Karthik Hullahalli

Assistant Professor

Microbiology & Immunology

Research Interests:

• Host-microbe interactions in bacterial infection

Education

PhD in Microbiology and Immunobiology,
Harvard University

Research Interests

Study of host-microbe interactions in bacterial infection, with particular emphasis on understanding the population dynamics of microbes within the host and the impacts of excessive inflammation on pathogen growth and spread. His lab leverages diverse approaches, including quantitative analysis of infection dynamics with barcoded bacteria, animal models of systemic infections, and cell culture-based assays of innate immunity. The long-term goal of this research is to mitigate the burden of infectious diseases by mechanistically dissecting the complex interplay between infectious microbes and the immune system and to leverage these insights for therapeutic treatment of bacterial infections.

Publications/Research Listings

1) Hullahalli K, Dailey KG, Acbay R, Suzuki M, Balazs GI, Waldor MK (2025). Reverse transcriptase
inhibitors diminish systemic proinflammatory responses to bacterial pathogens. mBio 16(2):e03412-24

2) Hullahalli K, Dailey KG, Hasegawa Y, Johnson WE, Waldor MK (2024). Reverse transcriptase
inhibitors prevent liver abscess formation during Escherichia coli bloodstream infection. PNAS
121(4):e2319162121

3) Hullahalli K, Dailey KG, Hasegawa Y, Torres E, Suzuki M, Zhang H, Threadgill DW, Navarro VM,
Waldor MK (2023). Genetic and immune determinants of E. coli liver abscess formation. PNAS
120(51):e2310053120

4) Hullahalli K, Dailey KG, Waldor MK (2023). Innate immune responses yield tissue-specific bottlenecks
that scale with pathogen dose. PNAS 120(37):e2309151120

5) Hullahalli K and Waldor MK (2021). Pathogen clonal expansion underlies multiorgan dissemination
and organ-specific outcomes during systemic infection. eLife 10:e70910

6) Hullahalli K, Pritchard JR, Waldor MK (2021). Refined quantification of infection bottlenecks and
pathogen dissemination with STAMPR. mSystems 6 (4):e00887-21

7) Hullahalli K, Rodrigues M, Nguyen UT, Palmer KL (2018). An attenuated CRISPR-Cas system in
Enterococcus faecalis permits DNA acquisition. mBio 9:e00414-18.

8) Hullahalli K*, Rodrigues M*, Palmer KL (2017). Exploiting CRISPR-Cas to manipulate Enterococcus
faecalis populations. eLife 6:e26664.

9) Hullahalli K, Rodrigues M, Schmidt BD, Li X, Bhardwaj P, Palmer KL (2015) Comparative analysis of
the orphan CRISPR locus in 242 Enterococcus faecalis strains. PLoS ONE 10(9):e0138890.

10) Xia L*, Hullahalli K*, Tian X, Yuan C, Pan F, Fan H, Waldor MK, Ma Z (2025). Lethal streptococcal
infection is associated with widened lymph node bottlenecks. bioRxiv 2025.01.29.635438

11) Peterson ST, Dailey KG*, Hullahalli K*, Sorobetea D, Matsuda R, Sewell J, Yost W, O’Neill R, Bobba
S, Apenes N, Sherman ME, Balazs GI, Assenmacher C, Cox A, Lanza M, Shin S, Waldor MK, Brodsky
IE (2025). TNF signaling maintains local restriction of bacterial founder populations in intestinal and
systemic sites during oral Yersinia infection. bioRxiv 2025.02.26.639286. Under review at mBio

12) Holmes CL, Dailey KG, Hullahalli K, Wilcox AE, Mason S, Moricz BS, Unverdorben L V., Waldor MK,
Bachman MA (2025). Patterns of Klebsiella pneumoniae bacteremic dissemination from the lung.
Nature Communications 16:785

13) Lebrun-Corbin M, Cheung B, Hullahalli K, Dailey KG, Bailey K, Waldor MK, Wunderlink M, Bachta
KER, Hauser A (2024). Pseudomonas aeruginosa population dynamics in a vancomycin-induced
murine model of gastrointestinal carriage. mBio e03136-24

14) Yuan C, Hullahalli K, Wang Y, Huang H, Liang Y, Fan H, Waldor MK, Ma Z (2024). Constitutive
glucose import in zoonotic Streptococci enables proliferation in cerebrospinal fluid. In revision at Nature
Microbiology

15) Chevée V, Hullahalli K, Dailey KG, Güereca L, Zhang C, Waldor MK, Portnoy DA (2024). Temporal
and spatial dynamics of Listeria monocytogenes central nervous system infection in mice. PNAS
121:e2320311121.

