Reassessment of Clinical Pathogens Diagnosed by Sub-urban Facilities of Dhaka: Necessity of Comprehensive Techniques to Manage Antibiotic Resistance

Shahnaz Fatema^a, Md Reaz Uddin^b, Siraje Arif Mahmud^b,c, Md. Jalal Uddin^a,^e, Ali Azam Talukder^a, MohibUllah Khondoker^d, Mohd. Raeed Jamiruddin^f, Nafisa Azmuda^a, Nihad Adnan^a*

Misidentification of bacterial pathogens may promote the dissemination of antibiotic resistance.

Abstract

Background: The determinative bacteriology currently available in the suburbs of Dhaka city mainly involves culture-based identification techniques. Incorporation of extensive biochemical characterization could enhance the efficiency of the existing methods and reduce the risk of wrong medication. The study was aimed, in this connection, at reassessment of clinical pathogens in the suburbs of Dhaka city through biochemical and molecular analysis. Methods: To assess the accuracy of identification of clinical pathogens by the diagnostic facilities of suburbs of Dhaka city, we were provided with previously identified clinical strains from different diagnostic facilities along with their clinical data. The etiological agents, were analyzed based on the cultural characteristics on different selective agar media and biochemical properties. The API20E profiles of the pathogens were analyzed to identify the organisms. Furthermore, to verify the results of API20E, 16s rRNA genes were sequenced and their phylogenetic relationship was checked in NCBI database. Result: The gram-negative clinical strains that the diagnostic facilities (DFI) provided were Escherichia coli, Klebsiella, and Pseudomonas. We further reassessed their identities among which two-third of those clinical strains were correctly identified as E. coli while half of those were correctly reported as Klebsiella. In addition to it, some of the DFI strains were also identified asEnterobacter, Yersinia, Acinetobacter, and as well as some unknown bacterial genera. These results were confirmed initially by biochemical tests followed by API20E and 16s rRNA sequencing. Finally, throughantibiogram we also observed that the reconfirmed E. coli and Klebsiella strains were resistant to various antibiotics, such as ampicillin, cefotaxime, ciprofloxacin, azithromycin etc. Conclusions:  Our findings allude to the fact that diagnostics facilities though are able to identify gram-negative bacteria within clinical strains, they are unable to identify the causative agents properly. We also hypothesize that misidentification of bacterial pathogens may promote the dissemination of antibiotic resistance.

Keywords:Misidentification, antibiotic resistance, suburb diagnostic facilities, reassessment.

Significance: Importance of the quality assurance of the service of the suburb diagnostic facilities to reduce the misuse of antibiotics.

Edited by: Sheikh Ariful Hoque, PhD, University of Dhaka, Dhaka, Bangladesh.

Abbreviations: DFI- diagnostic facility identified; AR- Antibiotic resistance; MDR- multi-drug resistance; NMR- nuclear magnetic resonance; MALDI-TOF- matrix-assisted laser desorption/ionization-time of flight; rRNA- ribosomal RNA; PCR- polymerase chain reaction.

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