Vulvovaginal candidiasis (VVC) is considered as a pervasive gynecological problem among women wor... more Vulvovaginal candidiasis (VVC) is considered as a pervasive gynecological problem among women worldwide. Owing to this fact, in the current study, we aimed at assessing the prevalence rate of spp. causing VVC in symptomatic pregnant women and their antifungal susceptibility pattern. This study was carried out in the tertiary care hospitals of Peshawar during the period of July 1, 2016 to December 31, 2016. The study group included 450 pregnant women in the age group of 17-44 years with symptoms of excessive vaginal discharge, pain and pruritis. In all, 108 pregnant women were culture positive for . Antimicrobial susceptibility testing (AST) was conducted on specimens against various azoles and polyene F group of antifungals. Out of 108 spp. isolated from vaginal swabs, there were 45 (41.7%) , 18 (16.7%) , 18 (16.7%) , 16 (14.8%) and 11 (10.2%) . According to age distribution, 27 years was the mean age. Pregnancy trimester distribution among patients was as follows: 21 (19.4%) patien...
Objective: To assess the utility of galactomannan and beta-D-glucan assays in the diagnosis of in... more Objective: To assess the utility of galactomannan and beta-D-glucan assays in the diagnosis of invasive aspergillosis in clinically suspected cases, and to compare their diagnostic potential to determine whether a combination of the two may result in an early and specific diagnosis. Methods: The descriptive cross-sectional case-control study was conducted at the Armed Forces Institute of Pathology, Rawalpindi, Pakistan, from April 1, 2017, to March 31, 2018, and comprised serum samples from clinically suspected invasive aspergillosis patients and healthy controls. The sera were tested for galactomannan and beta-D-glucan detection. Proven, probable and possible categories of invasive aspergillosis according to European Organisation for Research and Treatment of Cancer / Invasive Fungal Infections Cooperative Group and the National Institute of Allergy and Infectious Diseases Mycoses Study Group criteria. Galactomannan antigen was detected using a one-stage immunoenzymatic sandwich microplate assay. Beta-D-Glucan antigen was detected using a protease zymogen-based colorimetric assay. Sensitivity and positive / negative likelihood ratio of both the cases and the controls were calculated and compared. Results: Of the 178 subjects, 119(67%) were cases and 59(33%) were controls. Beta-D-glucan assay was more sensitive than galactomannan assay (91.6% versus 80.67%) whereas galactomannan assay was more specific than beta-D-glucan assay (86.44% versus 76.27%) in the diagnosis of invasive aspergillosis. The sensitivities of both assays decreased with decreasing probability of invasive aspergillosis, i.e., maximum sensitivities of both beta-D-glucan and galactomannan assays were for proven cases (100% versus 87.5%), followed by probable cases (89.29% versus 85.71%), and possible cases (91.57% versus 78.31%). Conclusion: Both beta-D-glucan and galactomannan assays seemed to play an encouraging role in the diagnosis of invasive aspergillosis in high-risk clinically suspected cases, with the former assay being more sensitive and the latter assay being more specific.
American journal of infection control, Jan 16, 2017
We sought to determine the incidence of bacterial biofilm-based catheter-associated urinary tract... more We sought to determine the incidence of bacterial biofilm-based catheter-associated urinary tract infections, identify variables affecting biofilm formation, and identify etiologic bacterial pathogens and antibiotic-resistance patterns associated with biofilm-based catheter-associated urinary tract infections (CAUTIs) in our setup. Patients who developed at least 2 symptoms of urinary tract infection after at least 2 days of indwelling urinary catheters were included. Urine was collected aseptically from catheter tubing and processed per standard microbiologic practices. Bacterial pathogens were identified on the basis of gram staining, colony morphology, and biochemical reactions. The detection of the biofilm was done using the tube adherence method. Drug susceptibility testing was done using the Kirby-Bauer disc diffusion method. Biofilm was detected in 73.4% isolates, whereas 26.6% of isolates were nonbiofilm producers. Mean duration of catheterization after which biofilm was det...
