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Article ; Online: Shiga toxin-producing Escherichia coli (STEC) stool multiplex PCR can replace culture for clinical diagnosis and follow-up.

Jääskeläinen, Anu E / Salmenlinna, Saara / Antikainen, Jenni / Sihvonen, Reetta / Ahava, Maarit / Tarkka, Eveliina / Pätäri-Sampo, Anu

APMIS : acta pathologica, microbiologica, et immunologica Scandinavica

2023 Volume 131, Issue 7, Page(s) 333–338

Abstract: Shiga toxin (stx)-producing Escherichia coli (STEC) causes potentially severe gastrointestinal infections. Due to its public health importance, control measures are required, and carriers may need to refrain from work or daycare when the risk of spread ... ...

Abstract	Shiga toxin (stx)-producing Escherichia coli (STEC) causes potentially severe gastrointestinal infections. Due to its public health importance, control measures are required, and carriers may need to refrain from work or daycare when the risk of spread to vulnerable people is high. We evaluated the use of direct stool multiplex PCR compared to culture for primary STEC diagnostics and for follow-up in order to update the national guidelines for STEC monitoring. We analyzed primary and follow-up samples of 236 STEC PCR-positive cases at HUSLAB, Helsinki, Finland in 2016-2017, altogether 858 samples. All STEC PCR-positive samples were inoculated on non-selective chromogenic agar plates. Culture positivity was confirmed from culture sweeps by PCR. 211 (89%) of the cases were culture positive in their primary sample. Of all primary and follow-up samples, 499 were PCR positive and of these 450 (90%) were culture positive. PCR-negative follow-up samples were available from 125 cases. Of these, 88 cases were followed for at least three consecutive PCR-negative samples. Two cases (2%) had culture-positive sample(s) after two consecutive PCR-negative samples. The median time for STEC clearance was 22-23 days. The laboratory-developed multiplex PCR test used in this study is a reliable method for STEC diagnostics and follow-up in a clinical laboratory. When non-selective methodology is used, the majority of PCR-positive samples (90%) are also culture positive. Furthermore, only two cases (2%) in our material had two consecutive PCR-negative samples followed by positive samples. Consequently, to demonstrate the clearance from STEC infection, we consider two PCR-negative follow-up samples sufficient. The Finnish national guidelines for STEC monitoring have been updated accordingly.
MeSH term(s)	Humans ; Shiga-Toxigenic Escherichia coli/genetics ; Multiplex Polymerase Chain Reaction ; Follow-Up Studies ; Escherichia coli Infections/diagnosis ; Bacteriological Techniques/methods ; Feces ; Escherichia coli Proteins/genetics
Chemical Substances	Escherichia coli Proteins
Language	English
Publishing date	2023-04-26
Publishing country	Denmark
Document type	Journal Article
ZDB-ID	93340-5
ISSN	1600-0463 ; 0903-4641
ISSN (online)	1600-0463
ISSN	0903-4641
DOI	10.1111/apm.13319
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Article ; Online: SARS-CoV-2 sample-to-answer nucleic acid testing in a tertiary care emergency department: evaluation and utility.

Jokela, Pia / Jääskeläinen, Anu E / Jarva, Hanna / Holma, Tanja / Ahava, Maarit J / Mannonen, Laura / Lappalainen, Maija / Kurkela, Satu / Loginov, Raisa

Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology

2020 Volume 131, Page(s) 104614

Abstract: Background: Rapid sample-to-answer tests for detection of SARS-CoV-2 are emerging and data on their relative performance is urgently needed.: Objectives: We evaluated the analytical performance of two rapid nucleic acid tests, Cepheid Xpert® Xpress ... ...

