Phenotypic and molecular characterization of Streptococcus pneumoniae serotype 3 isolates from blood and respiratory samples in Canada: CANWARD 2007–21
Abstract Background Lower respiratory infections and invasive disease caused by Streptococcus pneumoniae serotype 3 remain major clinical challenges around the world, despite widespread availability of updated vaccines. Methods As part of CANWARD, antimicrobial susceptibility testing and serotyping...
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description | Abstract
Background
Lower respiratory infections and invasive disease caused by Streptococcus pneumoniae serotype 3 remain major clinical challenges around the world, despite widespread availability of updated vaccines.
Methods
As part of CANWARD, antimicrobial susceptibility testing and serotyping were performed on all S. pneumoniae isolates from 2007 to 2021. A subset of 226/264 (85.6%) serotype 3 isolates were selected for WGS to determine sequence type (ST)/clonal cluster (CC) and correspondence of antimicrobial resistance determinants (erm, mefAE, tetM, cat, folA, folP) with resistance phenotype.
Results
Of the 3,039 S. pneumoniae isolates obtained from 2007 to 2021, 8.7% (n = 264) were serotype 3, with 64.0% of respiratory origin and 36.0% from blood. Of 226 sequenced serotype 3 isolates, 184 (81.4%) were ST180 (GPSC12). The proportion of ST8561 (single locus variant of ST180) increased from 7.2% to 16.6% during the study period. An increasing proportion of serotype 3 isolates had phenotypic resistance (P = 0.0007) and genetic resistance determinants (P = 0.004), comparing 2017–21 to 2007–11, largely due to a recently expanded ST180 clade with cat, tetM and mef determinants.
Conclusions
S. pneumoniae serotype 3 from GPSC12 continues to dominate throughout Canada, with an increase in the proportion of ST8561. The proportion of serotype 3 isolates that are phenotypically resistant and with genetic resistance determinants is increasing over time, reflecting a global increase in GPSC12 genotypes with known resistance determinants. Phylogenomic characterization of isolates collected over time and from around the world may facilitate improved treatment and enhanced prevention strategies, including new vaccines with activity against S. pneumoniae serotype 3. |
doi_str_mv | 10.1093/jac/dkae272 |
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Background
Lower respiratory infections and invasive disease caused by Streptococcus pneumoniae serotype 3 remain major clinical challenges around the world, despite widespread availability of updated vaccines.
Methods
As part of CANWARD, antimicrobial susceptibility testing and serotyping were performed on all S. pneumoniae isolates from 2007 to 2021. A subset of 226/264 (85.6%) serotype 3 isolates were selected for WGS to determine sequence type (ST)/clonal cluster (CC) and correspondence of antimicrobial resistance determinants (erm, mefAE, tetM, cat, folA, folP) with resistance phenotype.
Results
Of the 3,039 S. pneumoniae isolates obtained from 2007 to 2021, 8.7% (n = 264) were serotype 3, with 64.0% of respiratory origin and 36.0% from blood. Of 226 sequenced serotype 3 isolates, 184 (81.4%) were ST180 (GPSC12). The proportion of ST8561 (single locus variant of ST180) increased from 7.2% to 16.6% during the study period. An increasing proportion of serotype 3 isolates had phenotypic resistance (P = 0.0007) and genetic resistance determinants (P = 0.004), comparing 2017–21 to 2007–11, largely due to a recently expanded ST180 clade with cat, tetM and mef determinants.