COVID-19 has demonstrated that most countries’ public health systems and capacities are insuffici... more COVID-19 has demonstrated that most countries’ public health systems and capacities are insufficiently prepared to prevent a localised infectious disease outbreak from spreading. Strengthening national preparedness requires National Public Health Institutes (NPHIs), or their equivalent, to overcome practical challenges affecting timely access to, and use of, data that is critical to preparedness. Our situational analysis in collaboration with NPHIs in three countries—Ethiopia, Nigeria and Pakistan—characterises these challenges. Our findings indicate that NPHIs’ role necessitates collection and analysis of data from multiple sources that do not routinely share data with public health authorities. Since initiating requests for access to new data sources can be a lengthy process, it is essential that NPHIs are routinely monitoring a broad set of priority indicators that are selected to reflect the country-specific context. NPHIs must also have the authority to be able to request rapid...
This study was carried out at the department of Microbiology, Armed Forces Institute of Pathology... more This study was carried out at the department of Microbiology, Armed Forces Institute of Pathology, Rawalpindi, Pakistan. The purpose of this study was to find out the recovery rate of mycobacteria on MGIT 960 system and to compare it with the already in use Bactec 460 TB system. The study was carried out on various human clinical specimens submitted in our institute for culture of mycobacteria. All the specimens were processed as per the recommended protocol and inoculated into both MGIT 960 and Bactec 460 TB system. Our results showed that time to detection of mycoacteria on MGIT 960 was earlier as compared to Bactec 460 system while contamination rate on MGIT 960 system was more. In conclusion, the fully automated, rapid MGIT 960 system is better than the semi-automated Bactec 460 TB system and this system has been used as Gold standard in many parts of the world.
Background Inadvertent delays in access to appropriate therapeutic interventions in high-risk gro... more Background Inadvertent delays in access to appropriate therapeutic interventions in high-risk group coronavirus disease 2019 (COVID-19) patients contribute to mortality in patients with severe/critical disease presentation. Objectives The aim of this study was to determine the effect of timely admission to the hospital on mortality of patients with severe/critical COVID-19. Another secondary aspect of this study was to observe the efficacy of time-dependent use of corticosteroids on mortality of critical/severe COVID-19 patients. Methods Clinical data of 659 patients with severe/critical COVID-19, admitted to four major tertiary care hospitals from the Islamabad-Rawalpindi region of Pakistan was retrospectively collected from a period February–August 2020. Multivariate logistic regression analysis was carried out to determine the predictors of mortality in severe/critical COVID-19 patients. Results Out of a total of 659 patients, 469 (71.2%) patients died. Age > 60 years, presenc...
COVID-19 poses a great challenge to clinical and diagnostic services around the world. The need o... more COVID-19 poses a great challenge to clinical and diagnostic services around the world. The need of biosafety practices can never be emphasised more than under current circumstances. The four pillars of biosafety namely, leadership, standard operating procedures, personal protective equipment (PPE) and engineering controls must be employed for effective and safe practices in the clinical setting in general and laboratory settings in particular. Risk assessment must be carried out before meeting up the diagnostic challenge for COVID-19 and essential biorisk management measures are required to be taken. In our resource-poor settings, we need to adapt safe but cost-effective and improvised solutions to ensure safe handling of clinical samples from COVID-19 patients in the laboratories. The correct use of PPE and their suitable alternatives are available for selection and use. Disinfection of the lab areas and safe disposal of the clinical samples from such patients is also of paramount importance.
COVID-19 cases are alarmingly increasing in Pakistan since May 2020. Laboratory based surveillanc... more COVID-19 cases are alarmingly increasing in Pakistan since May 2020. Laboratory based surveillance system has been in place since the start of the pandemic. The genomic surveillance of SARS-CoV-2 strains isolated locally has been conducted based on partial ORF1b. The sequences were classified to show the phylogenetic correlation and showed 100% homology with those detected in neighboring countries India and China. The rapid increase in cases has led to development of robust strategies to enhance the laboratory testing capacity. We are currently meeting the country requirement to diagnose the virus in the community. Nonetheless, factors like recent ease in lockdown measures has led to massive rise in number of cases in few weeks time.
