Antimicrobial resistance is a serious global health threat, yet the drivers of its spread among humans are not fully understood. Antibiotics can enter the human gastrointestinal tract through the food chain, leading to the presence of low concentrations in the gut microbiota. However, the role of such traces in promoting the implantation of drug-resistant pathogens in the gut microbiota has never been explored in a controlled experimental setting. Using an in vitro model of the human gut microbiota, we tested whether traces of 19 antibiotics used in both human and veterinary medicine, alone or in combination, lead to the enrichment of Gram-negative pathogens producing extended-spectrum β-lactamases or carbapenemases. Twenty-eight strains of Gram-negative pathogens epidemic in humans (10 Escherichia coli, 6 Klebsiella pneumoniae, 5 Enterobacter hormaechei, 4 Acinetobacter baumannii, 3 Pseudomonas aeruginosa) were tested. We found that antibiotics at levels similar to those measured in the feces of healthy individuals (fluoroquinolones, 1-100 μg L-1; trimethoprim, 100 μg L-1; a mixture of fifteen veterinary antibiotics, 10-20 μg L-1) enriched the human gut microbiota with those resistant pathogens. Overall, the present study indicates that dietary consumption of some antibiotics can result in concentrations in the human colon sufficiently high to favor the implantation of exogenous antibiotic-resistant pathogens. These findings highlight the need to reassess permissible antibiotic concentrations in food and critically evaluate agricultural practices contributing to the contamination of animal- and plant-based products.

BACKGROUND:The occurrence of foreign body (FB) infections in patients with Staphylococcus aureus bacteraemia (SAB) can lead to serious complications. We therefore sought to evaluate the host risk factors and bacterial determinants associated with FB infection following SAB. METHODS:We retrospectively included patients hospitalized with a SAB and carrying FB, over a four-year period. Factors associated with FB infection were assessed with multivariable logistic regression analysis. Bacterial determinants (lineage and virulence factors) were determined using whole genome sequencing. RESULTS:We included 104 patients of whom 40 patients (38.5%) with FB infection. Factors associated with FB infection were community-acquired SAB (OR = 3.8; 95% confidence interval, CI [1.36-10.59]; p = 0.011), Charlson's score >3 (OR = 0.39; 95% CI [0.16.-0.99]; p = 0.048 and unknown source of infection (OR = 3.54; 95% CI [1.34-9.33]; p = 0.011). No clonal complex or virulence gene was associated with a risk of FB infection in patients with SAB. CONCLUSION:FB infection is frequent in patients with SAB, particularly when the bacteremia is community-acquired. Our results suggest that bacterial characteristics (clonal complex or virulence factors) are not involved in the occurrence of FB infection in patients with SAB.

In France, the use of essential oils to treat bacterial infections is common, with approximately 40% of cystic fibrosis patients regularly using these natural products to control infections caused by Pseudomonas aeruginosa often in combination with their antibiotic treatments. Previous research has demonstrated that prolonged exposure of P. aeruginosa PA14 to cinnamaldehyde (CNA), the main component of cinnamon essential oil, can select for mutants resistant to β-lactams through overproduction of the MexAB-OprM efflux pump, some of which are also hypersusceptible to aminoglycosides and colistin. We showed here that this hypersusceptibility is not due to an efflux defect, as the deletion of MexXY(OprM)-the specific efflux pump for aminoglycosides-still results in decreased minimum inhibitory concentrations of aminoglycosides. Genome sequencing of hypersusceptible mutants revealed mutations in the ATP synthase operon or its promoter (atpIBEFHAGDC). Surprisingly, although mutations in the atp operon reduced bacterial growth and ATP production, they are not uncommon in clinical strains. We found that ATP synthase alterations modified the respiratory chain and led to inner membrane hyperpolarization, likely enhancing positively charged antibiotic (aminoglycosides and colistin) uptake and susceptibility to these molecules. In addition, the modified respiratory chain increased the proton motive force, allowing the overproduction of the MexAB-OpM efflux pump, which protects bacteria from CNA and from the clinically relevant β-lactam antibiotics. Altogether, these results indicate a trade-off between CNA resistance and aminoglycoside/colistin susceptibility, a reaction that may question the survival of P. aeruginosa in the lung of CF patients possibly submitted to these therapeutic molecules.IMPORTANCEIn France, essential oils are widely used by cystic fibrosis patients (40%), often alongside antibiotic therapies, to help control Pseudomonas aeruginosa infections. Cinnamaldehyde from cinnamon essential oil appears to select for P. aeruginosa mutants that are resistant to β-lactam antibiotics due to the overproduction of the MexAB-OprM efflux pump and hypersusceptible to aminoglycosides and colistin. This increased susceptibility is associated with mutations in ATP synthase, which elevate the proton motive force (PMF) and facilitate both (i) increased uptake of positively charged antibiotics (aminoglycosides, colistin) and (ii) more efficient efflux of β-lactams via MexAB-OpM. Thus, the use of cinnamaldehyde may drive a trade-off in P. aeruginosa between β-lactam resistance and aminoglycosides/polymyxins susceptibility, potentially compromising bacterial persistence in the lung of patients.

