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Ullah A, Ul Haq M, Iqbal M, Irfan M, Khan S, Muhammad R, Ullah A, Khurram M, Alharbi M, Alasmari AF, Ahmad S. A computational quest for identifying potential vaccine candidates against Moraxella lacunata: a multi-pronged approach. J Biomol Struct Dyn 2024; 42:2976-2989. [PMID: 37177816 DOI: 10.1080/07391102.2023.2212793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/27/2023] [Indexed: 05/15/2023]
Abstract
Moraxella lacunata is an emerging gram-negative bacterium that is responsible for multiple nosocomial infections. The bacterium is evolving resistance to several antibiotics, and currently, no effective licensed vaccines are available, which warrants the search for new therapeutics. A multi-epitope-based vaccine has been designed for M. lacunata. The complete proteome of M. lacunata contains 10,110 core proteins. Subcellular localization analysis revealed the presence of five proteins in the extracellular matrix, while 19 proteins were predicted to be located in the outer membrane, and 21 proteins were predicted to be located in the periplasmic region. Only two proteins, the type VI secretion system tube protein (Hcp) and the transporter substrate-binding domain-containing protein, were selected for epitope prediction as they fulfilled all the criteria for being potential vaccine candidates. Shortlisted epitopes from the selected proteins were fused together using "GPGPG" linkers to overcome the limitations of single-epitope vaccines. Next, the cholera toxin-B adjuvant was attached to the peptide epitope using an EAAAK linker. Docking analysis was performed to examine the interaction between the vaccine and immune cell receptors, revealing robust intermolecular interactions and a stable binding conformation. Molecular dynamics simulation findings revealed no drastic changes in the binding conformation of complexes during the simulation period. The net binding free energy of vaccine-receptor complexes was estimated using the molecular mechanics energies combined with the Poisson-Boltzmann and surface area continuum solvation (MM-PBSA) method. The reported values were -586.38 kcal/mol, -283.74 kcal/mol, and -296.88 kcal/mol for the TLR-4-vaccine complex, MHC-I-vaccine complex, and MHC-II-vaccine complex, respectively. Furthermore, the molecular mechanics energies combined with the generalized Born and surface area continuum solvation (MM-GBSA) analysis predicted binding free energies of -596.69 kcal/mol, -287.39 kcal/mol, and -298.28 kcal/mol for the TLR-4-vaccine complex, MHC-I-vaccine complex, and MHC-II-vaccine complex, respectively. The theoretical vaccine design proposed in the study could potentially serve as a powerful therapeutic against targeted pathogens, subject to validation through experimental studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Asad Ullah
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Mahboob Ul Haq
- Department of Pharmacy, Abasyn University, Peshawar, Pakistan
| | - Madiha Iqbal
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Muhammad Irfan
- College of Dentistry, Department of Oral Biology, University of Florida, Gainesville, FL, USA
| | - Saifullah Khan
- Institute of Biotechnology and Microbiology, Bacha Khan University, Charsadda, Pakistan
| | - Riaz Muhammad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Amin Ullah
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | | | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah F Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
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Khan S, Irfan M, Hameed AR, Ullah A, Abideen SA, Ahmad S, Haq MU, El Bakri Y, Al-Harbi AI, Ali M, Haleem A. Vaccinomics to design a multi-epitope-based vaccine against monkeypox virus using surface-associated proteins. J Biomol Struct Dyn 2023; 41:10859-10868. [PMID: 36533379 DOI: 10.1080/07391102.2022.2158942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022]
Abstract
In 2022, the ongoing multi-country outbreak of monkeypox virus-now occurring outside Africa, too is a global health concern. Monkeypox is a zoonotic virus, which causes disease mainly in animals, and then it is transferred to humans. Recently, in the monkeypox epidemic, a large number of human cases emerged while the global health community worked to tackle the outbreak and save lives. Herein, a multi-epitope-based vaccine is designed against monkeypox virus using two surface-associated proteins: MPXVgp002 accession number > YP_010377003.1 and MPXVgp008 accession number > YP_010377007.1 proteins. These proteins were utilized for B- and T-cell epitopes prediction. The epitopes were further screened, and the screen filtered KCKDNEYRSR, RSCNTTHNR, and RTRRETGAS with the antigenicity scores of 0.5279, 0.5604, and 0.7628, respectively. Overall, the epitopes can induce immunity in 99.74% population of the world. Further, GPGPG linkers were used for joining the epitopes and EAAAK linker was used for adjuvant attachment. It has a three-dimensional structure modelled for retaining the structural stability. Three pairs of amino acid residues that were able to make disulfide bonds were chosen: Gly1-Ser82, Cys7-Tyr10, and Phe51-Ile55. Molecular docking of vaccine was done with toll-like receptors, viz., 2, 3, 4, and 8 immune cell receptors. The docking results revealed that the vaccine as potential molecule due to its better binding