Background: The first case of influenza A(H1N1)pdm09 was detected in Pakistan in June 2009. Since... more Background: The first case of influenza A(H1N1)pdm09 was detected in Pakistan in June 2009. Since then, it has continued to circulate causing considerable morbidity and mortality. The purpose of this study was to evaluate the evolutionary changes in influenza A(H1N1)pdm09 viruses from 2009 to 2016 and their relevance to the current vaccine viruses. Methods: Respiratory specimens (throat or nasopharyngeal swabs) were collected from patients with influenza-like illness and severe acute respiratory illness. Samples were processed following the protocol of the US Centers for Disease Control and Prevention. Sequencing and phylogenetic analysis of Haemagglutinin and neuraminidase genes were carried out on representative isolates of Pakistan viruses. Results: Between January 2009 and February 2016, out of 16,024 samples analysed, 1950 (12%) were positive for influenza A. During the pandemic period (2009-2010), influenza A(H1N1)pdm09 was the dominant strain with 366 out of 808 (45%) total influenza positive cases. In the post-pandemic period (2011-2016), a total of 1078 out of 1911 (56%) cases were positive for influenza A(H1N1)pdm09 with co-circulation of different influenza A subtypes. The Pakistan A(H1N1)pdm09 viruses belonged to two genetic clades: clade 7 in the pandemic period, and clade 7 (2011) and clade 6B (2015) in the postpandemic period. Sequence analysis of genes coding for surface glycoprotein's of Haemagglutinin and neuraminidase had a high degree of sequence similarity with corresponding genes of regional viruses circulating in SouthEast Asia. Conclusion: Influenza A(H1N1)pdm09 viruses from Pakistan clustered into two genetic clades, with cocirculation of some variants. Key substitutions in the receptor binding site and a few changes indicative of virulence were also detected in the post-pandemic strains. Continued monitoring of the viruses is essential for early identification of potential variants of high virulence and their relevance to current vaccine strains.
The COVID-19 epidemic is the latest evidence of critical gaps in our collective ability to monito... more The COVID-19 epidemic is the latest evidence of critical gaps in our collective ability to monitor country-level preparedness for health emergencies. The global frameworks that exist to strengthen core public health capacities lack coverage of several preparedness domains and do not provide mechanisms to interface with local intelligence. We designed and piloted a process, in collaboration with three National Public Health Institutes (NPHIs) in Ethiopia, Nigeria and Pakistan, to identify potential preparedness indicators that exist in a myriad of frameworks and tools in varying local institutions. Following a desk-based systematic search and expert consultations, indicators were extracted from existing national and subnational health security-relevant frameworks and prioritised in a multi-stakeholder two-round Delphi process. Eighty-six indicators in Ethiopia, 87 indicators in Nigeria and 51 indicators in Pakistan were assessed to be valid, relevant and feasible. From these, 14–16 i...
Objective: To compare the in vitro disk diffusion method and agar dilution method for sensitivity... more Objective: To compare the in vitro disk diffusion method and agar dilution method for sensitivity of Polymyxin B against multi drug resistant Acinetobacter baumannii. Study Design: Comparative cross sectional. Place and Duration of Study: The study was carried out in the department of Microbiology, Armed Forces Institute of Pathology (AFIP), Rawalpindi from 1st Dec 2016 to 30th Dec 2017. Methodology: Total 253 clinical specimens received from intensive care units with yielded growth of multidrug resistant Acinetobacter baumannii were evaluated for Polymyxin B susceptibility. Both Kirby bauer disk diffusion and agar dilution methods were compared with a reference method, broth microdilution. Results: Among 253 multidrug resistant isolates, 180 (71%) were extensively drug resistant and 221 (87%) were carbapenem resistant. Comparison of the disk diffusion and the MIC method by Agar dilution showed 100% correlation. 251 isolates were sensitive and 2 were resistant to Polymyxin B with MI...
Analysis of 17,782 whole-genome sequences submitted to GISAID exhibited several mutations mainly ... more Analysis of 17,782 whole-genome sequences submitted to GISAID exhibited several mutations mainly in the spike (S) gene. 1,2 During the current COVID-19 pandemic, identification of novel lineages of SARS-CoV-2 and tracking their geographic spread are essential to guide public health interventions and travel advice. We hereby report the detection and genetic characterization of two imported cases of the B.1.1.7 variant in Pakistan.
