Publications of Microbiology


  • Community case management of fast-breathing pneumonia with 3 days oral amoxicillin vs 5 days cotrimoxazole in children 2-59 months of age in rural Pakista​n: A cluster randomized trial. ​Ahmed S, Ariff S, Muhammed S, Rizvi A, Ahmed I, Soofi SB and Bhutta ZA.​ ​J Glob Health. 2022 Dec 29;12:04097.​ ​DOI: 10.7189/jogh.12.04097

  • ​COVID-19 antibody positivity over time and pregnancy outcomes in seven low-and-middle-income countries: A prospective, observational study of the Global Network for Women's and Children's Health Research. ​​Goldenberg RL, Saleem S, Billah SM, Kim J, Moore JL, Ghanchi NK, Haque R, Figueroa L, Ayala A, Lokangaka A, Tshefu A, Goudar SS, Kavi A, Somannavar M, Esamai F, Mwenechanya M, Chomba E, Patel A, Das P, Emonyi WI, Edidi S, Deshmukh M, Hossain B, Siraj S, Mazariegos M, Garces AL, Bauserman M, Bose CL, Petri WA Jr, Krebs NF, Derman RJ, Carlo WA, Liechty EA, Hibberd PL, Koso-Thomas M, Peres-da-Silva N, Nolen TL and McClure EM. ​BJOG. 2022 Dec 12. doi: 10.1111/1471-0528.17366.​ ​​DOI: 10.1111/1471-0528.17366

  • Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance.  Munk P, Brinch C, Møller FD, Petersen TN, He​ndriksen RS, Seyfarth AM, Kjeldgaard JS, Svendsen CA, van Bunnik B, Berglund F; Global Sewage Surveillance Consortium, Larsson DGJ, Koopmans M, Woolhouse M, Aarestrup FM. Nat Commun. 2022 Dec 1;13(1):7251.​ ​​DOI: 10.1038/s41467-022-34312-7.​​​ Collaborators​​ Rumina​ Ha​​san and Sadia Shakoor.​

  • Maternal infection and stillbirth: a review. McClure EM, Silver RM, Kim J, Ahmed I, Kallapur M, Ghanchi N, Nagmoti MB, Dhaded S, Aceituno A, Tikmani SS, Saleem S, Guruprasad G, Goudar SS and Goldenberg RL. ​J Matern Fetal Neonatal Med. 2022 Dec;35(23):4442-4450. DOI: 10.1080/14767058.2020.1852206.​​​

  • Exploring stakeholders' experiences and perceptions regarding barriers to effective surveillance of communicable diseases in a rural district of Pakistan: a qualitative study. Naeem I, Siddiqi S, Siddiqui AR, and Hasan R. BMJ Open. 2022 Nov 11;12(11):e067031. DOI: 10.1136/bmjopen-2022-067031.​

  • ​Drug-resistant bacterial infections: We need urgent ac​tion and investment that focus on the weakest link. Dolecek C, Shakoor S, Basnyat B, Okwor T and Sartorius B. PLoS Biol. 2022 Nov 16;20(11):e3001903.  DOI: 10.1371/journal.pbio.3001903


  • Comparative Analysis of Commercially Available Typhoid Point-of-Care Tests: Results of a Prospective and Hybrid Retrospective Multicenter Diagnostic Accuracy Study in Kenya and Pakistan. ​Sapkota J, Hasan R, Onsare R, Arafah S, Kariuki S, Shakoor S, Qamar F, Mundalo S, Njeru F, Too R, Ndegwa E, Andrews JR and Dittrich S​​.  J Clin Microbiol. 2022 Nov 30:e0100022. ​DOI: 10.1128/jcm.01000-22.​

  • Impact of a multifaceted intervention on physicians' knowledge, attitudes and practices in relation to pharmaceutical incentivisation: protocol for a randomised control trial. Noor MN, Khan M, Rahman-Shepherd A, Siddiqui AR, Khan SS, Azam I, Shakoor S and  Hasan R. 2022 Nov 4;12(11):e067233. ​​DOI: 10.1136/bmjopen-2022-067233​.​


