K. Hullahalli

Inducible transposon mutagenesis for genome-scale forward genetics

InducTn-seq improves transposon mutagenesis by enabling temporal control of transposition, generating diverse mutants and quantifying gene fitness across essential and non-essential genes.

Patterns of Klebsiella pneumoniae bacteremic dissemination from the lung

This study tracks Klebsiella pneumoniae dissemination from the lung using barcoding, revealing two distinct patterns of bacterial spread and their associated host and bacterial factors.

Innate immune responses yield tissue-specific bottlenecks that scale with pathogen dose

This study identifies tissue-specific bottlenecks in innate immune responses that scale with pathogen dose during E. coli infection.

Genetic and immune determinants of E. coli liver abscess formation

This study identifies host genetic and immune factors that determine susceptibility to E. coli liver abscesses in mice using spatial and single-cell transcriptomics.

Quantitative dose-response analysis untangles host bottlenecks to enteric infection

This study quantifies how host bottlenecks affect the founding population of Citrobacter rodentium during infection, showing that microbiota and dose influence pathogen establishment.

Targeted IS-element sequencing uncovers transposition dynamics during selective pressure in enterococci

This study uses IS-Seq to show that phage infection and antibiotic exposure drive IS256 diversification in enterococci, linking selective pressures to genome evolution.

Variation in supplemental carbon dioxide requirements defines lineage-specific antibiotic resistance acquisition in Neisseria gonorrhoeae

This study shows that metabolic variation in Neisseria gonorrhoeae, specifically CO2 dependence linked to a beta-carbonic anhydrase mutation, influences the likelihood of acquiring ciprofloxacin resistance.

Candidate undecaprenyl phosphate translocases enable conditional microbial fitness and pathogenesis

The paper identifies DUF368-containing proteins as undecaprenyl phosphate translocases essential for bacterial alkaline fitness and pathogenesis in Vibrio cholerae and Staphylococcus aureus.

Non-toxigenic Vibrio cholerae challenge strains for evaluating vaccine efficacy and inferring mechanisms of protection

This study develops non-toxigenic V. cholerae challenge strains to evaluate vaccine efficacy and infer protection mechanisms, showing they accurately measure colonization reduction and vibriocidal antibody responses.

Pathogen clonal expansion underlies multiorgan dissemination and organ-specific outcomes during systemic infection

This study shows that clonal expansion of rare bacterial clones drives organ-specific outcomes during systemic infection by E. coli.

Refined quantification of infection bottlenecks and pathogen dissemination with STAMPR

This paper introduces STAMPR, a method to improve the accuracy of measuring infection bottlenecks and pathogen dissemination using barcoded bacterial data.

Conjugative delivery of CRISPR-Cas9 for the selective depletion of antibiotic-resistant enterococci

This paper develops CRISPR-Cas antimicrobials delivered via conjugative plasmids to selectively remove antibiotic resistance genes from Enterococcus faecalis in vitro and in mice.

Enterococcus faecalis CRISPR-Cas is a robust barrier to conjugative antibiotic resistance dissemination in the murine intestine

This study shows that CRISPR-Cas in Enterococcus faecalis blocks antibiotic resistance plasmid dissemination in the mouse intestine but not in vitro.

Bacteriophage resistance alters antibiotic mediated intestinal expansion of enterococci

This study shows that phage resistance in enterococci reduces their intestinal colonization ability and antibiotic sensitivity, suggesting phage therapy could complement antibiotics in treating dysbiotic microbiota.

An attenuated CRISPR-Cas system in Enterococcus faecalis permits DNA acquisition

This paper shows that Enterococcus faecalis can transiently tolerate CRISPR-Cas targeting of its own DNA, enabling DNA acquisition and genome editing.