Phase 4 (2009 Deadline)
Prevalence, Species Distribution, and Trends in Resistance of Fungi Responsible for Invasive Mycoses in Pakistan
Mary E. Brandt, U.S. Centers for Disease Control and Prevention
Afia Zafar, Aga Khan University
Pakistani Funding (Department of State): $256,088
U.S. Funding (Department of State): $40,250
Project Dates on U.S. Side: November 15, 2010 - November 14, 2013 (Extended through September 30, 2014)
The rapid escalation of invasive fungal infections and their high mortality is an increasing global issue, as the introduction of aggressive medical treatments such as bone marrow transplants and chemotherapy along with the increased prevalence of immunosuppressive diseases including HIV have contributed to a rise in invasive fungal infections across the globe. However, to date there is little epidemiological data available on such infections and trends in Pakistan. With increasing numbers of HIV-infected individuals and post-transplant patients in Pakistan, fungal infections will pose significant healthcare challenge, and baseline information on prevalent fungal infections is essential in developing plans to manage such infections in the country. The goal of this project is to improve the diagnosis and management of fungal infections in the Pakistani population by building lab infrastructure and technical expertise in fungal diagnostics and epidemiology. The research team at Aga Khan University (AKU) will develop linkages with oncologists, orthopedic surgeons and other specialists to explore the frequency of various fungal species in immunocompromized and immunocompetent individuals. The Mycotic Diseases Branch of the Centers for Disease Control will provide support for training, molecular typing, and expert advice. The project should result in the development of baseline epidemiological data on prevalent fungi causing invasive diseases in the local community and contribute towards the formulation of local guidelines for treatment. In addition, this activity will also provide opportunities for training in detection and identification of medically important fungi to a large number of laboratory workers across the country, upgrading Pakistan’s mycology capabilities at the national level.
Over the past year, the project team saved 269 invasive fungal isolates for further workup in order to determine the spectrum of fungal pathogens associated with invasive fungal diseases in Pakistan. Dr. Kausar Jabeen, an MSc student in Medical Mycology from University College London, completed her bench work for molecular identification of molds under the supervision of Dr. Mary Brandt, CDC. Lab results continue to determine the frequency of occurrence and antifungal resistance among specific species of Candida associated with invasive disease through susceptibility test. On the basis of recent data and published studies (see publication list), a seminar is planned in late 2013 for medical microbiologists and infectious disease physicians to develop policies and guidelines for infection control and rational antifungal use. By conducting workshops throughout Pakistan, the PIs reported overall improvement in the standard of mycology diagnostic proficiency in clinical laboratories across Pakistan reflected by an increase in appropriate reporting and inclusion of fungal susceptibility testing in many laboratories. A simplified manual was prepared and distributed to all workshop participants, including technologists, laboratory doctors, and postgraduate residents. This grant also facilitated the MSc (Masters’ in Science in Medical Mycology degree) training of one of the co-investigators in the U.K. and higher level training of two postgraduates at CDC, Atlanta. As a result of multiple training activities and inclusion of both culture and non-culture based diagnostic methods, awareness of fungal infections among Pakistani clinicians has improved.
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2011 Show summary || Hide summary
A reduce in the budget caused 4-6 months delay for the project to start. In mid 2011, the project team started and collected more than 700 clinical fungal isolates and conducted preliminary analysis on the samples. They have been working in the direction to establish and develop proficiency in antifungal susceptibility testing for various spp of Candida. New equipment has been chosen and the team was waiting for funds to place the order.
2012 Show summary || Hide summary
On March 14, 2012, Dr. Zafar and her colleagues at AKU organized a continuing medical education workshop on “Challenges in diagnosis and management of fungal infections.” Some 200 participants attended, which including family physicians, dermatologists, medical residents, research ID fellows. On the research side of the project, 50 invasive strains were collected from blood, wounds, cerebrospinal fluid, and deep tissues between November 2011 and March 2012. Dr. Zafar’s lab has collected a total of 945 strains from 2006 to 2012. Two projects have been initiated for the identification and susceptibility testing of invasive yeasts directly from positive blood culture bottles and sterile body fluids with microscopic evidence of fungal infection. As of April 2012, 30 samples have been tested. Collaborative work with partner institutes has been further strengthened, with training provided for their technical staff and junior microbiologists. A joint publication by the Pakistani and U.S. researchers on the project (“Molecular identification of invasive yeasts including Candida in Pakistan: limitations of phenotypic identification”) has been accepted for publication by the Journal of the Pakistan Medical Associations
. The -700C° freezer being provided to AKU under this project was reported to have been shipped and arriving soon as of the time the most recent quarterly report was submitted (April 2012).
In the coming months, the researchers will continue their lab work, and they also plan to organize an advanced-level five-day mycology workshop for 15-25 candidates September 3-7, 2012. This workshop will be designed for junior microbiologists and microbiology residents, ID fellows and laboratory workers engaged in mycology laboratory work. They also plan to organize one-day workshops on the identification of yeasts and molds in other cities of Pakistan such as Lahore and Islamabad.
2013 Show summary || Hide summary
The project tasks were mainly carried out on the Pakistani side during spring 2013. The team continued with the collection work of clinical fungal isolates among which 30 yeasts and 6 molds were identified and stored for further workup. Meantime, the research team completed susceptibility testing for 100 isolates using disc diffusion method and 86 isolates using Yeast one sensititer method. On Feb 22, the team organized a workshop “Diagnosis of Fungal Infections in Clinical Laboratory” at Sheikh Zayed Hospital in Lahore. 28 participants including a diverse mix of medical microbiologists, laboratory technologists, infectious disease physicians and a few medical students from Lahore, Multan, and Rawalpindi attended the workshop. After the workshop, three presentations on this project were presented at the Annual Conference on Infectious Diseases Society of Pakistan on Feb 22-23 at Lahore. Two manuscripts writing are currently in process.
To determine the spectrum of fungal pathogens associated with invasive fungal disease in the country, the team continues the process of gathering isolates across the country. During the 2nd quarter, a total of 53 invasive isolates including 46 yeasts and 7 molds were saved. Under Dr. Brandt’s supervision, Dr. Kauser Jabeen completed the bench work for molecular identification of molds that are responsible for cerebral mycosis (fungal infection of brain) from formalin fixed paraffin embedded tissues. Regarding the second objective of the project: to determine the frequency of occurrence and antifungal resistance among specific species of Candida associated with invasive disease, and to track trends in their prevalence, the research team has been engaging in the following activities, the team analyzed antifungal susceptibility data of 100 isolates by using disc diffusion test and completed antifungal susceptibility test by Yeast one sensi-tier method for 165 isolates. The antifungal susceptibility data collected is currently being analyzed. For the next step, they plan to use these data to determine the prevalence of antifungal resistance, and later correlate the data with antifungal drug practices within the collaborating centers to promote rational antifungal utilization, especially in areas such as hospital ICUs where resistance can develop quickly. In addition, based on recent data and publications, the team will plan a seminar to take place in next quarter. The seminar will engage medical microbiologists and ID physicians to take initiatives to improve antifungal management and stewardship in the country through development of policies and guidelines.
In April, Dr. Seema Irfan, a faculty member of AKU, visited CDC to learn “advance molecular techniques to identify molds”. She performed molecular identification of 35 invasive molds that were isolated from this study. In addition, Dr. Irfan attended a hands-on workshop on “Laboratory Identification of Emerging Pathogenic Molds” from April 16th to 18th (courtesy of Dr. Brandt).