Dr. Bushra Moiz, Professor and Service Line Chief,​​

Department of Pathology and Laboratory Medicine​

Call of duty during torrential rains i​​n Karachi

Aneeta got up early in the morning as usual on July 25th to go to work. She works as a technologist in clinical laboratories of Aga Khan Hospital. Her home is far away, and she must travel an hour in a public bus to reach the workplace. Her father suggested her not to leave as heavy rains are anticipated to conti​​​nue for a few more days. Aneeta responded that she must leave and relieve her colleagues from work as many have worked for more than 16 hours on the previous day. As she left for her duty, she found the havoc caused by rains. The roads were full of water, buses and cars were half submerged, and for the first time she understood the meaning of urban flooding.

Aneeta is just one of the laboratory staff who worked tirelessly during recent rains and thunderstorms. While the city life was paralyzed, shops were shut down, people were afraid to leave their homes, there was a total calm in the laboratory. Staff was busy like any other working day. Patients' samples were collected as usual, no patient was turned away for the want of staff. All the tests were performed and not a single report got delayed. The laboratory continued to receive the usual workload as patients needing urgent diagnostics can't wait for an improvement in weather conditions. I observed a great sense of obligation and collegiality; staff offered to stay back for those who could not arrive. The others risk their lives to join the workforce for relieving the staff who had worked for more than usual hours. Every cloud has a silver lining and the abysmal situation in the city provided an opportunity for our staff to demonstrate professionalism and teamwork. Of course, our staff is never reluctant to respond to the call of duty, be it any adverse condition or extreme climate change.  ​


​​​​Dr. Joveria Farooqi, Assistant Professor and Consultant Microbiologist

Department of Pathology and Laboratory Medicine​

World Hepatitis Day

​Hepatitis is the inflammation of liver tissue, resulting in yellow discoloration of skin and eyes, and fever. There are several types of hepatitis, divided according to their causes. The most common cause of hepatitis is infectious, mainly by a group of viruses that​ specifically infect liver e.g., Hepatitis A, B, C, D and E viruses, but sometimes it may occur as part of another infection, like Dengue, Zika, Yellow fever, Crimean Congo fever, malaria, bacterial sepsis etc. Non-infectious hepatitis is usually related to drug toxicity. Hepatitis A, B, D and E can cause acute hepatitis, while B and C can cause chronic hepatitis, liver failure and even liver cancer. Viral hepatitis with HAV, HEV and HBV without HDV is usually subclinical or mild, but sometimes, it can become severe enough to result in hospitalization and possibly even death. 

Globally, viral hepatitis resulted in 1.4 million deaths in 2017, with more than 97% related to Hepatitis B and C, including liver failure and cancer (1). In Pakistan, approximately 12 million people suffer from hepatitis B or C, but the majority remain undiagnosed and untreated, leading to continued transmission in the population, complications, and death (2).

It is, therefore, important to diagnose hepatitis early, so that patient can be appropriately managed and monitored to determine response to treatment, and effectively vaccinate uninfected individuals against HBV.

Aga Khan Clinical Laboratories offer tests to diagnose early disease and also assess liver damage through hepatic enzyme levels and blood clotting, as well as specific tests for viral hepatitis. Different Hepatitis B antigens and antibodies can identify if the patient has acute or chronic HBV infection, whether they are infective, recovered, or immune. Antibodies against HAV, HCV, HDV and HEV can presumptively diagnose infection with these agents, while detecting DNA or RNA belonging to Hepatitis B, C and D viruses in serum can confirm it. Measuring the number of virus copies in blood over time can also guide physicians in how well the patient is responding to treatment.

HAV, HEV are transmitted through eating and drinking contaminated foods and drinks, while Hepatitis B, C and D are transmitted by exposure to infected blood and its products, or injury with contaminated sharp objects. The best way to prevent HBV and HCV infection is to adopt sharp-safety practices whenever dealing with blood products, needles, and during surgery through use of gloves, hand hygiene and safe handling of used items and equipment. For oral transmission of HAV and HEV, good hygiene and consuming safe food and water are the most effective measures. 

Vaccination is available for HBV and HAV. HBV vaccine is recommended at any age, and boosters may be necessary after 3 years if HBV antibody levels fall. HAV vaccine is offered to individuals travelling to countries with high rates of HAV infection from countries where HAV infection is rare. 


1. Thomas DL. Global Elimination of Chronic Hepatitis. N Engl J Med. 2019 May 23;380(21):2041-2050. doi: 10.1056/NEJMra1810477. PMID: 31116920.

