Pathology Commons^™

Allergic Bronchopulmonary Aspergillosis Misdiagnosed As Smear Negative Pulmonary Tuberculosis; A Retrospective Study From Pakistan, Nousheen Iqbal, Muhammad Dawood Amir Sheikh, Kauser Jabeen, Safia Awan, Muhammad Irfan

Section of Pulmonary & Critical Care

Background: Undiagnosed allergic bronchopulmonary aspergillosis (ABPA) can lead to chronic persistent symptoms. In country like Pakistan where tuberculosis (TB) is endemic, a significant proportion of ABPA patients are misdiagnosed as smear negative TB before reaching a diagnosis of ABPA due to chronicity of symptoms.This lead to empiric use of ATT(Anti-tuberculous therapy) and delay in primary diagnosis. The aim of the study is to determine such proportion of ABPA patients.|
Material and methods: This retrospective study was conducted at the outpatient pulmonology clinic of a tertiary care hospital in Karachi, Pakistan from January 2017 to December 2018. Xpert MTB/Rif, TB smear …

Is Covid-19 Impacting Cancer Screening In Pakistan? An Observational Study Of Cancer Screening Test Requests During The Pandemic, Sibtain Ahmed, Muhammad Abbas Abid, Noureen Niaz Ali, Junaid Ahmed, Imran Siddiqui

Department of Pathology and Laboratory Medicine

Background: The purpose of this study is to assess how the COVID-19 pandemic affected cancer screening at a large tertiary care setting in the city of Karachi, the third largest city in the world, and to identify if there has been any decrease in cancer screening during the ongoing pandemic.
Methods: A retrospective observational study was conducted at the clinical chemistry laboratory at the Department of Pathology & Laboratory Medicine, Aga Khan University Hospital (AKUH), Karachi Pakistan. Data for test volumes was extracted from the Integrated Laboratory Management System (ILMS) for the following tumor markers: CA19 Carbohydrate Antigen 19-9 (CA …

Availability Of Essential Diagnostics In Ten Low-Income And Middle-Income Countries: Results From National Health Facility Surveys, Harika Yadav, Devanshi Shah, Shahin Sayed, Susan Horton, Lee F. Schroeder

Pathology, East Africa

Background: Pathology and laboratory medicine diagnostics and diagnostic imaging are crucial to achieving universal health coverage. We analysed Service Provision Assessments (SPAs) from ten low-income and middle-income countries to benchmark diagnostic availability.

Methods: Diagnostic availabilities were determined for Bangladesh, Haiti, Malawi, Namibia, Nepal, Kenya, Rwanda, Senegal, Tanzania, and Uganda, with multiple timepoints for Haiti, Kenya, Senegal, and Tanzania. A smaller set of diagnostics were included in the analysis for primary care facilities compared with those expected at hospitals, with 16 evaluated in total. Surveys spanned 2004–18, including 8512 surveyed facilities. Country-specific facility types were mapped to basic primary …

Atypical Involvement Of Central Nervous System In Classic Hodgkin Lymphoma: A Case Report, Shanila Ahmed, Babar Irfan, Muhammad Raza, Ghulam Haider

Section of Haematology/Oncology

Background: Hodgkin lymphoma is a systemic disease that commonly involves the cervical, supraclavicular, and mediastinal lymph nodes. The involvement of central nervous system in Hodgkin lymphoma is extremely rare, and diagnosis is usually established using distinct morphological and immunohistochemical staining on the tissue biopsied. Extranodal presentation of HL is a rare occurrence. It has been evident that prognosis is encouraging in patients with disease that is limited to just central nervous system initially or as relapse, compared with involvement of multiple sites of relapse.
Case presentation: We herein report a case of a 35-year-old South-East Asian male with relapsed Hodgkin …

Role Of Gut Microbiome In Covid-19: An Insight Into Pathogenesis And Therapeutic Potential, Ikram Hussain, Gabriel Liu Yuan Cher, Muhammad Abbas Abid, Muhammad Bilal Abid

