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Davis Lab

Publications

Davis Lab Publications 

  1. Anil A, Braza RED, Liu B, Altouma V, Adedeji C, Welling A, Ellison AL, Check MH, Irnov I, Prescott R, Torres VJ, Davis KM. Staphylococcus aureus exhibits spatiotemporal heterogeneity in Sae activity during kidney abscess development. https://doi.org/10.1101/2025.07.08.663646
    -submitted as bioRxiv pre-print
     
  2. Cotten KL, McShane A, Dedon PC, Begley TJ, Davis KM. Loss of s2U tRNA modification induces antibiotic tolerance in Yersinia pseudotuberculosis. 
    -submitted as bioRxiv pre-print, https://doi.org/10.1101/2025.07.01.662621
     
  3. Greene J, Cotten KL, Snyder RA, Huiszoon RC, Chu S, Braza RED, Chapin AA, Stine JM, Bentley WE, Ghodssi R, Davis KM. Yersinia pseudotuberculosis growth arrest during type-III secretion system expression is associated with altered ribosomal protein expression and decreased gentamicin susceptibility. In press, PLoS Pathogens.
    -submitted as bioRxiv pre-print doi: https://doi.org/10.1101/2024.09.02.610769 PMID: 39282391
     
  4. Farhang PA, Cotten KL, Smith JC, Davis KM. Antibiotic-induced bacterial cell death. In the ‘Self-Induced Cell Death in Microorganisms’ volume (JM Hardwick and P Durand, eds) of the book series Current Topics in Microbiology and Immunology. Springer Nature. In press.
     
  5. Damarla M, Suresh K, Zheng L, Carino K, Turner M, Del Rosario O, D’Alessio F, Villabona-Rueda A, Aggarwal N, Mukandan A, D’Alessio A, Skandan N, Murray S, Gour N, Lajoie S, Davis KM, Shimoda LA, Punjabi N. Development of a preclinical model of ICU-associated sleep fragmentation and effects on pneumonia recovery in mice. In press, Am J Physiol Lung Cell Mol Physiol.
     
  6. Helaine S#, Conlon BP#, Davis KM#, Russell DG#. Host stress drives tolerance and persistence: the bane of anti-microbial therapeutics. 2024. Cell Host Microbe, 32(6):852-862. PMID: 38870901#co-corresponding authors.
     
  7. Dhakal S, Park HS, Seddu K, Lee J, Creisher PS, Seibert B, Davis KM, Hernandez IR, Maul RW, Klein SL. Estradiol mediates greater germinal center responses to influenza vaccination in female than male mice. 2024. mBio, e0032624. PMID: 38441028
    -submitted as bioRxiv pre-print, doi: https://doi.org/10.1101/2023.11.27.568847
     
  8. Cotten KL, Davis KM. Bacterial heterogeneity and antibiotic persistence: bacterial mechanisms utilized in the host environment. 2023. Microbiol Mol Biol Rev, 87(4):e0017422. PMID: 37962348
     
  9. Davis KM. mSphere of Influence: If virulence is energetically costly, how can it be maintained? 2023. mSphere, 8(5):e0031223. PMID: 37676232
     
  10. DeMourdant T, Rajkovic CJ, Tracz JA, Perdomo-Pantoja A, Judy BF, Hernandez VN, Lin J, Lazzari JL, Planchard RF,Dikeman DA, Archer NK, Davis KM, Gordon O, Witham TF. A Novel Rodent Model of Chronic Spinal Implant-Associated Infection. 2023. Spine J, 23(9):1389-1399. PMID: 37247639
     
  11. *Braza RE#, *Cotten KL#, Davis KM. Protocol for detecting Yersinia pseudotuberculosis nitric oxide (NO) exposure during in vitro growth. 2022. STAR Protoc, 3(4):101760. PMID: 36219561 (# equal contribution)
     
