​​​Publications of Microbiology​ 2024

October-December​​

  • ​Early warning systems for identifying severe maternal outcomes: findings from the WHO global maternal sepsis study. Chimwaza Y, Hunt A, Oliveira-Ciabati L, Bonnett L, Abalos E, Cuesta C, Souza JP, Bonet M, Brizuela V, Lissauer D; World Health Organization Global Maternal Sepsis Study Research Group. EClinicalMedicine. 2024 Dec 6;79:102981. doi: 10.1016/j.eclinm.2024.102981.​​ Collaborator: Dr Sadia Shakoor.​


  • Bacterial contamination of platelets concentrates in a lower middle-income country: Data from a single tertiary care hospital. Kumari B, Hasan M, Irfan S, Khalid A and Moiz B. Transfus Apher Sci. 2024 Dec;63(6):104018.​​​​​ ​DOI: 10.1016/j.transci.2024.104018.​​​


  • Addressing conflict of interest driving irrational prescribing of antibiotics in pluralistic health systems: an interventional study in Pakistan. Dr Rumina Hasan and Dr Sadia Shakoor were part of the group that led a recently released JPMA supplement https://jpma.org.pk/index.php/public_html/issue/view/98.


  • Physicians’ inclination towards standard guidelines and regulations on incentive based prescribing practices in Karachi. A mixed methods study design. Khan MS, Shepherd AR, Azizullah Z, Khan SS, Noor MN, Mark NV, Shakoor S, Hasan R, Siddiqui AR​​. A mixed methods study design. J Pak Med Assoc. 2024 Nov;74(11 (Supple-12)):S6-S10. ​https://jpma.org.pk/index.php/public_html/article/view/22842​. 


  • MRI differentiation of CNS fungal infections: correlating imaging features with microbiological and histopathological findings. Khandwala K, Farooqi J, Ali R, Bakhshi SK, Anwar SSM. Neuroradiology​. 2024 Nov 25. DOI: 10.1007/s00234-024-03510-z​

     

  • ​SARS-CoV-2 variants induce increased inflammatory gene expre​​ssion but reduced interferon responses and heme synthesis as compared with wild type strains. Merchant M, Ashra, J, Masood KI. et al. ​Sci Rep 14, 25734 (2024). https://doi.org/10.1038/s41598-024-76401-1​


  • Incentive-linked prescribing and the plights of p​atients: a qualitative study in Pakistan. Noor MN, Azizullah Z, Abbasi HS, Mark NV, Shepherd AR, Siddiqui AR, Khan MS, Hasan R, Shakoor S.  J Pak Med Assoc. 2024 Nov;74(11 (Supple-12)):S19-S23. DOI: 10.47391/JPMA.AKU-EPP-05​


  • Global burden of bacterial antimicrobial resistance 1990-2021: a systematic analysis with forecasts to 2050. ​GBD 2021 Antimicrobial Resistance Collaborators. ​Lancet. 2024 Sep 28;404(10459):1199-1226. doi: 10.1016/S0140-6736(24)01867-1. Epub 2024 Sep 16.​​ https://doi.org/10.1016/S0140-6736(24)01867-1​. Collaborator: Drs Rumina Syeda Hasan​ and Sadia Shakoor.​​

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  • Evaluation of a point-of-care multiplex immunochromatographic assay for the diagnosis of typhoid: results from a retrospective diagnostic accuracy study. Hasan R, Azizullah Z, Shams H, Dittrich S, Andrews JR, Charles RC, Esfandiari J, Gunasekera D, Tetteh KK, and Sapkota J. 2024. Journal of clinical microbiology, e0042824. Advance online publication. https://doi.org/10.1128/jcm.00428-24


