Finnish new variant of Chlamydia trachomatis escaping detection in the Aptima Combo 2 assay also present in Örebro County, Sweden, May 2019

Unemo, Magnus; Hansen, Marit; Hadad, Ronza; Lindroth, Ylva; Fredlund, Hans; Puolakkainen, Mirja; Sundqvist, Martin

doi:10.2807/1560-7917.es.2019.24.26.1900370

Cited by 17 publications

(33 citation statements)

References 10 publications

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“…The SNP was verified in both the forward and reverse strands of the sequenced V2 and V3 PCR products, with high quality values (Q-value > 30 by FinchTV, Geospiza). This SNP verifies that AC2 negative but ACT positive specimens contained the Finnish new variant of C. trachomatis (FI-nvCT) [18]. As this was the only mutation detected in the sequenced regions of the 23S rRNA gene, only primer pair V2 was used to amplify 29 additional AC2 negative/equivocal and ACT positive specimens, and the five AC2 positive specimens.…”

Section: Resultsmentioning

confidence: 65%

“…To streamline clinical sample testing with Aptima, Hologic is developing a new assay that specifically targets the FI-nvCT [20,22]. Recently, initial evaluation revealed that two cases of FI-nvCT have been identified in Sweden [18]. As ECDC has been notified and ECDC has informed public health officials in Europe, we expect more information on the epidemiology of FI-nvCT to accumulate.…”

Section: Discussionmentioning

confidence: 99%

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The Finnish New Variant of Chlamydia trachomatis with a Single Nucleotide Polymorphism in the 23S rRNA Target Escapes Detection by the Aptima Combo 2 Test

et al. 2019

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In 2019, more than 200 cases of Chlamydia trachomatis negative/equivocal by the Aptima Combo 2 assay (AC2, target: 23S rRNA) with slightly elevated relative light units (RLUs), but positive by the Aptima Chlamydia trachomatis assay (ACT, target: 16S rRNA) have been detected in Finland To identify the cause of the AC2 CT false-negative specimens, we sequenced parts of the CT 23S rRNA gene in 40 specimens that were AC2 negative/equivocal but ACT positive. A single nucleotide polymorphism (SNP; C1515T in the C. trachomatis 23S rRNA gene) was revealed in 39 AC2/ACT discordant specimens. No decrease in the number of mandatorily notified C. trachomatis cases was observed nationally in Finland in 2010–2019. When RLUs obtained for AC2 negative specimens were retrospectively evaluated in 2011–2019, a continuous increase in the proportion of samples with RLUs 10–19 was observed since 2014, and a slight increase in the proportion of samples with RLUs 20–84 in 2017–2019, indicating that the Finnish new variant of C. trachomatis might have been spreading nationally for several years. This emphasizes that careful surveillance of epidemiology, positivity rate and test performance are mandatory to detect any changes affecting detection of infections.

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Section: Resultsmentioning

confidence: 65%

Section: Discussionmentioning

confidence: 99%

The Finnish New Variant of Chlamydia trachomatis with a Single Nucleotide Polymorphism in the 23S rRNA Target Escapes Detection by the Aptima Combo 2 Test

et al. 2019

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“…The Finnish New Variant escaped detection by the Aptima Combo-2 test, which targets the 23S rRNA, but remained detectable by the Aptima CT test, which targets a sequence within the 16S rRNA sequence. The global distribution of the Finnish New Variant has yet to be determined, but it has also been detected in Sweden and further reports seem likely [80]. It is not known whether these isolates were imported from Finland or represent a separate evolutionary event-the former seems more likely given the close proximity of the two countries, but the latter cannot be ruled out until further investigations are completed.…”

Section: Implications On Diagnostic Target Choicementioning

confidence: 98%

The Nature and Extent of Plasmid Variation in Chlamydia trachomatis

et al. 2020

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Chlamydia trachomatis is an obligate intracellular pathogen of humans, causing both the sexually transmitted infection, chlamydia, and the most common cause of infectious blindness, trachoma. The majority of sequenced C. trachomatis clinical isolates carry a 7.5-Kb plasmid, and it is becoming increasingly evident that this is a key determinant of pathogenicity. The discovery of the Swedish New Variant and the more recent Finnish variant highlight the importance of understanding the natural extent of variation in the plasmid. In this study we analysed 524 plasmid sequences from publicly available whole-genome sequence data. Single nucleotide polymorphisms (SNP) in each of the eight coding sequences (CDS) were identified and analysed. There were 224 base positions out of a total 7550 bp that carried a SNP, which equates to a SNP rate of 2.97%, nearly three times what was previously calculated. After normalising for CDS size, CDS8 had the highest SNP rate at 3.97% (i.e., number of SNPs per total number of nucleotides), whilst CDS6 had the lowest at 1.94%. CDS5 had the highest total number of SNPs across the 524 sequences analysed (2267 SNPs), whereas CDS6 had the least SNPs with only 85 SNPs. Calculation of the genetic distances identified CDS6 as the least variable gene at the nucleotide level (d = 0.001), and CDS5 as the most variable (d = 0.007); however, at the amino acid level CDS2 was the least variable (d = 0.001), whilst CDS5 remained the most variable (d = 0.013). This study describes the largest in-depth analysis of the C. trachomatis plasmid to date, through the analysis of plasmid sequence data mined from whole genome sequences spanning 50 years and from a worldwide distribution, providing insights into the nature and extent of existing variation within the plasmid as well as guidance for the design of future diagnostic assays. This is crucial at a time when single-target diagnostic assays are failing to detect natural mutants, putting those infected at risk of a serious long-term and life-changing illness.