Department of Pathology and Laboratory Medicine

Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), resulted in an unprecedented global crisis. Although primarily a respiratory illness, dysregulated immune responses may lead to multi-organ dysfunction. Prior data showed that the resident microbial communities of gastrointestinal and respiratory tracts act as modulators of local and systemic inflammatory activity (the gut-lung axis). Evolving evidence now signals an alteration in the gut microbiome, brought upon either by cytokines from the infected respiratory tract or from direct infection of the gut, or both. Dysbiosis leads to a "leaky gut". The intestinal permeability then allows access to …

Relationship Between Estimated Average Glucose (Eag) And Fasting Plasma Glucose In A Cohort Of Pakistani Diabetic Subjects, Nanik Ram, Sibtain Ahmed, Saadia Sattar, Saira Furqan, Najmul Islam

Section of Diabetes, Endocrinology and Metabolism

Introduction: Scientific literature is scarce on the utility of estimated average glucose (eAG) from Pakistan. Hence, there is a dire need to evaluate the relationship between eAG and fasting plasma glucose (FPG), in order to enhance our understanding of eAG and its usefulness. This study aims to investigate the relationship between FPG and eAG in diabetic patients calculated using HbA1C.
Materials and methods: A retrospective study was conducted at the Aga Khan University, Karachi, Pakistan. The medical records of both genders in the age range of 18-60 years, presenting as outpatients at the endocrine clinic, labeled as DM, were reviewed …

High-Throughput Next-Generation Sequencing Respiratory Viral Panel: A Diagnostic And Epidemiologic Tool For Sars-Cov-2 And Other Viruses, Nikhil S. Sahajpal, Ashis K. Mondal, Allan Njau, Zachary Petty, Jiani Chen, Sudha Ananth, Pankaj Ahluwalia, Colin Williams, Ted M. Ross, Alka Chaubey

Pathology, East Africa

Two serious public health challenges have emerged in the current COVID-19 pandemic namely, deficits in SARS-CoV-2 variant monitoring and neglect of other co-circulating respiratory viruses. Additionally, accurate assessment of the evolution, extent, and dynamics of the outbreak is required to understand the transmission of the virus. To address these challenges, we evaluated 533 samples using a high-throughput next-generation sequencing (NGS) respiratory viral panel (RVP) that includes 40 viral pathogens. The performance metrics revealed a PPA, NPA, and accuracy of 95.98%, 85.96%, and 94.4%, respectively. The clade for pangolin lineage B that contains certain distant variants, including P4715L in ORF1ab, Q57H …

Labrad : Vol 46, Issue 4 - October 2021, Aga Khan University Hospital, Karachi

LABRAD - Departments of Pathology & Laboratory Medicine and Radiology Archives

• Role of Barcoding in a Clinical Laboratory to Reduce Pre-Analytical Errors
• Congenital Dyserythropoietic Anemia: The Morphological Diagnosis
• Digital Imaging in Hematology: A New Beginning
• Metabolomics: Identification of Fatty Acid Oxidation (FAO) Disorders
• Next-Generation Sequencing for HLA Genotyping
• Urine Metabolomics to identify Organic Academia
• Next-Generation Sequencing (NGS) of Solid Tumor
• Importance of using Genomic Tool in Microbial Identification
• Radiology Practice in 21st Century: Role of Artificial Intelligence
• Case Quiz
• Best of the Recent Past
• Polaroid

Impact Of Covid-19 On The Pre And Post Analytical Clinical Laboratory Testing Processes- A Performance Evaluation Study Using Six Sigma, Sibtain Ahmed, Farhat Jahan, Muhammad Umer Naeem Effendi, Farooq Ghani

Department of Pathology and Laboratory Medicine

Background: The aim of this study was to determine the impact of COVID-19 pandemic on the total testing process using six sigma metrics based on a comparison of pre and during pandemic periods.
Material & methods: The study duration was over 12 months, 6 months before and 6 months after the COVID-19 onset in Pakistan in March 2020 after the recognition of the first case, using quality indicators (QIs). QIs were chosen from a model of QIs recommended by the CAP. Analysis was performed using Six Sigma calculators and QIs were expressed in percentage (%) and Sigma value were computed. …

Super-Enhancer-Based Identification Of A Batf3/Il-2r-Module Reveals Vulnerabilities In Anaplastic Large Cell Lymphoma, Huan-Chang Liang, Mariantonia Costanza, Nicole Prutsch, Mark W. Zimmerman, Elisabeth Gurnhofer, Ivonne A. Montes-Mojarro, Brian J. Abraham, Nina Prokoph, Stefan Stoiber, Shahid Pervez

