Effectiveness of DArTseq markers application in genetic diversity and population structure of indigenous chickens in Eastern Province of Rwanda.

BACKGROUND: The application of biotechnologies which make use of genetic markers in chicken breeding is developing rapidly. Diversity Array Technology (DArT) is one of the current Genotyping-By-Sequencing techniques allowing the discovery of whole genome sequencing. In livestock, DArT has been applied in cattle, sheep, and horses. Currently, there is no study on the application of DArT markers in chickens. The aim was to study the effectiveness of DArTSeq markers in the genetic diversity and population structure of indigenous chickens (IC) and SASSO in the Eastern Province of Rwanda. METHODS: In total 87 blood samples were randomly collected from 37 males and 40 females of indigenous chickens and 10 females of SASSO chickens purposively selected from 5 sites located in two districts of the Eastern Province of Rwanda. Genotyping by Sequencing (GBS) using DArTseq technology was employed. This involved the complexity reduction method through digestion of genomic DNA and ligation of barcoded adapters followed by PCR amplification of adapter-ligated fragments. RESULTS: From 45,677 DArTseq SNPs and 25,444 SilicoDArTs generated, only 8,715 and 6,817 respectively remained for further analysis after quality control. The average call rates observed, 0.99 and 0.98 for DArTseq SNPs and SilicoDArTs respectively were quite similar. The polymorphic information content (PIC) from SilicoDArTs (0.33) was higher than that from DArTseq SNPs (0.22). DArTseq SNPs and SilicoDArTs had 34.4% and 34% of the loci respectively mapped on chromosome 1. DArTseq SNPs revealed distance averages of 0.17 and 0.15 within IC and SASSO chickens respectively while the respective averages observed with SilicoDArTs were 0.42 and 0.36. The average genetic distance between IC and SASSO chickens was moderate for SilicoDArTs (0.120) compared to that of DArTseq SNPs (0.048). The PCoA and population structure clustered the chicken samples into two subpopulations (1 and 2); 1 is composed of IC and 2 by SASSO chickens. An admixture was observed in subpopulation 2 with 12 chickens from subpopulation 1. CONCLUSIONS: The application of DArTseq markers have been proven to be effective and efficient for genetic relationship between IC and separated IC from exotic breed used which indicate their suitability in genomic studies. However, further studies using all chicken genetic resources available and large big sample sizes are required.

The Benefits and Harms of Antibiotic Prophylaxis for Urinary Tract Infection in Older Adults.

BACKGROUND: The role of antibiotics in preventing urinary tract infection (UTI) in older adults is unknown. We sought to quantify the benefits and risks of antibiotic prophylaxis among older adults. METHODS: We conducted a matched cohort study comparing older adults (≥66 years) receiving antibiotic prophylaxis, defined as antibiotic treatment for ≥30 days starting within 30 days of a positive culture, with patients with positive urine cultures who received antibiotic treatment but did not receive prophylaxis. We matched each prophylaxis recipient to 10 nonrecipients based on organism, number of positive cultures, and propensity score. Outcomes included (1) emergency department (ED) visit or hospitalization for UTI, sepsis, or bloodstream infection within 1 year; (2) acquisition of antibiotic resistance in urinary tract pathogens; and (3) antibiotic-related complications. RESULTS: Overall, 4.7% (151/3190) of UTI prophylaxis patients and 3.6% (n = 1092/30 542) of controls required an ED visit or hospitalization for UTI, sepsis, or bloodstream infection (hazard ratio [HR], 1.33; 95% confidence interval [CI], 1.12-1.57). Acquisition of antibiotic resistance to any urinary antibiotic (HR, 1.31; 95% CI, 1.18-1.44) and to the specific prophylaxis agent (HR, 2.01; 95% CI, 1.80-2.24) was higher in patients receiving prophylaxis. While the overall risk of antibiotic-related complications was similar between groups (HR, 1.08; 95% CI, .94-1.22), the risk of Clostridioidesdifficile and general medication adverse events was higher in prophylaxis recipients (HR [95% CI], 1.56 [1.05-2.23] and 1.62 [1.11-2.29], respectively). CONCLUSIONS: Among older adults with UTI, the harms of long-term antibiotic prophylaxis may outweigh their benefits.

