16S rDNA Sequencing analysis in identification of some multidrug resistant (MDR) bacterial isolates from clinical specimens

Abstract

Accurate identification of bacterial pathogens from clinical specimens and Multidrug Resistant (MDR) characterization is a key to empirical therapy.  Twelve (12) bacteria isolates from blood, urine and faecal samples were selected based on the ability to grow on Luria Bertani (LB) agar medium containing 100μg/ml ampicillin, identified by 16S rDNA PCR and sequencing. Identified isolates tagged; U01, U02, U03, U04, S08, U10 and U11 were  from urine specimens, S05, S06, S07 and S12 from stool, while B09 was from blood. The isolates were screened for MDR pattern according to Kirby-Bauer disc diffusion method. Conventional biochemical tests revealed that all the isolates are Escherichia coli. The 16S gene sequencing results confirmed that, ten (10) isolates had high similar sequence alignment with identified E. coli strains, while two are Enterobacter cloacae and P. aeruginosa. The antimicrobial susceptibility pattern shows that, most of the isolates (83.3%) were MDR. All the 12 isolates (100%) are resistant to Ampicillin, Cephalothin, Erythromycin, Fusidic acid, Novobiocin and Oxacillin, but sensitive to Colistin sulphate and Imipenem. Eleven isolates (91.7%) are resistant to Chloramphenicol, Cotrimoxazole, Streptomycin, Sulphatriad and Tetracycline. Eight of the 12 isolates (66.7%) are resistant to Ciprofloxacin and Ceftriaxone. Seven (58.3%) are resistant to Cefotaxime, Cefuroxime and Gentamycin. Nine (75%) are sensitive and three isolates (25%) are resistant to Augmentin. The high resistance to these antibacterial agents in this study was due to the indiscriminate use of first-line  common antibiotics like ampicillin in the study area, which is now substituted with Augmentin. Routine biochemical identification tests should always be confirmed with genotypic methods such as 16S gene sequencing, to avoid misdiagnosis, as variations do exist among some bacterial strains.

Keywords: Multidrug resistance, sequencing, 16S rDNA, E. coli, Enterobacter cloacae, P. aeruginosa.