Genus-Wide Assessment of Antibiotic Resistance in Lactobacillus spp
species are widely used as probiotics and starter cultures for a variety of foods, supported by a long history of safe usage. Although more than 35 species meet the European Food Safety Authority (EFSA) criteria for qualified presumption of safety status, the safety of species and their carriage of...
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creator | Campedelli, Ilenia Mathur, Harsh Salvetti, Elisa Clarke, Siobhán Rea, Mary C Torriani, Sandra Ross, R Paul Hill, Colin O'Toole, Paul W |
description | species are widely used as probiotics and starter cultures for a variety of foods, supported by a long history of safe usage. Although more than 35 species meet the European Food Safety Authority (EFSA) criteria for qualified presumption of safety status, the safety of
species and their carriage of antibiotic resistance (AR) genes is under continuing
review. To comprehensively update the identification of AR in the genus
, we determined the antibiotic susceptibility patterns of 182
type strains and compared these phenotypes to their genotypes based on genome-wide annotations of AR genes. Resistances to trimethoprim, vancomycin, and kanamycin were the most common phenotypes. A combination of homology-based screening and manual annotation identified genes encoding resistance to aminoglycosides (20 sequences), tetracycline (18), erythromycin (6), clindamycin (60), and chloramphenicol (42). In particular, the genes
and
, involved in resistance to aminoglycosides and clindamycin, respectively, were found in
spp. Acquired determinants predicted to code for tetracycline and erythromycin resistance were detected in
,
, and
, flanked in the genome by mobile genetic elements with potential for horizontal transfer.
species are generally considered to be nonpathogenic and are used in a wide variety of foods and products for humans and animals. However, many of the species examined in this study have antibiotic resistance levels which exceed those recommended by the EFSA, suggesting that these cutoff values should be reexamined in light of the genetic basis for resistance discussed here. Our data provide evidence for rationally revising the regulatory guidelines for safety assessment of lactobacilli entering the food chain as starter cultures, food preservatives, or probiotics and will facilitate comprehensive genotype-based assessment of strains for safety screening. |
doi_str_mv | 10.1128/AEM.01738-18 |
format | Article |
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species and their carriage of antibiotic resistance (AR) genes is under continuing
review. To comprehensively update the identification of AR in the genus
, we determined the antibiotic susceptibility patterns of 182
type strains and compared these phenotypes to their genotypes based on genome-wide annotations of AR genes. Resistances to trimethoprim, vancomycin, and kanamycin were the most common phenotypes. A combination of homology-based screening and manual annotation identified genes encoding resistance to aminoglycosides (20 sequences), tetracycline (18), erythromycin (6), clindamycin (60), and chloramphenicol (42). In particular, the genes
and
, involved in resistance to aminoglycosides and clindamycin, respectively, were found in
spp. Acquired determinants predicted to code for tetracycline and erythromycin resistance were detected in
,
, and
, flanked in the genome by mobile genetic elements with potential for horizontal transfer.
