scH16S‐Seq Maps Klebsiella pneumoniae ‐Associated Myeloid States and Reveals a CD38–NAD Immunometabolic Axis That Impairs Lysosomal Acidification in Sepsis

ABSTRACT

Sepsis arises from heterogeneous host‐cell states that influence bacterial clearance, yet single‐cell transcriptomic approaches do not directly connect microbial signals with host transcriptional programs. This study introduces single‐cell host–bacterial 16S co‐sequencing (scH16S‐seq), which couples host transcriptomes with barcode‐resolved bacterial 16S‐derived UMI signals to resolve bacterial signal‐enriched host‐cell states. Applied to Klebsiella pneumoniae (KP) sepsis, scH16S‐seq mapped cell‐associated bacterial 16S‐derived signals to discrete CD38 ⁺ myeloid states, including Acod1 ⁺ monocyte‐derived macrophages, Lyve1 ⁺ interstitial macrophages, and hypoxic neutrophils sharing inflammatory, hypoxic, and metabolically stressed programs. Increased myeloid CD38 expression is also observed across human sepsis cohorts. Mechanistically, KP induces CD38‐associated NAD ⁺ depletion, mitochondrial bioenergetic failure, reduced ATP, and impaired lysosomal acidification. CD38 inhibition, NAD‐related metabolic intervention, or Cd38 deficiency restores NAD homeostasis and mitochondrial function, whereas blockade of mitochondrial ATP synthesis or V‐ATPase‐dependent acidification attenuates lysosomal and antibacterial rescue. Lyz2‐Cre‐mediated Cd38 deletion improves bacterial control and sepsis outcomes in vivo. Together, scH16S‐seq resolves KP 16S signal‐enriched myeloid states and identifies a targetable CD38–NAD–mitochondrial–lysosomal axis linking immunometabolic dysfunction to impaired antibacterial defense in sepsis.