In high-income countries, dogs and cats are often considered members of the family. Because of this proximity, it has been suggested that pets and humans might exchange bacterial species from their gut microbiota, with multidrug resistant bacteria being of particular concern. The aim of this study was to compare the genomes of third-generation cephalosporin-resistant (3GC-R) Escherichia coli responsible for human and pet infections in Europe.Whole-genome sequencing data from 3GC-R E. coli isolated from clinical samples of humans, dogs and cats, and published in eight European studies were re-analyzed using bioinformatics tools. The acquired genes responsible for 3GC-R were identified. The sequence type (ST) of all genomes were assessed by multilocus sequence typing. Alpha and beta diversities were measured within and between the two populations.We included genomes of 1327 3GC-R E. coli isolated from humans and animals with 109 (8.2 %) being responsible for infections in dogs and cat, and 1218 (91.8 %) responsible for human infections. Alpha diversity analysis suggested greater diversity within ST and 3GC-R genes in the animal population. Beta diversity analysis by principal coordinate analysis separated animal and human strains. ST131 was more abundant in human strains (43.4 %) than in animal strains (14.7 %) (p < 0.001). Six STs, including ST372, were identified almost exclusively in 3GC-R E. coli from animal origin. The blaCTX-M-15 gene was more frequent in humans (49.24 %) than in companion animals (17.9 %) (p < 0.001). The resistance genes blaCMY-2 (30.8 %) and blaCTX-M-1 (15.4 %) were more frequent in E. coli isolated from pets (p < 0.001).We found that populations of 3GC-R E. coli responsible for human and pet infections in Europe do not overlap. Although it cannot rule out occasional transmission of bacteria between pets and humans within a household, it suggests that dogs and cats are not a major source of human infection with this antibiotic-resistant pathogen.

Pseudomonas aeruginosa is a major opportunistic pathogen responsible for severe infections in immunocompromised patients. The contamination of drinking water networks (DWNs) with this pathogen is underestimated, as it is mostly in the state of persister cells undetected by the recommended monitoring technique. We collected water samples from eight cities distant from each other and searched for P. aeruginosa using a culture-based method that resuscitates persister cells. The genomes of isolates were sequenced. Five DWNs of the eight tested (62.5%) were contaminated with P. aeruginosa, of which four were contaminated with high-risk clones (ST308, ST395). Surprisingly, the ST308 isolates retrieved from the four independent and distant DWNs were clonal. Most P. aeruginosa isolates shared a genomic island conferring tolerance to copper-ions. The population structure of the collection may result from both a common source of contamination by plumbing supplies and the selection of clones sharing genetic elements that presumably aided their propagation in DWNs.