Conclusions
S. pneumoniae serotype 3 from GPSC12 continues to dominate throughout Canada, with an increase in the proportion of ST8561. The proportion of serotype 3 isolates that are phenotypically resistant and with genetic resistance determinants is increasing over time, reflecting a global increase in GPSC12 genotypes with known resistance determinants. Phylogenomic characterization of isolates collected over time and from around the world may facilitate improved treatment and enhanced prevention strategies, including new vaccines with activity against S. pneumoniae serotype 3.</description><identifier>ISSN: 0305-7453</identifier><identifier>ISSN: 1460-2091</identifier><identifier>EISSN: 1460-2091</identifier><identifier>DOI: 10.1093/jac/dkae272</identifier><identifier>PMID: 39092981</identifier><language>eng</language><publisher>UK: Oxford University Press</publisher><subject>Adolescent ; Adult ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents - pharmacology ; Canada - epidemiology ; Child ; Child, Preschool ; Drug Resistance, Bacterial - genetics ; Female ; Genotype ; Humans ; Infant ; Male ; Microbial Sensitivity Tests ; Middle Aged ; Multilocus Sequence Typing ; Original Research ; Phenotype ; Pneumococcal Infections - epidemiology ; Pneumococcal Infections - microbiology ; Respiratory Tract Infections - epidemiology ; Respiratory Tract Infections - microbiology ; Serogroup ; Serotyping ; Streptococcus pneumoniae - classification ; Streptococcus pneumoniae - drug effects ; Streptococcus pneumoniae - genetics ; Streptococcus pneumoniae - isolation & purification ; Whole Genome Sequencing ; Young Adult</subject><ispartof>Journal of antimicrobial chemotherapy, 2024-10, Vol.79 (10), p.2653-2661</ispartof><rights>The Author(s) 2024. Published by Oxford University Press on behalf of British Society for Antimicrobial Chemotherapy. 2024</rights><rights>The Author(s) 2024. Published by Oxford University Press on behalf of British Society for Antimicrobial Chemotherapy.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c301t-585a902cf58a0ab58dcd48486de6b4067bd7fb6e691a8a0d7a5549959808ddb33</cites><orcidid>0000-0002-3238-0082 ; 0000-0002-1788-1794</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,780,784,885,1584,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/39092981$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Schellenberg, John J</creatorcontrib><creatorcontrib>Adam, Heather J</creatorcontrib><creatorcontrib>Baxter, Melanie R</creatorcontrib><creatorcontrib>Karlowsky, James A</creatorcontrib><creatorcontrib>Golden, Alyssa R</creatorcontrib><creatorcontrib>Martin, Irene</creatorcontrib><creatorcontrib>Zhanel, George G</creatorcontrib><title>Phenotypic and molecular characterization of Streptococcus pneumoniae serotype 3 isolates from blood and respiratory samples in Canada: CANWARD 2007–21</title><title>Journal of antimicrobial chemotherapy</title><addtitle>J Antimicrob Chemother</addtitle><description>Abstract
Background
Lower respiratory infections and invasive disease caused by Streptococcus pneumoniae serotype 3 remain major clinical challenges around the world, despite widespread availability of updated vaccines.
Methods
As part of CANWARD, antimicrobial susceptibility testing and serotyping were performed on all S. pneumoniae isolates from 2007 to 2021. A subset of 226/264 (85.6%) serotype 3 isolates were selected for WGS to determine sequence type (ST)/clonal cluster (CC) and correspondence of antimicrobial resistance determinants (erm, mefAE, tetM, cat, folA, folP) with resistance phenotype.
Results
Of the 3,039 S. pneumoniae isolates obtained from 2007 to 2021, 8.7% (n = 264) were serotype 3, with 64.0% of respiratory origin and 36.0% from blood. Of 226 sequenced serotype 3 isolates, 184 (81.4%) were ST180 (GPSC12). The proportion of ST8561 (single locus variant of ST180) increased from 7.2% to 16.6% during the study period. An increasing proportion of serotype 3 isolates had phenotypic resistance (P = 0.0007) and genetic resistance determinants (P = 0.004), comparing 2017–21 to 2007–11, largely due to a recently expanded ST180 clade with cat, tetM and mef determinants.
