Fig. 6. Lymphopenia and prolonged viral shedding are associated with blood recirculation of Enterobacteriaceae and Micrococcaceae DNA.

A Stacked bar charts showing the relative abundance of bacterial families obtained by 16S sequencing of the whole-blood samples in patients experiencing short-term viral RNA shedding (SVS) and long-term viral RNA shedding (LVS) among Cancer_FR1_TR. Only the top 15 most abundant bacterial families are represented (the others are in the category “Other”). B Linear discriminant analysis effect size (LEfSe) analysis displaying linear discriminant analysis score (LDA) of the blood bacterial taxa differentially recovered from SVS (orange) versus LVS (purple) patients (*P < 0.05 with Mann–Whitney test between the two groups of patients). C Mean (bar plots, +/− SEM) and individual values (dot plots) of relative proportions of Enterobacteriaceae (C, left panel) and Micrococcaceae (C, right panel) family members in SARS-CoV-2-positive and recovered patients. Significance between SVS and LVS patients was evaluated using Mann–Whitney test (*P < 0.05). D, E Spearman correlations between the relative proportions of Enterobacteriaceae with paired concentrations of CCL22 in serum (D) and with paired percentages of Granzyme B (GzB)⁺PD-1⁺ in Eomes^hiTCF-1^hi non-naive CD8⁺ measured in blood (E). F Idem as in A. considering segregating the cohort in two groups; ALC > 0.8 G/L and/or Ct >25 patients versus ALC < 0.8 G/L & Ct <25 patients. G LEfSe analysis displaying LDA score of the blood bacterial taxa significantly increased in ALC > 0.8 G/L and/or Ct >25 patients (gray) and ALC < 0.8 G/L & Ct <25 patients (red). The displayed bacterial taxa are significantly different (*P < 0.05 with Mann–Whitney test) between the two groups of patients. H Idem as in C segregating the cohort into the same two groups as in F. Significance between ALC > 0.8 G/L and/or Ct >25 patients and ALC < 0.8 G/L & Ct <25 patients was evaluated using the Mann–Whitney test (*P < 0.05).