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Introduction: Invasive mechanical ventilation (IMV) is frequently used as a life-supporting device in Pediatric Intensive Care Units (PICU). To date, there are few studies evaluating the impact of prolonged mechanical ventilation (PMV) in children which is associated with high morbidity and mortality. We aimed to determine the incidence and factors associated with PMV in PICU at our institution. Methods: A retrospective review was performed of children aged 1 month to 18 years who were admitted to the PICU at Chiang Mai University Hospital, Thailand between January and December 2020. PMV was defined if the duration of IMV was ≥ 96 hours. Baseline characteristics and factors associated with PMV were analyzed by descriptive statistics, and univariable and multivariable logistic regression analysis, respectively. A p-value of < 0.05 was considered significant. Results: Ninety-two episodes of IMV were performed in 90 children. The median (IQR) age of the children was 22.8 (7.2–111.9) months (male 64.1%). Forty-six of 92 (50%) children received PMV and 32.6% of children with PMV required a tracheostomy. Following multivariable analysis, factors associated with PMV were age <2 years old (OR 2.86, 95% CI 1.04–7.84, p = 0.041), male gender (OR 3.21, 95% CI 1.15–8.94, p = 0.026), and multiple antibiotics administration during PICU admission (OR 7.83, 95% CI 1.87–32.78, p = 0.005), respectively. Conclusions: Pediatric PMV was notably common, with younger age, male gender, and multiple antibiotic use contributing to higher risk. Developing weaning protocols and strategies to reduce PMV duration is crucial. [ABSTRACT FROM AUTHOR]

Background: Most US children with acute otitis media [AOM] receive prompt antibiotic treatment, though guidelines encourage watchful waiting. Previous systematic reviews of antibiotics versus watchful waiting have focused on symptom resolution and RCTs, limiting the assessment of serious, rare complications. We sought to evaluate these complications by including observational studies. Methods: RCTs and observational studies that compared antibiotics to placebo or watchful waiting for pediatric clinician diagnosed AOM were identified [PubMed/MEDLINE, Embase, Cochrane Database of Systematic Reviews, Central Register of Controlled Trials, and Web of Science] and reviewed for meta-analysis. Two reviewers independently extracted study characteristics, patient characteristics, and outcomes. We assessed publication bias, study bias with ROBINS-1 and RoB-2 and used random-effects models to assess treatment effects. Results: 24 studies were included. Antibiotics decreased the risk of acute mastoiditis [incidence 0.02%, RR 0.48, 95% CI 0.40–0.59; NNT 5,368]. This protective effect may be underestimated because of misclassification of non-suppurative conditions as AOM. Intracranial complications remained too rare to assess. Antibiotics markedly increased the risk of adverse effects [incidence 10.5%, RR 1.49, 1.27–1.73; NNH 23]. Studies used non-specific criteria for acute mastoiditis, potentially underestimating treatment effects. Conclusions: Prompt antibiotic therapy reduces the risk for some AOM complications. The NNT to prevent serious, rare complications is high, while the NNH is relatively low. Large-scale population-based observational studies using real-world datasets with validated measures of severe complications are needed to improve understanding of risk factors for serious AOM complications, facilitate more selective antibiotic therapy, and optimize individual outcomes and public health. [ABSTRACT FROM AUTHOR]

There is a rapid spread of antibiotic resistance in the environment. However, the impact of antibiotic resistance in drinking water is relatively underexplored. Thus, this study aimed to quantify antibiotic resistance genes (ARGs) and antibiotic residues in two drinking water production facilities (NW-E and NW-C) in North West Province, South Africa and link these parameters to bacterial communities. Physicochemical and ARG levels were determined using standard procedures. Residues (antibiotics and fluconazole) and ARGs were quantified using ultra-high performance liquid chromatography (UHPLC) chemical analysis and real-time PCR, respectively. Bacterial community compositions were determined by high-throughput 16S rRNA sequencing. Data were analysed using redundancy analysis and pairwise correlation. Although some physicochemical levels were higher in treated than in raw water, drinking water in NW-E and NW-C was safe for human consumption using the South African Water Quality Guideline (SAWQG). ARGs were detected in raw and treated water. In NW-E, the concentrations of ARGs (sul1, intl1, EBC, FOX, ACC and DHA) were higher in treated water than in raw water. Regarding antimicrobial agents, antibiotic and fluconazole concentrations were higher in raw than in treated water. However, in NW-C, trimethoprim concentrations were higher in raw than in treated water. Redundancy analysis showed that bacterial communities were not significantly correlated (Monte Carlo simulations, p-value >0.05) with environmental factors. However, pairwise correlation showed significant differences (p-value <0.05) for Armatimonas, CL500-29 marine group, Clade III, Dickeya and Zymomonas genera with environmental factors. The presence of ARGs and antibiotic residues in the current study indicated that antibiotic resistance is not only a clinical phenomenon but also in environmental settings, particularly in drinking water niches. Consumption of NW-E and NW-C treated water may facilitate the spread of antibiotic resistance among consumers. Thus, regulating and monitoring ARGs and antibiotic residues in drinking water production facilities should be regarded as paramount. [ABSTRACT FROM AUTHOR]

The excessive use of antibiotics has resulted in the contamination of the environment with antibiotic resistance genes (ARGs), posing a significant threat to public health. Wastewater treatment plants (WWTPs) are known to be reservoirs of ARGs and considered to be hotspots for horizontal gene transfer (HGT) between bacterial communities. However, most studies focused on the distribution and dissemination of ARGs in hospital and urban WWTPs, and little is known about their fate in industrial WWTPs. In this study, collected the 15 wastewater samples containing N,N-dimethylformamide (DMF) from five stages of the anaerobic anoxic aerobic (AAO) process in an industrial WWTPs. The findings revealed a stepwise decrease in DMF and chemical oxygen demand (COD) content with the progression of treatment. However, the number and abundances of ARGs increase in the effluents of biological treatments. Furthermore, the residues of DMF and the treatment process altered the structure of the bacterial community. The correlation analysis indicated that the shift in bacterial community structures might be the main driver for the dynamics change of ARGs. Interestingly, observed that the AAO process may acted as a microbial source and increased the total abundance of ARGs instead of attenuating it. Additionally, found that non-pathogenic bacteria had higher ARGs abundance than pathogenic bacteria in effluents. The study provides insights into the microbial community structure and the mechanisms that drive the variation in ARGs abundance in industrial WWTPs. [ABSTRACT FROM AUTHOR]

Surveillance methods of circulating antibiotic resistance genes (ARGs) are of utmost importance in order to tackle what has been described as one of the greatest threats to humanity in the 21st century. In order to be effective, these methods have to be accurate, quickly deployable, and scalable. In this study, we compare metagenomic shotgun sequencing (TruSeq DNA sequencing) of wastewater samples with a state-of-the-art PCR-based method (Resistomap HT-qPCR) on four wastewater samples that were taken from hospital, industrial, urban and rural areas. ARGs that confer resistance to 11 antibiotic classes have been identified in these wastewater samples using both methods, with the most abundant observed classes of ARGs conferring resistance to aminoglycoside, multidrug-resistance (MDR), macrolide-lincosamide-streptogramin B (MLSB), tetracycline and beta-lactams. In comparing the methods, we observed a strong correlation of relative abundance of ARGs obtained by the two tested methods for the majority of antibiotic classes. Finally, we investigated the source of discrepancies in the results obtained by the two methods. This analysis revealed that false negatives were more likely to occur in qPCR due to mutated primer target sites, whereas ARGs with incomplete or low coverage were not detected by the sequencing method due to the parameters set in the bioinformatics pipeline. Indeed, despite the good correlation between the methods, each has its advantages and disadvantages which are also discussed here. By using both methods together, a more robust ARG surveillance program can be established. Overall, the work described here can aid wastewater treatment plants that plan on implementing an ARG surveillance program. [ABSTRACT FROM AUTHOR]