Conclusions
S. pneumoniae serotype 3 from GPSC12 continues to dominate throughout Canada, with an increase in the proportion of ST8561. The proportion of serotype 3 isolates that are phenotypically resistant and with genetic resistance determinants is increasing over time, reflecting a global increase in GPSC12 genotypes with known resistance determinants. Phylogenomic characterization of isolates collected over time and from around the world may facilitate improved treatment and enhanced prevention strategies, including new vaccines with activity against S. pneumoniae serotype 3.</description><subject>Adolescent</subject><subject>Adult</subject><subject>Aged</subject><subject>Aged, 80 and over</subject><subject>Anti-Bacterial Agents - pharmacology</subject><subject>Canada - epidemiology</subject><subject>Child</subject><subject>Child, Preschool</subject><subject>Drug Resistance, Bacterial - genetics</subject><subject>Female</subject><subject>Genotype</subject><subject>Humans</subject><subject>Infant</subject><subject>Male</subject><subject>Microbial Sensitivity Tests</subject><subject>Middle Aged</subject><subject>Multilocus Sequence Typing</subject><subject>Original Research</subject><subject>Phenotype</subject><subject>Pneumococcal Infections - epidemiology</subject><subject>Pneumococcal Infections - microbiology</subject><subject>Respiratory Tract Infections - epidemiology</subject><subject>Respiratory Tract Infections - microbiology</subject><subject>Serogroup</subject><subject>Serotyping</subject><subject>Streptococcus pneumoniae - classification</subject><subject>Streptococcus pneumoniae - drug effects</subject><subject>Streptococcus pneumoniae - genetics</subject><subject>Streptococcus pneumoniae - isolation & purification</subject><subject>Whole Genome Sequencing</subject><subject>Young Adult</subject><issn>0305-7453</issn><issn>1460-2091</issn><issn>1460-2091</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNp9kT2P1DAQQC0E4paDih65Qkgo3Di2k5gGrZbjQzoB4kOU1sR2WB-JHezkpKXiP1Dx9_gl5NjlBA3VFPP0ZqRHyF0GjxgofnKO5sR-RlfW5TWyYqKCogTFrpMVcJBFLSQ_IrdyPgeASlbNTXLEFahSNWxFfrzZuhCn3egNxWDpEHtn5h4TNVtMaCaX_FecfAw0dvTdlNw4RRONmTMdg5uHGDw6ml26lDjKqc-xx8ll2qU40LaP0f42J5dHn3CKaUczDmO_ID7QDQa0-Jhu1q8-rt8-pSVA_fPb95LdJjc67LO7c5jH5MOz0_ebF8XZ6-cvN-uzwnBgUyEbiQpK08kGAVvZWGNFI5rKuqoVUNWtrbu2cpViuBC2RimFUlI10Fjbcn5Mnuy949wOzhoXpoS9HpMfMO10RK__3QS_1Z_ihWZMiOVbsRgeHAwpfpldnvTgs3F9j8HFOWsOTc1lLQAW9OEeNSnmnFx3dYeBvqypl5r6UHOh7_392hX7J98C3N8DcR7_a_oFx06s8Q</recordid><startdate>20241001</startdate><enddate>20241001</enddate><creator>Schellenberg, John J</creator><creator>Adam, Heather J</creator><creator>Baxter, Melanie R</creator><creator>Karlowsky, James A</creator><creator>Golden, Alyssa R</creator><creator>Martin, Irene</creator><creator>Zhanel, George G</creator><general>Oxford University Press</general><scope>TOX</scope><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>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-3238-0082</orcidid><orcidid>https://orcid.org/0000-0002-1788-1794</orcidid></search><sort><creationdate>20241001</creationdate><title>Phenotypic and molecular characterization of Streptococcus pneumoniae serotype 3 isolates from blood and respiratory samples in Canada: CANWARD 2007–21</title><author>Schellenberg, John J ; Adam, Heather J ; Baxter, Melanie R ; Karlowsky, James A ; Golden, Alyssa R ; Martin, Irene ; Zhanel, George G</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c301t-585a902cf58a0ab58dcd48486de6b4067bd7fb6e691a8a0d7a5549959808ddb33</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Adolescent</topic><topic>Adult</topic><topic>Aged</topic><topic>Aged, 80 and over</topic><topic>Anti-Bacterial Agents - pharmacology</topic><topic>Canada - epidemiology</topic><topic>Child</topic><topic>Child, Preschool</topic><topic>Drug Resistance, Bacterial - genetics</topic><topic>Female</topic><topic>Genotype</topic><topic>Humans</topic><topic>Infant</topic><topic>Male</topic><topic>Microbial Sensitivity Tests</topic><topic>Middle Aged</topic><topic>Multilocus Sequence Typing</topic><topic>Original Research</topic><topic>Phenotype</topic><topic>Pneumococcal Infections - epidemiology</topic><topic>Pneumococcal Infections - microbiology</topic><topic>Respiratory Tract Infections - epidemiology</topic><topic>Respiratory Tract Infections - microbiology</topic><topic>Serogroup</topic><topic>Serotyping</topic><topic>Streptococcus pneumoniae - classification</topic><topic>Streptococcus pneumoniae - drug