Abstract	Background: Rapid sample-to-answer tests for detection of SARS-CoV-2 are emerging and data on their relative performance is urgently needed. Objectives: We evaluated the analytical performance of two rapid nucleic acid tests, Cepheid Xpert® Xpress SARS-CoV-2 and Mobidiag Novodiag® Covid-19, in comparison to a combination reference of three large-scale PCR tests. Moreover, utility of the Novodiag® test in tertiary care emergency departments was assessed. Results: In the preliminary evaluation, analysis of 90 respiratory samples resulted in 100% specificity and sensitivity for Xpert®, whereas analysis of 107 samples resulted in 93.4% sensitivity and 100% specificity for Novodiag®. Rapid SARS-CoV-2 testing with Novodiag® was made available for four tertiary care emergency departments in Helsinki, Finland between 18 and 31 May, coinciding with a rapidly declining epidemic phase. Altogether 361 respiratory specimens, together with relevant clinical data, were analyzed with Novodiag® and reference tests: 355/361 of the specimens were negative with both methods, and 1/361 was positive in Novodiag® and negative by the reference method. Of the 5 remaining specimens, two were negative with Novodiag®, but positive with the reference method with late Ct values. On average, a test result using Novodiag® was available nearly 8 hours earlier than that obtained with the large-scale PCR tests. Conclusions: While the performance of novel sample-to-answer PCR tests need to be carefully evaluated, they may provide timely and reliable results in detection of SARS-CoV-2 and thus facilitate patient management including effective cohorting.
MeSH term(s)	Adolescent ; Adult ; Aged ; Aged, 80 and over ; Betacoronavirus ; COVID-19 ; COVID-19 Testing ; Child ; Child, Preschool ; Clinical Laboratory Techniques ; Coronavirus Infections/diagnosis ; Emergency Service, Hospital/statistics & numerical data ; Female ; Finland ; Humans ; Infant ; Infant, Newborn ; Male ; Middle Aged ; Molecular Diagnostic Techniques ; Nasopharynx/virology ; Nucleic Acid Amplification Techniques ; Pandemics ; Pneumonia, Viral/diagnosis ; SARS-CoV-2 ; Sensitivity and Specificity ; Tertiary Healthcare/statistics & numerical data ; Young Adult
Keywords	covid19
Language	English
Publishing date	2020-08-27
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1446080-4
ISSN	1873-5967 ; 1386-6532
ISSN (online)	1873-5967
ISSN	1386-6532
DOI	10.1016/j.jcv.2020.104614
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Article ; Online: Evaluation of three rapid lateral flow antigen detection tests for the diagnosis of SARS-CoV-2 infection

Jaaskelainen, Anu E / Ahava, Maarit J / Jokela, Pia / Szirovicza, Leonora / Pohjala, Sari / Vapalahti, Olli / Lappalainen, Maija / Hepojoki, Jussi / Kurkela, Satu

medRxiv

Abstract: Introduction The COVID-19 pandemic has led to high demand of diagnostic tools. Rapid antigen detection tests have been developed and many have received regulatory acceptance such as CE IVD or FDA markings. Their performance needs to be carefully assessed. ...

Abstract	Introduction The COVID-19 pandemic has led to high demand of diagnostic tools. Rapid antigen detection tests have been developed and many have received regulatory acceptance such as CE IVD or FDA markings. Their performance needs to be carefully assessed. Materials and Methods 158 positive and 40 negative retrospective samples collected in saline and analyzed by a laboratory-developed RT-PCR test were used to evaluate Sofia (Quidel), Standard Q (SD Biosensor), and Panbio (Abbott) rapid antigen detection tests (RADTs). A subset of the specimens was subjected to virus culture. Results The specificity of all RADTs was 100% and the sensitivity and percent agreement was 80% and 85% for Sofia, 81% and 85% for Standard Q, and 83% and 86% for Panbio, respectively. All three RADTs evaluated in this study reached a more than 90% sensitivity for samples with a high viral load as estimated from the low Ct values in the reference RT-PCR. Virus culture was successful in 80% of specimens with a Ct value <25. Conclusions As expected, the RADTs were less sensitive than RT-PCR. However, they benefit from the speed and ease of testing, and lower price as compared to RT-PCR. Repeated testing in appropriate settings may improve the overall performance.
Keywords	covid19
Language	English
Publishing date	2021-01-04
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2020.12.30.20249057
Database	COVID19

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Article: SARS-CoV-2 sample-to-answer nucleic acid testing in a tertiary care emergency department: evaluation and utility

Jokela, Pia / Jääskeläinen, Anu E / Jarva, Hanna / Holma, Tanja / Ahava, Maarit J / Mannonen, Laura / Lappalainen, Maija / Kurkela, Satu / Loginov, Raisa

J Clin Virol

Abstract: BACKGROUND: Rapid sample-to-answer tests for detection of SARS-CoV-2 are emerging and data on their relative performance is urgently needed. OBJECTIVES: We evaluated the analytical performance of two rapid nucleic acid tests, Cepheid Xpert® Xpress SARS- ... ...

