Publications of Microbiology



  • Prevalence of soil-transmitted helminths and associated risk factors among primary school children in Kandahar, Afghanistan: A cross-sectional analytical study.​ R​ahimi BA, Rafiqi N, Tareen Z, Kakar KA, Wafa MH, Stanikzai MH, Beg MA, Dost AK and Taylor WR.​ ​PLoS Negl Trop Dis. 2023 Sep 11;17(9):e0011614.​​ ​DOI: 10.1371/journal.pntd.0011614

  • ​Pathogens identified in the internal tissues and placentas of stillbirths: results from the prospective, observational PURPOSe study.​ ​Harakuni SU, Somannavar MS, Ghanchi NK, Ahmed I, Zafar A, Kim J, Tikmani SS, Hwang K, Saleem S, Goudar SS, Dhaded S, Guruprasad G, Yasmin H, Yogeshkumar S, Aceituno A, Silver RM, McClure EM, Goldenberg RL; PURPOSe Investigators. ​​BJOG. 2023 Sep;130(10):1238-1246. ​​DOI: 10.1111/1471-0528.17479

  • Placental inflammation and pregnancy outcomes: A pr​ospective, observational study in South Asia: The PURPOSe study. Ahmed I, Ghanchi NK, Sunder Tikmani S, Hwang K, Zafar A, Saleem S, Uddin Z, Harakuni S, Somannavar MS, Kulkarni V, Guruprasad G, Goudar SS, Kim J, McClure EM and Goldenberg RL.​ ​BJOG. 2023 Sep 6.​ DOI: 10.1111/1471-0528.17643

  • ​Investigating the impact​​​ of prior COVID-19 on IgG antibody and interferon γ responses after BBIBP-CorV vaccination in a disease endemic population: A prospective observational study.​​ Hasan Z, Masood KI, Qaiser S, Khan E, Hussain A, Ghous Z, Khan U, Yameen M, Hassan I, Nasir MI, Qazi MF, Memon HA, Ali S, Baloch S, Bhutta ZA, Veldhoen M, Pedro Simas J, Mahmood SF, Ghias K and Hussain R.​ Health Sci Rep. 2023 Sep 8;6(9):e1521. DOI: 10.1002/hsr2.1521

  • The PURPOSe cause of death study in stillbirths and neonatal deaths in India and Pakistan: A review.​ Goldenberg RL, Saleem S, Goudar SS, Moore J, Guruprasad G, Kulkarni V, Dhaded SM, Tikmani SS, Nausheen S, Masheer S, Kallapur MG, Ghanchi NK, Harakuni SU, Ahmed I, Hwang K, Yogeshkumar S, Somannavar MS, Yasmin H, Kim J, Bann CM, Silver RM, McClure EM; PURPOSe Study Group.​ ​BJOG. 2023 Aug 17.​​ ​DOI: 10.1111/1471-0528.17635. Collaborators Afia Zafar

  • Sequential viral introductions and spread of BA.1 across Pakistan provinces during the Omicron wave.​ Bukhari AR, Ashraf J, Kanji A, Rahman YA, Trovão NS, Thielen PM, Yameen M, Kanwar S, Khan W, Kabir F, Nisar MI, Merritt B, Hasan R, Spiro D, Rasmussen Z, Aamir UB and Hasan Z.​ BMC Genomics. 2023 Aug 3;24(1):432. DOI: 10.1186/s12864-023-09539-3​​

  • Morphological study of the placenta in deliveries with pre-ecla​mpsia​​: Results from a prospective, observational study in India and Pakistan (PURPOSe). Yogeshkumar S, Dhananjay S, Gowdar S, Gowdar G, Kulkarni V, Byranahalli S, Goudar SS, Dhaded SM, Somannavar MS, Tikamani SS, Sal​eem S, Ahmed I, Ghanchi NK, Uddin Z, Yasmin H, Jackson K, McClure EM and Goldenberg RL.​ BJOG. 2023 Aug 2.​ ​​DOI: 10.1111/1471-0528.17617

  • Group B streptococcal prevalence in internal organs and placentas of deceased neonates and stillbirths in South Asia. ​​Kallapur MG, Ghanchi NK, Harakuni SU, Somannavar MS, Ahmed I, Fogle​man E, Hwang K, Kim J, Saleem S, Goudar SS, Tikmani SS, Dhaded SM, Guruprasad G, Y​asmin H,​ Yogeshkumar S, McClure EM, Goldenberg RL; PURPOSe Study Group.​ ​BJOG. 2023 Aug 2.​ ​DOI: 10.1111/1471-0528.17614​. Collaborators:​ Afia Zafar

  • Cumulative antimicrobial susceptibilities for respiratory clinical isolates of Mycobacterium avium Complex, Mycobacterium kansasii, and Mycobacterium abscessus from Pakistan 2018 to 2022.​ ​Shakoor S, Shafiq S, Shahid A, Mir F, Ali R and Hasan R.​ Int J Mycobacteriol. 2023 Jul-Sep;12(3):310-315. DOI: 10.4103/ijmy.ijmy_136_23