species are generally considered to be nonpathogenic and are used in a wide variety of foods and products for humans and animals. However, many of the species examined in this study have antibiotic resistance levels which exceed those recommended by the EFSA, suggesting that these cutoff values should be reexamined in light of the genetic basis for resistance discussed here. Our data provide evidence for rationally revising the regulatory guidelines for safety assessment of lactobacilli entering the food chain as starter cultures, food preservatives, or probiotics and will facilitate comprehensive genotype-based assessment of strains for safety screening.</description><identifier>ISSN: 0099-2240</identifier><identifier>ISSN: 1098-5336</identifier><identifier>EISSN: 1098-5336</identifier><identifier>DOI: 10.1128/AEM.01738-18</identifier><identifier>PMID: 30366997</identifier><language>eng</language><publisher>United States: American Society for Microbiology</publisher><subject>Aminoglycosides ; Annotations ; Anti-Bacterial Agents - pharmacology ; Antibiotic resistance ; Antibiotics ; Chloramphenicol ; Chloromycetin ; Clindamycin ; Drug resistance ; Drug Resistance, Bacterial - genetics ; Erythromycin ; Food Microbiology ; Food safety ; Gene sequencing ; Genes ; Genomes ; Genotype & phenotype ; Genotypes ; Homology ; Horizontal transfer ; Kanamycin ; Lactobacillus ; Lactobacillus - drug effects ; Lactobacillus - genetics ; Phenotypes ; Probiotics ; Safety ; Species ; Spotlight ; Starter cultures ; Trimethoprim ; Vancomycin</subject><ispartof>Applied and environmental microbiology, 2019-01, Vol.85 (1)</ispartof><rights>Copyright © 2018 American Society for Microbiology.</rights><rights>Copyright American Society for Microbiology Jan 2019</rights><rights>Copyright © 2018 American Society for Microbiology. 2018 American Society for Microbiology</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c455t-9ae08efde9564cc2b59501edb3ed95ce1028da030ff2b4bb62d8827bedf3eafc3</citedby><cites>FETCH-LOGICAL-c455t-9ae08efde9564cc2b59501edb3ed95ce1028da030ff2b4bb62d8827bedf3eafc3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6293106/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6293106/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,727,780,784,885,3188,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30366997$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Björkroth, Johanna</contributor><creatorcontrib>Campedelli, Ilenia</creatorcontrib><creatorcontrib>Mathur, Harsh</creatorcontrib><creatorcontrib>Salvetti, Elisa</creatorcontrib><creatorcontrib>Clarke, Siobhán</creatorcontrib><creatorcontrib>Rea, Mary C</creatorcontrib><creatorcontrib>Torriani, Sandra</creatorcontrib><creatorcontrib>Ross, R Paul</creatorcontrib><creatorcontrib>Hill, Colin</creatorcontrib><creatorcontrib>O'Toole, Paul W</creatorcontrib><title>Genus-Wide Assessment of Antibiotic Resistance in Lactobacillus spp</title><title>Applied and environmental microbiology</title><addtitle>Appl Environ Microbiol</addtitle><description>species are widely used as probiotics and starter cultures for a variety of foods, supported by a long history of safe usage. Although more than 35 species meet the European Food Safety Authority (EFSA) criteria for qualified presumption of safety status, the safety of
species and their carriage of antibiotic resistance (AR) genes is under continuing
review. To comprehensively update the identification of AR in the genus
, we determined the antibiotic susceptibility patterns of 182
type strains and compared these phenotypes to their genotypes based on genome-wide annotations of AR genes. Resistances to trimethoprim, vancomycin, and kanamycin were the most common phenotypes. A combination of homology-based screening and manual annotation identified genes encoding resistance to aminoglycosides (20 sequences), tetracycline (18), erythromycin (6), clindamycin (60), and chloramphenicol (42). In particular, the genes
and
, involved in resistance to aminoglycosides and clindamycin, respectively, were found in
spp. Acquired determinants predicted to code for tetracycline and erythromycin resistance were detected in
,
, and
, flanked in the genome by mobile genetic elements with potential for horizontal transfer.