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“…AC2 negative/equivocal-ACT positive) signalled the presence of the new strain. Data collected in subsequent investigations suggested a recent emergence of FI-nvCT in south-western Finland, Norway and Sweden with relatively low prevalence (ca 1-6%) among patients with C. trachomatis infections [1,[3][4][5]. We have developed and validated a research-use only Aptima-format surveillance NAAT designed specifically to detect the FI-nvCT strain.…”

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confidence: 99%

Validation of an Aptima-format Finnish new variant of Chlamydia trachomatis (FI-nvCT) surveillance assay, 2019

et al. 2020

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The Finnish new variant of Chlamydia trachomatis (FI-nvCT) is escaping diagnostics in Finland, Norway and Sweden. We have developed and validated an Aptima-format nucleic acid amplification test (NAAT) designed specifically to detect the FI-nvCT. This NAAT has high sensitivity (100%) and specificity (100%) for the FI-nvCT strain, enabling further investigation of the geographic distribution, prevalence and transmission of this diagnostic-escape mutant in screening populations in Europe.In February 2019, investigation of discrepant nucleic acid amplification test (NAAT) results led to the discovery of a new genetic variant strain of Chlamydia trachomatis in south-western Finland [1]. This strain, designated Finnish new variant of C. trachomatis (FI-nvCT), harbours a single nt base mutation (C1515T; Escherichia coli numbering) in 23S rRNA. This mutation was determined to be the root cause for compromised detection of the organism by the Aptima Combo 2 (AC2) diagnostic test (Hologic Inc., San Diego, California, United States (US)), which targets C. trachomatis 23S rRNA [2,3]. Archived and newly received clinical specimens in Finland and Sweden with equivocal results or high-negative relative light units (RLU) from 15 to 99 in the AC2 test, and discrepant results between AC2 (target: 23S rRNA) and the separate Aptima Chlamydia trachomatis (ACT) test (target: 16S rRNA) (i.e. AC2 negative/equivocal-ACT positive) signalled the presence of the new strain. Data collected in subsequent investigations suggested a recent emergence of FI-nvCT in south-western Finland, Norway and Sweden with relatively low prevalence (ca 1-6%) among patients with C. trachomatis infections [1,3-5]. We have developed and validated a research-use only Aptima-format surveillance NAAT designed specifically to detect the FI-nvCT strain. This assay should facilitate further investigations to determine the geographic distribution, prevalence and transmission of this diagnostic-escape mutant. New Aptima-format surveillance assay for the Finnish new variant of Chlamydia trachomatisTo understand the geographic distribution, prevalence and transmission dynamics of the FI-nvCT strain nationally and internationally, we have developed an Aptima-format NAAT that sensitively and specifically detects FI-nvCT (23S rRNA gene C1515T mutation) but not wild-type (C1515) C. trachomatis strains. This research-use only test uses target capture and transcription-mediated amplification chemistries on the automated Panther instrument (Hologic Inc.) to isolate and amplify C. trachomatis 23S rRNA, and an acridinium ester probe to selectively detect the C→T mutation at position 1515. Validation and verification results for the Aptima-format surveillance assay for the Finnish new variant of C. trachomatisAll validation and verification studies of the new FI-nvCT assay were conducted according to Clinical Laboratory Standards Institute (CLSI) standard protocols used for in vitro diagnostic assay validation [6]. The cut-off value of the test (100,000 RLU) was initially establis...

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Finnish new variant of Chlamydia trachomatis escaping detection in the Aptima Combo 2 assay also present in Örebro County, Sweden, May 2019

Cited by 17 publications

References 10 publications

The Finnish New Variant of Chlamydia trachomatis with a Single Nucleotide Polymorphism in the 23S rRNA Target Escapes Detection by the Aptima Combo 2 Test

The Finnish New Variant of Chlamydia trachomatis with a Single Nucleotide Polymorphism in the 23S rRNA Target Escapes Detection by the Aptima Combo 2 Test

The Nature and Extent of Plasmid Variation in Chlamydia trachomatis

Validation of an Aptima-format Finnish new variant of Chlamydia trachomatis (FI-nvCT) surveillance assay, 2019

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