Role of Gut Microbiota in Statin-Associated New-Onset Diabetes-A Cross-Sectional and Prospective Analysis of the FINRISK 2002 Cohort

BACKGROUND

Dyslipidemia is treated effectively with statins, but treatment has the potential to induce new-onset type-2 diabetes. Gut microbiota may contribute to this outcome variability. We assessed the associations of gut microbiota diversity and composition with statins. Bacterial associations with statin-associated new-onset type-2 diabetes (T2D) risk were also prospectively evaluated.

METHODS

We examined shallow-shotgun-sequenced fecal samples from 5755 individuals in the FINRISK-2002 population cohort with a 17+-year-long register-based follow-up. Alpha-diversity was quantified using Shannon index and beta-diversity with Aitchison distance. Species-specific differential abundances were analyzed using general multivariate regression. Prospective associations were assessed with Cox regression. Applicable results were validated using gradient boosting.

RESULTS

Statin use associated with differing taxonomic composition (R2, 0.02%; q=0.02) and 13 differentially abundant species in fully adjusted models (MaAsLin; q<0.05). The strongest positive association was with Clostridium sartagoforme (β=0.37; SE=0.13; q=0.02) and the strongest negative association with Bacteroides cellulosilyticus (β=-0.31; SE=0.11; q=0.02). Twenty-five microbial features had significant associations with incident T2D in statin users, of which only Bacteroides vulgatus (HR, 1.286 [1.136-1.457]; q=0.03) was consistent regardless of model adjustment. Finally, higher statin-associated T2D risk was seen with [Ruminococcus] torques (ΔHRstatins, +0.11; q=0.03), Blautia obeum (ΔHRstatins, +0.06; q=0.01), Blautia sp. KLE 1732 (ΔHRstatins, +0.05; q=0.01), and beta-diversity principal component 1 (ΔHRstatin, +0.07; q=0.03) but only when adjusting for demographic covariates.

CONCLUSIONS

Statin users have compositionally differing microbiotas from nonusers. The human gut microbiota is associated with incident T2D risk in statin users and possibly has additive effects on statin-associated new-onset T2D risk.

Guidelines for microbiome studies in renal physiology

Gut microbiome research has increased dramatically in the last decade, including in renal health and disease. The field is moving from experiments showing mere association to causation using both forward and reverse microbiome approaches, leveraging tools such as germ-free animals, treatment with antibiotics, and fecal microbiota transplantations. However, we are still seeing a gap between discovery and translation that needs to be addressed, so that patients can benefit from microbiome-based therapies. In this guideline paper, we discuss the key considerations that affect the gut microbiome of animals and clinical studies assessing renal function, many of which are often overlooked, resulting in false-positive results. For animal studies, these include suppliers, acclimatization, baseline microbiota and its normalization, littermates and cohort/cage effects, diet, sex differences, age, circadian differences, antibiotics and sweeteners, and models used. Clinical studies have some unique considerations, which include sampling, gut transit time, dietary records, medication, and renal phenotypes. We provide best-practice guidance on sampling, storage, DNA extraction, and methods for microbial DNA sequencing (both 16S rRNA and shotgun metagenome). Finally, we discuss follow-up analyses, including tools available, metrics, and their interpretation, and the key challenges ahead in the microbiome field. By standardizing study designs, methods, and reporting, we will accelerate the findings from discovery to translation and result in new microbiome-based therapies that may improve renal health.

Genetic diversity and variation in antimicrobial-resistance determinants of non-serotype 2 Streptococcus suis isolates from healthy pigs

Streptococcus suis is a leading cause of bacterial meningitis in South-East Asia, with frequent zoonotic transfer to humans associated with close contact with pigs. A small number of invasive lineages are responsible for endemic infection in the swine industry, causing considerable global economic losses. A lack of surveillance and a rising trend in clinical treatment failure has raised concerns of growing antimicrobial resistance (AMR) among invasive S. suis. Gene flow between healthy and disease isolates is poorly understood and, in this study, we sample and sequence a collection of isolates predominantly from healthy pigs in Chiang Mai province, Northern Thailand. Pangenome characterization identified extensive genetic diversity and frequent AMR carriage in isolates from healthy pigs. Multiple AMR genes were identified, conferring resistance to aminoglycosides, lincosamides, tetracycline and macrolides. All isolates were non-susceptible to three or more different antimicrobial classes, and 75 % of non-serotype 2 isolates were non-susceptible to six or more classes (compared to 37.5 % of serotype 2 isolates). AMR genes were found on integrative and conjugative elements previously observed in other species, suggesting a mobile gene pool that can be accessed by invasive disease isolates. This article contains data hosted by Microreact.