affinity with toll-like receptors 2, 3, 4 and 8. Top complex in docking in with each receptor was selected based on lowest energy scores- -888.7 kcal/mol (TLR-2), -976.3 kcal/mol (TLR-3), -801.9 kcal/mol (TLR-4), and -955.4 kcal/mol (TLR-4)-were subjected to simulation. The docked complexes were evaluated in 500 ns of MD simulation. Throughout the simulation time, no significant deviation occurred. This confirmed that the vaccine as potential vaccine candidate to interact with immune cell receptors. This interaction is important for the immune system activation. In conclusion, the proposed vaccine construct against monkeypox could induce an effective immune response and speed up the vaccine development process. However, the study is completely based on the computational approach, hence, the experimental validation is required.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Saifullah Khan
- Institute of Biotechnology and Microbiology, Bacha Khan University, Charsadda, Pakistan
| | - Muhammad Irfan
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, USA
| | - Alaa R Hameed
- Department of Medical Laboratory Techniques, School of Life Sciences, Dijlah University College, Baghdad, Iraq
| | - Asad Ullah
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Syed Ainul Abideen
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Mahboob Ul Haq
- Department of Pharmacy, Abasyn University, Peshawar, Pakistan
| | - Youness El Bakri
- Department of Theoretical and Applied Chemistry, South Ural State University, Chelyabinsk, Russian Federation
| | - Alhanouf I Al-Harbi
- Department of Medical Laboratory, College of Applied Medical Sciences, Taibah University, Yanbu, Saudi Arabia
| | - Mahwish Ali
- Department of Biological Science, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Abdul Haleem
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
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Ullah A, Ullah Khan S, Haq MU, Ahmad S, Irfan M, Asif M, Muhseen ZT, Alkeraidees MS, Allemailem KS, Alrumaihi F, Almatroudi A. Computational study to investigate Proteus mirabilis proteomes for multi-epitope vaccine construct design. J Biomol Struct Dyn 2023; 41:10190-10201. [PMID: 36476074 DOI: 10.1080/07391102.2022.2153920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022]
Abstract
Proteus mirabilis is a gram-negative bacterium particularly known for its unique swarming ability. The swarming gives the bacteria ability to enhance adherence to the catheter surface and epithelium cells of the urethra to cause catheter associated urinary tract infections. P. mirabilis has evolved resistant to antibiotics. Additionally, there is an approved vaccine against P. mirabilis, thus demanding for identification of new vaccine targets. This gram-negative bacterium consists of 19,502 core proteins, out of which 19,063 are redundant proteins and remaining 439 are non-redundant proteins. The non-redundant proteins have 21 proteins present on the cell surface out of which 11 proteins are virulent. Antigenicity analysis predicted only 2 proteins as antigenic (fimbrial biogenesis outer membrane usher protein and ligand-gated channel protein). Four and seven B-cells epitopes were predicted from the former and later proteins, respectively. The predicted B-cells epitopes were used for T- cells epitopes prediction. The predicted epitopes were linked to each other through GPGPG linkers and joined with cholera toxin beta subunit adjuvant. A multi-epitopes vaccine construct consisting of 226 residues was docked with MHC-I, MHC-II and TLR-4. The best docked complex in each case has binding energy of -714.6, -744.6 and -829.5 kcal/mol, respectively. Moreover, the docking results were validated through molecular dynamics simulation and binding free energies estimation. The net energy of -137.2 kcal/mol was calculated for vaccine-MHC-I complex, -133.39 kcal/mol for vaccine-MHC-II and -158.68 kcal/mol for vaccine-TLR-4 complex. The designed vaccine construct could provoke immune responses against targeted pathogen and may be used in experimental testing.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Asad Ullah
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Saif Ullah Khan
- Institute of Biotechnology and Microbiology, Bacha Khan University, Charsadda, Pakistan
| | - Mahboob Ul Haq
- Department of Pharmacy, Abasyn University, Peshawar, Pakistan
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Muhammad Irfan
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Muhammad Asif
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Ziyad Tariq Muhseen
- Department of Pharmacy, Al-Mustaqbal University College, Hillah, Babylon, Iraq
| | - Monerh Saleh Alkeraidees
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Khaled S Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
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Ullah A, Shahid FA, Haq MU, Tahir ul Qamar M, Irfan M, Shaker B, Ahmad S, Alrumaihi F, Allemailem KS, Almatroudi A. An integrative reverse vaccinology, immunoinformatic, docking and simulation approaches towards designing of multi-epitopes based vaccine against monkeypox virus. J Biomol Struct Dyn 2023; 41:7821-7834. [PMID: 36129135 PMCID: PMC9527787 DOI: 10.1080/07391102.2022.2125441] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/11/2022] [Indexed: 12/31/2022]
Abstract
