The hazard of carbapenemase (OXA-181)-producing Escherichia coli spreading in pig and veal calf holdings in Italy in the genomics era: Risk of spill over and spill back between humans and animals
Carbapenemase-producing Enterobacterales (CPE) are considered a major public health issue. In the frame of the EU Harmonized AMR Monitoring program conducted in Italy in 2021, 21 epidemiological units of fattening pigs (6.98%; 95% CI 4.37–10.47%; 21/301) and four epidemiological units of bovines &am...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-11-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2022.1016895/full |
| _version_ | 1798017204520747008 |
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| author | Virginia Carfora Elena Lavinia Diaconu Angela Ianzano Paola Di Matteo Roberta Amoruso Elena Dell'Aira Luigi Sorbara Francesco Bottoni Flavia Guarneri Laura Campana Alessia Franco Patricia Alba Antonio Battisti |
| author_facet | Virginia Carfora Elena Lavinia Diaconu Angela Ianzano Paola Di Matteo Roberta Amoruso Elena Dell'Aira Luigi Sorbara Francesco Bottoni Flavia Guarneri Laura Campana Alessia Franco Patricia Alba Antonio Battisti |
| author_sort | Virginia Carfora |
| collection | DOAJ |
| description | Carbapenemase-producing Enterobacterales (CPE) are considered a major public health issue. In the frame of the EU Harmonized AMR Monitoring program conducted in Italy in 2021, 21 epidemiological units of fattening pigs (6.98%; 95% CI 4.37–10.47%; 21/301) and four epidemiological units of bovines <12 months (1.29%; 95% CI 0.35–3.27%, 4/310) resulted positive to OXA-48-like-producing E. coli (n = 24 OXA-181, n = 1 OXA-48). Whole Genome Sequencing (WGS) for in-depth characterization, genomics and cluster analysis of OXA-181-(and one OXA-48) producing E. coli isolated, was performed. Tracing-back activities at: (a) the fattening holding of origin of one positive slaughter batch, (b) the breeding holding, and (c) one epidemiologically related dairy cattle holding, allowed detection of OXA-48-like-producing E. coli in different units and comparison of further human isolates from fecal samples of farm workers. The OXA-181-producing isolates were multidrug resistant (MDR), belonged to different Sequence Types (STs), harbored the IncX and IncF plasmid replicons and multiple virulence genes. Bioinformatics analysis of combined Oxford Nanopore Technologies (ONT) long reads and Illumina short reads identified blaOXA-181 as part of a transposon in IncX1, IncX3, and IncFII fully resolved plasmids from 16 selected E. coli, mostly belonging to ST5229, isolated during the survey at slaughter and tracing-back activities. Although human source could be the most likely cause for the introduction of the blaOXA-181-carrying IncX1 plasmid in the breeding holding, concerns arise from carbapenemase OXA-48-like-producing E. coli spreading in 2021 in Italian fattening pigs and, to a lesser extent, in veal calf holdings. |
| first_indexed | 2024-04-11T16:03:17Z |
| format | Article |
| id | doaj.art-e52517b408f1465596cd9cc8ba7f4c94 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-04-11T16:03:17Z |
| publishDate | 2022-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-e52517b408f1465596cd9cc8ba7f4c942022-12-22T04:14:54ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2022-11-011310.3389/fmicb.2022.10168951016895The hazard of carbapenemase (OXA-181)-producing Escherichia coli spreading in pig and veal calf holdings in Italy in the genomics era: Risk of spill over and spill back between humans and animalsVirginia Carfora0Elena Lavinia Diaconu1Angela Ianzano2Paola Di Matteo3Roberta Amoruso4Elena Dell'Aira5Luigi Sorbara6Francesco Bottoni7Flavia Guarneri8Laura Campana9Alessia Franco10Patricia Alba11Antonio Battisti12Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e Della Toscana “M. Aleandri”, Rome, ItalyDepartment of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e Della Toscana “M. Aleandri”, Rome, ItalyDepartment of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e Della Toscana “M. Aleandri”, Rome, ItalyDepartment of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e Della Toscana “M. Aleandri”, Rome, ItalyDepartment of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e Della Toscana “M. Aleandri”, Rome, ItalyDepartment of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e Della Toscana “M. Aleandri”, Rome, ItalyDepartment of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e Della Toscana “M. Aleandri”, Rome, ItalyDepartment of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e Della Toscana “M. Aleandri”, Rome, ItalySede