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Machine-learning prediction of resistance to sub-inhibitory antimicrobial concentrations from Escherichia coli genomes [article]

Sam Benkwitz-Bedford, Martin Palm, Talip Yasir Demirtas, Ville Mustonen, Anne Farewell, Jonas Warringer, Danesh Moradigaravand, Leopold Parts
2021 bioRxiv   pre-print
We used machine-learning to predict the population doubling time and yield of >1,400 genetically diverse E. coli expanding under exposure to three sub-inhibitory concentrations of six classes of antimicrobials  ...  Besides therapeutic concentrations of antimicrobials in healthcare settings, the presence of sub-inhibitory antimicrobial residues in the environment and in the clinics selects for antimicrobial resistance  ...  C) Prediction of the resistant 75 phenotypes using labels inferred from the predicted bimodal distributions for three 76 antimicrobials.  ... 
doi:10.1101/2021.03.26.437296 fatcat:bd74x26mz5cl7kyyz5l4exvnni

Effect of Antimicrobial Treatment on the Dynamics of Ceftiofur Resistance in Enterobacteriaceae from Adult California Dairy Cows

David B Sheedy, Emmanuel Okello, Deniece R Williams, Katie Precht, Elisa Cella, Terry W Lehenbauer, Sharif S Aly
2021 Microorganisms  
Dairy farm use of antimicrobial drugs (AMD) is a risk for the selection of antimicrobial resistance (AMR); however, these resistance dynamics are not fully understood.  ...  Samples from AMD treated cows had peak counts of resistant Enterobacteriaceae during AMD treatment and returned to baseline counts by 3-4 days post-treatment at 8 µg/mL.  ...  The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.  ... 
doi:10.3390/microorganisms9040828 pmid:33919743 pmcid:PMC8070714 fatcat:oxrvqqptkfcbtgxtzgxmgvw3fa

Direct Antimicrobial Resistance Prediction from MALDI-TOF mass spectra profile in clinical isolates through Machine Learning [article]

Caroline Weis, Aline Cuénod, Bastian Rieck, Felipe Llinares-López, Olivier Dubuis, Susanne Graf, Claudia Lang, Michael Oberle, Kirstine K. Soegaard, Michael Osthoff, Karsten Borgwardt, Adrian Egli
2020 bioRxiv   pre-print
We present a revolutionary approach to predict resistance with unmatched speed within 24h, using calibrated logistic regression and LightGBM-classifiers trained on species-specific MALDI-TOF mass spectrometry  ...  Early administration of effective antimicrobial treatments improves the outcome of infections. Culture-based antimicrobial resistance testing allows for tailored treatments, but takes up to 96h.  ...  based antimicrobial resistance prediction.  ... 
doi:10.1101/2020.07.30.228411 fatcat:p7pzogqegvdsbdzbtrpzteagbi

Changes in resistance among coliform bacteraemia associated with a primary care antimicrobial stewardship intervention: A population-based interrupted time series study

Virginia Hernandez-Santiago, Peter G. Davey, Dilip Nathwani, Charis A. Marwick, Bruce Guthrie, Nicola Low
2019 PLoS Medicine  
Primary care antimicrobial stewardship interventions can improve antimicrobial prescribing, but there is less evidence that they reduce rates of resistant infection.  ...  This study examined changes in broad-spectrum antimicrobial prescribing in the community and resistance in people admitted to hospital with community-associated coliform bacteraemia associated with a primary  ...  Because of the shape of the resistance time series (Fig 1, right-hand panels), we conducted two types of post hoc sensitivity analysis for resistance to each of the three antimicrobials.  ... 
doi:10.1371/journal.pmed.1002825 pmid:31173597 pmcid:PMC6555503 fatcat:qqe2t5t4tfgxnkwhqeomy6x5ey

A stepwise introduction of a successful antimicrobial stewardship program. Experience from a tertiary care university hospital in Western, Saudi Arabia

Maha Alawi, Bayan Darwesh
2016 Saudi Medical Journal  
A multidisciplinary team supervised antibiotic use and regulated pharmacy dispensations of a list of restricted antimicrobials (RAs).  ...  Methods: Prospective data were collected from an ASP that was gradually introduced between April 2012 and December 2013 in 6 hospital departments, over successive periods of 3 months each.  ...  Statistical test used One-way analysis of variance and post hoc multiple comparisons analysis (Tukey Kramer test) Figure 4 - 4 Hospital consumption of broad-spectrum antimicrobials per department as  ... 
doi:10.15537/smj.2016.12.15739 pmid:27874151 pmcid:PMC5303774 fatcat:vq2n7pkzqrcelnzsdgnyjgx5ui