Monkeypox is a viral zoonotic disease that is caused by the monkeypox virus (MPXV) and is mainly transmitted to human through close contact with an infected person, animal, or fomites which is contaminated by the virus. In the present research work, reverse vaccinology and several other bioinformatics and immunoinformatics tools were utilized to design multi-epitopes-based vaccine against MPXV by exploring three probable antigenic extracellular proteins: cupin domain-containing protein, ABC transporter ATP-binding protein and DUF192 domain-containing protein. Both cellular and humoral immunity induction were the main concerning qualities of the vaccine construct, hence from selected proteins both B and T-cells epitopes were predicted. Antigenicity, allergenicity, toxicity, and water solubility of the predicted epitopes were assessed and only probable antigenic, non-allergic, non-toxic and good water-soluble epitopes were used in the multi-epitopes vaccine construct. The developed vaccine was found to be potentially effective against MPXV and to be highly immunogenic, cytokine-producing, antigenic, non-toxic, non-allergenic, and stable. Additionally, to increase stability and expression efficiency in the host E. coli, disulfide engineering, codon adaptation, and in silico cloning were employed. Molecular docking and other biophysical approaches were utilized to evaluate the binding mode and dynamic behavior of the vaccine construct with TLR-2, TLR-4, and TLR-8. The outcomes of the immune simulation demonstrated that both B and T cells responded more strongly to the vaccination component. The detailed in silico analysis concludes that the proposed vaccine will induce a strong immune response against MPXV infection, making it a promising target for additional experimental trials.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Asad Ullah
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Farah Ali Shahid
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Mahboob Ul Haq
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
- Department of Pharmacy, Abasyn University, Peshawar, Pakistan
| | - Muhammad Tahir ul Qamar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Irfan
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Bilal Shaker
- Department of Biomedical Engineering, Chung-Ang University, Seoul, South Korea
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Khaled S. Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
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Al-Harbi AI, Ullah A, Almanaa TN, Gul F, Khan S, Waheed Y, Ul Haq M, Muhammad R, Khurram M, Ullah A, Ahmad S. A chemoinformatic-biophysics based approach to identify novel anti-virulent compounds against Pseudomonas aeruginosa disulfide-bond protein A1. J Biomol Struct Dyn 2023:1-10. [PMID: 37551016 DOI: 10.1080/07391102.2023.2245470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
The conventional course of drug discovery is a lengthy, expensive and complex process and often experiences a high failure rate. This in-silico based study screened novel drug molecules against Pseudomonas aeruginosa disulfide-bond protein A1 (PaDsbA1; PDB ID of 4ZL7) using a variety of chemoinformatic and biophysics approaches. The structure-based virtual screening identified three antipseudomonal compounds (BDC_30129064, BDC_20699588 and BDC_25329008) that targeted PaDsbA1 enzyme with a binding energy score of -7.8 kcal/mol, -7.7 kcal/mol and -7.7 kcal/mol, respectively. The compounds revealed deep binding at the enzyme active pocket with close distance hydrogen bond interactions with Thr46, Pro55, Val58, Arg62, His88, and Asp180. The co-crystalized hexaethylene glycol revealed a binding energy of -6.02 kcal/mol. The docked compounds were further subjected to molecular dynamics simulation analysis in order to check the dynamic movements of docked complexes. The complexes reported no drastic changes during simulation time. In the simulation, stable compounds binding and docked conformation were accomplished. The docking and simulation results were validated using free binding energies calculation through molecular mechanics with generalized born surface area solvation and molecular mechanics Poisson Boltzmann surface area (MMGBSA/MMPBSA) approaches. The net binding energy estimated by MMGBSA for BDC_30129064, BDC_20699588 and BDC_25329008 was -75.07 kcal/mol, -77.87 kcal/mol and -59.1 kcal/mol, respectively while that of MMPBSA for the compounds was -72.47 kcal/mol, -78.99 kcal/mol and -60.991 kcal/mol, respectively. The physiochemical properties of the selected compounds indicated them to be physiochemically stable with good absorption, distribution, metabolism and elimination properties. From the above observations and predictions, the compounds can be recommended for further experimental validation in order to decipher their anti-virulence capacity in blocking disulfide bond formation in P. aeruginosa.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Alhanouf I Al-Harbi
- Department of Medical Laboratory, College of Applied Medical Sciences, Taibah University, Yanbu, Saudi Arabia
| | - Asad Ullah
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar, Pakistan
| | - Taghreed N Almanaa
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Farah Gul
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Saifullah Khan
- Institute of Biotechnology and Microbiology, Bacha Khan University, Charsadda, Pakistan
| | - Yasir Waheed
