Large-scale CRISPRi and transcriptomics of Staphylococcus epidermidis identify genetic factors implicated in commensal-pathogen lifestyle versatility

Staphylococcus (S.) epidermidis is a ubiquitous human commensal skin bacterium and prevalent nosocomial pathogen, but genetic factors underlying this lifestyle plasticity are incompletely understood. We developed a large-scale CRISPR interference (CRISPRi) screen complemented by transcriptional profiling (RNA-seq) across 24 conditions and piloted droplet-based CRISPRi. We identified putative essential genes, demonstrated the importance of trace metal uptake under stress, and identified condition-specific essential genes. Additionally, we demonstrate the considerable transcriptional plasticity of S. epidermidis, postulating a mechanism by which nitrogen metabolism is linked to lifestyle versatility in response to hyperosmotic challenges, and performed a comprehensive analysis of survival under acid stress, hypothesizing a role for cell wall modification as crucial. This study represents one of the first large-scale CRISPRi studies in prokaryotes and the first to integrate transcriptomics data across multiple conditions. Our results provide a valuable benchmarking analysis for CRISPRi screens and are rich resource for other staphylococcal researchers.

Complete Genome Sequences of Two Staphylococcus saccharolyticus Strains Isolated from Prosthetic Joint Infections

ABSTRACT Staphylococcus saccharolyticus is a human skin bacterium and is occasionally associated with prosthetic joint infections (PJIs). Here, we report the complete genome sequences of two strains that were isolated from shoulder and hip PJIs. The genomes show signs of reductive evolution; around 21% of all coding sequences are inactivated by frameshift mutations.

Consequences of Long-term Exposure to Increased Salinity on the Amphibian Skin Bacterium Erwinia Toletana

Amphibian’s skin bacterial community may help them to cope with several types of environmental perturbations, including osmotic stress caused by increased salinity. This work aimed at assessing if an amphibian skin bacterium could increase its tolerance to NaCl after a long-term exposure to this salt. A strain of Erwinia toletana, isolated from the skin of Pelophylax perezi, was exposed to two salinity scenarios (of 18g/L of NaCl): (i) long-term exposure (for 46 days; Et-NaCl) and (ii) long-term exposure followed by a recovery period, (exposure for 30 days to NaCl and then to LB medium for 16 days; Et-R). After exposure, the sensitivity of E. toletana clonal populations to NaCl was assessed by testing 6 NaCl concentrations (LB medium spiked with NaCl) plus a control (LB medium). Genotypic alterations were assessed by PCR-based molecular typing method (BOX-PCR). Results shown that tolerance of E. toletana to NaCl slightly increased after the long-term exposure, EC50 for growth were: 22.5g/L (8.64-36.4) for Et-LB; 30.3g/L (23.2-37.4) for Et-NaCl, and 26.1g/L (19.3-32.9) for Et-R. Differences in metabolic activity were observed between Et-LB and Et-R and Et-NaCl and Et-R suggesting the use of different substrates by this bacterium when exposed to salinized environments. NaCl-induced genotypic alterations were not detected. This work suggests that E. toletana exposed to low levels of salinity, activate different metabolic pathways to cope with osmotic stress. Which may be further explored to be used in bioaugmentation procedures in natural populations of amphibians exposed to salinization.

Tadpole body size and behaviour alter the social acquisition of a defensive bacterial symbiont

Individual differences in host phenotypes can generate heterogeneity in the acquisition and transmission of microbes. Although this has become a prominent factor of disease epidemiology, host phenotypic variation might similarly underlie the transmission of microbial symbionts that defend against pathogen infection. Here, we test whether host body size and behaviour influence the social acquisition of a skin bacterium, Janthinobacterium lividum , which in some hosts can confer protection against infection by Batrachochytrium dendrobatidis , the causative agent of the amphibian skin disease chytridiomycosis. We measured body size and boldness (time spent in an open field) of green frog tadpoles and haphazardly constructed groups of six individuals. In some groups, we exposed one individual in each group to J. lividum and, in other groups, we inoculated a patch of aquarium pebbles to J. lividum . After 24 h, we swabbed each individual to estimate the presence of J. lividum on their skin. On average, tadpoles acquired nearly four times more bacteria when housed with an exposed individual compared to those housed with a patch of inoculated substrate. When tadpoles were housed with an exposed group-mate, larger and ‘bolder’ individuals acquired more bacteria. These data suggest that phenotypically biased acquisition of defensive symbionts might generate biased patterns of mortality from the pathogens against which they protect.

Response to Comment on “A commensal strain of Staphylococcus epidermidis protects against skin neoplasia” by Nakatsuji et al.

Kozmin et al. contend that observations previously reported regarding the antimicrobial and antitumor activities of 6-N-hydroxy aminopurine (6-HAP) were incorrect. Their conclusions rely on poorly characterized reagents and focus strictly on in vitro techniques without validation in relevant mammalian model systems. We are pleased to be able to illuminate the weaknesses in their technical comment. The totality of current results continues to support our original conclusion that a strain of the common human commensal skin bacterium, Staphylococcus epidermidis, produces 6-HAP that can inhibit tumor growth.