Selected Publications

The mechanism by which phenotypic heterogeneity is generated within a bacterial population and leads to colistin heteroresistance has been unclear. Heteroresistance is a form of antibiotic resistance in which a minor subpopulation of resistant cells coexists with a majority susceptible population. Colistin heteroresistance is common among Enterobacter isolates, threatens its utility as a therapeutic, and has become a model to study the fundamental bases of heteroresistance. Here, we identify the sigma factor σE  as the source of heterogeneity in colistin resistance. Single-cell tracking revealed that σE  is active in 1% of the population, and only those cells survive colistin exposure. However, σE expression and heterogeneity were insufficient for survival, as a mutant lacking the PhoPQ system controlling lipid A modifications necessary for colistin resistance retained heterogeneity but lost resistance. These findings lead to a paradigm in heteroresistance; the combinatorial action of regulatory systems, encompassing a heterogeneity generator and a distinct resistance generator, gives rise to colistin heteroresistance.

Heteroresistance is a form of antibiotic resistance in which a phenotypically unstable subpopulation of resistant cells coexists with a majority susceptible population. Many mechanisms of heteroresistance are unclear and the impact of the extracellular environment on this phenomenon is unknown. Studying fosfomycin heteroresistance in Enterobacter cloacae complex, we observed that glucose availability greatly increased the frequency of the resistant subpopulation. Glucose downregulated the glycerol and fosfomycin importer GlpT via catabolite repression. Heteroresistance was generated by heterogeneity in single-cell expression of GlpT, in addition to expression of fosA, which acted as a resistance enhancer. Due to the impact of environmental glucose on glpT expression, we observed that the resistant subpopulation was more frequent during infection in murine models of hyperglycemia/diabetes. Thus, we reveal a paradigm where heterogeneity in response to the environment tunes resistant subpopulation frequency, which suggests that the metabolic context of infection in specific disease states may be important to consider in treatment decisions.

We sought to uncover the mechanism of heteroresistance to cefiderocol, a novel β-lactam developed to resist β-lactamases including extended-spectrum-β-lactamases (ESBLs), which has been recently reported but poorly understood. We observe HR to cefiderocol among clinical isolates collected before its use. The resistant subpopulation in Enterobacter is a continuum; increasing copy number of a gene encoding an ESBL ineffective against cefiderocol mediates increased resistance in decreasing numbers of cells. We observe that ESBL activity correlates with the level of amplification, and thus that increased copy number can compensate for poor enzymatic activity.. These data provide insights into factors controlling dynamics of HR and how bacteria can use gene amplification to flexibly confront new antibiotic threats.

Hypervirulent Klebsiella pneumoniae (hvKp) has emerged as a concerning global pathogen. hvKp is more virulent than classical K. pneumoniae (cKp) and capable of causing community-acquired infections, often in healthy individuals. hvKp is carried in the gastrointestinal tract, which contributes to its spread in the community and healthcare settings. hvKp arose as a leading cause of pyogenic liver abscesses. In addition to liver abscesses, hvKp is distinct from cKp in its ability to metastasize to distant sites, including most commonly the eye, lung and central nervous system (CNS). The genetic determinants of hypervirulence are often found on large virulence plasmids as well as chromosomal mobile genetic elements which can be used as biomarkers to distinguish hvKp from cKp clinical isolates. These distinct virulence determinants of hvKp include up to four siderophore systems for iron acquisition, increased capsule production, K1 and K2 capsule types, and the colibactin toxin.  This review details the distinguishing features of hypervirulent K. pneumoniae