A comparative study of SAR-CoV-2 detection using RT-PCR based testing from a nasopharyngeal swab versus indwelling tracheostomy in patients with a tracheostomy

Background Nasopharyngeal swab RT-PCR is the standard procedure for COVID-19 testing. In patients with tracheostomy with an altered airway that bypasses the nasopharynx, the yield of samples from different sites is unknown. This information will be essential for formulating a sample collection method for COVID-19 RT-PCR testing in patients undergoing tracheostomy. Methods This was a cross-sectional study. Nasopharyngeal swabs and tracheal secretion (via closed-circuit secretion suction) samples were collected from 100 patients with a non-plugging tracheostomy tube at Thammasat University Hospital, Pathum Thani, Thailand. The participants were aged between 1-96 years old for screening purposes during the pandemic. The detection results and cycle threshold (Ct) values from each site were analyzed using McNemar’s test with a 95% confidence interval. Results Four participants had positive results. One patient tested positive only for the nasopharyngeal swab, whereas the other tested positive only for the tracheal secretion sample. No statistically significant difference was found between the discordant and concordant groups (P = 1). Conclusions We found two discordant results among the four positive cases in the 100 patients. One patient tested positive only from the nasopharyngeal swab, whereas the other tested positive only from the tracheal sample. The percentage of agreement was 98, and the kappa coefficient value was 65.64% (p <0.001). According to these results, one sample from the nasopharynx or tracheal tube should be sufficient to determine the infection status of low-risk patients. For highly suspicious cases, multisite sampling should be performed. This study showed discordance in COVID-19 RT-PCR screening results using samples from nasopharyngeal swabs and tracheal secretions in tracheotomized patients. A multiple-site sample is suggested for highly suspicious patients with tracheostomy.