Ontology type: schema:ScholarlyArticle Open Access: True
2019-12
AUTHORSMary Wandia Kivata, Margaret Mbuchi, Fredrick Lunyagi Eyase, Wallace Dimbuson Bulimo, Cecilia Katunge Kyanya, Valerie Oundo, Simon Wachira Muriithi, Ben Andagalu, Wilton Mwema Mbinda, Olusegun O Soge, R Scott McClelland, Willy Sang, James D Mancuso
ABSTRACTBACKGROUND: Phenotypic fluoroquinolone resistance was first reported in Western Kenya in 2009 and later in Coastal Kenya and Nairobi. Until recently gonococcal fluoroquinolone resistance mechanisms in Kenya had not been elucidated. The aim of this paper is to analyze mutations in both gyrA and parC responsible for elevated fluoroquinolone Minimum Inhibitory Concentrations (MICs) in Neisseria gonorrhoeae (GC) isolated from heterosexual individuals from different locations in Kenya between 2013 and 2017. METHODS: Antimicrobial Susceptibility Tests were done on 84 GC in an ongoing Sexually Transmitted Infections (STI) surveillance program. Of the 84 isolates, 22 resistant to two or more classes of antimicrobials were chosen for analysis. Antimicrobial susceptibility tests were done using E-test (BioMerieux) and the results were interpreted with reference to European Committee on Antimicrobial Susceptibility Testing (EUCAST) standards. The isolates were sub-cultured, and whole genomes were sequenced using Illumina platform. Reads were assembled de novo using Velvet, and mutations in the GC Quinolone Resistant Determining Regions identified using Bioedit sequence alignment editor. Single Nucleotide Polymorphism based phylogeny was inferred using RaxML. RESULTS: Double GyrA amino acid substitutions; S91F and D95G/D95A were identified in 20 isolates. Of these 20 isolates, 14 had an additional E91G ParC substitution and significantly higher ciprofloxacin MICs (p = 0.0044*). On the contrary, norfloxacin MICs of isolates expressing both GyrA and ParC QRDR amino acid changes were not significantly high (p = 0.82) compared to MICs of isolates expressing GyrA substitutions alone. No single GyrA substitution was found in the analyzed isolates, and no isolate contained a ParC substitution without the simultaneous presence of double GyrA substitutions. Maximum likelihood tree clustered the 22 isolates into 6 distinct clades. CONCLUSION: Simultaneous presence of amino acid substitutions in ParC and GyrA has been reported to increase gonococcal fluoroquinolone resistance from different regions in the world. Our findings indicate that GyrA S91F, D95G/D95A and ParC E91G amino acid substitutions mediate high fluoroquinolone resistance in the analyzed Kenyan GC. More... »
PAGES76
http://scigraph.springernature.com/pub.10.1186/s12866-019-1439-1
DOIhttp://dx.doi.org/10.1186/s12866-019-1439-1
DIMENSIONShttps://app.dimensions.ai/details/publication/pub.1113300166
PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/30961546
JSON-LD is the canonical representation for SciGraph data.
TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT
[
{
"@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json",
"about": [
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/1108",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Medical Microbiology",
"type": "DefinedTerm"
},
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/11",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Medical and Health Sciences",
"type": "DefinedTerm"
}
],
"author": [
{
"affiliation": {
"alternateName": "Karatina University",
"id": "https://www.grid.ac/institutes/grid.448671.8",
"name": [
"Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology (JKUAT), P.O Box 62,000-00200, Thika, Kenya. marywandia086@gmail.com.",
"Department of Biological and Physical Science, Karatina University (KarU), P.O Box 1957-10101, Karatina, Kenya. marywandia086@gmail.com."