  • A successful UN High-Level Meeting on antimicrobial resistance must build on the 2023 UN High-Level Meeting on tuberculosis. Cirillo D, Anthony R, Gagneux S, Horsburgh CR Jr, Hasan R, Darboe S, Laniado-Laborin R, Probandari A, Tukvadze N, Arcêncio RA, Bimba J, S, Brighenti S, Chesov D, Chiang, C Y, Kalmambetova G, Knight G, Konstantynovska O, Kruse A, Lange C, Mayanja-Kizza H, Hauser J. 2024. The Lancet. Global health, 12(8), e1225–e1226. https://doi.org/10.1016/S2214-109X(24)00229-8​


  • Chromoblastomycosis: A Single Centre Clinical Laboratory Experience of Seven Years (2016-2022) and Literature Review From Pakistan. Zeeshan M, Fatima S, Farooqi J, Owais R, Ahmed A, Jabeen K, and Zafar A. 2024. Mycoses, 67(9), e13796. https://doi.org/10.1111/myc.13796


  • Advancing medical laboratory practice in Pakistan: insights from a focus group study on technologists' training needs. Khan FMA, Moiz B, Rehman J, Majid H, Zeeshan M, Jafri L, and Khan AH. 2024. BMC medical education, 24(1), 938. https://doi.org/10.1186/s12909-024-05836-x​


  • Linezolid-resistant Enterococcus faecium clinical isolates from Pakistan: a genomic anal​ysis. Nasir SAR, Zeeshan M, Hasan R, Farooqi J, Jabeen K, ​Khan E, Ghanchi N. et al. BMC Microbiol 24, 347. 2​024. https://doi.org/10.1186/s12866-024-03491-2


  • Disparities in age and gender-specific SARS-CoV-2 diagnostic testing trends: a retrospective study from Pakistan. Ghanchi NK, Masood KI, Qazi MF, Shahid S, Nasir A, Mahmood SF, Ansar Z, Nisar MI, and Hasan Z. 2024.  BMC public health, 24(1), 2629. https://doi.org/10.1186/s12889-024-19958-w​


  • Evaluation of hydroxychloroquine or chloroquine for the prevention of COVID-19 (COPCOV): A double-blind, randomised, placebo-controlled trial. Schilling WHK, Mukaka M, Callery JJ, Llewelyn MJ, Cruz CV, Dhorda M, Ngernseng T, Waithira N, Ekkapongpisit M, Watson JA, Chandna A, Nelwan EJ, Hamers RL, Etyang A, Beg MA, Sow S, Yavo W, Allabi AC, Basnyat B, Sharma SK, COPCOV Collaborative Group. 2024.  PLoS medicine, 21(9), e1004428. https://doi.org/10.1371/journal.pmed.1004428​

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  • Correction: IgG antibodies to SARS-CoV-2 in asymptomatic blood donors at two time points in Karachi. Hasan M, Moiz B, Qaiser S, Masood KI, Ghous Z, Hussain A, Ali N, Simas JP, Veldhoen M, Alves P, Abidi SH, Ghias K, Khan E, Hasan Z. ​​PLoS One. 2024 Dec 12;19(12):e0315960. doi: 10.1371/journal.pone.0315960. Erratum for: PLoS One. 2022 Aug 24;17(8):e0271259. ​​​DOI: 10.1371/journal.pone.0315960​

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  • ​Role of Xpert PCR kit in assessing MRSA colonization in medical and surgical units of a tertiary care teaching hospital. Ashraf MA, Irfan S, Baig A, Zeeshan SM, Khan H, Ahmed I, Virani N, and Roshan R. 2024.  BMC infectious diseases, 24(1), 1096. https://doi.org/10.1186/s12879-024-09710-5​​.

