Risk factors and outcomes of secondary co-infections in hospitalised COVID-19 patients in Malaysia: a case control study

Hospitalised COVID-19 patients are susceptible to co-infections. This study aims to evaluate the risk factors and outcomes of secondary co-infections in hospitalised COVID-19 patients in Malaysia. A total of 929 COVID-19 patients were admitted to our centre from January 2021 to December 2022. Thirty-four cases of secondary co-infections among hospitalised COVID-19 patients were identified using standard microbiology culture. A control group of 136 hospitalised COVID-19 patients without secondary infections, admitted during the same period, was randomly selected. Additionally, 48 archived COVID-19 samples were analysed for primary co-infections involving 33 respiratory pathogens using multiplex real-time reverse transcription polymerase chain reaction (RT-PCR). The prevalence of secondary co-infections in hospitalised COVID-19 patients was 3.7%. Thirty-nine pathogens were isolated where Acinetobacter baumannii and Candida spp. were among the commonest isolated pathogens (4 isolates each, 10.3%). Significant factors associated with secondary co-infections included longer hospital stay (p ≤ 0.001) and hypertension (p = 0.032). Laboratory findings associated with secondary co-infections were thrombocytopenia (p = 0.021) and elevated alkaline phosphatase (p = 0.024). Among patients with secondary co-infections, 52.9% died, compared to only 14.7% in the control group (p = 0.008), highlighting the poor clinical outcomes of patients with co-infections. Secondary co-infections were also significantly associated with ICU admission (p = 0.045). Out of 48 archived samples, 32 samples (66.7%) were found to have positive respiratory pathogens of primary co-infection. Although secondary co-infections occurred in a relatively small subset of hospitalised COVID-19 patients, their profound association with fatal outcomes underscores the need for heightened clinical vigilance when these specific risk factors are present.