Pathology Commons^™

Glycogen Storage Diseases-Time To Flip The Outdated Diagnostic Approach Centered On Liver Biopsy With The Molecular Testing, Sibtain Ahmed, Bushra Afroze

Department of Pathology and Laboratory Medicine

The glycogen storage diseases (GSDs) are a group of inherited metabolic disorders that result from a defect in any one of several enzymes required for either glycogen synthesis or glycogen degradation. The traditional diagnostic approach is based on the invasive hepatic or muscle biopsies, which are neither cost effective nor convenient. Molecular (gene testing) has emerged over the course of past few years as a robust alternative diagnostic tool, which not only confirms the diagnosis of GSDs but also clearly differentiates the types of GSDs allowing the initiation of the type-specific appropriate treatment for the particular type of GSDs. The …

Use Of Pefloxacin As A Surrogate Marker To Detect Ciprofloxacin Susceptibility In Salmonella Enterica Serotypes Typhi And Paratyphi A, Safia Moin, Mohammad Zeeshan, Sidra Laiq, Ahmed Raheem, Afia Zafar

Department of Pathology and Laboratory Medicine

Objective: To determine the use of pefloxacin as a surrogate marker to detect fluoroquinolone (ciprofloxacin) susceptibility against Salmonella enterica serotypes Typhi and Paratyphi A.
Methods: The prospective, descriptive cross-sectional study was conducted at the Aga Khan University Hospital, Karachi, from September 2016 to March 2018, and comprised Salmonella Typhi and Paratyphi A isolates of blood cultures. Disk susceptibility tests and broth microdilution to test minimum inhibitory concentration were performed as per standard guidelines. Data was analysed using SPSS 21.
Results: Of the 138 isolates, 91(66%) were intermediate resistant to ciprofloxacin but were resistant to pefloxacin, 42(30%) were resistant to both …

Acute Mesenteric Thrombosis: A Hematologist Perspective, Bushra Moiz, Zaid Muslim, Zahraa Farrukh Siddiqui, Hasnain Zafar

Department of Pathology and Laboratory Medicine

No abstract provided.

Is It T3 Thyrotoxicosis? A Case Of Falsely Elevated Tri-Iodothyronine (T3) Levels Leading To A Diagnosis Of Multiple Myeloma, Nanik Ram, Saira Furqan, Sibtain Ahmed

Section of Diabetes, Endocrinology and Metabolism

We are presenting a case of falsely elevated T3 levels in a patient due to interference from monoclonal immunoglobulins. A 56-year-old, clinically euthyroid man referred to the endocrinology clinic of the Aga Khan university, Karachi Pakistan, for possible T3 thyrotoxicosis after thyroid function tests revealed total T3 >12.32 nmol/L (reference range 0.6-2.79), normal TSH, and total T4 level. There was a mismatch in clinical and laboratory parameters and preliminary laboratory results were suggestive of thyroid binding globulin abnormalities. Further evaluation in this context unmasked multiple myeloma. The presence of monoclonal immunoglobulins can lead to assay interference and spurious results. To …

Worldwide Network For Blood And Marrow Transplantation Recommendations For Establishing A Hematopoietic Stem Cell Transplantation Program In Countries With Limited Resources, Part Ii: Clinical, Technical, And Socioeconomic Considerations, Mahmoud Aljurf, Daniel Weisdorf, Shahrukh Hashmi, Amr Nassar, Eliane Gluckman, Mohamad Mohty, Doug Rizzo, Marcelo Pasquini, Mehdi Hamadani, Salman Adil

Department of Pathology and Laboratory Medicine

The development of hematopoietic stem cell transplantation (HSCT) programs can face significant challenges in most developing countries because such endeavors must compete with other government health care priorities, including the delivery of basic services. Although this is may be a limiting factor, these countries should prioritize development of the needed expertise to offer state-of-the-art treatments, including transplantation, by providing financial, technological, legal, ethical, and other needed support. This would prove beneficial in providing successful programs customized to the needs of their population and potentially provide long-term cost savings by circumventing the need for their citizens to seek care abroad. The …