Purpose: Acinetobacter baumannii antibiotic resistant infections in high-risk patients are a grea... more Purpose: Acinetobacter baumannii antibiotic resistant infections in high-risk patients are a great challenge for researchers and clinicians worldwide. In an effort to achieve potent bactericidal outcomes, a novel chitosan-mastoparan nanoconstruct (Mast-Cs NC) was designed and assessed for its therapeutic potential through in silico, in vitro and in vivo experimentation against clinical multidrug-resistant (MDR) A. baumannii. Methods: Optimized 3D structures of mastoparan and chitosan were coupled computationally through an ionic cross-linker to generate a circular ring of chitosan encasing mastoparan. The complex was assessed for interactions and stability through molecular dynamic simulation (MDS). Binding pocket analysis was used to assess the protease-peptide interface. Mast-Cs NC were prepared by the ionic gelation method. Mast-Cs NC were evaluated in vitro and in vivo for their therapeutic efficacy against drug-resistant clinical A. baumannii. Results: MDS for 100 ns showed stable bonds between chitosan and mastoparan; the first at chitosan oxygen atom-46 and mastoparan isoleucine carbon atom with a distance of 2.77 Å, and the second between oxygen atom-23 and mastoparan lysine nitrogen atom with a distance of 2.80 Å, and binding energies of −3.6 and −7.4 kcal/mol, respectively. Mast-Cs complexes approximately 156 nm in size, with +54.9 mV zeta potential and 22.63% loading capacity, offered >90% encapsulation efficiency and were found to be geometrically incompatible with binding pockets of various proteases. The MIC 90 of Mast-Cs NC was significantly lower than that of chitosan (4 vs 512 μg/mL, respectively, p<0.05), with noticeable bacterial damage upon morphological analysis. In a BALB/c mouse sepsis model, a significant reduction in bacterial colony count in the Mast-Cs treated group was observed compared with chitosan and mastoparan alone (p<0.005). Mast-Cs maintained good biocompatibility and cytocompatibility. Conclusion: Novel mastoparan-loaded chitosan nanoconstructs signify a successful strategy for achieving a synergistic bactericidal effect and higher therapeutic efficacy against MDR clinical A. baumannii isolates. The Mast-Cs nano-drug delivery system could work as an alternative promising treatment option against MDR A. baumannii.
A large outbreak of extensively drug-resistant (XDR) Salmonella enterica serotype Typhi infection... more A large outbreak of extensively drug-resistant (XDR) Salmonella enterica serotype Typhi infections is ongoing in Pakistan, predominantly in Sindh Province. Here, we report the sequencing and characterization of five XDR Salmonella Typhi isolates from the Punjab province of Pakistan that are closely related to the outbreak strain and carry the same IncY plasmid.
The increasing prevalence of chronic infections, with frequent exposure to broad-spectrum antibio... more The increasing prevalence of chronic infections, with frequent exposure to broad-spectrum antibiotics for repeated and prolonged hospitalizations, favors the emergence of nosocomial infection by Gram-positive bacteria, such as outbreaks of Corynebacterium striatum. Cornyebacteria are gram-positive non spore forming rods. Many species are part of the normal skin and mucosal flora of humans. The clinical significance of C. striatum has recently been established. C. striatum has recently been reported to cause a variety of infections including pneumonia, endocarditis, septic arthritis, cerebrospinal fluid infection, surgical site infections and septicemia. In this study, describing three cases of Corynebacterium striatum that are attributed to health care associated infections and presented as post-surgical wound infection and hospital acquired pneumonia. The three cases include a case of a 68 years old lady who was readmitted with fever, pain and purulent discharge from surgical wound of the lower back, a 57 years old man who was readmitted 2 months after a road traffic accident with surgical wound infection of forearm and a 25 years old man on respiratory support after a head injury with ventilator associated pneumonia.
OBJECTIVE To study the immunohistochemical expression of vascular endothelial growth factors in u... more OBJECTIVE To study the immunohistochemical expression of vascular endothelial growth factors in urothelial tumours of bladder and its possible association with tumour characteristics and microvessel density. METHODS The cross-sectional descriptive study was conducted at the Histopathology Department of the Armed Forces Institute of Pathology, Rawalpindi, Pakistan, from July 2011 to December 2012, and comprised cases of non-invasive and invasive urothelial tumours of the bladder. The microvessel density and expression of vascular endothelial growth factors A, C, D were evaluated by immunohistochemistry. Specimens of transurethral bladder biopsies and surgical resection were examined. The cases were classified into non-invasive (stage pTa ) and invasive groups as well as low-grade and high-grade groups. The presence of in-situ component was evaluated in each category. To assess the microvessel density, highly vascularised foci ('hot spots') after immuno-staining with CD34 were...
