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Background  Gas-producing perianal abscess raises the possibility of clostridial infection, with  Clostridium perfringens  being the most common causative agent, which is highly lethal if untreated timely. As the treatment of clostridial infections often differs from that of non-clostridial infections, which they may closely resemble, the importance of accurate pathogenic organism identification cannot be overemphasized. The 16S rDNA of bacteria is highly conserved within a species and among species of the same genus but demonstrates substantial variation between different species, thus making it a suitable genomic candidate for bacterial detection and identification.    Case presentation  Here, we report the case of a 53-year-old patient who was admitted to the hospital for a gas-producing perianal abscess. The patient was managed with ceftizoxime and ornidazole and then received debridement and drainage at the lesion on the second day after admission. The bacterial cultures of the patient isolates from the debridement showed a coinfection of  Escherichia coli  and  Enterococcus faecium . Although perianal redness and swelling subsided obviously after the surgery, the patient was febrile to 38.3℃ with his left upper thigh red and swollen, aggravated with tenderness and crepitus. Considering insufficient debridement and the risk of incorrect identification of pathogens, a second debridement and drainage were performed 4 days after the primary operation, and 16S rDNA sequencing of the isolates implicated  Clostridium perfringens  infection. Given the discrepancies in diagnostic results and the treatment outcomes,  Enterococcus faecium  was identified as sample contamination, and a diagnosis of coinfection of  Clostridium perfringens  and  Escherichia coli  in gas-producing perianal abscess was confirmed. The patient was then successfully treated with meropenem and vancomycin and was discharged at 27 days of admission.    Conclusions  This case represents the first report of coinfection of both clostridial and non-clostridial organisms in gas-producing perianal abscess and the first case reporting the use of 16S rDNA sequencing in the diagnosis of perianal abscess. Timely pathogen identification is critical for treating gas-producing perianal abscess and an antibiotic regimen covering both aerobic and anaerobic organisms is recommended before true pathogens are identified.    Supplementary Information  The online version contains supplementary material available at 10.1186/s13099-021-00457-x.

Coinfection of Clostridium perfringens and Escherichia coli in gas-producing perianal abscess diagnosed by 16S rDNA sequencing: a case report