  • ​P​revalence of familial hy​percholesterolemia in a country-wide laboratory network in Pakistan: 10-year data from 988, 306 patients. Farhad A, Noorali AA, Tajuddin S, Khan SD, Ali M, Chunara R, Khan AH, Zafar A, Merchant A, Bokhari SS, Virani SS and Samad Z. ​Prog Cardiovasc Dis. 2023 Jul-Aug;79:19-27.​ ​DOI: 10.1016/j.pcad.2023.07.00

  • ​​Early recognition and management of matern​al sepsis in Pakistan: a feasibility study of the implementation of FAST-M intervention. ​Ahmed SI, Rind GK, Sikandar R, Raza A, Khowaja BMH, Parveen F, Khan S, Memon N, Jahangir A, Mirza DN, Cheshire J, Dunlop CL, Shakoor S, Barolia R, Sheikh L, Saleem S, Coomar​​asamy A and Lissauer D.​ ​BMJ Open. 2023 Jul 30;13(7):e069135. ​​​DOI: 10.1136/bmjopen-2022-0691​​35

  • ​Enterobacterales draft genome sequences: 15 historical (1998-2004) and 30 contemporary (2015-2016) clinical isolates from Pakistan​​. Crawford MA, Lascols C, Lomonaco S, Timme RE, Fisher DJ, Anderson K, Hodge DR, Morse SA, Pillai SP, Sharma SK, Khan E, Allard MW and Hughes MA.​​​ ​Microbiol Resour Announc. 2023 Jul 28:e0016323. ​​​​DOI: 10.1128/MRA.00163-23

  • Data usefulness in determining cause of stillbirth in South Asia.​ Goldenberg RL, Hwang K, Saleem S, Tikmani SS, Yogeshkumar S, Kulkani V, Ghanchi N, Harakuni S, Ahmed I, Uddin Z, Goudar SS, Guruprasad G, Dhaded S, Goco N, Silver RM and McClure EM.​ ​​BJOG. 2023 Jul 20. DOI: 10.1111/1471-0528.17592

  • Overlooked Candida glabrata petites are echinocandin tolerant, induce host inflammatory responses, and display poor in vivo fitness.​ Arastehfar A, Daneshnia F, Hovhannisyan H, Fuentes D, Cabrera N, Quintin C, Ilkit M, Ünal N, Hilmioğlu-Polat S, Jabeen K, Zaka S, Desai JV, Lass-Flörl C, Shor E, Gabaldon T and Perlin DS.​ ​​​2023 Jun 16:2023.0​​6.15.545195.​DOI: 10.1101/2023.06.15.545195

  • ​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, Sha​rif S, Aftab W, Shakoor S, Khan M and Hasan R.​ Health Sociol Rev. 2023 Jul;32(2):198-212. DOI: 10.1080/14461242.2022.2139628

  • Incentivisation practices and t​heir influence on physicians' prescriptions: A qualitative analysis of practice and policy in Pakistan.​ Khan M, Rahman-Shepherd A, Noor MN, Sharif S, Hamid M, Aftab W, Isani AK, Khan RI, Hasan R, Shakoor S and Siddiqi S.​ PLOS Glob Public Health. 2023 Jun 29;3(6):e0001890.​ DOI: 10.1371/journal.pgph.0001890

  • ​Pregnancy outcomes in preterm multiple gestations: Results from a prospective study in India and Pakistan (PURPOSe). ​Guruprasad G, Raghoji CR, Dhaded SM, Tikmani SS, Saleem S, Goudar SS, Hwang K, Yogeshkumar S, Somannavar MS, Reza S, Yasmin H, Moore JL, Bann CM, McClure EM, Goldenberg RL; PURPOSe Study Group.​ ​BJOG. 2023 Jul 20. ​​DOI: 10.1111/1471-0528.17602​ Collaborators​​:​ Afia Zafar and Najia Ghanchi

  • Neonatal mortality among preterm infants admitted to neonatal intensive care units in India and Pakistan: A prospective study.​​​​​ Saleem S, Tikmani SS, Goudar SS, Hwang K, Dhaded S, Gurupra​​sad G, Nadig NG, Kusagur VB, Patil LGC, Siddartha ES, Yogeshkumar S, Somannavar MS, Roujani S, Khan M, Shaikh M, Hanif M, Bann CM, McClure EM, Goldenberg RL; PURPOSE Study Group.​ BJOG. 2023 Jul 20. DOI: 10.1111/1471-0528.17581 Collaborators​​: Afia Zafar and Najia Ghanchi

  • Investigation of multidrug-resistant plasmids from carbapenemase-producing Klebsiella pneumoniae clinical isolates from Pakistan.​ Lascols C, Cherney B, Conley AB, Rishishwar L, Crawford MA, Morse SA, Fisher DJ, Anderson K, Hodge DR, Pillai SP, Hughes MA, Khan E and Sue D. Front Microbiol. 2023 Jun 29;14:1192097.​ ​DOI: 10.3389/fmicb.2023.1192097