Alveolar echinococcosis (AE) is a rare but severe disease that affects more than 18,000 people worldwide per year. The complete sequencing of the mitochondrial genome of Echinococcus multilocularis has made it possible to study the genetic diversity of the parasite and its spatial and temporal evolution. We amplified the whole mitochondrial genome by PCR, using one uniplex and two multiplex reactions to cover the 13,738 bp of the mitogenome, and then sequenced the amplicons with Illumina technology. In total, 113 samples from Europe, Asia, , the Arctic and North America were analyzed. Three major haplogroups were found: HG1, which clustered samples from Alaska (including Saint-Lawrence Island), Yakutia (Russia) and Svalbard; HG2, with samples from Asia, North America and Europe; and HG3, subdivided into three micro-haplogroups. HG3a included samples from North America and Europe, whereas HG3b and HG3c only include samples from Europe. In France, HG3a included samples from patients more recently diagnosed in a region outside the historical endemic area. A fourth putative haplogroup, HG4, was represented by only one isolate from Olkhon Island (Russia). The increased discriminatory power of the complete sequencing of the E. multilocularis mitogenome has made it possible to highlight four distinct geographical clusters, one being divided into three micro-haplogroups in France.

Recent efforts have been made to review the state of the art on a variety of questions and targets in paleoparasitology, including protozoan taxa. Meanwhile, these efforts seemed to let aside Cryptosporidium, and we then intended to review its paleoparasitological record to assess its past distribution and favored detection methods, and eventually highlight needed research trajectories. This review shows that contrary to other parasites, most of the positive results came from South-American sites and coprolites rather than sediment samples, highlighting the need to test this kind of material, notably in Europe where many negative results were reported in the published literature from sediment samples. Moreover, aDNA-based detections are nearly absent from the paleoparasitological record of this parasite, though punctually shown successful. With their potential to address the evolutionary history of Cryptosporidium species, notably through their 18S rRNA tree, aDNA-based approaches should be encouraged in the future. In sum, and though the limits of currently used methods and materials remain unclear, this review highlights the potential role of coprolites and aDNA for the study of Cryptosporidium species in the past and how this history shaped their current diversity and distribution, notably among human populations but also farm animals.

Aim: We used genome-based typing data with the aim of identifying the routes of acquisition of Pseudomonas aeruginosa by patients hospitalized in a medical intensive care unit (MICU) over a long period in a non-epidemic context.Methods: This monocentric prospective study took place over 10 months in 2019 in a 15 -bed MICU that applies standard precautions of hygiene. Lockable sink traps installed at all water points of use were bleach disinfected twice a week. We sampled all sink traps weekly to collect 404 P. aeruginosa environmental isolates and collected all P. aeruginosa isolates (N = 115) colonizing or infecting patients (N = 65). All isolates had their pheno-typic resistance profile determined and their genome sequenced, from which we identified resistance determinants and assessed the population structure of the collection at the nucleotide level to identify events of P. aeruginosa transmission.Findings: All sink traps were positive for P. aeruginosa, each sink trap being colonized for several months by one or more clones. The combination of genomic and spatiotemporal data identified one potential event of P. aeruginosa transmission from a sink trap to a patient (1/65, 1.5%) and six events of patient cross-transmission, leading to the contamination of five patients (5/65, 7.7%). All transmitted isolates were fully susceptible to b-lactams and aminoglycosides.Conclusions: Genome-based typing revealed the contamination of patients by P. aeruginosa originating from sink traps to be infrequent (1.5%) in an MICU with sink trap -bleaching measures, and that only 7.7% of the patients acquired P. aeruginosa originating from another patient.(c) 2023 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

The animal reservoir of Enterobacterales producing Extended-Spectrum-β-Lactamases (ESBL) and plasmid-borne cephalosporinases (pAmpC) is a global concern. Using genome data, we analyzed a population of Escherichia coli and Salmonella species resistant to third-generation cephalosporins (3GC-R) recovered from healthy food animals (HA) and diseased food animals (DA) across Europe. Among the isolates collected from HA (n = 4,498) and DA (n = 833) in up to twelve European countries, 62 (1.4%) and 45 (5.4%) were 3GC-R, respectively. The genomes of these 3GC-R 107 isolates were sequenced to identify blaESBL and blaAmpC, sequence types (STs), virulence-associated genes, and Salmonella serovars. We also assessed their population structure using core genome multilocus sequence typing. The 78 3GC-R Escherichia coli originated from poultry (n = 27), swine (n = 26), and cattle (n = 25). Almost all (n = 77; 98.7%) harbored at least one blaESBL or blaAmpC, with blaCTX-M-1 predominating. We identified 51 STs, with ST10 and ST101 being the most frequent. The population of 3GC-R E. coli was polyclonal. The 29 3GC-R Salmonella spp. were mostly retrieved from healthy broiler (96.5%). blaCMY-2 dominated in this population. We found two clusters of CMY-2-producing Salmonella spp. in Germany: one with 15 isolates of S. Heidelberg isolates and another with six S. Minnesota, all of them with blaCMY-2. Our results confirm the low prevalence of 3GC-R E. coli and Salmonella spp. in HA and DA. blaCTX-M-1 was dominating in a highly diverse population of E. coli. 3GC-R E.coli isolated from HA and DA were genetically unrelated, with high clonal diversity suggesting multiple origins of contamination. This contrasted with the clonal population of 3GC-R Salmonella spp. in which blaCMY-2 dominated through two dominant serovars in this collection.