Vulvovaginal candidiasis (VVC) is considered as a pervasive gynecological problem among women wor... more Vulvovaginal candidiasis (VVC) is considered as a pervasive gynecological problem among women worldwide. Owing to this fact, in the current study, we aimed at assessing the prevalence rate of spp. causing VVC in symptomatic pregnant women and their antifungal susceptibility pattern. This study was carried out in the tertiary care hospitals of Peshawar during the period of July 1, 2016 to December 31, 2016. The study group included 450 pregnant women in the age group of 17-44 years with symptoms of excessive vaginal discharge, pain and pruritis. In all, 108 pregnant women were culture positive for . Antimicrobial susceptibility testing (AST) was conducted on specimens against various azoles and polyene F group of antifungals. Out of 108 spp. isolated from vaginal swabs, there were 45 (41.7%) , 18 (16.7%) , 18 (16.7%) , 16 (14.8%) and 11 (10.2%) . According to age distribution, 27 years was the mean age. Pregnancy trimester distribution among patients was as follows: 21 (19.4%) patien...
Objective: To assess the utility of galactomannan and beta-D-glucan assays in the diagnosis of in... more Objective: To assess the utility of galactomannan and beta-D-glucan assays in the diagnosis of invasive aspergillosis in clinically suspected cases, and to compare their diagnostic potential to determine whether a combination of the two may result in an early and specific diagnosis. Methods: The descriptive cross-sectional case-control study was conducted at the Armed Forces Institute of Pathology, Rawalpindi, Pakistan, from April 1, 2017, to March 31, 2018, and comprised serum samples from clinically suspected invasive aspergillosis patients and healthy controls. The sera were tested for galactomannan and beta-D-glucan detection. Proven, probable and possible categories of invasive aspergillosis according to European Organisation for Research and Treatment of Cancer / Invasive Fungal Infections Cooperative Group and the National Institute of Allergy and Infectious Diseases Mycoses Study Group criteria. Galactomannan antigen was detected using a one-stage immunoenzymatic sandwich microplate assay. Beta-D-Glucan antigen was detected using a protease zymogen-based colorimetric assay. Sensitivity and positive / negative likelihood ratio of both the cases and the controls were calculated and compared. Results: Of the 178 subjects, 119(67%) were cases and 59(33%) were controls. Beta-D-glucan assay was more sensitive than galactomannan assay (91.6% versus 80.67%) whereas galactomannan assay was more specific than beta-D-glucan assay (86.44% versus 76.27%) in the diagnosis of invasive aspergillosis. The sensitivities of both assays decreased with decreasing probability of invasive aspergillosis, i.e., maximum sensitivities of both beta-D-glucan and galactomannan assays were for proven cases (100% versus 87.5%), followed by probable cases (89.29% versus 85.71%), and possible cases (91.57% versus 78.31%). Conclusion: Both beta-D-glucan and galactomannan assays seemed to play an encouraging role in the diagnosis of invasive aspergillosis in high-risk clinically suspected cases, with the former assay being more sensitive and the latter assay being more specific.
American journal of infection control, Jan 16, 2017
We sought to determine the incidence of bacterial biofilm-based catheter-associated urinary tract... more We sought to determine the incidence of bacterial biofilm-based catheter-associated urinary tract infections, identify variables affecting biofilm formation, and identify etiologic bacterial pathogens and antibiotic-resistance patterns associated with biofilm-based catheter-associated urinary tract infections (CAUTIs) in our setup. Patients who developed at least 2 symptoms of urinary tract infection after at least 2 days of indwelling urinary catheters were included. Urine was collected aseptically from catheter tubing and processed per standard microbiologic practices. Bacterial pathogens were identified on the basis of gram staining, colony morphology, and biochemical reactions. The detection of the biofilm was done using the tube adherence method. Drug susceptibility testing was done using the Kirby-Bauer disc diffusion method. Biofilm was detected in 73.4% isolates, whereas 26.6% of isolates were nonbiofilm producers. Mean duration of catheterization after which biofilm was det...
