Sequencing of fosA: A Rapid and Inexpensive Method for Discriminating Klebsiella pneumoniae CC258 from Other Clones
Typing carbapenem-resistant Klebsiella pneumoniae (CR-KPN) is crucial in controlling their dissemination and solving outbreaks. In this context, we searched for an effective, faster, and cheaper alternative technique to type KPN by analyzing the fosA KP sequence. We analyzed the nucleotide sequences...
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Veröffentlicht in: | Microbial drug resistance (Larchmont, N.Y.) N.Y.), 2022-11, Vol.28 (11), p.137-1042 |
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creator | Ribeiro, Ághata Cardoso da Silva Santos, Fernanda Fernandes Moses, Ikechukwu Benjamin Minarini, Luciene Andrade da Rocha Gales, Ana Cristina |
description | Typing carbapenem-resistant
Klebsiella pneumoniae
(CR-KPN) is crucial in controlling their dissemination and solving outbreaks. In this context, we searched for an effective, faster, and cheaper alternative technique to type KPN by analyzing the
fosA
KP
sequence. We analyzed the nucleotide sequences of chromosomal
fosA
KP
gene in 350 KPN genomes (70 per sequence type [ST] or clonal complex [CC]). Assembly genomes were randomly downloaded from NCBI and annotated using RAST in PATRIC platform. The isolate STs were verified using multilocus sequence typing 2.0 by the Center for Genomic Epidemiology. Chromosomally encoded
fosA
KP
was confirmed in MLplasmid, and the sequence alignments were performed in Clustal Omega. The amino acid sequences were analyzed using SNAP2 and SMART platforms. Out of the 70 genomes analyzed for each ST/CC, we observed 100%
fosA
sequence identity for CC258/11, ST15, ST307, and ST101. For ST16, only two
fosA
sequences were different from each other. We observed differences in amino acid sequences at positions 25 and 79 (ST16) and 86 (ST16, ST101). The C-terminal (amino acid 138, 139, 140) was different for each cluster. None of these polymorphisms is related to the protein active site. Moreover, L25Q (ST16) polymorphism was predicted to probably affect the protein function. We observed that chromosomal
fosA
KP
sequences from KPN are highly conserved in ST15, ST307, ST16, ST101, and CC258/11, suggesting
fosA
KP
sequencing as an alternative, easier, faster, and less expensive technique in identifying epidemiological STs for KPN, and discriminating them from CC258/11. |
doi_str_mv | 10.1089/mdr.2022.0081 |
format | Article |
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Klebsiella pneumoniae
(CR-KPN) is crucial in controlling their dissemination and solving outbreaks. In this context, we searched for an effective, faster, and cheaper alternative technique to type KPN by analyzing the
fosA
KP
sequence. We analyzed the nucleotide sequences of chromosomal
fosA
KP
gene in 350 KPN genomes (70 per sequence type [ST] or clonal complex [CC]). Assembly genomes were randomly downloaded from NCBI and annotated using RAST in PATRIC platform. The isolate STs were verified using multilocus sequence typing 2.0 by the Center for Genomic Epidemiology. Chromosomally encoded
fosA
KP
was confirmed in MLplasmid, and the sequence alignments were performed in Clustal Omega. The amino acid sequences were analyzed using SNAP2 and SMART platforms. Out of the 70 genomes analyzed for each ST/CC, we observed 100%
fosA
sequence identity for CC258/11, ST15, ST307, and ST101. For ST16, only two
fosA
sequences were different from each other. We observed differences in amino acid sequences at positions 25 and 79 (ST16) and 86 (ST16, ST101). The C-terminal (amino acid 138, 139, 140) was different for each cluster. None of these polymorphisms is related to the protein active site. Moreover, L25Q (ST16) polymorphism was predicted to probably affect the protein function. We observed that chromosomal
fosA
KP
sequences from KPN are highly conserved in ST15, ST307, ST16, ST101, and CC258/11, suggesting
fosA
KP
