<i>Bifidobacterium breve</i> PRL2020: Antibiotic-Resistant Profile and Genomic Detection of Antibiotic Resistance Determinants
Antibiotics are one of the greatest scientific achievements of modern medicine, but excessive use is creating challenges for the future of medicine. Antibiotic resistance (AR) is thought to cause changes in bowel habits and an increased risk of gastroenteritis, but it may also increase the risk of o...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-06-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/11/7/1649 |
| _version_ | 1797588235431444480 |
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| author | Francesco Di Pierro Ilenia Campedelli Patrick De Marta Fabio Fracchetti Antonio Del Casale Ilaria Cavecchia Mariarosaria Matera Massimiliano Cazzaniga Alexander Bertuccioli Luigina Guasti Nicola Zerbinati |
| author_facet | Francesco Di Pierro Ilenia Campedelli Patrick De Marta Fabio Fracchetti Antonio Del Casale Ilaria Cavecchia Mariarosaria Matera Massimiliano Cazzaniga Alexander Bertuccioli Luigina Guasti Nicola Zerbinati |
| author_sort | Francesco Di Pierro |
| collection | DOAJ |
| description | Antibiotics are one of the greatest scientific achievements of modern medicine, but excessive use is creating challenges for the future of medicine. Antibiotic resistance (AR) is thought to cause changes in bowel habits and an increased risk of gastroenteritis, but it may also increase the risk of overweight, obesity, autoimmune and atopic diseases, and a low response to vaccines and cancer, likely mediated by antibiotic-induced gut dysbiosis. Probiotic add-on therapy could partially prevent antibiotic-induced gut dysbiosis, but their antibiotic sensitivity features likely limits this potential. The EFSA (European Food Safety Authority) guidelines consider the use of probiotics whose antibiotic-resistant profile could be transferable an important hazard. Recently, a strain of <i>B. breve</i> (PRL2020) has shown to be resistant to amoxicillin and amoxicillin-clavulanate (AC) by applying the microdilution protocol according EFSA guidelines. After verifying that horizontal gene transfer is unlikely to take place, this feature suggests its concomitant use with these specific antibiotics. The results of our tests demonstrated that the strain PRL2020 is indeed endowed with amoxicillin- and AC-resistant properties and that it is also insensitive to ampicillin. In-depth analysis of the annotated genome sequence of <i>B. breve</i> PRL2020 was employed to query the Comprehensive Antibiotic Resistance Database (CARD) using Resistance Gene Identifier (RGI) software (version 5.2.1). The similarity among the AR determinants found was studied through nucleotide sequence alignment, and it was possible to verify not only the absence of genes explaining these features in the flanking regions but also the presence of genetic sequences (<i>rpoB</i> and <i>erm(X)</i>) putatively responsible for rifampicin and erythromycin resistance. Both features are not phenotypically expressed, and for these antibiotics, the strain is within the EFSA limits. Analysis of the flanking regions of these genes revealed possible mobile elements upstream and downstream only in the case of the <i>erm(X)</i> gene, but the features of the Insertion Sequences (IS) are described as not to cause horizontal transfer. Our findings on strain PRL2020 demonstrate that its AR profile is compatible with antibiotics when taken with the aim of reducing the risk of dysbiosis. |
| first_indexed | 2024-03-11T00:49:16Z |
| format | Article |
| id | doaj.art-d6c39e9f3b0b4efb91d4c3a3c657ef60 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-11T00:49:16Z |
| publishDate | 2023-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-d6c39e9f3b0b4efb91d4c3a3c657ef602023-11-18T20:34:28ZengMDPI AGMicroorganisms2076-26072023-06-01117164910.3390/microorganisms11071649<i>Bifidobacterium breve</i> PRL2020: Antibiotic-Resistant Profile and Genomic Detection of Antibiotic Resistance DeterminantsFrancesco Di Pierro0Ilenia Campedelli1Patrick De Marta2Fabio Fracchetti3Antonio Del Casale4Ilaria Cavecchia5Mariarosaria Matera6Massimiliano Cazzaniga7Alexander Bertuccioli8Luigina Guasti9Nicola Zerbinati10Scientific & Research Department, Velleja Research, 20125 Milan, ItalyMicrobion, San Giovanni Lupatoto, 37057 Verona, ItalyMicrobion, San Giovanni Lupatoto, 37057 Verona, ItalyMicrobion, San Giovanni Lupatoto, 37057 Verona, ItalyMicrobion, San