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Supranational TB Reference Laboratory in Karachi, Pakistan
Address:
Rumina Hasan (rumina.hasan@aku@edu)
Sadia Shakoor (sadia.shakoor@aku.edu)
TB Supranational Reference Laboratory, Karachi
Department of Pathology and Laboratory Medicine
Aga Khan University
Stadium Road, POBox 3500,
Karachi 74800, Pakistan
The Mycobacteriology test menu offers a range of conventional and molecular based tests for the diagnosis of tuberculosis and non-tuberculous mycobacterial infections. Including smear microscopy, solid and liquid (MGIT) culture, 1st and 2nd line drug sensitivity testing, Xpert MTB/RIF, MTBDRplus
Current links and partnerships outside of SRLN
SRL also works closely with the WHO EMRO and with the EMR_GLC. It participates in GLC activities and review missions within the region.
Description
The SRL Karachi is part of the Clinical Laboratory and the Department of Pathology and Laboratory Medicine at the Aga Khan University (AKU). The Aga Khan University Hospital (AKUH) in Karachi is accredited by the Joint Commission International (JCIA). AKUH Clinical Laboratory is a full service laboratory, supported by regional and several Stat Laboratories. It further includes over 225 Laboratory Collection outlets (phlebotomy stations) around the country and an extensive specimen transport network. The SRL is housed in a Biosafety Level 3 facility and includes trained and experienced technical staff and medically qualified clinical microbiology faculty.
Structure and organization
The Microbiology Section of the Clinical Laboratory includes the SRL. The Section Head; a clinical microbiologist works with a team of eleven clinical microbiology faculty (including 6 with a special interest in tuberculosis). The laboratory also has a Sectional Manager who works with charge technologists as well as senior and staff technologists. The Section Head reports to the Chair Department of Pathology and Laboratory Medicine as well as to the Service Line Chief and Director Clinical Laboratories, while the Sectional Manager reports to the Business Manager and ultimately to the Chief Operating Officer Outreach Services AKUH-Karachi.
Services provided by the SRL
The laboratory offers diagnostic microbiology services and works with the Molecular Pathology Section for molecular microbiology testing. The sectional faculty also participate in infection control activities within the hospital. The Laboratory offers training for clinical microbiology residents, laboratory technologists, graduates as well as for undergraduate medical students. It further organises continuous medical education programs for general practitioners and for specialists.
Additional information:
Research activities
Research focus includes pathogenesis of mycobacterial diseases, antimicrobial resistance a molecular epidemiology of M. tuberculosis strains.
Publications
1. Z Hasan, M.Tanveer, A Kanji, et al Spoligotyping of Mycobacteruim tuberculosis isolates in Pakistan reveals MDR associated Beijing strains and the predominance of a Central Asian type strain. J. Clinical Microbiology May 2006; 44(5):1763-1768.
2. A Ali, Z Hasan, MTanveer, et al Characterization of Mycobacterium tuberculosis Central Asian Strain1 (CAS1) using Mycobacterial Interspersed Repetitive Unit (MIRU-VNTR) BMC Microbiol. 2007 Aug 9;7:76.
3. Javaid A, Hasan R, Zafar A, Ghafoor A, et al Prevalence of primary multidrug resistance to anti-tuberculosis drugs in Pakistan. Int J Tuberc Lung Dis. 2008 Mar;12(3):326-31.
4. M Tanveer, Z Hasan, AR Siddiqui, et al Genotyping and Drug resistance patterns of M.tuberculosis strains in Pakistan. BMC Infect Dis. 2008 Dec 24;8(1):171.
5. Ali A, Hasan Z, Moatter T, Tanveer M, Hasan R M. tuberculosis Central Asian Strain 1 MDR isolates have more mutations in rpoB and katG genes compared with other genotypes. Scand J Infect Dis. 2009;41(1):37-44.
6. R Hasan, K Jabeen, V Mehraj et al Trends of Mycobacterium Tuberculosis resistance in Pakistan (1990-2007). Int J Infect Dis. 2009 Apr 13.
7. S Shakoor, M Tanveer, Y Rafiq et al Prevalence of ST26 among untreated smear-positive tuberculosis patients from Karachi indicating ongoing transmission. Scand J Infect Dis. 2009 Aug 13:1-6.