],
"type": "Organization"
},
"familyName": "Kivata",
"givenName": "Mary Wandia",
"type": "Person"
},
{
"affiliation": {
"alternateName": "Kenya Medical Research Institute",
"id": "https://www.grid.ac/institutes/grid.33058.3d",
"name": [
"US Army Medical Research Directorate-Africa, P.O Box 606, 00621, Village Market, Nairobi, Kenya.",
"Kenya Medical Research Institute (KEMRI), P. O. Box 54840-00200, Nairobi, Kenya."
],
"type": "Organization"
},
"familyName": "Mbuchi",
"givenName": "Margaret",
"type": "Person"
},
{
"affiliation": {
"alternateName": "Jomo Kenyatta University of Agriculture and Technology",
"id": "https://www.grid.ac/institutes/grid.411943.a",
"name": [
"US Army Medical Research Directorate-Africa, P.O Box 606, 00621, Village Market, Nairobi, Kenya.",
"Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology (JKUAT), P.O Box 62,000-00200, Thika, Kenya."
],
"type": "Organization"
},
"familyName": "Eyase",
"givenName": "Fredrick Lunyagi",
"type": "Person"
},
{
"affiliation": {
"alternateName": "University of Nairobi",
"id": "https://www.grid.ac/institutes/grid.10604.33",
"name": [
"US Army Medical Research Directorate-Africa, P.O Box 606, 00621, Village Market, Nairobi, Kenya.",
"Department of Biochemistry, School of Medicine, University of Nairobi, P.O. Box 30197, GPO, 00100, Nairobi, Kenya."
],
"type": "Organization"
},
"familyName": "Bulimo",
"givenName": "Wallace Dimbuson",
"type": "Person"
},
{
"affiliation": {
"name": [
"US Army Medical Research Directorate-Africa, P.O Box 606, 00621, Village Market, Nairobi, Kenya."
],
"type": "Organization"
},
"familyName": "Kyanya",
"givenName": "Cecilia Katunge",
"type": "Person"
},
{
"affiliation": {
"name": [
"US Army Medical Research Directorate-Africa, P.O Box 606, 00621, Village Market, Nairobi, Kenya."
],
"type": "Organization"
},
"familyName": "Oundo",
"givenName": "Valerie",
"type": "Person"
},
{
"affiliation": {
"name": [
"US Army Medical Research Directorate-Africa, P.O Box 606, 00621, Village Market, Nairobi, Kenya."
],
"type": "Organization"
},
"familyName": "Muriithi",
"givenName": "Simon Wachira",
"type": "Person"
},
{
"affiliation": {
"name": [
"US Army Medical Research Directorate-Africa, P.O Box 606, 00621, Village Market, Nairobi, Kenya."
],
"type": "Organization"
},
"familyName": "Andagalu",
"givenName": "Ben",
"type": "Person"
},
{
"affiliation": {
"alternateName": "Karatina University",
"id": "https://www.grid.ac/institutes/grid.448671.8",
"name": [
"Department of Biological and Physical Science, Karatina University (KarU), P.O Box 1957-10101, Karatina, Kenya."
],
"type": "Organization"
},
"familyName": "Mbinda",
"givenName": "Wilton Mwema",
"type": "Person"
},
{
"affiliation": {
"name": [
"Department of Global Health and Medicine, University of Washington, 325 9th Avenue, Box 359931, Seattle, WA, 98104, USA."
],
"type": "Organization"
},
"familyName": "Soge",
"givenName": "Olusegun O",
"type": "Person"
},
{
"affiliation": {
"name": [
"Department of Global Health and Medicine, University of Washington, 325 9th Avenue, Box 359931, Seattle, WA, 98104, USA."
],
"type": "Organization"
},
"familyName": "McClelland",
"givenName": "R Scott",
"type": "Person"
},
{
"affiliation": {
"alternateName": "Kenya Medical Research Institute",
"id": "https://www.grid.ac/institutes/grid.33058.3d",
"name": [
"US Army Medical Research Directorate-Africa, P.O Box 606, 00621, Village Market, Nairobi, Kenya.",
"Kenya Medical Research Institute (KEMRI), P. O. Box 54840-00200, Nairobi, Kenya."