Objective: High prevalence of sexually transmitted infections (STIs) combined with poor antimicrobial stewardship are drivers of STI antimicrobial resistance (AMR) especially in resource-limited settings where syndromic case management (SCM) is the norm. We characterized patterns of antibiotic use prior to clinic attendance and study enrollment in Ugandan men with urethral discharge syndrome (UDS), evaluated in-clinic prescribing, and the performance characteristics of SCM. Methods: Participants were recruited from government clinics participating in an existing gonococcal surveillance program in Kampala, Uganda. Questionnaires including antimicrobial use prior to attendance, prior episodes of UDS, penile swabs, and blood samples were collected. Bivariable and multivariable logistic regression models were used to estimate odds ratios (OR) for preselected factors likely to be associated with antibiotic use. In-clinic antibiotic treatment data were extracted from clinical notes, and the performance of SCM against laboratory-based STI diagnoses was evaluated. Findings: Between October 2019 and November 2020, 100(40%) of 250 men with UDS reported taking antibiotics in the 14days prior to attending the clinic. Of these 210(84%) had at least one curable STI and 20% had a reactive point-of-care HIV test. Multivariable analysis demonstrated significant associations between recent antimicrobial use and duration of UDS symptoms <6 days (OR 2.98(95%CI 1.07,8.36), p = 0.038), and sex with women only (OR 0.08(95%CI 0.01,0.82),p = 0.038). The sensitivity of SCM ranged from 80.0% to 94.4%; specificity was low between 5.6% and 33.1%. The positive predictive value of SCM ranged from 2.4(95%CI 0.7,6.0) for trichomoniasis to 63.4(95%CI 56.5,69.9) for gonorrhea. Conclusion: Pre-enrollment antibiotic use was common in this population at high risk of STI and HIV. Combined with the poor specificity of SCM for male UDS, extensive antibiotic use is a likely driver of STI-AMR in Ugandan men. Interventions to improve antimicrobial stewardship and deliver affordable diagnostics to augment SCM and decrease overtreatment of STI syndromes are required. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic has imposed an enormous burden on health care systems around the world. Simultaneously, many countries have reported a decrease in the incidence of other infectious diseases, such as acute respiratory infections, leading to a decline in outpatient antibiotic use. The aim of this study is to assess the impact of the COVID-19 pandemic on outpatient antibiotic prescribing in Finland during the first 2 years of the pandemic. We used nationwide register data, applied descriptive methods, and conducted an interrupted time series analysis (ITSA) using ARIMA modelling. Results from the ARIMA modelling showed that at the baseline, before the pandemic, the level of monthly number of antibiotic prescriptions was 248,560 (95% CI: 224,261 to 272,856; p<0.001) and there was a decreasing trend of 1,202 in monthly number of prescriptions (95% CI: -2,107 to -262; p<0.01). After the COVID-19 pandemic began, there was a statistically significant decline of 48,470 (95% CI: -76,404 to -20,535, p<0.001) prescriptions (-19.5% from the baseline level). The greatest decrease in antibiotic prescribing was observed among children aged 0–17 years. While antibiotic prescribing declined in all antibiotic groups associated with respiratory tract infections, the decrease from 2019 to 2020 was the largest with azithromycin (52.6%), amoxicillin (44.8%), and doxycycline (43.8%). Future studies should continue exploring antibiotic prescribing trends during the COVID-19 pandemic and beyond. [ABSTRACT FROM AUTHOR]

Background: Resistance to antibiotics is rising and threatens future antibiotic effectiveness. 'Antibiotic targeting' ensures patients who may benefit from antibiotics receive them, while being safely withheld from those who may not. Point-of-care tests may assist with antibiotic targeting by allowing primary care clinicians to establish if symptomatic patients have a viral, bacterial, combined, or no infection. However, because organisms can be harmlessly carried, it is important to know if the presence of the virus/bacteria is related to the illness for which the patient is being assessed. One way to do this is to look for associations with more severe/prolonged symptoms and test results. Previous research to answer this question for acute respiratory tract infections has given conflicting results with studies has not having enough participants to provide statistical confidence. Aim: To undertake a synthesis of IPD from both randomised controlled trials (RCTs) and observational cohort studies of respiratory tract infections (RTI) in order to investigate the prognostic value of microbiological data in addition to, or instead of, clinical symptoms and signs. Methods: A systematic search of Cochrane Central Register of Controlled Trials, Ovid Medline and Ovid Embase will be carried out for studies of acute respiratory infection in primary care settings. The outcomes of interest are duration of disease, severity of disease, repeated consultation with new/worsening illness and complications requiring hospitalisation. Authors of eligible studies will be contacted to provide anonymised individual participant data. The data will be harmonised and aggregated. Multilevel regression analysis will be conducted to determine key outcome measures for different potential pathogens and whether these offer any additional information on prognosis beyond clinical symptoms and signs. Trial registration: PROSPERO Registration number: CRD42023376769. [ABSTRACT FROM AUTHOR]

Background: This paper aims to estimate the prevalence of antibiotic use for diarrhea among under-five children (u5c) in low- and middle-income countries (LMICs) using data from 112 Demographic Health Surveys (DHS) conducted between 2006 and 2018. The focus is on understanding the extent of antibiotic usage for managing diarrhea, a condition characterized by frequent loose or watery bowel movements that can lead to severe dehydration. Methods and findings: A cross-sectional study design was employed in the DHS. The prevalence of antibiotic use for diarrhea among under-five children was estimated by analyzing DHS data from 2006 to 2018 and using the R statistical programming language. Out of a total of 12,69,944 children under five included in this study, 1,80,067 children had diarrhea and 19,502 children had bloody diarrhea. The overall prevalence of diarrhea estimated at ~14% (prevalence = 0.142; 95% CI = 0.141, 0.142). Among the children with diarrhea, 47,755 child received antibiotic treatment, resulting a prevalence of ~27% (prevalence = 0.27, 95% CI = 0.26, 0.27) globally. Central Asia had the highest prevalence of antibiotic use at ~55% (prevalence = (967/1748) = 0.55, 95% CI = 0.52, 0.59), followed by the Europe region with a prevalence of ~44% (prevalence = (5483/12502) = 0.44, 95% CI = 0.43, 0.45). In the South East and Central Asia region, DHS conducted between 2006 and 2018, showed the highest prevalence of antibiotic use in DHS 2007 (~44%), DHS 2012 (~49%), DHS 2016 (~40%) and DHS 2017 (~65%). The linear trend analysis showed an upward trend for using antibiotic of diarrhea in the South East and Central Asia region. Conclusions: The Central Asia region had the highest proportion of antibiotic use, with an estimated prevalence of ~55% (95% CI = 0.52, 0.59). The Europe region followed closely with a prevalence of ~44% (95% CI = 0.43, 0.45). The South East Asia region had the lowest prevalence of antibiotic use estimated at ~23% (95% CI = 0.22, 0.24), with a gradual increasing trend. [ABSTRACT FROM AUTHOR]

Background: Inappropriate use of antibiotics can promote bacterial resistance, which is a growing public health concern. As children are amongst the highest recipients of antibiotics, understanding the drivers of parental decisions towards their children's antibiotic use is imperative for the development of strategies to assist parents in making more informed decisions. This is particularly relevant to the decisions of parents living in resource-limited settings. This study explored the perspectives and practices of parents living in a rural setting about the use of antibiotics in their children. Methods: Three focus group interviews were conducted with 10 parents of children under 12yrs, living in rural and remote areas of the Northern Territory, Australia. A focus group guide was developed to facilitate discussions, which was informed by the Theory of Planned Behaviour. Transcripts were analysed abductively using thematic analysis. Findings: Four themes emerged explaining factors that contributed to parent decisions about their children's antibiotic use: 1) Parental knowledge, attitudes and decision making; 2) Perceptions of antimicrobial resistance; 3) Healthcare challenges; 4) Behaviours with antibiotics. While parents demonstrated accurate knowledge of the indications for antibiotic use, their decisions about the need for antibiotics were often driven by fear of serious illness. This fear was exacerbated by resource limitations associated with living in a resource-limited setting. Additional drivers of parental decision making included what parents have read or heard from both medical and non-medical networks, underscoring the importance of Social Norms in predicting behavioural intentions. Conclusion: Mothers living in remote areas experiencing reduced access to health services may make decisions about antibiotic use out of fear and based on the advice of their personal network when they perceive their child is vulnerable to a health threat. Findings from this study provide guidance for future research in the prediction of antibiotic use behaviours and for context-specific interventions. [ABSTRACT FROM AUTHOR]

