Whole genome sequencing of Brucella melitensis isolated from 57 patients in Germany reveals high diversity in strains from Middle East
Brucellosis, a worldwide common bacterial zoonotic disease, has become quite rare in Northern and Western Europe. However, since 2014 a significant increase of imported infections caused by Brucella (B.) melitensis has been noticed in Germany. Patients predominantly originated from Middle East inclu...
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| description | Brucellosis, a worldwide common bacterial zoonotic disease, has become quite rare in Northern and Western Europe. However, since 2014 a significant increase of imported infections caused by Brucella (B.) melitensis has been noticed in Germany. Patients predominantly originated from Middle East including Turkey and Syria. These circumstances afforded an opportunity to gain insights into the population structure of Brucella strains. Brucella-isolates from 57 patients were recovered between January 2014 and June 2016 with culture confirmed brucellosis by the National Consultant Laboratory for Brucella. Their whole genome sequences were generated using the Illumina MiSeq platform. A whole genome-based SNP typing assay was developed in order to resolve geographically attributed genetic clusters. Results were compared to MLVA typing results, the current gold-standard of Brucella typing. In addition, sequences were examined for possible genetic variation within target regions of molecular diagnostic assays. Phylogenetic analyses revealed spatial clustering and distinguished strains from different patients in either case, whereas multiple isolates from a single patient or technical replicates showed identical SNP and MLVA profiles. By including WGS data from the NCBI database, five major genotypes were identified. Notably, strains originating from Turkey showed a high diversity and grouped into seven subclusters of genotype II. MLVA analysis congruently clustered all isolates and predominantly matched the East Mediterranean genetic clade. This study confirms whole-genome based SNP-analysis as a powerful tool for accurate typing of B. melitensis. Furthermore it allows special allocation and therefore provides useful information on the geographic origin for trace-back analysis. However, the lack of reliable metadata in public databases often prevents a resolution below geographic regions or country levels and corresponding precise trace-back analysis. Once this obstacle is resolved, WGS-derived bacterial typing adds an important method to complement epidemiological surveys during outbreak investigations. This is the first report of a detailed genetic investigation of an extensive collection of B. melitensis strains isolated from human cases in Germany. |
| doi_str_mv | 10.1371/journal.pone.0175425 |
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However, since 2014 a significant increase of imported infections caused by Brucella (B.) melitensis has been noticed in Germany. Patients predominantly originated from Middle East including Turkey and Syria. These circumstances afforded an opportunity to gain insights into the population structure of Brucella strains. Brucella-isolates from 57 patients were recovered between January 2014 and June 2016 with culture confirmed brucellosis by the National Consultant Laboratory for Brucella. Their whole genome sequences were generated using the Illumina MiSeq platform. A whole genome-based SNP typing assay was developed in order to resolve geographically attributed genetic clusters. Results were compared to MLVA typing results, the current gold-standard of Brucella typing. In addition, sequences were examined for possible genetic variation within target regions of molecular diagnostic assays. Phylogenetic analyses revealed spatial clustering and distinguished strains from different patients in either case, whereas multiple isolates from a single patient or technical replicates showed identical SNP and MLVA profiles. By including WGS data from the NCBI database, five major genotypes were identified. Notably, strains originating from Turkey showed a high diversity and grouped into seven subclusters of genotype II. MLVA analysis congruently clustered all isolates and predominantly matched the East Mediterranean genetic clade. This study confirms whole-genome based SNP-analysis as a powerful tool for accurate typing of B. melitensis. Furthermore it allows special allocation and therefore provides useful information on the geographic origin for trace-back analysis. However, the lack of reliable metadata in public databases often prevents a resolution below geographic regions or country levels and corresponding precise trace-back analysis. Once this obstacle is resolved, WGS-derived bacterial typing adds an important method to complement epidemiological surveys during outbreak investigations. This is the first report of a detailed genetic investigation of an extensive collection of B. melitensis strains isolated from human cases in Germany.