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Articles 1 - 19 of 19
Full-Text Articles in Medicine and Health Sciences
Substitution Spectra Of Sars-Cov-2 Genome From Pakistan Reveals Insights Into The Evolution Of Variants Across The Pandemic, Javaria Ashraf, Sayed Ali Raza Bukhari, Akber Kanji, Tulaib Iqbal, Maliha Yameen, Waqasuddin Khan, Zahra Hasan
Substitution Spectra Of Sars-Cov-2 Genome From Pakistan Reveals Insights Into The Evolution Of Variants Across The Pandemic, Javaria Ashraf, Sayed Ali Raza Bukhari, Akber Kanji, Tulaib Iqbal, Maliha Yameen, Waqasuddin Khan, Zahra Hasan
Department of Pathology and Laboratory Medicine
Changing morbidity and mortality due to COVID-19 across the pandemic has been linked with factors such as the emergence of SARS-CoV-2 variants and vaccination. Mutations in the Spike glycoprotein enhanced viral transmission and virulence. We investigated whether SARS-CoV-2 mutation rates and entropy were associated COVID-19 in Pakistan, before and after the introduction of vaccinations. We analyzed 1,705 SARS-CoV-2 genomes using the Augur phylogenetic pipeline. Substitution rates and entropy across the genome, and in the Spike glycoprotein were compared between 2020, 2021 and 2022 (as periods A, B and C). Mortality was greatest in B whilst cases were highest during C. …
Adapting International Clinical Trials During Covid-19 And Beyond, Kamala Thriemer, Kamala Thriemer, Mohammad Shafiul Alam, Bipin Adhikari, Rupam Tripura, Mohammad Sharif Hossain, Michael Christian, Najia Bano Ghanchi, Hellen Mnjala, Muhammad Asim
Adapting International Clinical Trials During Covid-19 And Beyond, Kamala Thriemer, Kamala Thriemer, Mohammad Shafiul Alam, Bipin Adhikari, Rupam Tripura, Mohammad Sharif Hossain, Michael Christian, Najia Bano Ghanchi, Hellen Mnjala, Muhammad Asim
Department of Pathology and Laboratory Medicine
Background: The COVID-19 pandemic and resulting restrictions, particularly travel restrictions, have had significant impact on the conduct of global clinical trials. Our clinical trials programme, which relied on in-person visits for training, monitoring and capacity building across nine low- and middle-income countries, had to adapt to those unprecedented operational challenges. We report the adaptation of our working model with a focus on the operational areas of training, monitoring and cross-site collaboration.
The new working model: Adaptations include changing training strategies from in-person site visits with three or four team members to a multi-pronged virtual approach, with generic online training for …
Diagnostic Accuracy Of Different Cut-Off Values Of Adenosine Deaminase Levels In Tuberculous Pleural Effusion, Kiran Iqbal Masood, Shayan Shahid, Kauser Jabeen, Joveria Farooqi, Sabeika Raza Kerawala, Muhammad Irfan
Diagnostic Accuracy Of Different Cut-Off Values Of Adenosine Deaminase Levels In Tuberculous Pleural Effusion, Kiran Iqbal Masood, Shayan Shahid, Kauser Jabeen, Joveria Farooqi, Sabeika Raza Kerawala, Muhammad Irfan
Department of Pathology and Laboratory Medicine
Objective: To assess the diagnostic accuracy of different cut-off values of pleural fluid adenosine deaminase levels as a diagnostic method for tuberculous pleural effusion.
Method: The prospective study was conducted from 2014 to 2016 at the Aga Khan University Hospital, Karachi, and comprised pleural fluid samples of adult patients with and without tuberculosis which were tested for adenosine deaminase levels, and divided into tuberculosis group A and non-tuberculosis group B. Sensitivity, specificity, negative predictive value and positive predictive value were calculated using different cut-offs. Data was analysed using IBM SPSS (Statistical Package for Social Sciences) version 21.0 (IBM Corp., Armonk, …
Drug-Resistant Bacterial Infections: We Need Urgent Action And Investment That Focus On The Weakest Link, Christiane Dolecek, Sadia Shakoor, Buddha Basnyat, Tochi Okwor, Benn Sartorius
Drug-Resistant Bacterial Infections: We Need Urgent Action And Investment That Focus On The Weakest Link, Christiane Dolecek, Sadia Shakoor, Buddha Basnyat, Tochi Okwor, Benn Sartorius
Department of Pathology and Laboratory Medicine
Despite high mortality and morbidity, drug-resistant bacterial infections remain the forgotten pandemic. We argue for strengthening of diagnostics, WASH (water, sanitation, and hygiene) and infection prevention and control to reduce drug-resistant infections, as an integral part of sustainable high-quality health services, particularly in low- and middle-income countries.