- Office of Research, Innovation and Commercialization, Shaheed Zulfiqar Ali Bhutto Medical University (SZABMU), Islamabad, Pakistan
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
| | - Mahboob Ul Haq
- Department of Pharmacy, Abasyn University, Peshawar, Pakistan
| | - Riaz Muhammad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | | | - Ameen Ullah
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
- Department of Computer Science, Virginia Tech, United States
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
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Quddus S, Liaqat Z, Azam S, Haq MU, Ahmad S, Alharbi M, Khan I. Identification of Efflux Pump Mutations in Pseudomonas aeruginosa from Clinical Samples. Antibiotics (Basel) 2023; 12:antibiotics12030486. [PMID: 36978353 PMCID: PMC10044530 DOI: 10.3390/antibiotics12030486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/23/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023] Open
Abstract
Efflux pumps are a specialized tool of antibiotic resistance used by Pseudomonas aeruginosa to expel antibiotics. The current study was therefore conducted to examine the expression of MexAB-OprM and MexCD-OprJ efflux pump genes. In this study, 200 samples were collected from Khyber Teaching Hospital (KTH) and Hayatabad Medical Complex (HMC) in Peshawar, Pakistan. All the isolates were biochemically identified by an Analytical Profile Index kit and at the molecular level by Polymerase Chain Reaction (PCR) utilizing specific primers for the OprL gene. A total of 26 antibiotics were tested in the current study using the guidelines of the Clinical and Laboratory Standard Institute (CLSI) and high-level resistance was shown to amoxicillin-clavulanic acid (89%) and low-level to chloramphenicol (1%) by the isolates. The antibiotic-resistant efflux pump genes MexA, MexB, OprM, MexR, MexC, MexD, OprJ, and NfxB were detected in 178 amoxicillin-clavulanic acid-resistant isolates. Mutations were detected in MexA, MexB, and OprM genes but no mutation was found in the MexR gene as analyzed by I-Mutant software. Statistical analysis determined the association of antibiotics susceptibility patterns by ANOVA: Single Factor p = 0.05. The in silico mutation impact on the protein structure stability was determined via the Dynamut server, which revealed the mutations might increase the structural stability of the mutants. The docking analysis reported that MexA wild protein showed a binding energy value of −6.1 kcal/mol with meropenem and the mexA mutant (E178K) value is −6.5 kcal/mol. The mexB wild and mutant binding energy value was −5.7 kcal/mol and −8.0 kcal/mol, respectively. Efflux pumps provide resistance against a wide range of antibiotics. Determining the molecular mechanisms of resistance in P. aeruginosa regularly will contribute to the efforts against the spread of antibiotic resistance globally.
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Affiliation(s)
- Sonia Quddus
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar 25120, Pakistan
| | - Zainab Liaqat
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar 25120, Pakistan
| | - Sadiq Azam
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar 25120, Pakistan
| | - Mahboob Ul Haq
- Department of Pharmacy, Abasyn University, Peshawar 25000, Pakistan
| | - Sajjad Ahmad
- Department of Computer Science and Physics, Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24060, USA
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ibrar Khan
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar 25120, Pakistan
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Fatima R, Yaqoob A, Qadeer E, Khan MA, Ghafoor A, Jamil B, Haq MU, Ahmed N, Baig S, Rehman A, Abbasi Q, Khan AW, Ikram A, Hicks JP, Walley J. Community- vs. hospital-based management of multidrug-resistant TB in Pakistan. Int J Tuberc Lung Dis 2022; 26:929-933. [PMID: 36163662 DOI: 10.5588/ijtld.21.0695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Multidrug-resistant TB (MDR-TB) treatment takes 18-24 months and is complex, costly and isolating. We provide trial evidence on the WHO Pakistan recommendation for community-based care rather than hospital-based care.METHODS Two-arm, parallel-group, superiority trial was conducted in three programmatic management of drug-resistant TB hospitals in Punjab and Sindh Provinces, Pakistan. We enrolled 425 patients with MDR-TB aged >15 years through block randomisation in community-based care (1-week hospitalisation) or hospital-based care (2 months hospitalisation). Primary outcome was treatment success.RESULTS Among 425 patients with MDR-TB, 217 were allocated to community-based care and 208 to hospital-based care. Baseline characteristics were similar between the community and hospitalised arms, as well as in selected sites. Treatment success was 74.2% (161/217) under community-based care and 67.8% (141/208) under hospital-based care, giving a covariate-adjusted risk difference (community vs. hospital model) of 0.06 (95% CI -0.02 to 0.15; P = 0.144).CONCLUSIONS We found no clear evidence that community-based care was more or less effective than hospital-based care model. Given the other substantial advantages of community-based care over hospital based (e.g., more patient-friendly and accessible, with lower treatment costs), this supports the adoption of the community-based care model, as recommended by the WHO.