Antimicrobial resistance (AMR) is a silent pandemic that has claimed millions of lives, and resulted in long-term disabilities, limited treatment options, and high economic costs associated with the healthcare burden. Given the rising prevalence of AMR, which is expected to pose a challenge to current empirical antibiotic treatment strategies, we sought to summarize the available data on knowledge, attitudes, and practices regarding AMR in Ethiopia. Articles were searched in international electronic databases. Microsoft Excel spreadsheet and STATA software version 16 were used for data extraction and analysis, respectively. The Preferred Reporting Items for Systematic Reviews and Meta-Analysis 2020 checklist was followed. The methodological quality of the studies included was assessed by the Joana Briggs Institute critical appraisal checklists. The random-effect meta-analysis model was used to estimate Der Simonian-Laird's pooled effect. Statistical heterogeneity of the meta-analysis was checked through Higgins and Thompson's I2 statistics and Cochran's Q test. Publication bias was investigated by funnel plots, and the regression-based test of Egger for small study effects with a P value < 0.05 was considered to indicate potential reporting bias. In addition, sensitivity and subgroup meta-analyses were performed. Fourteen studies with a total of 4476 participants met the inclusion criteria. Overall, the pooled prevalence of good AMR knowledge was 51.53% [(95% confidence interval (CI): 37.85, 65.21), I2 = 99.0%, P <0.001]. The pooled prevalence of favorable attitudes and good practices were 63.43% [(95% CI: 42.66, 84.20), I2 = 99.6, P <0.001], and 48.85% [(95% CI: 38.68, 59.01), I2 = 93.1, P <0.001] respectively. In conclusion, there is a significant knowledge and practice gap on AMR among the general public, patients, and livestock producers. As a result, we call for greater educational interventions to raise awareness and build a strong national AMR narrative. [ABSTRACT FROM AUTHOR]

Antimicrobial resistance (AMR) is one of the key public health concerns the world is facing today. The effect of antibiotic awareness campaigns (AACs) on consumer behaviour has been documented in the literature with mixed results. Understanding the mechanism for how AACs affect target populations is vital in designing effective and tailored campaigns. Using structural equation modelling our study examined the relationships among people's exposure to antibiotic awareness campaigns, knowledge of AMR prevention, AMR risk perception, and intention to seek antibiotic treatment. This study also tested the moderating effect of anxiety and societal responsibility on preventing AMR, and on their intention to demand antibiotic treatment mediated by knowledge of AMR prevention and risk-perception. Primary data was generated using an online survey of 250 Western Australian parents. We tested our hypotheses using reliability and validity tests and structural equation modelling. Our results show that exposure to AACs alone may not be enough to change parental intention to demand antibiotic prescription for their children. Parental risk perception of AMR and parental anxiety affect intention to demand antibiotics, and the view that AMR is a social responsibility has a moderating effect on intention to demand antibiotics. These factors could be considered and combine messaging strategies in designing future antibiotic awareness campaigns. [ABSTRACT FROM AUTHOR]

Antibiotics are frequently prescribed for children in the outpatient setting. Although sometimes necessary, antibiotic use is associated with important downstream effects including the development of antimicrobial resistance among human and environmental microorganisms. Current outpatient stewardship efforts focus on guiding appropriate antibiotic prescribing practices among providers, but little is known about parents' understanding of antibiotics and appropriate disposal of leftover antibiotics. To help bridge this gap, we conducted a qualitative study to assess parental understanding of their children's antibiotics, their adherence to antibiotic instructions, and their disposal practices. We conducted a semi-structured interview with parents of 13 children diagnosed with acute respiratory illnesses and prescribed antibiotics in an urban outpatient clinic. We found that parents had limited understanding of how antibiotics work. Although they received instructions about antibiotic use during the healthcare visit, adherence to the prescription and appropriate disposal of antibiotics was suboptimal. Limited baseline understanding of antibiotics, their prior experiences with antibiotics, perceptions about their social networks' antibiotic use, and information provided to them by healthcare providers may influence these behaviors. Our findings can inform educational efforts of outpatient stewardship programs to help optimize parental understanding of how to use and dispose of their children's antibiotics. [ABSTRACT FROM AUTHOR]

Background: After admission to hospital, COVID-19 progresses in a substantial proportion of patients to critical disease that requires intensive care unit (ICU) admission. Methods: In a pragmatic, non-blinded trial, 387 patients aged 40–90 years were randomised to receive treatment with SoC plus doxycycline (n = 192) or SoC only (n = 195). The primary outcome was the need for ICU admission as judged by the attending physicians. Three types of analyses were carried out for the primary outcome: "Intention to treat" (ITT) based on randomisation; "Per protocol" (PP), excluding patients not treated according to randomisation; and "As treated" (AT), based on actual treatment received. The trial was undertaken in six hospitals in India with high-quality ICU facilities. An online application serving as the electronic case report form was developed to enable screening, randomisation and collection of outcomes data. Results: Adherence to treatment per protocol was 95.1%. Among all 387 participants, 77 (19.9%) developed critical disease needing ICU admission. In all three primary outcome analyses, doxycycline was associated with a relative risk reduction (RRR) and absolute risk reduction (ARR): ITT 31.6% RRR, 7.4% ARR (P = 0.063); PP 40.7% RRR, 9.6% ARR (P = 0.017); AT 43.2% RRR, 10.8% ARR (P = 0.007), with numbers needed to treat (NTT) of 13.4 (ITT), 10.4 (PP), and 9.3 (AT), respectively. Doxycycline was well tolerated with not a single patient stopping treatment due to adverse events. Conclusions: In hospitalized COVID-19 patients, doxycycline, a safe, inexpensive, and widely available antibiotic with anti-inflammatory properties, reduces the need for ICU admission when added to SoC. [ABSTRACT FROM AUTHOR]

This study aimed to investigate the presence and persistence of antibiotics in wastewater of four typical pharmaceutical manufactories in China and receiving water bodies and suggest the removal of antibiotics by the wastewater treatment process. It also evaluated the environmental impact of antibiotic residues through wastewater discharge into receiving water bodies. The results indicated that thirteen antibiotics were detected in wastewater samples with concentrations ranging from 57.03 to 726.79 ng/L. Fluoroquinolones and macrolides were the most abundant antibiotic classes found in wastewater samples, accounting for 42.5% and 38.7% of total antibiotic concentrations, respectively, followed by sulfonamides (16.4%) and tetracyclines (2.4%). Erythromycin-H2O, lincomycin, ofloxacin, and trimethoprim were the most frequently detected antibiotics; among these antibiotics, the concentration of ofloxacin was the highest in most wastewater samples. No significant difference was found in different treatment processes used to remove antibiotics in wastewater samples. More than 50% of antibiotics were not completely removed with a removal efficiency of less than 70%. The concentration of detected antibiotics in the receiving water bodies was an order of magnitude lower than that in the wastewater sample due to dilution. An environmental risk assessment showed that lincomycin and ofloxacin could pose a high risk at the concentrations detected in effluents and a medium risk in their receiving water bodies, highlighting a potential hazard to the health of the aquatic ecosystem. Overall, The investigation was aimed to determine and monitor the concentration of selected antibiotics in 4 typical PMFs and their receiving water bodies, and to study the removal of these substances in PMFs. This study will provide significant data and findings for future studies on antibiotics-related pollution control and management in water bodies. [ABSTRACT FROM AUTHOR]

Veterinary medicine uses antibiotics randomly for treatment and growth promotion. Milk of dairy animals contains substantial quantities of antibiotics that have harmful effects on health. It is therefore necessary to test commercially available milk using immunological, chromatographic, or microbiological methods to confirm the absence of antibiotic residues. This study aims to perform a microbiological test, followed by a quantitative confirmation analysis, on raw milk to assess the presence of antibiotic residues. Tests were conducted on 200 milk samples collected from markets and farms in Saudi Arabia and Egypt. The microbial inhibitor test (Delvotest SP-NT) revealed that 40 samples were positive for antibiotic residues. The positive samples were further tested using liquid chromatography-tandem mass spectrometry (LC-MS/MS) as a confirmatory quantitative test for 29 antibiotics that belong to five groups: tetracyclines, sulfonamides, fluoroquinolones, macrolides, and lactamases. Only four samples tested positive for oxytetracycline residues above the maximum residue limit. Based on these results, researchers suggest a monitoring system that considers both microbial and HPLC-MS/MS methods when detecting antibiotic residues in bovine milk. The analysis of risk to human health revealed that antibiotic residues at the detected levels do not pose any health risks to consumers. [ABSTRACT FROM AUTHOR]