sequencing as an alternative, easier, faster, and less expensive technique in identifying epidemiological STs for KPN, and discriminating them from CC258/11.</description><identifier>ISSN: 1076-6294</identifier><identifier>EISSN: 1931-8448</identifier><identifier>DOI: 10.1089/mdr.2022.0081</identifier><language>eng</language><publisher>New Rochelle: Mary Ann Liebert, Inc., publishers</publisher><subject>Amino acid sequence ; Amino acids ; Epidemiology ; Gene polymorphism ; Genomes ; Klebsiella ; Klebsiella pneumoniae ; Multilocus sequence typing ; Nucleotides ; Polymorphism ; Proteins</subject><ispartof>Microbial drug resistance (Larchmont, N.Y.), 2022-11, Vol.28 (11), p.137-1042</ispartof><rights>2022, Mary Ann Liebert, Inc., publishers</rights><rights>Copyright Mary Ann Liebert, Inc. Nov 2022</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c272t-4b4d314a3cd65a862e735154e85042af1a6ee4b3b1bb987bf5c0e8c54a9e8a673</citedby><cites>FETCH-LOGICAL-c272t-4b4d314a3cd65a862e735154e85042af1a6ee4b3b1bb987bf5c0e8c54a9e8a673</cites><orcidid>0000-0002-4997-0505 ; 0000-0003-0913-768X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27915,27916</link.rule.ids></links><search><creatorcontrib>Ribeiro, Ághata Cardoso da Silva</creatorcontrib><creatorcontrib>Santos, Fernanda Fernandes</creatorcontrib><creatorcontrib>Moses, Ikechukwu Benjamin</creatorcontrib><creatorcontrib>Minarini, Luciene Andrade da Rocha</creatorcontrib><creatorcontrib>Gales, Ana Cristina</creatorcontrib><title>Sequencing of fosA: A Rapid and Inexpensive Method for Discriminating Klebsiella pneumoniae CC258 from Other Clones</title><title>Microbial drug resistance (Larchmont, N.Y.)</title><description>Typing carbapenem-resistant
Klebsiella pneumoniae
(CR-KPN) is crucial in controlling their dissemination and solving outbreaks. In this context, we searched for an effective, faster, and cheaper alternative technique to type KPN by analyzing the
fosA
KP
sequence. We analyzed the nucleotide sequences of chromosomal
fosA
KP
gene in 350 KPN genomes (70 per sequence type [ST] or clonal complex [CC]). Assembly genomes were randomly downloaded from NCBI and annotated using RAST in PATRIC platform. The isolate STs were verified using multilocus sequence typing 2.0 by the Center for Genomic Epidemiology. Chromosomally encoded
fosA
KP
was confirmed in MLplasmid, and the sequence alignments were performed in Clustal Omega. The amino acid sequences were analyzed using SNAP2 and SMART platforms. Out of the 70 genomes analyzed for each ST/CC, we observed 100%
fosA
sequence identity for CC258/11, ST15, ST307, and ST101. For ST16, only two
fosA
sequences were different from each other. We observed differences in amino acid sequences at positions 25 and 79 (ST16) and 86 (ST16, ST101). The C-terminal (amino acid 138, 139, 140) was different for each cluster. None of these polymorphisms is related to the protein active site. Moreover, L25Q (ST16) polymorphism was predicted to probably affect the protein function. We observed that chromosomal
fosA
KP
sequences from KPN are highly conserved in ST15, ST307, ST16, ST101, and CC258/11, suggesting
fosA
KP
sequencing as an alternative, easier, faster, and less expensive technique in identifying epidemiological STs for KPN, and discriminating them from CC258/11.</description><subject>Amino acid sequence</subject><subject>Amino acids</subject><subject>Epidemiology</subject><subject>Gene polymorphism</subject><subject>Genomes</subject><subject>Klebsiella</subject><subject>Klebsiella pneumoniae</subject><subject>Multilocus sequence typing</subject><subject>Nucleotides</subject><subject>Polymorphism</subject><subject>Proteins</subject><issn>1076-6294</issn><issn>1931-8448</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><recordid>eNqFkTtPwzAUhSMEEqUwsltiYUnxM3HYqvCqKKrEY46c5Ia6SuxgJwj-PY7KxMJ07_Cdo3PviaJzghcEy-yqq92CYkoXGEtyEM1IxkgsOZeHYcdpEic048fRifc7jLEgCZtF_gU-RjCVNu_INqixfnmNluhZ9bpGytRoZeCrB-P1J6AnGLa2DpBDN9pXTnfaqGGSPrZQeg1tq1BvYOys0QpQnlMhUeNshzbDFhzKW2vAn0ZHjWo9nP3OefR2d_uaP8Trzf0qX67jiqZ0iHnJa0a4YlWdCCUTCikTRHCQAnOqGqISAF6ykpRlJtOyERUGWQmuMpAqSdk8utz79s6GI_1QdCH1FNKAHX1B02BPEy55QC_-oDs7OhPSTZTIGA2_DFS8pypnvXfQFH34gXLfBcHFVEERKiimCoqpgsCzPT8xyphWQwlu-Ef1A8WYiis</recordid><startdate>20221101</startdate><enddate>20221101</enddate><creator>Ribeiro, Ághata Cardoso da Silva</creator><creator>Santos, Fernanda Fernandes</creator><creator>Moses, Ikechukwu Benjamin</creator><creator>Minarini, Luciene Andrade da Rocha</creator><creator>Gales, Ana Cristina</creator><general>Mary Ann Liebert, Inc., publishers</general><general>Mary Ann Liebert, Inc</general><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7QP</scope><scope>7QR</scope><scope>7T7</scope><scope>7TK</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-4997-0505</orcidid><orcidid>https://orcid.org/0000-0003-0913-768X</orcidid></search><sort><creationdate>20221101</creationdate><title>Sequencing