Assessment During Covid-19: Quality Assurance Of An Online Open Book Formative Examination For Undergraduate Medical Students, Javeria Rehman, Rahila Ali Mazhar, Azam Afzal, Sara Shakil, Amber Shahmim Sultan, Romana Idress, Syeda Sadia Fatima
Assessment During Covid-19: Quality Assurance Of An Online Open Book Formative Examination For Undergraduate Medical Students, Javeria Rehman, Rahila Ali Mazhar, Azam Afzal, Sara Shakil, Amber Shahmim Sultan, Romana Idress, Syeda Sadia Fatima
Department of Pathology and Laboratory Medicine
Background: The spread of COVID-19 pandemic in early 2020 compelled all the educational activities, including medical education to be shifted from face-to-face interaction to a virtual platform. This shift provided opportunities for exploring online assessment modalities. One such assessment method is an online open book exam which is a unique concept in medical education of Pakistan. Limited information is available in literature regarding open book exam for the basic science subjects. Hence, the objective of the study was to determine the quality of the open book exam administered as a pilot project to the first-year medical students.
Methods: It was …
Emergence Of A Multidrug-Resistant And Virulent Streptococcus Pneumoniae Lineage Mediates Serotype Replacement After Pcv13: An International Whole-Genome Sequencing Study, Stephanie W. Lo, Kate Mellor, Robert Cohen, Alba Redin Alonso, Sophie Belman, Narender Kumar, Paulina A. Hawkins, Rebecca A. Gladstone, Sadia Shakoor, Muhammad Imran Nisar
Emergence Of A Multidrug-Resistant And Virulent Streptococcus Pneumoniae Lineage Mediates Serotype Replacement After Pcv13: An International Whole-Genome Sequencing Study, Stephanie W. Lo, Kate Mellor, Robert Cohen, Alba Redin Alonso, Sophie Belman, Narender Kumar, Paulina A. Hawkins, Rebecca A. Gladstone, Sadia Shakoor, Muhammad Imran Nisar
Department of Pathology and Laboratory Medicine
Background: Serotype 24F is one of the emerging pneumococcal serotypes after the introduction of pneumococcal conjugate vaccine (PCV). We aimed to identify lineages driving the increase of serotype 24F in France and place these findings into a global context.
Methods: Whole-genome sequencing was performed on a collection of serotype 24F pneumococci from asymptomatic colonisation (n=229) and invasive disease (n=190) isolates among individuals younger than 18 years in France, from 2003 to 2018. To provide a global context, we included an additional collection of 24F isolates in the Global Pneumococcal Sequencing (GPS) project database for analysis. A Global Pneumococcal Sequence Cluster …
Igg Antibodies To Sars-Cov-2 In Asymptomatic Blood Donors At Two Time Points In Karachi, Muhammad Hasan, Bushra Moiz, Shama Qaiser, Kiran I. Masood, Zara Ghous, Areeba Hussain, Natasha Bahadur Ali, Syed Hani Abidi, Kulsoom Ghias, Erum Khan, Zahra Hasan
Igg Antibodies To Sars-Cov-2 In Asymptomatic Blood Donors At Two Time Points In Karachi, Muhammad Hasan, Bushra Moiz, Shama Qaiser, Kiran I. Masood, Zara Ghous, Areeba Hussain, Natasha Bahadur Ali, Syed Hani Abidi, Kulsoom Ghias, Erum Khan, Zahra Hasan
Department of Pathology and Laboratory Medicine
Introduction: An estimated 1.5 million cases were reported in Pakistan until 23 March, 2022. However, SARS-CoV-2 PCR testing capacity has been limited and the incidence of COVID-19 infections is unknown. Volunteer healthy blood donors can be a control population for assessment of SARS-CoV-2 exposure in the population. We determined COVID-19 seroprevalence during the second pandemic wave in Karachi in donors without known infections or symptoms in 4 weeks prior to enrollment.