Fluro(quinolones) is an important class of antibiotic used widely in both human and veterinary medicine. Resistance to fluro(quinolones) can be acquired by either chromosomal point mutations or plasmid-mediated quinolone resistance (PMQR). There is a lack of studies on the prevalence of PMQR in organisms from environmental sources in Bangladesh. In this study, we investigated the occurrence of PMQR genes in E. coli from various water sources and analysed associations between multi-drug resistance (MDR) and resistance to extended spectrum β-lactam antibiotics. We analysed 300 E. coli isolates from wastewaters of urban live-bird markets (n = 74) and rural households (n = 80), rural ponds (n = 71) and river water samples (n = 75) during 2017–2018. We isolated E. coli by filtering 100 ml of water samples through a 0.2μm cellulose membrane and incubating on mTEC agar media followed by identification of isolated colonies using biochemical tests. We selected one isolate per sample for detection of PMQR genes by multiplex PCR and tested for antibiotic susceptibility by disc diffusion. Clonal relatedness of PMQR-positive isolates was evaluated by enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR). About 66% (n = 199) of E. coli isolates harbored PMQR-genes, predominantly qnrS (82%, n = 164) followed by aac(6')-lb-cr (9%, n = 17), oqxAB (7%, n = 13), qnrB (6%, n = 11) and qepA (4%, n = 8). Around 68% (n = 135) of PMQR-positive isolates were MDR and 92% (n = 183) were extended spectrum β-lactamase (ESBL)-producing of which the proportion of positive samples was 87% (n = 159) for blaCTX-M-1' 34% (n = 62) for blaTEM, 9% (n = 16) for blaOXA-1,blaOXA-47 and blaCMY-2, and 2% (n = 4) for blaSHV. Further, 16% (n = 32) of PMQR-positive isolates were resistant to carbapenems of which 20 isolates carried blaNDM-1. Class 1 integron (int1) was found in 36% (n = 72) of PMQR-positive E. coli isolates. PMQR genes were significantly associated with ESBL phenotypes (p≤0.001). The presence of several PMQR genes were positively associated with ESBL and carbapenemase encoding genes such as qnrS with blaCTXM-1 (p<0.001), qnrB with blaTEM (p<0.001) and blaOXA-1 (p = 0.005), oqxAB and aac(6')-lb-cr with blaSHV and blaOXA-1 (p<0.001), qnrB with blaNDM-1 (p<0.001), aac(6')-lb-cr with blaOXA-47 (p<0.001) and blaNDM-1 (p = 0.002). Further, int1 was found to correlate with qnrB (p<0.001) and qepA (p = 0.011). ERIC-PCR profiles allowed identification of 84 of 199 isolates with 85% matching profiles which were further grouped into 33 clusters. Only 5 clusters had isolates (n = 11) with identical ERIC-PCR profiles suggesting that PMQR-positive E. coli isolates are genetically heterogeneous. Overall, PMQR-positive MDR E. coli were widely distributed in aquatic environments of Bangladesh indicating poor wastewater treatment and highlighting the risk of transmission to humans and animals. [ABSTRACT FROM AUTHOR]

Objectives: Antibiotics are important for improving animal health and production. However, the deposition of its residues in food of animal origin intended for human consumption at non-permissible levels has generated global health concern and the need to tackle this using the "One Health Approach". This study assessed the knowledge and practice of 286 cattle handlers in Kwara State, Nigeria. Methods: A web-based cross sectional online survey using a semi-structured questionnaire was conducted from November to December, 2019. Univariate, bivariate and multivariate analyses were performed at 95% confidence interval to determine predictors of good knowledge and practices towards Antibiotic Residues in Meat and Milk among cattle handlers. Results: This study revealed that majority (52.7% n = 165/286) of the cattle handlers were not aware of antibiotic residues. Knowledge and practices regarding antibiotic residues were generally poor among the study population; 36.7% and 35.5% had satisfactory knowledge and practice respectively. The age (p = 0.026), gender (p = 0.006) and business duration (p = 0.001) of participants were significantly associated with their knowledge of antimicrobial residues. The effect of education on knowledge was modified by age. The odds of having poor knowledge on antibiotic residues increased 4 times among participants who were ≤40 years old than those above 40 years (Stratum Specific OR = 3.65; CI = 1.2, 11.1; p = 0.026). Knowledge levels of participants were statistically associated with their practice levels p<0.05 (OR = 2.43; CI = 1.45. 4.06; p = 0.0006). Conclusion: This implies that poor knowledge is a risk factor to having poor practice among cattle handlers. Deliberate efforts towards educating cattle farmers on best farm practices in antibiotic use would prevent antibiotic residues in meat and milk. Also, an effective surveillance system for monitoring the use of veterinary drugs in Kwara State, Nigeria is crucial. [ABSTRACT FROM AUTHOR]

Antibiotic resistance genes (ARGs) are emerging contaminants causing serious global health concern. Interventions to address this concern include improving our understanding of methods for treating waste material of human and animal origin that are known to harbor ARGs. Anaerobic digestion is a commonly used process for treating dairy manure, and although effective in reducing ARGs, its mechanism of action is not clear. In this study, we used three ARGs to conducted a longitudinal bench scale anaerobic digestion experiment with various temperatures (28, 36, 44, and 52°C) in triplicate using fresh dairy manure for 30 days to evaluate the reduction of gene abundance. Three ARGs and two mobile genetic elements (MGEs) were studied: sulfonamide resistance gene (sulII), tetracycline resistance genes (tetW), macrolide-lincosamide-streptogramin B (MLSB) superfamily resistance genes (ermF), class 1 integrase gene (intI1), and transposase gene (tnpA). Genes were quantified by real-time quantitative PCR. Results show that the thermophilic anaerobic digestion (52°C) significantly reduced (p < 0.05) the absolute abundance of sulII (95%), intI1 (95%), tnpA (77%) and 16S rRNA gene (76%) after 30 days of digestion. A modified Collins–Selleck model was used to fit the decay curve, and results suggest that the gene reduction during the startup phase of anaerobic digestion (first 5 days) was faster than the later stage, and reductions in the first five days were more than 50% for most genes. [ABSTRACT FROM AUTHOR]

Introduction: Antimicrobial resistance is (AMR) an emerging global public health problem. Rationale use of antibiotic can prevent the rise of antimicrobial resistance. The objective of this study was to understand the knowledge, attitude and practice on antibiotic usage and AMR among the veterinarians and para-veterinarians in Bhutan. Method: A cross-sectional questionnaire survey among the veterinarians and para-veterinarians was conducted from June to July 2020. A score of one to the correct answers and zero for the wrong answers was allotted to each respondent answers. The total score was added and those who scored above the mean was categorized as having good knowledge and favourable attitude. Result: A total of 219 animal health workers participated in this study. The mean knowledge score was 12.05 ±1.74 with 38.8% of the respondents having good knowledge on antibiotic use and AMR. Similarly, the mean scores for the attitude level were 8.32±1.61 with 51% them having favorable attitude towards antibiotic usage and AMR. The mean practice score was 3.83±1.06 with 77% of them having good practices on antibiotic use. The respondents who read national plan on AMR were found to have good knowledge on antibiotics and AMR (AOR: 2.39; 95% CI: 1.19–4.82). The female respondents (AOR: 2.16; 95% CI: 1.01–4.61), respondents from the eastern region (AOR: 2.53; 95% CI: 1.18–5.44), west central (AOR: 3; 95% CI: 1.30–6.92), animal health supervisors (AOR: 9.77; 95% CI: 1.98–48.29), and livestock production supervisors (AOR: 2.77; 95% CI: 1.21–6.35) have favorable attitude towards antibiotics and AMR. Conclusions: Our study identified that most animal health workers in Bhutan had poor knowledge on antibiotics usage and AMR. Therefore, regular awareness education on antibiotics and AMR in the form of refresher course/training must be provided to the animal health workers in the country to avoid inappropriate use of antibiotics. [ABSTRACT FROM AUTHOR]

