# Immune-adaptive pathogen variation reveals targetable mediators of gram-positive bacterial killing in macrophages **Authors:** Clark D. Russell, Jennifer Marshall, Brian J. McHugh, Bartosz J. Michno, Justyna Cholewa-Waclaw, Gonzalo Yebra, Jelimo Chepsat, Gareth-Rhys Jones, Martin P. McHugh, Nicola N. Lynskey, Stephen A. Renshaw, Tomasz K. Prajsnar, J. Kenneth Baillie, J. Ross Fitzgerald, David H. Dockrell PMC · DOI: 10.1126/sciadv.aea0375 · Science Advances · 2026-02-27 ## TL;DR This study uses evolving bacteria to identify host factors that help macrophages kill gram-positive bacteria and suggests new therapeutic strategies. ## Contribution A novel method using immune-adaptive pathogen variation to identify host defense mediators and repurpose drugs for bacterial infections. ## Key findings - ACOD1, NAMPT, and P2RX7 were validated as host defense factors against gram-positive bacteria. - The antihistamine clemastine was repurposed to enhance bacterial killing via P2RX7. - Pathogen-centric screening revealed therapeutic opportunities for host-directed therapies. ## Abstract Host-directed therapies for bacterial infections can provide an adjunct or alternative to conventional antimicrobials, mitigating the impact of antimicrobial resistance. However, therapeutically targetable mediators of innate immune bacterial killing remain elusive. We hypothesized that immune-adaptive pathogen evolution could provide an informative perspective on this problem. We examined the interaction of a genetically diverging hypervirulent Streptococcus pneumoniae (pneumococcus) serotype with macrophages, identifying closely phylogenetically related isolates with differential susceptibility to intracellular killing. We reasoned that macrophage genes relatively suppressed during pathogen escape from killing were likely to encode mediators normally promoting bacterial killing. This led to the validation of ACOD1 and its product itaconate, NAMPT, and P2RX7 as host defense factors against pneumococci and related gram-positive pathogens. Last, we repurposed the antihistamine clemastine to augment phagolysosomal bacterial killing, via P2RX7, as a candidate host-directed therapy against pneumococci and vancomycin-resistant Enterococcus faecium. Overall, we show that pathogen-centric host screening can aid identification of microbicidal responses as targets for host-directed therapies. Immune-adaptive pathogen variation is a tool to identify mediators of macrophage bacterial killing and therapeutic opportunities. ## Linked entities - **Genes:** ACOD1 (aconitate decarboxylase 1) [NCBI Gene 730249], NAMPT (nicotinamide phosphoribosyltransferase) [NCBI Gene 10135], P2RX7 (purinergic receptor P2X 7) [NCBI Gene 5027] - **Chemicals:** clemastine (PubChem CID 26987) - **Species:** Streptococcus pneumoniae (taxon 1313), Enterococcus faecium (taxon 1352) ## Full-text entities - **Genes:** IL1B (interleukin 1 beta) [NCBI Gene 3553] {aka IL-1, IL1-BETA, IL1F2, IL1beta}, Xcl1 (chemokine (C motif) ligand 1) [NCBI Gene 16963] {aka ATAC, LTN, Lptn, SCM-1, SCM-1a, Scyc1}, Il1b (interleukin 1 beta) [NCBI Gene 16176] {aka IL-1beta, Il-1b}, Nampt (nicotinamide phosphoribosyltransferase) [NCBI Gene 59027] {aka 1110035O14Rik, NAmPRTase, Pbef, Pbef1, Visfatin}, Il27 (interleukin 27) [NCBI Gene 246779] {aka IL-27, IL-27-A, IL-27p28, IL27-A, Il30, p28}, Ms4a4a (membrane-spanning 4-domains, subfamily A, member 4A) [NCBI Gene 666907] {aka EG666907}, Sphk1 (sphingosine kinase 1) [NCBI Gene 20698] {aka 1110006G24Rik, Sk1, Spk1}, Hcar2 (hydroxycarboxylic acid receptor 2) [NCBI Gene 80885] {aka Gpr109a, Gpr109b, HM74, Niacr1, PUMA-G, Pumag}, Ncoa7 (nuclear receptor coactivator 7) [NCBI Gene 211329] {aka 9030406N13Rik}, Ifng (interferon gamma) [NCBI Gene 15978] {aka IFN-g, If2f, Ifg}, Mmp12 (matrix metallopeptidase 12) [NCBI Gene 17381] {aka MME, Mmel}, CASP1 (caspase 1) [NCBI Gene 834] {aka ICE, IL1BC, P45}, IL1RN (interleukin 1 receptor antagonist) [NCBI Gene 3557] {aka CRMO2, DIRA, ICIL-1RA, IL-1RN, IL-1ra, IL-1ra3}, Csf1 (colony stimulating factor 1 (macrophage)) [NCBI Gene 12977] {aka BAP025, Csfm, MCSF, Mhdabap25, PG-M-CSF, op}, Csf2 (colony stimulating factor 2 (granulocyte-macrophage)) [NCBI