Monitoring and surveillance of antimicrobial resistance in microorganisms associated with aquatic animals

P Smith, V Alday-Sanz, J Matysczak, G Moulin, C R Lavilla-Pitogo, D Prater
2013 Rev Sci Tech Off Int Epizoot  
It is further recommended that, for the purpose of evaluating antimicrobial resistance trends, such as emerging resistance, the data generated by these protocols should be interpreted by the application  ...  Internationally harmonised standard test protocols and interpretive criteria have, to a large extent, been developed to monitor antimicrobial resistance in bacterial species capable of infecting humans  ...  resistance trends in relevant microorganisms iii) explore the potential relationship between antimicrobial resistance in aquatic animal microorganisms and the use of antimicrobial agents iv) detect the  ... 
pmid:24547661 fatcat:72hrapfbkfd5pheec2bloh7z2y

Predictive utility of swab screening for vancomycin-resistant Enterococcus in selection of empiric antibiotics for Enterococcus sterile-site infections: a retrospective cohort study

Ian Brasg, Marion Elligsen, Derek MacFadden, Nick Daneman
2017 CMAJ Open  
of VRE of 83% among patients with a prior positive swab result. 25 Post-test probability of vancomycin resistance Interpretation We explored the utility of swab screening for VRE in predicting vancomycin  ...  We calculated confidence intervals (CIs) using the Clopper-Pearson exact method, with the efficient score method used for negative predictive value in the "immediate" group (described below) and the log  ... 
doi:10.9778/cmajo.20170034 pmid:28814382 pmcid:PMC5621943 fatcat:bs6ytugeurhgxf4xrtumr3eemm

Impact of azithromycin on the clinical and antimicrobial effectiveness of tobramycin in the treatment of cystic fibrosis

Dave P. Nichols, Carrie L. Happoldt, Preston E. Bratcher, Silvia M. Caceres, James F. Chmiel, Kenneth C. Malcolm, Milene T. Saavedra, Lisa Saiman, Jennifer L. Taylor-Cousar, Jerry A. Nick
2017 Journal of Cystic Fibrosis  
Background-Concomitant use of oral azithromycin and inhaled tobramycin occurs in approximately half of US cystic fibrosis (CF) patients. Recent data suggest that this combination may be antagonistic.  ...  Methods-Test the hypothesis that azithromycin reduces the clinical benefits of tobramycin by analyses of clinical trial data, in vitro modeling of P. aeruginosa antibiotic killing, and regulation of the  ...  Our bacterial culture methods are distinct from those used in prior testing and it is not known which in vitro model may best predict clinical response.  ... 
doi:10.1016/j.jcf.2016.12.003 pmid:28025037 pmcid:PMC5492972 fatcat:v6zjbosgnfb7bldi6oukoas57a

In vitro evaluation of the anti-bacterial effect of two preparations of platelet rich plasma compared with cefazolin and whole blood

Jessica Intravia
2014 Muscles Ligaments and Tendons Journal  
The company had no influence on study design, data collection or interpretation of the results or the final manuscript.  ...  Given the small group sizes (n=4), the lowest possible p value that could be reached with post hoc non-parametric testing was 0.0625 therefore the threshold for significance with post hoc testing was 0.1  ...  Post hoc comparisons were performed with the Wilcoxon rank-sum test and sign-rank test.  ... 
doi:10.11138/mltj/2014.4.1.079 fatcat:i7cwoxvcjjfttat7j2upnuyv7m

Technology to support integrated Antimicrobial Stewardship Programs: a user centered and stakeholder driven development approach

Nienke Beerlage-de Jong, Lisette Van Gemert-Pijnen, Jobke Wentzel, Ron Hendrix, Liseth Siemons
2017 Infectious Disease Reports  
We highlight how to combat the dangerous rise of antimicrobial resistance in the future.  ...  The rise of antimicrobial resistance (AMR) is a severe global health problem. Tackling this problem requires the prudent prescribing of antimicrobials.  ...  Nor is surveillance currently used to predict antimicrobial resistance problems and upcoming outbreaks of diseases due to the lack of advanced analytics.  ... 
doi:10.4081/idr.2017.6829 pmid:28458796 pmcid:PMC5391533 fatcat:mtazwkc2ijg2dpigr5oj4biani

Clinical Prediction Tool To Identify Patients with Pseudomonas aeruginosa Respiratory Tract Infections at Greatest Risk for Multidrug Resistance