species are generally considered to be nonpathogenic and are used in a wide variety of foods and products for humans and animals. However, many of the species examined in this study have antibiotic resistance levels which exceed those recommended by the EFSA, suggesting that these cutoff values should be reexamined in light of the genetic basis for resistance discussed here. Our data provide evidence for rationally revising the regulatory guidelines for safety assessment of lactobacilli entering the food chain as starter cultures, food preservatives, or probiotics and will facilitate comprehensive genotype-based assessment of strains for safety screening.</description><subject>Aminoglycosides</subject><subject>Annotations</subject><subject>Anti-Bacterial Agents - pharmacology</subject><subject>Antibiotic resistance</subject><subject>Antibiotics</subject><subject>Chloramphenicol</subject><subject>Chloromycetin</subject><subject>Clindamycin</subject><subject>Drug resistance</subject><subject>Drug Resistance, Bacterial - genetics</subject><subject>Erythromycin</subject><subject>Food Microbiology</subject><subject>Food safety</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genomes</subject><subject>Genotype & phenotype</subject><subject>Genotypes</subject><subject>Homology</subject><subject>Horizontal transfer</subject><subject>Kanamycin</subject><subject>Lactobacillus</subject><subject>Lactobacillus - drug effects</subject><subject>Lactobacillus - genetics</subject><subject>Phenotypes</subject><subject>Probiotics</subject><subject>Safety</subject><subject>Species</subject><subject>Spotlight</subject><subject>Starter cultures</subject><subject>Trimethoprim</subject><subject>Vancomycin</subject><issn>0099-2240</issn><issn>1098-5336</issn><issn>1098-5336</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpdkU1LJDEQhoOs6Phx8ywNe_Gw7VaS7kxyEYbBdRdGFkTxGJJ09W6kpzN2dQv-e-PHiuupDvXw8lY9jB1xOOVc6O-L88tT4HOpS6632IyD0WUtpfrCZgDGlEJUsMv2iO4AoAKld9iuBKmUMfMZW15gP1F5GxssFkRItMZ-LFJbLPox-pjGGIorpEij6wMWsS9WLozJuxC7bqKCNpsDtt26jvDwbe6zmx_n18uf5er3xa_lYlWGqq7H0jgEjW2DplZVCMLXpgaOjZfYmDogB6EbBxLaVvjKeyUarcXcY9NKdG2Q--zsNXcz-TU2IRcdXGc3Q1y74dEmF-3_mz7-tX_Sg1XCSA4qB5y8BQzpfkIa7TpSwK5zPaaJrOBCGT7XAjL69RN6l6ahz-dlKj-7qo3hmfr2SoUhEQ3YvpfhYJ_t2GzHvtixXGf8-OMB7_A_HfIJNr-LoQ</recordid><startdate>20190101</startdate><enddate>20190101</enddate><creator>Campedelli, Ilenia</creator><creator>Mathur, Harsh</creator><creator>Salvetti, Elisa</creator><creator>Clarke, Siobhán</creator><creator>Rea, Mary C</creator><creator>Torriani, Sandra</creator><creator>Ross, R Paul</creator><creator>Hill, Colin</creator><creator>O'Toole, Paul W</creator><general>American Society for Microbiology</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7QO</scope><scope>7SN</scope><scope>7SS</scope><scope>7ST</scope><scope>7T7</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>SOI</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20190101</creationdate><title>Genus-Wide Assessment of Antibiotic Resistance in Lactobacillus spp</title><author>Campedelli, Ilenia ; Mathur, Harsh ; Salvetti, Elisa ; Clarke, Siobhán ; Rea, Mary C ; Torriani, Sandra ; Ross, R Paul ; Hill, Colin ; O'Toole, Paul W</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c455t-9ae08efde9564cc2b59501edb3ed95ce1028da030ff2b4bb62d8827bedf3eafc3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Aminoglycosides</topic><topic>Annotations</topic><topic>Anti-Bacterial Agents - pharmacology</topic><topic>Antibiotic resistance</topic><topic>Antibiotics</topic><topic>Chloramphenicol</topic><topic>Chloromycetin</topic><topic>Clindamycin</topic><topic>Drug resistance</topic><topic>Drug Resistance, Bacterial - genetics</topic><topic>Erythromycin</topic><topic>Food Microbiology</topic><topic>Food safety</topic><topic>Gene sequencing</topic><topic>Genes</topic><topic>Genomes</topic><topic>Genotype & phenotype</topic><topic>Genotypes</topic><topic>Homology</topic><topic>Horizontal transfer</topic><topic>Kanamycin</topic><topic>Lactobacillus</topic><topic>Lactobacillus - drug effects</topic><topic>Lactobacillus - genetics</topic><topic>Phenotypes</topic><topic>Probiotics</topic><topic>Safety</topic><topic>Species</topic><topic>Spotlight</topic><topic>Starter