool for research and product development.” PloS one 14(3), e0214088.
Comas, I., et al. (2013). "Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans." Nature Genetics 45: 1176-1182.
Firdessa, R., et al. (2013). "Mycobacterial lineages causing pulmonary and extrapulmonary tuberculosis, Ethiopia." Emerg Infect Dis 19: 460-463.
Gagneux, S. & Small, P.M. (2007). “Global phylogeography of Mycobacterium tuberculosis and implications for tuberculosis product development.” Lancet Infect Dis. 7(5):328-37.
Ioerger, T.R., et al. (2010). “Variation among genome sequences of H37Rv strains of Mycobacterium tuberculosis from multiple laboratories.” J Bacteriol.192(14):3645-53.
Ngabonziza, J.C.S., et al. (2020). “A sister lineage of the Mycobacterium tuberculosis complex discovered in the African Great Lakes region.” Nat Commun 11, 2917.