Lung microbiome alterations and secondary-infections in lethal COVID-19

Lung microbiome alterations and secondary-infections in lethal COVID-19

In a recent study posted to the medRxiv* preprint server, researchers examined how an interplay of host and microbial factors weakened immunity leading to secondary infections in coronavirus disease 2019 (COVID-19)-infected individuals.

Study: Host and microbiome features of secondary infections in lethal covid-19. Image Credit: MDGRPHCS/Shutterstock

The scientific data demonstrating host and microbial factors that drive secondary infections following severe disease and contributing to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-related mortality is unavailable. 

About the study

In the present study, researchers used a combination of autopsies with microbial cultivation and ribonucleic acid (RNA) sequencing to gain pathophysiological insights into COVID-19 progression, define major organ pathologies and specify secondary infections.

They autopsied 20 COVID-19 cases and 14 control subjects according to the Centers for Disease Control and Prevention (CDC) guidelines in the county of Styria in a biosafety level 3 (BSL-3) facility, designed for post-mortem examinations and sample collection.

They used standard procedures to process, stain, and prepare formalin-fixed paraffin-embedded (FFPE) lung tissue specimens for histopathological examinations. From each autopsied case, at least two specimens/lobes of a lung were taken into account to examine the variations in COVID-19 representation and assess histopathological lung features.

Study findings

COVID-19 lung pathology is multifaceted, and two discriminators of its lethal course are diffuse alveolar damage (DAD) and the presence of secondary infections. Notably, SARS-CoV-2-induced direct DAD was found to be chronologically divergent from DAD due to secondary infections, thus provoking entirely different host reactions.

Up to 42% of cases developed secondary infections. Subsequently, in one case, secondary infections due to Staphylococcus aureusEnterococcus faecium, or Klebsiella pneumonia, as well as fungi, such as Candida spp. and the mold Rhizopus microspores were identified. These typical agents of secondary infections have also been observed in patients with influenza, SARS, and Middle East respiratory syndrome (MERS).

In case #16, the authors observed multiple pathogens, including K. pneumoniaS. aureus, and C. glabrata, indicating polymicrobial infections. They were present in cultures and detected via libraries for RNA sequencing (RNAseq). In addition, five COVID-19 cases yielded RNA transcripts of Epstein Barr virus (EBV), detected by RNA in situ hybridization of lung tissues. EBV emergence indicated endogenous reactivation due to weakened immunity.

Single-cell transcriptomic studies showed myeloid cells in bronchioloalveolar lavage fluids (BALF) specimens from COVID-19 patients. Moreover, high proportions of proinflammatory macrophages were observed.

Generally, M1-type macrophages dominate early DAD, whereas later DAD stages show increased M2-types involved in tissue repair with immunosuppressive features, thus indicating that later (organizing) phases of DAD might be more prone to acquiring secondary infections.

Past studies have discussed direct complement activation by the SARS-CoV-2 spike protein. Additionally, these studies have shown that complement factors, including C1q deposit in vessels and epithelial cells of lungs and skin during COVID-19. Overall, complement activation has been discussed linked to COVID-19-related respiratory failure and in the context of fibrin-clot formation and endothelial injury.

The current study findings suggested another pathophysiological role of the complement system in COVID-19; subsequently, authors observed that immune complexes formed by SARS-CoV-2 antigens and antibodies activated complement factors, such as complement component 1q (C1q) that perpetuated immune impairment during SARS-CoV infection. 

The clearance of apoptotic and necrotic cells by phagocytes occurs through efferocytosis. During efferocytosis, phagocytes also produce anti-inflammatory cytokines to suppress inflammation. Subsequently, C1q and molecules released from apoptotic and necrotic cells formed complexes that conferred uptake and induced a tolerogenic state. Notably, this binding that occurred between C1q and leukocyte-associated immunoglobulin-like receptor 1 (LAIR-1) restricted the production of type I interferons impairing antiviral defense during COVID-19. 

Subsequently, the "DAD2" subtype observed in the current study showed increased macrophages, C1q, and LAIR-1 representing cases with a lowered immune tone prone to the development of secondary infections. Overall, the progression of exudative DAD into fibrotic DAD indicated healing of severe acute lung injury (ALI) characterized by reduced inflammation, with involvement of immune suppressive factors, such as transforming growth factor-beta 1 (TGF-β1) and LAIR-1 recognizing collagens during this disease phase. Together, the synergistic induction of a tolerogenic state, including inhibitory immune-checkpoints and increased (apoptotic) immune-cell death, perpetuated immune failure in COVID-19.


The lung microbiome of COVID-19 patients showed a reduced taxonomic richness but harbored a diverse spectrum of bacterial and fungal pathogen typically associated with secondary lung infections. Polymicrobial infections and the relatively high proportion of EBV with the induction of inhibitory immune checkpoints suggested an impaired immunity in COVID-19 lungs. 

Overall, the study highlighted alterations of the local immunity during COVID-19, wherein immune impairment led to weakened antimicrobial defense facilitating the development of secondary infections following SARS-CoV-2-infection.

Although the authors could not identify clinical parameters correlated with secondary infections that provided a mechanistic understanding of why secondary infections develop following viral infections, the findings strongly supported the idea that lung immunity is impaired during COVID-19, driving these infections. 

Further studies should focus on understanding the molecular pathways in more detail for unraveling chronological phases of immuno-suppression during COVID-19. This data could prove helpful in the development of potential COVID-19 therapies counteracting secondary infections not only in COVID-19 but other diseases. For this research, autopsy specimens and associated molecular data might serve as a valuable resource.

*Important notice

medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Journal reference:
  • Zacharias, M. et al. (2022) "Host and microbiome features of secondary infections in lethal covid-19". medRxiv. doi: 10.1101/2022.02.18.22270995.

Posted in: Medical Science News | Medical Research News | Disease/Infection News

Tags: Antibodies, Anti-Inflammatory, Candida, Cell, Cell Death, Coronavirus, Coronavirus Disease COVID-19, covid-19, Cytokines, Enterococcus, fungi, Growth Factor, Hybridization, immunity, Immunoglobulin, Inflammation, Influenza, Interferons, Leukocyte, Lungs, Microbiome, mold, Mortality, Pathogen, Pathology, Phagocytes, Pneumonia, Protein, Receptor, Research, Respiratory, Ribonucleic Acid, RNA, RNA Sequencing, SARS, SARS-CoV-2, Severe Acute Respiratory, Severe Acute Respiratory Syndrome, Skin, Spike Protein, Staphylococcus aureus, Syndrome, Virus

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Neha Mathur

Neha is a digital marketing professional based in Gurugram, India. She has a Master’s degree from the University of Rajasthan with a specialization in Biotechnology in 2008. She has experience in pre-clinical research as part of her research project in The Department of Toxicology at the prestigious Central Drug Research Institute (CDRI), Lucknow, India. She also holds a certification in C++ programming.

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