Discontinuing Contact Precautions for Vancomycin-Resistant Enterococcus (VRE) Is Associated With Rising VRE Bloodstream Infection Rates in Ontario Hospitals, 2009-2018: A Quasi-experimental Study.

In Ontario, Canada, since 2012, some hospitals discontinued contact precautions for vancomycin-resistant Enterococcus (VRE). Between 2009 and 2018, there was an associated rise in VRE bloodstream infections in hospitals where contact precautions were discontinued but not in hospitals that maintained contact precautions. These data suggest contact precautions are important for hospital VRE control programs.

Comparing prescribing and dispensing databases to study antibiotic use: a validation study of the Electronic Medical Record Administrative data Linked Database (EMRALD).

BACKGROUND: Monitoring and studying community antibiotic use is a critical component in combating rising antimicrobial resistance. OBJECTIVES: To validate an electronic medical record dataset containing antibiotic prescriptions and to quantify some important differences between prescribing and dispensing databases. METHODS: We evaluated antibiotics prescribed and dispensed to patients ≥65 years of age during 2011-15. We compared the EMRALD prescribing database with the validated Ontario Drug Benefit (ODB) dispensing database. Using ODB as the gold standard and limiting to EMRALD physicians, we calculated sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) with 95% CIs. We also compared the relative change in antibiotic use prescribed by all physicians to this population over time between the databases using Poisson regression models. RESULTS: In this population, 74% of all antibiotics dispensed were from non-EMRALD physicians. Trends in use were discordant over time. When we limited ODB to EMRALD prescribers only to assess the validity of EMRALD data, we observed good sensitivity and excellent specificity for correctly identifying antibiotics at 85% (95% CI 84%-85%) and 98% (95% CI 98%-98%), respectively. The PPV was 78% (95% CI 78%-78%) and the NPV was 99% (95% CI 99%-99%). All performance measures were higher among the highest prescribing physicians. CONCLUSIONS: We demonstrated EMRALD is well suited for studying antibiotic prescribing by EMRALD physicians. However, due to the frequency with which patients receive antibiotic prescriptions from their non-primary care physicians, we caution against the use of non-population-based prescribing databases to infer antibiotic use rates or trends over time.

Effect of incorporation of thermo-regulatory genes into exotic layers on egg production and quality under tropical environment.

A breed development strategy aimed at making exotic layers (Lohmann Brown) more productive under tropical environment using thermo-regulatory genes is underway at Akate Farms in Kumasi, Ghana. The present experiment was carried out to find out the effect of the genes on egg production in hot and humid environments. Three genetic groups comprising naked-neck, frizzle and their normally feathered sibs were obtained after successive generations of crossing between naked-neck and frizzle cocks and Lohmann brown hens. A total of 270 18-week-old pullets, 90 each of the 3 groups, were selected randomly and assigned to a completely randomized design experiment with 3 replicates, with 30 birds in each replicate group and kept up to a period of 72 weeks. The birds were kept in a partitioned open-sided deep-litter house constructed with sandcrete blocks with 30 pullets in each compartment. They were fed ad libitum with layer diets containing 18 % crude protein and 2,800 kcal ME/kg. Results obtained showed that the crossbred naked-neck and frizzle phenotypes produced eggs at a significantly (P < 0.05) higher rates than their normally feathered sibs and also out-performed their normally feathered sibs in other egg production parameters measured, even though they all segregated from similar parents. This is an indication of the favourable effect of the genes on egg production under hot and humid environments.

Phenotypic characterization and analysis of genetic diversity between commercial crossbred and indigenous chickens from three different agro-ecological zones using DArT-Seq technology.