  • ​​Etiology of Acute Infectious Meningitis and Meningoencephalitis in Karachi, Pakistan: Retrospective Observational Study from a Tertiary Care Center​. ​Shakoor S, Fatima T, Mir F, Shahid A, Shaheen N, Khan E and Jamil B. ​Am J Trop Med Hyg. 2023 Jul 17:tpmd230182.​DOI: 10.4269/ajtmh.23-0182


  • ​​​Whole-genome sequencing reveals genotypic resistance in phenotypically susceptible Mycobacterium tuberculosis clinical isolates. Hasan Z, Razzak SA, Kanji A, Shakoor S and Hasan R.​ ​Int J Mycobacteriol. 2023 Apr-Jun;12(2):179-183.​ DOI: 10.4103/ijmy.ijmy_101_23

  • ​Laboratory service relocation: experience and lessons learned from relocating a biosaf​ety level-3 clinical mycobacteriology service to a new facility.​ ​Shakoor S, Ahmed I, Wahab K, Shafiq S, Shahid A, Chishti S, Ghulam H and Hasan R.​ ​Int J Mycobacteriol. 2023 Apr-Jun;12(2):184-191. DOI: 10.4103/ijmy.ijmy_98_23

  • Correction: Ceftriaxone resistant Salmonella enterica serovar Paratyphi A identified in a case of ent​eric fever: first case report from Pakistan. ​​​​Irfan S, Hasan Z, Qamar FN, Ghanchi N, Ashraf J, Kanji A, Razzak SA, Greig D, Nair S and Hasan R.​​ BMC Infect Dis. 2023 May 23;23(1):346. ​​​DOI: 10.1186/s12879-023-08321-w.​

  • ​Ceftriaxone resistant Salmonella enterica serovar Paratyphi A identified in a case of enteric fever: first case report from Pakistan.​​​ Irfan S, Hasan Z, Qamar F, Ghanchi N, Ashraf J, Kanji A, Razzak S, Greig D, Nair S and Hasan R. BMC Infect Dis. 2023 Apr 26;23(1):267.​​ ​​DOI: 10.1186/s12879-023-08152-9


  • ​​​​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. 2023 Mar;130(4):366-376.​ ​DOI: 10.1111/1471-0528.17366.​

  • Community-acquired meningoencephalitis due to concomitant infection caused by Naegleria fowleri and Streptococcus pneum​oniae from Karachi, Pakistan: A Case Report. Ghanchi NK, Bibi S, Sultan BA and Zafar A. J Pak Med Assoc. 2023 Feb;73(2):396-398. DOI: 10.47391/JPMA.4690.​

  • ​Adapting international clinical trials during COVID-19 and beyond.​ ​Thriemer K, Degaga TS, Alam MS, Adhikari B, Tripura R, Hossain MS, Christian M, Ghanchi NK, Mnjala H, Weston S, Ley B, Rumaseb A, Tadesse D, Teferi T, Yilma D, Lee G, Unger H, Sutanto I, Pasaribu AP, Ghimire P, Beg MA and Price RN. Clin Trials. 2023 Feb 11:17407745231154215. DOI: 10.1177/17407745231154215

  • ​Socioecological factors linked with pharmaceutical inc​entive-driven prescribing in Pakistan. ​Noor MN, Rahman-Shepherd A, Siddiqui AR, Aftab W, Shakoor SHasan R and Khan M. BMJ Glob Health. 2023 Feb;6(Suppl 3):e010853. ​DOI: 10.1136/bmjgh-2022-010853.​

  • ​The Landscape of Stem Cell Research in Pakistan. ​Ahmad S,​ Zeeshan S, Hussain A, Hasan R, Ghias K, Mian A and Enam SA. ​​J Pak Med Assoc. 2023 Feb;73(Suppl 1)(2):S19-S24. DOI: 10.47391/JPMA.AKUS-04.​​​

  • ​Pathogens Identified by Minimally Invasive Tissu​e Sampling in India and Pakistan From Preterm Neonatal Deaths: The PURPOSE Study. ​Ghanchi NKAhmed 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. 2023 Feb 8;76(3):e1004-e1011. DOI: 10.1093/cid/ciac747.​

  • ​Diagnostic accuracy of different cut-off values of adenosine deaminase leve​ls in tuberculous pleural effusion. Masood KI, Shahid S, Jabeen KFarooqi J, Kerawala SR and Irfan M. ​J Pak Med Assoc. 2023 Jan;73(1):13-16. ​DOI: 10.47391/JPMA.4773.​​​ ​

  • Post-COVID-19 Pneumocystis pneumonia cases from Pakistan: an observational study. Niamatul​​lah H, Nasir N, Jabeen K, Rattani S, Farooqi JGhanchi N and Irfan M​. Access Microbiol. 2023 Jan 5;5(1):acmi000406. ​​​DOI: 10​.1099/acmi.0.000406.​

  • ​​Author Correction: Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance.​ ​Munk P, Brinch C, Møller FD, Petersen TN, Hendriksen 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. 2023 Jan 12;14(1):178. doi: 10.1038/s41467-023-35890-w. Erratum for: Nat Commun. 2022 Dec 1;13(1):7251. DOI: 10.1038/s41467-023-35890-w.​ Collaborators Rumina Hasan and Sadia Shakoor.