| Objective As the cost of omics and high-throughput sequencing continues to decrease,their applications were becoming more widespread in the research community.Meanwhile,the Coronavirus Disease 2019(COVID-19)pandemic is posing new challenges to nosocomial infection control.It is of great significance to clarify the bacterial and fungal community structure of the hospital environment,especially during the COVID-19 pandemic,for removing infectious sources,improving hospital infection prevention and control measures,and reducing the incidence of hospital infection.Therefore,in this study,the bacteria and fungi on the hospital surface were monitored by amplicon sequencing technology to clarify the community structure.Besides,the distribution characteristics of the bacterial and fungal pathogens were studied by combining the bioinformatics analysis and statistical analysis,and the possible hospital infection risk was assessed accordingly.Methods A total of 126 environmental samples were collected from three hospitals during the COVID-19 pandemic.After nucleic acid extraction of samples and library construction in the laboratory,17,722,444 16S ribosomal Ribo Nucleic Acid(rRNA)and 13,159,610 Internal Transcribed Spacer(ITS)rRNA sequences were obtained by amplicon sequencing.The 16S rRNA sequences and ITS rRNA sequences were filtered by deblur and dada2,and 6,093 and 13,514 representative sequences were obtained respectively.The taxonomy and annotation were based on Greengenes and UNITE database.The a diversity and β diversity of samples were calculated according to the distribution of representative sequences.Then,edgeR was used to compare the differences,and Linear discriminant analysis Effect Size(LEfSe)was used to determine the dominant species.Finally,after the phylogenetic relationships were preliminarily constructed with representative sequences of high abundance,BugBase was used to predict the phenotypes of bacterial communities.Finally,functional prediction was completed through Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2(PICRUSt2)and FAPROTAX database.Results On environmental surfaces in the three hospitals during the COVID-19 pandemic,Firmicutes(51.6%)and Bacteroidetes(25%)were the dominant bacteria,while Ascomycota(39.4%)and Basidiomycota(14.2%)were the dominant fungi.In this study,amplicon sequencing was used to identify potential pathogens,including 12 bacterial and 29 fungal pathogens.Differences in bacterial and fungal community composition were compared among outdoor environments,public areas,inpatient areas,and restricted areas.Finally,phenotypic prediction and functional analysis showed that the ratio of Gram-negative bacteria to Gram-positive bacteria was about 3:7.The proportions of pressure-tolerant bacteria in A,B and C hospitals were 88.9%,93.0%and 93.8%,respectively.The proportion of anaerobic bacteria in outdoor environments,public area,inpatient area and restricted area was 39.6%,77.7%,87.9%and 79.6%,respectively.Finally,there were broader similarities in the community structure of fungi compared to bacteria.Conclusions The application of amplicon sequencing technology in pathogen monitoring in hospital environment can solve the problem of difficult culture of some microorganisms to a certain extent.The monitoring results,combined with molecular epidemiological analysis,were helpful to identify the source of infection,discover potential transmission routes,and help researchers understand the structural characteristics of microbial communities and the internal relationship among species.In this study.bacterial and fungal community structure and distribution characteristics were identified in three healthcare facilities during the COVID-19 pandemic,and some important phenotypes were predicted.We found that the prevention and control of β-lactam and polymyxin resistant bacterial infections should be paid more attention. |
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