Associations of healthy food choices with gut microbiota profiles

BACKGROUND

Diet has a major influence on the human gut microbiota, which has been linked to health and disease. However, epidemiological studies on associations of a healthy diet with the microbiota utilizing a whole-diet approach are still scant.

OBJECTIVES

To assess associations between healthy food choices and human gut microbiota composition, and to determine the strength of association with functional potential.

METHODS

This population-based study sample consisted of 4930 participants (ages 25-74; 53% women) in the FINRISK 2002 study. Intakes of recommended foods were assessed using a food propensity questionnaire, and responses were transformed into healthy food choices (HFC) scores. Microbial diversity (alpha diversity) and compositional differences (beta diversity) and their associations with the HFC score and its components were assessed using linear regression. Multiple permutational multivariate ANOVAs were run from whole-metagenome shallow shotgun-sequenced samples. Associations between specific taxa and HFC were analyzed using linear regression. Functional associations were derived from Kyoto Encyclopedia of Genes and Genomes orthologies with linear regression models.

RESULTS

Both microbial alpha diversity (β/SD, 0.044; SE, 6.18 × 10-5; P = 2.21 × 10-3) and beta diversity (R2, 0.12; P ≤ 1.00 × 10-3) were associated with the HFC score. For alpha diversity, the strongest associations were observed for fiber-rich breads, poultry, fruits, and low-fat cheeses (all positive). For beta diversity, the most prominent associations were observed for vegetables, followed by berries and fruits. Genera with fiber-degrading and SCFA-producing capacities were positively associated with the HFC score. The HFC score was associated positively with functions such as SCFA metabolism and synthesis, and inversely with functions such as fatty acid biosynthesis and the sulfur relay system.

CONCLUSIONS

Our results from a large, population-based survey confirm and extend findings of other, smaller-scale studies that plant- and fiber-rich dietary choices are associated with a more diverse and compositionally distinct microbiota, and with a greater potential to produce SCFAs.

Taxonomic signatures of cause-specific mortality risk in human gut microbiome

The collection of fecal material and developments in sequencing technologies have enabled standardised and non-invasive gut microbiome profiling. Microbiome composition from several large cohorts have been cross-sectionally linked to various lifestyle factors and diseases. In spite of these advances, prospective associations between microbiome composition and health have remained uncharacterised due to the lack of sufficiently large and representative population cohorts with comprehensive follow-up data. Here, we analyse the long-term association between gut microbiome variation and mortality in a well-phenotyped and representative population cohort from Finland (n = 7211). We report robust taxonomic and functional microbiome signatures related to the Enterobacteriaceae family that are associated with mortality risk during a 15-year follow-up. Our results extend previous cross-sectional studies, and help to establish the basis for examining long-term associations between human gut microbiome composition, incident outcomes, and general health status.

Domestication of Campylobacter jejuni NCTC 11168

Reference and type strains of well-known bacteria have been a cornerstone of microbiology research for decades. The sharing of well-characterized isolates among laboratories has run in parallel with research efforts and enhanced the reproducibility of experiments, leading to a wealth of knowledge about trait variation in different species and the underlying genetics. Campylobacter jejuni strain NCTC 11168, deposited at the National Collection of Type Cultures in 1977, has been adopted widely as a reference strain by researchers worldwide and was the first Campylobacter for which the complete genome was published (in 2000). In this study, we collected 23 C. jejuni NCTC 11168 reference isolates from laboratories across the UK and compared variation in simple laboratory phenotypes with genetic variation in sequenced genomes. Putatively identical isolates, identified previously to have aberrant phenotypes, varied by up to 281 SNPs (in 15 genes) compared to the most recent reference strain. Isolates also display considerable phenotype variation in motility, morphology, growth at 37 °C, invasion of chicken and human cell lines, and susceptibility to ampicillin. This study provides evidence of ongoing evolutionary change among C. jejuni isolates as they are cultured in different laboratories and highlights the need for careful consideration of genetic variation within laboratory reference strains. This article contains data hosted by Microreact.