Determinants Of Campylobacter Infection And Association With Growth And Enteric Inflammation In Children Under 2 Years Of Age In Low-Resource Settings, Md Ahshanul Haque, James A. Platts-Mills, Estomih Mduma, Ladaporn Bodhidatta, Pascal Bessong, Sadia Shakoor, Gagandeep Kang, Margaret N. Kosek, Aldo A M Lima, Zulfiqar Ahmed Bhutta

Department of Pathology and Laboratory Medicine

Campylobacter species infections have been associated with malnutrition and intestinal inflammation among children in low-resource settings. However, it remains unclear whether that association is specific to Campylobacter jejuni/coli. The aim of this study was to assess the association between both all Campylobacter species infections and Campylobacter jejuni/coli infections on growth and enteric inflammation in children aged 1-24 months. We analyzed data from 1715 children followed from birth until 24 months of age in the MAL-ED birth cohort study, including detection of Campylobacter species by enzyme immunoassay and Campylobacter jejuni/coli by quantitative PCR in stool samples. Myeloperoxidase (MPO) concentration in stool, …

Plasma Cell Leukemia Mimicking Hairy Cell Leukemia: Extended Role Of Immunophenotyping In Correct Diagnosis, Ayesha Majeed Memon, Natasha Ali

Department of Pathology and Laboratory Medicine

No abstract provided.

Prevalence Of Malaria Reported During Summer And Winter At A Tertiary Care Hospital In Karachi, Pakistan, Fazal M. Arain, Aisha Memon, Roohi Jamal, Ahmed Raheem Buksh, Mohammad Asim Beg

Department of Biological & Biomedical Sciences

This study was designed to determine the prevalence and type of malaria cases that presented throughout the year 2014 in a tertiary care hospital in Karachi, Pakistan. A total of 1099 cases, (377 females, 722 males) were reported. Plasmodium vivax (P. vivax) was discovered in 93.7% cases compared to 6.3% Plasmodium falciparum (P. falciparum). Based on the highest and lowest weather temperatures, in summer (June, July and August) and in winter (December, January and February) were differentiated. The number of cases were greater during summer months compared to winter. Interestingly, the ratio of P. falciparum to P. vivax during winter …

Perceptions Of Health Professionals Regarding Minimally Invasive Tissue Sampling (Mits) To Identify The Cause Of Death In Stillbirths And Neonates: Results From A Qualitative Study, Anam Shahil Feroz, Anum Shiraz Ali, Mohsina Noor Ibrahim, Elizabeth M. Mcclure, Shiyam Sunder Tikmani, Sayyeda Reza, Zahid Abbasi, Afia Zafar, Sameen Siddiqi, Sarah Saleem

Community Health Sciences

Background: Pakistan is considered to be one of the riskiest places in the world for childbirth as measured by its high stillbirth and neonatal mortality rates. Complete diagnostic autopsy remains the gold standard to determine the cause of death (CoD); however, it is not routinely implemented due to religious objections, sociocultural beliefs, limited resources and low demand from physicians and families. Recently, minimally invasive tissue sampling (MITS) using needle biopsies of multiple tissues to obtain tissue for histological examination and organism identification with PCR has been developed and promoted to determine CoD in low-resource areas. To ensure successful implementation of …

Methicillin Resistant Staphylococcus Aureus Outbreak In A Neonatal Intensive Care Unit, Seema Irfan, Imran Ahmed, Farida Lalani, Naureen Anjum, Nadia Mohammad, Maria Owais, Afia Zafar

Department of Pathology and Laboratory Medicine

The global and national burden of communicable and noncommunicable diseases continues to rise, thus making access to Healthcare workers (HCWs) colonized with methicillin-resistant Staphylococcus aureus (MRSA) may pose transmission risk to vulnerable patients including neonates. This study reports an MRSA outbreak in a level-II neonatal intensive care unit (NICU) of a secondary care hospital in Pakistan. Once identified, an infection control team from the parent hospital visited the facility, risk factors were listed and infection control measures taken to control the outbreak. Screening cultures of NICU staff and environmental cultures from NICU were obtained for the presence of MRSA. Five …

