Publications by John McKinney | EPFL Graph Search

A hermetically closed sample chamber enables time-lapse nano-characterization of pathogenic microorganisms in vitro

John McKinney, Santiago Harald Andany, Georg Fantner, Navid Asmari Saadabad

Pathogenic microorganisms, such as pathogenic mycobacteria, pose a global health burden. Studying these organisms is crucial for gaining detailed knowledge about the pathogens and the diseases they cause. To handle pathogenic organisms, specific biosafety ...

ROYAL SOC CHEMISTRY2025

Open-source microscope add-on for structured illumination microscopy

Matthias Lütolf, Theo Lasser, Aleksandra Radenovic, John McKinney, Georg Fantner, Olivier François Venzin, Mélanie Thérèse Marie Hannebelle, Tomas Lukes, Samuel Mendes Leitão, Antonius Chrisnandy, Chiara Toniolo, Andrew Charles Oates, Prabhu Prasad Swain, Nathan Cyprien Arsène Ronceray

Super-resolution techniques expand the abilities of researchers who have the knowledge and resources to either build or purchase a system. This excludes the part of the research community without these capabilities. Here we introduce the openSIM add-on to ...

Nature Portfolio2024

Revitalizing antibiotic discovery and development through in vitro modelling of in-patient conditions

John McKinney, Alexandre Louis André Persat

In vitro models mimicking in-patient conditions have the potential to yield exciting opportunities for antibiotic research and revitalize future antibiotic discovery and development. ...

Nature Portfolio2024

Mechanical morphotype switching as an adaptive response in mycobacteria

John McKinney, Georg Fantner, Chiara Toniolo

Invading microbes face a myriad of cidal mechanisms of phagocytes that inflict physical damage to microbial structures. How intracellular bacterial pathogens adapt to these stresses is not fully understood. Here, we report the discovery of a virulence mech ...

Amer Assoc Advancement Science2024

UROPOT: study protocol for a randomized, double-blind phase I/II trial for metabolism-based potentiation of antimicrobial prophylaxis in the urological tract

John McKinney

Background: Urinary tract catheters, including Double-J or ureteral stents, are prone to bacterial colonization forming biofilms and leading to asymptomatic bacteriuria. In the context of asymptomatic bacteriuria, endourological procedures causing mucosa-i ...

2024

Mechanopathology of biofilm-like Mycobacterium tuberculosis cords

Nicolas Jean Philippe Guex, Graham Knott, John McKinney, Neeraj Dhar, Jessica Sordet, Maxime Jan, Kunal Sharma, Mélanie Thérèse Marie Hannebelle, Vivek Vijay Thacker, Richa Mishra

Mycobacterium tuberculosis (Mtb) cultured axenically without detergent forms biofilm-like cords, a clinical identifier of virulence. In lung-on-chip (LoC) and mouse models, cords in alveolar cells contribute to suppression of innate immune signaling via nu ...

Cell Press2023

Uptake-independent killing of macrophages by extracellular Mycobacterium tuberculosis aggregates

John McKinney, Neeraj Dhar, Chiara Toniolo

Mycobacterium tuberculosis (Mtb) infection is initiated by inhalation of bacteria into lung alveoli, where they are phagocytosed by resident macrophages. Intracellular Mtb replication induces the death of the infected macrophages and the release of bacteri ...

WILEY2023

Investigating the composition and recruitment of the mycobacterial ImuA'-ImuB-DnaE2 mutasome

John McKinney, Neeraj Dhar, Zela Alexandria-Mae Martin

A DNA damage-inducible mutagenic gene cassette has been implicated in the emergence of drug resistance in Mycobacterium tuberculosis during anti-tuberculosis (TB) chemotherapy. However, the molecular composition and operation of the encoded 'mycobacterial ...

Elife Sciences Publ Ltd2023

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 outc ...

AMER SOC MICROBIOLOGY2022

Seeing and Touching the Mycomembrane at the Nanoscale

John McKinney, Georg Fantner

Mycobacteria have unique cell envelopes, surface properties and growth dynamics, which all play a part in the ability of these important pathogens to infect, evade host immunity, disseminate and to resist antibiotic challenges. Recent atomic force microsco ...