There is an urgent requirement to identify which clinical settings are in most need of COVID-19 tests and the priority role(s) for tests in these settings to accelerate the development of tests fit for purpose in health and social care across the UK. This study sought to identify and prioritize unmet clinical needs for COVID-19 tests across different settings within the UK health and social care sector via an online survey of health and social care professionals and policymakers. Four hundred and forty-seven responses were received between 22nd May and 15th June 2020. Hospitals and care homes were recognized as the settings with the greatest unmet clinical need for COVID-19 diagnostics, despite reporting more access to laboratory molecular testing than other settings. Hospital staff identified a need for diagnostic tests for symptomatic workers and patients. In contrast, care home staff expressed an urgency for screening at the front door to protect high-risk residents and limit transmission. The length of time to test result was considered a widespread problem with current testing across all settings. Rapid tests for staff were regarded as an area of need across general practice and dental settings alongside tests to limit antibiotics use. [ABSTRACT FROM AUTHOR]

Optimizing the gene transformation factors can be considered as the first and foremost step in successful genetic engineering and genome editing studies. However, it is usually difficult to achieve an optimized gene transformation protocol due to the cost and time-consuming as well as the complexity of this process. Therefore, it is necessary to use a novel computational approach such as machine learning models for analyzing gene transformation data. In the current study, three individual machine learning models including Multi-Layer Perceptron (MLP), Adaptive Neuro-Fuzzy Inference System (ANFIS), and Radial Basis Function (RBF) were developed for forecasting Agrobacterium-mediated gene transformation in chrysanthemum based on eleven input variables including Agrobacterium strain, optical density (OD), co-culture period (CCP), and different antibiotics including kanamycin (K), vancomycin (VA), cefotaxime (CF), hygromycin (H), carbenicillin (CA), geneticin (G), ticarcillin (TI), and paromomycin (P). Consequently, best-obtained results were used in the fusion process by bagging method. Results showed that ensemble model with the highest R2 (0.83) had superb performance in comparison with all other individual models (MLP:063, RBF:0.69, and ANFIS: 0.74) in the validation set. Also, ensemble model was linked to Fruit fly optimization algorithm (FOA) for optimizing gene transformation, and the results showed that the maximum gene transformation efficiency (37.54%) can be achieved from EHA105 strain with 0.9 OD600, for 3.8 days CCP, 46.43 mg/l P, 9.54 mg/l K, 18.62 mg/l H, and 4.79 mg/l G as selection antibiotics and 109.74 μg/ml VA, 287.63 μg/ml CF, 334.07 μg/ml CA and 87.36 μg/ml TI as antibiotics in the selection medium. Moreover, sensitivity analysis demonstrated that input variables have a different degree of importance in gene transformation system in the order of Agrobacterium strain > CCP > K > CF > VA > P > OD > CA > H > TI > G. Generally, the developed hybrid model in this study (ensemble model-FOA) can be employed as an accurate and reliable approach in future genetic engineering and genome editing studies. [ABSTRACT FROM AUTHOR]

Self-medication and antibiotic utilization without healthcare oversight may lead to delayed appropriate treatment, transmission of communicable infections, untoward adverse events, and contribute to antimicrobial resistance. Previous data suggest people obtain over-the-counter (OTC) animal antibiotics for their personal use. This study examined the availability of OTC fish antibiotics online and the documented intent for self-medication. The authors conducted a web-based cross-sectional study using Google search engine to identify vendor websites selling fish antibiotics in the United States. Vendor websites were included if product information, consumer reviews, and comments were publicly available. Nine fish antibiotics were chosen due to their possibility of having consequences to human misuse. The cost and availability of fish antibiotics was recorded. The proportion of reviews and comments related to human consumption was calculated. Consumer review traffic based on "likes" and "dislikes" received was compared between human- and non-human consumption-related reviews. Selected fish antibiotics were purchased and evaluated for physical appearance and compared to FDA-approved available equivalents. We found 24 website vendors with online ordering available for OTC fish antibiotics. Cost varied significantly by antibiotic and quantity ranging from USD $8.99 to $119.99. There were 2,288 reviews documented for the 9 selected antibiotics being sold. Among consumer reviews, 2.4% were potentially associated with human consumption. Human consumption-related reviews constituted 30.2% of all "likes" received and 37.5% of all "dislikes" received. Human consumption-related reviews received an average of 9.2 likes compared to 0.52 likes for non-human consumption-related reviews. The 8 fish antibiotics purchased were consistent with FDA-approved equivalents in physical appearance. Although infrequent, antibiotics intended for fish use are being purchased online without a prescription for self-medication to circumvent professional medical care. Reviews related to human consumption generate significant online traffic compared to reviews unrelated to human consumption. [ABSTRACT FROM AUTHOR]

The use of veterinary antibiotics is largely unregulated in low-income countries. Consequently, food producers rarely observe drug withdrawal periods, contributing to drug residues in food products. Drug residues in milk can cause immunogenic reactions in people, and selectively favor antibiotic-resistant bacteria in unpasteurized products. We quantified the prevalence of antibiotic residues in pasteurized and unpasteurized milk, and antibiotic-resistant bacteria from unpasteurized milk sold within Kibera, an informal settlement in Nairobi, Kenya. Ninety-five milk samples (74 pasteurized and 21 unpasteurized) were collected from shops, street vendors or vending machines, and tested for the presence of β-lactam and tetracycline residues using IDEXX SNAP kits. MacConkey agar without- and with antibiotics (ampicillin, 32 μg/ml; tetracycline, 16 μg/ml) was used to enumerate presumptive E. coli based on colony morphology (colony forming units per ml, CFU/ml). β-lactam and tetracycline residues were found in 7.4% and 3.2% of all milk samples, respectively. Residues were more likely to be present in unpasteurized milk samples (5/21, 23.8%) compared to pasteurized samples (5/75, 6.8%); P = 0.039. Two thirds of unpasteurized samples (14/21, 66.7%) contained detectable numbers of presumptive E. coli (mean 3.5 Log10 CFU/ml) and of these, 92.8% (13/14) were positive for ampicillin- (mean 3.2 Log10 CFU/ml) and 50% (7/14) for tetracycline-resistant E. coli (mean 3.1 Log10 CFU/ml). We found no relationship between the presence of antibiotic residues and the presence of antibiotic-resistant E. coli in unpasteurized milk sold within Kibera (P > 0.2). [ABSTRACT FROM AUTHOR]

The objectives of this study were to comprehensively investigate the occurrence, distribution, and mobility of antibiotic resistant genes (ARGs) in the biofilm, water, and sediment from a section of the Weihe-river, in the northern Henan province, China. The abundances of nine ARGs belonging to four commonly used antibiotic classes (tetracyclines, sulfonamides, fluoroquinolones, and multidrug) and class 1 integron-integrase gene (intI1) were quantified. Sulfonamides gene (sulI) accounted for the highest percentage of detected ARGs in most sampling sites, including in water, biofilm, and sediment. Among the resistance genes, IntI1 and sul1 were significantly correlated (r>0.800, p<0.01) with a fecal coliform (FC) detected in the biofilm, and there was also a significantly positive correlation between the abundances of 16SrRNA and intI1 in the biofilms. Compared with the sediment and water samples, the biofilms contained sufficient nutrients to promote bacterial reproduction. Under sufficient total nitrogen and phosphorus concentrations, the horizontal gene transfer due to intI1 plays a key role in the formation and migration of ARGs within biofilms. [ABSTRACT FROM AUTHOR]

Background: Antibiotic resistance is one of the major global health emergencies. One potential source of dissemination of resistant bacteria is mass gatherings, e.g. mass bathing events. We evaluated the physicochemical parameters of water quality and the antibiotic resistance pattern in commensal Escherichia coli from river-water and river-sediment in pre-, during- and post-mass bathing events in river Kshipra, Central India. Method/Design: Water and sediment samples were collected from three selected points during eight mass bathing events during 2014–2016. Water quality parameters (physical, chemical and microbiological) were analyzed using standard methods. In river water and sediment samples, antibiotic susceptibility patterns of isolated E. coli to 17 antibiotics were tested. Results: pH, turbidity and dissolved oxygen were significantly lower and total dissolved solid, free carbon dioxide were higher during mass bathing, whilst TSS, BOD and COD were lowest in pre-bathing and highest in post-bathing period. E.coli with multi drug resistance (MDR) or extended spectrum beta-lactamase (ESBL) production were between 9–44% and 6–24%, respectively in river-water as well as river-sediment. Total coliform count/ml and E. coli count were higher during-and post-bathing in river water than in pre-bathing period. Thus, the percentage of resistance was significantly higher during and post-bathing period (p<.05) than in pre-bathing. Colony forming unit (CFU)/ml in river-sediment was much higher than in river-water. Percentage of resistance was significantly higher in river-water (p<.05) than in river-sediment. Conclusions: Antibiotic resistance in E.coli isolated from the Kshipra River showed significant variation during mass bathing events. Guidelines and regulatory standards are needed to control environmental dissemination of resistant bacteria. [ABSTRACT FROM AUTHOR]