Labrad : Vol 45, Issue 3 - October 2019, Aga Khan University Hospital, Karachi

LABRAD - Departments of Pathology & Laboratory Medicine and Radiology Archives

• Therapeutic Drug Monitoring for Antibiotics in Infections
• Biomarkers of Sepsis
• Serum Procalcitonin Level - Marker of Bacterial Infection
• Bone Marrow Findings in Malaria
• Antibiogram: A Clinicians’ Reference for Antibiotic Selection
• Laboratory Diagnosis of Meningitis
• Detection of Pneumocystis Jirovecii by PCR
• Microbiology Quiz
• Radiology Pathology Correlation- Orthopedic Pathology
• Role of Imaging in the Diagnosis and Management of Hepatic Abscess
• The Best of the Past
• Microbiology Quiz’s Answer
• Polaroid

Infections In Patients With Multiple Myeloma Treated With Conventional Chemotherapy: A Single-Center, 10-Year Experience In Pakistan, Mohammad Faizan Zahid, Natasha Ali, Myra Nasir, Maria Haider Baig, Mustafa Iftikhar, Syed Usman Bin Mahmood, Arhama Malik, Sara Atif, Mohammad Asim Beg

Department of Pathology and Laboratory Medicine

Introduction: Multiple myeloma (MM) is a common hematologic malignancy with variable degrees of immunodeficiency. Disease- and treatment-related compromise of the immune system predisposes patients to infections, which are a major cause of morbidity and mortality.
Objective: We aimed to establish the incidence and main characteristics of infections in MM patients treated at our center over a 10-year period.
Method and results: Of the 412 patients retrospectively analyzed, 154 (37.4%) were documented to have at least one episode of infection and were included in this study. A total of 244 infectious episodes were documented. The most common site of infection was …

Xpert® Mtb/Rif Assay On Formalin-Fixed Paraffin-Embedded Tissues In The Diagnosis Of Extrapulmonary Tuberculosis, Allan Njau, Samuel Gakinya, Shahin Sayed, Zahir Moloo

Pathology, East Africa

Background: Diagnosis of extrapulmonary tuberculosis continues to be a challenge due to the complexity of the causative organism and the wide array of pathologic features seen in this infection. Xpert MTB/RIF can be used on fresh or frozen tissue specimens for diagnosis of tuberculosis with good results. However, there is little data on its use with formalin-fixed paraffin-embedded (FFPE) tissues.

Objectives: The aim of this study was to demonstrate the potential utility of Xpert MTB/RIF and to compare its performance to Ziehl-Neelsen staining for the detection of Mycobacterium tuberculosis from FFPE tissues using histological features from haematoxylin and eosin staining …

Vitamin D Status And Risk Of Incident Tuberculosis Disease: A Nested Case-Control Study, Systematic Review, And Individual-Participant Data Meta-Analysis, Omowunmi Aibana, Chuan-Chin Huang, Said Aboud, Alberto Arnedo-Pena, Mercedes C. Becerra, Juan Bautista Bellido-Blasco, Ramesh Bhosale, Roger Calderon, Rabia Hussain, Najeeha Talat Iqbal

Department of Pathology and Laboratory Medicine

Background: Few studies have evaluated the association between preexisting vitamin D deficiency and incident tuberculosis (TB). We assessed the impact of baseline vitamins D levels on TB disease risk.
Methods and Findings: We assessed the association between baseline vitamin D and incident TB in a prospective cohort of 6,751 HIV-negative household contacts of TB patients enrolled between September 1, 2009, and August 29, 2012, in Lima, Peru. We screened for TB disease at 2, 6, and 12 months after enrollment. We defined cases as household contacts who developed TB disease at least 15 days after enrollment of the index patient. …

Antimicrobial Sensitivity Pattern, Demographic Findings And Risk Factors Amongst Meningitis And Non-Meningitis Invasive Streptococcus Pneumoniae At Aga Khan University Hospital Clinical Laboratory, Karachi, Pakistan, Seema Irfan, Joveria Farooqi, Afia Zafar, Haresh Kumar

Department of Pathology and Laboratory Medicine

Objective: To determine the resistance rate of penicillin and ceftriaxone amongst invasive meningitis and nonmeningitis isolates of streptococcus pneumoniae. Methods: The prospective cross-sectional study was conducted from January 2011 to March 2014 at the Clinical Microbiology Laboratory of Aga Khan University, Karachi, and comprised all invasive strains of streptococcus pneumoniae. Penicillin and ceftriaxone susceptibilities were performed and interpreted based on minimum inhibitory concentration breakpoints recommended by Clinical and Laboratory Standards Institute guidelines. Data was analysed using Stata 12.
Result: There were 163 strains isolated from sterile body fluids of 109 patients. Of the total, 46(28%) samples were meningitic while 117(72%) …