American Society for Microbiology2021

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

Graham Knott, John McKinney, Neeraj Dhar, François Signorino-Gelo, Kunal Sharma, Vivek Vijay Thacker, Maria Clapés Cabrer

2021

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

Graham Knott, John McKinney, Neeraj Dhar, François Signorino-Gelo, Kunal Sharma, 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 anti ...

2021

Microfluidic-assisted bioprinting of tissues and organoids at high cell concentrations

Philippe Renaud, Arnaud Bertsch, John McKinney, Ludovic Serex, Kunal Sharma

Despite its simplicity, which makes it the most commonly used bioprinting method today, extrusion-based bioprinting suffers from its inability to reproduce the complex tissue architecture found in organs. Generally, this printing method allows for the disp ...

IOP PUBLISHING LTD2021

Revealing Antibiotic Tolerance of the Mycobacterium smegmatis Xanthine/Uracil Permease Mutant Using Microfluidics and Single-Cell Analysis

John McKinney, Neeraj Dhar, Meltem Elitas

To reveal rare phenotypes in bacterial populations, conventional microbiology tools should be advanced to generate rapid, quantitative, accurate, and high-throughput data. The main drawbacks of widely used traditional methods for antibiotic studies include ...

MDPI2021

A biphasic growth model for cell pole elongation in mycobacteria

Joëlle Xiao Yuan Ven, John McKinney, Gaëlle Madeleine Vuaridel, Georg Fantner, Mélanie Thérèse Marie Hannebelle, Haig Alexander Eskandarian, Chiara Toniolo

Mycobacteria grow by inserting new cell wall material in discrete zones at the cell poles. This pattern implies that polar growth zones must be assembled de novo at each division, but the mechanisms that control the initiation of new pole growth are unknow ...

Nature Research2020

Overlapping and essential roles for molecular and mechanical mechanisms in mycobacterial cell division

John McKinney, Georg Fantner, Pascal Damian Odermatt, Adrian Pascal Nievergelt, Mélanie Thérèse Marie Hannebelle, Haig Alexander Eskandarian

Mechanisms to control cell division are essential for cell proliferation and survival. Bacterial cell growth and division require the coordinated activity of peptidoglycan synthases and hydrolytic enzymes to maintain mechanical integrity of the cell wall. ...

2020

Do chance encounters between heterogeneous cells shape the outcome of tuberculosis infections?

John McKinney, Ophélie Rutschmann, Chiara Toniolo

The sum of all of the interactions between single bacteria and host cells determines if an infection is cleared, controlled, or progresses at the whole host-organism level. These individual interactions have independent trajectories defined by diverse and ...

2020

A lung-on-chip model of early Mycobacterium tuberculosis infection reveals an essential role for alveolar epithelial cells in controlling bacterial growth

John McKinney, Neeraj Dhar, Kunal Sharma, Vivek Vijay Thacker

We establish a murine lung-on-chip infection model and use time-lapse imaging to reveal the dynamics of host-Mycobacterium tuberculosis interactions at an air-liquid interface with a spatiotemporal resolution unattainable in animal models and to probe the ...

2020

Preexisting variation in DNA damage response predicts the fate of single mycobacteria under stress

John McKinney, Neeraj Dhar, Giulia Manina, Lalit Kumar Singh

Clonal microbial populations are inherently heterogeneous, and this diversification is often considered as an adaptation strategy. In clinical infections, phenotypic diversity is found to be associated with drug tolerance, which in turn could evolve into g ...

2019

Time-Lapse Atomic Force Microscopy Reveals New End Take Off (Neto) Dynamics in Mycobacteria

Joëlle Xiao Yuan Ven, John McKinney, Georg Fantner, Adrian Pascal Nievergelt, Mélanie Thérèse Marie Hannebelle, Haig Alexander Eskandarian, Chiara Toniolo

CELL PRESS2019