| Summary: | Abstract Background Managing surgical site infections, with negative culture report in routine diagnosis is a common dilemma in microbiology accounting more than 30% worldwide. The present study attempted to identify the presence of bacterial spp. if any in wound aspirates/swabs of culture negative surgical site infections of hospitalised patients using molecular tools. Methods Ninety-seven patients with post-operative SSI whose wound swabs/aspirate were negative in the conventional aerobic culture after 72 h of incubation were analysed by 16S rRNA gene specific broad range PCR. The amplified DNA fragments were sequenced by Sanger DNA sequencing method and homology of the sequence were matched using NCBI BLAST (NCBI, USA) Results Of the 97 patients, 16S rRNA based broad range PCR assay could identify the presence of bacterial pathogen in 53(54.63%) cases, of which 29 isolates were supposed to be of viable but non-culturable bacteria (VBNC), 07 were of obligatory anaerobes and 13 were of unculturable bacteria, 04 were with poly bacterial infections. Conclusions Our study highlights the usefulness of PCR assay in detecting the presence of any VBNC, anaerobes and unculturable bacteria in SSI patients regardless of how well the bacteria may or may not grow in culture. Measures should be taken to use anaerobic culture system and PCR diagnosis along with conventional culture to detect the VBNC and unculturable bacteria where Gram stain is positive for better patient care.
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