Indigenous and were used to study genetic diversity and population structure analyses. Polymorphism information content (PIC) values ranged from 0.0 to 0.5, with 21,285 SNP markers (35%) being in the lowest PIC value range (0 to 0.15) while 13,511 (commercial chickens have developed unique adaptations to their environments, which may include nutrition, pathogens, and thermal stress. Besides, environmental pressures and artificial selection have generated significant genome-wide divergence in chickens, as those selection pressures contribute a considerable evolutionary force to phenotypic and genotypic differentiation. Herein, we determined genomic diversity of indigenous chickens from semi-deciduous rainforest (SDR), coastal savannah (CS) and Guinea savannah (GS) agro-ecological zones (AEZs) in Ghana and commercial crossbreds (CC) reared at the Kwame Nkrumah University of Science and Technology (KNUST). We generated SNP markers from 82 chickens (62 indigenous chicken ecotypes and 26 commercial crossbred ecotype) using DArT-Seq technology. A total of 85,396 SNP markers were generated and after filtering the data, 58,353 markers 21%) were in the highest PIC value range (0.45 to 0.50). The CC were more genetically diverse than the indigenous birds, with the highest expected heterozygosity value of 0.220. Between the commercial crossbreds population and the indigenous ecotypes, pairwise FST values were estimated to be 0.105 between CS, 0.096 between SDF, and 0.133 between GS. Furthermore, PCA analysis showed that the CC, SDF and GS chickens clustered together and are genetically distant from the commercial crossbred. We herein show that chickens from the AEZs studied can be considered as one population. However, due the abundance of agro-byproducts in the SDR compared to the CS and GS, chickens from the SDR AEZ had better growth compared to their counterparts. It is suggested that the genetic diversity within the local ecotypes could form the basis for genetic improvement.

A comparative study of population structure and genetic diversity of commercial and indigenous chickens from different agro-ecological zones in Ghana using SilicoDArT and SNP markers.

Chicken production, both in the local and commercial sectors, contributes significantly to human livelihood and food security. Precise use of diverse genetic resources is primary in breeding programs. The study analyzed the genetic diversity and population structure of commercial chickens and indigenous chicken ecotypes from three different agro-ecological zones (Semi-Deciduous Rainforest Zone, Guinea Savannah, and Coastal Savannah) using SilicoDArT and SNP markers, utilizing whole-genome sequencing and phenotypic data. Phenotypic data were collected from 72 indigenous chicken ecotypes across the three AEZs, and 32 commercial birds kept at the Kwame Nkrumah University of Science and Technology (KNUST). DNA samples used for sequencing were obtained from 88 chickens (62 indigenous chicken ecotypes and 26 commercial chickens). A total of 54,995 SilicoDArT and 85,396 SNPs markers were generated from DArTseq genotyping. After filtering, 44,784 SilicoDArT and 58,353 SNP were used for genetic diversity and population structure analysis. Both markers showed high reproducibility and call rate. Polymorphic information content (PIC) values ranged from 0.00 to 0.50, while ≥ 50 % showed PIC values more than the median. Furthermore, we obtained FST values, Nei's genetic distance, dendrogram analysis, and principal component analysis (PCA) of commercial and indigenous chickens. The FST and Nei's genetic distance showed that there is high genetic diversity between the commercial chickens and the indigenous chicken ecotypes. However, there was low genetic diversity among the indigenous chicken ecotypes. The PCA analysis indicated a clear separation between the commercial and indigenous chicken ecotypes, while no clear separation was observed between the indigenous chicken ecotypes. The phenotypic data and the dendrogram indicated that naked and frizzle genes do not markedly alter the genetics of indigenous and commercial birds, and their influence on economic traits may be solely determined by the prevailing environmental conditions. The results indicate that there is high genetic differentiation between commercial and indigenous chickens based on SilicoDArT and SNP markers. The indigenous chickens from the agro-ecological zones have low genetic diversity and might have a common origin. Naked neck and frizzle genes do not markedly alter the genetic performance of birds in terms of economic traits. Therefore, the superiority of birds carrying these genes in economic traits may be solely due to environmental variation.

Local chickens in East African region: their production and potential.

Indigenous chickens (IC) contribute socioeconomically to household food security in the region of East Africa. However, their potential and improvement are not well documented. This review is aimed at exploring the production and potential of indigenous chickens in East Africa. The various tools for literature search such as google search and Google scholars, agricultural journals, animal sciences and health journals, poultry related journals, and country online databases were used to gather information. IC were primarily reared by women and were kept predominantly under scavenging systems where the conditions of management (feeding, housing, and health care) are poor. They presented a high variation in their reproduction and production characteristics. The products (meat and eggs) were of good quality and preferred by the local consumers. Despite the variation and potential of IC, improvements in the village system were constrained by diseases and loss due to Newcastle, Gumboro, and Ecto-endo parasites and predators. Farmers primarily used traditional methods to control the diseases, and some used conventional medications and vaccines. Due to the potential of IC, the exploration of various strategies for improvement supported by the details of their genetic variability and adaptation as well as different management conditions was a goal of this review.