Materials and methods: We enrolled 558 healthy blood donors at the Aga Khan University Hospital between December 2020 and February 2021. ABO blood groups were determined. Serum IgG reactivity …
Characterisation Of Drug-Resistant Mycobacterium Tuberculosis Mutations And Transmission In Pakistan, Gary Napier, Anwar Sheed Khan, Abdul Jabbar, Muhammad Tahir Khan, Sajid Ali, Muhammad Qasim, Noor Mohammad, Rumina Hasan, Zahra Hasan, Susana Campino
Characterisation Of Drug-Resistant Mycobacterium Tuberculosis Mutations And Transmission In Pakistan, Gary Napier, Anwar Sheed Khan, Abdul Jabbar, Muhammad Tahir Khan, Sajid Ali, Muhammad Qasim, Noor Mohammad, Rumina Hasan, Zahra Hasan, Susana Campino
Department of Pathology and Laboratory Medicine
Tuberculosis, caused by Mycobacterium tuberculosis, is a high-burden disease in Pakistan, with multi-drug (MDR) and extensive-drug (XDR) resistance, complicating infection control. Whole genome sequencing (WGS) of M. tuberculosis is being used to infer lineages (strain-types), drug resistance mutations, and transmission patterns-all informing infection control and clinical decision making. Here we analyse WGS data on 535 M. tuberculosis isolates sourced across Pakistan between years 2003 and 2020, to understand the circulating strain-types and mutations related to 12 anti-TB drugs, as well as identify transmission clusters. Most isolates belonged to lineage 3 (n = 397; 74.2%) strain-types, and were MDR (n = …
A Streptococcus Pneumoniae Lineage Usually Associated With Pneumococcal Conjugate Vaccine (Pcv) Serotypes Is The Most Common Cause Of Serotype 35b Invasive Disease In South Africa, Following Routine Use Of Pcv, Kedibone M. Ndlangisa, Mignon Du Plessis, Stephani Lo, Linda De Gouveia, Chrispin Chaguza, Martin Antonio, Brenda Kwambana-Adams, Jennifer Cornick, Dean B. Everett, Sadia Shakoor
A Streptococcus Pneumoniae Lineage Usually Associated With Pneumococcal Conjugate Vaccine (Pcv) Serotypes Is The Most Common Cause Of Serotype 35b Invasive Disease In South Africa, Following Routine Use Of Pcv, Kedibone M. Ndlangisa, Mignon Du Plessis, Stephani Lo, Linda De Gouveia, Chrispin Chaguza, Martin Antonio, Brenda Kwambana-Adams, Jennifer Cornick, Dean B. Everett, Sadia Shakoor
Department of Pathology and Laboratory Medicine
Pneumococcal serotype 35B is an important non-conjugate vaccine (non-PCV) serotype. Its continued emergence, post-PCV7 in the USA, was associated with expansion of a pre-existing 35B clone (clonal complex [CC] 558) along with post-PCV13 emergence of a non-35B clone previously associated with PCV serotypes (CC156). This study describes lineages circulating among 35B isolates in South Africa before and after PCV introduction. We also compared 35B isolates belonging to a predominant 35B lineage in South Africa (GPSC5), with isolates belonging to the same lineage in other parts of the world. Serotype 35B isolates that caused invasive pneumococcal disease in South Africa in …
Development And Validation Of Standard And Real Patient Gallstone Library Using Fourier Transform Infra-Red Spectroscopy, Lena Jafri, Muhammad Abbas Abid, Humera Asif, Syed Bilal Hashmi, Hafsa Majid, Farooq Ghani, Sibtain Ahmed, Imran Siddiqui, Aysha Habib
Development And Validation Of Standard And Real Patient Gallstone Library Using Fourier Transform Infra-Red Spectroscopy, Lena Jafri, Muhammad Abbas Abid, Humera Asif, Syed Bilal Hashmi, Hafsa Majid, Farooq Ghani, Sibtain Ahmed, Imran Siddiqui, Aysha Habib
Department of Pathology and Laboratory Medicine
Background: Analysis of the constituents of gallstones using various spectroscopic techniques assists in identification of the pathogenesis of gallstones. In the current study, using Fourier Transform Infra-Red (FTIR) Spectroscopy, a Gallstone Standard Library (GSL) and a Gallstone Real Patients' Library (GRPL) were developed and validated for gallstone composition analysis.