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Affiliation(s)
- R Fatima
- Common Management Unit (TB, HIV/AIDS and Malaria), Islamabad, Pakistan
| | - A Yaqoob
- Common Management Unit (TB, HIV/AIDS and Malaria), Islamabad, Pakistan, University of Bergen, Bergen, Norway
| | - E Qadeer
- Ministry of National Health Services, Regulations and Coordination, Islamabad, Pakistan
| | - M A Khan
- Association for Social Development, Islamabad, Pakistan
| | - A Ghafoor
- National TB Control Program, Islamabad, Pakistan
| | - B Jamil
- Common Management Unit (TB, HIV/AIDS and Malaria), Islamabad, Pakistan
| | - M U Haq
- University of Bergen, Bergen, Norway, National TB Control Program, Islamabad, Pakistan
| | - N Ahmed
- Ojha Institute of Chest Diseases, Karachi, Pakistan
| | - S Baig
- Ojha Institute of Chest Diseases, Karachi, Pakistan
| | - A Rehman
- Gulab Devi Chest Hospital, Lahore, Pakistan
| | - Q Abbasi
- TB Samli Sanatorium Hospital, Murree, Pakistan
| | - A W Khan
- National TB Control Program, Islamabad, Pakistan
| | - A Ikram
- National Institute of Health, Islamabad, Pakistan
| | - J P Hicks
- Nuffield Centre for International Health and Development, Leeds Institute of Health Sciences, University of Leeds, UK
| | - J Walley
- Nuffield Centre for International Health and Development, Leeds Institute of Health Sciences, University of Leeds, UK
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Haq MU, Hinderaker SG, Fatima R, Qadeer E, Habib H, Hussain K, Khan AW. Are pulmonary tuberculosis patients identified by active and by passive case detection different? A cross sectional study in Pakistan. Int J Infect Dis 2022; 121:39-46. [PMID: 35489633 DOI: 10.1016/j.ijid.2022.04.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Active tuberculosis (TB) case finding by 'extended contact screening' (ECS), was tested during 2013-15. OBJECTIVES Our objective was to compare the characteristics of pulmonary TB patients detected by ECS with patients detected by routine passive case finding (PCF). METHODS This cross sectional study was based on data collected through ECS and routine program data in Lahore, Faisalabad and Rawalpindi districts and Islamabad in 2015. Characteristics of patients detected by ECS and PCF were compared. RESULTS In 12114 patients with pulmonary TB in the study, 4604 (38%) were detected by ECS, 4052 (88%) had bacteriological confirmation. Males represented 56.2%(95%CI 54.8-57.6) in ESC and 49.7%(95%CI 48.6-50.8) in PCF; bacteriologically confirmed cases was 88.0%(95%CI 87.1-88.9) in ECS and 50.3%(95%CI 49.2-51.4). By regression analysis we found that compared to adults aged 15-44 years, children under 15 had higher chance of being detected by ECS (adjusted odds ratio (OR) 2.69; 95%CI 2.21-3.28). There was a higher chance of being detected by ECS in Faisalabad (adjusted OR 2.57; 95%CI 2.01-3.29) compared to Islamabad. CONCLUSION Extended contact screening detected a higher proportion of men and children than routine case finding; both these groups are more often undetected by routine TB control.
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Affiliation(s)
- Mahboob Ul Haq
- University of Bergen, Norway; Management Unit (HIV/AIDS, TB & Malaria), Islamabad, Pakistan.