July-September

  • Temporary persistence of bedaquiline-resistant mycobacterium tuberculosis Isolates under bedaquiline pressure as a model to explore resistance mechanisms. Saeed DK, Shakoor S, Hasan Z, Razzak SA, Ashraf J, Azizullah Z, Kanji A, and Hasan R. Department of Pathology and Laboratory Medicine. 2024. https://doi.org/10.4103/ijmy.ijmy_121_24​


  • Advancing medical laboratory practice in Pakistan: insights from a focus group study on technologists' training needs. Khan FMA, Moiz B, Rehman J, Majid H, Zeeshan M, Jafri L, and Khan AH. BMC Med Educ. 2024 Aug ​28;24(1):938. DOI: 10.1186/s12909-024-05836-x


  • Non-granulomatous meningoencephalitis with Balamuthia mandr​​illaris mi​micking a tumor: First confirmed case from Pakistan. ​Javed Z, Hussain MM, Ghanchi N, Gilani A, and Enam SA.​ Surg Neurol Int. 2024 Jul 12;15:238. DOI: 10.25259/SNI_181_2024​


  • ​​Pneumococcal carriage and changes in serotype distribution post- PCV13 introduction in children in Matiari, Pakistan. Iqbal I, Shahid S, Kanwar S, Kabir F, Umrani F, Ahmed S, Khan W, Qazi MF, Aziz F, Muneer S, Kalam A, Hotwani A, Mehmood J, Qureshi AK, Hasan Z, Shakoor S, Mirza S, McGee L, Lo SW, Kumar N, Azam I, Bentley SD, Jehan F, Nisar MI. ​Vaccine. 2024 Aug 20;42(23):126238. ​​DOI: 10.1016/j.vaccine.2024.126238.​

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  • WHO global research priorities for antimicrobial resistance in human health. Bertagnolio S, Dobreva Z, Centner CM, Olaru ID, Donà D, Bur​zo S, Huttner BD, Chaillon A, Gebreselassie N, Wi T, Hasso-Agopsowicz M, Allegranzi B, Sati H, Ivanovska V, Kothari KU, Balkhy HH, Cassini A, Hamers RL, Weezenbeek KV; WHO Research Agenda for AMR in Human Health Collaborators. Lancet Microbe. 2024 Aug 12:100902. DOI: 10.1016/S2666-5247(24)00134-4. Collaborator: Sadia Shakoor and Joveria Farooqi​


  • ​​The Second International Collaborative Mycology Conference: evidence-informed fight against fungal diseases in Pakistan. Farooqi J, Bongomin F, Hasan R, Nasir N, Irfan M, Mahmood SF, Zafar A, Mir F, Nizamuddin S, and Jabeen K. Ther Adv Infect Dis. 2024 Sep 6;11:20499361241272510.​ ​DOI: 10.1177/20499361241272510


  • ​A successful UN High-Level Meeting on antimicrobial resistance must build on the 2023 UN High-Level Meeting on tuberculosis. ​Cirillo D, Anthony R, Gagneux S, Horsburgh CR Jr, Hasan R, Darboe S, Laniado-Laborin R, Probandari A, Tukvadze N, Arcêncio RA, Bimba JS, Brighenti S, Chesov D, Chiang CY, Kalmambetova G, Knight G, Konstantynovska O, Kruse A, Lange C, Mayanja-Kizza H, McBryde E, Min J, Sanchez-Montalva A, Sulis G, Tsogt B, Van Der Walt M, Yeboah-Manu D and Hauser J. ​Lancet Glob Health. 2024 Aug;12(8):e1225-e1226. ​DOI: 10.1016/S2214-109X(24)00229-8


  • ​Longevity of immune response following a single dose of typhoid conjugate vaccine against Salmonella Typhi among children in Hyderabad, Pakistan. Qamar FN, Qureshi S, Haq Z, Yousafzai T, Qazi I, Irfan S, Iqbal N, Amalik Z, Hotwani A, Ali Q, Fatima I, Rahman N, Carter AS and Seidman JC.​ Int J Infect Dis. 2024 Jul 20:107187. DOI: 10.1016/j.ijid.2024.107187​



April-June​​

  • Healthcare consumers' perceptions of incentive-linked prescribing: A scoping review.​ Noor MN, Abbasi HS, van Der Mark N, Azizullah Z, Linton J, Rahman-Shepherd A, Siddiqui AR, Kha​​n MS, Hasan R and Shakoor S.​ ​PLOS Glob Public Health. 2024 Jun 27;4(6):e0003026. ​​DOI: 10.1371/journal.pgph.0003026.