Department of Pathology and Laboratory Medicine

Anaplastic large cell lymphoma (ALCL), an aggressive CD30-positive T-cell lymphoma, comprises systemic anaplastic lymphoma kinase (ALK)-positive, and ALK-negative, primary cutaneous and breast implant-associated ALCL. Prognosis of some ALCL subgroups is still unsatisfactory, and already in second line effective treatment options are lacking. To identify genes defining ALCL cell state and dependencies, we here characterize super-enhancer regions by genome-wide H3K27ac ChIP-seq. In addition to known ALCL key regulators, the AP-1-member BATF3 and IL-2 receptor (IL2R)-components are among the top hits. Specific and high-level IL2R expression in ALCL correlates with BATF3 expression. Confirming a regulatory link, IL-2R-expression decreases following BATF3 knockout, and …

Concomitant Bilateral Mandibular Cemento-Ossifying Fibroma And Cementoblastoma: Case Report Of An Extremely Rare Occurrence, Madiha Bilal Qureshi, Muhammad Usman Tariq, Jamshid Abdul Ghafar, Muhammad Raza, Nasir Ud Din

Department of Pathology and Laboratory Medicine

Background: Cemento-ossifying fibroma (COF) and cementoblastoma (CB) are rare benign odontogenic tumors with a predilection for the mandible. Cemento-ossifying fibroma is a fibro-osseous lesion that originates in the tooth bearing areas of jaw and shows cementum-like tissue in a fibrotic stroma. Cementoblastoma is classically related to roots of teeth with the presence of calcified cementum-like material. To date, only a single case of concomitant unilateral COF and CB has been reported in the literature.
Case presentation: We present an unusual case of a 37-year-old female who presented with two discrete bilateral swellings in the right and left mandible for 10 …

Editorial: Vitamin D Deficiency And Sufficiency In Reproduction And Bone Metabolism, Rehana Rehman, Faiza Alam, Mukhtiar Baig, Aysha Habib Khan, Naseer Ahmed

Department of Biological & Biomedical Sciences

No abstract provided.

Comparative Analysis Of N95 Respirators Fit Testing With Commercially Available And In House Reagent, Erum Khan, Joveria Farooqi, Humaira Shafaq, Kaleem Ullah Khushik, Syed Shamim Raza, Sara Khan, Zohra Rafiq, Bushra Ahmed, Shazia Chisti, Kehkashan Imtiaz, Hasnain Zafar, Afia Zafar

Department of Pathology and Laboratory Medicine

Background: Due to COVID-19, thousands of healthcare workers have been affected and have lost their lives in the line of duty. For the protection of healthcare workers, WHO and CDC have made standard guidelines and requirements for PPE use. N95 masks are amongst the most readily used PPE by healthcare professionals and it is highly recommended by OSHA that every make and model of N95 should go through a fit test at least once in a year.
Method: A total of 30 randomly selected healthcare professionals (who were a regular user of N95 respiratory masks) were subjected to assess in-house …

Diagnosis And Management Of Diffuse Large B-Cell Lymphoma: Society Of Medical Oncology, Pakistan Society Of Hematology, And Pakistan Society Of Clinical Oncology Joint Clinical Practice Guideline, Raheel Iftikhar, Muhammad Ayaz Mir, Munira Moosajee, Kamran Rashid, Syed Waqas Bokhari, Ahmed Nadeem Abbasi, Tahir Sultan Shamsi, Mohammad Usman Shaikh, Natasha Bahadur Ali, Salman Adil

Section of Haematology/Oncology

Diffuse large B-cell lymphoma (DLBCL) is the commonest non-Hodgkin lymphoma encountered by hematopathologists and oncologists. Management guidelines for DLBCL are developed and published by countries with high income and do not cater for practical challenges faced in resource-constrained settings. This report by a multidisciplinary panel of experts from Pakistan is on behalf of three major national cancer societies: Society of Medical Oncology Pakistan, Pakistan Society of Hematology, and Pakistan Society of Clinical Oncology. The aim is to develop a practical and standardized guideline for managing DLBCL in Pakistan, keeping in view local challenges, which are similar across most of the …