2. WHO EMRO | Prevention and control of hepatitis | Programmes | Pakistan. Last updated 2022​


Dr. Lena Jafri, Section Head, Chemical Pathology

Metabolomics Book Club - A New Teaching Learning Strategy in Chemical Pathology

My interests in metabolomics

Metabolomics is defined as the complete analysis of metabolites in a biological specimen. It is an evolving technology that holds promise to inform the practice of precision medicine. Developments in the techniques of analytical clinical chemistry and metabolomics are the source of the rapid evolution of a new omics era. 

The introduction of the science of metabolomics in the Section of Chemical Pathology at Aga Khan University, Karachi Pakistan pertains to important platforms: analytical techniques like GCMS, FTIR, HPLC and LCMSMS. With the introduction of mass spectrometers and HPLC in the section almost 8-9 years ago metabolic profiling of patients suspected of having inherited metabolic disorders can be done. We have screened > 22000 high risk children and adults in past 8 years and have identified around 40 disorders using these cutt​ing-edge technologies. The Biochemical Genetics Laboratory in the section has established some targeted metabolomics panels for quantitation of selected groups of metabolites using mass spectrometry specifically for inherited metabolic disorders and new-born screening (LCMSMS). My interest in this field grew as I got involved in reviewing the mass spectrometer chromatograms and reporting these rare disorders.

The Book Club

To facilitate understanding of metabolomics and to e​​​nhance the science of metabolomics amongst pathologists, residents, technologists and scientists a monthly activity of 'Metabolomics Book Club' was initiated in the section of Chemical Pathology, Department of Pathology and Laboratory Medicine at Aga Khan University. The method of teaching and learning was that the participants facilitate the discussion and are at the same level of understanding by the end of the one-hour long monthly session.

Selected Book

After a thorough rev​​iew, “Metabolomics: From Fundamentals to Clinical Applications" was selected to be the book for discussion. It provides a comprehensive review of th​e journey of metabolomics and carries the readers through the basic concepts and clinical applications of metabolomics in medicine. Each chapter focuses on a separate aspect of metabolomics, from sample preparations and recent advancements to data interpretation and statistical analysis. This book also focuses on surveying and providing a gap analysis on metabolic phenotyping with a focus on targeted and untargeted based metabolomics from an instrumental, technical point-of-view discussing the state-of-the-art instrumentation, pre- to post- analytical aspects as well as an overall future necessity for biomarker discovery. The book serves as an updated guide for experienced researchers of metabolomics, while also providing essential information for novices in the field. As such, this book served to be the perfect fit for the diverse participants in the book club on metabolomics.​


​Dr Zaib Un Nisa 

Chief Resident , Department of Pathology and Laboratory Medicine

 (January, 2022 - Present)​

Year 4 Resident, Section of Chemical Pathology

​"The Unsung Warriors" ​

At the beginning of 2020, I had just entered my second year of postgraduate residency training in Chemical Pathology at Aga Khan University. After my first year of learning to get used to the ropes, I was slowly getting used to the grueling routine of residency. I naively thought I was ready for the challenges that would come my way, but little did I know that something as unpredictable as COVID-19 was on the cards. 

When a nationwide lockdown was announced, it seemed like we were thrown into an apocalypse. Initially, I was among those staff members who were detached from routine laboratory work due to limited staff attendance subsequent to the lockdown. Even though I enjoyed the brief unplanned break and stayed with my family in my hometown of Quetta, I was virtually connected to the laboratory and performed my required duties. Attending lectures and regular staff trainings online was also anxiety inducing as none of us were prepared for this shift to digitalization, but ultimately we learned how to cope with the change. 

When I returned to my workplace in April, I felt like I was stepping into a prison. The environment that I had gotten accustomed to working in was functioning in a limited capacity. From my perspective as a human, I could see how the lockdown had created psychological insecurities in patients about visiting a laboratory which could act as a high-risk environment for catching disease.

However, as a front-line warrior I could also observe how the patient inflow had been affected. Like all laboratories, AKUH clinical laboratory also had a critical role to play in the diagnosis and surveillance of COVID from the beginning, however, it also acted as a referral center for COVID-19 testing, and thus catered to test requests from across the country. This resulted in the phlebotomy staff frequently falling short. Many of our junior residents were called to perform nasopharyngeal swab testing in the on-site COVID testing area, which also affected our residents’ on-call rota. A sense of doom hung heavy over our heads as all of us were among those highly exposed, and the masked faces of friends merely looked like a magnified COVID-19 machine. As a hostelite, my mobility was doubly restricted, and communication with peers and friends was extremely limited, which added to the depressing emotions. The gym and sports track that I previously used to unwind at was also closed and going back to my hostel room only reminded me of what challenges the next day had in store for me. It felt like there was no break. 

But ultimately, I realized that COVID was here to stay. And when I begrudgingly accepted the change I found that it became more palatable. In my fellow residents, I found long-lasting friendships. Our ability to quickly think of solutions and create opportunities out of disruptions even surprised us as we were able to knock problems out of the park. 