  • ​The healthcare field as a marketplace: general practitioners, pharmaceutical companies, and profit-led prescribing in Pakistan. Noor MN, Liverani M, Bryant J, Rahman-Shepherd A, Sharif S, Aftab W, Shakoor S, Khan M and Hasan R. ​Health Sociol Rev. 2022 Nov 2:1-15.​​ ​​​DOI: 10.1080/14461242.2022.2139628.​

  • The causes of preterm neonatal deaths in India and Pakistan (PURPOSe): a prospective cohort study.Dhaded SM, Saleem S, Goudar SS, Tikmani SS, Hwang K, Guruprasad G, Aradhya GH, Kusagur VB, Patil LGC, Yogeshkumar S, Somannavar MS, Reza S, Roujani S, Raza J, Yasmin H, Aceituno A, Parlberg L, Kim J, Moore J, Bann CM, Silver RM, Goldenberg RL, McClure EM; PURPOSe study group. Lancet Glob Health. 2022 Nov;10(11):e1575-e1581.​​ ​DOI: 10.1016/S2214-109X(22)00384-9. ​Collaborators Afia Zafar, Imran Ahmed and Najia Ghanchi.​

  • Poliovirus Immunity among Children Aged 6-11 and 36-48 Months in 14 Polio High-Risk Provinces of Afghanistan: A Health-Facility-Based Study. oofi SB, Martinez M, Farag NH, Hendley WS, Ehrhardt D, Ahmed I, Hussain I, Weldon W and Kassem AM.​ Vaccines (Basel). 2022 Oct 16;10(10):1726.​ S​ DOI: 10.3390/vaccines10101726.​

  • Screening for arboviruses in healthy blood donors: Experience from Karachi, Pakistan. Khan MA, Imtiaz K, Shafaq H, Farooqi J, Hassan M, Zafar A, Long MT, Barr KL and Khan E.​ Virol Sin. 2022 Oct;37(5):774-777. ​​DOI: 10.1016/j.virs.2022.07.008.​


  • Bedaquiline resistant Mycobacterium tuberculosis clinical isolates with and without rv0678 mutations have similar growth patterns under varying BDQ drug pressure. Saeed DK, Ashraf J, Hasan Z, Shakoor S, Kanji A and Hasan R. ​Tuberculosis (Edinb). 2022 Sep 28;137:102266. DOI: 10.1016/​

  • Fungal isolation from wound samples submitted for culture at a tertiary care hospital laboratory. ​​​Farooqi J, Ladak AA, Shaheen N and Jabeen K.​​ ​2022 Aug;72(8):1622-1625.​​​ DOI: 10.47391/JPMA.2105.​

  • Practices and predictors of menstrual hygiene management material use among adolescent and young women in rural Pakistan: A cross-sectional assessment. W​asan Y, Baxter JB, Rizvi A, Shaheen F, Junejo Q, Abro MA, Hussain A, Ahmed I, Soofi SB, Bhutta ZA.​ J Glob Health. 2022 Aug 10;12:04059. DOI: 10.7189/jogh.12.04059.​

  • ​Analysis of fks1 and fks2 gene mutations in invasive Candida glabrata s​​trains from Pakistan. Memon S, Ghanchi NK, Zafar U, Farooqi J, Zaka S and Jabeen K. Mycoses. 2022 Sep 15. DOI: 10.1111/myc.13527.​

  • Comparison of risk factors and outco​​​me of patients with and without COVID-19-associated pulmonary aspergillosis from Pakistan: A case-control study. Nasir N, Farooqi J, Zubair SM, Ayub M, Khan S, Wiqar MH, Mahmood SF and Jabeen K. ​​Mycoses. 2022 Sep 15. ​DOI: 10.1111/myc.13529.​

  • Pathogens Identified by Minimally Invasive Tissue Sampling in India and Pakistan from Preterm Neonatal Deaths: The PURPOSe Study. Ghanchi​​ NK, Ahmed I, Kim J, Harakuni S, Somannavar MS, Zafar A, Tikmani SS, Saleem S, Goudar SS, Dhaded SM, Guruprasad G, Yogeshkumar S, Hwang K, Aceituno A, Silver RM, McClure EM and Goldenberg RL. Clin Infect Dis. 2022 Sep 15:ciac747.  ​DOI: 10.1093/cid/ciac747

