Abstract:
:Salmonella enterica serovar Heidelberg is the second most frequently occurring serovar in Quebec and the third-most prevalent in Canada. Given that conventional pulsed-field gel electrophoresis (PFGE) subtyping for common Salmonella serovars, such as S. Heidelberg, yields identical subtypes for the majority of isolates recovered, public health laboratories are desperate for new subtyping tools to resolve highly clonal S. Heidelberg strains involved in outbreak events. As PFGE was unable to discriminate isolates from three epidemiologically distinct outbreaks in Quebec, this study was conducted to evaluate whole-genome sequencing (WGS) and phylogenetic analysis as an alternative to conventional subtyping tools. Genomes of 46 isolates from 3 Quebec outbreaks (2012, 2013, and 2014) supported by strong epidemiological evidence were sequenced and analyzed using a high-quality core genome single-nucleotide variant (hqSNV) bioinformatics approach (SNV phylogenomics [SNVphyl] pipeline). Outbreaks were indistinguishable by conventional PFGE subtyping, exhibiting the same PFGE pattern (SHEXAI.0001/SHEBNI.0001). Phylogenetic analysis based on hqSNVs extracted from WGS separated the outbreak isolates into three distinct groups, 100% concordant with the epidemiological data. The minimum and maximum number of hqSNVs between isolates from the same outbreak was 0 and 4, respectively, while >59 hqSNVs were measured between 2 previously indistinguishable outbreaks having the same PFGE and phage type, thus corroborating their distinction as separate unrelated outbreaks. This study demonstrates that despite the previously reported high clonality of this serovar, the WGS-based hqSNV approach is a superior typing method, capable of resolving events that were previously indistinguishable using classic subtyping tools.
journal_name
J Clin Microbioljournal_title
Journal of clinical microbiologyauthors
Bekal S,Berry C,Reimer AR,Van Domselaar G,Beaudry G,Fournier E,Doualla-Bell F,Levac E,Gaulin C,Ramsay D,Huot C,Walker M,Sieffert C,Tremblay Cdoi
10.1128/JCM.02200-15subject
Has Abstractpub_date
2016-02-01 00:00:00pages
289-95issue
2eissn
0095-1137issn
1098-660Xpii
JCM.02200-15journal_volume
54pub_type
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journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.25.10.1854-1859.1987
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更新日期:1987-04-01 00:00:00
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journal_title:Journal of clinical microbiology
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journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.31.3.665-670.1993
更新日期:1993-03-01 00:00:00
abstract::Given that the integration of human papillomavirus type 16 (HPV16) into the host genome occurs preferentially with the disruption of the E2 gene, a ratio of E2 to E7 gene copies is often used as a marker for integration. It is largely undetermined, however, whether ratio estimates are affected by HPV intratypic variat...
journal_title:Journal of clinical microbiology
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doi:10.1128/JCM.02115-08
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journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.39.12.4328-4331.2001
更新日期:2001-12-01 00:00:00
abstract::Several biochemical test systems were studied for their potential usefulness for the examination of strains of Campylobacter species. Most (81%) of the C. jejuni strains hydrolyzed sodium hippurate, but strains of C. fetus, C. sputorum, and C. fecalis did not. Some (46%) of the C. jejuni strains and all of the C. sput...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.15.6.1065-1073.1982
更新日期:1982-06-01 00:00:00
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journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.19.1.4-7.1984
更新日期:1984-01-01 00:00:00
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journal_title:Journal of clinical microbiology
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更新日期:1987-01-01 00:00:00
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journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.02303-10
更新日期:2011-05-01 00:00:00
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journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.36.4.979-982.1998
更新日期:1998-04-01 00:00:00
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journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.20.3.473-477.1984
更新日期:1984-09-01 00:00:00
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journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.34.6.1355-1358.1996
更新日期:1996-06-01 00:00:00
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journal_title:Journal of clinical microbiology
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doi:10.1128/JCM.01288-14
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pub_type: 杂志文章
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journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.25.11.2090-2093.1987
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journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.1.6.504-508.1975
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journal_title:Journal of clinical microbiology
pub_type: 临床试验,杂志文章,多中心研究
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journal_title:Journal of clinical microbiology
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doi:10.1128/JCM.28.8.1813-1817.1990
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journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.42.7.3256-3261.2004
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journal_title:Journal of clinical microbiology
pub_type: 杂志文章
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journal_title:Journal of clinical microbiology
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journal_title:Journal of clinical microbiology
pub_type: 杂志文章
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更新日期:2006-07-01 00:00:00
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journal_title:Journal of clinical microbiology
pub_type: 杂志文章
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更新日期:2009-10-01 00:00:00
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journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.32.2.473-476.1994
更新日期:1994-02-01 00:00:00
abstract::Between November 1983 and January 1984, 13 cases of Candida parapsilosis endophthalmitis occurred in Florida, Georgia, and Tennessee in patients who had had an intraocular lens implantation (IOLI) or cataract extraction with an IOLI. This outbreak followed the introduction in July 1983 of a new brand of balanced salt ...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.24.4.625-628.1986
更新日期:1986-10-01 00:00:00
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journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.22.2.157-160.1985
更新日期:1985-08-01 00:00:00
abstract::Blastomyces dermatitidis and Histoplasma capsulatum are dimorphic fungi that often cause self-limited respiratory infections. However, they may also cause severe disseminated disease, depending on the level of the exposure to the organism and the host immune status. In addition, patients with infections caused by thes...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.00673-11
更新日期:2011-09-01 00:00:00