],
"type": "Organization"
},
"familyName": "Sang",
"givenName": "Willy",
"type": "Person"
},
{
"affiliation": {
"name": [
"US Army Medical Research Directorate-Africa, P.O Box 606, 00621, Village Market, Nairobi, Kenya."
],
"type": "Organization"
},
"familyName": "Mancuso",
"givenName": "James D",
"type": "Person"
}
],
"citation": [
{
"id": "https://doi.org/10.1093/bioinformatics/btu033",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1000848409"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/jac/dkg040",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1001547949"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/s12864-016-3407-6",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1001575154",
"https://doi.org/10.1186/s12864-016-3407-6"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/s12864-016-3407-6",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1001575154",
"https://doi.org/10.1186/s12864-016-3407-6"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1371/journal.pone.0011147",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1001774801"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/jac/dkl301",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1009846427"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1128/aac.28.3.393",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1011003570"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/nar/gkt1099",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1015010527"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.3103/s0891416815030027",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1015511212",
"https://doi.org/10.3103/s0891416815030027"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.2165/00003495-199958002-00003",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1016558667",
"https://doi.org/10.2165/00003495-199958002-00003"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1097/olq.0b013e318248a85f",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1016670577"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1097/olq.0b013e318248a85f",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1016670577"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/s0167-4781(98)00126-2",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1019193864"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1136/sti.74.1.59",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1020230426"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1136/sti.74.1.59",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1020230426"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/bioinformatics/btp352",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1023014918"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1111/j.1365-2958.1994.tb01297.x",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1024734357"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1111/j.1365-2958.2008.06424.x",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1029023953"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1136/sti.2010.048777",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1029089850"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1136/sti.2010.048777",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1029089850"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1136/sti.72.4.295",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1029573228"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1136/sti.72.4.295",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1029573228"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/s1369-5274(99)00008-9",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1030816117"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1128/aac.46.9.2811-2820.2002",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1034082955"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1128/aac.00155-11",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1035105075"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/bioinformatics/btp324",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1038266369"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1101/gr.074492.107",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1051720574"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1128/cmr.00010-14",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1052136002"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/jac/24.suppl_a.183",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1059732430"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1128/jb.179.13.4123-4128.1997",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1062726011"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1128/aac.43.10.2468",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1074529254"
],
"type": "CreativeWork"
},
{
"id": "https://app.dimensions.ai/details/publication/pub.1078031046",
"type": "CreativeWork"
},
{
"id": "https://app.dimensions.ai/details/publication/pub.1080745583",
"type": "CreativeWork"
},
{
"id": "https://app.dimensions.ai/details/publication/pub.1081951528",
"type": "CreativeWork"
},
{
"id": "https://app.dimensions.ai/details/publication/pub.1082672378",
