Characterization of Clostridioides difficile strains isolated from manure and digestate in five agricultural biogas plants.

Clostridioides difficile strains were isolated from manure and digestate samples from five biogas plants in France. The objective of this study was to characterize these isolates using PCR ribotyping, wgMLST, a multiplex PCR targeting genes encoding for the main virulence factors, i.e. tcdA, tcdB, cdtA and cdtB, and antimicrobial susceptibility assays. The 54 strains characterized were all positive for tcdA and tcdB and 83% (45/54) were positive for the binary toxin genes. PCR ribotypes 126 (59%) and 078 (37%) were predominant, and wgMLST analysis of 18 isolates showed close proximity of strains within a single biogas plant. Samples from the biogas plant supplied with cattle and poultry manure displayed the largest variety in PCR ribotypes. The in vitro activities of nine antimicrobial agents were determined. All the strains were susceptible to vancomycin and metronidazole, which are currently considered first-line treatments for C. difficile infection in humans. All the strains were resistant to clindamycin. The results of this study show that a high percentage of C. difficile strains present in the French biogas plants investigated are toxigenic strains from PCR ribotypes also commonly found in humans.

Local outbreak of Clostridioides difficile PCR-Ribotype 018 investigated by multi locus variable number tandem repeat analysis, whole genome multi locus sequence typing and core genome single nucleotide polymorphism typing.

The prevalence of Clostridioides difficile PCR-ribotype (RT) 018 is low in Europe but variations are observed across countries. We report here the first RT 018-related outbreak in France that took place in 4 geriatric units (GU) in Strasbourg, France. From January to December 2017, 38 patients were diagnosed with C. difficile infection (CDI). Strains were first characterized by PCR ribotyping: 19 out of 38 (50%) strains belonged to RT 018. These strains as well as 12 RT 018 isolated in other French healthcare facilities and 2 strains of RT 018 isolated in the GU in 2015 were characterized by multi locus variable-number tandem repeat (VNTR) analysis (MLVA), whole genome multi locus sequence typing (wgMLST) and core genome single nucleotide polymorphism typing (cgSNP). The MLVA indicated that 15 out of 19 epidemic strains of RT 018 were included in 2 Clonal Complexes (CC). Four RT 018 strains from the outbreak did not belong to the CC. The wgMLST and cgSNP typing analysis revealed a single CC that included 19 strains from the geriatric unit (17 from GU in 2017 and 2 from GU in 2015) and 4 strains (33%) from other healthcare facilities (HCF). Our results suggest that a specific RT 018 clone has spread in the geriatric unit and has evolved slowly over time. MLVA, wgMLST and cgSNP typing results provided fairly consistent information but wgMLST and cgSNP typing better separated epidemic strains from non-epidemic strains. Compared to wgMLST, the cgSNP typing did not provide additional information.

A high-fat diet alters genome-wide DNA methylation and gene expression in SM/J mice.

BACKGROUND: While the genetics of obesity has been well defined, the epigenetics of obesity is poorly understood. Here, we used a genome-wide approach to identify genes with differences in both DNA methylation and expression associated with a high-fat diet in mice. RESULTS: We weaned genetically identical Small (SM/J) mice onto a high-fat or low-fat diet and measured their weights weekly, tested their glucose and insulin tolerance, assessed serum biomarkers, and weighed their organs at necropsy. We measured liver gene expression with RNA-seq (using 21 total libraries, each pooled with 2 mice of the same sex and diet) and DNA methylation with MRE-seq and MeDIP-seq (using 8 total libraries, each pooled with 4 mice of the same sex and diet). There were 4356 genes with expression differences associated with diet, with 184 genes exhibiting a sex-by-diet interaction. Dietary fat dysregulated several pathways, including those involved in cytokine-cytokine receptor interaction, chemokine signaling, and oxidative phosphorylation. Over 7000 genes had differentially methylated regions associated with diet, which occurred in regulatory regions more often than expected by chance. Only 5-10% of differentially methylated regions occurred in differentially expressed genes, however this was more often than expected by chance (p = 2.2 × 10- 8). CONCLUSIONS: Discovering the gene expression and methylation changes associated with a high-fat diet can help to identify new targets for epigenetic therapies and inform about the physiological changes in obesity. Here, we identified numerous genes with altered expression and methylation that are promising candidates for further study.

Evaluation of a novel molecular assay to diagnose toxigenic strains of Clostridium difficile.

The objective of this study was to evaluate the Amplidiag C. difficile+027® assay, a new molecular method that detects toxin B gene in stool samples and identifies the hypervirulent 027 strain, to diagnose Clostridium difficile infections. The assay was compared to the reference method i.e. toxigenic culture. Amplidiag C. difficile+027® assay was prospectively evaluated from 309 diarrheal stool specimens of patients suspected of C. difficile infection. Forty-five (14.6%) stools were positive by toxigenic culture and 11 (3.6%) stools gave discordant results with the molecular method. PR027 was not recovered during the study. After resolving the discrepant results, the sensitivity, specificity, positive and negative predictive values of Amplidiag C. difficile+027® assay were 91.1% [CI 95% 77.9-97.1], 99.6% [CI 95% 97.6-100], 97.6% [CI 95% 85.9-99.9] and 98.5% [CI 95% 96-99.5], respectively compared to toxigenic culture. This assay is sensitive compared to the toxigenic culture.

Molecular epidemiology and antimicrobial resistance patterns of Clostridioides difficile isolates in Algerian hospitals.

