Amplifying the possibilities: Long awaited new PCR equipment arrives in Karachi

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Category: Infrastructure support

After a long wait, a piece of vital equipment, the “CFX96 Touch™ Real-Time PCR Detection System”, co-funded by the Global Network for Neglected Tropical Diseases (NTDs) and the University of Karachi, has now arrived at the International Center for Chemical and Biological Sciences (ICCBS).  The machine (a white box with screen – visible in the right of the picture) now enables Network members Iqbal Choudhary, Sammer Yousuf and the Karachi team to use the polymerase chain reaction technique (PCR) DNA amplifying technology to identify genetic variations between strains of Leishmania parasites, causing leishmaniasis.  This purchase is also a behind-the-scenes administrative triumph for international collaboration, highlighting some of the bureaucratic difficulties we navigate with our NTD Network colleagues in developing countries.
Leishmaniasis is a major health challenge in Pakistan, with cases reported in all provinces and almost all major cities.  Skin-based forms (cutaneous leishmaniasis, CL), caused by Leishmania major and L. tropica, are most common, affecting around 15,000–20,000 people each year.1,2  Whilst not lethal, the open sores and scars caused by CL, often on the face or hands, have a devastating and life-long impact.  Sufferers experience social stigma, resulting in isolation and exclusion from employment opportunities.  Women are particularly victimized, as the scars mean they are often considered unacceptable for marriage.3

Visceral, cutaneous and muco-cutaneous forms of leishmaniasis occur in tropical areas across Asia, Africa and South America. Leishmania parasites are spread by sandflies (Phlebotomus spp, above left) and infect white blood cells (below left); the disease presents clinically in either a visceral form (above, right) which is lethal if untreated, or as cutaneous sores (right, below) causing disfiguring scars. Images: Wikimedia Commons.

In nearby India, the CL epidemic has developed widespread clinical resistance to the first-line treatment, pentavalent antimonials.4  The resistance of CL in Pakistan is currently unknown.
The team at ICCBS will use the new PCR machine to look for the presence of genetic mutations conveying drug resistance in parasites isolated from across Pakistan, and cross-check these with resistance to these treatments in the lab.  The PCR method uses short pieces of DNA (primers) which ‘stick’ to the mutated gene sequence, if present, and making multiple copies of this gene which raises a signal detected by the machine – confirming the presence of the mutation in the parasite DNA.  This will enable the team to develop a map of drug-specific resistance mutations across the CL strains in Pakistan, informing a more patient-appropriate choice of treatment.
Whilst the need for a PCR machine is clear, navigating the purchase was laborious.  Pakistani processes of fairness required that the team at ICCBS advertise in newspapers for companies to bid for the task of supplying the machine, and obtain three independent tenders, before they could proceed.  Further delays resulted from arranging a second funding source.  This specialised (and so expensive) item exceeds the NTD Network’s £10,000 cut-off for single laboratory equipment purchases.  Finally, the ICCBS in Pakistan were able to cover the shortfall –some US$13.000.  The delivery of this machine in Karachi is therefore truly an international administrative triumph.
NTD Network members in Pakistan are already leading their region’s efforts to discover new anti-leishmanial lead compounds from natural sources.  The ICCBS staff are now using the new PCR system to support their plans to train researchers in how to analyse infective strains of Leishmania, and to assess natural product-derived compounds for anti-leishmanial activity.  Their ambition is for the ICCBS at the University of Karachi to become a Hub for leishmaniasis research for the whole of Pakistan.
As part of this effort, NTD Network members Iqbal and Sammer from ICCBS, along with Paul Denny (Durham UK) and others are offering an international student training workshop in Karachi this November  For further information, and details of how to apply for an NTD Network travel bursary, please visit our events page.



1 World Health Organization. Leishmaniasis country profile – 2010: Pakistan. Available at (accessed July 2019).

2 World Health Organization. Leishmaniasis country profile – 2015: Pakistan (accessed July 2019).

  1. Kassi M, et al. PLOS Negl Trop Dis 2008; 2(10): e259
  2. Haldar AK, et al. Mol Biol Int 2011; 2011: 571242.