Abstract	BACKGROUND: Rapid sample-to-answer tests for detection of SARS-CoV-2 are emerging and data on their relative performance is urgently needed. OBJECTIVES: We evaluated the analytical performance of two rapid nucleic acid tests, Cepheid Xpert® Xpress SARS-CoV-2 and Mobidiag Novodiag® Covid-19, in comparison to a combination reference of three large-scale PCR tests. Moreover, utility of the Novodiag® test in tertiary care emergency departments was assessed. RESULTS: In the preliminary evaluation, analysis of 90 respiratory samples resulted in 100% specificity and sensitivity for Xpert®, whereas analysis of 107 samples resulted in 93.4% sensitivity and 100% specificity for Novodiag®. Rapid SARS-CoV-2 testing with Novodiag® was made available for four tertiary care emergency departments in Helsinki, Finland between 18 and 31 May, coinciding with a rapidly declining epidemic phase. Altogether 361 respiratory specimens, together with relevant clinical data, were analyzed with Novodiag® and reference tests: 355/361 of the specimens were negative with both methods, and 1/361 was positive in Novodiag® and negative by the reference method. Of the 5 remaining specimens, two were negative with Novodiag®, but positive with the reference method with late Ct values. On average, a test result using Novodiag® was available nearly 8â¯hours earlier than that obtained with the large-scale PCR tests. CONCLUSIONS: While the performance of novel sample-to-answer PCR tests need to be carefully evaluated, they may provide timely and reliable results in detection of SARS-CoV-2 and thus facilitate patient management including effective cohorting.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #731821
Database	COVID19

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Article ; Online: SARS-CoV-2 sample-to-answer nucleic acid testing in a tertiary care emergency department

Jokela, Pia / Jääskeläinen, Anu E. / Jarva, Hanna / Holma, Tanja / Ahava, Maarit J / Mannonen, Laura / Lappalainen, Maija / Kurkela, Satu / Loginov, Raisa

Journal of Clinical Virology

evaluation and utility

2020 Volume 131, Page(s) 104614

Keywords	Virology ; Infectious Diseases ; covid19
Language	English
Publisher	Elsevier BV
Publishing country	us
Document type	Article ; Online
ZDB-ID	1446080-4
ISSN	1873-5967 ; 1386-6532
ISSN (online)	1873-5967
ISSN	1386-6532
DOI	10.1016/j.jcv.2020.104614
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Multi-laboratory evaluation of ReaScan TBE IgM rapid test, 2016 to 2017.

Albinsson, Bo / Jääskeläinen, Anu E / Värv, Kairi / Jelovšek, Mateja / GeurtsvanKessel, Corine / Vene, Sirkka / Järhult, Josef D / Reusken, Chantal / Golovljova, Irina / Avšič-Županc, Tatjana / Vapalahti, Olli / Lundkvist, Åke

Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin

2020 Volume 25, Issue 12

Abstract: BackgroundTick-borne encephalitis (TBE) is a potentially severe neurological disease caused by TBE virus (TBEV). In Europe and Asia, TBEV infection has become a growing public health concern and requires fast and specific detection.AimIn this ... ...