Whole-Genome Sequence-Informed Maldi-Tof Ms Diagnostics Reveal Importance Of Klebsiella Oxytoca Group In Invasive Infections: A Retrospective Clinical Study, Aline Cuénod, Daniel Wüthrich, Helena M. B. Seth-Smith, Chantal Ott, Christian Gehringer, Frédéric Foucault, Roxanne Mouchet, Ali Kassim, Gunturu Revathi, Deborah R. Vogt

Pathology, East Africa

Background: Klebsiella spp. are opportunistic pathogens which can cause severe infections, are often multi-drug resistant and are a common cause of hospital-acquired infections. Multiple new Klebsiella species have recently been described, yet their clinical impact and antibiotic resistance profiles are largely unknown. We aimed to explore Klebsiella group- and species-specific clinical impact, antimicrobial resistance (AMR) and virulence.

Methods: We analysed whole-genome sequence data of a diverse selection of Klebsiella spp. isolates and identified resistance and virulence factors. Using the genomes of 3594 Klebsiella isolates, we predicted the masses of 56 ribosomal subunit proteins and identified species-specific marker masses. …

Higher Entropy Observed In Sars-Cov-2 Genomes From The First Covid-19 Wave In Pakistan, Najia Karim Ghanchi, Asghar Nasir, Kiran I. Masood, Syed Hani Abidi, Syed Faisal Mahmood, Akber Kanji, Safina Abdul Razzak, Waqasuddin Khan, Saba Shahid, Maliha Yameen, Ali Raza, Javaria Ashraf, Zeeshan Ansar Ahmed, Mohammad Buksh Dharejo, Nazneen Islam, Zahra Hasan, Rumina Hasan

Department of Pathology and Laboratory Medicine

Background: We investigated the genome diversity of SARS-CoV-2 associated with the early COVID-19 period to investigate evolution of the virus in Pakistan.
Materials and methods: We studied ninety SARS-CoV-2 strains isolated between March and October 2020. Whole genome sequences from our laboratory and available genomes were used to investigate phylogeny, genetic variantion and mutation rates of SARS-CoV-2 strains in Pakistan. Site specific entropy analysis compared mutation rates between strains isolated before and after June 2020.
Results: In March, strains belonging to L, S, V and GH clades were observed but by October, only L and GH strains were present. The …

Acute Generalized Exanthematous Pustulosis Induced By Cetuximab, Sadia Masood, Mohammad Rizwan, Saira Fatima, Palwasha Jalil

Department of Medicine

A wide variety of diseases and drugs can cause cutaneous pustular eruptions. Acute generalized exanthematous pustulosis (AGEP) is a unique drug-induced dermatosis clinically presented as erythematous papular and pustular eruption, usually caused by certain systemic drugs. We are presenting a very rare association of AGEP with a biological agent, cetuximab. A male aged 66 years, who was recently diagnosed with a case of squamous cell carcinoma of glottis, presented in the dermatology clinic with a recent onset of fever and widespread pustular eruption over the face, trunk, and limbs. The eruption was noted after the injection of cetuximab given for …

Discrepancy Between Pcr Based Sars-Cov-2 Tests Suggests The Need To Re-Evaluate Diagnostic Assays, Zain Mushtaq, Sadia Shakoor, Akber Kanji, Najma Shaheen, Asghar Nasir, Zeeshan Ansar Ahmed, Imran Ahmed, Syed Faisal Mahmood, Rumina Hasan, Zahra Hasan

Section of Internal Medicine

Objective: We investigated the discrepancy between clinical and PCR-based diagnosis of COVID-19. We compared results of ten patients with mild to severe COVID-19. Respiratory samples from all cases were tested on the Roche SARS-CoV-2 (Cobas) assay, Filmarray RP2.1 (bioMereiux) and TaqPath™ COVID19 (Thermofisher) PCR assays.
Results: Laboratory records of ten patients with mild to severe COVID-19 were examined. Initially, respiratory samples from the patients were tested as negative on the SARS-CoV-2 Roche® assay. Further investigation using the BIOFIRE® Filmarray RP2.1 assay identified SARS-CoV-2 as the pathogen in all ten cases. To investigate possible discrepancies between PCR assays, additional testing was …

