One Day in Denmark: Comparison of Phenotypic and Genotypic Antimicrobial Susceptibility Testing in Bacterial Isolates From Clinical Settings
Antimicrobial susceptibility testing (AST) should be fast and accurate, leading to proper interventions and therapeutic success. Clinical microbiology laboratories rely on phenotypic methods, but the continuous improvement and decrease in the cost of whole-genome sequencing (WGS) technologies make t...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-06-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2022.804627/full |
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| author | Ana Rita Rebelo Valeria Bortolaia Valeria Bortolaia Pimlapas Leekitcharoenphon Dennis Schrøder Hansen Hans Linde Nielsen Hans Linde Nielsen Svend Ellermann-Eriksen Michael Kemp Bent Løwe Røder Niels Frimodt-Møller Turid Snekloth Søndergaard John Eugenio Coia Claus Østergaard Henrik Westh Henrik Westh Frank M. Aarestrup |
| author_facet | Ana Rita Rebelo Valeria Bortolaia Valeria Bortolaia Pimlapas Leekitcharoenphon Dennis Schrøder Hansen Hans Linde Nielsen Hans Linde Nielsen Svend Ellermann-Eriksen Michael Kemp Bent Løwe Røder Niels Frimodt-Møller Turid Snekloth Søndergaard John Eugenio Coia Claus Østergaard Henrik Westh Henrik Westh Frank M. Aarestrup |
| author_sort | Ana Rita Rebelo |
| collection | DOAJ |
| description | Antimicrobial susceptibility testing (AST) should be fast and accurate, leading to proper interventions and therapeutic success. Clinical microbiology laboratories rely on phenotypic methods, but the continuous improvement and decrease in the cost of whole-genome sequencing (WGS) technologies make them an attractive alternative. Studies evaluating the performance of WGS-based prediction of antimicrobial resistance (AMR) for selected bacterial species have shown promising results. There are, however, significant gaps in the literature evaluating the applicability of WGS as a diagnostics method in real-life clinical settings against the range of bacterial pathogens experienced there. Thus, we compared standard phenotypic AST results with WGS-based predictions of AMR profiles in bacterial isolates without preselection of defined species, to evaluate the applicability of WGS as a diagnostics method in clinical settings. We collected all bacterial isolates processed by all Danish Clinical Microbiology Laboratories in 1 day. We randomly selected 500 isolates without any preselection of species. We performed AST through standard broth microdilution (BMD) for 488 isolates (n = 6,487 phenotypic AST results) and compared results with in silico antibiograms obtained through WGS (Illumina NextSeq) followed by bioinformatics analyses using ResFinder 4.0 (n = 5,229 comparisons). A higher proportion of AMR was observed for Gram-negative bacteria (10.9%) than for Gram-positive bacteria (6.1%). Comparison of BMD with WGS data yielded a concordance of 91.7%, with discordant results mainly due to phenotypically susceptible isolates harboring genetic AMR determinants. These cases correspond to 6.2% of all isolate-antimicrobial combinations analyzed and to 6.8% of all phenotypically susceptible combinations. We detected fewer cases of phenotypically resistant isolates without any known genetic resistance mechanism, particularly 2.1% of all combinations analyzed, which corresponded to 26.4% of all detected phenotypic resistances. Most discordances were observed for specific combinations of species-antimicrobial: macrolides and tetracycline in streptococci, ciprofloxacin and β-lactams in combination with β-lactamase inhibitors in Enterobacterales, and most antimicrobials in Pseudomonas aeruginosa. WGS has the potential to be used for surveillance and routine clinical microbiology. However, in clinical microbiology settings and especially for certain species and antimicrobial agent combinations, further developments in AMR gene databases are needed to ensure higher concordance between in silico predictions and expected phenotypic AMR profiles. |
| first_indexed | 2024-04-12T18:06:17Z |
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| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-04-12T18:06:17Z |
| publishDate | 2022-06-01 |
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| series | Frontiers in Microbiology |
| spelling | doaj.art-70a0a9c126dd47b39337e2fa0f134bf12022-12-22T03:21:59ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2022-06-011310.3389/fmicb.2022.804627804627One Day in Denmark: Comparison of Phenotypic and Genotypic Antimicrobial Susceptibility Testing in Bacterial Isolates From Clinical SettingsAna Rita Rebelo0Valeria Bortolaia1Valeria Bortolaia2Pimlapas Leekitcharoenphon3Dennis Schrøder Hansen4Hans Linde Nielsen5Hans Linde Nielsen6Svend Ellermann-Eriksen7Michael Kemp8Bent Løwe Røder9Niels Frimodt-Møller10Turid Snekloth Søndergaard11John Eugenio Coia12Claus Østergaard13Henrik Westh14Henrik Westh15Frank M. Aarestrup16National Food Institute, Technical University of Denmark, Kongens Lyngby, DenmarkNational Food Institute, Technical University of Denmark, Kongens Lyngby, DenmarkDepartment of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, DenmarkNational Food Institute, Technical University of Denmark, Kongens Lyngby, DenmarkDepartment of Clinical Microbiology, Herlev and Gentofte Hospital, Herlev, DenmarkDepartment of Clinical Microbiology, Aalborg University Hospital, Aalborg, DenmarkDepartment of Clinical Medicine, Aalborg University, Aalborg, DenmarkDepartment of