John McKinney

Professor John McKinney received his Ph.D. from The Rockefeller University (New York, NY) in 1994 for studies on cell cycle regulation in Saccharomyces cerevisiae in the laboratory of Fred Cross. From 1995 to 1998, he was a postdoctoral fellow in the laboratory of William Jacobs at the Albert Einstein College of Medicine (Bronx, NY), where he studied mechanisms of persistence in Mycobacterium tuberculosis . In 1999, he returned to Rockefeller University to establish his own laboratory as an Assistant (1999-2004) and then Associate (2004-2007) Professor. In July 2007, the lab relocated to the Global Health Institute in the School of Life Sciences at the École Polytechnique Fédérale de Lausanne (EPFL) in Switzerland, where McKinney is Professor and Head of the Laboratory of Microbiology and Microsystems (LMIC). Our research focuses on understanding the mechanistic basis of bacterial persistence in the context of host immunity and antimicrobial therapy, using M. tuberculosis as a "model" system.

Preexisting Heterogeneity of Inducible Nitric Oxide Synthase Expression Drives Differential Growth of Mycobacterium tuberculosis in Macrophages

John McKinney, Ophélie Rutschmann, Chiara Toniolo

Mycobacterium tuberculosis infection is initiated by the inhalation and implantation of bacteria in the lung alveoli, where they are phagocytosed by macrophages. Even a single bacterium may be sufficient to initiate infection. Thereafter, the clinical outcome is highly variable between individuals, ranging from sterilization to active disease, for reasons that are not well understood. Here, we show that the rate of intracellular bacterial growth varies markedly between individual macrophages, and this heterogeneity is driven by cell-to-cell variation of inducible nitric oxide synthase (iNOS) activity. At the single-cell level, iNOS expression fluctuates over time, independent of infection or activation with gamma interferon. We conclude that chance encounters between individual bacteria and host cells randomly expressing different levels of an antibacterial gene can determine the outcome of single-cell infections, which may explain why some exposed individuals clear the bacteria while others develop progressive disease. IMPORTANCE In this report, we demonstrate that fluctuations in the expression of antimicrobial genes can define how single host cells control bacterial infections. We show that preexisting cell-to-cell variation in the expression of a single gene, that for inducible nitric oxide synthase, is sufficient to explain why some macrophages kill intracellular M. tuberculosis while others fail to control bacterial replication, possibly leading to disease progression. We introduce the concept that chance encounters between heterogeneous bacteria and host cells can determine the outcome of a host-pathogen interaction. This concept is particularly relevant for all the infectious diseases in which the number of interacting pathogens and host cells is small at some point during the infection.

AMER SOC MICROBIOLOGY2022

Dynamic persistence of UPEC intracellular bacterial communities in a human bladder-chip model of urinary tract infection

Neeraj Dhar, John McKinney, Kunal Sharma, François Signorino-Gelo, Thomas Marie Simonet, Vivek Vijay Thacker

Uropathogenic Escherichia coli (UPEC) proliferate within superficial bladder umbrella cells to form intracellular bacterial communities (IBCs) during early stages of urinary tract infections. However, the dynamic responses of IBCs to host stresses and antibiotic therapy are difficult to assess in situ. We develop a human bladder-chip model wherein umbrella cells and bladder microvascular endothelial cells are co-cultured under flow in urine and nutritive media respectively, and bladder filling and voiding mimicked mechanically by application and release of linear strain. Using time-lapse microscopy, we show that rapid recruitment of neutrophils from the vascular channel to sites of infection leads to swarm and neutrophil extracellular trap formation but does not prevent IBC formation. Subsequently, we tracked bacterial growth dynamics in individual IBCs through two cycles of antibiotic administration interspersed with recovery periods which revealed that the elimination of bacteria within IBCs by the antibiotic was delayed, and in some instances, did not occur at all. During the recovery period, rapid proliferation in a significant fraction of IBCs reseeded new foci of infection through bacterial shedding and host cell exfoliation. These insights reinforce a dynamic role for IBCs as harbours of bacterial persistence, with significant consequences for non-compliance with antibiotic regimens.

2021

Preexisting Heterogeneity of Inducible Nitric Oxide Synthase Expression Drives Differential Growth of Mycobacterium tuberculosis in Macrophages

John McKinney, Ophélie Rutschmann, Chiara Toniolo

AMER SOC MICROBIOLOGY2022

Preexisting Heterogeneity of Inducible Nitric Oxide Synthase Expression Drives Differential Growth of Mycobacterium tuberculosis in Macrophages

Dynamic persistence of UPEC intracellular bacterial communities in a human bladder-chip model of urinary tract infection

Early invasion of the bladder wall by solitary bacteria protects UPEC from antibiotics and neutrophil swarms in an organoid model

Preexisting Heterogeneity of Inducible Nitric Oxide Synthase Expression Drives Differential Growth of Mycobacterium tuberculosis in Macrophages

Early invasion of the bladder wall by solitary bacteria protects UPEC from antibiotics and neutrophil swarms in an organoid model

Dynamic persistence of UPEC intracellular bacterial communities in a human bladder-chip model of urinary tract infection