Our Experience Of Treating Adult Bone Lymphoma, A Retrospective Cross-Sectional Study In A Tertiary Care Center, Aga Khan University Hospital, Karachi, Masood Umer, Muhammad Younus Khan Durrani, Javeria Saeed, Nasir Ud Din

Section of Orthopaedic Surgery

Objective: To determine the experience at the Aga Khan University Hospital in diagnosing and treating adult patients with primary lymphoma of bone.
Methodology: All patients with Primary lymphoma of bone (PLB) that were diagnosed and/or treated at Aga Khan University Hospital, Karachi from 2005 to 2019 were included as part of this study.
Results: There were 17 patients with PLB including 13 (76.5%) males and 4 (23.5%) females with a mean age of 44 ± 16.5 years. Nine patients were between 30-59 years of age at diagnosis. The mean follow-up time of patients was 80±46.7 months. Six patients had tumours …

Prevalence And Determinants Of Inappropriate Antibiotic Dispensing At Private Drug Retail Outlets In Urban And Rural Areas Of Indonesia: A Mixed Methods Study, Luh Putu Lila Wulandari, Mishal Khan, Marco Liverani, Astri Ferdiana, Yusuf Ari Mashuri, Ari Probandari, Tri Wibawa, Neha Batura, Gill Schierhout, John Kaldor

Department of Pathology and Laboratory Medicine

Introduction: The aim of this mixed-method study was to determine the extent and determinants of inappropriate dispensing of antibiotics by licensed private drug retail outlets in Indonesia.
Methods: Standardised patients (SPs) made a total of 495 visits to 166 drug outlets (community pharmacies and drug stores) between July and August 2019. The SPs presented three clinical cases to drug outlet staff: parent of a child at home with diarrhoea; an adult with presumptive tuberculosis (TB); and an adult with upper respiratory tract infection (URTI). The primary outcome was the dispensing of an antibiotic without prescription, with or without the client …

Synchronous Primary Diffuse Large B-Cell Lymphoma And Papillary Thyroid Carcinoma: A Case Report Highlighting "Lymphoma First Approach", Rahim Dhanani, Ambreen Abdullah Unar, Muhammad Hassan Danish, Hamdan Ahmed Pasha, Ummiya Tahir, Mubasher Ikram

Section of Otolaryngology, Head & Neck Surgery

Papillary thyroid carcinoma (PTC) is the most common type of all thyroid carcinomas and accounts for up to 90% of all thyroid malignancies. It is the most indolent form of the disease and has an excellent prognosis. On the other hand, Primary thyroid lymphoma (PTL) is a rare entity accounting for only about 1% to 5% of all thyroid malignancies and only 2% of extranodal lymphomas. Synchronous PTC and PTL is a very rare condition and only a few cases have been reported in the literature up till now. We report one such case in a 52-year-old lady who was …

Establishing Reference Interval For Thyroid-Stimulating Hormone In Children Below Two-Year Ages In Pakistani Population, Siraj Muneer, Imran Siddiqui, Hafsa Majid, Lena Jafri, Khadija N Humayun, Sibtain Ahmed, Aysha Habib Khan

Department of Pathology and Laboratory Medicine

Introduction: Reference intervals (RIs) of thyroid-stimulating hormone (TSH) and free thyroxine (FT4) are age, assay and population specific. Currently, the age and assay-specific RIs for TSH are not available for children under two years of age. This study aimed to establish reference intervals for serum concentrations of TSH and FT4 in healthy children aged 1-24 months as per CLSI C28-A3 guidelines.
Methods: This prospective cross-sectional study was conducted in children from 1 to 24 months visiting the clinical laboratory for serum vitamin D testing but without any recent illness, hospitalization, medication and history of maternal thyroid diseases from August 2018 …

Follicular Thyroid Carcinoma In A Developing Country: A 10-Year Retrospective Study, Abdul Aziz, Qamar Masood, Saadia Sattar, Saira Fatima, Najmul Islam

