Application of artificial intelligence to the in silico assessment of antimicrobial resistance and risks to human and animal health presented by priority enteric bacterial pathogens.

Application of artificial intelligence to the in silico assessment of antimicrobial resistance and risks to human and animal health presented by priority enteric bacterial pathogens. Can Commun Dis Rep. 2020 Jun 04;46(6):180-185 Authors: Steinkey R, Moat J, Gannon V, Zovoilis A, Laing C Abstract Each year, approximately one in eight Canadians are affected by foodborne illness, either through outbreaks or sporadic illness, with animals being the major reservoir for the pathogens. Whole genome sequence analyses are now routinely implemented by public and animal health laboratories to define epidemiological disease clusters and to identify potential sources of infection. Similarly, a number of bioinformatics tools can be used to identify virulence and antimicrobial resistance (AMR) determinants in the genomes of pathogenic strains. Many important clinical and phenotypic characteristics of these pathogens can now be predicted using machine learning algorithms applied to whole genome sequence data. In this overview, we compare the ability of support vector machines, gradient-boosted decision trees and artificial neural networks to predict the levels of AMR within Salmonella enterica and extended-spectrum β-lactamase (ESBL) producing Escherichia coli. We show that minimum inhibitory concentrations (MIC) for each of 13 antimicrobials for S. enterica strains can be accurately determined, and that ESBL-producing E. coli strains can be accurately classified a...
Source: Can Commun Dis Rep - Category: Infectious Diseases Authors: Tags: Can Commun Dis Rep Source Type: research

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Abstract Background: The 21st century has seen a wide range of diseases resulting from zoonotic infections, of which bacterial infections have led to outbreaks of food-borne diseases. Aim: The study looks at bacterial pathogen carriage by farm rats and their antimicrobial susceptibility, with the view of providing insights for antimicrobial surveillance. Method: Farm rats of Rattus rattus species where randomly collected alive from farms in Al-Ahsa using food baits. They were anaesthetize with urethane within 4 h of collection and were unconscious for the collection of samples. Basic bacteriologic...
Source: Environmental Health Insights - Category: Environmental Health Authors: Tags: Environ Health Insights Source Type: research
Dhiviya Prabaa Muthuirulandi Sethuvel, Naveen Kumar Devanga Ragupathi, Yamuna Devi Bakthavatchalam, Saranya Vijayakumar, Rosemol Varghese, Chaitra Shankar, Jobin John Jacob, Karthick Vasudevan, Divyaa Elangovan, Veeraraghavan BalajiIndian Journal of Medical Microbiology 2019 37(2):147-162 The prime goal of molecular epidemiology is to identify the origin and evolution of pathogens, which can potentially influence the public health worldwide. Traditional methods provide limited information which is not sufficient for outbreak investigation and studying transmission dynamics. The recent advancement of next-generation sequen...
Source: Indian Journal of Medical Microbiology - Category: Microbiology Authors: Source Type: research
ConclusionsThis report confirms 12 azithromycin-resistantSalmonella Typhi strains and one Paratyphi A strain. The molecular basis of this resistance is one mutation in the AcrB protein at position 717. This is the first report demonstrating the impact of this non-synonymous mutation in conferring macrolide resistance in a clinical setting. With increasing azithromycin use, strains with R717 mutations may spread and be acquired by XDR strains. An azithromycin-resistant XDR strain would shift enteric fever treatment from outpatient departments, where patients are currently treated with oral azithromycin, to inpatient departm...
Source: PLoS Neglected Tropical Diseases - Category: Tropical Medicine Authors: Source Type: research
koh Disease outbreaks caused by the ingestion of contaminated vegetables and fruits pose a significant problem to human health. The sources of contamination of these food products at the preharvest level of agricultural production, most importantly, agricultural soil and irrigation water, serve as potential reservoirs of some clinically significant foodborne pathogenic bacteria. These clinically important bacteria include: Klebsiella spp., Salmonella spp., Citrobacter spp., Shigella spp., Enterobacter spp., Listeria monocytogenes and pathogenic E. coli (and E. coli O157:H7) all of which have the potential to cause dise...