| | | | - Razia Fatima
- Management Unit (HIV/AIDS, TB & Malaria), Islamabad, Pakistan
| | - Ejaz Qadeer
- Pakistan Institute of Medical Sciences, Islamabad, Pakistan; Ministry of National Health Services Regulations and Coordination Islamabad, Pakistan
| | - Hammad Habib
- Management Unit (HIV/AIDS, TB & Malaria), Islamabad, Pakistan
| | - Kashif Hussain
- Ministry of National Health Services Regulations and Coordination Islamabad, Pakistan
| | - Abdul Wali Khan
- Management Unit (HIV/AIDS, TB & Malaria), Islamabad, Pakistan; Ministry of National Health Services Regulations and Coordination Islamabad, Pakistan
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Ullah W, Wali A, Haq MU, Yaqoob A, Fatima R, Khan GM. Public-Private Mix Models of Tuberculosis Care in Pakistan: A High-Burden Country Perspective. Front Public Health 2021; 9:703631. [PMID: 34447737 PMCID: PMC8383070 DOI: 10.3389/fpubh.2021.703631] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/09/2021] [Indexed: 12/03/2022] Open
Abstract
Introduction: Pakistan ranks fifth in the globally estimated burden of tuberculosis (TB) case incidence. Annually, a gap of 241,688 patients with TB exists between estimated TB incidence and actual TB case notification in Pakistan. These undetected/missed TB cases initiate TB care from providers in the private healthcare system who are less motivated to notify patients to the national database that leads to significant underdetection of actual TB cases in the Pakistani community. To engage these private providers in reaching out to missing TB cases, a national implementation trial of the Public–Private Mix (PPM) model was cohesively launched by National TB Control Program (NTP) Pakistan in 2014. The study aims to assess the implementation, contribution, and relative treatment outcomes of cohesively implemented PPM model in comparison to the non-PPM model. Methods: A retrospective record review of all forms (new and relapse) patients with TB notified from July 2015 to June 2016 was conducted both for PPM- and non-PPM models. Results: The PPM model was implemented in 92 districts in total through four different approaches and contributed 25% (81,016 TB cases) to the national TB case notification. The PPM and non-PPM case notification showed a strong statistical difference in proportions among compared variables related to gender (p < 0.001), age group (p < 0.000), and province (p < 0.000). Among PPM approaches, general practitioners and non-governmental-organization facilities achieve a treatment success of 94–95%; private hospitals achieve 82% success, whereas Parastatals are unable to follow more than half of their notified TB cases. Discussion: The PPM model findings in Pakistan are considerably consistent with countries that have prioritized PPM for an increasing trend in the TB case notification to their national TB control programs. Different PPM approaches need to be scaled up in terms of PPM implemented districts, PPM coverage, PPM coverage efficiency, and PPM coverage outcome in the Pakistani healthcare system in the future.
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Affiliation(s)
- Waseem Ullah
- Department of Pharmacy, Quaid-i-Azam University Islamabad, Islamabad, Pakistan.,Department of Pharmacy Practice, Shifa Tameer-e-Millat University Islamabad, Islamabad, Pakistan
| | - Ahmad Wali
- Health Department, Provincial Tuberculosis Control Program Balochistan, Quetta, Pakistan
| | - Mahboob Ul Haq
- Policy Strategy and Drug Management Unit, National Tuberculosis Control Program, Islamabad, Pakistan
| | - Aashifa Yaqoob
- Research Unit, National Tuberculosis Control Program, Islamabad, Pakistan
| | - Razia Fatima
- Research Unit, National Tuberculosis Control Program, Islamabad, Pakistan
| | - Gul Majid Khan
- Department of Pharmacy, Quaid-i-Azam University Islamabad, Islamabad, Pakistan.,Islamia College University, Peshawar, Pakistan
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Khan A, Afzal S, Yaqoob A, Fatima R, Ul Haq M, Junaid K, Nadir A. Epidemiology of viral hepatitis B and C in Punjab, Pakistan: a multicenter cross-sectional study, 2017-18. F1000Res 2019. [DOI: 10.12688/f1000research.20174.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Background: Globally, approximately 240 million people are chronically infected with hepatitis B virus (HBV) and hepatitis C virus (HCV), which are responsible for 96% of all hepatitis-related mortality. Pakistan has the second highest prevalence of HCV in the world. Methods: We conducted this study to ascertain the prevalence and potential risk factors associated with HBV and HCV infections in Punjab. A multi-center cross-sectional study was conducted, involving 24 Hepatitis Prevention and Treatment Clinics of the Pakistan Kidney and Liver Institute and Research Center clinics, Lahore. A total of 141,705 individuals who visited the clinics during 2017-18 were included for seroprevalence analysis of hepatitis B (HBsAg) and C (Anti-HCV). In addition, 12,427 individuals from the main group underwent detailed face-to-face interviews based on a predesigned questionnaire for risk factor assessment. Results: The overall prevalence for HBV and HCV was 8.4% and 42.7%, respectively. Of those with HCV infection, 4.2% had a co-infection. The transgender population had a higher seroprevalence of HBV (11.8%) and HCV (58.8%). Higher HBV seroprevalence was found in a younger age group (16-30 years), while the older age group (>61 years) had a higher HCV seroprevalence. Geographically, Muzaffargarh district had the highest HBV seroprevalence at 26%, followed by Rajanpur district (20.3%). HCV seroprevalence was significantly (P value <0.05) higher in Shujabad district (66.4%), followed by Muzaffargarh (65.2%). Using multivariable logistic regression analysis, age, gender, intravenous injections, hijama therapy, dental procedure, circumcision by barbers, barber shaving, hospitalization and having had surgical procedures were all found to be significant risk factors (OR >1; p<0.05) for HBV and HCV. Conclusions: There is an urgent need for proper implementation of preventive and control strategies, as well as formal evaluation and monitoring mechanisms. Sustainable and adequate funding of public-sector hepatitis programs is also an extremely important area that should not be neglected.