cultures</topic><topic>Trimethoprim</topic><topic>Vancomycin</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Campedelli, Ilenia</creatorcontrib><creatorcontrib>Mathur, Harsh</creatorcontrib><creatorcontrib>Salvetti, Elisa</creatorcontrib><creatorcontrib>Clarke, Siobhán</creatorcontrib><creatorcontrib>Rea, Mary C</creatorcontrib><creatorcontrib>Torriani, Sandra</creatorcontrib><creatorcontrib>Ross, R Paul</creatorcontrib><creatorcontrib>Hill, Colin</creatorcontrib><creatorcontrib>O'Toole, Paul W</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Environment Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>Environment Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Applied and environmental microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Campedelli, Ilenia</au><au>Mathur, Harsh</au><au>Salvetti, Elisa</au><au>Clarke, Siobhán</au><au>Rea, Mary C</au><au>Torriani, Sandra</au><au>Ross, R Paul</au><au>Hill, Colin</au><au>O'Toole, Paul W</au><au>Björkroth, Johanna</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genus-Wide Assessment of Antibiotic Resistance in Lactobacillus spp</atitle><jtitle>Applied and environmental microbiology</jtitle><addtitle>Appl Environ Microbiol</addtitle><date>2019-01-01</date><risdate>2019</risdate><volume>85</volume><issue>1</issue><issn>0099-2240</issn><issn>1098-5336</issn><eissn>1098-5336</eissn><abstract>species are widely used as probiotics and starter cultures for a variety of foods, supported by a long history of safe usage. Although more than 35 species meet the European Food Safety Authority (EFSA) criteria for qualified presumption of safety status, the safety of
species and their carriage of antibiotic resistance (AR) genes is under continuing
review. To comprehensively update the identification of AR in the genus
, we determined the antibiotic susceptibility patterns of 182
type strains and compared these phenotypes to their genotypes based on genome-wide annotations of AR genes. Resistances to trimethoprim, vancomycin, and kanamycin were the most common phenotypes. A combination of homology-based screening and manual annotation identified genes encoding resistance to aminoglycosides (20 sequences), tetracycline (18), erythromycin (6), clindamycin (60), and chloramphenicol (42). In particular, the genes
and
, involved in resistance to aminoglycosides and clindamycin, respectively, were found in
spp. Acquired determinants predicted to code for tetracycline and erythromycin resistance were detected in
,
, and
, flanked in the genome by mobile genetic elements with potential for horizontal transfer.
species are generally considered to be nonpathogenic and are used in a wide variety of foods and products for humans and animals. However, many of the species examined in this study have antibiotic resistance levels which exceed those recommended by the EFSA, suggesting that these cutoff values should be reexamined in light of the genetic basis for resistance discussed here. Our data provide evidence for rationally revising the regulatory guidelines for safety assessment of lactobacilli entering the food chain as starter cultures, food preservatives, or probiotics and will facilitate comprehensive genotype-based assessment of strains for safety screening.</abstract><cop>United States</cop><pub>American Society for Microbiology</pub><pmid>30366997</pmid><doi>10.1128/AEM.01738-18</doi><oa>free_for_read</oa></addata></record> |
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source | MEDLINE; American Society for Microbiology Journals; PubMed Central; Alma/SFX Local Collection |
subjects | Aminoglycosides Annotations Anti-Bacterial Agents - pharmacology Antibiotic resistance Antibiotics Chloramphenicol Chloromycetin Clindamycin Drug resistance Drug Resistance, Bacterial - genetics Erythromycin Food Microbiology Food safety Gene sequencing Genes Genomes Genotype & phenotype Genotypes Homology Horizontal transfer Kanamycin Lactobacillus Lactobacillus - drug effects Lactobacillus - genetics Phenotypes Probiotics Safety Species Spotlight Starter cultures Trimethoprim Vancomycin |
title | Genus-Wide Assessment of Antibiotic Resistance in Lactobacillus spp |
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