Beyond Sequencing: Re-Visiting Annotations For Pjl As A Test Case, Waqasuddin Khan, Aisha Ghani, Muhammad Bilal Azmi, Safina Abdul Razzak

Department of Paediatrics and Child Health

Objectives: Current developments in sequencing techniques have enabled rapid and high-throughput generation of sequence data. however, there is a growing gap between the generation of raw sequencing data and the extraction of meaningful biological information. variant annotation is a crucial step in the analysis of genome sequencing data. incorrect or incomplete annotations can cause researchers to dilute interesting variants in a pool of false positives. we require consistent, accurate and reliable annotation of variants for making diagnostic and treatment decisions. current annotation depends on the set of transcripts, and software used can be managed, with sufficient care, in the research …

Metastatic Breast Cancer In Kenya: Presentation, Pathologic Characteristics, And Patterns-Findings From A Tertiary Cancer Center, Etoroabasi Ekpe, Asim Jamal, Jasmit Shah, Judith S. Jacobson, Shahin Sayed

Internal Medicine, East Africa

Purpose: The purpose of this research was to describe the sociodemographic and clinical characteristics of Kenyan women with metastatic breast cancer diagnosed and treated at Aga Khan University Hospital in Nairobi, Kenya from 2012 to 2018.

Patients and Methods: We reviewed charts of Kenyan women with metastatic breast cancer and analyzed sociodemographic data, breast cancer risk factors, and tumor characteristics associated with stage at diagnosis, receptor status (ie, estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2 [HER2]), and site of metastasis using χ2, analysis of variance, two-sample t tests, and logistic regressions.

Results: A total of 125 …

Acinetobacter Infections: A Retrospective Study To Determine In Hospital Mortality Rate And Clinical Factors Associated With Mortality, Rajiv Patel, Jasmit Shah, Gunturu Revathi, Wangari Siika, Reena Shah

Internal Medicine, East Africa

A retrospective case series of acinetobacter infections at a tertiary hospital in Nairobi was conducted to determine the mortality rate and factors associated with mortality. Over an eight-year period, 80 clinically significant infections were identified. The majority of infections were ventilator-associated pneumonia (40%) and bloodstream infections (30%). Eighty-six percent of the isolates were multi-drug resistant. The mortality rate in the study cohort was 45%. Twelve patients grew Acinetobacter spp. within 48 h of hospitalization, and three of these patients had no prior healthcare contact. The mean Sequential Organ Failure Assessment score was associated with mortality from acinetobacter infections.

Labrad : Vol 45, Issue 2 - July 2019, Aga Khan University Hospital, Karachi

LABRAD - Departments of Pathology & Laboratory Medicine and Radiology Archives

• Novel Molecular Technique for Identifying Respiratory Tract Pathogens
• Role of Serum Galactomannan (GM) Assay in Diagnosing Invasive Aspergillosis (IA)
• Factor VIII Inhibitor – A Diagnostic Approach
• PET/CT Hybrid Imaging Technology at Aga Khan University Hospital
• Diagnostic Tests for Von Willebrand Disease
• Iron Deficiency Anemia
• Sweat Testing for Diagnosis of Cystic Fibrosis
• Flow Cytometric Identification of Abnormal B-Cells
• Direct Immunofluorescence in Bullous Skin Disorders
• Radiology-Pathology Correlation; Orthopedic Pathology
• Fecal Elastase: A Marker For Exocrine Pancreatic Function
• Edward Syndrome: Rare Autosomal Aneuploidy
• Sirolimus in Renal Transplant
• Latest Trends in Clinical Laboratory Science Technology
• Radiology-Neuropathology Correlation
• Nuchal Translucency Scan
• Bio-risk Management System in …

Unique Classification Of Parathyroid Dysfunction In Patients With Transfusion Dependent Thalassemia Major Using Nomogram: A Cross Sectional Study, Hafsa Majid, Lena Jafri, Jamsheer Jehangir Talati, Sibtain Ahmed, Bushra Moiz, Aysha Habib Khan