  • ​IgG antibodies to SARS-CoV-2 in asymptomatic blood donors at two time points in Karachi. PLoS One. Hasan M, Moiz B, Q​​​aiser S, Masood KI, Ghous Z, Hussain A, Ali N, Simas JP, Veldhoen M, Alves P, Abidi SH, Ghias K, Khan E, Hasan Z. 2022 Aug 24;17(8):e0271259. ​DOI: 10.1371/journal.pone.0271259

  • ​Emergence of a multidrug-resistant and virulent Streptococcus pneumoniae lineage mediates serotype replacement after PCV13: an international whole-genome ​​​sequencing study. Lancet Microbe. 2022 Aug 16:S2666-5247(22)00158-6. ​Lo SW, Mellor K, Cohen R, Alonso AR, Belman S, Kumar N, Hawkins PA, Gladstone RA, von Gottberg A, Veeraraghavan B, Ravikumar KL, Kandasamy R, Pollard SAJ, Saha SK, Bigogo G, Antonio M, Kwambana-Adams B, Mirza S, Shakoor S, Nisar I, Cornick JE, Lehmann D, Ford RL, Sigauque B, Turner P, Moïsi J, Obaro SK, Dagan R, Diawara I, Skoczyńska A, Wang H, Carter PE, Klugman KP, Rodgers G, Breiman RF, McGee L, Bentley SD, Almagro CM, Varon E; Global Pneumococcal Sequencing Consortium. ​​​​​DOI: 10.1016/S2666-5247(22)00158-6

  • Field evaluation of typhoid conjuga​te vaccine in a catch-up campaign among children aged 9 months to 15 years in Sindh, Pakistan. ​Thobani RS, Yousafzai MT, Sultana S, Kazi AM, Jan M, Rafey A, Khan A, Irfan S, Ujjan IU, Brown N, Mårtensson A and Qamar FN. Vaccine. 2022 Aug 6:S0264-410X(22)00840-4. DOI: 10.1016/j.vaccine.2022.06.072

  • Blended team based learning sessions to enhance medical students' engagement. ​Jabee​n K, Ah​​med I, Fatima SS and Ghias K. Med Educ. 2022 Aug;56(8):858. ​​​DOI: 10.1111/medu.14834

  • The causes of stillbirths in south Asia: results from a prospective study in India and Pakistan (PURPOSe). McClure EM, Saleem S, Goudar SS, Tikmani SS, Dhaded SM, Hwang K, Guruprasad G, Shobha D, Sarvamangala B, Yogeshkumar S, Somannavar MS, Roujani S, Reza S, Raza J, Yasmin H, Aceituno A, Parlberg L, Kim J, Bann CM, Silver RM, Goldenberg RL; PURPOSe Study Group. Lancet Glob Health. 2022 Jul;10(7):e970-e977.​​ ​​​Collaborators​- ​Afia Zafar​​, Imran Ahmed and​ Najia Ghanchi. ​​DOI: 10.1016/S2214-109X(22)00180-2.

  • Reporting of mycetoma cases from skin and soft tissue biopsies over a period of ten years: A single center report and literature review from Pakistan.​ Zeeshan M, Fatima S, Farooqi J, Jabeen K, Ahmed A, Haq A, Arif MO and Zafar A. PLoS Negl Trop Dis. 2022 Jul 29;16(7):e0010607. DOI: 10.1371/journal.pntd.0010607.​

  •  Incidence of typhoid and paratyphoid fever in Bangladesh, Nepal, and Pakistan: results of the Surveillance for Enteric Fever in Asia Project.​ Garrett DO, Longley AT, Aiemjoy K, Yousafzai MT, Hemlock C, Yu AT, Vaidya K, Tamrakar D, Saha S, Bogoch II, Date K, Saha S, Islam MS, Sayeed KMI, Bern C, Shakoor S, Dehraj IF, Mehmood J, Sajib MSI, Islam M, Thobani RS, Hotwani A, Rahman N, Irfan S, Naga SR, Memon AM, Pradhan S, Iqbal K, Shrestha R, Rahman H, Hasan MM, Qazi SH, Kazi AM, Saddal NS, Jamal R, Hunzai MJ, Hossain T, Marks F, Carter AS, Seidman JC, Qamar FN, Saha SK, Andrews JR, Luby SP.Lancet Glob Health. 2022 Jul;10(7):e978-e988. ​​​​DOI: 10.1016/S2214-109X(22)00119-X.​