Cockroach allergens have a greater impact on asthma morbidity than those from dust mites, cats, and dogs. The American cockroach (Periplaneta americana) and the German cockroach (Blattella germanica) are most frequently responsible for sensitization. The worldwide prevalence of allergic sensitization has been estimated at 2 to 26 % and is influenced by unfavorable socioeconomic conditions. Exposure is generally measured by determining antigen levels in dust or through insect trapping. We developed a real-time quantitative PCR (qPCR) method to provide an objective measurement of B. germanica levels in dwellings. The specificity of the qPCR primers and TaqMan® hydrolysis probe was validated in silico with 18S rRNA sequences. No amplification was observed for other species of cockroaches, with the exception of Blattella nipponica, which is not common indoors. From 2018 to 2021, exposure to B. germanica was detected and quantified in 27 of 389 dwellings in Bourgogne-Franche-Comté (mean = 333.8; median = 9.1 and maximum = 5304 copy number equivalents) and in 236 of 3193 ELFE cohort dwellings in mainland France in 2011 (mean = 15.6; median < 1 and maximum = 1275 copy number equivalents). The distribution of dwellings testing positive for cockroaches (7 %) differed among the 12 regions of France: <1 % in two regions, between 1 and 5 % in eight regions, 16.5 % in two regions and 35 % around Paris. Exposure measurements by the EDC sampling and qPCR methods are effective ways to assess the exposure to cockroaches in dwellings. A knowledge of the level of exposure to cockroaches is particularly important for asthmatic patients, particularly those not allergic to other common antigens.

The Acinetobacter baumannii clonal lineage ST25 has been identified in humans and animals and found associated with outbreaks globally. To highlight possible similarities among ST25 A. baumannii of animal and human origins and to gather clues on the dissemination and evolution of the ST25 lineage, we conducted a phylogenetic analysis on n = 106 human and n = 35 animal A. baumannii ST25 genomes, including 44 sequenced for this study. Resistance genes and their genetic background were analyzed, as well. ST25 genomes are clustered into four clades: two are widespread in South America, while the other two are largely distributed in Europe, Asia and America. One particular clade was found to include the most recent strains and the highest number of acquired antibiotic resistance genes. OXA-23-type carbapenemase was the most common. Other resistance genes such as blaNDM-1, blaPER-7, and armA were found embedded in complex chromosomal regions present in human isolates. Genomic similarity among multidrug resistant ST25 isolates of either animal or human origin was revealed, suggesting cross-contaminations between the two sectors. Tracking the clonal complex ST25 between humans and animals should provide new insights into the mode of dissemination of these bacteria, and should help defining strategies for preserving global health.

Core genome multilocus sequence typing (cgMLST) has gained in popularity for bacterial typing since whole-genome sequencing (WGS) has become affordable. We introduce here pyMLST, a new complete, stand-alone, free and open source pipeline for cgMLST analysis. pyMLST can create or import a core genome database. For each gene, the first allele is aligned against the bacterial genome of interest using BLAT. Incomplete genes are aligned using MAFT. All data are stored in a SQLite database. pyMLST accepts assembly genomes or raw data (with the option pyMLST-KMA) as input. To evaluate our new tool, we selected three genome collections of major bacterial pathogens (Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus) and compared them with pyMLST, pyMLST-KMA, ChewBBACA, SeqSphere and the variant calling approach. We compared the sensitivity, precision and false-positive rate for each method with those of the variant calling approach. Minimal spanning trees were generated with each type of software to evaluate their interest in the context of a bacterial outbreak. We found that pyMLST-KMA is a convenient screening method to avoid assembling large bacterial collections. Our data showed that pyMLST (free, open source, available in Galaxy and pipeline ready) performed similarly to the commercial SeqSphere and performed better than ChewBBACA and pyMLST-KMA.