Territoriale di Brescia, Laboratorio Diagnostica Generale, Istituto Zooprofilattico Sperimentale Della Lombardia e Dell’Emilia-Romagna “Bruno Ubertini”, Brescia, ItalyAgenzia Tutela Della Salute, Brescia, ItalyDepartment of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e Della Toscana “M. Aleandri”, Rome, ItalyDepartment of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e Della Toscana “M. Aleandri”, Rome, ItalyDepartment of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e Della Toscana “M. Aleandri”, Rome, ItalyCarbapenemase-producing Enterobacterales (CPE) are considered a major public health issue. In the frame of the EU Harmonized AMR Monitoring program conducted in Italy in 2021, 21 epidemiological units of fattening pigs (6.98%; 95% CI 4.37–10.47%; 21/301) and four epidemiological units of bovines <12 months (1.29%; 95% CI 0.35–3.27%, 4/310) resulted positive to OXA-48-like-producing E. coli (n = 24 OXA-181, n = 1 OXA-48). Whole Genome Sequencing (WGS) for in-depth characterization, genomics and cluster analysis of OXA-181-(and one OXA-48) producing E. coli isolated, was performed. Tracing-back activities at: (a) the fattening holding of origin of one positive slaughter batch, (b) the breeding holding, and (c) one epidemiologically related dairy cattle holding, allowed detection of OXA-48-like-producing E. coli in different units and comparison of further human isolates from fecal samples of farm workers. The OXA-181-producing isolates were multidrug resistant (MDR), belonged to different Sequence Types (STs), harbored the IncX and IncF plasmid replicons and multiple virulence genes. Bioinformatics analysis of combined Oxford Nanopore Technologies (ONT) long reads and Illumina short reads identified blaOXA-181 as part of a transposon in IncX1, IncX3, and IncFII fully resolved plasmids from 16 selected E. coli, mostly belonging to ST5229, isolated during the survey at slaughter and tracing-back activities. Although human source could be the most likely cause for the introduction of the blaOXA-181-carrying IncX1 plasmid in the breeding holding, concerns arise from carbapenemase OXA-48-like-producing E. coli spreading in 2021 in Italian fattening pigs and, to a lesser extent, in veal calf holdings.https://www.frontiersin.org/articles/10.3389/fmicb.2022.1016895/fullcarbapenem-resistant EnterobacteralesOXA-48-like carbapenemasesOXA-181 carbapenemaseslong-read sequencingWhole Genome Sequencingplasmids |
| spellingShingle | Virginia Carfora Elena Lavinia Diaconu Angela Ianzano Paola Di Matteo Roberta Amoruso Elena Dell'Aira Luigi Sorbara Francesco Bottoni Flavia Guarneri Laura Campana Alessia Franco Patricia Alba Antonio Battisti The hazard of carbapenemase (OXA-181)-producing Escherichia coli spreading in pig and veal calf holdings in Italy in the genomics era: Risk of spill over and spill back between humans and animals Frontiers in Microbiology carbapenem-resistant Enterobacterales OXA-48-like carbapenemases OXA-181 carbapenemases long-read sequencing Whole Genome Sequencing plasmids |
| title | The hazard of carbapenemase (OXA-181)-producing Escherichia coli spreading in pig and veal calf holdings in Italy in the genomics era: Risk of spill over and spill back between humans and animals |
| title_full | The hazard of carbapenemase (OXA-181)-producing Escherichia coli spreading in pig and veal calf holdings in Italy in the genomics era: Risk of spill over and spill back between humans and animals |
| title_fullStr | The hazard of carbapenemase (OXA-181)-producing Escherichia coli spreading in pig and veal calf holdings in Italy in the genomics era: Risk of spill over and spill back between humans and animals |
| title_full_unstemmed | The hazard of carbapenemase (OXA-181)-producing Escherichia coli spreading in pig and veal calf holdings in Italy in the genomics era: Risk of spill over and spill back between humans and animals |
| title_short | The hazard of carbapenemase (OXA-181)-producing Escherichia coli spreading in pig and veal calf holdings in Italy in the genomics era: Risk of spill over and spill back between humans and animals |
| title_sort | hazard of carbapenemase oxa 181 producing escherichia coli spreading in pig and veal calf holdings in italy in the genomics era risk of spill over and spill back between humans and animals |
| topic | carbapenem-resistant Enterobacterales OXA-48-like carbapenemases OXA-181 carbapenemases long-read sequencing Whole Genome Sequencing plasmids |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2022.1016895/full |
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