A pilot study of dietary fibres on pathogen growth in an ex vivo colonic model reveals their potential ability to limit vancomycin-resistant Enterococcus expansion

Aim: Dietary fibre is important for shaping gut microbiota. The aim of this pilot study was to investigate the impact of dietary fibres on pathogen performance in the presence of gut microbiota. Methods: In an ex vivo gut model, pooled faecal samples were spiked with a cocktail of representative gastrointestinal pathogens and fermented with yeast β-glucan for 24 hours, after which 16S rRNA amplicon sequencing and short-chain and branched-chain fatty acid (SCFA and BCFA) analyses were performed. In addition, oat β-glucan, arabinoxylan, yeast β-glucan, and galactooligosaccharides were each tested against individual representative pathogens and pathogen growth was assessed via qPCR. Glucose served as a control carbon source. Results: Based on 16S rRNA amplicon sequencing, yeast β-glucan selected for higher proportions of Bacteroides (P = 0.0005, ~6 fold) and Clostridia (P = 0.005, ~3.6 fold) while species of Escherichia/Shigella (P = 0.021, ~2.8 fold) and Lactobacillus (P = 0.007, ~ 15.7-fold) were higher in glucose. Pathogen relative abundance did not differ between glucose and yeast β-glucan. In the absence of pathogens, higher production of BCFAs (P = 0.002) and SCFAs (P = 0.002) fatty acids was observed for fibre group(s). For individual pathogens, yeast β-glucan increased growth of Escherichia coli, Salmonella typhimurium, and Listeria monocytogenes (P < 0.05), arabinoxylan increased S. typhimurium (P < 0.05). Tested fibres decreased vancomycin-resistant Enterococcus faecium (P < 0.05), with yeast β-glucan causing a 1-log reduction (P < 0.01), while galactooligosaccharides decreased L. monocytogenes (P < 0.05). Conclusion: Tested fibres differentially influenced the growth of pathogens, but yeast β-glucan could represent a dietary strategy to help limit vancomycin-resistant enterococci (VRE) expansion in the gut.

Effect of diet on pathogen performance in the microbiome

Intricate interactions among commensal bacteria, dietary substrates and immune responses are central to defining microbiome community composition, which plays a key role in preventing enteric pathogen infection, a dynamic phenomenon referred to as colonisation resistance. However, the impact of diet on sculpting microbiota membership, and ultimately colonisation resistance has been overlooked. Furthermore, pathogens have evolved strategies to evade colonisation resistance and outcompete commensal microbiota by using unique nutrient utilisation pathways, by exploiting microbial metabolites as nutrient sources or by environmental cues to induce virulence gene expression. In this review, we will discuss the interplay between diet, microbiota and their associated metabolites, and how these can contribute to or preclude pathogen survival.

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.

Three New Escherichia coli Phages from the Human Gut Show Promising Potential for Phage Therapy

With the emergence of multi-drug resistant bacteria the use of bacteriophages (phages) is gaining renewed interest as promising anti-microbial agents. The aim of this study was to isolate and characterize phages from human fecal samples. Three new coliphages, ɸAPCEc01, ɸAPCEc02 and ɸAPCEc03, were isolated. Their phenotypic and genomic characteristics, and lytic activity against biofilm, and in combination with ciprofloxacin, were investigated. All three phages reduced the growth of E. coli strain DPC6051 at multiplicity of infection (MOI) between 10-3 and 105. A cocktail of all three phages completely inhibited the growth of E. coli. The phage cocktail also reduced biofilm formation and prevented the emergence of phage-resistant mutants which occurred with single phage. When combined with ciprofloxacin, phage alone or in cocktail inhibited the growth of E. coli and prevented the emergence of resistant mutants. These three new phages are promising biocontrol agents for E. coli infections.

What makes quality assurance effective? Results from a randomized, controlled trial in 16 primary care group practices

OBJECTIVES

The authors estimate separately contributions of each component intervention to overall effectiveness of quality assurance cycles used to improve practice performance.

METHODS

In a randomized, controlled trial, experimental cycles of quality assurance were conducted for eight patient-care guidelines, with two experimental cycles assigned to each of 16 group practices. For three separate interventions per cycle, practitioners: (1) were notified of the name of the experimental guideline, (2) discussed criteria of conformance to the guideline, and (3) received feedback on performance. Actions taken in response to interventions were documented. Using medical records data for a baseline year and for 3 months after each intervention and an additional 9 months, the authors scored each practice for conformance to two experimental guidelines and to control guidelines.

RESULTS

For all patient-care guidelines combined, and for four of five guidelines showing improvement, knowledge of guidelines and review criteria alone produced no change. After feedback, performance improved and improvement persisted for at least 9 months. The number of corrective actions implemented contributed significantly to effectiveness of quality assurance.

CONCLUSIONS

Feedback to providers of data on their performance is a more powerful stimulus for quality improvement than is knowledge of guidelines or discussion of review criteria.

