Distinct anal microbiome is correlated with anal cancer precursors in MSM with HIV.

OBJECTIVES: Anal cancer risk is elevated in MSM with HIV (MSMWH). Anal high-risk human papillomavirus (hr-HPV) infection is necessary but insufficient to develop high-grade squamous intraepithelial lesion (HSIL), the anal cancer precursor, suggesting additional factors. We sought to determine whether the microbiome of the anal canal is distinct by comparing it with the microbiome of stool. We also sought to determine whether changes in the anal microbiome are associated with HSIL among MSMWH. DESIGN: Cross-sectional comparison of the microbiome of the anal canal with the microbiome of stool in MSMWH and cross-sectional comparison of the anal microbiome of MSMWH with anal HSIL with the anal microbiome of MSMWH without anal HSIL. METHODS: Sterile swabs were used to sample the anus of MSMWH for microbiome and HPV testing, followed by high-resolution anoscopy. Stool samples were mailed from home. 16S sequencing was used for bacterial identification. Measures of alpha diversity, beta diversity, and differential abundance analysis were used to compare samples. RESULTS: One hundred sixty-six anal samples and 103 matching stool samples were sequenced. Beta diversity showed clustering of stool and anal samples. Of hr-HPV-positive MSMWH, 31 had HSIL and 13 had no SIL. Comparison of the microbiome between these revealed 28 different species. The highest-fold enrichment among MSMWH/hr-HPV/HSIL included pro-inflammatory and carcinogenic Prevotella, Parasuterella, Hungatella, Sneathia, and Fusobacterium species. The anti-inflammatory Anaerostipes caccae showed the greatest reduction among MSMWH/hr-HPV/HSIL. CONCLUSION: The anal microbiome is distinct from stool. A pro-inflammatory and carcinogenic environment may be associated with anal HSIL.

A global microbiome survey of vineyard soils highlights the microbial dimension of viticultural terroirs.

The microbial biodiversity found in different vitivinicultural regions is an important determinant of wine terroir. It should be studied and preserved, although it may, in the future, be subjected to manipulation by precision agriculture and oenology. Here, we conducted a global survey of vineyards' soil microbial communities. We analysed soil samples from 200 vineyards on four continents to establish the basis for the development of a vineyard soil microbiome's map, representing microbial biogeographical patterns on a global scale. This study describes vineyard microbial communities worldwide and establishes links between vineyard locations and microbial biodiversity on different scales: between continents, countries, and between different regions within the same country. Climate data correlates with fungal alpha diversity but not with prokaryotes alpha diversity, while spatial distance, on a global and national scale, is the main variable explaining beta-diversity in fungal and prokaryotes communities. Proteobacteria, Actinobacteria and Acidobacteria phyla, and Archaea genus Nitrososphaera dominate prokaryotic communities in soil samples while the overall fungal community is dominated by the genera Solicoccozyma, Mortierella and Alternaria. Finally, we used microbiome data to develop a predictive model based on random forest analyses to discriminate between microbial patterns and to predict the geographical source of the samples with reasonable precision.

Local Network Properties of Soil and Rhizosphere Microbial Communities in Potato Plantations Treated with a Biological Product Are Important Predictors of Crop Yield.

Understanding the effectiveness and potential mechanism of action of agricultural biological products under different soil profiles and crops will allow more precise product recommendations based on local conditions and will ultimately result in increased crop yield. This study aimed to use bulk soil and rhizosphere microbial composition and structure to evaluate the potential effect of a Bacillus amyloliquefaciens inoculant (strain QST713) on potatoes and to explore its relationship with crop yield. We implemented next-generation sequencing (NGS) and bioinformatics approaches to assess the bacterial and fungal biodiversity in 185 soil samples, distributed over four different time points-from planting to harvest-from three different geographical locations in the United States. In addition to location and sampling time (which includes the difference between bulk soil and rhizosphere) as the main variables defining the microbiome composition, the microbial inoculant applied as a treatment also had a small but significant effect in fungal communities and a marginally significant effect in bacterial communities. However, treatment preserved the native communities without causing a detectable long-lasting effect on the alpha- and beta-diversity patterns after harvest. Using information about the application of the microbial inoculant and considering microbiome composition and structure data, we were able to train a Random Forest model to estimate if a bulk soil or rhizosphere sample came from a low- or high-yield block with relatively high accuracy (84.6%), concluding that the structure of fungal communities gives us more information as an estimator of potato yield than the structure of bacterial communities. IMPORTANCE Our results reinforce the notion that each cultivar on each location recruits a unique microbial community and that these communities are modulated by the vegetative growth stage of the plant. Moreover, inoculation of a Bacillus amyloliquefaciens strain QST713-based product on potatoes also changed the abundance of specific taxonomic groups and the structure of local networks in those locations where the product caused an increase in the yield. The data obtained, from in-field assays, allowed training a predictive model to estimate the yield of a certain block, identifying microbiome variables-especially those related to microbial community structure-even with a higher predictive power than the geographical location of the block (that is, the principal determinant of microbial beta-diversity). The methods described here can be replicated to fit new models in any other crop and to evaluate the effect of any agricultural input in the composition and structure of the soil microbiome.