Department of Pathology and Laboratory Medicine

Introduction: Hypoparathyroidism is a rare complication of iron overload in patients with transfusion dependent β thalassemia major (β-TM). We aim to determine the prevalence of parathyroid dysfunction in patients with β-TM.
Methods:Diagnosed cases of transfusion dependent β-TM between 5 and 17 years of age were recruited from outpatient clinics of a non-profit organization in Karachi, Pakistan. Blood and urine samples were collected in fasting to determine Ca, P, Alb, Mg, Cr 25OHD and iPTH. Patients were grouped on the basis of upper and lower levels of Ca, 25OHD and iPTH for assessing parathyroid dysfunction into primary hypoparathyroidism [low calcium …

Current Laboratory Techniques Commonly Used For The Detection Of Molecular Biomarkers And Potential Technologies On The Horizon, Muhammad Shariq Shaikh, Zeeshan Ansar Ahmed

Department of Pathology and Laboratory Medicine

No abstract provided.

Antimicrobial Susceptibility Against Metronidazole And Carbapenem In Clinical Anaerobic Isolates From Pakistan, Kauser Jabeen, Yusra Shafquat, Joveria Farooqi, Kiran Mehmood, Seema Irfan, Rumina Hasan, Afia Zafar

Department of Pathology and Laboratory Medicine

Background: Globally metronidazole and carbapenem resistance in anaerobic organisms is increasing necessitating continuous surveillance to guide selection of empirical treatment. In this study we have determined metronidazole resistance in anaerobes using MIC Evaluator strips (M.I.C.E strips). Carbapenem resistance was evaluated only in metronidazole resistant isolates.
Material and methods: The study was conducted at the Aga Khan University (AKU) Hospital laboratory, Karachi, Pakistan (2014–2017). Metronidazole and imipenem resistance was evaluated using M.I.C.E strips and minimum inhibitory concentrations (MICs) were interpreted using Clinical Laboratory Standards Institute (CLSI) criteria. Clinical details including demographics, prolonged hospital stay, malignancy, transplant, dialysis, diabetes, site of infection …

Solitary Brain Metastasis: A Rare Initial Presentation Of Prostate Carcinoma, Asim Hafiz, Muneeb Uddin Karim, Bilal Mazhar Qureshi, Adnan Jabbar, Zubair Ahmad

Department of Radiation Oncology

Cerebral metastasis as an initial clinical presentation of prostate carcinoma is extremely rare. Usually, patients have widespread metastasis in the body before presenting with brain metastasis. In the absence of extensive metastasis, especially without bony metastasis, only brain metastasis is an unusual presentation of the disease. We report a case of a 59-years-old patient who presented with a lack of concentration and decreased vision. Magnetic resonance imaging (MRI) of the brain revealed a large right parietal-occipital space-occupying lesion. He underwent surgery and the pathological diagnosis of the tumor turned out to be metastatic prostate carcinoma. Further evaluation by a whole-body …

Analysis Of Candida Auris Fungemia At A Single Facility In Kenya, Rodney Adam, Gunturu Revathi, Nancy Okinda, Melanie Fontaine, Jasmit Shah, Elizabeth Kagotho, Mariana Castanheira, Michael A. Pfaller, Daniel Maina

Pathology, East Africa

Objectives: Candida auris emerged as a human pathogen in 2009 and has subsequently been identified around the world as a cause of invasive candidiasis. We did an analysis from a single institution in order to analyze risk factors and outcomes for C. auris candidemia.

Methods: Patients with candidemia were identified by the electronic medical record and reviewed for risk factors and outcome. Candida isolates were identified by Vitek2 as Candida haemulonii, but species determinations for 21 of the isolates using published molecular and proteomic methods identified all as C. auris.

Findings: From September 2010 to December 2016, C. auris accounted …

Blood Film Says It All! Rare Case Of Congenital Ttp Misdiagnosed As Itp, Ayesha Majeed Memon, Natasha Ali

Department of Pathology and Laboratory Medicine

We report a case of a 16-year-old female who presented with bleeding diathesis. Peripheral blood film examination was consistent with microangiopathic hemolytic anemia with 7% fragmented red blood cells. The ADAMTS13 level was 40 ng/ml (reference range: 630-850 ng/ml). She responded to plasma exchange therapy and methylprednisolone and was discharged in a stable condition.