Giovanni Lupatoto, 37057 Verona, ItalyMicrobiomic Department, Koelliker Hospital, 10134 Turin, ItalyDepartment of Pediatric Emergencies, Misericordia Hospital, 58100 Grosseto, ItalyScientific & Research Department, Velleja Research, 20125 Milan, ItalyDepartment of Biomolecular Sciences, University of Urbino Carlo Bo, 61122 Urbino, ItalyDepartment of Medicine and Surgery, University of Insubria, 21100 Varese, ItalyDepartment of Medicine and Surgery, University of Insubria, 21100 Varese, ItalyAntibiotics are one of the greatest scientific achievements of modern medicine, but excessive use is creating challenges for the future of medicine. Antibiotic resistance (AR) is thought to cause changes in bowel habits and an increased risk of gastroenteritis, but it may also increase the risk of overweight, obesity, autoimmune and atopic diseases, and a low response to vaccines and cancer, likely mediated by antibiotic-induced gut dysbiosis. Probiotic add-on therapy could partially prevent antibiotic-induced gut dysbiosis, but their antibiotic sensitivity features likely limits this potential. The EFSA (European Food Safety Authority) guidelines consider the use of probiotics whose antibiotic-resistant profile could be transferable an important hazard. Recently, a strain of <i>B. breve</i> (PRL2020) has shown to be resistant to amoxicillin and amoxicillin-clavulanate (AC) by applying the microdilution protocol according EFSA guidelines. After verifying that horizontal gene transfer is unlikely to take place, this feature suggests its concomitant use with these specific antibiotics. The results of our tests demonstrated that the strain PRL2020 is indeed endowed with amoxicillin- and AC-resistant properties and that it is also insensitive to ampicillin. In-depth analysis of the annotated genome sequence of <i>B. breve</i> PRL2020 was employed to query the Comprehensive Antibiotic Resistance Database (CARD) using Resistance Gene Identifier (RGI) software (version 5.2.1). The similarity among the AR determinants found was studied through nucleotide sequence alignment, and it was possible to verify not only the absence of genes explaining these features in the flanking regions but also the presence of genetic sequences (<i>rpoB</i> and <i>erm(X)</i>) putatively responsible for rifampicin and erythromycin resistance. Both features are not phenotypically expressed, and for these antibiotics, the strain is within the EFSA limits. Analysis of the flanking regions of these genes revealed possible mobile elements upstream and downstream only in the case of the <i>erm(X)</i> gene, but the features of the Insertion Sequences (IS) are described as not to cause horizontal transfer. Our findings on strain PRL2020 demonstrate that its AR profile is compatible with antibiotics when taken with the aim of reducing the risk of dysbiosis.https://www.mdpi.com/2076-2607/11/7/1649LMG S-32458amoxicillinclavulanic aciderythromycinrifaximinampicillin |
| spellingShingle | Francesco Di Pierro Ilenia Campedelli Patrick De Marta Fabio Fracchetti Antonio Del Casale Ilaria Cavecchia Mariarosaria Matera Massimiliano Cazzaniga Alexander Bertuccioli Luigina Guasti Nicola Zerbinati <i>Bifidobacterium breve</i> PRL2020: Antibiotic-Resistant Profile and Genomic Detection of Antibiotic Resistance Determinants Microorganisms LMG S-32458 amoxicillin clavulanic acid erythromycin rifaximin ampicillin |
| title | <i>Bifidobacterium breve</i> PRL2020: Antibiotic-Resistant Profile and Genomic Detection of Antibiotic Resistance Determinants |
| title_full | <i>Bifidobacterium breve</i> PRL2020: Antibiotic-Resistant Profile and Genomic Detection of Antibiotic Resistance Determinants |
| title_fullStr | <i>Bifidobacterium breve</i> PRL2020: Antibiotic-Resistant Profile and Genomic Detection of Antibiotic Resistance Determinants |
| title_full_unstemmed | <i>Bifidobacterium breve</i> PRL2020: Antibiotic-Resistant Profile and Genomic Detection of Antibiotic Resistance Determinants |
| title_short | <i>Bifidobacterium breve</i> PRL2020: Antibiotic-Resistant Profile and Genomic Detection of Antibiotic Resistance Determinants |
| title_sort | i bifidobacterium breve i prl2020 antibiotic resistant profile and genomic detection of antibiotic resistance determinants |
| topic | LMG S-32458 amoxicillin clavulanic acid erythromycin rifaximin ampicillin |
| url | https://www.mdpi.com/2076-2607/11/7/1649 |
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