Identifying targets for improvement using a nationally standardized survey: Surgical antimicrobial prophylaxis in orthopedic surgery.

BACKGROUND: Surgical antimicrobial prophylaxis (SAP) is commonly administered in orthopedic procedures. Research regarding SAP appropriateness for specific orthopedic procedures is limited and is required to facilitate targeted orthopedic prescriber behavior change. OBJECTIVES: To describe SAP prescribing and appropriateness for orthopedic procedures in Australian hospitals. DESIGN, SETTING, AND PARTICIPANTS: Multicenter, national, quality improvement study with retrospective analysis of data collected from Australian hospitals via Surgical National Antimicrobial Prescribing Survey (Surgical NAPS) audits from January 1, 2016, to April 15, 2019, were analyzed. METHODS: Logistic regression identified hospital, patient and surgical factors associated with appropriateness. Adjusted appropriateness was calculated from the multivariable model. Additional subanalyses were conducted on smaller subsets to calculate the adjusted appropriateness for specific orthopedic procedures. RESULTS: In total, 140 facilities contributed to orthopedic audits in the Surgical NAPS, including 4,032 orthopedic surgical episodes and 6,709 prescribed doses. Overall appropriateness was low, 58.0% (n = 3,894). This differed for prescribed procedural (n = 3,978, 64.7%) and postprocedural doses (n = 2,731, 48.3%). The most common reasons for inappropriateness, when prophylaxis was required, was timing for procedural doses (50.9%) and duration for postprocedural prescriptions (49.8%). The adjusted appropriateness of each orthopedic procedure group was low for procedural SAP (knee surgery, 54.1% to total knee joint replacement, 74.1%). The adjusted appropriateness for postprocedural prescription was also low (from hand surgery, 40.7%, to closed reduction fractures, 68.7%). CONCLUSIONS: Orthopedic surgical specialties demonstrated differences across procedural and postprocedural appropriateness. The metric of appropriateness identifies targets for quality improvement and is meaningful for clinicians. Targeted quality improvement projects for orthopedic specialties need to be developed to support optimization of antimicrobial use.

Gut microbiome composition and risk factors in a large cross-sectional IBS cohort.

Objective: Irritable bowel syndrome (IBS) is a common gastrointestinal disorder that is difficult to diagnose and treat due to its inherent heterogeneity and unclear aetiology. Although there is evidence suggesting the importance of the microbiome in IBS, this association remains poorly defined. In the current study, we aimed to characterise a large cross-sectional cohort of patients with self-reported IBS in terms of microbiome composition, demographics, and risk factors. Design: Individuals who had previously submitted a stool sample for 16S microbiome sequencing were sent a comprehensive survey regarding IBS diagnosis, demographics, health history, comorbidities, family history, and symptoms. Log ratio-transformed abundances of microbial taxa were compared between individuals reporting a diagnosis of IBS without any comorbidities and individuals reporting no health conditions. Univariable testing was followed by a multivariable logistic regression model controlling for relevant confounders. Results: Out of 6386 respondents, 1692 reported a diagnosis of IBS without comorbidities and 1124 reported no health conditions. We identified 3 phyla, 15 genera, and 19 species as significantly associated with IBS after adjustment for confounding factors. Demographic risk factors include a family history of gut disorders and reported use of antibiotics in the last year. Conclusion: The results of this study confirm important IBS risk factors in a large cohort and support a connection for microbiome compositional changes in IBS pathogenesis. The results also suggest clinical relevance in monitoring and investigating the microbiome in patients with IBS. Further, the exploratory models described here provide a foundation for future studies.

Appropriateness of Surgical Antimicrobial Prophylaxis Practices in Australia.

