Virotyping and genetic antimicrobial susceptibility testing of porcine ETEC/STEC strains and associated plasmid types
IntroductionEnterotoxigenic Escherichia coli (ETEC) infections are the most common cause of secretory diarrhea in suckling and post-weaning piglets. For the latter, Shiga toxin-producing Escherichia coli (STEC) also cause edema disease. This pathogen leads to significant economic losses. ETEC/STEC s...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-04-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1139312/full |
| _version_ | 1797844952539987968 |
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| author | Nick Vereecke Nick Vereecke Sander Van Hoorde Daniel Sperling Sebastiaan Theuns Bert Devriendt Eric Cox |
| author_facet | Nick Vereecke Nick Vereecke Sander Van Hoorde Daniel Sperling Sebastiaan Theuns Bert Devriendt Eric Cox |
| author_sort | Nick Vereecke |
| collection | DOAJ |
| description | IntroductionEnterotoxigenic Escherichia coli (ETEC) infections are the most common cause of secretory diarrhea in suckling and post-weaning piglets. For the latter, Shiga toxin-producing Escherichia coli (STEC) also cause edema disease. This pathogen leads to significant economic losses. ETEC/STEC strains can be distinguished from general E. coli by the presence of different host colonization factors (e.g., F4 and F18 fimbriae) and various toxins (e.g., LT, Stx2e, STa, STb, EAST-1). Increased resistance against a wide variety of antimicrobial drugs, such as paromomycin, trimethoprim, and tetracyclines, has been observed. Nowadays, diagnosing an ETEC/STEC infection requires culture-dependent antimicrobial susceptibility testing (AST) and multiplex PCRs, which are costly and time-consuming.MethodsHere, nanopore sequencing was used on 94 field isolates to assess the predictive power, using the meta R package to determine sensitivity and specificity and associated credibility intervals of genotypes associated with virulence and AMR.ResultsGenetic markers associated with resistance for amoxicillin (plasmid-encoded TEM genes), cephalosporins (ampC promoter mutations), colistin (mcr genes), aminoglycosides (aac(3) and aph(3) genes), florfenicol (floR), tetracyclines (tet genes), and trimethoprim-sulfa (dfrA genes) could explain most acquired resistance phenotypes. Most of the genes were plasmid-encoded, of which some collocated on a multi-resistance plasmid (12 genes against 4 antimicrobial classes). For fluoroquinolones, AMR was addressed by point mutations within the ParC and GyrA proteins and the qnrS1 gene. In addition, long-read data allowed to study the genetic landscape of virulence- and AMR-carrying plasmids, highlighting a complex interplay of multi-replicon plasmids with varying host ranges.ConclusionOur results showed promising sensitivity and specificity for the detection of all common virulence factors and most resistance genotypes. The use of the identified genetic hallmarks will contribute to the simultaneous identification, pathotyping, and genetic AST within a single diagnostic test. This will revolutionize future quicker and more cost-efficient (meta)genomics-driven diagnostics in veterinary medicine and contribute to epidemiological studies, monitoring, tailored vaccination, and management. |
| first_indexed | 2024-04-09T17:30:42Z |
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| id | doaj.art-b526d18587884f9d8a2ccb48d6830edc |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-04-09T17:30:42Z |
| publishDate | 2023-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-b526d18587884f9d8a2ccb48d6830edc2023-04-18T06:08:32ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2023-04-011410.3389/fmicb.2023.11393121139312Virotyping and genetic antimicrobial susceptibility testing of porcine ETEC/STEC strains and associated plasmid typesNick Vereecke0Nick Vereecke1Sander Van Hoorde2Daniel Sperling3Sebastiaan Theuns4Bert Devriendt5Eric Cox6Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, BelgiumPathoSense BV, Lier, BelgiumLaboratory of Immunology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, BelgiumCEVA Santé Animale, Libourne, FranceLaboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, BelgiumLaboratory of Immunology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, BelgiumLaboratory of Immunology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, BelgiumIntroductionEnterotoxigenic Escherichia coli (ETEC) infections are the most common cause of secretory diarrhea in suckling and post-weaning piglets. For the latter, Shiga toxin-producing Escherichia coli (STEC) also cause edema disease. This pathogen leads to significant economic losses. ETEC/STEC strains can be distinguished from general E. coli by the presence of different host colonization factors (e.g., F4 and F18 fimbriae) and various toxins (e.g., LT, Stx2e, STa, STb, EAST-1). Increased resistance against a wide variety of antimicrobial drugs, such as paromomycin, trimethoprim, and tetracyclines, has been observed. Nowadays, diagnosing an ETEC/STEC infection requires culture-dependent antimicrobial susceptibility testing (AST) and multiplex PCRs, which are costly and time-consuming.MethodsHere, nanopore sequencing was used on 94 field isolates to assess the predictive power, using the meta R package to determine sensitivity and specificity and associated credibility intervals of genotypes associated with virulence and AMR.ResultsGenetic markers associated with resistance for amoxicillin (plasmid-encoded TEM genes), cephalosporins (ampC promoter mutations), colistin (mcr genes), aminoglycosides (aac(3) and aph(3) genes), florfenicol (floR), tetracyclines (tet genes), and trimethoprim-sulfa (dfrA genes) could explain most acquired resistance phenotypes. Most of the genes were plasmid-encoded, of which some collocated on a multi-resistance plasmid (12 genes against 4 antimicrobial classes). For fluoroquinolones, AMR was addressed by point mutations within the ParC and GyrA proteins and the qnrS1 gene. In addition, long-read data allowed to study the genetic landscape of virulence- and AMR-carrying plasmids, highlighting a complex interplay of multi-replicon plasmids with varying host ranges.ConclusionOur results showed promising sensitivity and specificity for the detection of all common virulence factors and most resistance genotypes. The use of the identified genetic hallmarks will contribute to the simultaneous identification, pathotyping, and genetic AST within a single diagnostic test. This will revolutionize future quicker and more cost-efficient (meta)genomics-driven diagnostics in veterinary medicine and contribute to epidemiological studies, monitoring, tailored vaccination, and management.https://www.frontiersin.org/articles/10.3389/fmicb.2023.1139312/fullpathogenic Escherichia coliedema diseasenanopore sequencingantibiotic resistancegenomics |
| spellingShingle | Nick Vereecke Nick Vereecke Sander Van Hoorde Daniel Sperling Sebastiaan Theuns Bert Devriendt Eric Cox Virotyping and genetic antimicrobial susceptibility testing of porcine ETEC/STEC strains and associated plasmid types Frontiers in Microbiology pathogenic Escherichia coli edema disease nanopore sequencing antibiotic resistance genomics |
| title | Virotyping and genetic antimicrobial susceptibility testing of porcine ETEC/STEC strains and associated plasmid types |
| title_full | Virotyping and genetic antimicrobial susceptibility testing of porcine ETEC/STEC strains and associated plasmid types |
| title_fullStr | Virotyping and genetic antimicrobial susceptibility testing of porcine ETEC/STEC strains and associated plasmid types |
| title_full_unstemmed | Virotyping and genetic antimicrobial susceptibility testing of porcine ETEC/STEC strains and associated plasmid types |
| title_short | Virotyping and genetic antimicrobial susceptibility testing of porcine ETEC/STEC strains and associated plasmid types |
| title_sort | virotyping and genetic antimicrobial susceptibility testing of porcine etec stec strains and associated plasmid types |
| topic | pathogenic Escherichia coli edema disease nanopore sequencing antibiotic resistance genomics |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1139312/full |
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