  • ​Clinical characteris​tics, outcome, and factors associated with mortality of pulmonary mucormycosis: a retrospective single-center study from Pakistan. ​​Khalid R, Khanum I, Habib K, Ali AS, Farooqi J, Iqbal N, Ejaz T, Jabeen K, and Irfan M.​​ Ther Adv Infect Dis. 2024 May 6;11:20499361241251744.​​ DOI: 10.1177/20499361241251744.​


  • ​Microbiological Evaluation of Commercial Hand Sanitisers Available in Pakistan Using European Standard and Membrane Filtration Method.​​​ Ashraf MA, and Irfan S. ​​J Coll Physicians Surg Pak. 2024 Jun;34(6):667-671. ​DOI: 10.29271/jcpsp.2024.06.667.​


  • Efflux pump gene single nucleotide variants associated with resistance in Mycobacterium tuberculosis isolates with discrepant drug genotypes. ​​Hasan Z, Razzak SA, Kanji A, Shakoor S, and Hasan R.​  J Glob Antimicrob Resist. 2024 May 22:S2213-7165(24)00095-X. ​​DOI: 10.1016/j.jgar.2024.05.006.​


  • Value of 3‑D‑Printed Swabs for Respiratory Sampling and Testing. Hasan Z, Iqbal A, Ahmed I, Khan MA, Jabeen K,  Islam N, Khan E and Sayani S. ​Received: 28 June 2023 / Accepted: 24 July 2023. Biomedical Materials & Devices. https://doi.org/10.1007/s44174-023-00120-w.

  • ​Temporal changes in SARS-CoV-2 clearance kinetics and the optimal design of antiviral pharmacodynamic studies: an individual patient data meta-analysis of a randomised, controlled, adaptive platform study (PLATCOV). Wongnak P, Schilling WHK, Jittamala P, Boyd S, Luvira V, Siripoon T, Ngamprasertchai T, Batty EM, Singh S, Kouhathong J, Pagornrat W, Khanthagan P, Hanboonkunupakarn B, Poovorawan K, Mayxay M, Chotivanich K, Imwong M, Pukrittayakamee S, Ashley EA, Dondorp AM, Day NPJ, Teixeira MM, Piyaphanee W, Phumratanaprapin W, White NJ, Watson JA; PLATCOV Collaborative Group: Najia Ghanchi and M Asim Beg.  Lancet Infect Dis. 2024 Apr 24:S1473-3099(24)00183-X. doi:10.1016/S1473-3099(24)00183-X.​

  • Clinical and nutritional correlates of bacterial diarrhoea aetiology in young children: a secondary cross-sectional analysis of the ABCD trial. Somji S, Ashorn P, Manji K, Ahmed T, Chisti M, Dhingra U, Sazawal S, Singa B, Walson JL, Pavlinac P, Bar-Zeev N, Houpt E, Dube Q, Kotloff K, Sow S, Yousafzai MT, Qamar F, Bahl R, De Costa A, Simon​ J, Sudfeld CR, Duggan CP; ABCD Study Group. BMJ Paediatr Open. 2024 Apr 11;8(1):e002448. DOI: 10.1136/bmjpo-2023-002448. Collaborator: Sadia Shakoor​​


