Phenotypic and genotypic characterization of antimicrobial resistant Escherichia coli isolated from ready-to-eat food in Singapore using disk diffusion, broth microdilution and whole genome sequencing methods

This study aimed to determine the antimicrobial resistance (AMR) profiles of Escherichia coli isolated from ready-to-eat (RTE) food sold in retail food premises in Singapore. In this study, a total of 99 E. coli isolates from poultry-based dishes (n = 77) and fish-based dishes (n = 22), obtained bet...

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Main Authors: Guo, Siyao, Tay, Moon Yue Feng, Aung, Kyaw Thu, Seow, Kelyn Lee Ghee, Ng, Lee Ching, Purbojati, Rikky Wenang, Drautz-Moses, Daniela Isabel, Schuster, Stephan Christoph, Schlundt, Joergen
Other Authors: School of Chemical and Biomedical Engineering
Format: Article
Language:English
Published: 2021
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Online Access:https://hdl.handle.net/10356/146979
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spelling sg-ntu-dr.10356-1469792021-03-16T03:00:10Z Phenotypic and genotypic characterization of antimicrobial resistant Escherichia coli isolated from ready-to-eat food in Singapore using disk diffusion, broth microdilution and whole genome sequencing methods Guo, Siyao Tay, Moon Yue Feng Aung, Kyaw Thu Seow, Kelyn Lee Ghee Ng, Lee Ching Purbojati, Rikky Wenang Drautz-Moses, Daniela Isabel Schuster, Stephan Christoph Schlundt, Joergen School of Chemical and Biomedical Engineering School of Biological Sciences Singapore Centre for Environmental Life Sciences and Engineering (SCELSE) NTU Food Technology Centre Engineering::Chemical engineering Whole Genome Sequencing Antimicrobial Resistance This study aimed to determine the antimicrobial resistance (AMR) profiles of Escherichia coli isolated from ready-to-eat (RTE) food sold in retail food premises in Singapore. In this study, a total of 99 E. coli isolates from poultry-based dishes (n = 77) and fish-based dishes (n = 22), obtained between 2009 and 2014, were included for disk diffusion testing. Of the 99 isolates, 24 (24.2%) were resistant to at least one antimicrobial agent. These isolates were then subjected to broth microdilution testing against 33 antimicrobial agents, including beta-lactams, aminoglycosides, tetracycline, fluoroquinolones and polymyxin E (also known as colistin) to determine the minimum inhibitory concentration (MIC) of isolates. Finally, whole genome sequence (WGS) was carried out on the strains in order to correlate resistant phenotypes to putative antimicrobial-related genes. Of the 24 isolates, 15 (62.5%) were found to be resistant to three or more classes of antimicrobials and thus were defined as multidrug resistant strains. Two isolates (8.3%) were confirmed as Extended-Spectrum Beta-Lactamase (ESBL)-producing E. coli by double-disk synergy test. Based on WGS data, online analysis tool ResFinder detected 7 classes of AMR genes and resistance-related chromosomal point mutations in 19 of the 24 E. coli isolates. Prediction of AMR using WGS data was evaluated for six antimicrobials including ampicillin, chloramphenicol, colistin, fluoroquinolones, tetracycline and trimethoprim. By analyzing the WGS contigs using BLASTn and KmerFinder, quinolone resistance genes, ESBL genes and transferable colistin resistance gene mcr-1 and mcr-5 were determined to be located on plasmids, which could pose a greater risk of AMR transfer among bacteria. Mutations were detected in four isolates within genes previously shown to confer resistance to quinolones (gyrA and parE) and tetracycline (rrsB). This study showed the presence of AMR E. coli isolates in RTE food, and raises a concern on the possible transmission of AMR bacteria from food to humans. Nanyang Technological University National Environmental Agency (NEA) This study was supported by the National Environment Agency (NEA) and Nanyang Technological University Research Initiative. Authors would like to thank Man Ling Chau and Ramona Alikiiteaga Gutiérrez for manuscript vetting, and thank Food Hygiene team members in the Environmental Health Institute of NEA for providing isolates and experimental guidance. 2021-03-16T03:00:10Z 2021-03-16T03:00:10Z 2019 Journal Article Guo, S., Tay, M. Y. F., Aung, K. T., Seow, K. L. G., Ng, L. C., Purbojati, R. W., Drautz-Moses, D. I., Schuster, S. C. & Schlundt, J. (2019). Phenotypic and genotypic characterization of antimicrobial resistant Escherichia coli isolated from ready-to-eat food in Singapore using disk diffusion, broth microdilution and whole genome sequencing methods. Food Control, 99, 89-97. https://dx.doi.org/10.1016/j.foodcont.2018.12.043 0956-7135 0000-0001-7409-0262 0000-0003-4326-9512 https://hdl.handle.net/10356/146979 10.1016/j.foodcont.2018.12.043 2-s2.0-85060025206 99 89 97 en Food Control © 2019 Elsevier Ltd. All rights reserved.