Clinical Microbiology, Aarhus University Hospital, Aarhus, DenmarkDepartment of Clinical Microbiology, Odense University Hospital, Odense, DenmarkDepartment of Clinical Microbiology, Slagelse Hospital, Slagelse, DenmarkDepartment of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark0Department of Clinical Microbiology, Hospital of Southern Jutland, Sønderborg, Denmark1Department of Clinical Microbiology, Hospital of South West Jutland, Esbjerg, Denmark2Department of Clinical Microbiology, Vejle Hospital, Vejle, Denmark3Department of Clinical Microbiology, Hvidovre Hospital, Copenhagen University Hospital – Amager and Hvidovre, Hvidovre, Denmark4Department of Clinical Medicine, University of Copenhagen, Copenhagen, DenmarkNational Food Institute, Technical University of Denmark, Kongens Lyngby, DenmarkAntimicrobial susceptibility testing (AST) should be fast and accurate, leading to proper interventions and therapeutic success. Clinical microbiology laboratories rely on phenotypic methods, but the continuous improvement and decrease in the cost of whole-genome sequencing (WGS) technologies make them an attractive alternative. Studies evaluating the performance of WGS-based prediction of antimicrobial resistance (AMR) for selected bacterial species have shown promising results. There are, however, significant gaps in the literature evaluating the applicability of WGS as a diagnostics method in real-life clinical settings against the range of bacterial pathogens experienced there. Thus, we compared standard phenotypic AST results with WGS-based predictions of AMR profiles in bacterial isolates without preselection of defined species, to evaluate the applicability of WGS as a diagnostics method in clinical settings. We collected all bacterial isolates processed by all Danish Clinical Microbiology Laboratories in 1 day. We randomly selected 500 isolates without any preselection of species. We performed AST through standard broth microdilution (BMD) for 488 isolates (n = 6,487 phenotypic AST results) and compared results with in silico antibiograms obtained through WGS (Illumina NextSeq) followed by bioinformatics analyses using ResFinder 4.0 (n = 5,229 comparisons). A higher proportion of AMR was observed for Gram-negative bacteria (10.9%) than for Gram-positive bacteria (6.1%). Comparison of BMD with WGS data yielded a concordance of 91.7%, with discordant results mainly due to phenotypically susceptible isolates harboring genetic AMR determinants. These cases correspond to 6.2% of all isolate-antimicrobial combinations analyzed and to 6.8% of all phenotypically susceptible combinations. We detected fewer cases of phenotypically resistant isolates without any known genetic resistance mechanism, particularly 2.1% of all combinations analyzed, which corresponded to 26.4% of all detected phenotypic resistances. Most discordances were observed for specific combinations of species-antimicrobial: macrolides and tetracycline in streptococci, ciprofloxacin and β-lactams in combination with β-lactamase inhibitors in Enterobacterales, and most antimicrobials in Pseudomonas aeruginosa. WGS has the potential to be used for surveillance and routine clinical microbiology. However, in clinical microbiology settings and especially for certain species and antimicrobial agent combinations, further developments in AMR gene databases are needed to ensure higher concordance between in silico predictions and expected phenotypic AMR profiles.https://www.frontiersin.org/articles/10.3389/fmicb.2022.804627/fullwhole-genome sequencing (WGS)antimicrobial resistance (AMR)antimicrobial resistance genes (ARGs)genotypephenotypeconcordance |
| spellingShingle | Ana Rita Rebelo Valeria Bortolaia Valeria Bortolaia Pimlapas Leekitcharoenphon Dennis Schrøder Hansen Hans Linde Nielsen Hans Linde Nielsen Svend Ellermann-Eriksen Michael Kemp Bent Løwe Røder Niels Frimodt-Møller Turid Snekloth Søndergaard John Eugenio Coia Claus Østergaard Henrik Westh Henrik Westh Frank M. Aarestrup One Day in Denmark: Comparison of Phenotypic and Genotypic Antimicrobial Susceptibility Testing in Bacterial Isolates From Clinical Settings Frontiers in Microbiology whole-genome sequencing (WGS) antimicrobial resistance (AMR) antimicrobial resistance genes (ARGs) genotype phenotype concordance |
| title | One Day in Denmark: Comparison of Phenotypic and Genotypic Antimicrobial Susceptibility Testing in Bacterial Isolates From Clinical Settings |
| title_full | One Day in Denmark: Comparison of Phenotypic and Genotypic Antimicrobial Susceptibility Testing in Bacterial Isolates From Clinical Settings |
| title_fullStr | One Day in Denmark: Comparison of Phenotypic and Genotypic Antimicrobial Susceptibility Testing in Bacterial Isolates From Clinical Settings |
| title_full_unstemmed | One Day in Denmark: Comparison of Phenotypic and Genotypic Antimicrobial Susceptibility Testing in Bacterial Isolates From Clinical Settings |
| title_short | One Day in Denmark: Comparison of Phenotypic and Genotypic Antimicrobial Susceptibility Testing in Bacterial Isolates From Clinical Settings |
| title_sort | one day in denmark comparison of phenotypic and genotypic antimicrobial susceptibility testing in bacterial isolates from clinical settings |
| topic | whole-genome sequencing (WGS) antimicrobial resistance (AMR) antimicrobial resistance genes (ARGs) genotype phenotype concordance |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2022.804627/full |
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