Abstract	BackgroundTick-borne encephalitis (TBE) is a potentially severe neurological disease caused by TBE virus (TBEV). In Europe and Asia, TBEV infection has become a growing public health concern and requires fast and specific detection.AimIn this observational study, we evaluated a rapid TBE IgM test, ReaScan TBE, for usage in a clinical laboratory setting.MethodsPatient sera found negative or positive for TBEV by serological and/or molecular methods in diagnostic laboratories of five European countries endemic for TBEV (Estonia, Finland, Slovenia, the Netherlands and Sweden) were used to assess the sensitivity and specificity of the test. The patients' diagnoses were based on other commercial or quality assured in-house assays, i.e. each laboratory's conventional routine methods. For specificity analysis, serum samples from patients with infections known to cause problems in serology were employed. These samples tested positive for e.g. Epstein-Barr virus, cytomegalovirus and
MeSH term(s)	Antibodies, Viral/blood ; Encephalitis Viruses, Tick-Borne/immunology ; Encephalitis, Tick-Borne/diagnosis ; Encephalitis, Tick-Borne/epidemiology ; Encephalitis, Tick-Borne/immunology ; Female ; Humans ; Immunoenzyme Techniques ; Immunoglobulin M/blood ; Male ; Predictive Value of Tests ; Sensitivity and Specificity
Chemical Substances	Antibodies, Viral ; Immunoglobulin M
Language	English
Publishing date	2020-03-26
Publishing country	Sweden
Document type	Journal Article ; Observational Study
ZDB-ID	1338803-4
ISSN	1560-7917 ; 1025-496X
ISSN (online)	1560-7917
ISSN	1025-496X
DOI	10.2807/1560-7917.ES.2020.25.12.1900427
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Zs.A 5066: Show issues

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Article ; Online: Real-life clinical sensitivity of SARS-CoV-2 RT-PCR test in symptomatic patients.

PloS one

2021 Volume 16, Issue 5, Page(s) e0251661

Abstract: Background: Understanding the false negative rates of SARS-CoV-2 RT-PCR testing is pivotal for the management of the COVID-19 pandemic and it has implications for patient management. Our aim was to determine the real-life clinical sensitivity of SARS- ... ...

Abstract	Background: Understanding the false negative rates of SARS-CoV-2 RT-PCR testing is pivotal for the management of the COVID-19 pandemic and it has implications for patient management. Our aim was to determine the real-life clinical sensitivity of SARS-CoV-2 RT-PCR. Methods: This population-based retrospective study was conducted in March-April 2020 in the Helsinki Capital Region, Finland. Adults who were clinically suspected of SARS-CoV-2 infection and underwent SARS-CoV-2 RT-PCR testing, with sufficient data in their medical records for grading of clinical suspicion were eligible. In addition to examining the first RT-PCR test of repeat-tested individuals, we also used high clinical suspicion for COVID-19 as the reference standard for calculating the sensitivity of SARS-CoV-2 RT-PCR. Results: All 1,194 inpatients (mean [SD] age, 63.2 [18.3] years; 45.2% women) admitted to COVID-19 cohort wards during the study period were included. The outpatient cohort of 1,814 individuals (mean [SD] age, 45.4 [17.2] years; 69.1% women) was sampled from epidemiological line lists by systematic quasi-random sampling. The sensitivity (95% CI) for laboratory confirmed cases (repeat-tested patients) was 85.7% (81.5-89.1%) inpatients; 95.5% (92.2-97.5%) outpatients, 89.9% (88.2-92.1%) all. When also patients that were graded as high suspicion but never tested positive were included in the denominator, the sensitivity (95% CI) was: 67.5% (62.9-71.9%) inpatients; 34.9% (31.4-38.5%) outpatients; 47.3% (44.4-50.3%) all. Conclusions: The clinical sensitivity of SARS-CoV-2 RT-PCR testing was only moderate at best. The relatively high false negative rates of SARS-CoV-2 RT-PCR testing need to be accounted for in clinical decision making, epidemiological interpretations, and when using RT-PCR as a reference for other tests.
MeSH term(s)	Adult ; Aged ; COVID-19 Nucleic Acid Testing/methods ; COVID-19 Nucleic Acid Testing/standards ; False Negative Reactions ; Female ; Humans ; Male ; Middle Aged ; Random Allocation ; Reagent Kits, Diagnostic/standards
Chemical Substances	Reagent Kits, Diagnostic
Language	English
Publishing date	2021-05-21
Publishing country	United States
Document type	Evaluation Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0251661
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Article ; Online: European subtype tick-borne encephalitis virus in Ixodes persulcatus ticks.