A GWAS on Helicobacter pylori strains points to genetic variants associated with gastric cancer risk

Background

Helicobacter pylori are stomach-dwelling bacteria that are present in about 50% of the global population. Infection is asymptomatic in most cases, but it has been associated with gastritis, gastric ulcers and gastric cancer. Epidemiological evidence shows that progression to cancer depends upon the host and pathogen factors, but questions remain about why cancer phenotypes develop in a minority of infected people. Here, we use comparative genomics approaches to understand how genetic variation amongst bacterial strains influences disease progression.

Results

We performed a genome-wide association study (GWAS) on 173 H. pylori isolates from the European population (hpEurope) with known disease aetiology, including 49 from individuals with gastric cancer. We identified SNPs and genes that differed in frequency between isolates from patients with gastric cancer and those with gastritis. The gastric cancer phenotype was associated with the presence of babA and genes in the cag pathogenicity island, one of the major virulence determinants of H. pylori, as well as non-synonymous variations in several less well-studied genes. We devised a simple risk score based on the risk level of associated elements present, which has the potential to identify strains that are likely to cause cancer but will require refinement and validation.

Conclusion

There are a number of challenges to applying GWAS to bacterial infections, including the difficulty of obtaining matched controls, multiple strain colonization and the possibility that causative strains may not be present when disease is detected. Our results demonstrate that bacterial factors have a sufficiently strong influence on disease progression that even a small-scale GWAS can identify them. Therefore, H. pylori GWAS can elucidate mechanistic pathways to disease and guide clinical treatment options, including for asymptomatic carriers.

Electronic supplementary material

The online version of this article (10.1186/s12915-018-0550-3) contains supplementary material, which is available to authorized users.

Epistasis analysis uncovers hidden antibiotic resistance-associated fitness costs hampering the evolution of MRSA

Background

Fitness costs imposed on bacteria by antibiotic resistance mechanisms are believed to hamper their dissemination. The scale of these costs is highly variable. Some, including resistance of Staphylococcus aureus to the clinically important antibiotic mupirocin, have been reported as being cost-free, which suggests that there are few barriers preventing their global spread. However, this is not supported by surveillance data in healthy communities, which indicate that this resistance mechanism is relatively unsuccessful.

Results

Epistasis analysis on two collections of MRSA provides an explanation for this discord, where the mupirocin resistance-conferring mutation of the ileS gene appears to affect the levels of toxins produced by S. aureus when combined with specific polymorphisms at other loci. Proteomic analysis demonstrates that the activity of the secretory apparatus of the PSM family of toxins is affected by mupirocin resistance. As an energetically costly activity, this reduction in toxicity masks the fitness costs associated with this resistance mutation, a cost that becomes apparent when toxin production becomes necessary. This hidden fitness cost provides a likely explanation for why this mupirocin-resistance mechanism is not more prevalent, given the widespread use of this antibiotic.

Conclusions

With dwindling pools of antibiotics available for use, information on the fitness consequences of the acquisition of resistance may need to be considered when designing antibiotic prescribing policies. However, this study suggests there are levels of depth that we do not understand, and that holistic, surveillance and functional genomics approaches are required to gain this crucial information.

Electronic supplementary material

The online version of this article (10.1186/s13059-018-1469-2) contains supplementary material, which is available to authorized users.