COVID-19 has demonstrated that most countries’ public health systems and capacities are insuffici... more COVID-19 has demonstrated that most countries’ public health systems and capacities are insufficiently prepared to prevent a localised infectious disease outbreak from spreading. Strengthening national preparedness requires National Public Health Institutes (NPHIs), or their equivalent, to overcome practical challenges affecting timely access to, and use of, data that is critical to preparedness. Our situational analysis in collaboration with NPHIs in three countries—Ethiopia, Nigeria and Pakistan—characterises these challenges. Our findings indicate that NPHIs’ role necessitates collection and analysis of data from multiple sources that do not routinely share data with public health authorities. Since initiating requests for access to new data sources can be a lengthy process, it is essential that NPHIs are routinely monitoring a broad set of priority indicators that are selected to reflect the country-specific context. NPHIs must also have the authority to be able to request rapid...
This study was carried out at the department of Microbiology, Armed Forces Institute of Pathology... more This study was carried out at the department of Microbiology, Armed Forces Institute of Pathology, Rawalpindi, Pakistan. The purpose of this study was to find out the recovery rate of mycobacteria on MGIT 960 system and to compare it with the already in use Bactec 460 TB system. The study was carried out on various human clinical specimens submitted in our institute for culture of mycobacteria. All the specimens were processed as per the recommended protocol and inoculated into both MGIT 960 and Bactec 460 TB system. Our results showed that time to detection of mycoacteria on MGIT 960 was earlier as compared to Bactec 460 system while contamination rate on MGIT 960 system was more. In conclusion, the fully automated, rapid MGIT 960 system is better than the semi-automated Bactec 460 TB system and this system has been used as Gold standard in many parts of the world.
Background Inadvertent delays in access to appropriate therapeutic interventions in high-risk gro... more Background Inadvertent delays in access to appropriate therapeutic interventions in high-risk group coronavirus disease 2019 (COVID-19) patients contribute to mortality in patients with severe/critical disease presentation. Objectives The aim of this study was to determine the effect of timely admission to the hospital on mortality of patients with severe/critical COVID-19. Another secondary aspect of this study was to observe the efficacy of time-dependent use of corticosteroids on mortality of critical/severe COVID-19 patients. Methods Clinical data of 659 patients with severe/critical COVID-19, admitted to four major tertiary care hospitals from the Islamabad-Rawalpindi region of Pakistan was retrospectively collected from a period February–August 2020. Multivariate logistic regression analysis was carried out to determine the predictors of mortality in severe/critical COVID-19 patients. Results Out of a total of 659 patients, 469 (71.2%) patients died. Age > 60 years, presenc...
COVID-19 poses a great challenge to clinical and diagnostic services around the world. The need o... more COVID-19 poses a great challenge to clinical and diagnostic services around the world. The need of biosafety practices can never be emphasised more than under current circumstances. The four pillars of biosafety namely, leadership, standard operating procedures, personal protective equipment (PPE) and engineering controls must be employed for effective and safe practices in the clinical setting in general and laboratory settings in particular. Risk assessment must be carried out before meeting up the diagnostic challenge for COVID-19 and essential biorisk management measures are required to be taken. In our resource-poor settings, we need to adapt safe but cost-effective and improvised solutions to ensure safe handling of clinical samples from COVID-19 patients in the laboratories. The correct use of PPE and their suitable alternatives are available for selection and use. Disinfection of the lab areas and safe disposal of the clinical samples from such patients is also of paramount importance.
COVID-19 cases are alarmingly increasing in Pakistan since May 2020. Laboratory based surveillanc... more COVID-19 cases are alarmingly increasing in Pakistan since May 2020. Laboratory based surveillance system has been in place since the start of the pandemic. The genomic surveillance of SARS-CoV-2 strains isolated locally has been conducted based on partial ORF1b. The sequences were classified to show the phylogenetic correlation and showed 100% homology with those detected in neighboring countries India and China. The rapid increase in cases has led to development of robust strategies to enhance the laboratory testing capacity. We are currently meeting the country requirement to diagnose the virus in the community. Nonetheless, factors like recent ease in lockdown measures has led to massive rise in number of cases in few weeks time.
