Co-infections and superinfections with other pathogens in patients with SARS-CoV-2 have often been reported. However, there is no clarity on the frequency of co-infection and superinfections by other pathogens and associated clinical outcomes among patients having SARS-CoV-2 infection.

While co-infection has been defined as the recovery of other respiratory pathogens in SARS-CoV-2 infected patients at the time of diagnosis of SARS-CoV-2 infection, superinfection has been defined as recovery of other respiratory pathogens during treatment of SARS-CoV-2 infection.

A meta-analysis has been published recently in PLOS One which noted that 19% of patients with COVID-19 had co-infection with other pathogens, while 24% patients with COVID-19 had a superinfection. The meta-analysis included 118 studies, of which around half were retrospective cohort studies, 35% case series, and 9% prospective cohort studies.

Sixty seven of the studies (57%) reported on co-infections, 44 (37%) reported on superinfections, and 7 (6%) reported on both co-infections and superinfections in COVID-19 patients. 

• The pooled prevalence of co-infection was 19% (95% confidence interval [CI] 14-25; I2 = 98%), with the highest prevalence seen in non-ICU patients (29%). The pooled prevalence of superinfection was 24%, with the highest being in ICU patients (41%).
• Bacterial superinfections had a prevalence of 20%, which was followed by viral co-infections at 10%, bacterial co-infections at 8% and fungal superinfections at 8%. Viral superinfections and fungal co-infections had a prevalence of 4% each. 
• Among patients with co-infections, the most common causative bacteria included Klebsiella pneumoniae, Streptococcus pneumoniae and Staphylococcus aureus. The most common viruses in patients with co-infections included influenza type A, influenza type B and respiratory syncytial virus. Aspergillus was the most commonly identified fungus among patients with a co-infection.
• In patients with superinfections, the most frequent bacteria included Acinetobacter spp., Pseudomonas and Escherichia coli, while the most frequently detected virus was Rhinovirus. Candida sp. was the most frequently identified fungus.
• The mortality risk was higher among patients with a co-infection or superinfection compared to those with only SARS-CoV-2 infection (odds ratio [OR] 3.31).

The data presented in the meta-analysis has significant implications. The authors emphasize that protocols for respiratory virus diagnostic testing must consider the fact that co-infection with SARS-CoV-2 is common. Management approach must also involve co-infection evaluation in order to provide adequate treatment for SARS-CoV-2 as well as the co-infection.

Dr Shashank R Joshi

MD, DM, FICP, FACP (USA), FACE(USA), FRCP (Lon, Glsg & Edin)

(Padma Shri Awardee)

Chair, International Diabetes Federation Southeast Asia

Dean, Indian College of Physicians (2020-21)

Endocrinologist, Joshi Clinic, Lilavati Hospital, & Bhatia Hospital

Member, Covid 19 Maharashtra State Task Force

President, Association of Physicians of India (API) (2014-15)

Past-President, Endocrine Society of India (2015-16)

Past President, RSSDI (Research Society for the Study of Diabetes in India 2011)

Past President, AIAARO (All India Association of Advancement for Research in Obesity),

Past Chapter Chair India American Association of Clinical Endocrinology

Past President, International College of Nutrition