Singapore's Antimicrobial Resistance (AMR) national strategic action plan includes inappropriate use of antimicrobials in food-producing animals as a specific priority. Although the use of antibiotics and other drugs are monitored by regulatory bodies, food fish farmers are allowed to buy and administer antimicrobials without a veterinary prescription. We conducted a qualitative study of Singaporean food fish farmers to understand patterns and determinants of antibiotic use, their knowledge of antibiotic resistance, as well as perceptions of on-farm infection prevention and control measures. During the interview, participants were asked about their farming processes, farm infrastructure, antibiotic use and any disease prevention measures. Thematic analysis of participants' interviews showed that antibiotic for growth promotion and infection prevention was uncommon among local food fish farmers. The following three main themes influenced participants' decisions to use antibiotics in their practice: 1) individual factors, 2) local regulatory factors as well as 3) market-related factors. Individual factors included their personal experience and knowledge both with antibiotics as well as with alternate options. In terms of local regulatory factors, we found that regular oversight was a strong deterrent in antibiotic use. Last, at the market level, the relatively high price of antibiotics in Singapore coupled with stiff competition was a strong disincentive for participants to use antibiotics in their farming practice. These factors were also influential in their relationships with local regulatory bodies as well as their counterparts. Although industries differ significantly across countries, lessons learnt from Singapore's food fish farming demonstrate the importance of an environment where multi-dimensional factors come together to discourage the irrational use of antibiotics in food animal production. In addition, our results allow greater insight into food fish farmers' perspectives on infection control and form a basis from which further research work can be undertaken. [ABSTRACT FROM AUTHOR]

Background: Given their geographical proximity but differences in cultural and religious dietary customs, we hypothesize that children from the three main ethnic populations (Han, Hui, and Tibetan) residing in the Qinghai–Tibetan Plateau region differs in their non-iatrogenic antibiotic loads. Methods: To determine the antibiotic burden of the school children unrelated to medical treatment, we quantified the antibiotic residues in morning urine samples from 92 Han, 72 Tibetan, and 85 Muslim Hui primary school children aged 8 to 12 years using high-performance liquid chromatography-tandem mass spectrometry, and performed correlation analysis between these data and concurrent dietary nutrition assessments. Results: Sixteen of the 18 targeted antibiotics (4 macrolides, 3 β-lactams, 2 tetracyclines, 4 quinolones, 3 sulfonamides, and 2 aminoanols) were identified in the urine samples with an overall detection frequency of 58.63%. The detection frequency of the six antibiotic classes ranged from 1.61% to 32.53% with ofloxacin showing the single highest frequency (18.47%). Paired comparison analysis revealed significant differences in antibiotic distribution frequency among groups, with Tibetans having higher enrofloxacin (P = 0.015) and oxytetracycline (P = 0.021) than Han children. Norfloxacin (a human/veterinary antibiotic) was significantly higher in the Hui children than in the Han children (P = 0.024). Dietary nutrient intake assessments were comparable among participants, showing adequate levels of essential vitamins and minerals across all three ethnic groups. However, significant differences in specific foods were observed among groups, notably in lower fat consumption in the Hui group. Conclusions: The introduction and accumulation of antibiotic residues in school children through non-iatrogenic routes (food or environmental sources) poses a serious potential health risk and merits closer scrutiny to determine the sources. While the exact sources of misused or overused antibiotics remains unclear, further study can potentially correlate ethnicity-specific dietary practices with the sources of contamination. [ABSTRACT FROM AUTHOR]

There are growing demands to ensure animal health and, from a broader perspective, animal welfare, especially for farmed animals. In addition to the newly developed welfare assessment protocols, which provide a harmonised method to measure animal health during farm visits, the question has been raised whether data from existing data collections can be used for an assessment without a prior farm visit. Here, we explore the possibilities of developing animal health scores for fattening pig herds using a) official meat inspection results, b) data on antibiotic usage and c) data from the QS (QS Qualität und Sicherheit GmbH) Salmonella monitoring programme in Germany. The objective is to aggregate and combine these register-like data into animal health scores that allow the comparison and benchmark of participating pig farms according to their health status. As the data combined in the scores have different units of measure and are collected in different abattoirs with possibly varying recording practices, we chose a relative scoring approach using z-transformations of different entrance variables. The final results are aggregated scores in which indicators are combined and weighted based on expert opinion according to their biological significance for animal health. Six scores have been developed to describe different focus areas, such as "Respiratory Health", "External Injuries/ Alterations", "Animal Management", "Antibiotic Usage", "Salmonella Status" and "Mortality". These "focus" area scores are finally combined into an "Overall Score". To test the scoring method, existing routine data from 1,747 pig farm units in Germany are used; these farm units are members of the QS Qualität und Sicherheit GmbH (QS) quality system. In addition, the scores are directly validated for 38 farm units. For these farm units, the farmers and their veterinarians provided their perceptions concerning the actual health status and existing health problems. This process allowed a comparison of the scoring results with actual health information using kappa coefficients as a measure of similarity. The score testing of the focus area scores using real information resulted in normalised data. The results of the validation showed satisfactory agreement between the calculated scores for the project farm units and the actual health information provided by the related farmers and veterinarians. In conclusion, the developed scoring method could become a viable benchmark and risk assessment instrument for animal health on a larger scale under the conditions of the German system. [ABSTRACT FROM AUTHOR]

Background: Currently, various tools exist to evaluate knowledge and awareness of antibiotic use and antimicrobial resistance (AMR) and are applied by various organizations. Previous systematic reviews have focused mainly on study findings such as levels of knowledge and AMR awareness. However, the survey procedures and data instruments used ought to be scrutinized as well, since they are important contributors to credible results. This review aims to assess the study methods and procedures of existing population-based surveys and explore key components which determine the general population's levels of knowledge and awareness of antibiotic use and AMR. Methods: We searched existing literature for population -based surveys which sought knowledge and awareness of antibiotic use or AMR in the general population. Databases searched included Ovid, MEDLINE and EMBASE, PsycINFO and Scopus, domestic journals and gray literature sources. Population-based cross-sectional studies published in English or Thai from January 2000 to December 2018 were included in the review. Quality assessment was conducted using the 'Appraisal Tool for Cross-Sectional Studies' (AXIS). Results: All 22 studies included in the analysis had clear objectives focusing on assessing people's levels of knowledge, awareness, attitudes and behavior relating to antibiotic use and awareness of AMR. These studies had employed appropriate methodologies for population-based cross-sectional surveys relative to research questions. More than half of studies (14 out of 22) had scientifically soundly designed methodologies which captured the representativeness of the population; whereas the remaining studies had unclear sample size estimations, inappropriate sample frames and selection biases. Half of the studies had tested the validity and reliability of the questionnaire. The common questions used by these surveys were categorized into four themes: behavior related to antibiotic use, knowledge and awareness of antibiotic use, knowledge and awareness of AMR and others such as receiving information about antibiotic use and AMR or cross-cutting issues like self-medication. Conclusion: This review identified four key features of good practices in antibiotic use and awareness surveys: a) clear survey objective; b) scientifically sound sampling techniques ensuring representativeness; c) strategies for recruitment of samples and survey administration methods; and d) credible measurement to prevent non-sampling biases. During questionnaire design, the health systems context in terms of access to health services and antibiotics should be taken into account. In conclusion, to maximize the use of surveys, the application of findings in surveys and associated factors related to antibiotic use and AMR should primarily generate public health interventions and target specific groups to make progress in solving AMR problems. [ABSTRACT FROM AUTHOR]