Virtual learning collaboratives to improve urine culturing and antibiotic prescribing in long-term care: controlled before-and-after study.

BACKGROUND: Urine culturing practices are highly variable in long-term care and contribute to overprescribing of antibiotics for presumed urinary tract infections. The purpose of this study was to evaluate the use of virtual learning collaboratives to support long-term care homes in implementing a quality improvement programme focused on reducing unnecessary urine culturing and antibiotic overprescribing. METHODS: Over a 4-month period (May 2018-August 2018), 45 long-term care homes were self-selected from five regions to participate in virtual learning collaborative sessions, which provided an orientation to a quality improvement programme and guidance for implementation. A process evaluation complemented the use of a controlled before-and-after study with a propensity score matched control group (n=127) and a difference-in-difference analysis. Primary outcomes included rates of urine cultures performed and urinary antibiotic prescriptions. Secondary outcomes included rates of emergency department visits, hospital admission and mortality. An 18-month baseline period was compared with a 16-month postimplementation period with the use of administrative data sources. RESULTS: Rates of urine culturing and urinary antibiotic prescriptions per 1000 resident days decreased significantly more among long-term care homes that participated in learning collaboratives compared with matched controls (differential reductions of 19% and 13%, respectively, p<0.0001). There was no statistically significant changes to rates of emergency department visits, hospital admissions or mortality. These outcomes were observed with moderate adherence to the programme model. CONCLUSIONS: Rates of urine culturing and urinary antibiotic prescriptions declined among long-term care homes that participated in a virtual learning collaborative to support implementation of a quality improvement programme. The results of this study have refined a model to scale this programme in long-term care.

Antibiotic susceptibility reporting and association with antibiotic prescribing: a cohort study.

OBJECTIVE: Selective reporting of antibiotic susceptibility test results may help guide appropriate antibiotic prescribing, particularly for urinary tract infections. Our objective was to describe laboratory urine culture susceptibility reporting practices and to estimate their impact on antibiotic prescribing in outpatients. METHODS: We examined all positive urine cultures with Escherichia coli, Klebsiella pneumoniae, or Proteus mirabilis associated with an antibiotic prescription among outpatients over 65 years of age in Ontario, Canada from 2014 through 2017. We evaluated antibiotic prescribing in the empirical window (1-3 days before culture result) and in the directed window (0-5 days after culture result). Unadjusted and adjusted odds ratios were reported to estimate the association between reporting and prescribing. RESULTS: In total 113 780 eligible urine cultures from 48 laboratories were included in the study cohort. Susceptibility reporting practices were highly variable between laboratories, with a range across antibiotics from norfloxacin (n = 5/48, 10.4% reporting) to nitrofurantoin (n = 40/48, 83.3% reporting). Reporting antibiotic susceptibility was associated with increased odds of prescribing that antibiotic in the directed window (aOR 2.98, 95%CI 2.07-4.28). At the laboratory level, the proportion of urine cultures reporting specific antibiotic susceptibility results was also associated with an increase in prescribing of that antibiotic in the empirical window (adjusted OR 1.23, 95%CI 1.13-1.33, per 25% increase in reporting). CONCLUSIONS: Laboratory reporting of antibiotic susceptibility results for urine cultures is associated with empirical and directed prescribing of the reported antibiotics. Laboratories can play an important role in guiding appropriate antibiotic selection for urinary indications.

Patient- and hospital-level predictors of vancomycin-resistant Enterococcus (VRE) bacteremia in Ontario, Canada.