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0175425</identifier><identifier>PMID: 28388689</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Analysis ; Bacteria ; Bacteriology ; Biodiversity ; Biology and Life Sciences ; Brucella melitensis - genetics ; Brucella melitensis - isolation & purification ; Brucellosis ; Clustering ; Clusters ; Computer and Information Sciences ; Deoxyribonucleic acid ; Diagnostic systems ; DNA ; DNA sequencing ; Earth Sciences ; Ecology and Environmental Sciences ; Epidemiology ; Gene sequencing ; Genes, Bacterial ; Genetic diversity ; Genomes ; Genotypes ; Germany ; Humans ; Medicine and Health Sciences ; Middle East ; Multilocus Sequence Typing ; Outbreaks ; Patients ; People and Places ; Phylogenetics ; Phylogeny ; Polymorphism, Single Nucleotide ; Population structure ; Research and Analysis Methods ; Single-nucleotide polymorphism ; Spatial analysis ; Strains (organisms) ; Zoonoses</subject><ispartof>PloS one, 2017-04, Vol.12 (4), p.e0175425-e0175425</ispartof><rights>COPYRIGHT 2017 Public Library of Science</rights><rights>2017 Georgi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2017 Georgi et al 2017 Georgi et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-58d68f947e8a33e94b6f2803213d696a6d7093e237576f3947e290275645c3203</citedby><cites>FETCH-LOGICAL-c692t-58d68f947e8a33e94b6f2803213d696a6d7093e237576f3947e290275645c3203</cites><orcidid>0000-0003-4013-8808</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5384748/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5384748/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79343,79344</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/28388689$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Georgi, Enrico</creatorcontrib><creatorcontrib>Walter, Mathias C</creatorcontrib><creatorcontrib>Pfalzgraf, Marie-Theres</creatorcontrib><creatorcontrib>Northoff, Bernd H</creatorcontrib><creatorcontrib>Holdt, Lesca M</creatorcontrib><creatorcontrib>Scholz, Holger C</creatorcontrib><creatorcontrib>Zoeller, Lothar</creatorcontrib><creatorcontrib>Zange, Sabine</creatorcontrib><creatorcontrib>Antwerpen, Markus H</creatorcontrib><title>Whole genome sequencing of Brucella melitensis isolated from 57 patients in Germany reveals high diversity in strains from Middle East</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Brucellosis, a worldwide common bacterial zoonotic disease, has become quite rare in Northern and Western Europe. 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Phylogenetic analyses revealed spatial clustering and distinguished strains from different patients in either case, whereas multiple isolates from a single patient or technical replicates showed identical SNP and MLVA profiles. By including WGS data from the NCBI database, five major genotypes were identified. Notably, strains originating from Turkey showed a high diversity and grouped into seven subclusters of genotype II. MLVA analysis congruently clustered all isolates and predominantly matched the East Mediterranean genetic clade. This study confirms whole-genome based SNP-analysis as a powerful tool for accurate typing of B. melitensis. Furthermore it allows special allocation and therefore provides useful information on the geographic origin for trace-back analysis. However, the lack of reliable metadata in public databases often prevents a resolution below geographic regions or country levels and corresponding precise trace-back analysis. Once this obstacle is resolved, WGS-derived bacterial typing adds an important method to complement epidemiological surveys during outbreak investigations. This is the first report of a detailed genetic investigation of an extensive collection of B. melitensis strains isolated from human cases in Germany.</description><subject>Analysis</subject><subject>Bacteria</subject><subject>Bacteriology</subject><subject>Biodiversity</subject><subject>Biology and Life Sciences</subject><subject>Brucella melitensis - genetics</subject><subject>Brucella melitensis - isolation & purification</subject><subject>Brucellosis</subject><subject>Clustering</subject><subject>Clusters</subject><subject>Computer and Information Sciences</subject><subject>Deoxyribonucleic acid</subject><subject>Diagnostic systems</subject><subject>DNA</subject><subject>DNA sequencing</subject><subject>Earth Sciences</subject><subject>Ecology and Environmental Sciences</subject><subject>Epidemiology</subject><subject>Gene sequencing</subject><subject>Genes, Bacterial</subject><subject>Genetic diversity</subject><subject>Genomes</subject><subject>Genotypes</subject><subject>Germany</subject><subject>Humans</subject><subject>Medicine and Health Sciences</subject><subject>Middle East</subject><subject>Multilocus Sequence