  • The international and intercontinental spread and expansion of antimicrobial-resistant Salmonella Typhi: a genomic epidemiology study.​ da Silva KE, Tanmoy AM, Pragasam AK, Iqbal J, Sajib MSI, Mutreja A, Veeraraghavan B, Tamrakar D, Qamar FN, Dougan G, Bogoch I, Seidman JC, Shakya J, Vaidya K, Carey ME, Shrestha R, Irfan S, Baker S, Luby SP, Cao Y, Dyson ZA, Garrett DO, John J, Kang G, Hooda Y, Saha SK, Saha S, Andrews JR.  Lancet Microbe. 2022 Jun 21:S2666-5247(22)00093-3. ​​​DOI: 10.1016/S2666-5247(22)00093-3.​

  • How conflicts of interest hinder effective regulation of healthcare: an analysis of antimicrobial use regulation in Cambodia, Indonesia and Pakistan. ​Khan MRahman-Shepherd ABory SHasan R. et al. ​BMJ Global Health 2022;7:e008596.​ ​​​​

  • External quality assessment (EQA) combined ​with on-site technical evaluation for capacity building in clinical microbiology laboratories in Pakistan. Saeed, Noureen & Zeeshan, M & Saeed, D & Farooqi, J & Shakoor, S & Ahmed, I & Jabeen, K & Rao, J & Hasan, R. (2022). Accreditation and Quality Assurance. 27. 1-8. 10.1007/s00769-022-01495-x. DOI:10.1007/s00769-022-01495-x.

  • ​Dynamics of IgG antibody responses to SARS-CoV-2 reveals insight into immunity during the early pandemic period in Pakistan. Masood, K & Qaiser, S & Abidi, S & Khan, E & Mahmood, S & Hussain, A & Ghous, Z & Imtiaz, K & Ali, N & Hayat, H & Memon, H & Yameen, M & Ali, S & Baloch, S & Lakhani, G & Alves, P & Iqbal, N & Ahmed, K & Iqbal, J. Karachi, Pakistan. (2022).  DOI:10.2139/ssrn.4065417.

  • Risk factors and outcome of pulmonary aspergillosis in critically ill coronavirus disease 2019 patients-a multinational observational study by the European Confederation of Medical Mycology. Prattes, J., Wauters, J., Giacobbe, D. R., Salmanton-García, J., Maertens, J., Bourgeois, M., Reynders, M., Rutsaert, L., Van Regenmortel, N., Lormans, P., Feys, S., Reisinger, A. C., Cornely, O. A., Lahmer, T., Valerio, M., Delhaes, L., Jabeen, K., Steinmann, J., Chamula, M., Bassetti, M., … ECMM-CAPA Study Group (2022). Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases, 28(4), 580–587.


  • Characterisation of drug-resistant Mycobacterium tuberculosis mutations and transmission in Pakistan. Napier, G., Khan, A. S., Jabbar, A., Khan, M. T., Ali, S., Qasim, M., Mohammad, N., Hasan, R., Hasan, Z., Campino, S., Ahmad, S., Khattak, B., Waddell, S. J., Khan, T. A., Phelan, J. E., & Clark, T. G. (2022).  Scientific reports, 12(1), 7703.


  • ​​​​A Streptococcus pneumoniae lineage usually associated with pneumococcal conjugate vaccine (PCV) serotypes is the most common cause of serotype 35B invasive disease in South Africa, following routine use of PCV. Ndlangisa KM, du Plessis M, Lo S, de Gouveia L, Chaguza C, Antonio M, Kwambana-Adams B, Cornick J, Everett DB, Dagan R, Hawkins PA, Beall B, Corso A, Grassi Almeida SC, Ochoa TJ, Obaro S, Shakoor S, Donkor ES, Gladstone RA, Ho PL. The Global Pneumococcal Sequencing Consortium. Microbial genomics. 2022 April;8(4), 10.1099/mgen.0.000746.​