institution Nanyang Technological University
building NTU Library
continent Asia
country Singapore
Singapore
content_provider NTU Library
collection DR-NTU
language English
topic Engineering::Chemical engineering
Whole Genome Sequencing
Antimicrobial Resistance
spellingShingle Engineering::Chemical engineering
Whole Genome Sequencing
Antimicrobial Resistance
Guo, Siyao
Tay, Moon Yue Feng
Aung, Kyaw Thu
Seow, Kelyn Lee Ghee
Ng, Lee Ching
Purbojati, Rikky Wenang
Drautz-Moses, Daniela Isabel
Schuster, Stephan Christoph
Schlundt, Joergen
Phenotypic and genotypic characterization of antimicrobial resistant Escherichia coli isolated from ready-to-eat food in Singapore using disk diffusion, broth microdilution and whole genome sequencing methods
description This study aimed to determine the antimicrobial resistance (AMR) profiles of Escherichia coli isolated from ready-to-eat (RTE) food sold in retail food premises in Singapore. In this study, a total of 99 E. coli isolates from poultry-based dishes (n = 77) and fish-based dishes (n = 22), obtained between 2009 and 2014, were included for disk diffusion testing. Of the 99 isolates, 24 (24.2%) were resistant to at least one antimicrobial agent. These isolates were then subjected to broth microdilution testing against 33 antimicrobial agents, including beta-lactams, aminoglycosides, tetracycline, fluoroquinolones and polymyxin E (also known as colistin) to determine the minimum inhibitory concentration (MIC) of isolates. Finally, whole genome sequence (WGS) was carried out on the strains in order to correlate resistant phenotypes to putative antimicrobial-related genes. Of the 24 isolates, 15 (62.5%) were found to be resistant to three or more classes of antimicrobials and thus were defined as multidrug resistant strains. Two isolates (8.3%) were confirmed as Extended-Spectrum Beta-Lactamase (ESBL)-producing E. coli by double-disk synergy test. Based on WGS data, online analysis tool ResFinder detected 7 classes of AMR genes and resistance-related chromosomal point mutations in 19 of the 24 E. coli isolates. Prediction of AMR using WGS data was evaluated for six antimicrobials including ampicillin, chloramphenicol, colistin, fluoroquinolones, tetracycline and trimethoprim. By analyzing the WGS contigs using BLASTn and KmerFinder, quinolone resistance genes, ESBL genes and transferable colistin resistance gene mcr-1 and mcr-5 were determined to be located on plasmids, which could pose a greater risk of AMR transfer among bacteria. Mutations were detected in four isolates within genes previously shown to confer resistance to quinolones (gyrA and parE) and tetracycline (rrsB). This study showed the presence of AMR E. coli isolates in RTE food, and raises a concern on the possible transmission of AMR bacteria from food to humans.
author2 School of Chemical and Biomedical Engineering
author_facet School of Chemical and Biomedical Engineering
Guo, Siyao
Tay, Moon Yue Feng
Aung, Kyaw Thu
Seow, Kelyn Lee Ghee
Ng, Lee Ching
Purbojati, Rikky Wenang
Drautz-Moses, Daniela Isabel
Schuster, Stephan Christoph
Schlundt, Joergen
format Article
author Guo, Siyao
Tay, Moon Yue Feng
Aung, Kyaw Thu
Seow, Kelyn Lee Ghee
Ng, Lee Ching
Purbojati, Rikky Wenang
Drautz-Moses, Daniela Isabel
Schuster, Stephan Christoph
Schlundt, Joergen
author_sort Guo, Siyao
title Phenotypic and genotypic characterization of antimicrobial resistant Escherichia coli isolated from ready-to-eat food in Singapore using disk diffusion, broth microdilution and whole genome sequencing methods
title_short Phenotypic and genotypic characterization of antimicrobial resistant Escherichia coli isolated from ready-to-eat food in Singapore using disk diffusion, broth microdilution and whole genome sequencing methods
title_full Phenotypic and genotypic characterization of antimicrobial resistant Escherichia coli isolated from ready-to-eat food in Singapore using disk diffusion, broth microdilution and whole genome sequencing methods
title_fullStr Phenotypic and genotypic characterization of antimicrobial resistant Escherichia coli isolated from ready-to-eat food in Singapore using disk diffusion, broth microdilution and whole genome sequencing methods
title_full_unstemmed Phenotypic and genotypic characterization of antimicrobial resistant Escherichia coli isolated from ready-to-eat food in Singapore using disk diffusion, broth microdilution and whole genome sequencing methods
title_sort phenotypic and genotypic characterization of antimicrobial resistant escherichia coli isolated from ready-to-eat food in singapore using disk diffusion, broth microdilution and whole genome sequencing methods
publishDate 2021
url https://hdl.handle.net/10356/146979
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