Rapid culture-independent loop-mediated isothermal amplification detection of antimicrobial resistance markers from environmental water samples

Liam Burke; Louise O'Connor; Dearbháile Morris; Terry J. Smith

doi:10.1111/1751-7915.14227

Rapid culture-independent loop-mediated isothermal amplification detection of antimicrobial resistance markers from environmental water samples

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Abstract

Environmental water is considered one of the main vehicles for the transmission of antimicrobial resistance (AMR), posing an increasing threat to humans and animals health. Continuous efforts are being made to eliminate AMR; however, the detection of AMR pathogens from water samples often requires at least one culture step, which is time-consuming and can limit sensitivity. In this study, we employed comparative genomics to identify the prevalence of AMR genes within among: Escherichia coli, Klebsiella, Salmonella enterica and Acinetobacter, using publicly available genomes. The mcr-1, blaKPC (KPC-1 to KPC-4 alleles), blaOXA-48, blaOXA-23 and blaVIM (VIM-1 and VIM-2 alleles) genes are of great medical and veterinary significance, thus were selected as targets for the development of isothermal loop-mediated amplification (LAMP) detection assays. We also developed a rapid and sensitive sample preparation method for an integrated culture-independent LAMP-based detection from water samples. The developed assays successfully detected the five AMR gene markers from pond water within 1 h and were 100% sensitive and specific with a detection limit of 0.0625 μg/mL and 10 cfu/mL for genomic DNA and spiked bacterial cells, respectively. The integrated detection can be easily implemented in resource-limited areas to enhance One Health AMR surveillances and improve diagnostics.

Original language	English (Ireland)
Pages (from-to)	977-989
Number of pages	13
Journal	Microbial Biotechnology
Volume	16
Issue number	5
DOIs	https://doi.org/10.1111/1751-7915.14227
Publication status	Published - 1 Feb 2023

Authors (Note for portal: view the doc link for the full list of authors)

Authors
Marwa M. Hassan; Arnoud H. M. van Vliet; Owen Higgins; Liam P. Burke; Alexandra Chueiri; Louise O'Connor; Dearbháile Morris; Terry J. Smith; Roberto M. La Ragione
Hassan, MM; van Vliet, AMH; Higgins, O; Burke, LP; Chueiri, A; OConnor, L; Morris, D; Smith, TJ; La Ragione, RM.
Marwa M. Hassan, Arnoud H. M. van Vliet, Owen Higgins, Liam P. Burke, Alexandra Chueiri, Louise O'Connor, Dearbháile Morris, Terry J. Smith, Roberto M. La Ragione

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10.1111/1751-7915.14227

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abstract = "Environmental water is considered one of the main vehicles for the transmission of antimicrobial resistance (AMR), posing an increasing threat to humans and animals health. Continuous efforts are being made to eliminate AMR; however, the detection of AMR pathogens from water samples often requires at least one culture step, which is time-consuming and can limit sensitivity. In this study, we employed comparative genomics to identify the prevalence of AMR genes within among: Escherichia coli, Klebsiella, Salmonella enterica and Acinetobacter, using publicly available genomes. The mcr-1, blaKPC (KPC-1 to KPC-4 alleles), blaOXA-48, blaOXA-23 and blaVIM (VIM-1 and VIM-2 alleles) genes are of great medical and veterinary significance, thus were selected as targets for the development of isothermal loop-mediated amplification (LAMP) detection assays. We also developed a rapid and sensitive sample preparation method for an integrated culture-independent LAMP-based detection from water samples. The developed assays successfully detected the five AMR gene markers from pond water within 1 h and were 100\% sensitive and specific with a detection limit of 0.0625 μg/mL and 10 cfu/mL for genomic DNA and spiked bacterial cells, respectively. The integrated detection can be easily implemented in resource-limited areas to enhance One Health AMR surveillances and improve diagnostics.",

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Rapid culture-independent loop-mediated isothermal amplification detection of antimicrobial resistance markers from environmental water samples

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