Characterization of Microbial Co-infections in the Respiratory Tract of hospitalized COVID-19 patients

Abstract

<jats:p>Summary Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic of Coronavirus disease 2019 (COVID-19). However, microbial composition of the respiratory tract and other infected tissues, as well as their possible pathogenic contributions to varying degrees of disease severity in COVID-19 patients remain unclear. Method Between January 27 and February 26, 2020, serial clinical specimens (sputum, nasal and throat swab, anal swab and feces) were collected from a cohort of hospitalized COVID-19 patients, including 8 mildly and 15 severely ill patients (requiring ICU admission and mechanical ventilation), in the Guangdong province, China. Total RNA was extracted and ultra-deep metatranscriptomic sequencing was performed in combination with laboratory diagnostic assays. Co-infection rates, the prevalence and abundance of microbial communities in these COVID-19 patients were determined. Findings Notably, respiratory microbial co-infections were exclusively found in 84.6% of severely ill patients (11/13), among which viral and bacterial co-infections were detected by sequencing in 30.8% (4/13) and 69.2% (9/13) of the patients, respectively. In addition, for 23.1% (3/13) of the patients, bacterial co-infections with Burkholderia cepacia complex (BCC) and Staphylococcus epidermidis were also confirmed by bacterial culture. Further, a time-dependent, secondary infection of B. cenocepacia with expressions of multiple virulence genes in one severely ill patient was demonstrated, which might be the primary cause of his disease deterioration and death one month after ICU admission. Interpretation Our findings identified distinct patterns of co-infections with SARS-CoV-2 and various respiratory pathogenic microbes in hospitalized COVID-19 patients in relation to disease severity. Detection and tracking of BCC-associated nosocomial infections are recommended to improve the pre-emptive treatment regimen and reduce fatal outcomes of hospitalized patients infected with SARS-CoV-2. Funding National Science and Technology Major Project of China, National Major Project for Control and Prevention of Infectious Disease in China, the emergency grants for prevention and control of SARS-CoV-2 of Ministry of Science and Technology and Guangdong province, Guangdong Provincial Key Laboratory of Genome Read and Write, Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, and Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics.</jats:p>

Humoral response to SARS-CoV-2 by healthy and sick dogs during COVID-19 pandemic in Spain

“…It is interesting to note that mycoplasma coinfections are very common in COVID-19 human patients 24 and it also has been suggested that a co-infection or activation of latent mycoplasma infections in COVID-19 disease may be important in determining a fatal disease course. 25,26 Normally, the therapy response when treating respiratory tract diseases with drugs (antibiotics, bronchodilators, anti-inflammatories, antitussives, decongestants, mucolytics, mucokinetics or expectorants) is adequate or complete, nevertheless our patients did not respond adequately to the therapeutic protocol. A major pathogen has not been detected in our patients, so at the moment the causative agent of the pathologies is unknown.…”

The role of co-infections and secondary infections in patients with COVID-19

“…Although no additional viruses were documented in any of the patients, the bacteria and fungi isolated were more closely related to those nosocomial pathogens described above. The additional studies from China confirmed indicated the occurrence of co-pathogens in patients with SARS-CoV-2 infection [53,54].…”

“…A number of mostly retrospective studies have been reported from China [49][50][51][52][53][54], the US [55][56][57], the UK [58,59], Spain [60], France [61] and Iran [62], that investigated what the authors call "co-infections" in patients with COVID-19 infection. However, when reviewing several of these studies, it is not entirely clear that these were true co-infections, rather than superinfections, as defined above.…”

COVID-19 and Antimicrobial Resistance: Data from the Greek Electronic System for the Surveillance of Antimicrobial Resistance—WHONET-Greece (January 2018–March 2021)

“…A thorough search into the literature (January 2020–June 2021) revealed many studies trying to address the AMR issue in the pandemic era. The main issues refer to patients with COVID-19 who may receive antimicrobial therapy (a) without a microbiological confirmation of the bacterial co-infection [ 18 , 31 , 32 , 33 , 34 , 35 , 36 ] and (b) often in the absence of a microbiological confirmation of the diagnosis [ 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 ]. Lai et al [ 24 ] recorded the consumption of antibiotics in January–June 2019 vs. January–June 2020 in The National Taiwan University Hospital.…”