Methods: The study was conducted at the Department of Pathology & Laboratory Medicine, Aga Khan University, Pakistan. Pure standards (cholesterol, calcium carbonate, bilirubin and bile salts) and gallstone specimens were analyzed using FTIR Nicolet iS-5 Spectrometer from Thermo Fisher Scientific, USA. Thermo Scientific™ QCheck™ algorithm, embedded within the OMNIC™ software, was …
Lymphoma With Tuberculous Granulomas, Jyoti Mohan Lal, Anila Rashid
Lymphoma With Tuberculous Granulomas, Jyoti Mohan Lal, Anila Rashid
Department of Pathology and Laboratory Medicine
Chronic granulomatous inflammation is a common finding in lymphoproliferative disorders (LPDs), but it is important to exclude coexisting mycobacterium tuberculosis (MTB) especially in patients from areas of high endemicity. This case emphasizes the relevance of performing MTB culture on bone marrow exhibiting LPD and concomitant granulomas
Upregulated Type I Interferon Responses In Asymptomatic Covid-19 Infection Are Associated With Improved Clinical Outcome, Kiran I. Masood, Maliha Yameen, Javeria Ashraf, Saba Shahid, Syed Faisal Mahmood, Asghar Nasir, Nosheen Nasir, Bushra Jamil, Najia Karim Ghanchi, Iffat Khanum, Safina Abdul Razzak, Akber Kanji, Rabia Hussain, Martin E. Rottenberg, Zahra Hasan
Upregulated Type I Interferon Responses In Asymptomatic Covid-19 Infection Are Associated With Improved Clinical Outcome, Kiran I. Masood, Maliha Yameen, Javeria Ashraf, Saba Shahid, Syed Faisal Mahmood, Asghar Nasir, Nosheen Nasir, Bushra Jamil, Najia Karim Ghanchi, Iffat Khanum, Safina Abdul Razzak, Akber Kanji, Rabia Hussain, Martin E. Rottenberg, Zahra Hasan
Department of Pathology and Laboratory Medicine
Understanding key host protective mechanisms against SARS-CoV-2 infection can help improve treatment modalities for COVID-19. We used a blood transcriptome approach to study biomarkers associated with differing severity of COVID-19, comparing severe and mild Symptomatic disease with Asymptomatic COVID-19 and uninfected Controls. There was suppression of antigen presentation but upregulation of inflammatory and viral mRNA translation associated pathways in Symptomatic as compared with Asymptomatic cases. In severe COVID-19, CD177 a neutrophil marker, was upregulated while interferon stimulated genes (ISGs) were downregulated. Asymptomatic COVID-19 cases displayed upregulation of ISGs and humoral response genes with downregulation of ICAM3 and TLR8. Compared across …
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
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 …
Diagnostic Accuracy And Agreement Between Four Phenotypic Carbapenemase Detection Tests Among Enterobacterales, Fizza Farooqui, Seema Irfan, Sidra Laiq
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, …
Plasmodium In The Bone Marrow: Case Series From A Hospital In Pakistan, 2007-2015, Muhammad Shariq Shaikh, Basim Ali, Mahin Janjua, Ayesha Akbar, Syed Arish Haider, Bushra Moiz, Ahmed Raheem Buksh, John Kevin Baird, Mohammad Asim Beg
Plasmodium In The Bone Marrow: Case Series From A Hospital In Pakistan, 2007-2015, Muhammad Shariq Shaikh, Basim Ali, Mahin Janjua, Ayesha Akbar, Syed Arish Haider, Bushra Moiz, Ahmed Raheem Buksh, John Kevin Baird, Mohammad Asim Beg
Department of Pathology and Laboratory Medicine
Background: Malaria is a life-threatening, multisystem disease caused by the plasmodial parasite with a global incidence of approximately 229 million annually. The parasites are known to have unique and crucial interactions with various body tissues during its life cycle, notably the liver, spleen, and recent work has shown the bone marrow to be a reservoir of infection.