T. P. Lodise, C. D. Miller, J. Graves, J. P. Furuno, J. C. McGregor, B. Lomaestro, E. Graffunder, L.-A. McNutt
2006 Antimicrobial Agents and Chemotherapy  
Despite the increasing prevalence of multiple-drug-resistant (MDR) Pseudomonas aeruginosa, the factors predictive of MDR have not been extensively explored.  ...  Identifying these risk factors enabled us to develop a prediction tool to assess the risk of resistance and thus guide empirical antibiotic therapy.  ...  No other potential conflicts of interest exist for the rest of us.  ... 
doi:10.1128/aac.00851-06 pmid:17158943 pmcid:PMC1797724 fatcat:wyhxxqwhx5dxlo4hp6pdyj5yre

Moderate positive predictive value of a multiplex real-time PCR on whole blood for pathogen detection in critically ill patients with sepsis

Kirsten van de Groep, on behalf of the MARS consortium, Martine P. Bos, Meri R. J. Varkila, Paul H. M. Savelkoul, David S. Y. Ong, Lennie P. G. Derde, Nicole P. Juffermans, Tom van der Poll, Marc J. M. Bonten, Olaf L. Cremer
2019 European Journal of Clinical Microbiology and Infectious Diseases  
This study aimed at determining the positive predictive value (PPV) of BSI-PCR in critically ill patients with sepsis.  ...  BSI-PCR may complement conventional cultures and expedite the microbiological diagnosis of sepsis in ICU patients, but improvements in positive predictive value of the test are warranted before its implementation  ...  Members Open Access This article is distributed under the terms of the Creative Comm ons Attribution 4.0 International License (http:// creativecommons.org/licenses/by/4.0/), which permits unrestricted use  ... 
doi:10.1007/s10096-019-03616-w pmid:31243596 pmcid:PMC6778535 fatcat:y45iv2fzu5c5djbeo2fdregt2m

In vitro evaluation of the anti-bacterial effect of two preparations of platelet rich plasma compared with cefazolin and whole blood

J. Intravia, D.A. Allen, T.JS. Durant, M.B.R. McCarthy, R. Russell, K. Beitzel, M.P. Cote, F. Dias, A.D. Mazzocca
2019 Muscles Ligaments and Tendons Journal  
Methods.  ...  whole blood and Cefazolin were added to experimental reaction tubes, each containing a single bacterial inoculum of Staphylococcus aureus (S. aureus), Staphylococcus epidermidis (S. epi), methicillin-resistant  ...  The company had no influence on study design, data collection or interpretation of the results or the final manuscript.  ... 
doi:10.32098/mltj.01.2014.14 fatcat:lhn3btv3enb7nkwgsbz5egrs6y

In vitro evaluation of the anti-bacterial effect of two preparations of platelet rich plasma compared with cefazolin and whole blood

Jessica Intravia, Donald A Allen, Thomas Js Durant, Mary Beth R McCarthy, Ryan Russell, Knut Beitzel, Mark P Cote, Feliciano Dias, Augustus D Mazzocca
2014 Muscles Ligaments and Tendons Journal  
whole blood and Cefazolin were added to experimental reaction tubes, each containing a single bacterial inoculum of Staphylococcus aureus (S. aureus), Staphylococcus epidermidis (S. epi), methicillin-resistant  ...  The company had no influence on study design, data collection or interpretation of the results or the final manuscript.  ...  Given the small group sizes (n=4), the lowest possible p value that could be reached with post hoc non-parametric testing was 0.0625 therefore the threshold for significance with post hoc testing was 0.1  ... 
pmid:24932452 pmcid:PMC4049655 fatcat:ozdart4w5bb4lebrrzwzb3af74

Prediction of Staphylococcus aureus Antimicrobial Resistance by Whole-Genome Sequencing

N. C. Gordon, J. R. Price, K. Cole, R. Everitt, M. Morgan, J. Finney, A. M. Kearns, B. Pichon, B. Young, D. J. Wilson, M. J. Llewelyn, J. Paul (+4 others)
2014 Journal of Clinical Microbiology  
In this study, we aimed to develop a genotypic prediction method for antimicrobial susceptibilities.  ...  WGS is a promising alternative to culture methods for resistance prediction in S. aureus and ultimately other major bacterial pathogens.  ...  (3) and Stoesser et al. (4) reported on resistance prediction using a simple BLAST method.  ... 
doi:10.1128/jcm.03117-13 pmid:24501024 pmcid:PMC3993491 fatcat:vv24qtzqdfdljdqpxypo2jf4d4
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