Whole genome sequencing and antibiotic diffusion assays, provide new insight on drug resistance in the genus Pedobacter
ABSTRACT A total of four strains of the ‘environmental superbug’ Pedobacter isolated from sludge produced at Norwegian drinking water treatment plants, were characterized by whole genome sequencing and antibiotic susceptibility assays. As with previous studies on members of this genus, we found that...
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| Veröffentlicht in: | FEMS microbiology ecology 2020-06, Vol.96 (6), p.1 |
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| creator | Ullmann, Ingvild Falkum Nygaard, Anders Benteson Tunsjø, Hege Smith Charnock, Colin |
| description | ABSTRACT
A total of four strains of the ‘environmental superbug’ Pedobacter isolated from sludge produced at Norwegian drinking water treatment plants, were characterized by whole genome sequencing and antibiotic susceptibility assays. As with previous studies on members of this genus, we found that the isolates were multi-drug resistant, and that this resistance included clinically important beta-lactams, aminoglycosides and the fluoroquinolone ciprofloxacin. Using the minION sequencing platform (Oxford Nanopore Technologies) combined with HiSeq PE150 Illumina sequencing data, the four isolates were assembled into genomes of single contigs. Analysis of the genomes revealed potential genetic factors possibly underlying some of the specific resistances observed. Metallo-beta-lactamase activity was detected in one isolate, and the same isolate contained a putative metallo-betalactamase gene resembling pedo-2. Furthermore, several genes related to multidrug efflux systems were found using the resistance database CARD. Additionally, the present study extends our knowledge on the phylogeny of this genus, adding four new genomes to the existing 50.
Whole genome sequencing of the environmental superbugs™ Pedobacter spp. provides insights on their multi-drug resistance. |
| doi_str_mv | 10.1093/femsec/fiaa088 |
| format | Article |
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A total of four strains of the ‘environmental superbug’ Pedobacter isolated from sludge produced at Norwegian drinking water treatment plants, were characterized by whole genome sequencing and antibiotic susceptibility assays. As with previous studies on members of this genus, we found that the isolates were multi-drug resistant, and that this resistance included clinically important beta-lactams, aminoglycosides and the fluoroquinolone ciprofloxacin. Using the minION sequencing platform (Oxford Nanopore Technologies) combined with HiSeq PE150 Illumina sequencing data, the four isolates were assembled into genomes of single contigs. Analysis of the genomes revealed potential genetic factors possibly underlying some of the specific resistances observed. Metallo-beta-lactamase activity was detected in one isolate, and the same isolate contained a putative metallo-betalactamase gene resembling pedo-2. Furthermore, several genes related to multidrug efflux systems were found using the resistance database CARD. Additionally, the present study extends our knowledge on the phylogeny of this genus, adding four new genomes to the existing 50.
Whole genome sequencing of the environmental superbugs™ Pedobacter spp. provides insights on their multi-drug resistance.</description><identifier>ISSN: 0168-6496</identifier><identifier>EISSN: 1574-6941</identifier><identifier>DOI: 10.1093/femsec/fiaa088</identifier><identifier>PMID: 32386210</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Aminoglycosides ; Analysis ; Antibiotics ; Antimicrobial agents ; Ciprofloxacin ; Contamination ; Distribution ; DNA sequencing ; Drinking water ; Drug resistance ; Drug resistance in microorganisms ; Ecology ; Efflux ; Environmental aspects ; Gene sequencing ; Genetic aspects ; Genetic factors ; Genomes ; Gram-negative bacteria ; Metallo-β-lactamase ; Metallography ; Microbiology ; Multidrug resistance ; Nucleotide sequencing ; Phylogeny ; Porosity ; Sludge ; Water treatment ; Water treatment plants ; Whole genome sequencing ; β Lactamase ; β-Lactam antibiotics</subject><ispartof>FEMS microbiology ecology, 2020-06, Vol.96 (6), p.1</ispartof><rights>FEMS 2020. 2020</rights><rights>FEMS 2020.</rights><rights>COPYRIGHT 2020 Oxford University Press</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c519t-74f5636243fa159621ff6f6c40c1df8688b28684b9d87adf3d91d1a2925fc2ed3</citedby><cites>FETCH-LOGICAL-c519t-74f5636243fa159621ff6f6c40c1df8688b28684b9d87adf3d91d1a2925fc2ed3</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/PMC7254926/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7254926/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,724,777,781,882,1599,27905,27906,53772,53774</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32386210$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Ullmann, Ingvild Falkum</creatorcontrib><creatorcontrib>Nygaard, Anders Benteson</creatorcontrib><creatorcontrib>Tunsjø, Hege Smith</creatorcontrib><creatorcontrib>Charnock, Colin</creatorcontrib><title>Whole genome sequencing and antibiotic diffusion assays, provide new insight on drug resistance in the genus Pedobacter</title><title>FEMS microbiology ecology</title><addtitle>FEMS Microbiol Ecol</addtitle><description>ABSTRACT
A total of four strains of the ‘environmental superbug’ Pedobacter isolated from sludge produced at Norwegian drinking water treatment plants, were characterized by whole genome sequencing and antibiotic susceptibility assays. As with previous studies on members of this genus, we found that the isolates were multi-drug resistant, and that this resistance included clinically important beta-lactams, aminoglycosides and the fluoroquinolone ciprofloxacin. Using the minION sequencing platform (Oxford Nanopore Technologies) combined with HiSeq PE150 Illumina sequencing data, the four isolates were assembled into genomes of single contigs. Analysis of the genomes revealed potential genetic factors possibly underlying some of the specific resistances observed. Metallo-beta-lactamase activity was detected in one isolate, and the same isolate contained a putative metallo-betalactamase gene resembling pedo-2. Furthermore, several genes related to multidrug efflux systems were found using the resistance database CARD. Additionally, the present study extends our knowledge on the phylogeny of this genus, adding four new genomes to the existing 50.