  12. *Molom-Ochir S, Davis KM. Effects of temperature on hand sanitizer efficiency†. 2022. Journal of Emerging Investigators, 5:1-5. †manuscript completed as part of an outreach partnership with S. Molom-Ochir and Governor Thomas Johnson Middle School
     
  13. Liu B, Braza RE, Cotten KL, Davidson RK, Davis KM. NO-stressed Y. pseudotuberculosis have decreased cell division rates in the mouse spleen. 2022. Infect Immun, 90(8): e0016722. PMID: 35862700
    -submitted as bioRxiv pre-print, doi: https://doi.org/10.1101/2021.08.04.455180
     
  14. Alvarez-Manzo HS#, Davidson RK#, Van Cauwelaert de Wyels J, Cotten KL, Nguyen BH, Xiao M, Zhu Z, Anthony J, van Opijnen T, Davis KM. Yersinia pseudotuberculosis doxycycline tolerance strategies include modulating expression of genes linked to cell permeability and tRNA modification. 2022. PLoS Pathogens, 18(5):e1010556. PMID: 35576231 (# equal contribution)
    -submitted as bioRxiv pre-print, doi: https://doi.org/10.1101/2021.11.01.466809
     
  15. Gordon O, Lee D, Liu B, Langevin B, Ordonez AA, Dikeman DA, Shafiq B, Thompson JM, Sponseller PD, Flavahan K, Lodge MA, Rowe SP, Dannals RF, Ruiz-Bedoya CA, Read TD, Peloquin CA, Archer NK, Miller LS, Davis KM, Gobburu JVS, Jain  SK. Dynamic PET-facilitated Modeling and High-dose Rifampin Regimens for Staphylococcus aureus Orthopedic Implant Associated Infections. 2021. Sci Transl Med, 13(622):eabl6851. doi: 10.1126/scitranslmed.abl6851. PMID: 34851697 
     
  16. Patel P, O’Hara BJ, Aunins E, Davis KM.  Modifying TIMER to generate a slow-folding DsRed derivative for optimal use in quickly-dividing bacteria. 2021. PLoS Pathog, 17(7):e1009284. PMID: 34214139 
    -submitted as bioRxiv pre-print, doi: https://doi.org/10.1101/2021.01.12.426338
     
  17. Davidson RK, Davis KM.  Yersinia pseudotuberculosis: cultivation, storage, and methods for introducing DNA. 2020. Curr Protoc Microbiol, 59(1):e122. PMID: 33079471
     
  18. Raneses JR, Ellison AL, Liu, B, Davis KM. Subpopulations of stressed Y. pseudotuberculosis preferentially survive doxycycline treatment within host tissues. 2020. mBio, 11(4):e00901-20.PMID: 32753491
    -also submitted as bioRxiv pre-print, doi: https://doi.org/10.1101/2020.04.13.039222
     
  19. Clark SA, Thibault D, Shull LM, Davis KM, Aunins E, van Opijnen T, Isberg RR. Topologically correct synthetic reconstruction of pathogen social behavior found during Yersinia growth in deep tissue sites. 2020. eLife, 9:e58106. PMID: 32543373 **also submitted as bioRxiv pre-print, https://doi.org/10.1101/2020.04.27.065144
     
  20. Davis KM. For the greater (bacterial) good: heterogeneous expression of energetically costly virulence factors. Review. 2020. Infect Immun, 88(7):e00911-19. PMID: 32041785
     
  21. Davis KM, Krupp J, Clark S, Isberg RR. Iron-sulfur cluster repair contributes to Yersinia pseudotuberculosis survival within deep tissues. 2019. Infect Immun, 87(10):e00533-19. PMID: 31331956
     
  22. Davis KM, Isberg RR. One for all, but not all for one: social behavior during bacterial diseases. Review. 2019. Trends Microbiol, 27(1):64-74. PMID: 30243514
     
  23. Davis KM. All Yersinia are not created equal: phenotypic adaptation to distinct niches within mammalian tissues. Review. 2018. Front Cell Infect Microbiol, 8:261. PMID 30128305
     