Growth in open-source hardware designs combined with the low-cost of high performance optoelectronic and robotics components has supported a resurgence of in-house custom lab equipment development. We describe a low cost (below $700), open-source, fully customizable high-throughput imaging system for analytical microbiology applications. The system comprises a Raspberry Pi camera mounted on an aluminium extrusion frame with 3D-printed joints controlled by an Arduino microcontroller running open-source Repetier Host Firmware. The camera position is controlled by simple G-code scripts supplied from a Raspberry Pi singleboard computer and allow customized time-lapse imaging of microdevices over a large imaging area. Open-source OctoPrint software allows remote access and control. This simple yet effective design allows high-throughput microbiology testing in multiple formats including formats for bacterial motility, colony growth, microtitre plates and microfluidic devices termed 'lab-on-a-comb' to screen the effects of different culture media components and antibiotics on bacterial growth. The open-source robot design allows customization of the size of the imaging area; the current design has an imaging area of ~420 × 300mm, which allows 29 'lab-on-a-comb' devices to be imaged which is equivalent 3480 individual 1μl samples. The system can also be modified for fluorescence detection using LED and emission filters embedded on the PiCam for more sensitive detection of bacterial growth using fluorescent dyes. [ABSTRACT FROM AUTHOR]

In Denmark, American mink (Neovison vison) have been bred for their fur since the mid-1920s. Mink escaping from farms may supply the feral population. Often, it is of biological and management interest to separate the population of feral mink (i.e. mink caught in the wild) in two groups: 1) mink born on farms i.e., escapees, and 2) mink born in the wild. In this study, two methods were used for separating feral mink into the two groups: a) Comparison of body length of farmed mink and feral mink, and b) Presence of a biomarker (tetracycline: an oral antibiotic used on mink farms). A total of 367 wild caught mink (from the mainland of Denmark and the island of Bornholm), and 147 mink from farms, collected during the period 2014–2018, were used for the analysis of body length. For the testing of tetracycline (TC) as a biomarker, 78 mink from farms where there was knowledge about TC treatment (with or without) were examined for fluorescent markings in the canine teeth. Results from both univariate analyses and Gaussian mixture model analysis demonstrated clear divisions between the mean body length (mean ± S.E., range) of farmed males (52.1 cm ± 0.4, 48–68) and farmed females (mean 44.0 ± 0.2, 40–50), and between farmed mink and wild caught mink. Mixture analysis identified two groups within each sex of the wild caught mink, one assigned to farmed mink (born in captivity) and another group of smaller mink suspected of being born in the wild. On Bornholm, the mean (±SD, range) length of males born in the wild was 43.7cm (± 0.3, 36–57) and for females 37.5cm (± 0.3, 32–45). The mean length (±SD, range) of males born in the wild in the mainland of Denmark was 42.5cm (± 2.3, 36–46) and for females 36.1cm (± 1.0, 34–37). Among the feral mink from mainland Denmark, 28.4% of males and 21.6% of females were identified as escapees, while 0% of the males and 1% of the females were identified as escapees among the wild caught mink on Bornholm. Eight percent of mink from farms using tetracycline were false negatives, while no false positives were found among mink from farms not using TC. TC fluorescence was found in five of 217 mink caught in the wild equivalent to 22% escapees in mainland Denmark. No TC markings were found in mink caught in the wild on Bornholm. In conclusion, both methods a) the body length of mink, and b) fluorescent biomarkers in canine teeth are considered as useful tools to identifing mink that have escaped from farms. [ABSTRACT FROM AUTHOR]

Inappropriate antibiotic prescribing is a cause of antimicrobial resistance. Acute Respiratory Tract Infections (ARTI) are common diseases for those antibiotics are most likely prescribed in outpatient setting. To clarify factors associated with antibiotic prescribing for non-bacterial acute respiratory tract infections (NB-ARTI) and identify targets for reducing inappropriate prescribing for NB-ARTI in Japan. We conducted a retrospective, observational study using longitudinal claims data between April 2012 and June 2017. We assessed the rate of and factors associated with inappropriate antibiotic prescribing in outpatient settings for all NB-ARTI consultations included in the database. The mean monthly antibiotic prescribing rate per 100 NB-ARTI consultations during the study period was 31.65. The monthly antibiotic prescribing rate per 100 NB-ARTI consultations decreased by 19.2% from April 2012 to June 2017. Adolescents (13–18 years) and adults of working age (19–29 and 30–39 years) were more likely prescribed antibiotics compared with elderly patients ≥ 60 years (aOR: 1.493 [95%CI: 1.482–1.503], 1.585 [95%CI: 1.575–1.595], and 1.507 [95%CI: 1.498–1.516], respectively). Outpatient clinics registered as internal medicine or ear, nose, and throat specialty were more likely to prescribe antibiotics than those of paediatric specialty or other specialties. Among health facility type, clinics without beds (aOR 2.123 [95%CI: 2.113–2.133]) and clinics with beds (aOR: 1.752 [95%CI: 1.7371–1.767]) prescribed significantly more antibiotics for NB-ARTI than outpatient departments inside general hospitals. Inappropriate antibiotic prescribing for NB-ARTI is common in Japan. Although the antibiotic prescribing rate has decreased, further interventions are required to promote antimicrobial stewardship (ASP). Education and awareness for adults and promotion of ASP among physicians in clinics without beds are key drivers to reduce inappropriate antibiotic prescribing in Japan. [ABSTRACT FROM AUTHOR]

In the present study, antibiotic residues were detected in milk samples collected from the dairy herds located in Karnataka, India, by microbiological assay. Subsequently, the detected antibiotics were identified as azithromycin and tetracycline, by high-performance liquid chromatography, further both the antibiotics detected in the cow milk samples were found to be at high concentration (9708.7 and 5460 μg kg-1, respectively). We then investigated the effects of temperature and pH on the stabilities of azithromycin and tetracycline to determine the degradation rate constant k using first-order kinetic equation. Results indicated that significant reduction in stability and antibacterial activity of azithromycin solution when subjected to 70 and 100°C for 24 h. While stability of tetracycline was significantly reduced when subjected to 70 and 100°C for 24 h. However no significant reduction in antibacterial activity of tetracycline was observed at respective temperatures when compared with that of control. In addition, the stabilities of azithromycin and tetracycline were found to be decreased in acidic pH 4–5. The results of the present study revealed the high risk of contamination of milk sample with veterinary antibiotics and also demonstrated the effect of temperature and pH on stability of antibiotics. Therefore the study suggest that the qualitative and quantitative screening of milk for the presence of antibiotics need to be strictly performed to ensure safe drinking milk for consumers. [ABSTRACT FROM AUTHOR]

One of the biggest challenges of health care systems worldwide is the increasing number of pathogenic bacteria resistant to a growing number of antibiotics. In this respect, class 1 integrons which are part of mobile genetic elements can confer several phenotypes including resistance to a broad range of antibiotic classes, heavy metals and biocides. They are linked to common resistance genes and have penetrated pathogenic and commensal bacteria likewise. Therefore its relative prevalence can be a proxy for antimicrobial resistance and anthropogenic pollution. Household environments are areas with a high influx of bacteria from humans, animals and foods, and biocides and detergents are frequently used. In this study we aimed to investigate the relative prevalence of class 1 integrons in household environments, in relation to the number of antibiotic and benzalkonium chloride resistant phenotypes of a sample point, for the validation of the relative prevalence of class 1 integrons as a screening tool for multi-resistance. Kitchen sink and bathroom sink U-bends, dishwasher, washing machines and toothbrushes of 28 households were probed. Copies /mL of class 1 integron integrase gene and 16SrDNA gene were determined by qPCR and bacteria of the respective sample were isolated on ampicillin selective agar plates, followed by the determination of the species and phenotypic resistance profiles. The relative prevalence of class 1 integrons in relation to 16SrDNA was calculated and correlated to phenotypic resistance. Our findings show a high relative prevalence of class 1 integrons in water reticulation systems of household environments and in particular shower U-bends. Furthermore, prevalence of class 1 integrons correlates strongly (rs = 0.95) with total phenotypic resistance at a sample point and suggest that a standardized assay determining the relative prevalence of class 1 integrons could be used as a useful screening tool in the assessment of multi-resistance in environmental samples. [ABSTRACT FROM AUTHOR]

