Culture and PCR based detection of bacteria causing urinary tract infection in urine specimen

Detection of bacteria causing UTI

  • Ghulam Sarwar Pirkani Bolan University of Medical & Health Sciences, Quetta
  • Mohammad Arif Awan
  • Ferhat Abbas
  • Mohammad Din
Keywords: Urinary Tract Infection (UTI), Antimicrobial susceptibility, Disc diffusion, Multi Drug Resistance, blaNDM1


Objectives: Urinary tract infections are the second most common bacterial infections occurring at all ages and both sexes. The increasing rate of antibiotic resistance is a global concern. The use of routinely used antibiotics is resulting in treatment failure. The objective of this study was to diagnose the urinary tract infections by routine culture sensitivity test and by molecular methods.

Methods: This study was conducted in Microbiology laboratory, Bolan Medical Complex Hospital, Quetta, from July 1st to 31st March 2019. Isolates were identified biochemically by API20E & API20NE. Antibiogram was performed using disc diffusion Kirby Bauer technique. The 16S rDNA gene approach was used for molecular identification of bacterial isolates. The presence of the blaNDM-1 gene was identified by polymerase chain reaction (PCR).

Results: We isolated 146 bacterial isolates namely Escherichia coli (n=99) 67.80%, Klebsiella pneumoniae (n=33) 22.60%, Pseudomonas aeruginosa (n=11) 7.53% and Proteus mirabilis (n=3) 2.05% from 2032 urine samples. The resistance pattern was dominated by Multi Drug Resistance (MDR). Remarkably, four isolates of Escherichia coli (n=3) and Klebsiella pneumoniae (n=1) were displaying resistance against a range of antibiotics used in the study, including carbapenems but sensitive to tigecycline and polymyxins only, suggesting extensive drug resistance having blaNDM-1 gene.

Conclusion: This is the first report on direct molecular detection of bacterial pathogens from urinary tract infected patients in Balochistan. The presence of blaNDM-1 in different bacterial species and their extensive drug resistance pattern poses a significant clinical threat. Molecular detection of bacteria and resistant gene may reduce the diagnostic time of patients.


How to cite this:
Pirkani GS, Awan MA, Abbas F, Din M. Culture and PCR based detection of bacteria causing urinary tract infection in urine specimen. Pak J Med Sci. 2020;36(3):391-395. doi:

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

How to Cite
Pirkani, G. S., Awan, M. A., Abbas, F., & Din, M. (2020). Culture and PCR based detection of bacteria causing urinary tract infection in urine specimen: Detection of bacteria causing UTI. Pakistan Journal of Medical Sciences, 36(3).
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