BACKGROUND:Using genomic data, we determined the origin of MRSA ST398 isolates responsible for invasive infection in patients with no known livestock contact.METHODS:We sequenced the genome of seven MSSA and four MRSA ST398 isolates from patients with invasive infections between 2013 and 2017, using the Illumina technique. Prophage-associated virulence genes and resistance genes were identified. To determine the origin of the isolates, their genome sequences were included in phylogenetic analysis also encompassing the ST398 genomes available on NCBI.RESULTS:All isolates carried the φSa3 prophage, but with variations in the immune evasion cluster: type C in MRSA isolates, and type B in MSSA isolates. All MSSA belonged to the spa type t1451. MRSA strains had the same SCCmec type IVa (2B) cassette and belonged to spa types t899, t4132, t1939 and t2922. All MRSA harbored the tetracycline resistance gene, tet(M). Phylogenetic analysis revealed that MSSA isolates belonged to a cluster of human-associated isolates, while MRSA isolates belonged to a cluster containing livestock-associated MRSA.CONCLUSION:We showed that the clinical isolates MRSA and MSSA ST398 have different origins. An acquisition of virulence genes by livestock-associated MRSA isolates allows them to induce an invasive infection in human.

Background Intestinal inflammation, dysbiosis, intestinal permeability (IP), and bacterial translocation (BT) have been identified in patients with spondyloarthritis but the time at which they appear and their contribution to the pathogenesis of the disease is still a matter of debate. Objectives To study the time-course of intestinal inflammation (I-Inf), IP, microbiota modification BT in a rat model of reactive arthritis, the adjuvant-induced arthritis model (AIA). Methods Analysis was performed at 3 phases of arthritis in control and AIA rats: preclinical phase (day 4), onset phase (day 11), and acute phase (day 28). IP was assessed by measuring levels of zonulin and ileal mRNA expression of zonulin. I-inf was assessed by lymphocyte count from rat ileum and by measuring ileal mRNA expression of proinflammatory cytokines. The integrity of the intestinal barrier was evaluated by levels of iFABP. BT and gut microbiota were assessed by LPS, soluble CD14 levels, and 16S RNA sequencing in mesenteric lymph node and by 16S rRNA sequencing in stool, respectively. Results Plasma zonulin levels increased at the preclinical and onset phase in the AIA group. Plasma levels of iFABP were increased in AIA rats at all stages of the arthritis course. The preclinical phase was characterized by a transient dysbiosis and increased mRNA ileal expression of IL-8, IL-33, and IL-17. At the onset phase, TNF-α, IL-23p19, and IL-8 mRNA expression were increased. No changes in cytokines mRNA expression were observed at the acute phase. Increased CD4 + and CD8 + T cell number was measured in the AIA ileum at day 4 and day 11. No increase in BT was observed. Conclusion These data show that intestinal changes precede the development of arthritis but argue against a strict “correlative” model in which arthritis and gut changes are inseparable.

Human papillomavirus (HPV) 16 exhibits different variants that may differ in their carcinogenic risk. To identify some high-risk variants, we sequenced and compared HPV16 whole genomes obtained from a longitudinal cohort of 34 HPV16-infected women who had either spontaneously cleared their infection (clearance group or "C"), or developed cervical high-grade lesions following a viral persistence (group persistence or "P"). Phylogenetic analysis of paired samples obtained at the beginning (C0 or P0) and at the end (C2 or P2) of the follow-up (median intervals between C0-C2 and between P0-P2 were 16 and 36.5 months, respectively) revealed a low genetic variability within the host compared to the genetic interhost diversity. By comparing our HPV16 sequences to a reference sequence, we observed 301 different substitutions, more often transitions (60.9%) than transversions (39.1%), that occurred throughout the viral genome, but with a low frequency in E6 and E7 oncogenes (10 and 9 substitutions), suggesting a high conservation of these genes. Deletions and insertions were mostly observed in intergenic regions of the virus. The only significant substitution found between the subgroups C2 and P2 was observed in the L2 gene (L330F), with an unclear biological relevance. Our results suggest a low longitudinal intrahost evolution of HPV16 sequences and no correlation between genetic variations and clinical evolution.