I am now in my fourth year of residency as the Chief Resident, in my final tuning to become a chemical pathologist. I strongly believe that the roadblocks that COVID-19 threw our way have prepared me for all kinds of unpredictability. Show me a river, I’ll make it an ocean, throw me a rock, I’ll make it a tunnel!


​Dr Sana Brohi

​Chief Resident

(January, 2021 to December, 2021)

"You cannot separate passion from pathology any more than you can separate a person’s spirit from his body” - Richard Selzer

On behalf of Pathology residents, I welcome you to the webpage of the Department of Pathology and Laboratory Medicine, Aga Khan University (AKU), Karachi, Pakistan. 


​​Each year, the department offers residency in its four sections i.e Chemical pathology,​ Haematology, Histopathology and Microbiology. As we all know, residency training has a huge impact on our career; hence residency in Pathology and Laboratory Medicine at AKU allows residents to work with challenging cases in the presence of expert faculty. Each year, a number of residents are enrolled in the department who are offered focused and in-depth learning environments in each section. Residents are encouraged to use their clinical judgment to recommend or approve laboratory tests. ​The department also motivates residents to do research and further develop their​ academic and clinical skills through rotations. The training programme involves individual sign-out sessions with faculty; teaching sessions including didactic lectures, slide sessions, and journal clubs, inte​rdepartmental sessions such as multidisciplinary tumor boards as well as faculty forums on monthly basis, where national and international speakers are invited to deliver talk on wide range of topics covering different aspects of pathology. There is a good workspace for residents, including desks, microscopes, and computers. There is always a senior resident around if a junior resident has a query about a specimen or case, to get advice on a diagnosis or need to switch calls. Similarly, our faculty is always available in assisting residents. Hence, residency at AKU is a unique experience and it's an outstanding place to train for a career in pathology. 


​​A​ Journey of 30-Long years at Section of Histopathology

Dr Shahid Pervez​​

I joined Aga​ Khan University three decades ago on June 16th, 1991 as ‘Assistant Professor’ and in June 15, 2021, completed thirty years of my full-time service here. I must admit that if it was not for AKU, like so many others, in all probability I would have ended up somewhere outside Pakistan. So, what is special about AKU which kept me here to date?

The reason wasn't financial remuneration as I started on a very modest salary package and there were many opportunities around the globe offering far better financial packages. Second common reason quoted by many who come back from abroad is to live with their parents; this was again not the case for me as my father passed away when I was only 19 years old and my mother was with me and willing to travel abroad. In a nutshell it was foremost living on my own soil and serving my own people and country in my humble capacity even if it was a drop in the ocean and secondly it was the Pathology department of AKU, located in a 3rd world country but with a vision and infrastructure of the first world. It has been most fulfilling for me to have an opportunity to teach and train some of the brightest minds of the nation at undergraduate, graduate, and postgraduate levels as well as practice a specialty at a place where there is so much diversity. I have an invaluable opportunity to interact with highly motivated young medical students and FCPS trainees behind the microscope, supervise PhD students, work on original local research and publish and disseminate knowledge. This is my true legacy; to see my students working and serving at various leadership positions around the globe. Last but not the least, to be able to make a small contribution to patient management. By clinching a correct diagnosis, we pathologists who largely work behind the scenes make conclusive grounds for a proper treatment to follow, hence save lives.​​


A journey to a more compassionate way of living 

​Shamsha Punjwani

I am struggling, burnt out, anxious and overwhelmed about daily life. I dive into projects and check tasks off my list, trying to climb my way up to the next level of success. Yet I somehow still never feel like enough, no matter how many achievements acquired. It seems I am always working on something else, yet I am never satisfied. I yearn for the sweet taste of approval and acknowledgment, while disconnecting myself from the world around me. Welcome to my blog. Many wonderful thing have happened to me in the department, including accomplishments, plans, and progress on initiatives. I have served in many roles and have had a wonderful career.

I think we can all relate to feeling this way at some point in our lives. I know I can. For a long time, I did everything I could to prove th​at I was worthy of something. However, finally realizing that no matter how many times I worked on changing the world around me, I still didn’t feel good internally. Changing everything on the outside simply did nothing to change what I thought of myself on the inside. That’s what really counts, how you feel about yourself that is  really important. 

Well, there are a few ways to feel about yourself 

  1. ​I became an observer of my own life: 

  2. I wanted to know the true me by self-reflection

  3. Influencing people in a positive way 

  4. Learning to be content 

Embrace that recollection. Try and find it everyday. You’ll find that you feel more refreshed and full of energy to tackle challenges of the day or whatever comes up.

Good luck and learn to use mindfulness! 

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