A randomized controlled trial of quality assurance in sixteen ambulatory care practices

A crossover randomized controlled trial of cycles of quality assurance in 16 primary care (8 medical, 8 pediatric) group practices was conducted. Of four medical and four pediatric tasks important to patient outcome, two were randomly assigned to experimental intervention (a quality assurance cycle), and two were also measured and used as blinded controls for each medical or pediatric group practice. Task performance was measured in each group for 12 months prior to, 9 months during, and 9 months after the experimental intervention, using as a performance score the percentage of evaluation criteria failed of those applicable to a case. As a result of quality assurance intervention, quality of performance was significantly improved in two of the tasks (P less than 0.0001, with 6.7, and 9.8 percentage points improvement), and marginally improved in one task (P = 0.06, 5.7 percentage points improvement). Surprisingly, tasks with lower perceived effect on patient health (low physician motivation) had greater improvement in quality. Unimproved tasks were associated with the perceived need for delivery system changes beyond the immediate control of the individual practitioner.

Resource requirements for evaluating ambulatory health care

We implemented the most frequently used form of quality assurance activity: abstracting information on the quality of patient care from medical records and communicating findings to providers in 16 ambulatory care groups. Site providers accepted the evaluation criteria, agreed that deficiencies in care were detected, and, for some medical tasks, effected improvements in care. Direct costs in 1980 dollars for the quality assurance cycle including data system development were $46 per evaluated case. Per-case costs varied considerably among tasks, decreased with larger numbers of cases and as experience grew, and were reduced through computerization. Measured costs were high due to: a demanding research design; our extended accounting of direct, indirect, and induced costs; and the substantial resource requirements of rigorously performed evaluations.

Quality assurance in eight adult medicine group practices

Four evaluations of ambulatory medical care tasks were developed for use in quality assurance. The evaluations used medical records data and explicit criteria incorporating branching logic. They were implemented in eight general medicine provider groups in two teaching hospitals and six related health centers. Agreement with criteria among 316 provider responses to questionnaires varied from 57% to 100%. The percentage of cases with one or more variation from evaluation criteria, confirmed on peer review to have a deficiency in care, ranged by task from 6% to 42%, with substantial variation between sites. Physician reviewers from each site varied in leniency. Numbers of actions taken to correct deficiencies ranged by site and task from zero to six. Multisite evaluations revealed differences in performance and efforts to improve that are not apparent when each site conducts its own evaluations. More uniformly effective and impartial quality assurance is needed to correct some important deficiencies in care observed in this study.

A method for evaluating performance of ambulatory pediatric tasks

Four evaluations of ambulatory pediatric tasks were used for quality assurance in eight pediatric group practices situated in two teaching hospitals and six related health centers. The evaluations used criteria incorporating branching logic to judge the quality of care revealed in data abstracted from medical records. Performance was evaluated for follow-up of positive urine cultures, assessment and follow-up of otitis media, initial assessment for gastroenteritis, and "well child" care for infants. A computerized data system was developed to process evaluation data and produce easily read reports. This work is part of a controlled trial of the feasibility, cost, and effectiveness of quality assurance as a means to improve patient care, but this preliminary report concerns only the principles for design of the evaluations and their use in quality assurance. Acceptance of evaluations by site providers was high: of 203 provider responses to a survey, only four reported disagreement with the criteria. Rates of cases "variant" from criteria and found on peer review to represent deficiencies in care, when averaged across sites, ranged by task from 1% to 47% of cases evaluated. In most sites, providers planned and implemented actions to correct these deficiencies. It is noted that improvements in care may increase costs of care.

The cost of quality assurance in medicine

Cost analysis has been frequently neglected in program evaluations but is currently of high relevance in policy decisions on quality assurance in medicine. The Ambulatory Care Medical Audit Demonstration (ACMAD) Project implemented and evaluated a program of medical record-based quality assurance in eleven sites for nine medical topics. Total direct costs for the project were $1.22 million over five years; indirect costs, $694,000. A computerized data system enabled disaggregation of the cost data by person, timing, type of work, project phase, health topic, health center, and research or operational nature. Of the costs incurred, 79% were for operational reasons, with 21% incurred for research reasons. Costs per audited case were 31% higher in hospitals than in neighborhood health centers. Audit topics of low per-case costs tended to have automated case findings, straightforward and limited abstracting, little need to examine multiple visits, and a low proportion of case-found patients ineligible for audit.

Evaluation of operational failures in clinical decision making

Medical decision analysts are interested in the changes in health benefits from inappropriate ordering of tests, imperfect information from tests, and imperfect results of treatments. Operational failures in the decision-making sequence, caused by human and system factors, may also alter health benefits. An evaluation of operational failures in follow-up of positive urine cultures in pediatric patients is reported. Branching criteria were developed by physician representatives from each of eight pediatric group practices to evaluate the care of patients aged 6 months to 16 years, inclusive. Of 858 cases evaluated, 52 percent failed at one or more nodes in the criteria sequence. Rates of failure at individual nodes among cases reaching these nodes varied from 2 percent to 48 percent. Like those of other researchers, our findings suggest that decision analyses that do not take operational failures into consideration may inaccurately predict the yield of health benefits achieved in actual practice.