Genome Comparison of Erythromycin Resistant Campylobacter from Turkeys Identifies Hosts and Pathways for Horizontal Spread of erm(B) Genes

Pathogens in the genus Campylobacter are the most common cause of food-borne bacterial gastro-enteritis. Campylobacteriosis, caused principally by Campylobacter jejuni and Campylobacter coli, is transmitted to humans by food of animal origin, especially poultry. As for many pathogens, antimicrobial resistance in Campylobacter is increasing at an alarming rate. Erythromycin prescription is the treatment of choice for clinical cases requiring antimicrobial therapy but this is compromised by mobility of the erythromycin resistance gene erm(B) between strains. Here, we evaluate resistance to six antimicrobials in 170 Campylobacter isolates (133 C. coli and 37 C. jejuni) from turkeys. Erythromycin resistant isolates (n = 85; 81 C. coli and 4 C. jejuni) were screened for the presence of the erm(B) gene, that has not previously been identified in isolates from turkeys. The genomes of two positive C. coli isolates were sequenced and in both isolates the erm(B) gene clustered with resistance determinants against aminoglycosides plus tetracycline, including aad9, aadE, aph(2″)-IIIa, aph(3')-IIIa, and tet(O) genes. Comparative genomic analysis identified identical erm(B) sequences among Campylobacter from turkeys, Streptococcus suis from pigs and Enterococcus faecium and Clostridium difficile from humans. This is consistent with multiple horizontal transfer events among different bacterial species colonizing turkeys. This example highlights the potential for dissemination of antimicrobial resistance across bacterial species boundaries which may compromise their effectiveness in antimicrobial therapy.

Biofilm Morphotypes and Population Structure among Staphylococcus epidermidis from Commensal and Clinical Samples

Bacterial species comprise related genotypes that can display divergent phenotypes with important clinical implications. Staphylococcus epidermidis is a common cause of nosocomial infections and, critical to its pathogenesis, is its ability to adhere and form biofilms on surfaces, thereby moderating the effect of the host’s immune response and antibiotics. Commensal S. epidermidis populations are thought to differ from those associated with disease in factors involved in adhesion and biofilm accumulation. We quantified the differences in biofilm formation in 98 S. epidermidis isolates from various sources, and investigated population structure based on ribosomal multilocus typing (rMLST) and the presence/absence of genes involved in adhesion and biofilm formation. All isolates were able to adhere and form biofilms in in vitro growth assays and confocal microscopy allowed classification into 5 biofilm morphotypes based on their thickness, biovolume and roughness. Phylogenetic reconstruction grouped isolates into three separate clades, with the isolates in the main disease associated clade displaying diversity in morphotype. Of the biofilm morphology characteristics, only biofilm thickness had a significant association with clade distribution. The distribution of some known adhesion-associated genes (aap and sesE) among isolates showed a significant association with the species clonal frame. These data challenge the assumption that biofilm-associated genes, such as those on the ica operon, are genetic markers for less invasive S. epidermidis isolates, and suggest that phenotypic characteristics, such as adhesion and biofilm formation, are not fixed by clonal descent but are influenced by the presence of various genes that are mobile among lineages.

Progressive genome-wide introgression in agricultural Campylobacter coli

Hybridization between distantly related organisms can facilitate rapid adaptation to novel environments, but is potentially constrained by epistatic fitness interactions among cell components. The zoonotic pathogens Campylobacter coli and C. jejuni differ from each other by around 15% at the nucleotide level, corresponding to an average of nearly 40 amino acids per protein-coding gene. Using whole genome sequencing, we show that a single C. coli lineage, which has successfully colonized an agricultural niche, has been progressively accumulating C. jejuni DNA. Members of this lineage belong to two groups, the ST-828 and ST-1150 clonal complexes. The ST-1150 complex is less frequently isolated and has undergone a substantially greater amount of introgression leading to replacement of up to 23% of the C. coli core genome as well as import of novel DNA. By contrast, the more commonly isolated ST-828 complex bacteria have 10–11% introgressed DNA, and C. jejuni and nonagricultural C. coli lineages each have <2%. Thus, the C. coli that colonize agriculture, and consequently cause most human disease, have hybrid origin, but this cross-species exchange has so far not had a substantial impact on the gene pools of either C. jejuni or nonagricultural C. coli. These findings also indicate remarkable interchangeability of basic cellular machinery after a prolonged period of independent evolution.