Typing</subject><subject>Outbreaks</subject><subject>Patients</subject><subject>People and Places</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Population structure</subject><subject>Research and Analysis Methods</subject><subject>Single-nucleotide polymorphism</subject><subject>Spatial analysis</subject><subject>Strains 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genome sequencing of Brucella melitensis isolated from 57 patients in Germany reveals high diversity in strains from Middle East</title><author>Georgi, Enrico ; Walter, Mathias C ; Pfalzgraf, Marie-Theres ; Northoff, Bernd H ; Holdt, Lesca M ; Scholz, Holger C ; Zoeller, Lothar ; Zange, Sabine ; Antwerpen, Markus H</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-58d68f947e8a33e94b6f2803213d696a6d7093e237576f3947e290275645c3203</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Analysis</topic><topic>Bacteria</topic><topic>Bacteriology</topic><topic>Biodiversity</topic><topic>Biology and Life Sciences</topic><topic>Brucella melitensis - genetics</topic><topic>Brucella melitensis - isolation & purification</topic><topic>Brucellosis</topic><topic>Clustering</topic><topic>Clusters</topic><topic>Computer and Information Sciences</topic><topic>Deoxyribonucleic 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zoonotic disease, has become quite rare in Northern and Western Europe. However, since 2014 a significant increase of imported infections caused by Brucella (B.) melitensis has been noticed in Germany. Patients predominantly originated from Middle East including Turkey and Syria. These circumstances afforded an opportunity to gain insights into the population structure of Brucella strains. Brucella-isolates from 57 patients were recovered between January 2014 and June 2016 with culture confirmed brucellosis by the National Consultant Laboratory for Brucella. Their whole genome sequences were generated using the Illumina MiSeq platform. A whole genome-based SNP typing assay was developed in order to resolve geographically attributed genetic clusters. Results were compared to MLVA typing results, the current gold-standard of Brucella typing. In addition, sequences were examined for possible genetic variation within target regions of molecular diagnostic assays. Phylogenetic analyses revealed spatial clustering and distinguished strains from different patients in either case, whereas multiple isolates from a single patient or technical replicates showed identical SNP and MLVA profiles. By including WGS data from the NCBI database, five major genotypes were identified. Notably, strains originating from Turkey showed a high diversity and grouped into seven subclusters of genotype II. MLVA analysis congruently clustered all isolates and predominantly matched the East Mediterranean genetic clade. This study confirms whole-genome based SNP-analysis as a powerful tool for accurate typing of B. melitensis. Furthermore it allows special allocation and therefore provides useful information on the geographic origin for trace-back analysis. However, the lack of reliable metadata in public databases often prevents a resolution below geographic regions or country levels and corresponding precise trace-back analysis. Once this obstacle is resolved, WGS-derived bacterial typing adds an important method to complement epidemiological surveys during outbreak investigations. This is the first report of a detailed genetic investigation of an extensive collection of B. melitensis strains isolated from human cases in Germany.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>28388689</pmid><doi>10.1371/journal.pone.0175425</doi><tpages>e0175425</tpages><orcidid>https://orcid.org/0000-0003-4013-8808</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | PloS one, 2017-04, Vol.12 (4), p.e0175425-e0175425 |
| issn | 1932-6203 1932-6203 |
| language | eng |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; Free Full-Text Journals in Chemistry; Public Library of Science (PLoS) |
| subjects | Analysis Bacteria Bacteriology Biodiversity Biology and Life Sciences Brucella melitensis - genetics Brucella melitensis - isolation & purification Brucellosis Clustering Clusters Computer and Information Sciences Deoxyribonucleic acid Diagnostic systems DNA DNA sequencing Earth Sciences Ecology and Environmental Sciences Epidemiology Gene sequencing Genes, Bacterial Genetic diversity Genomes Genotypes Germany Humans Medicine and Health Sciences Middle East Multilocus Sequence Typing Outbreaks Patients People and Places Phylogenetics Phylogeny Polymorphism, Single Nucleotide Population structure Research and Analysis Methods Single-nucleotide polymorphism Spatial analysis Strains (organisms) Zoonoses |
| title | Whole genome sequencing of Brucella melitensis isolated from 57 patients in Germany reveals high diversity in strains from Middle East |
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