Gene 12981] {aka CSF, Csfgm, GMCSF, Gm-CSf, MGI-IGM}, Acod1 (aconitate decarboxylase 1) [NCBI Gene 16365] {aka CAD, Irg1}, Gzmb (granzyme B) [NCBI Gene 14939] {aka CCP-1/C11, CCP1, Ctla-1, Ctla1, GZB}, Txnip (thioredoxin interacting protein) [NCBI Gene 56338] {aka 1200008J08Rik, Hyplip1, THIF, Tbp-2, VDUP1}, Il23a (interleukin 23, alpha subunit p19) [NCBI Gene 83430] {aka IL-23, p19}, NLRP3 (NLR family pyrin domain containing 3) [NCBI Gene 114548] {aka AGTAVPRL, AII, AVP, C1orf7, CIAS1, CLR1.1}, Tnfaip3 (tumor necrosis factor, alpha-induced protein 3) [NCBI Gene 21929] {aka A20, Tnfip3}, Cstb (cystatin B) [NCBI Gene 13014] {aka Stfb}, IFNG (interferon gamma) [NCBI Gene 3458] {aka IFG, IFI, IMD69}, Gapdh (glyceraldehyde-3-phosphate dehydrogenase) [NCBI Gene 14433] {aka Gapd}, P2rx7 (purinergic receptor P2X, ligand-gated ion channel, 7) [NCBI Gene 18439] {aka P2X(7), P2X7R}, Lamp3 (lysosomal-associated membrane protein 3) [NCBI Gene 239739] {aka 1200002D17Rik, Cd208, DC-LAMP, DCLAMP, LAMP, TSC403}, Npc2 (NPC intracellular cholesterol transporter 2) [NCBI Gene 67963] {aka 2700012J19Rik, HE1}, nampt1 (nicotinamide phosphoribosyltransferase 1) [NCBI Gene 100330160] {aka nampta} - **Diseases:** gram (MESH:D016908), Inflammation (MESH:D007249), liver abscesses (MESH:D008100), bacteraemia (MESH:C531821), streptococcal and (MESH:D013290), chronic granulomatous disease (MESH:D006105), pneumococcal pneumonia (MESH:D011018), COPD (MESH:D029424), Infection (MESH:D007239), hMDMs (MESH:D055501), pneumococcal disease (MESH:D011008), septic shock (MESH:D012772), HIV-1 infection (MESH:D015658), invasive disease (MESH:D009361), bacterial infection (MESH:D001424), dysfunction (MESH:D006331) - **Chemicals:** streptomycin (MESH:D013307), diphenhydramine (MESH:D004155), Itaconate (MESH:C005229), Bafilomycin A1 (MESH:C040929), gentamicin (MESH:D005839), FK866 (MESH:C480543), GlutaMAX (MESH:C054122), nicotinamide (MESH:D009536), water (MESH:D014867), benzyl-penicillin (MESH:D010400), vancomycin (MESH:D014640), Clemastine (MESH:D002974), dimethyl itaconate (MESH:C518953), NMN (MESH:D009537), dextran (MESH:D003911), YVAD-FMK (MESH:C425776), DQ-Red (-), penicillin (MESH:D010406), KN-62 (MESH:C063302), NAD+ (MESH:D009243), acetate (MESH:D000085), saponin (MESH:D012503), DMSO (MESH:D004121), 4',6-diamidino-2-phenylindole (MESH:C007293), d-glucose (MESH:D005947), polystyrene (MESH:D011137), l-glutamine (MESH:D005973), Citrate (MESH:D019343), ATP (MESH:D000255), lipid (MESH:D008055), paraformaldehyde (MESH:C003043), lipopolysaccharide (MESH:D008070) - **Species:** Mus musculus (house mouse, species) [taxon 10090], Enterobacter cloacae complex (species group) [taxon 354276], Klebsiella pneumoniae (species) [taxon 573], Streptococcus pneumoniae (species) [taxon 1313], Streptococcus pyogenes (species) [taxon 1314], Salmonella enterica (species) [taxon 28901], Ovis aries (domestic sheep, species) [taxon 9940], Streptococcus pneumoniae ST 618 (strain) [taxon 525380], Mycobacterium tuberculosis (species) [taxon 1773], Bacteria Latreille et al. 1825 (Bacteria stick insect, genus) [taxon 629395], Staphylococcus aureus (species) [taxon 1280], Homo sapiens (human, species) [taxon 9606], Streptococcus pneumoniae D39 (strain) [taxon 373153], Burkholderia pseudomallei (species) [taxon 28450], Danio rerio (leopard danio, species) [taxon 7955], Leishmania (subgenus) [taxon 38568], Listeria monocytogenes (species) [taxon 1639], Legionella pneumophila (species) [taxon 446], Enterococcus faecium (species) [taxon 1352], Streptococcus agalactiae (species) [taxon 1311] - **Cell lines:** ST618 — Cricetulus griseus (Chinese hamster), Spontaneously immortalized cell line (CVCL_4590), C57BL/6J — Mus musculus (Mouse), Transformed cell line (CVCL_C0MW), /6NJ — Mus musculus (Mouse), Hybridoma (CVCL_KS11) ## Full text _Full body text omitted from this summary view._ Fetch the complete paper as Markdown: https://tomesphere.com/paper/PMC12947864/full.md ## Figures 6 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12947864/full.md ## References 118 references — full list in the complete paper: https://tomesphere.com/paper/PMC12947864/full.md --- Source: https://tomesphere.com/paper/PMC12947864