Microbial co-infections in COVID-19: Associated microbiota and underlying mechanisms of pathogenesis

M Nazmul Hoque; Salma Akter; Israt Dilruba Mishu; M Rafiul Islam; M Shaminur Rahman; Masuda Akhter; Israt Islam; Mehedi Mahmudul Hasan; Md Mizanur Rahaman; Munawar Sultana; Tofazzal Islam; M Anwar Hossain

doi:10.1016/j.micpath.2021.104941

Microbial co-infections in COVID-19: Associated microbiota and underlying mechanisms of pathogenesis

Microb Pathog. 2021 Jul:156:104941. doi: 10.1016/j.micpath.2021.104941. Epub 2021 May 4.

Affiliations

¹ Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh; Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh.
² Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh; Department of Microbiology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh.
³ Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh.
⁴ Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh; Department of Fisheries and Marine Science, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh.
⁵ Institute of Biotechnology and Genetic Engineering (IBGE), BSMRAU, Gazipur, 1706, Bangladesh.
⁶ Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh; Jashore University of Science and Technology, Jashore, 7408, Bangladesh. Electronic address: hossaina@du.ac.bd.

Abstract

The novel coronavirus infectious disease-2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has traumatized the whole world with the ongoing devastating pandemic. A plethora of microbial domains including viruses (other than SARS-CoV-2), bacteria, archaea and fungi have evolved together, and interact in complex molecular pathogenesis along with SARS-CoV-2. However, the involvement of other microbial co-pathogens and underlying molecular mechanisms leading to extortionate ailment in critically ill COVID-19 patients has yet not been extensively reviewed. Although, the incidence of co-infections could be up to 94.2% in laboratory-confirmed COVID-19 cases, the fate of co-infections among SARS-CoV-2 infected hosts often depends on the balance between the host's protective immunity and immunopathology. Predominantly identified co-pathogens of SARS-CoV-2 are bacteria such as Streptococcus pneumoniae, Staphylococcus aureus, Klebsiella pneumoniae, Haemophilus influenzae, Mycoplasma pneumoniae, Acinetobacter baumannii, Legionella pneumophila and Clamydia pneumoniae followed by viruses including influenza, coronavirus, rhinovirus/enterovirus, parainfluenza, metapneumovirus, influenza B virus, and human immunodeficiency virus. The cross-talk between co-pathogens (especially lung microbiomes), SARS-CoV-2 and host is an important factor that ultimately increases the difficulty of diagnosis, treatment, and prognosis of COVID-19. Simultaneously, co-infecting microbiotas may use new strategies to escape host defense mechanisms by altering both innate and adaptive immune responses to further aggravate SARS-CoV-2 pathogenesis. Better understanding of co-infections in COVID-19 is critical for the effective patient management, treatment and containment of SARS-CoV-2. This review therefore necessitates the comprehensive investigation of commonly reported microbial co-pathogens amid COVID-19, their transmission pattern along with the possible mechanism of co-infections and outcomes. Thus, identifying the possible co-pathogens and their underlying molecular mechanisms during SARS-CoV-2 pathogenesis may shed light in developing diagnostics, appropriate curative and preventive interventions for suspected SARS-CoV-2 respiratory infections in the current pandemic.

Keywords: COVID-19; Microbial co-infections; Molecular pathogenesis; SARS-CoV-2.

Publication types

Review

MeSH terms

COVID-19*
Coinfection*
Communicable Diseases*
Humans
Microbiota*
SARS-CoV-2