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Fatima R, Haq MU, Yaqoob A, Mahmood N, Ahmad KL, Osberg M, Makayova J, Hymoff A, Hanson C. Delivering Patient-Centered Care in a Fragile State: Using Patient-Pathway Analysis to Understand Tuberculosis-Related Care Seeking in Pakistan. J Infect Dis 2017; 216:S733-S739. [PMID: 29117348 PMCID: PMC5853661 DOI: 10.1093/infdis/jix380] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Background Pakistan has the sixth largest population in the world and boasts the fifth greatest burden of tuberculosis. The Government of Pakistan has set the ambitious goal of zero deaths due to tuberculosis and universal access to tuberculosis care by 2020. Successfully reaching these goals is dependent on the country’s capacity to diagnose and successfully treat an estimated 200000 unnotified or missing patients with tuberculosis. Methods A patient-pathway analysis (PPA) was conducted at the national level, as well as for each of the 4 provinces, to assess the alignment between patient care seeking and the availability of tuberculosis diagnostic and treatment services. Results Almost 90% of patients initiated care in the private sector, which accounts for only 15% of facilities with the capacity for tuberculosis diagnosis and treatment. Across the country, nearly 50% of tuberculosis microscopy laboratories were located in public-sector–basic health units and regional health centers. However, very few patients initiated care in these facilities. Overall, tuberculosis case detection was high given the low likelihood of patients reaching facilities with the capacity for tuberculosis service delivery during their first visit. Discussion Improving the engagement of the informal sector and lower-level clinicians will improve the efficiency and timeliness of tuberculosis diagnosis for patients in Pakistan. Concurrently, the apparent strength of the referral networks connecting community-level workers and private clinicians to the public sector for tuberculosis diagnosis and treatment suggests that strengthening the capacity of the public sector could be valuable.
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Affiliation(s)
- Razia Fatima
- National Tuberculosis Control Program, Islamabad, Pakistan
| | - Mahboob Ul Haq
- National Tuberculosis Control Program, Islamabad, Pakistan
| | - Aashifa Yaqoob
- National Tuberculosis Control Program, Islamabad, Pakistan
| | - Nasir Mahmood
- National Tuberculosis Control Program, Islamabad, Pakistan
| | | | | | | | | | - Christy Hanson
- Bill and Melinda Gates Foundation, Seattle, Washington.,Macalester College, St Paul, Minnesota
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Qadeer E, Fatima R, Haq MU, Yaqoob A, Kyaw NTT, Shah S, Das M, Isaakidis P. Yield of facility-based verbal screening amongst household contacts of patients with multi-drug resistant tuberculosis in Pakistan. J Clin Tuberc Other Mycobact Dis 2017; 7:22-27. [PMID: 31723697 PMCID: PMC6850254 DOI: 10.1016/j.jctube.2017.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 01/03/2017] [Accepted: 01/31/2017] [Indexed: 11/24/2022] Open
Abstract
Background Household contacts of multidrug-resistant tuberculosis (MDR-TB) patients are at a high risk of getting infected with TB/MDR-TB, therefore symptomatic or vulnerable individuals should be screened and treated early. Methods A cross-sectional study was conducted among household contacts of MDR-TB patients in three high-burden TB sites in Pakistan from July 2013 to June 2014. MDR-TB index patients were asked to provide a list of all members of their household and were asked whether any of them had TB symptoms such as productive cough, fever, weight loss and night sweat ("facility-based verbal screening"). Symptomatic contacts were defined as presumptive TB cases and were invited for investigations at the facility. Those who did not come were paid a home-visit. Confirmed TB/MDR-TB patients were registered in the nearest treatment facility. Results Of 209 MDR-TB index patients, 1467 household contacts were identified and screened, 95 of them children < 5 years. Of these 172 (12%) were symptomatic. Most common symptoms were cough 157 (91%) and fever 107 (62%). 58 (34%) presumptive TB contacts were not investigated. Of total contacts, 56 (3.8%) were diagnosed with TB, among them 54(96%) with MDR-TB and 2(4%) with drug-susceptible-TB. The number needed to screen (NNS) to identify a new MDR-TB case among adult household contacts was 27 and among presumptive adult and pediatric TB contacts was three. All 56 confirmed patients were registered for treatment. Conclusion Screening household contacts of MDR-TB index cases may be considered a feasible and high yield option, in high-burden, low-resource settings within Pakistan. The number of presumptive TB contacts required to screen to identify a new MDR-TB case was unusually low, indicating an effective strategy that could easily be scaled-up. The screening and management of vulnerable adults and children living with patients having TB of any form is a major priority in the combined efforts to end TB.