Section of Diabetes, Endocrinology and Metabolism

Background: The most common endocrine tumor is thyroid cancer. Follicular thyroid carcinoma (FTC) accounts for 5-10% of all thyroid cancers. Patients with FTC frequently present with more advanced diseases and a higher occurrence of distant metastases because of the propensity of vascular invasion. FTC is mainly treated with surgery while radioactive iodine (RAI) therapy is the main adjuvant therapy according to the American Thyroid Association guidelines.
Methodology: This was a retrospective observational study of FTC patients aged 18 and above conducted at a tertiary care hospital in Karachi from January 01, 2010 to December 31, 2019.
Results: A total of …

Comparison Of Antimicrobial Efficacy Of Calcipex And Metapex In Endodontic Treatment Of Chronic Apical Periodontitis: A Randomised Controlled Trial Study Protocol, Momina Motiwala, Saqib Habib, Rabia Ghafoor, Seema Irfan

Section of Dental-Oral Maxillofacial Surgery

Introduction: Various intracanal medicaments have been used in cases of chronic apical periodontitis for appropriate disinfection of the root canal system to eliminate microbes especially from the inaccessible areas. Calcium hydroxide is the most common intracanal medicament available in various forms, but its effectiveness with or without iodoform using microbial culture is unknown. Therefore, our aim is to compare the antimicrobial efficacy of Calcipex and Metapex in endodontic treatment of teeth presenting with chronic apical periodontitis by assessing the bacterial load reduction.
Method and analysis: 60 single rooted teeth of patients with diagnosis of chronic apical periodontitis will be selected …

Gut Integrity And Duodenal Enteropathogen Burden In Undernourished Children With Environmental Enteric Dysfunction, Zehra Jamil, Najeeha Talat Iqbal, Romana Idress, Zubair Ahmad, Kamran Sadiq, Junaid Iqbal, Sana Syed, Aneeta Hotwani, Furqan Kabir, Kumail Ahmed, Sheraz Ahmed, Fayyaz Umrani, Fatima Aziz, Adil Kalam, Syed Asad Ali

Department of Biological & Biomedical Sciences

Environmental enteric dysfunction (EED) is a subclinical condition of intestinal inflammation, barrier dysfunction and malabsorption associated with growth faltering in children living in poverty. This study explores association of altered duodenal permeability (lactulose, rhamnose and their ratio) with higher burden of enteropathogen in the duodenal aspirate, altered histopathological findings and higher morbidity (diarrhea) that is collectively associated with linear growth faltering in children living in EED endemic setting. In a longitudinal birth cohort, 51 controls (WHZ > 0, HAZ > -1.0) and 63 cases (WHZ< -2.0, refractory to nutritional intervention) were recruited. Anthropometry and morbidity were recorded on monthly bases up to 24 months of age. Dual sugar assay of urine collected after oral administration of lactulose and rhamnose was assessed in 96 children from both the groups. Duodenal histopathology (n = 63) and enteropathogen analysis of aspirate via Taqman array card (n = 60) was assessed in only cases. Giardia was the most frequent pathogen and was associated with raised L:R ratio (p = 0.068). Gastric microscopy was more sensitive than duodenal aspirate in H. pylori detection. Microscopically confirmed H. pylori negatively correlated with HAZ at 24 months (r = -0.313, p = 0.013). Regarding histopathological parameters, goblet cell reduction significantly correlated with decline in dual sugar excretion (p< 0.05). Between cases and controls, there were no significant differences in the median (25th, 75th percentile) of urinary concentrations (μg/ml) of lactulose [27.0 (11.50, 59.50) for cases vs. 38.0 (12.0, 61.0) for controls], rhamnose [66.0 (28.0, 178.0) vs. 86.5 (29.5, 190.5)] and L:R ratio [0.47 (0.24, 0.90) vs. 0.51 (0.31, 0.71)] respectively. In multivariable regression model, 31% of variability in HAZ at 24 months of age among cases and controls was explained by final model including dual sugars. In conclusion, enteropathogen burden is associated with altered histopathological features and intestinal permeability. In cases and controls living in settings of endemic enteropathy, intestinal permeability test may predict linear growth. However, for adoption as a screening tool for EED, further validation is required due to its complex intestinal pathophysiology.