Whole genome sequencing of the environmental superbugs™ Pedobacter spp. provides insights on their multi-drug resistance.</description><subject>Aminoglycosides</subject><subject>Analysis</subject><subject>Antibiotics</subject><subject>Antimicrobial agents</subject><subject>Ciprofloxacin</subject><subject>Contamination</subject><subject>Distribution</subject><subject>DNA sequencing</subject><subject>Drinking water</subject><subject>Drug resistance</subject><subject>Drug resistance in microorganisms</subject><subject>Ecology</subject><subject>Efflux</subject><subject>Environmental aspects</subject><subject>Gene sequencing</subject><subject>Genetic aspects</subject><subject>Genetic factors</subject><subject>Genomes</subject><subject>Gram-negative bacteria</subject><subject>Metallo-β-lactamase</subject><subject>Metallography</subject><subject>Microbiology</subject><subject>Multidrug resistance</subject><subject>Nucleotide sequencing</subject><subject>Phylogeny</subject><subject>Porosity</subject><subject>Sludge</subject><subject>Water treatment</subject><subject>Water treatment plants</subject><subject>Whole genome sequencing</subject><subject>β Lactamase</subject><subject>β-Lactam 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genome sequencing and antibiotic diffusion assays, provide new insight on drug resistance in the genus Pedobacter</title><author>Ullmann, Ingvild Falkum ; Nygaard, Anders Benteson ; Tunsjø, Hege Smith ; Charnock, Colin</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c519t-74f5636243fa159621ff6f6c40c1df8688b28684b9d87adf3d91d1a2925fc2ed3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Aminoglycosides</topic><topic>Analysis</topic><topic>Antibiotics</topic><topic>Antimicrobial agents</topic><topic>Ciprofloxacin</topic><topic>Contamination</topic><topic>Distribution</topic><topic>DNA sequencing</topic><topic>Drinking water</topic><topic>Drug resistance</topic><topic>Drug resistance in microorganisms</topic><topic>Ecology</topic><topic>Efflux</topic><topic>Environmental aspects</topic><topic>Gene sequencing</topic><topic>Genetic aspects</topic><topic>Genetic 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Colin</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Whole genome sequencing and antibiotic diffusion assays, provide new insight on drug resistance in the genus Pedobacter</atitle><jtitle>FEMS microbiology ecology</jtitle><addtitle>FEMS Microbiol Ecol</addtitle><date>2020-06-01</date><risdate>2020</risdate><volume>96</volume><issue>6</issue><spage>1</spage><pages>1-</pages><issn>0168-6496</issn><eissn>1574-6941</eissn><abstract>ABSTRACT
A total of four strains of the ‘environmental superbug’ Pedobacter isolated from sludge produced at Norwegian drinking water treatment plants, were characterized by whole genome sequencing and antibiotic susceptibility assays. As with previous studies on members of this genus, we found that the isolates were multi-drug resistant, and that this resistance included clinically important beta-lactams, aminoglycosides and the fluoroquinolone ciprofloxacin. Using the minION sequencing platform (Oxford Nanopore Technologies) combined with HiSeq PE150 Illumina sequencing data, the four isolates were assembled into genomes of single contigs. Analysis of the genomes revealed potential genetic factors possibly underlying some of the specific resistances observed. Metallo-beta-lactamase activity was detected in one isolate, and the same isolate contained a putative metallo-betalactamase gene resembling pedo-2. Furthermore, several genes related to multidrug efflux systems were found using the resistance database CARD. Additionally, the present study extends our knowledge on the phylogeny of this genus, adding four new genomes to the existing 50.
Whole genome sequencing of the environmental superbugs™ Pedobacter spp. provides insights on their multi-drug resistance.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>32386210</pmid><doi>10.1093/femsec/fiaa088</doi><oa>free_for_read</oa></addata></record> |
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| source | Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Oxford Journals Open Access Collection; PubMed Central |
| subjects | Aminoglycosides Analysis Antibiotics Antimicrobial agents Ciprofloxacin Contamination Distribution DNA sequencing Drinking water Drug resistance Drug resistance in microorganisms Ecology Efflux Environmental aspects Gene sequencing Genetic aspects Genetic factors Genomes Gram-negative bacteria Metallo-β-lactamase Metallography Microbiology Multidrug resistance Nucleotide sequencing Phylogeny Porosity Sludge Water treatment Water treatment plants Whole genome sequencing β Lactamase β-Lactam antibiotics |
| title | Whole genome sequencing and antibiotic diffusion assays, provide new insight on drug resistance in the genus Pedobacter |
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