INTRODUCTION: Clostridioides difficile is a major pathogen responsible for hospital-associated diarrhoea. This study investigated the molecular epidemiology and antibiotic resistance of C. difficile isolates in five Algerian hospitals. METHODOLOGY: Between 2016 and 2019, faecal specimens were collected from in-patients and were cultured for C. difficile. Isolates were characterised by toxin genes detection, Polymerase Chain Reaction (PCR)-ribotyping, Multilocus Sequence Typing (MLST), antimicrobial susceptibility testing against a panel of antibiotics, and screened for antimicrobial resistance genes. RESULTS: Out of 300 patient stools tested, 18 (6%) were positive for C. difficile by culture, and were found to belong to 11 different ribotypes (RT) and 12 sequence types (ST): RT 085/ST39, FR 248/ST259, FR 111/ST48, RT 017/ST37, RT 014/ST2, RT 014/ST14, FR 247/new ST, RT 005/ST6, RT 029/ST16, RT 039/ST26, RT 056/ST34 and RT 446/ST58. MLST analysis assigned the isolates to two clades, 1 and 4. Clade 4 was more homogeneous, as it mainly included non-toxigenic isolates. Three toxin gene profiles were detected, two toxigenic, A+B+CDT- (33.3%) and A-B+CDT- (11%); and one non-toxigenic, A-B-CDT- (55.5%). All C. difficile isolates were susceptible to metronidazole, vancomycin and moxifloxacin. CONCLUSIONS: Overall prevalence of C. difficile in our healthcare settings was 6%. Antibiotic resistance rates ranged from 72.2% (clindamycin) to 16.6% (tetracycline). This study highlighted a relatively high genetic diversity in term of ribotypes, sequence types, toxin and antibiotic resistance patterns, in the C. difficile isolates. Further larger studies are needed to assess the true extent of C. difficile infections in Algeria.

Characterization of Non-Toxigenic Clostridioides difficile Strains Isolated from Preterm Neonates and In Vivo Study of Their Protective Effect.

In a previous monocentric study in preterm neonates (PN), we described a high Clostridioides difficile colonization rate (74%) with two uncommon non-toxigenic strains (NTCD) belonging to PCR-ribotype (RT) (CE)847 and (CE)032. To determine the extent of carriage of both NTCD in other spatio-temporal settings, strains isolated in PN stools from two multicenter cohorts were characterized by PCR-ribotyping, MLVA and MLST. We also evaluated the protective role of two NTCD from these RT against C. difficile infection in a hamster caecitis model. Animals were administered either each NTCD alone (n = 7), or followed by a 027 strain (n = 9). A control group received only the 027 strain (n = 8). Clinical activity and colonization by C. difficile in stools were monitored daily until death or sacrifice at D20. We isolated 18 RT(CE)032 (ST-83) strains and 2 RT(CE)847 (ST-26) strains among 247 PN from both cohorts. Within each RT, strains were genetically related. The survival rate was significantly increased when animals received a RT(CE)847 or (CE)032 strain before the 027 strain (4/9 deaths, p = 0.029; 1/9 death, p = 0.0004, respectively). We describe two predominant uncommon NTCD strains, in a PN population from different healthcare facilities. Both NTCD provide a potential protection against C. difficile infection.

The effect of dietary fat on behavior in mice.

PURPOSE: Obesity is linked to cognitive dysfunction in humans and rodents, and its effects can be passed on to the next generation. However, the extent of these effects is not well understood. The purpose of this study was to determine the effect of a prenatal maternal high-fat diet and an individual high-fat diet in inbred mice. METHODS: We varied maternal diet and offspring diet to test the hypothesis that a high-fat diet would increase anxiety, reduce activity levels, and impair nest-building. First, we fed a high-fat (HF) or low-fat (LF) diet to genetically identical female Small (SM/J) mice and mated them with LF males. We cross-fostered all offspring to LF-fed SM/J nurses and weaned them onto an HF or LF diet. We weighed the mice weekly and we tested anxiety with the Open Field Test, activity levels with instantaneous scan sampling, and nest building using the Deacon Scale. RESULTS: Diet significantly affected weight, with HF females weighing 28.2 g (± 1.4 g SE) and LF females weighing 15.1 g (± 1.6 g SE) at 17 weeks old. The offspring's own diet had major behavioral effects. HF mice produced more fecal boli and urinations in the Open Field Test, built lower-quality nests, and had lower activity in adulthood than LF mice. The only trait that a prenatal maternal diet significantly affected was whether the offspring built their nests inside or outside of a hut. CONCLUSIONS: Offspring diet, but not prenatal maternal diet, affected a wide range of behaviors in these mice.

Maternal high-fat diet associated with altered gene expression, DNA methylation, and obesity risk in mouse offspring.

We investigated maternal obesity in inbred SM/J mice by assigning females to a high-fat diet or a low-fat diet at weaning, mating them to low-fat-fed males, cross-fostering the offspring to low-fat-fed SM/J nurses at birth, and weaning the offspring onto a high-fat or low-fat diet. A maternal high-fat diet exacerbated obesity in the high-fat-fed daughters, causing them to weigh more, have more fat, and have higher serum levels of leptin as adults, accompanied by dozens of gene expression changes and thousands of DNA methylation changes in their livers and hearts. Maternal diet particularly affected genes involved in RNA processing, immune response, and mitochondria. Between one-quarter and one-third of differentially expressed genes contained a differentially methylated region associated with maternal diet. An offspring high-fat diet reduced overall variation in DNA methylation, increased body weight and organ weights, increased long bone lengths and weights, decreased insulin sensitivity, and changed the expression of 3,908 genes in the liver. Although the offspring were more affected by their own diet, their maternal diet had epigenetic effects lasting through adulthood, and in the daughters these effects were accompanied by phenotypic changes relevant to obesity and diabetes.