Migraine diagnosis and management in general emergency departments in France

Background

We conducted a prospective study of patients admitted to 22 general emergency departments in France over 1 week.

Patients and methods

Of 15,835 adult patients, 483 (3.1%) had headache and 98 (0.6%) had migraine.

Results

Compared with the migraine population in France, our migraine patients were similar in terms of proportion of female patients (75%) and mean age (37.6 ± 13.8 years) but presented earlier in their disease course. Patients sought emergency treatment because of a severe attack (49%) or because of ineffective treatment (20%). Non-opioid analgesics excluding non-steroidal anti-inflammatory drugs (NSAIDs), and NSAIDs, were most commonly prescribed as acute treatment, yet it took more than 48 h for symptom resolution in 36% of 92 follow-up patients.

Conclusions

Results suggest there is room for improvement in choice of agents prescribed. We propose additional education and training of clinicians to improve adherence to clinical practice guidelines.

Evaluating patient satisfaction with specific migraine therapy based on initial treatment expectations: the PAX study

AIMS AND OBJECTIVES

The PAX study was a naturalistic, prospective survey evaluating treatment expectations and satisfaction in a typical French migraine population.

METHODS

A total of 1710 patients were recruited by 489 general practitioners across France. Despite a high drop-out rate (due to one or more deviations from protocol and/or missing data), the analysable per-protocol population (PPP) patients (n = 615) remained representative with regard to the overall migraine population. Patients ranked expectations according to four criteria at baseline, and were asked to report satisfaction for each criterion at baseline and for six consecutive attacks. The highest-ranked treatment expectation was rapid relief of headache, followed by pain-free response, relief of associated symptoms, and ability to carry on present activity, respectively.

RESULTS

At inclusion, >50% of patients were using non-specific medications (analgesics, NSAIDs), and 30% reported global satisfaction with treatment. At the end of the survey, >75% of patients were using specific medications (predominantly triptans), and global treatment satisfaction increased to 83%, independent of treatment expectation rankings at baseline.

CONCLUSIONS

These survey results suggest that satisfaction with acute migraine treatment increases when specific medications are prescribed, irrespective of which treatment expectation is considered most important at baseline. This emphasizes the need for improvements in the management of migraine, to ensure that optimal treatment is being provided with regard to pharmacological intervention.

luxS-based quorum-sensing signaling affects Biofilm formation in Streptococcus mutans

BACKGROUND

Quorum sensing (QS) is a process by which bacteria communicate with diffusible chemical signaling molecules called autoinducers (AIs). The autoinducer-2 signal (AI-2) produced by the LuxS protein mediates interspecies communication among Gram-positive and Gram-negative bacteria. In this study, we report that luxS-dependent QS is involved in the formation of Streptococcus mutans biofilms.

METHODS

An S. mutans luxS mutant was constructed, and the differences in growth and biofilm formation were compared between the wild-type strain and the mutant strain. To quantificationally analyze the kinetic biofilm formation of the mutant strain, an assay of BioFilm Ring Test(R) was applied.

RESULTS

There is a small increase in the growth of the luxS mutant strain after the stationary phase, compared with the parent strain. However during the exponential period, there were no significant differences. Using the BioFilm Ring Test(R), it was demonstrated that this luxS mutation was able to accelerate biofilm formation on a polystyrene surface during the mid-exponential growth phase. With 1% glucose treatment, even greater differences were observed between the mutant strain and its parental strain.

CONCLUSION

These data suggest that a luxS-dependent signal may play an important role in the biofilm formation of S. mutans.

Disability and quality of life of patients with knee or hip osteoarthritis in the primary care setting and factors associated with general practitioners' indication for prosthetic replacement within 1 year

OBJECTIVE

To assess disability and health-related quality of life (HRQoL) of patients with knee or hip OA in primary care and to determine factors associated with GPs' opinion that their patients will need prosthetic replacement within 1 year after the consultation.

DESIGN

A cross-sectional national survey.

SETTING

Primary care in France.

