Gut and respiratory resistome in COVID-19 patients, China

The antibiotic resistome is the collection of all the ARGs present in an individual. Whether an individual susceptibility to infection and the eventual severity of COVID-19 is influenced by their respiratory tract antibiotic resistome is unknown. Additional, whether a relationship exists between the respiratory tract and gut ARGs composition has not been fully explored. We recruited 66 patients with COVID-19 at three disease stages and conducted a metagenome sequencing analysis of 143 sputum and 97 fecal samples obtained from them. Respiratory tract, gut metagenomes, and PBMC transcriptomes are analyzed to compare the gut and respiratory tract ARGs of ICU and non-ICU patients and determine relationships between ARGs and immune response. Among the respiratory tract ARGs, we found that Aminoglycoside, Multidrug and Vancomycin are increased in ICU patients compared with nICU patients. In the gut, we found that Multidrug, Vancomycin and Fosmidomycin were increased in ICU patients. We discovered that the relative abundances of Multidrug were significantly correlated with clinical indices, and there was a significantly positive correlation between ARGs and microbiota in respiratory tract and gut. We found that immune related pathways in PBMC were enhanced, and they were correlated with Multidrug, Vancomycin and Tetracycline ARGs. Based on the ARG types, we built a respiratory tract-gut ARG combined random-forest classifier to distinguish ICU COVID-19 patients from nICU patients with an AUC of 0.969. Cumulatively, our findings provide some of the first insights into the dynamic alterations of respiratory tract and gut antibiotic resistome in the progression of COVID-19 and disease severity. They also provide a better understanding of how this disease affects different cohorts of patients. As such, these findings should contribute to better diagnosis and treatment scenarios.

Classified as human lower respiratory / gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.75. Assay shotgun_dna.

• host study.description · “We recruited 66 patients with COVID-19”
• host run.host_tax_id · “9606”
• body site study.description · “143 sputum and 97 fecal samples”

218 runs over 218 samples · mean 9.73 Gbp per run (median 9.95 Gbp, total 2,121.24 Gbp; 218 runs with a base count) · layout PAIRED 218 · platform ILLUMINA 218 · models Illumina HiSeq 2500 (218) · 92% of runs with a Sandpiper profile · first public 2024-01-28

Shen Y first · Qu W · Yu F · Zhang D · Zou Q · Han D · Xie M · Chen X · Yuan L · Lou B · Xie G · Wang R · Yang X · Chen W · Wang Q · Teng Y · Dong Y · Huang L · Bao J · Liu C · Wu W · Shen E · Fan L · Timko MP · Zheng S · Chen Y last

PRJNA950577.csv.gz (6.6 KB) · parquet (79.7 KB) — all 218 samples, every field with route and confidence · PRJNA950577_determinations.csv.gz (15.3 KB) — 1,962 evidence rows