  • ​Azithromycin for Bacterial Watery Diarrhea: A Reanalysis of the AntiBiotics for Children With Severe Diarrhea (ABCD) Trial Incorporating Molecular Diagnostics. Pavlinac PB, Platts-Mills JA, Liu J, Atlas HE, Gratz J, Operario D, Rogawski McQuade ET, Ahmed D, Ahmed T, Alam T, Ashorn P, Badji H, Bahl R, Bar-Zeev N, Chisti MJ, Cornick J, Chauhan A, De Costa A, Deb S, Dhingra U, Dube Q, Duggan CP, Freyne B, Gumbi W, Hotwani A, Kabir M, Islam O, Kabir F, Kasumba I, Kibwana U, Kotloff KL, Khan SS, Maiden V, Manji K, Mehta A, Ndeketa L, Praharaj I, Qamar FN, Sazawal S, Simon J, Singa BO, Somji S, Sow SO, Tapia MD, Tigoi C, Toure A, Walson JL, Yousafzai MT, Houpt ER; AntiBiotics for Children with severe Diarrhea (ABCD) Study Group. J Infect Dis. 2024 Apr 12;229(4):988-998.​​ ​DOI: 10.1093/infdis/jiad252. Collaborator: Sadia Shakoor​


  • Pneumocystis pneumonia in HIV-positive and non-HIV patients: a retrospective comparative study from a lower-middle income country. ​​​Ayub M, Bin Ali Zubairi M, Ghanchi N, Awan S, Jabeen K and Zubairi A.​ ​​Monaldi Arch Chest Dis. 2024 Apr 3. DOI: 10.4081/monaldi.2024.2810.


  • Successful Treatment of Confirmed Naegleria fowleri Primary Amebic Meningoencephalitis.​ Burqi AMK, Satti L, Mahboob S, Anwar SOZ, Bizanjo M, Rafique M, Ghanchi NK. Emerg Infect Dis. 2024 Apr;30(4):803-805. ​​DOI: 10.3201/eid3004.230979.


January-March​​​

  • Identification of Invasive Filamentous Mold Isolates Using DNA Sequencing: Experience of a Clinical Laboratory in a Resource‑limited Setting. Irfan S, Zeeshan M, Ghanchi N, Jabeen K and Zafar A. Biomedical and Biotechnology Research Journal 8(1):p 67-71, Jan–Mar 2024. | DOI: 10.4103/bbrj.bbrj_3_24​​.


  • "Caught In Each Other's Traps": Factors Perpetuating Incentive-Linked Prescribing Deals Between Physicians and the Pharmaceutical Industry. Khan MS, Rahman-Shepherd A, Noor MN, Siddiqui AR, Goodman C, Wiseman V, Isani AK, Aftab W, Sharif S, Shakoor S, Siddiqi S and Hasan R. ​Int J Health Policy Manag. 2024 Mar 17. ​​​DOI: 10.34172/ijhpm.2024.821​​3.​


  • ​Genomic analysis of clinical Aeromonas isolates reveals genetic diversity but little evidence of genetic determinants for diarrhoeal disease. Microb Genom. 2024 Mar;10(3). ​​Klemm EJ, Nisar MI, Bawn M, Nasrin D, Qamar FN, Page A, Qadri F, Shakoor S, Zaidi AK, Levine MM, Dougan G, Kingsley RA.​ Microb Genom. 2024 Mar;10(3).​​​​​ DOI: 10.1099/mgen.0.001211.​


  • ​GBD 2021 Tuberculosis Collaborators. Global, regional, and national age-specific progress towards the 2020 milestones of the WHO End TB Strategy: a systematic analysis for the Global Burden of Disease Study 2021. ​​Lancet Infect Dis. 2024 Mar 19:S1473-3099(24)00007-0.​ ​DOI: 10.1016/S1473-3099(24)00007-0. Collaborator: Rumina Syeda Hasan​


  • Aetiology and use of antibiotics in pregnancy-related infections: results of the WHO Global Maternal Sepsis Study (GLOSS), 1-week inception cohort. Ribeiro-do-Valle CC, Bonet M, Brizuela V, Abalos E, Baguiya A, Bellissimo-Rodrigues F, Budianu M, Puscasiu L, Knight M, Lissauer D, Dunlop C, Jacob ST, Shakoor S, Gadama L, Assarag B, Souza JP, Cecatti JG; WHO GLOSS research group.​ Ann Clin Microbiol Antimicrob. 2024 Feb 24;23(1):21. DOI: 10.1186/s12941-024-00681-8​


  • ​WHO model list of essential in vitro diagnostics: strengthening diagnostics capacity to transform health care for all. Trapani D, Garcia PJ​, Schroeder L, Abdul-Ghani R, Hansali A, Offutalu PN, Sewell W, Shakoor S, Yunfeng L, Hashimoto N, Moussy FG, Aceves Capri A and Fleming K. Lancet Glob Health. 2024 Mar;12(3):e364-e365.  DOI: 10.1016/S2214-109X(23)00568-5​.