The Role Of Interspecies Recombination In The Evolution Of Antibiotic-Resistant Pneumococci, Joshua C. D'Aeth, Mark Pg Van Der Linden, Lesley Mcgee, Herminia De Lencastre, Paul Turner, Jae-Hoon Song, Stephanie W. Lo, Rebecca A. Gladstone, Gps Consortium, Sadia Shakoor

Department of Pathology and Laboratory Medicine

Multidrug-resistant Streptococcus pneumoniae emerge through the modification of core genome loci by interspecies homologous recombinations, and acquisition of gene cassettes. Both occurred in the otherwise contrasting histories of the antibiotic-resistant S. pneumoniae lineages PMEN3 and PMEN9. A single PMEN3 clade spread globally, evading vaccine-induced immunity through frequent serotype switching, whereas locally circulating PMEN9 clades independently gained resistance. Both lineages repeatedly integrated Tn916-type and Tn1207.1-type elements, conferring tetracycline and macrolide resistance, respectively, through homologous recombination importing sequences originating in other species. A species-wide dataset found over 100 instances of such interspecific acquisitions of resistance cassettes and flanking …

Indirect Determination Of Serum Creatinine Reference Intervals In A Pakistani Pediatric Population Using Big Data Analytics, Sibtain Ahmed, Jakob Zierk, Imran Siddiqui, Aysha Habib Khan

Department of Pathology and Laboratory Medicine

Background: The indirect methods of reference intervals (RI) establishment based on data mining are utilized to overcome the ethical, practical challenges and the cost associated with the conventional direct approach.
Aim: To generate RIs for serum creatinine in children and adolescents using an indirect statistical tool.
Methods: Data mining of the laboratory information system was performed for serum creatinine analyzed from birth to 17 years for both genders. The timeline was set at six years from January 2013 to December 2018. Microsoft Excel 2010 and an indirect algorithm developed by the German Society of Clinical Chemistry and Laboratory Medicine's Working …

Diagnostic Accuracy And Agreement Between Four Phenotypic Carbapenemase Detection Tests Among Enterobacterales, Fizza Farooqui, Seema Irfan, Sidra Laiq

Department of Pathology and Laboratory Medicine

Introduction: Carbapenem-resistant Enterobacterales (CREs) are becoming increasingly popular as a cause of hospital-acquired infections that are difficult to treat and are frequently reported as causes of outbreaks in various hospitals. Conventional culturing techniques take at least 2 days to report a case as carbapenem resistant, and it is therefore important to detect such resistance mechanisms as early as possible.
Methods: This study aimed to compare the diagnostic performance of Carba NP, modified Hodge test (MHT), ethylenediaminetetraacetic acid (EDTA) disk synergy test (DST), and the modified carbapenem inactivation method (mCIM). This study was done at Microbiology Laboratory, Aga Khan University Hospital, …

Online Assessment In Undergraduate Medical Education: Challenges And Solutions From A Lmic University, Syeda Sadia Fatima, Romana Idrees, Kauser Jabeen, Saniya Sabzwari, Sadaf Khan

Department of Biological & Biomedical Sciences

Background and objectives: The Covid-19 pandemic has caused large-scale disruption in almost all educational programs across the world. Planning and rapid implementation of assessment through an online format presents the next set of novel challenges that must be addressed by academic administrations across the globe.
Methods: This cross-sectional study was conducted between March to August 2020 at the Aga Khan University Medical College. Two hundred medical students of year 1 and 2 participated in the study. We describe the planning, processes, and outcomes of online assessments using video communication platforms conducted at a private university in Pakistan. Standardized protocols were …

A Prospective Observational Study Of Community Acquired Pneumonia In Kenya: The Role Of Viral Pathogens, Jamila Nambafu, Mary Achakolong, Fridah Mwendwa, Jumaa Bwika, Felix Riunga, Samuel Gitau, Hanika Patel, Rodney Adam

Internal Medicine, East Africa

Background: Lower respiratory tract infections continue to contribute significantly to morbidity and mortality across all age groups globally. In sub-Saharan Africa, many studies of community acquired pneumonia in adults have focused on HIV-infected patients and little attention has been given to risk factors and etiologic agents in an urban area with a more moderate HIV prevalence.

Methods: We prospectively enrolled 77 patients admitted to a 280 bed teaching hospital in Kenya with radiographically confirmed community acquired pneumonia from May 2019 to March 2020. The patients were followed for etiology and clinical outcomes. Viral PCR testing was performed using …