Community structure of environmental microorganisms associated with COVID-19 affected patients

Abstract

To clarify the characteristics and distribution of hospital environmental microbiome associated with confirmed COVID-19 patients. Environmental samples with varying degrees of contamination which were associated with confirmed COVID-19 patients were collected, including 13 aerosol samples collected near eight patients in different wards, five swabs from one patient’s skin and his personal belongings, and two swabs from the surface of positive pressure respiratory protective hood and the face shield from a physician who had close contact with one patient. Metagenomic next-generation sequencing (mNGS) was used to analyze the composition of the microbiome. One of the aerosol samples (near patient 4) was detected positive for COVID-19, and others were all negative. The environmental samples collected in different wards possessed protean compositions and community structures, the dominant genera including Pseudomonas, Corynebacterium, Neisseria, Staphylococcus, Acinetobacter, and Cutibacterium. Top 10 of genera accounted for more than 76.72%. Genera abundance and proportion of human microbes and pathogens radiated outward from the patient, while the percentage of environmental microbes increased. The abundance of the pathogenic microorganism of medical supplies is significantly higher than other surface samples. The microbial compositions of the aerosol collected samples nearby the patients were mostly similar to those from the surfaces of the patient's skin and personal belongings, but the abundance varied greatly. The positive rate of COVID-19 RNA detected from aerosol around patients in general wards was quite low. The ward environment was predominantly inhabited by species closely related to admitted patients. The spread of hospital microorganisms via aerosol was influenced by the patients’ activity.

Simultaneous monitoring of SARS-CoV-2 and bacterial profiles from the air of hospital environments with COVID-19-affected patients

“…None of the air samples collected in the ICU ward of this study was found positive to SARS-CoV-2, according to the Allplex 2019-nCoV Assay which has an analytical sensitivity of 50 copies per reaction (3 viral copies per microliter of sample). Our results are consistent with those from previous studies, which detected SARS-CoV-2 at very low rates, likely for weak ability of the virus to be transmitted by aerosol particles (Ghaffari et al, 2021 ; Hemati et al, 2021 ; Liu et al, 2020 ; López et al, 2021 ; Zhang et al, 2021 ). The first study on the SARS-CoV-2 detection in air samples was performed by Liu et al ( 2020 ) using a droplet digital Polymerase Chain Reaction (ddPCR) method, which was carried out according to the manufacturer’s instructions for the QX200 Droplet Digital PCR System (Bio-Rad).…”

“…Both samples were taken from the places which had higher concentrations of PM. Zhang et al ( 2021 ) collected 12 bioaerosol samples and 7 swab samples from the environments hosting COVID-19 patients in ICU hospital wards. DNA was extracted and purified from 200 μl aerosol samples or swabs according to the instruction of DNA Mini kit DP316 (Tiangen).…”

Compositional Data Analysis of 16S rRNA Gene Sequencing Results from Hospital Airborne Microbiome Samples

“…More specifically, Table 2 displays positive and significant ρ values among Corynebacterium and Staphylococcus (0.92), Acinetobacter and Pseudomonas (0.77), Bacteroides and Prevotella (0.78), Bacteroides and Streptococcus (0.76), and Prevotella and Streptococcus (0.83). The comparison of these results with the hierarchical clustering of clades on the left-side of Figure 1 c shows that the detected significant proportionalities between the abovementioned pairs of pathogenic genera correspond to double clades in the dendrogram of Figure 1 c. Moreover, these pathogens may all cause hospital-associated infections, as discussed in the previous section (e.g., [ 58 , 61 , 69 , 76 , 77 , 78 , 79 ]). The high proportionalities found among Bacteroides , Prevotella, and Streptococcus can also be due to the fact that they are commonly found in the upper respiratory tract (e.g., [ 80 , 81 ]).…”

“…Corynebacterium , Sphingomonas , and Staphylococcus are the only three genera detected in all the samples with high and positive CLR values, as reported in Table S1 . In fact, they are among the prevailing genera within hospital wards (e.g., [ 60 , 61 ]). Corynebacterium is a skin colonizer that also has been isolated in patients after prolonged hospitalization (e.g., [ 61 , 62 ]).…”

“…In fact, they are among the prevailing genera within hospital wards (e.g., [ 60 , 61 ]). Corynebacterium is a skin colonizer that also has been isolated in patients after prolonged hospitalization (e.g., [ 61 , 62 ]). Sphingomonas may be responsible for some nosocomial infections from environmental exposure [ 62 ].…”