In recent years, several reports pointed out the role of protein oxidation in seed longevity, notably regarding the oxidation of methionine (Met) residues to methionine sulfoxide (MetO) in proteins. To further consider this question, we present a handy proteomic method based on the use of two-dimensional diagonal electrophoresis (2Dd) and cyanogen bromide (CNBr) cleavage, which we refer to as 2Dd-CNBr. CNBr treatment of proteins causes the non-enzymatic hydrolysis of peptide bonds on the carboxyl side of reduced Met residues. However, Met oxidation causes a lack of cleavage, thus modifying the electrophoretic mobility of CNBr-induced peptides. This approach was first validated using bovine serum albumin as a model protein, which confirmed the possibility of distinguishing between oxidized and non-oxidized forms of Met-containing peptides in gels. Then, the 2Dd-CNBr method was applied to the Arabidopsis thaliana seed protein extract in a control (non-oxidized) condition and in an oxidized one (as obtained following hypochlorous acid treatment). Twenty-four oxidized Met residues in 19 proteins identified by mass spectrometry were found to be surface exposed in these proteins. In the three-dimensional environment of the oxidized Met, we detected amino acid residues that could be converted by oxidation (carbonylation) or by phosphorylation, suggesting a possible interplay between Met oxidation and the other protein modifications. The identification of the proteins oxidatively modified in Met residues revealed the finding that MetO-containing proteins are related to seed longevity. Based on these results, we suggest that the method presently described also has the potential for wider applications.

Seed germination and subsequent seedling growth affect the final yield and quality of the crop. Seed germination is defined as a series of processes that begins with water uptake by a quiescent dry seed and ends with the elongation of embryonic axis. Rice is an important cereal crop species, and during seed germination, two tissues function in a different manner; the embryo grows into a seedling as the next generation and the endosperm is responsible for nutritional supply. Toward understanding the integrated roles of each tissue at the transcriptional, translational, and metabolic production levels during germination, an exhaustive "multi-omics" analysis was performed by combining transcriptomics, label-free shotgun proteomics, and metabolomics on rice germinating embryo and endosperm, independently. Time-course analyses of the transcriptome and metabolome in germinating seeds revealed a major turning point in the early phase of germination in both embryo and endosperm, suggesting that dramatic changes begin immediately after water imbibition in the rice germination program at least at the mRNA and metabolite levels. In endosperm, protein profiles mostly showed abundant decreases corresponding to 90% of the differentially accumulated proteins. An ontological classification revealed the shift from the maturation to the germination process where over-represented classes belonged to embryonic development and cellular amino acid biosynthetic processes. In the embryo, 19% of the detected proteins are differentially accumulated during germination. Stress response, carbohydrate, fatty acid metabolism, and transport are the main functional classes representing embryo proteome change. Moreover, proteins specific to the germinated state were detected by both transcriptomic and proteomic approaches and a major change in the network operating during rice germination was uncovered. In particular, concomitant changes of hormonal metabolism-related proteins (GID1L2 and CNX1) implicated in GAs and ABA metabolism, signaling proteins, and protein turnover events emphasized the importance of such biological networks in rice seeds. Using metabolomics, we highlighted the importance of an energetic supply in rice seeds during germination. In both embryo and endosperm, starch degradation, glycolysis, and subsequent pathways related to these cascades, such as the aspartate-family pathway, are activated during germination. A relevant number of accumulated proteins and metabolites, especially in embryos, testifies the pivotal role of energetic supply in the preparation of plant growth. This article summarizes the key genetic pathways in embryo and endosperm during rice seed germination at the transcriptional, translational, and metabolite levels and thereby, emphasizes the value of combined multi-omics approaches to uncover the specific feature of tissues during germination.