  24. Davis KM, Isberg RR. Defining heterogeneity within bacterial populations via single cell approaches. Review. 2016. Bioessays, 38(8):782-90. PMID: 27273675 ncbi.nlm.nih.gov/pubmed/27273675
     
  25. Chen Y, Lin Y, Davis KM, Wang Q, Rnjak-Kovacina J, Li C, Isberg RR, Kumamoto CA, Mecsas J, Kaplan DL. Robust bioengineered 3D functional human intestinal epithelium. 2015. Sci Rep, 5: 1370 PMID: 26374193 ncbi.nlm.nih.gov/pubmed/26374193
     
  26. Asrat S#, Davis KM#, Isberg RR. Modulation of the host innate immune and inflammatory response by translocated bacterial proteins. Review. 2015. Cell Microbiol, 17(6): 785-95. (# equal contribution) PMID: 25850689 ncbi.nlm.nih.gov/pubmed/25850689
     
  27. Davis KM, Mohammadi S, Isberg RR. Community behavior and spatial regulation within a bacterial microcolony in deep tissue sites serves to protect again host attack. 2015. Cell Host Microbe, 17(1): 21-31. PMID: 25500192 ncbi.nlm.nih.gov/pubmed/25500192
     
  28. Davis KM, Isberg RR. Plague’s partners in crime. Preview. 2014. Immunity, 41(3): 347-349. PMID: 25238090 ncbi.nlm.nih.gov/pubmed/25238090
     
  29. Davis KM, Nakamura S, Weiser JN. Nod2-sensing of lysozyme-digested peptidoglycan promotes macrophage recruitment and clearance of S. pneumoniae colonization in mice. 2011. J Clin Invest, 121(9): 3666-3676. PMID: 21841315 ncbi.nlm.nih.gov/pubmed/21841315
     
  30. Nakamura S, Davis KM, Weiser JN. Synergistic stimulation of type I interferons during influenza virus coinfection promotes Streptococcus pneumoniae colonization in mice. 2011. J Clin Invest, 121(9): 3657-3665. PMID: 21841308 ncbi.nlm.nih.gov/pubmed/21841308
     
  31. Davis KM, Weiser JN. Modifications to the peptidoglycan backbone help bacteria to establish infection. Review. 2011. Infect Immun, 79(2): 562-570. PMID: 21041496 ncbi.nlm.nih.gov/pubmed/21041496
     
  32. Clarke TB, Davis KM, Lysenko ES, Zhou AY, Yu Y, Weiser JN. Recognition of peptidoglycan from the microbiota by Nod1 enhances systemic innate immunity. 2010. Nat Med, 16(2): 228-231. PMID: 20081863 ncbi.nlm.nih.gov/pubmed/20081863
     
  33. Davis KM, Akinbi HT, Standish AJ, Weiser JN. Resistance to mucosal lysozyme compensates for the fitness deficit of peptidoglycan modifications by Streptococcus pneumoniae. 2008. PLoS Pathog,4(12): e1000241. PMID: 19079576 ncbi.nlm.nih.gov/pubmed/19079576
     
  34. Dunlap PV, Davis KM, Tomiyama S, Fujino M, Fukui A. Developmental and microbiological analysis of the inception of bioluminescent symbiosis in the marine fish Nuchequula nuchalis (Perciformes: Leiognathidae). 2008. Appl Environ Microbiol, 74(24): 7471-7481. PMID: 18978090 ncbi.nlm.nih.gov/pubmed/18978090
     
  35. Ji G, Zheng J, Shen Y, Wu X, Jiang R, Lin Y, Loke JC, Davis KM, Reese GJ, Li QQ. Predictive modeling of plant messenger RNA polyadenylation sites. 2007. BMC Bioinformatics, 8(1): 43. PMID: 17286857 ncbi.nlm.nih.gov/pubmed/17286857