16) Hotinger JA, Campbell IW, Hullahalli K, Osaki A, Waldor MK (2025). Quantification of Salmonella
enterica serovar Typhimurium population dynamics in murine infection using a highly diverse barcoded
library. eLife13:RP101388

17) Landau LM, Chaudhary N, Tien YC, Rogozinska M, Joshi S, Yao C, Crowley J, Hullahalli K, Campbell
IW, Waldor MK, Haigis M, Kagan JC (2024). pLxIS-containing domains are biochemically flexible
regulators of interferons and metabolism. Molecular Cell 84(13), 2436-2454

18) Basta DW*, Campbell IC*, Sullivan EJ, Hotinger JA, Hullahalli K, Waldor MK (2024). Inducible
transposon mutagenesis for genome-scale forward genetics. bioRxiv 2024.05.21.595064. Accepted for
publication at Nature Microbiology

19) White MT, Zhang H, Eckhard U, Hullahalli K, Wu S, Queen J, Gomis-Ruth FX, Waldor MK, Sears CL
(2023). A procarcinogenic bacterial metalloprotease binds claudin-4 to mediate toxicity on colonic
epithelial cells. In revision at Nature

20) Campbell IW, Hullahalli K, Turner JR, Waldor MK (2023). Quantitative dose-response analysis
untangles host bottlenecks to enteric infection. Nature Communications 14(1), 456

21) Kirsch JM, Ely S, Stellfox ME, Hullahalli K, Luong P, Palmer KL, Van Tyne D, Duerkop BA (2023).
Targeted IS-element sequencing uncovers transposition dynamics during selective pressure in
enterococci. PLoS Pathogens 19(6):e1011424

22) Rubin DHF, Ma KC, Westervelt KA, Hullahalli K, Waldor MK, Grad YH (2023). CanB is a metabolic
mediator of antibiotic resistance in Neisseria gonorrhoeae. Nature Microbiology 18(1), 28-39

23) Sit B*, Srisuknimit V*, Bueno E*, Zingl F, Hullahalli K, Cava F, Waldor MK (2023). Undecaprenyl
phosphate translocases confer conditional microbial fitness. Nature 10.1038/s41586-022-05569-1

24) Fakoya B, Hullahalli K, Rubin DHF, Leitner DR, Chilengi R, Sack D, and Waldor MK (2021) Nontoxigenic
Vibrio Cholerae challenge strains for evaluating vaccine efficacy and inferring mechanisms of
protection. mBio 13:e00539-22

25) Zhang T, Sasabe J, Hullahalli K, Sit B, Waldor MK (2020). Increased Listeria monocytogenes
dissemination and altered population dynamics in Muc2-deficient mice. Infection and Immunity
89(4):e00667-20

26) Rodrigues M, McBride SW, Hullahalli K, Palmer KL, Duerkop BA (2019). Conjugative delivery of
CRISPR-Cas9 for the selective depletion of antibiotic-resistant enterococci. Antimicrobial Agents and
Chemotherapy 63(11):e01454-19

27) Price VJ, McBride SW, Hullahalli K, Chatterjee A, Duerkop BA, Palmer KL (2019). Enterococcus
faecalis CRISPR-Cas is a robust barrier to conjugative antibiotic resistance dissemination in the murine
intestine. mSphere 10(4):e01775-19

28) Chatterjee A, Johnson CN, Luong P, Hullahalli K, McBride SW, Schubert AM, Palmer KL, Carlson PE,
Duerkop BA (2019). Bacteriophage resistance alters antibiotic mediated intestinal expansion of
enterococci. Infection and Immunity 87(6):e00085-19