Machine Learning Approaches for Epidemiological Investigations of Food-Borne Disease Outbreaks

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 sequencing (WGS) is becoming more accessible and affordable, it is increasingly used as a routine tool for the detection of pathogens, and has the potential to differentiate between outbreak strains that are closely related, identify virulence/resistance genes and provide improved understanding of transmission events within hours to days. In most cases, the computational pipeline of WGS data analysis can be divided into four (though, not necessarily consecutive) major steps: de novo genome assembly, genome characterization, comparative genomics and inference of phylogeny or phylogenomics. In each step, ML could be used to increase the speed and potentially the accuracy (provided increasing amounts of high-quality input data) of identification of the source of ongoing out- breaks, leading to more efficient treatment and prevention of additional cases. In this r...
Source: Frontiers in Microbiology - Category: Microbiology Source Type: research

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CONCLUSION: Prevalence of antibiotic use was high not only versus other hospitals in the region but globally including Africa, coupled with significant evidence of sub-optimal prescribing. Swift action is needed to improve future prescribing to reduce AMR. One or two areas should initially be targeted for quality improvement including development of local guidelines, documentation of antibiotic indications and/or stop/review dates. PMID: 33034234 [PubMed - as supplied by publisher]
Source: Expert Review of Anti-Infective Therapy - Category: Infectious Diseases Tags: Expert Rev Anti Infect Ther Source Type: research
Publication date: Available online 10 October 2020Source: Journal of Genetics and GenomicsAuthor(s): Chengqi Wang, Justin Gibbons, Swamy R. Adapa, Jenna Oberstaller, Xiangyun Liao, Min Zhang, John H. Adams, Rays H.Y. Jiang
Source: Journal of Genetics and Genomics - Category: Genetics & Stem Cells Source Type: research
CONCLUSIONS: Xyloglucan/gelose plus ORS was effective and safe in treating acute diarrhea in children. PMID: 33028102 [PubMed - as supplied by publisher]
Source: Expert Review of Gastroenterology and Hepatology - Category: Gastroenterology Tags: Expert Rev Gastroenterol Hepatol Source Type: research
Conclusions: (1) Data at our center suggests at least a regional implementation gap in GBS screening and IAP. (2) The decline in the resistance rate ofE. coli for all antimicrobial substances might indicate that the reduction of prenatal antibiotics use is beneficial and that neonatal antibiotic stewardship programs should include pregnant women as well.What is Known:• GBS screening and intrapartum antibiotic prophylaxis led to a 32%-reduction in GBS disease in Germany with a 0.75 (92:122) ratio of early-onset disease to late-onset disease in 2009–2010.• Prenatal antibiotic use might increase the risk of E....
Source: European Journal of Pediatrics - Category: Pediatrics Source Type: research
Publication date: Available online 9 October 2020Source: The Journal of Allergy and Clinical Immunology: In PracticeAuthor(s): Manuel Jorge Rial, Marcela Valverde, Victoria del Pozo, Francisco Javier González-Barcala, Carlos Martínez-Rivera, Xavier Muñoz, José María Olaguibel, Vicente Plaza, Elena Curto, Santiago Quirce, Pilar Barranco, Javier Domínguez-Ortega, Joaquin Mullol, César Picado, Antonio Valero, Irina Bobolea, Ebymar Arismendi, Paula Ribó, Joaquín Sastre
Source: The Journal of Allergy and Clinical Immunology: In Practice - Category: Allergy & Immunology Source Type: research
Authors: Abdeta D, Kebede N, Giday M, Terefe G, Abay SM Abstract Microbial resistance to the few conventional antitrypanosomal drugs, increasing resistance of vectors to insecticides, lack of effective vaccines, and adverse effects of the existing antitrypanosomal drugs justify the urgent need for effective, tolerable, and affordable drugs. We assessed antitrypanosomal effects of the hydromethanolic extract of Echinops kebericho Mesfin roots against Trypanosoma congolense field isolate using in vitro and in vivo techniques. Parasite load, packed cell volume (PCV), body weight, and rectal temperature in Swiss albino...
Source: Evidence-based Complementary and Alternative Medicine - Category: Complementary Medicine Tags: Evid Based Complement Alternat Med Source Type: research
Conclusion: This study demonstrates that the crude extract of A. hispidum DC, one of the plants used traditionally to treat malaria, inhibits the growth of P. falciparum in vitro and could be a potential source of antimalarial drug. The report has highlighted genotoxic and cytotoxic effects of the selected plant extracts on human leukocytes as well. PMID: 33029160 [PubMed]
Source: Evidence-based Complementary and Alternative Medicine - Category: Complementary Medicine Tags: Evid Based Complement Alternat Med Source Type: research
This study investigated antibacterial-producing Streptomyces isolated from the gut of estuarine fish Chanos chanos, emphasizing screening for the producer of peptide-containing antibacterial compounds. Eighteen isolates were found during preliminary screening, in which four isolates showed the best antibacterial activities. Based on the morphological, physiological, and biochemical characterization, as well as 16S rRNA partial sequencing, all of the four isolates belonged to Streptomyces. Three isolates were suspected as novel isolate candidates based on homology presentations and phylogenetic tree analysis. Disk-diffusion...
Source: International Journal of Microbiology - Category: Microbiology Tags: Int J Microbiol Source Type: research
Trump plans in-person rally on Monday as next presidential debate cancelled; Europe records 100,000 daily cases for first time; Canada at ‘tipping point’. Follow latest updatesEurope: Spain declares emergency in Madrid as Berlin emerges as hotspotUK workers to get two-thirds of wages if firms told to shutAustralia: Is Victoria ready to come out of lockdown?US presidential debate cancelled – live updatesSee all our coronavirus coverage5.42amBSTMy colleagueLuke Henriques-Gomes has this story giving you a summary of the main Covid-19 stories from Australia.A main point of the day has beenVictoria ’s pr...
Source: Guardian Unlimited Science - Category: Science Authors: Tags: Coronavirus outbreak Infectious diseases Science World news France Trump administration Donald Trump Source Type: news
(Nagoya University) Using the model Orobanchaceae parasitic plant Phtheirospermum japonicum, scientists have discerned the molecular mechanisms underlying plant parasitism and cross-species grafting, pinpointing enzymeβ-1,4-glucanase (GH9B3) as an important contributor to both phenomena. Targeting this enzyme may help control plant parasitism in crops.
Source: EurekAlert! - Biology - Category: Biology Source Type: news
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