BACKGROUND: Data are limited on risk factors for vancomycin-resistant Enterococcus (VRE) bacteremia. METHODS: All patients with a confirmed VRE bacteremia in Ontario, Canada, between January 2009 and December 2013 were linked to provincial healthcare administrative data sources and frequency matched to 3 controls based on age, sex, and aggregated diagnosis group. Associations between predictors and VRE bacteremia were estimated by generalized estimating equations and summarized using odds ratios (ORs) and corresponding 95% confidence intervals (CIs). RESULTS: In total, 217 cases and 651 controls were examined. In adjusted analyses, patient-level predictors included bone marrow transplant (OR 106.99 [95% CI 12.19-939.26]); solid organ transplant (OR 17.17 [95% CI 4.95-59.54]); any cancer (OR 8.64 [95% CI 3.88-19.21]); intensive care unit (ICU) admission (OR 6.81 [95% CI 3.53-13.13]); heart disease (OR 5.27 [95% CI 2.00-13.90]); and longer length of stay (OR 1.07 per day [95% CI 1.06-1.09]). Hospital-level predictors included hospital size (per increase in 100 beds (OR 1.26 [95% CI 1.07-1.48]) and teaching hospitals (OR 3.87 [95% CI 1.85-8.08]). CONCLUSIONS: Patients with a bone marrow transplant, solid organ transplant, cancer, or who are admitted to the ICU are at highest risk of VRE bacteremia, particularly at large hospitals and teaching hospitals.

Influence of an independent quarterly audit on publicly reported vancomycin-resistant enterocococi bacteremia data in Ontario, Canada.

BACKGROUND: All Ontario hospitals are mandated to self-report vancomycin-resistant enterocococi (VRE) bacteremias to Ontario's Ministry of Health and Long-term Care for public reporting purposes. Independent quarterly audits of publicly reported VRE bacteremias between September 2013 and June 2015 were carried out by Public Health Ontario. VRE bacteremia case-reporting errors between January 2009 and August 2013 were identified by a single retrospective audit. METHODS: Employing a quasiexperimental pre-post study design, the relative risk of VRE bacteremia reporting errors before and after quarterly audits were modeled using Poisson regression adjusting for hospital type, case counts reported to the Ministry of Health and Long-term Care, and autocorrelation via generalized estimating equation. RESULTS: Overall, 24.5% (126 out of 514) of VRE bacteremias were reported in error; 114 out of 367 (31%) VRE bacteremias reported before quarterly audits and 12 out of 147 (8.1%) reported after audits were found to be incorrect. In adjusted analysis, quarterly audits of VRE bacteremias were associated with significant reductions in reporting errors when compared with before quarterly auditing (relative risk, 0.17; 95% confidence interval, 0.05-0.63). Risk of reporting errors among community hospitals were greater than acute teaching hospitals of the region (relative risk, 4.39; 95% CI, 3.07-5.70). CONCLUSIONS: This study found independent quarterly audits of publicly reported VRE bacteremias to be associated with significant reductions in reporting errors. Public reporting systems should consider adopting routine data audits and hospital-targeted training to improve data accuracy.

VRE and VSE Bacteremia Outcomes in the Era of Effective VRE Therapy: A Systematic Review and Meta-analysis.

BACKGROUND Prior data suggest that vancomycin-resistant Enterococcus (VRE) bacteremia is associated with worse outcomes than vancomycin-sensitive Enterococcus (VSE) bacteremia. However, many studies evaluating such outcomes were conducted prior to the availability of effective VRE therapies. OBJECTIVE To systematically review VRE and VSE bacteremia outcomes among hospital patients in the era of effective VRE therapy. METHODS Electronic databases and grey literature published between January 1997 and December 2014 were searched to identify all primary research studies comparing outcomes of VRE and VSE bacteremias among hospital patients, following the availability of effective VRE therapies. The primary outcome was all-cause, in-hospital mortality, while total hospital length of stay (LOS) was a secondary outcome. All meta-analyses were conducted in Review Manager 5.3 using random-effects, inverse variance modeling. RESULTS Among all the studies reviewed, 12 cohort studies and 1 case control study met inclusion criteria. Similar study designs were combined in meta-analyses for mortality and LOS. VRE bacteremia was associated with increased mortality compared with VSE bacteremia among cohort studies (odds ratio [OR], 1.80; 95% confidence interval [CI], 1.38-2.35; I2=0%; n=11); the case-control study estimate was similar, but not significant (OR, 1.93; 95% CI, 0.97-3.82). LOS was greater for VRE bacteremia patients than for VSE bacteremia patients (mean difference, 5.01 days; 95% CI, 0.58-9.44]; I2=0%; n=5). CONCLUSIONS Despite the availability of effective VRE therapy, VRE bacteremia remains associated with an increased risk of in-hospital mortality and LOS when compared to VSE bacteremia. Infect. Control Hosp. Epidemiol. 2015;37(1):26-35.