Source: International Journal of Environmental Research and Public Health - Category: Environmental Health Authors: Tags: Review Source Type: research
Foodborne diseases (FBDs) are infections of the gastrointestinal tract caused by foodborne pathogens (FBPs) such as bacteria (Salmonella, Listeria monocytogenes and Shiga toxin-producing E. coli (STEC)) and several viruses, but also parasites and some fungi. Artificial intelligence (AI) and its sub-discipline machine learning (ML) are re-emerging and gaining an ever increasing popularity in the scientific community and industry, and could lead to actionable knowledge in diverse ranges of sectors including epidemiological investigations of FBD outbreaks and antimicrobial resistance (AMR). As genotyping using whole-genome se...
Source: Frontiers in Microbiology - Category: Microbiology Source Type: research
Conclusion This study revealed that Enterococcus species with biofilm potentials and extracellular virulence properties extensively occur in retail RTE shrimps. A significant number of isolated strains are resistant to antibiotics and harbor resistant and virulent genes, denoting a significant route of resistance and virulence dissemination to bacteria in humans. There is an inadequate understanding of the intricacies of antibiotic-resistant enterococci of food origin that belong to enterococci aside from E. faecium and E. faecalis. Findings from this study reveal detailed antibiotic resistance of E. durans, E. casselifla...
Source: Frontiers in Microbiology - Category: Microbiology Source Type: research
This study revealed that a diverse group of plasmids, carrying AR genes, are responsible for the phenotypic resistance seen in Salmonella isolated from United States food animals. It was also determined that many plasmids carry similar ARCs. Introduction Non-typhoidal Salmonella enterica is one of the most common causes of foodborne illnesses globally, with an estimated 1.2 million cases each year in the United States alone (CDC, 2013). Symptoms range from self-limiting gastrointestinal illness to sepsis. These infections can lead to death unless treated with antibiotics (Crump et al., 2015). Unfortunately, antimic...
Source: Frontiers in Microbiology - Category: Microbiology Source Type: research
In this study, a “species” is defined as a unique AMR profile, including the profile corresponding to susceptibility to all tested antimicrobials. The AMR profile (or antibiogram) of an isolate is the combination of AMR phenotype (susceptible or non-susceptible) to each drug tested. SR reflects the richness of AMR profiles without weighting of abundance. SE and SD are measures in which both SR and relative abundance are taken into account. The BP diversity index is related to the proportion of isolates with the most common AMR profile. Changes in antimicrobial testing protocol could impact upon results, partic...
Source: Frontiers in Microbiology - Category: Microbiology Source Type: research
Conclusion In this study, a self-transmissible IncN2 plasmid bearing blaNDM was detected in ST405 E. coli, which is a globally disseminated lineage. We highlight the dissemination potential of IncN2 plasmids harboring blaNDM. The presence of blaNDM mediated by plasmids in the high-risk clone ST405 E. coli linked with multiple virulence genes and resistance genes is increasing, which may create health concerns. Author Contributions YJ and ZL designed the experiments. YH analyzed the data and wrote the manuscript. CS and XG prepared the table and figures. YB carried out the bacteria identification. Funding The study was...
Source: Frontiers in Microbiology - Category: Microbiology Source Type: research
In conclusion, association rule mining is an effective tool for identifying patterns of multidrug resistance within antimicrobial susceptibility testing data and evaluating the statistical and biological significance of the patterns. Rule quality measures used to sort and differentiate rules should be tested using resampling procedures to minimize the false discovery rate. Rule mining identified consistent multidrug resistance patterns involving beta-lactams, sulfisoxazole, tetracycline, gentamicin, and streptomycin in E. coli isolated from chicken carcasses and meat between 2004 and 2012. The generally low rule overlap su...
Source: Frontiers in Microbiology - Category: Microbiology Source Type: research
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