Clinical considerations on antimicrobial resistance potential of complex microbiological samples
Antimicrobial resistance (AMR) is one of our greatest public health challenges. Targeted use of antibiotics (ABs) can reduce the occurrence and spread of AMR and boost the effectiveness of treatment. This requires knowledge of the AB susceptibility of the pathogens involved in the disease. Therapeut...
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PeerJ Inc.
2025-01-01
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| author | Norbert Solymosi Adrienn Gréta Tóth Sára Ágnes Nagy István Csabai Csongor Feczkó Tamás Reibling Tibor Németh |
| author_facet | Norbert Solymosi Adrienn Gréta Tóth Sára Ágnes Nagy István Csabai Csongor Feczkó Tamás Reibling Tibor Németh |
| author_sort | Norbert Solymosi |
| collection | DOAJ |
| description | Antimicrobial resistance (AMR) is one of our greatest public health challenges. Targeted use of antibiotics (ABs) can reduce the occurrence and spread of AMR and boost the effectiveness of treatment. This requires knowledge of the AB susceptibility of the pathogens involved in the disease. Therapeutic recommendations based on classical AB susceptibility testing (AST) are based on the analysis of only a fraction of the bacteria present in the disease process. Next and third generation sequencing technologies allow the identification of antimicrobial resistance genes (ARGs) present in a bacterial community. Using this metagenomic approach, we can map the antimicrobial resistance potential (AMRP) of a complex, multi-bacterial microbial sample. To understand the interpretiveness of AMRP, the concordance between phenotypic AMR properties and ARGs was investigated by analyzing data from 574 Escherichia coli strains of five different studies. The overall results show that for 44% of the studied ABs, phenotypically resistant strains are genotypically associated with a 90% probability of resistance, while for 92% of the ABs, the phenotypically susceptible strains are genotypically susceptible with a 90% probability. ARG detection showed a phenotypic prediction with at least 90% confidence in 67% of ABs. The probability of detecting a phenotypically susceptible strain as resistant based on genotype is below 5% for 92% of ABs. While the probability of detecting a phenotypically resistant strain as susceptible based on genotype is below 5% for 44% of ABs. We can assume that these strain-by-strain concordance results are also true for bacteria in complex microbial samples, and conclude that AMRP obtained from metagenomic ARG analysis can help choose efficient ABs. This is illustrated using AMRP by a canine external otitis sample. |
| format | Article |
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| institution | Kabale University |
| issn | 2167-8359 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | PeerJ Inc. |
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| spelling | doaj-art-53af4d679ddb4dfd962babb2c38399ad2025-01-30T15:05:09ZengPeerJ Inc.PeerJ2167-83592025-01-0113e1880210.7717/peerj.18802Clinical considerations on antimicrobial resistance potential of complex microbiological samplesNorbert Solymosi0Adrienn Gréta Tóth1Sára Ágnes Nagy2István Csabai3Csongor Feczkó4Tamás Reibling5Tibor Németh6Centre for Bioinformatics, University of Veterinary Medicine, Budapest, HungaryCentre for Bioinformatics, University of Veterinary Medicine, Budapest, HungaryDepartment of Physics of Complex Systems, Eötvös Loránd University, Budapest, HungaryDepartment of Physics of Complex Systems, Eötvös Loránd University, Budapest, HungaryCentre for Bioinformatics, University of Veterinary Medicine, Budapest, HungaryCentre for Bioinformatics, University of Veterinary Medicine, Budapest, HungaryDepartment and Clinic of Surgery and Ophthalmology, University of Veterinary Medicine, Budapest, HungaryAntimicrobial resistance (AMR) is one of our greatest public health challenges. Targeted use of antibiotics (ABs) can reduce the occurrence and spread of AMR and boost the effectiveness of treatment. This requires knowledge of the AB susceptibility of the pathogens involved in the disease. Therapeutic recommendations based on classical AB susceptibility testing (AST) are based on the analysis of only a fraction of the bacteria present in the disease process. Next and third generation sequencing technologies allow the identification of antimicrobial resistance genes (ARGs) present in a bacterial community. Using this metagenomic approach, we can map the antimicrobial resistance potential (AMRP) of a complex, multi-bacterial microbial sample. To understand the interpretiveness of AMRP, the concordance between phenotypic AMR properties and ARGs was investigated by analyzing data from 574 Escherichia coli strains of five different studies. The overall results show that for 44% of the studied ABs, phenotypically resistant strains are genotypically associated with a 90% probability of resistance, while for 92% of the ABs, the phenotypically susceptible strains are genotypically susceptible with a 90% probability. ARG detection showed a phenotypic prediction with at least 90% confidence in 67% of ABs. The probability of detecting a phenotypically susceptible strain as resistant based on genotype is below 5% for 92% of ABs. While the probability of detecting a phenotypically resistant strain as susceptible based on genotype is below 5% for 44% of ABs. We can assume that these strain-by-strain concordance results are also true for bacteria in complex microbial samples, and conclude that AMRP obtained from metagenomic ARG analysis can help choose efficient ABs. This is illustrated using AMRP by a canine external otitis sample.https://peerj.com/articles/18802.pdfAntimicrobial resistanceGenomicsComplex microbial sampleClinical metagenomics |
| spellingShingle | Norbert Solymosi Adrienn Gréta Tóth Sára Ágnes Nagy István Csabai Csongor Feczkó Tamás Reibling Tibor Németh Clinical considerations on antimicrobial resistance potential of complex microbiological samples PeerJ Antimicrobial resistance Genomics Complex microbial sample Clinical metagenomics |
| title | Clinical considerations on antimicrobial resistance potential of complex microbiological samples |
| title_full | Clinical considerations on antimicrobial resistance potential of complex microbiological samples |
| title_fullStr | Clinical considerations on antimicrobial resistance potential of complex microbiological samples |
| title_full_unstemmed | Clinical considerations on antimicrobial resistance potential of complex microbiological samples |
| title_short | Clinical considerations on antimicrobial resistance potential of complex microbiological samples |
| title_sort | clinical considerations on antimicrobial resistance potential of complex microbiological samples |
| topic | Antimicrobial resistance Genomics Complex microbial sample Clinical metagenomics |
| url | https://peerj.com/articles/18802.pdf |
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