8. M Ejaz, AR Siddiqui, Y Rafiq et al Prevalence of Multi-drug resistance TB and its associated Risk factors in Karachi Pakistan. Trans R Soc Trop Med Hyg. 2010 Aug;104(8):511-7.
9. R Hasan, K Jabeen, A Ali, et al Extensively Drug Resistant Tuberculosis; A Perspective from Pakistan. Emerg Infect Dis. (2010) Sep;16(9):1473-5.
10. Rafiq Y, Jabeen K, Hasan R et al Fluoroquinolone resistance amongst Mycobacterium tuberculosis strains from Karachi, Pakistan; Data from community based field clinics. Antimicrob Agents Chemother. 2010 Dec 6.
11. K Jabeen, S Shakoor, S Chishti et al Increasing trend of fluoroquinolone resistance in Mycobacterium tuberculosis isolates from Pakistan (2005-2009). Emerg Infect Dis. 2011; 17 (3): 564-565
12. A Kanji, Z Hasan, M Tanveer et al Presence of RD149 deletions in the M. tuberculosis Central Asian Strain1 isolates affects growth and TNFα induction in THP-1 monocytes. PloS ONE August 2011. Volume 6 (8) e24178.
13. A Ali, R Hasan, K Jabeen et al Characterization of mutations conferring extensive drug resistance (XDR) to M. tuberculosis isolates in Pakistan. Antimicrobial Agents and Chemotherapy, Dec. 2011; Vol. 55(12): 5654–5659.
14. A Ayaz, Z Hasan, S Jafri et al Characterising M. tuberculosis isolates from Karachi, Pakistan: Drug resistance and genotypes. International Journal of Infectious Diseases 2012; 16(2012) e303-e309.
15. S Batra, A Ayaz, A Murtaza et al Childhood Tuberculosis in Household Contacts of Newly Diagnosed TB Patients. PLoS ONE 2012; 7(7): e40880
16. N Fasih, Y Rafiq, K Jabeen et al High Isoniazid Resistance Rates in Rifampicin Susceptible Mycobacterium tuberculosis Pulmonary Isolates from Pakistan. PLoS One. 2012;7(11):e50551.
17. I Ahmed, K Jabeen, R Inayat, R Hasan Susceptibility testing of extensively drug resistant and pre-extensively drug resistant Mycobacterium tuberculosis against levofloxacin, linezolid, and amoxicillin-clavulanate. Antimicrob. Agents Chemother. June 2013; 57:6 2522-2525.
18. Marais BJ, Lönnroth K, Lawn SD, Migliori GB et al Tuberculosis comorbidity with communicable and non-communicable diseases: integrating health services and control efforts. Lancet Infect Dis. 2013 May;13(5):436-48.
19. MS Khan, MS Khan, R Hasan, P Godfrey-Faussett. Unusual sex differences in tuberculosis notifications across Pakistan and the role of environmental factors. Eastern Mediterranean Health Journal 2013; 19(9): 821-825.
20. S Shakoor, FN Qamar, F Mir et al Are TB control programmes in South Asia ignoring children with disease? A situational analysis. Arch Dis Child 2015 Feb; 100(2): 198-205 doi:10.1136/archdischild-2013-304816.
21. A Ali et al. Whole genome sequencing based characterization of extensively drug-resistant Mycobacterium tuberculosis isolates from Pakistan PLoS One. 2015 Feb 26;10(2):e0117771.
22. K Jabeen, S Shakoor, R Hasan Fluoroquinolone resistant tuberculosis; implications in settings with weak healthcare systems. Invited review Int J. Infec Dis (2015) Mar;32:118-23
23. Coll F, McNerney R, Preston MD, et al Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Genome Med. 2015 May 27;7(1):51.
24. OA Dar, RHasan, J.et al Exploring the evidence base for national and regional policy interventions to combat resistance. The Lancet; Antimicrobials: access and sustainable effectiveness. Lancet. 2015 Nov 17. pii: S0140-6736(15)00520-6.
25. JE Phelan, F Coll, I Bergval et al Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages. BMC Genomics 2016 17:151 http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2467-y
Trainings
Regular trainings for technologists and clinical microbiology trainees
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