Tissue compartmentalization enables; Salmonella; persistence during chemotherapy

Antimicrobial chemotherapy can fail to eradicate the pathogen, even in the absence of antimicrobial resistance. Persisting pathogens can subsequently cause relapsing diseases. In vitro studies suggest various mechanisms of antibiotic persistence, but their in vivo relevance remains unclear because of the difficulty of studying scarce pathogen survivors in complex host tissues. Here, we localized and characterized rare surviving; Salmonella; in mouse spleen using high-resolution whole-organ tomography. Chemotherapy cleared >99.5% of the; Salmonella; but was inefficient against a small; Salmonella; subset in the white pulp. Previous models could not explain these findings: drug exposure was adequate,; Salmonella; continued to replicate, and host stresses induced only limited; Salmonella; drug tolerance. Instead, antimicrobial clearance required support of; Salmonella; -killing neutrophils and monocytes, and the density of such cells was lower in the white pulp than in other spleen compartments containing higher; Salmonella; loads. Neutrophil densities declined further during treatment in response to receding; Salmonella; loads, resulting in insufficient support for; Salmonella; clearance from the white pulp and eradication failure. However, adjunctive therapies sustaining inflammatory support enabled effective clearance. These results identify uneven; Salmonella; tissue colonization and spatiotemporal inflammation dynamics as main causes of; Salmonella; persistence and establish a powerful approach to investigate scarce but impactful pathogen subsets in complex host environments

Efficient Dual-Negative Selection for Bacterial Genome Editing

We describe a versatile method for chromosomal gene editing based on classical consecutive single-crossovers. The method exploits rapid plasmid construction using Gibson assembly, a convenient E. coli donor strain, and efficient dual-negative selection for improved suicide vector resolution. We used this method to generate in frame deletions, insertions and point mutations in Salmonella enterica with limited hands-on time. Similar strategies allowed efficient gene editing also in Pseudomonas aeruginosa and multi-drug-resistant (MDR) Escherichia coli clinical isolates

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

Erratum to: Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition) (Autophagy, 12, 1, 1-222, 10.1080/15548627.2015.1100356

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