PARTICIPANTS

1471 GPs and 4183 patients with hip or knee OA.

MEASURES

Pain on an 11-point numeric scale (0-10), disability on the Western Ontario and MacMaster Universities Osteoarthritis Index (WOMAC) (1-100) and Lequesne index (0-24), and quality of life on the Medical Outcomes Study 36-item Short Form (MOS SF-36; 0-100).

RESULTS

We analyzed records of 4121 patients (2540 knee, 1581 hip OA). Patients with knee or hip OA exhibited high and similar levels of pain (5.2+/-2.1 and 5.3+/-2.3) and disability (Lequesne score: 12.0+/-4.2 and 11.8+/-4.3; WOMAC score: 45.7+/-19.3 and 45.2+/-17.3) The decrease in HRQoL was similar for patients with either location of the disease. GPs more often considered that their patients with hip OA would need prosthetic replacement within 1 year (28.1%) than those with knee OA (15.8%). Most factors associated with GPs' opinion were identified for both locations of disease and were related to disability and pain levels.

CONCLUSIONS

In the primary care setting, patients with knee or hip OA have similar, high disability levels and substantially low HRQoL. Patients' disability seems to play a central role in GPs' opinion of the need for their patients with either type of OA to undergo prosthetic replacement within 1 year.

Should aggregate scores of the Medical Outcomes Study 36-item Short Form Health Survey be used to assess quality of life in knee and hip osteoarthritis? A national survey in primary care

OBJECTIVE

To assess the relevance of using the aggregate physical component score (PCS) and mental component score (MCS) of the Medical Outcomes Study 36-item Short Form Health Survey (SF-36) for patients with knee and hip osteoarthritis (OA).

METHODS

We conducted a cross-sectional national survey in a primary care setting in France. A total of 1474 general practitioners enrolled 4183 patients with hip or knee OA. Construct validity of PCS and MCS was assessed by convergent and divergent validity and factor analysis.

RESULTS

Records of 4133 patients (98.8%) were analyzed (2540 knee, 1593 hip OA). PCS mean scores were 32.0+/-8.4 and 31.8+/-8.4 and MCS scores 47.1+/-11.0 and 46.8+/-11.1, for knee and hip OA, respectively. Acceptable convergent and divergent validity was observed, and correlation between PCS and MCS mean scores was low (r=0.14). However, factor analysis performed on the eight subscale scores failed to support the use of PCS and MCS aggregate scores. It extracted two factors which were similar for both OA types and differed from the a priori stratification. Scores for two subscales usually attributed to MCS - emotional role and social functioning - were shared between factors, and scores for another subscale - general health perception - usually belonging to the PCS was in the mental component factor.

CONCLUSIONS

Our results suggest that aggregate scores from the PCS and MCS of the SF-36 as they are currently defined may not be optimal for used in hip and knee OA patients to assess health-related quality of life.

Development and psychometric validation of a new patient satisfaction instrument: The osteoARthritis Treatment Satisfaction (ARTS) questionnaire

Given the increasing interest in treatment satisfaction research and the lack of a specific questionnaire in osteoarthritis (OA), we developed and explored the psychometric properties of the osteoARthritis Treatment Satisfaction (ARTS) questionnaire. The ARTS questionnaire which consists of 18 items was developed in French following the analysis of semi-structured interviews performed among 20 OA participants, five rheumatologists and five general practitioners. Psychometric properties were assessed in France on a cross-sectional sample of 797 OA participants and test-retest reliability was evaluated in an independent sample of 111 clinically stable OA participants who filled-in the questionnaire within a 7.7 (+/- 3.1) day interval. Using principal component analysis, four scales were identified: Treatment advantages (seven items), Treatment convenience (three items), Treatment confidence (two items) and Satisfaction with physician (six items). Item convergent and item discriminant validity were satisfactory. Internal consistency provided evidence of reliability and lack of redundancy (Cronbach's alphas ranged from 0.66 to 0.86). Test-retest reliability was acceptable for two out of four scales (intraclass correlations coefficients (ICC) ranged from 0.61 to 0.75). Significant between groups differences were found on the ARTS scales, demonstrating the known groups validity of the ARTS questionnaire. The responsiveness of the ARTS is still to be documented.