Feline immunodeficiency virus (FIV) is a naturally occurring Lentivirus causing acquired immunodeficiency syndrome in felines. It is considered a useful non-primate model to study HIV infection, and to test anti-HIV vaccine. Similarly to HIV, FIV enters cells via a mechanism involving a surface glycoprotein named gp36. C8 is a short synthetic peptide corresponding to the residues 770777 of gp36 membrane proximal external region (MPER). It elicits antiviral activity by inhibiting the fusion of the FIV and host cell membrane. C8 is endowed with evident membrane binding property, inducing alteration of the phospholipid bilayer and membrane fusion. The presence and the position of tryptophan residues in C8 are important for antiviral activity: the C8 derivative C6a, obtained by truncating the N-terminal 770771 residues, exhibits conserved antiviral activity, while the C8 derivative C6b, derived from the truncation of the C-terminal 776777 is nearly inactive. To elucidate the structural factors that induce the different activity profiles of C6a and C6b, in spite of their similarity, we investigated the structural behaviour of the two peptides in membrane mimicking environments. Conformational data on the short peptides C6a and C6b, matched to those of their parent peptide C8, allow describing a pharmacophore model of antiviral fusion inhibitors. This includes the essential structural motifs to design new simplified molecules overcoming the pharmacokinetic and high cost limitations affecting the antiviral entry inhibitors that currently are in therapy. [ABSTRACT FROM AUTHOR]

Two Pseudomonas strains, identified as closely related to Pseudomonas tolaasii, were isolated from milk of a farm with frequent false-positive Delvotest results for screening putative antibiotic residues in raw milk executed as part of the regulatory quality programme. Growth at 5 to 7°C of these isolates in milk resulted in high lipolysis and the production of bacterial inhibitors. The two main bacterial inhibitors have a molecular weight of 1168.7 and 1140.7 Da respectively, are heat-tolerant and inhibit Geobacillus stearothermophilus var. calidolactis, the test strain of most of the commercially available microbiological inhibitor tests for screening of antibiotic residues in milk. Furthermore, these bacterial inhibitors show antimicrobial activity against Staphylococcus aureus, Bacillus cereus and B. subtilis and also interfere negatively with yoghurt production. Following their isolation and purification with RP-HPLC, the inhibitors were identified by NMR analysis as cyclic lipodepsipeptides of the viscosin group. Our findings bring to light a new challenge for quality control in the dairy industry. By prolonging the refrigerated storage of raw milk, the keeping quality of milk is influenced by growth and metabolic activities of psychrotrophic bacteria such as pseudomonads. Besides an increased risk of possible spoilage of long shelf-life milk, the production at low temperature of natural bacterial inhibitors may also result in false-positive results for antibiotic residue screening tests based on microbial inhibitor assays thus leading to undue production loss. [ABSTRACT FROM AUTHOR]

Owing to their potential for systematic analysis, complex networks have been widely used in proteomics. Representing a protein structure as a topology network provides novel insight into understanding protein folding mechanisms, stability and function. Here, we develop a new feature to reveal correlations between residues using a protein structure network. In an original attempt to quantify the effects of several key residues on catalytic residues, a power function was used to model interactions between residues. The results indicate that focusing on a few residues is a feasible approach to identifying catalytic residues. The spatial environment surrounding a catalytic residue was analyzed in a layered manner. We present evidence that correlation between residues is related to their distance apart: most environmental parameters of the outer layer make a smaller contribution to prediction; and (ii) catalytic residues tend to be located near key positions in enzyme folds. Feature analysis revealed satisfactory performance for our features, which were combined with several conventional features in a prediction model for catalytic residues using a comprehensive data set from the Catalytic Site Atlas. Values of 88.6% for sensitivity and 88.4% for specificity were obtained by 10-fold cross-validation. These results suggest that these features reveal the mutual dependence of residues and are promising for further study of structure-function relationship. [ABSTRACT FROM AUTHOR]

LRR-kinases constitute the largest subfamily of receptor-like kinases in plants and regulate a wide variety of processes related to development and defense. Through a reiterative process of sequence analysis and re-annotation, we identified 309 LRR-kinase genes in the rice genome (Nipponbare). Among them, 127 genes in the Rice Annotation Project Database and 85 in Refseq of NCBI were amended (in addition, 62 LRR-kinase genes were not annotated in Refseq). The complete set of LRR-kinases was characterized. These LRR-kinases were classified into five groups according to phylogenetic analysis, and the genes in groups 1, 2, 3 and 4 usually have fewer introns than those in group 5. The introns in the LRR domain, which are highly conserved in regards to their positions and configurations, split the first Leu or other amino residues at this position of the 'xxLxLxx' motif with phase 2 and usually separate one or more LRR repeats exactly. Tandemly repeated LRR motifs have evolved from exon duplication, mutation and exon shuffling. The extensive distribution and diversity of the LRR-kinase genes have been mainly generated by tandem duplication and mutation after whole genome duplication. Positive selection has made a limited contribution to the sequence diversity after duplication, but positively selected sites located in the LRR domain are thought to involve in the protein-protein interaction. [ABSTRACT FROM AUTHOR]

Background: Histone demethylase, JMJD2A, specifically recognizes and binds to methylated lysine residues at histone H3 and H4 tails (especially trimethylated H3K4 (H3K4me3), trimethylated H3K9 (H3K9me3) and di,trimethylated H4K20 (H4K20me2, H4K20me3)) via its tandem tudor domains. Crystal structures of JMJD2A-tudor binding to H3K4me3 and H4K20me3 peptides are available whereas the others are not. Complete picture of the recognition of the four histone peptides by the tandem tudor domains yet remains to be clarified. Methodology/Principal Findings: We report a detailed molecular dynamics simulation and binding energy analysis of the recognition of JMJD2A-tudor with four different histone tails. 25 ns fully unrestrained molecular dynamics simulations are carried out for each of the bound and free structures. We investigate the important hydrogen bonds and electrostatic interactions between the tudor domains and the peptide molecules and identify the critical residues that stabilize the complexes. Our binding free energy calculations show that H4K20me2 and H3K9me3 peptides have the highest and lowest affinity to JMJD2A-tudor, respectively. We also show that H4K20me2 peptide adopts the same binding mode with H4K20me3 peptide, and H3K9me3 peptide adopts the same binding mode with H3K4me3 peptide. Decomposition of the enthalpic and the entropic contributions to the binding free energies indicate that the recognition of the histone peptides is mainly driven by favourable van der Waals interactions. Residue decomposition of the binding free energies with backbone and side chain contributions as well as their energetic constituents identify the hotspots in the binding interface of the structures. Conclusion: Energetic investigations of the four complexes suggest that many of the residues involved in the interactions are common. However, we found two receptor residues that were related to selective binding of the H3 and H4 ligands. Modifications or mutations on one of these residues can selectively alter the recognition of the H3 tails or the H4 tails. [ABSTRACT FROM AUTHOR]

The article offers information regarding a study which aims to provide NMR structural and dynamic properties of an insoluble SH3 mutant with a naturally-occurring insertion of Val22 at the tip of the diverging turn. It is mentioned that according to the results, regardless of whether the residue is Val, Ala, Asp or Arg, the insertion will render the first hNck2 SH3 domain to be insoluble in buffers. It is stated that comparison of the chemical shift deviations reveals that while in V22-SH3 the second helical region is similarly populated as in the wild-type SH3 at pH 2.0, the first helical region is largely unformed.

Background: The number of available structures of large multi-protein assemblies is quite small. Such structures provide phenomenal insights on the organization, mechanism of formation and functional properties of the assembly. Hence detailed analysis of such structures is highly rewarding. However, the common problem in such analyses is the low resolution of these structures. In the recent times a number of attempts that combine low resolution cryo-EM data with higher resolution structures determined using X-ray analysis or NMR or generated using comparative modeling have been reported. Even in such attempts the best result one arrives at is the very course idea about the assembly structure in terms of trace of the Ca atoms which are modeled with modest accuracy. Methodology/Principal Findings: In this paper first we present an objective approach to identify potentially solvent exposed and buried residues solely from the position of Ca atoms and amino acid sequence using residue type-dependent thresholds for accessible surface areas of Ca. We extend the method further to recognize potential protein-protein interface residues. Conclusion/ Significance: Our approach to identify buried and exposed residues solely from the positions of Ca atoms resulted in an accuracy of 84%, sensitivity of 83-89% and specificity of 67-94% while recognition of interfacial residues corresponded to an accuracy of 94%, sensitivity of 70-96% and specificity of 58-94%. Interestingly, detailed analysis of cases of mismatch between recognition of interface residues from Ca positions and all-atom models suggested that, recognition of interfacial residues using Ca atoms only correspond better with intuitive notion of what is an interfacial residue. Our method should be useful in the objective analysis of structures of protein assemblies when positions of only Ca positions are available as, for example, in the cases of integration of cryo-EM data and high resolution structures of the components of the assembly. [ABSTRACT FROM AUTHOR]