of fosA: A Rapid and Inexpensive Method for Discriminating Klebsiella pneumoniae CC258 from Other Clones</title><author>Ribeiro, Ághata Cardoso da Silva ; Santos, Fernanda Fernandes ; Moses, Ikechukwu Benjamin ; Minarini, Luciene Andrade da Rocha ; Gales, Ana Cristina</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c272t-4b4d314a3cd65a862e735154e85042af1a6ee4b3b1bb987bf5c0e8c54a9e8a673</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Amino acid sequence</topic><topic>Amino acids</topic><topic>Epidemiology</topic><topic>Gene polymorphism</topic><topic>Genomes</topic><topic>Klebsiella</topic><topic>Klebsiella pneumoniae</topic><topic>Multilocus sequence typing</topic><topic>Nucleotides</topic><topic>Polymorphism</topic><topic>Proteins</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ribeiro, Ághata Cardoso da Silva</creatorcontrib><creatorcontrib>Santos, Fernanda Fernandes</creatorcontrib><creatorcontrib>Moses, Ikechukwu Benjamin</creatorcontrib><creatorcontrib>Minarini, Luciene Andrade da Rocha</creatorcontrib><creatorcontrib>Gales, Ana Cristina</creatorcontrib><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Neurosciences Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Microbial drug resistance (Larchmont, N.Y.)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ribeiro, Ághata Cardoso da Silva</au><au>Santos, Fernanda Fernandes</au><au>Moses, Ikechukwu Benjamin</au><au>Minarini, Luciene Andrade da Rocha</au><au>Gales, Ana Cristina</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Sequencing of fosA: A Rapid and Inexpensive Method for Discriminating Klebsiella pneumoniae CC258 from Other Clones</atitle><jtitle>Microbial drug resistance (Larchmont, N.Y.)</jtitle><date>2022-11-01</date><risdate>2022</risdate><volume>28</volume><issue>11</issue><spage>137</spage><epage>1042</epage><pages>137-1042</pages><issn>1076-6294</issn><eissn>1931-8448</eissn><abstract>Typing carbapenem-resistant
Klebsiella pneumoniae
(CR-KPN) is crucial in controlling their dissemination and solving outbreaks. In this context, we searched for an effective, faster, and cheaper alternative technique to type KPN by analyzing the
fosA
KP
sequence. We analyzed the nucleotide sequences of chromosomal
fosA
KP
gene in 350 KPN genomes (70 per sequence type [ST] or clonal complex [CC]). Assembly genomes were randomly downloaded from NCBI and annotated using RAST in PATRIC platform. The isolate STs were verified using multilocus sequence typing 2.0 by the Center for Genomic Epidemiology. Chromosomally encoded
fosA
KP
was confirmed in MLplasmid, and the sequence alignments were performed in Clustal Omega. The amino acid sequences were analyzed using SNAP2 and SMART platforms. Out of the 70 genomes analyzed for each ST/CC, we observed 100%
fosA
sequence identity for CC258/11, ST15, ST307, and ST101. For ST16, only two
fosA
sequences were different from each other. We observed differences in amino acid sequences at positions 25 and 79 (ST16) and 86 (ST16, ST101). The C-terminal (amino acid 138, 139, 140) was different for each cluster. None of these polymorphisms is related to the protein active site. Moreover, L25Q (ST16) polymorphism was predicted to probably affect the protein function. We observed that chromosomal
fosA
KP
sequences from KPN are highly conserved in ST15, ST307, ST16, ST101, and CC258/11, suggesting
fosA
KP
sequencing as an alternative, easier, faster, and less expensive technique in identifying epidemiological STs for KPN, and discriminating them from CC258/11.</abstract><cop>New Rochelle</cop><pub>Mary Ann Liebert, Inc., publishers</pub><doi>10.1089/mdr.2022.0081</doi><tpages>906</tpages><orcidid>https://orcid.org/0000-0002-4997-0505</orcidid><orcidid>https://orcid.org/0000-0003-0913-768X</orcidid></addata></record> |
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issn | 1076-6294 1931-8448 |
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source | Alma/SFX Local Collection |
subjects | Amino acid sequence Amino acids Epidemiology Gene polymorphism Genomes Klebsiella Klebsiella pneumoniae Multilocus sequence typing Nucleotides Polymorphism Proteins |
title | Sequencing of fosA: A Rapid and Inexpensive Method for Discriminating Klebsiella pneumoniae CC258 from Other Clones |
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