  • ​Estimating the subnational prevalence of antimicro​bial resistant Salmonella enterica serovars Typhi and Paratyphi A infections in 75 endemic countries, 1990-2019: a modelling study. GRAM Typhoid Collaborators. Lancet Glob Health. 2024 Mar;12(3):e406-e418.​ ​​​DOI: 10.1016/S2214-109X(23)00585-5. Collaborators: ​Rumina Hasan an​​d Sadia Shakoor.


  • ​Malaria in Pregnancy: ​Meta-Analyses of Prevalence and Associated Complications. ​​Das JK, Lakhani S, Rahman AR, Siddiqui F, Ali Padhani Z, Rashid Z, Mahmud O, Naqvi SK, Amir Naseem H, Jehanzeb H, Kumar S and Beg MA.​ ​2024 Feb 13:1-130. Epidemiol Infect. DOI: 10.1017/S0950268824000177.​


  • What happens when private general practitioners receive incentivisation offers from pharmaceutical sales representatives? A qualitative study in Pakistan. Noor MN, Rahman-Shepherd A, Khan SS, Hasan R, Siddiqui AR, Azam I, Bhutto F, Isani AK, Siddiqi S, Khan RI, Shakoor S and Khan M.​ 20​24 Feb 1:13558196241230853.  J Health Serv Res Policy. DOI: 10.1177/13558196241230853.​


  • ​Implementation and Long-term Efficacy of a Multifa​ceted Intervention to Reduc​​e Central Line-Associated Bloodstream Infections in Intensive Care Units of a Low Middle-Income Country. ​Latif A, Ali W, Haleem S, Mahmood F, Munir T, Virani N, Khan H, Qadir M, Roshan R, Hooda K, Khan NM, Zafar A and Pronovost P.​ 2024 Feb 7:S0196-6553(24)00060-9. Am J Infect Control. ​DOI: 10.1016/j.ajic.2024.02.001.​


  • ​​Building Research Capacity in Low- and Middle-Income Countries and Pandemic Preparedness: Lessons Learned and Future Directions. Kilmarx PH, Goraleski KA, Khan E, Lindo JF and Saravia NG.​ 2024 Jan 23:tpmd230675. Am J Trop Med Hyg.​​​DOI: 10.4269/ajtmh.23-0675.​


  • Strain features of pneumococcal isolates in the pre- and post-PCV10 era in Pakistan.  ​Javaid N, Lo SW, Nisar MI, Basharat A, Jaleel H, Rasool K, Sultana Q, Kabir F, Hotwani A, Breiman RF, Bentley SD, Shakoor S and Mirza S. 2024 Jan;10(1):00​​​1163. ​​Microb Genom. DOI: 10.1099/mgen.0.001163.​

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  • Fluconazole-resistant Candida parapsilosis complex candidemia and analysis of mutations in the ERG11 gene from Pakistan. Zeeshan M, Memon S, Malick A, Naqvi SF, Farooqi J, Ghanchi NK and Jabeen K. Mycoses. 2024 Jan;67(1):e13677. ​​DOI: 10.1111/myc.13677​


  • Daptomycin MICs by Broth Microdilution Method Against Staphylococcus aureus in Clinical Specimens: A Cross-Sectional Study from Pakistan. Zeeshan M, Ahmed I, Irfan S, Khan MA and Zafar A.​  2024 Jan;34(1):27-31. J Coll Physicians Surg Pak.​​DOI: 10.29271/jcpsp.2024.01.27.​