Mutational Landscape Of Head And Neck Squamous Cell Carcinomas In A South Asian Population, Kulsoom Ghias, Sadiq S. Rehmani, Safina Abdul Razzak, Sarosh Madani, M Kamran Azim, Rashida Ahmed, Mumtaz J Khan

Department of Biological & Biomedical Sciences

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer type globally and contributes significantly to burden of disease in South Asia. In Pakistan, HNSCC is anmong the most commonly diagnosed cancer in males and females. The increasing regional burden of HNSCC along with a unique set of risk factors merited a deeper investigation of the disease at the genomic level. Whole exome sequencing of HNSCC samples and matched normal genomic DNA (n=7) was performed. Significant somatic single nucleotide variants (SNVs) were identified and pathway analysis performed to determine frequently affected signaling pathways. We identified significant, novel …

Chimeric Antigen T Cell Receptor Treatment In Hematological Malignancies, Natasha Ali

Department of Pathology and Laboratory Medicine

No abstract provided.

Safety And Efficacy Of Bendamustine In The Conditioning Regimen For Autologous Stem Cell Transplantation In Patients With Relapsed/Refractory Lymphoma, Munira Moosajee, Samad Jehangir, Sobia Sawani, Tariq Muhammed, N. Ali, Usman Shaikh, Salman Adil

Section of Haematology/Oncology

Background: Bendamustine is an attractive option for the management of both de novo and relapsed lymphomas. It is being increasingly used in the conditioning regimen for autologous stem cell transplantation (SCT) and can be an alternative to the traditionally-used carmustine. In this study, we aimed to determine the safety and efficacy of bendamustine in the conditioning regimen for autologous SCT in refractory/relapsed lymphomas.
Methods: We designed a descriptive study to evaluate bendamustine in combination with etoposide, cytarabine, and melphalan (BeEAM) in the conditioning regimen for autologous SCT.
Results: Fourteen patients (median age, 28 yr) with Hodgkin's lymphoma (HL) (N=8), non-Hodgkin's …

Perceptions Of Parents And Religious Leaders Regarding Minimal Invasive Tissue Sampling To Identify The Cause Of Death In Stillbirths And Neonates: Results From A Qualitative Study, Anam Shahil Feroz, Mohsina Noor Ibrahim, Elizabeth M. Mcclure, Anum Shiraz Ali, Shiyam Sunder Tikmani, Sayyeda Reza, Zahid Abbasi, Jamal Raza, Haleema Yasmin, Khadija Bano, Afia Zafar, Sameen Siddiqi, Robert L. Goldenberg, Sarah Saleem

Community Health Sciences

Background: Recently, the minimal invasive tissue sampling (MITS) procedure has been developed to support determination of the cause of death as an alternate to conventional autopsy, especially in countries where complete diagnostic autopsy is not routine. To assess the feasibility of implementation of the MITS procedure for a study to determine cause of death in premature births and stillbirths in south Asia, we explored the views and perceptions of parents and religious leaders on the acceptability of MITS.
Methods: A qualitative study was conducted at the National Institute of Child Health (NICH) hospital of Karachi, Pakistan. Focus group discussions (FGDs) …

Diffuse Large B-Cell Lymphoma In Kenya: Myc, Bcl2, And The Cell Of Origin, Jonathan Wawire, Shahin Sayed, Zahir Moloo, Aliyah R. Sohani

Pathology, East Africa

Purpose: Diffuse large B-cell lymphoma (DLBCL) is the most commonly diagnosed non-Hodgkin lymphoma in adults in Kenya. Cell of origin (COO) and double expression of MYC and BCL2 are two important prognostic factors for DLBCL. A small subset (5% to 10%) of DLBCL cases show positivity for CD5 and are associated with poor prognosis, whereas CD30 antigen, seen in up to 10% of cases, may be a useful target for therapy. We sought to determine the prevalence of MYC/BCL2 double expression, COO, and proportion of Epstein-Barr virus positivity among patients with DLBCL diagnosed at a tertiary referral laboratory in Kenya. …