effects</topic><topic>Streptococcus pneumoniae - genetics</topic><topic>Streptococcus pneumoniae - isolation & purification</topic><topic>Whole Genome Sequencing</topic><topic>Young Adult</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Schellenberg, John J</creatorcontrib><creatorcontrib>Adam, Heather J</creatorcontrib><creatorcontrib>Baxter, Melanie R</creatorcontrib><creatorcontrib>Karlowsky, James A</creatorcontrib><creatorcontrib>Golden, Alyssa R</creatorcontrib><creatorcontrib>Martin, Irene</creatorcontrib><creatorcontrib>Zhanel, George G</creatorcontrib><collection>Oxford Journals Open Access Collection</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Journal of antimicrobial chemotherapy</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Schellenberg, John J</au><au>Adam, Heather J</au><au>Baxter, Melanie R</au><au>Karlowsky, James A</au><au>Golden, Alyssa R</au><au>Martin, Irene</au><au>Zhanel, George G</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Phenotypic and molecular characterization of Streptococcus pneumoniae serotype 3 isolates from blood and respiratory samples in Canada: CANWARD 2007–21</atitle><jtitle>Journal of antimicrobial chemotherapy</jtitle><addtitle>J Antimicrob Chemother</addtitle><date>2024-10-01</date><risdate>2024</risdate><volume>79</volume><issue>10</issue><spage>2653</spage><epage>2661</epage><pages>2653-2661</pages><issn>0305-7453</issn><issn>1460-2091</issn><eissn>1460-2091</eissn><abstract>Abstract
Background
Lower respiratory infections and invasive disease caused by Streptococcus pneumoniae serotype 3 remain major clinical challenges around the world, despite widespread availability of updated vaccines.
Methods
As part of CANWARD, antimicrobial susceptibility testing and serotyping were performed on all S. pneumoniae isolates from 2007 to 2021. A subset of 226/264 (85.6%) serotype 3 isolates were selected for WGS to determine sequence type (ST)/clonal cluster (CC) and correspondence of antimicrobial resistance determinants (erm, mefAE, tetM, cat, folA, folP) with resistance phenotype.
Results
Of the 3,039 S. pneumoniae isolates obtained from 2007 to 2021, 8.7% (n = 264) were serotype 3, with 64.0% of respiratory origin and 36.0% from blood. Of 226 sequenced serotype 3 isolates, 184 (81.4%) were ST180 (GPSC12). The proportion of ST8561 (single locus variant of ST180) increased from 7.2% to 16.6% during the study period. An increasing proportion of serotype 3 isolates had phenotypic resistance (P = 0.0007) and genetic resistance determinants (P = 0.004), comparing 2017–21 to 2007–11, largely due to a recently expanded ST180 clade with cat, tetM and mef determinants.
Conclusions
S. pneumoniae serotype 3 from GPSC12 continues to dominate throughout Canada, with an increase in the proportion of ST8561. The proportion of serotype 3 isolates that are phenotypically resistant and with genetic resistance determinants is increasing over time, reflecting a global increase in GPSC12 genotypes with known resistance determinants. Phylogenomic characterization of isolates collected over time and from around the world may facilitate improved treatment and enhanced prevention strategies, including new vaccines with activity against S. pneumoniae serotype 3.</abstract><cop>UK</cop><pub>Oxford University Press</pub><pmid>39092981</pmid><doi>10.1093/jac/dkae272</doi><tpages>9</tpages><orcidid>https://orcid.org/0000-0002-3238-0082</orcidid><orcidid>https://orcid.org/0000-0002-1788-1794</orcidid><oa>free_for_read</oa></addata></record> |
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subjects | Adolescent Adult Aged Aged, 80 and over Anti-Bacterial Agents - pharmacology Canada - epidemiology Child Child, Preschool Drug Resistance, Bacterial - genetics Female Genotype Humans Infant Male Microbial Sensitivity Tests Middle Aged Multilocus Sequence Typing Original Research Phenotype Pneumococcal Infections - epidemiology Pneumococcal Infections - microbiology Respiratory Tract Infections - epidemiology Respiratory Tract Infections - microbiology Serogroup Serotyping Streptococcus pneumoniae - classification Streptococcus pneumoniae - drug effects Streptococcus pneumoniae - genetics Streptococcus pneumoniae - isolation & purification Whole Genome Sequencing Young Adult |
title | Phenotypic and molecular characterization of Streptococcus pneumoniae serotype 3 isolates from blood and respiratory samples in Canada: CANWARD 2007–21 |
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