Methods: This study is a case series of patients in whom examination of bone marrow revealed malarial parasites. A retrospective record review of 35 parasite-positive bone marrow specimens examined at Aga Khan University Hospital (AKUH), Karachi, Pakistan, over the years 2007 to 2015 …
Antimicrobial Resistance And Covid-19: Intersections And Implications, Gwenan M. Knight, Rebecca E. Glover, C Finn Mcquaid, Ioana D. Olaru, Karin Gallandat, Quentin J. Leclerc, Naomi M. Fuller, Sam J. Willcocks, Rumina Hasan, Esther Van Kleef, Clare Ir Chandler
Antimicrobial Resistance And Covid-19: Intersections And Implications, Gwenan M. Knight, Rebecca E. Glover, C Finn Mcquaid, Ioana D. Olaru, Karin Gallandat, Quentin J. Leclerc, Naomi M. Fuller, Sam J. Willcocks, Rumina Hasan, Esther Van Kleef, Clare Ir Chandler
Department of Pathology and Laboratory Medicine
Before the coronavirus 2019 (COVID-19) pandemic began, antimicrobial resistance (AMR) was among the top priorities for global public health. Already a complex challenge, AMR now needs to be addressed in a changing healthcare landscape. Here, we analyse how changes due to COVID-19 in terms of antimicrobial usage, infection prevention, and health systems affect the emergence, transmission, and burden of AMR. Increased hand hygiene, decreased international travel, and decreased elective hospital procedures may reduce AMR pathogen selection and spread in the short term. However, the opposite effects may be seen if antibiotics are more widely used as standard healthcare pathways break …
Comparison Of Clinical Presentation And Out-Comes Of Chikungunya And Dengue Virus Infections In Patients With Acute Undifferentiated Febrile Illness From The Sindh Region Of Pakistan, Uzma Shahid, Joveria Farooqi, Kelli L. Barr, Syed Faisal Mahmood, Bushra Jamil, Kehkashan Imtiaz, Zahida Azizullah, Faisal Malik, Dhani Prakoso, Maureen T. Long, E. Khan
Comparison Of Clinical Presentation And Out-Comes Of Chikungunya And Dengue Virus Infections In Patients With Acute Undifferentiated Febrile Illness From The Sindh Region Of Pakistan, Uzma Shahid, Joveria Farooqi, Kelli L. Barr, Syed Faisal Mahmood, Bushra Jamil, Kehkashan Imtiaz, Zahida Azizullah, Faisal Malik, Dhani Prakoso, Maureen T. Long, E. Khan
Department of Pathology and Laboratory Medicine
Background: Arboviruses are a cause of acute febrile illness and outbreaks worldwide. Recent outbreaks of Chikungunya virus (CHIKV) in dengue endemic areas have alarmed clinicians as unique clinical features differentiating CHIKV from Dengue virus (DENV) are limited. This has complicated diagnostic efforts especially in resource limited countries where lab testing is not easily available. Therefore, it is essential to analyse and compare clinical features of laboratory confirmed cases to assist clinicians in suspecting possible CHIKV infection at time of clinical presentation.
Methodology: A prospective point prevalence study was conducted, with the hypothesis that not all patients presenting with clinical suspicion …
Post Tuberculosis Treatment Infectious Complications, Desmond Hsu, Muhammad Irfan, Kauser Jabeen, Nousheen Iqbal, Rumina Hasan, Giovanni Battista Migliori, Alimuddin Zumla, Dina Visca, Rosella Centis, Simon Tiberi
Post Tuberculosis Treatment Infectious Complications, Desmond Hsu, Muhammad Irfan, Kauser Jabeen, Nousheen Iqbal, Rumina Hasan, Giovanni Battista Migliori, Alimuddin Zumla, Dina Visca, Rosella Centis, Simon Tiberi
Department of Pathology and Laboratory Medicine
Following greater attention and follow-up of patients with treated pulmonary tuberculosis (TB), it has emerged that infections are more likely to occur in this cohort of patients. This comes as no surprise, as pulmonary TB is a destructive process that leads to cicatrization, alteration of parenchyma, bronchiectasis, and scarring of the lung, with reduction of lung volumes and an impact on pulmonary function. In addition to relapse and re-infection with TB, other pathogens are increasingly recognized in post-TB patients. This paper serves as a summary and guide on how to approach the post-TB patient with new signs and symptoms of …
Integrating Standardized Whole Genome Sequence Analysis With A Global Mycobacterium Tuberculosis Antibiotic Resistance Knowledgebase, Rumina Hasan, Matthew Ezewudo, Amanda Borens, Álvaro Chiner-Oms, Paolo Miotto, Leonid Chindelevitch, Angela M. Starks, Debra Hanna, Richard Liwsk, Matteo Zignol
Integrating Standardized Whole Genome Sequence Analysis With A Global Mycobacterium Tuberculosis Antibiotic Resistance Knowledgebase, Rumina Hasan, Matthew Ezewudo, Amanda Borens, Álvaro Chiner-Oms, Paolo Miotto, Leonid Chindelevitch, Angela M. Starks, Debra Hanna, Richard Liwsk, Matteo Zignol
Department of Pathology and Laboratory Medicine
Drug-resistant tuberculosis poses a persistent public health threat. The ReSeqTB platform is a collaborative, curated knowledgebase, designed to standardize and aggregate global Mycobacterium tuberculosis complex (MTBC) variant data from whole genome sequencing (WGS) with phenotypic drug susceptibility testing (DST) and clinical data. We developed a unified analysis variant pipeline (UVP) ( https://github.com/CPTR-ReSeqTB/UVP ) to identify variants and assign lineage from MTBC sequence data. Stringent thresholds and quality control measures were incorporated in this open source tool. The pipeline was validated using a well-characterized dataset of 90 diverse MTBC isolates with conventional DST and DNA Sanger sequencing data. The UVP exhibited …