Objectives: To assess the extent to which food items are a source of extended-spectrum beta-lactamase (ESBL) -producing Escherichia coli (ESBL-Ec) and ESBL-producing Klebsiella pneumoniae (ESBL-Kp) for humans in five European cities. Methods: We sampled 122 human polluted (hp)-environments (sewers and polluted rivers, as a proxy of human contamination) and 714 food items in Besancon (France), Geneva (Switzerland), Sevilla (Spain), Tubingen (Germany) and Utrecht (The Netherlands). A total of 254 ESBL-Ec and 39 ESBL-Kp isolates were cultured. All genomes were fully sequenced to compare their sequence types (ST) and core genomes, along with the distribution of bla(ESBL) genes and their genetic supports (i.e. chromosome or plasmid). Results: Sequence data revealed that ESBL-Ec and ESBL-Kp isolates from hp-environments were genetically different from those contaminating food items. ESBL-Ec ST131 was widespread in the hp-environment (21.5% of the isolates) but absent from the food items tested. ESBL-Ec ST10 was in similar proportions in hp-environments and food items (15 and 10 isolates, respectively) but mostly carried reservoir-specific bla(ESBL). bla(CTX-M-1) and bla(SHV-12) predominated in food-related E. coli isolates (32% and 34% of the isolates, respectively), whereas bla(CTX-M-15) and bla(CTX-M-27) predominated in isolates from hp-environments (52% and 15% of the isolates, respectively). Conclusions: We found a very limited connection between ESBL-Ec and ESBL-Kp populations retrieved in food items and from hp-environments and bla(ESBL). This suggests that human-to-human contamination, rather than the food chain, is possibly the most frequent route of ESBL-Ec and ESBL-Kp transmission in high-income countries. (C) 2021 The Authors. Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases.

This present study addresses the question of the composition of both prokaryotic and eukaryotic mi-crobial communities outside, at the entrance and inside the prehistoric Aze cave using a metabarcoding survey. The results showed that cave bacteria as well as Eukaryote phototrophs richness were negatively correlated with the distance from the cave entrance. In fact, outside the cave, richness, diversity and spe-cific OTUs were significantly higher in comparison to the entrance and the bottom of the cave. Moreover, this study reported that each section of the cave host different communities. The differences in commu-nities provide a better understanding of the microorganism sources in the Aze show cave. (c) 2022 Published by Elsevier Masson SAS on behalf of Consiglio Nazionale delle Ricerche (CNR).

Cinnamaldehyde (CNA), the main component of cinnamon essential oil, is one of the most active plant compounds against nosocomial pathogen Pseudomonas aeruginosa. Exposure of wild-type strain PA14 (MIC 700 µg/mL) for 5 to 10 days to fixed (900 µg/mL) or increasing (from 900 to 1400 µg/mL) concentrations of this natural antibacterial resulted in emergence of resistant mutants CNA-A1 to A3, and CNA-B1 to B7, respectively. Genome sequencing experiments showed that each of CNA-A1 to A3 mutants differed from PA14 by one SNP, and a slight increase in CNA resistance level (from 700 to 900 µg/mL). By comparison, mutants B1 to B7 were more resistant (up to 1100 µg/mL); each of them harbored multiple SNPs (from 24 to 39) likely as a consequence of alteration of DNA mismatch repair gene mutS. Of the ten mutants selected, eight contained mutations in gene nalC, which indirectly downregulates expression of the operon that codes for multidrug efflux system MexAB-OprM, and showed increased resistance (up to 16-fold versus PA14) to antibiotic molecules exported by the pump, including ß-lactams and fluoroquinolones. Of the six mutants with the highest CNA resistance, five were no longer motile because of alteration of genes flgJ, fliE and/or pilJ genes. Altogether, our data show that P. aeruginosa is able to adapt to strong electrophilic molecules such as CNA by upregulating its intrinsic efflux pump MexAB-OprM, and through less well-characterized pleiotropic changes. Whether multidrug-resistant mutants can emerge in patients using cinnamon essential oil as self-medication needs to be assessed further.