Background: The first case of influenza A(H1N1)pdm09 was detected in Pakistan in June 2009. Since... more Background: The first case of influenza A(H1N1)pdm09 was detected in Pakistan in June 2009. Since then, it has continued to circulate causing considerable morbidity and mortality. The purpose of this study was to evaluate the evolutionary changes in influenza A(H1N1)pdm09 viruses from 2009 to 2016 and their relevance to the current vaccine viruses. Methods: Respiratory specimens (throat or nasopharyngeal swabs) were collected from patients with influenza-like illness and severe acute respiratory illness. Samples were processed following the protocol of the US Centers for Disease Control and Prevention. Sequencing and phylogenetic analysis of Haemagglutinin and neuraminidase genes were carried out on representative isolates of Pakistan viruses. Results: Between January 2009 and February 2016, out of 16,024 samples analysed, 1950 (12%) were positive for influenza A. During the pandemic period (2009-2010), influenza A(H1N1)pdm09 was the dominant strain with 366 out of 808 (45%) total influenza positive cases. In the post-pandemic period (2011-2016), a total of 1078 out of 1911 (56%) cases were positive for influenza A(H1N1)pdm09 with co-circulation of different influenza A subtypes. The Pakistan A(H1N1)pdm09 viruses belonged to two genetic clades: clade 7 in the pandemic period, and clade 7 (2011) and clade 6B (2015) in the postpandemic period. Sequence analysis of genes coding for surface glycoprotein's of Haemagglutinin and neuraminidase had a high degree of sequence similarity with corresponding genes of regional viruses circulating in SouthEast Asia. Conclusion: Influenza A(H1N1)pdm09 viruses from Pakistan clustered into two genetic clades, with cocirculation of some variants. Key substitutions in the receptor binding site and a few changes indicative of virulence were also detected in the post-pandemic strains. Continued monitoring of the viruses is essential for early identification of potential variants of high virulence and their relevance to current vaccine strains.
The COVID-19 epidemic is the latest evidence of critical gaps in our collective ability to monito... more The COVID-19 epidemic is the latest evidence of critical gaps in our collective ability to monitor country-level preparedness for health emergencies. The global frameworks that exist to strengthen core public health capacities lack coverage of several preparedness domains and do not provide mechanisms to interface with local intelligence. We designed and piloted a process, in collaboration with three National Public Health Institutes (NPHIs) in Ethiopia, Nigeria and Pakistan, to identify potential preparedness indicators that exist in a myriad of frameworks and tools in varying local institutions. Following a desk-based systematic search and expert consultations, indicators were extracted from existing national and subnational health security-relevant frameworks and prioritised in a multi-stakeholder two-round Delphi process. Eighty-six indicators in Ethiopia, 87 indicators in Nigeria and 51 indicators in Pakistan were assessed to be valid, relevant and feasible. From these, 14–16 i...
Objective: To compare the in vitro disk diffusion method and agar dilution method for sensitivity... more Objective: To compare the in vitro disk diffusion method and agar dilution method for sensitivity of Polymyxin B against multi drug resistant Acinetobacter baumannii. Study Design: Comparative cross sectional. Place and Duration of Study: The study was carried out in the department of Microbiology, Armed Forces Institute of Pathology (AFIP), Rawalpindi from 1st Dec 2016 to 30th Dec 2017. Methodology: Total 253 clinical specimens received from intensive care units with yielded growth of multidrug resistant Acinetobacter baumannii were evaluated for Polymyxin B susceptibility. Both Kirby bauer disk diffusion and agar dilution methods were compared with a reference method, broth microdilution. Results: Among 253 multidrug resistant isolates, 180 (71%) were extensively drug resistant and 221 (87%) were carbapenem resistant. Comparison of the disk diffusion and the MIC method by Agar dilution showed 100% correlation. 251 isolates were sensitive and 2 were resistant to Polymyxin B with MI...
Analysis of 17,782 whole-genome sequences submitted to GISAID exhibited several mutations mainly ... more Analysis of 17,782 whole-genome sequences submitted to GISAID exhibited several mutations mainly in the spike (S) gene. 1,2 During the current COVID-19 pandemic, identification of novel lineages of SARS-CoV-2 and tracking their geographic spread are essential to guide public health interventions and travel advice. We hereby report the detection and genetic characterization of two imported cases of the B.1.1.7 variant in Pakistan.