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Affiliation(s)
- Ejaz Qadeer
- National Tuberculosis Control Program Pakistan (NTP), Islamabad, Pakistan
| | - Razia Fatima
- National Tuberculosis Control Program Pakistan (NTP), Islamabad, Pakistan
| | - Mahboob Ul Haq
- National Tuberculosis Control Program Pakistan (NTP), Islamabad, Pakistan
| | - Aashifa Yaqoob
- National Tuberculosis Control Program Pakistan (NTP), Islamabad, Pakistan
| | - Nang Thu Thu Kyaw
- International Union Against Tuberculosis and Lung Disease (IUATLD), Myanmar
| | - Safieh Shah
- Médecins Sans Frontières - Operational Research Unit, Luxembourg City, Luxembourg
| | | | - Petros Isaakidis
- Médecins Sans Frontières - Operational Research Unit, Luxembourg City, Luxembourg.,Médecins Sans Frontières, Delhi, India
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Qadeer E, Fatima R, Yaqoob A, Tahseen S, Ul Haq M, Ghafoor A, Asif M, Straetemans M, Tiemersma EW. Population Based National Tuberculosis Prevalence Survey among Adults (>15 Years) in Pakistan, 2010-2011. PLoS One 2016; 11:e0148293. [PMID: 26863617 PMCID: PMC4749340 DOI: 10.1371/journal.pone.0148293] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 01/15/2016] [Indexed: 12/04/2022] Open
Abstract
Background We aimed to determine the prevalence of pulmonary tuberculosis (TB) amongst the adult population in 2010–2011 in Pakistan. Method A nationwide cross-sectional survey with multistage cluster sampling was conducted among adults (≥15 years) in 95 clusters in 2010–2011. All consenting participants were screened for cough and by chest X-ray. Participants with presumptive TB submitted two sputum samples for smear microscopy, culture, and molecular testing if needed. The TB prevalence estimates were adjusted for missing data and the cluster design. Result Of 131,329 eligible individuals, 105,913 (81%) participated in the survey, of whom 10,471 (9.9%) were eligible for sputum examination. We found 341 bacteriologically positive TB cases of whom 233 had sputum smear-positive TB. The adjusted prevalence estimates for smear and bacteriologically positive TB were 270/100,000 (95% confidence interval (CI) 217–323), and 398/100,000 (95% CI 333–463), respectively. Only 61% of the diagnosed TB cases screened positive on symptoms (cough >2wks), whereas the other TB cases were detected based on X-ray abnormalities. The TB prevalence increased with age and was 1.8 times higher among men than women. The prevalence-to-notification ratio of smear-positive TB was 3.1 (95% CI 2.5–3.7), was higher among men than women, and increased with age. Conclusion Our data suggest that there is under-detection and/or -notification of TB, especially among men and elderly. TB control should be strengthened specifically in these risk groups. X-ray examination should be combined with symptom screening to enhance case detection.
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Affiliation(s)
- Ejaz Qadeer
- National Tuberculosis Control Program Pakistan, Islamabad, Pakistan
| | - Razia Fatima
- National Tuberculosis Control Program Pakistan, Islamabad, Pakistan
| | - Aashifa Yaqoob
- National Tuberculosis Control Program Pakistan, Islamabad, Pakistan
| | - Sabira Tahseen
- National Tuberculosis Control Program Pakistan, Islamabad, Pakistan
| | - Mahboob Ul Haq
- National Tuberculosis Control Program Pakistan, Islamabad, Pakistan
| | - Abdul Ghafoor
- National Tuberculosis Control Program Pakistan, Islamabad, Pakistan
| | - Muhammad Asif
- National Tuberculosis Control Program Pakistan, Islamabad, Pakistan
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Haq MU. Four bridges to cross. People Planet 2002; 1:8-9. [PMID: 12344707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
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