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1128/aac.40.4.1020",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1082975041"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.bjm.2017.06.001",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1090652512"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.4103/ijmr.ijmr_730_15",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1099907662"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.17221/7883-vetmed",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1100968579"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/infdis/jiy240",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1103566869"
],
"type": "CreativeWork"
}
],
"datePublished": "2019-12",
"datePublishedReg": "2019-12-01",
"description": "BACKGROUND: Phenotypic fluoroquinolone resistance was first reported in Western Kenya in 2009 and later in Coastal Kenya and Nairobi. Until recently gonococcal fluoroquinolone resistance mechanisms in Kenya had not been elucidated. The aim of this paper is to analyze mutations in both gyrA and parC responsible for elevated fluoroquinolone Minimum Inhibitory Concentrations (MICs) in Neisseria gonorrhoeae (GC) isolated from heterosexual individuals from different locations in Kenya between 2013 and 2017.\nMETHODS: Antimicrobial Susceptibility Tests were done on 84 GC in an ongoing Sexually Transmitted Infections (STI) surveillance program. Of the 84 isolates, 22 resistant to two or more classes of antimicrobials were chosen for analysis. Antimicrobial susceptibility tests were done using E-test (BioMerieux) and the results were interpreted with reference to European Committee on Antimicrobial Susceptibility Testing (EUCAST) standards. The isolates were sub-cultured, and whole genomes were sequenced using Illumina platform. Reads were assembled de novo using Velvet, and mutations in the GC Quinolone Resistant Determining Regions identified using Bioedit sequence alignment editor. Single Nucleotide Polymorphism based phylogeny was inferred using RaxML.\nRESULTS: Double GyrA amino acid substitutions; S91F and D95G/D95A were identified in 20 isolates. Of these 20 isolates, 14 had an additional E91G ParC substitution and significantly higher ciprofloxacin MICs (p\u2009=\u20090.0044*). On the contrary, norfloxacin MICs of isolates expressing both GyrA and ParC QRDR amino acid changes were not significantly high (p\u2009=\u20090.82) compared to MICs of isolates expressing GyrA substitutions alone. No single GyrA substitution was found in the analyzed isolates, and no isolate contained a ParC substitution without the simultaneous presence of double GyrA substitutions. Maximum likelihood tree clustered the 22 isolates into 6 distinct clades.\nCONCLUSION: Simultaneous presence of amino acid substitutions in ParC and GyrA has been reported to increase gonococcal fluoroquinolone resistance from different regions in the world. Our findings indicate that GyrA S91F, D95G/D95A and ParC E91G amino acid substitutions mediate high fluoroquinolone resistance in the analyzed Kenyan GC.",
"genre": "research_article",
"id": "sg:pub.10.1186/s12866-019-1439-1",
"inLanguage": [
"en"
],
"isAccessibleForFree": true,
"isPartOf": [
{
"id": "sg:journal.1024253",
"issn": [
"1471-2180"
],
"name": "BMC Microbiology",
"type": "Periodical"
},
{
"issueNumber": "1",
"type": "PublicationIssue"
},
{
"type": "PublicationVolume",
"volumeNumber": "19"
}
],
"name": "gyrA and parC mutations in fluoroquinolone-resistant Neisseria gonorrhoeae isolates from Kenya.",
"pagination": "76",
"productId": [
{
"name": "doi",
"type": "PropertyValue",
"value": [
"10.1186/s12866-019-1439-1"
]
},
{
"name": "dimensions_id",
"type": "PropertyValue",
"value": [
"pub.1113300166"
]
},
{
"name": "nlm_unique_id",
"type": "PropertyValue",
"value": [
"100966981"
]
},
{
"name": "pubmed_id",
"type": "PropertyValue",
"value": [
"30961546"
]
}
],
"sameAs": [
"https://doi.org/10.1186/s12866-019-1439-1",
"https://app.dimensions.ai/details/publication/pub.1113300166"
],
"sdDataset": "articles",
"sdDatePublished": "2019-04-15T09:03",
"sdLicense": "https://scigraph.springernature.com/explorer/license/",
"sdPublisher": {
"name": "Springer Nature - SN SciGraph project",
"type": "Organization"
},
"sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000375_0000000375/records_91464_00000001.jsonl",
"type": "ScholarlyArticle",
"url": "https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-019-1439-1"
}
]Download the RDF metadata as: json-ld nt turtle xml License info
JSON-LD is a popular format for linked data which is fully compatible with JSON.
curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/s12866-019-1439-1'
N-Triples is a line-based linked data format ideal for batch operations.
curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/s12866-019-1439-1'
Turtle is a human-readable linked data format.
curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s12866-019-1439-1'
RDF/XML is a standard XML format for linked data.
curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/s12866-019-1439-1'
This table displays all metadata directly associated to this object as RDF triples.
267 TRIPLES
21 PREDICATES
63 URIs
20 LITERALS
8 BLANK NODES