Purpose: Acinetobacter baumannii antibiotic resistant infections in high-risk patients are a grea... more Purpose: Acinetobacter baumannii antibiotic resistant infections in high-risk patients are a great challenge for researchers and clinicians worldwide. In an effort to achieve potent bactericidal outcomes, a novel chitosan-mastoparan nanoconstruct (Mast-Cs NC) was designed and assessed for its therapeutic potential through in silico, in vitro and in vivo experimentation against clinical multidrug-resistant (MDR) A. baumannii. Methods: Optimized 3D structures of mastoparan and chitosan were coupled computationally through an ionic cross-linker to generate a circular ring of chitosan encasing mastoparan. The complex was assessed for interactions and stability through molecular dynamic simulation (MDS). Binding pocket analysis was used to assess the protease-peptide interface. Mast-Cs NC were prepared by the ionic gelation method. Mast-Cs NC were evaluated in vitro and in vivo for their therapeutic efficacy against drug-resistant clinical A. baumannii. Results: MDS for 100 ns showed stable bonds between chitosan and mastoparan; the first at chitosan oxygen atom-46 and mastoparan isoleucine carbon atom with a distance of 2.77 Å, and the second between oxygen atom-23 and mastoparan lysine nitrogen atom with a distance of 2.80 Å, and binding energies of −3.6 and −7.4 kcal/mol, respectively. Mast-Cs complexes approximately 156 nm in size, with +54.9 mV zeta potential and 22.63% loading capacity, offered >90% encapsulation efficiency and were found to be geometrically incompatible with binding pockets of various proteases. The MIC 90 of Mast-Cs NC was significantly lower than that of chitosan (4 vs 512 μg/mL, respectively, p<0.05), with noticeable bacterial damage upon morphological analysis. In a BALB/c mouse sepsis model, a significant reduction in bacterial colony count in the Mast-Cs treated group was observed compared with chitosan and mastoparan alone (p<0.005). Mast-Cs maintained good biocompatibility and cytocompatibility. Conclusion: Novel mastoparan-loaded chitosan nanoconstructs signify a successful strategy for achieving a synergistic bactericidal effect and higher therapeutic efficacy against MDR clinical A. baumannii isolates. The Mast-Cs nano-drug delivery system could work as an alternative promising treatment option against MDR A. baumannii.
A large outbreak of extensively drug-resistant (XDR) Salmonella enterica serotype Typhi infection... more A large outbreak of extensively drug-resistant (XDR) Salmonella enterica serotype Typhi infections is ongoing in Pakistan, predominantly in Sindh Province. Here, we report the sequencing and characterization of five XDR Salmonella Typhi isolates from the Punjab province of Pakistan that are closely related to the outbreak strain and carry the same IncY plasmid.
The increasing prevalence of chronic infections, with frequent exposure to broad-spectrum antibio... more The increasing prevalence of chronic infections, with frequent exposure to broad-spectrum antibiotics for repeated and prolonged hospitalizations, favors the emergence of nosocomial infection by Gram-positive bacteria, such as outbreaks of Corynebacterium striatum. Cornyebacteria are gram-positive non spore forming rods. Many species are part of the normal skin and mucosal flora of humans. The clinical significance of C. striatum has recently been established. C. striatum has recently been reported to cause a variety of infections including pneumonia, endocarditis, septic arthritis, cerebrospinal fluid infection, surgical site infections and septicemia. In this study, describing three cases of Corynebacterium striatum that are attributed to health care associated infections and presented as post-surgical wound infection and hospital acquired pneumonia. The three cases include a case of a 68 years old lady who was readmitted with fever, pain and purulent discharge from surgical wound of the lower back, a 57 years old man who was readmitted 2 months after a road traffic accident with surgical wound infection of forearm and a 25 years old man on respiratory support after a head injury with ventilator associated pneumonia.
OBJECTIVE To study the immunohistochemical expression of vascular endothelial growth factors in u... more OBJECTIVE To study the immunohistochemical expression of vascular endothelial growth factors in urothelial tumours of bladder and its possible association with tumour characteristics and microvessel density. METHODS The cross-sectional descriptive study was conducted at the Histopathology Department of the Armed Forces Institute of Pathology, Rawalpindi, Pakistan, from July 2011 to December 2012, and comprised cases of non-invasive and invasive urothelial tumours of the bladder. The microvessel density and expression of vascular endothelial growth factors A, C, D were evaluated by immunohistochemistry. Specimens of transurethral bladder biopsies and surgical resection were examined. The cases were classified into non-invasive (stage pTa ) and invasive groups as well as low-grade and high-grade groups. The presence of in-situ component was evaluated in each category. To assess the microvessel density, highly vascularised foci ('hot spots') after immuno-staining with CD34 were...
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