Importance: Surgical antimicrobial prophylaxis (SAP) is a common indication for antibiotic use in hospitals and is associated with high rates of inappropriateness. Objective: To describe the SAP prescribing practices and assess hospital, surgical, and patient factors associated with appropriate SAP prescribing. Design, Setting, and Participants: Multicenter, national, quality improvement study with retrospective analysis of data collected from Australian hospitals via Surgical National Antimicrobial Prescribing Survey audits from January 1, 2016, to June 30, 2018. Data were analyzed using multivariable logistic regression. Crude estimates of appropriateness were adjusted for factors included in the model by calculating estimated marginal means and presented as adjusted-appropriateness with 95% confidence intervals. Main Outcomes and Measures: Adjusted appropriateness and factors associated with inappropriate prescriptions. Results: A total of 9351 surgical episodes and 15 395 prescriptions (10 740 procedural and 4655 postprocedural) were analyzed. Crude appropriateness of total prescriptions was 48.7% (7492 prescriptions). The adjusted appropriateness of each surgical procedure group was low for procedural SAP, ranging from 33.7% (95% CI, 26.3%-41.2%) for dentoalveolar surgery to 68.9% (95% CI, 63.2%-74.5%) for neurosurgery. The adjusted appropriateness of postprocedural prescriptions was also low, ranging from 21.5% (95% CI, 13.4%-29.7%) for breast surgery to 58.7% (95% CI, 47.9%-69.4%) for ophthalmological procedures. The most common reason for inappropriate procedural SAP was incorrect timing (44.9%), while duration greater than 24 hours was the most common reason for inappropriate postprocedural SAP (54.3%). Conclusions and Relevance: High rates of inappropriate procedural and postprocedural antimicrobial use were demonstrated across all surgical specialties. Reasons for inappropriateness, such as timing and duration, varied according to the type of SAP and surgical specialty. These findings highlight the need for improvement in SAP prescribing and suggest potential targeted areas for action.

Statistical Process Control Charts for Monitoring Staphylococcus aureus Bloodstream Infections in Australian Health Care Facilities.

BACKGROUND: Staphylococcus aureus bloodstream infection (SAB) in health care settings contributes significantly to mortality, and improved processes are associated with reduced burden of infection. In Australia, health care-associated SAB (HA-SAB) rates are reported as a health care performance indicator, but standardized methods for analyzing longitudinal data are not applied. Our objective was to evaluate the utility of statistical process control chart methodology for reporting HA-SAB and flagging higher than expected rates. METHODS: A real-world test data set was defined as HA-SAB surveillance data collected by 155 Australian health care facilities between June 1, 2015, and June 30, 2017. This included 788 HA-SAB events, corresponding to an overall rate of 0.7 HA-SAB events per 10 000 occupied bed-days. The u-chart was selected as an appropriate tool, given the need for reporting natural units (HA-SAB rates) to a range of stakeholders. Facility-level data were plotted as u-charts, applying warning and control limits (2- and 3-SD thresholds, respectively). RESULTS: Sixty-eight of the 155 participating facilities (43.9%) observed at least 1 HA-SAB event during the studied period. Using the traditional method of Poisson modeling, 56 of these 68 facilities demonstrated overdispersion with variance-to-mean ratio spanning 1.03 to 42.82. Modeling by negative binomial (NB) distribution was therefore applied to enhance functionality. CONCLUSION: The u-chart is an accessible method for monitoring HA-SAB, interpretable by a range of stakeholders. We demonstrate the benefit of NB modeling to account for overdispersion, providing an effective tool to avoid inappropriate flags while maintaining early detection of out-of-control systems throughout a wide range of health care settings.

Prevalence of infections and antimicrobial prescribing in Australian aged care facilities: Evaluation of modifiable and nonmodifiable determinants.

BACKGROUND: Infections in aged care residents are associated with poor outcomes, and inappropriate antimicrobial prescribing contributes to adverse events, such as the emergence of antimicrobial resistance. The objective of this study was to identify resident- and facility-level factors associated with infection and antimicrobial prescribing in Australian aged care residents. METHODS: Using data captured by a national point-prevalence survey (the Aged Care National Antimicrobial Prescribing Survey), risk and protective factors were determined by multivariate Poisson regression. RESULTS: In 2017, 292 facilities were surveyed. Infection prevalence was 2.9% (95% confidence interval [CI], 2.6%-3.2%), and antimicrobial use prevalence was 8.9% (95% CI, 8.4%-9.4%). Resident-level factors associated with infection prevalence included urinary catheterization and hospital admission within the last 30 days; facility-level factors included state and multipurpose service provision. Resident-level factors associated with antimicrobial prescribing included infection signs and symptoms; facility-level factors included state, nonmetropolitan locality, and not-for-profit status. Availability of guidelines for urinary tract infection (UTI) management was associated with reduced antimicrobial prescribing. CONCLUSIONS: Looking ahead, reports should be peer grouped by significant facility-level factors. Priority should be given to implementing UTI management guidelines and prevention of infection in residents with indwelling urinary catheters. Enhanced monitoring and prevention strategies are required for residents recently admitted to hospital.