Jääskeläinen, Anu E / Tonteri, Elina / Sironen, Tarja / Pakarinen, Laura / Vaheri, Antti / Vapalahti, Olli

Emerging infectious diseases

2011 Volume 17, Issue 2, Page(s) 323–325

MeSH term(s)	Animals ; Arthropod Vectors/virology ; Arvicolinae/virology ; Communicable Diseases, Emerging/epidemiology ; Communicable Diseases, Emerging/transmission ; Communicable Diseases, Emerging/virology ; Encephalitis Viruses, Tick-Borne/genetics ; Encephalitis Viruses, Tick-Borne/immunology ; Encephalitis Viruses, Tick-Borne/isolation & purification ; Encephalitis, Tick-Borne/epidemiology ; Encephalitis, Tick-Borne/transmission ; Encephalitis, Tick-Borne/virology ; Finland/epidemiology ; Humans ; Ixodes/virology ; Mice ; Phylogeny ; Prevalence ; RNA, Viral/blood ; Rodent Diseases/epidemiology ; Rodent Diseases/transmission ; Rodent Diseases/virology
Chemical Substances	RNA, Viral
Language	English
Publishing date	2011-02-04
Publishing country	United States
Document type	Letter
ZDB-ID	1380686-5
ISSN	1080-6059 ; 1080-6040
ISSN (online)	1080-6059
ISSN	1080-6040
DOI	10.3201/eid1702.101487
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Zs.A 4778: Show issues

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Article: Rate of evolution and molecular epidemiology of tick-borne encephalitis virus in Europe, including two isolations from the same focus 44 years apart

Uzcátegui, Nathalie Y / Sironen, Tarja / Golovljova, Irina / Jääskeläinen, Anu E / Välimaa, Hannamari / Lundkvist, Åke / Plyusnin, Alexander / Vaheri, Antti / Vapalahti, Olli

Journal of general virology. 2012 Apr., v. 93, no. Pt Pt_4

2012

Abstract: Tick-borne encephalitis virus (TBEV) is a member of the family FLAVIVIRIDAE: It is transmitted by Ixodes spp. ticks in a cycle involving rodents and small mammals. TBEV has three subtypes: European, Siberian and Far Eastern. The virus causes thousands of ...

Abstract	Tick-borne encephalitis virus (TBEV) is a member of the family FLAVIVIRIDAE: It is transmitted by Ixodes spp. ticks in a cycle involving rodents and small mammals. TBEV has three subtypes: European, Siberian and Far Eastern. The virus causes thousands of cases of meningoencephalitis in Europe annually, with an increasing trend. The increase may be attributed to a complex network of elements, including climatic, environmental and socio-economic factors. In an attempt to understand the evolutionary history and dispersal of TBEV, to existing genetic data we add two novel complete ORF sequences of TBEV strains from northern Europe and the completion of the genome of four others. Moreover, we provide a unique measure for the natural rate of evolution of TBEV by studying two isolations from the same forest on an island in Åland archipelago 44 years apart. For all isolates, we analysed the phylogeny, rate of evolution and probable time of radiation of the different TBEV strains. The results show that the two lineages of TBEV in different Ixodes species have evolved independently for approximately 3300 years. Notably, rapid radiation of TBEV-Eur occurred approximately 300 years ago, without the large-scale geographical clustering observed previously for the Siberian subtype. The measurements from the natural rate of evolution correlated with the estimates done by phylogenetic programs, demonstrating their robustness.
Keywords	Ixodes ; Tick-borne encephalitis virus ; forests ; genome ; geographical distribution ; meningoencephalitis ; molecular epidemiology ; open reading frames ; phylogeny ; rodents ; small mammals ; socioeconomic factors ; ticks ; viruses ; Finland ; Northern European region
Language	English
Dates of publication	2012-04
Size	p. 786-796.
Publishing place	Society for General Microbiology
Document type	Article
ZDB-ID	219316-4
ISSN	1465-2099 ; 0022-1317
ISSN (online)	1465-2099
ISSN	0022-1317
DOI	10.1099/vir.0.035766-0
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Rate of evolution and molecular epidemiology of tick-borne encephalitis virus in Europe, including two isolations from the same focus 44 years apart.

Uzcátegui, Nathalie Y / Sironen, Tarja / Golovljova, Irina / Jääskeläinen, Anu E / Välimaa, Hannamari / Lundkvist, Åke / Plyusnin, Alexander / Vaheri, Antti / Vapalahti, Olli

The Journal of general virology

2011 Volume 93, Issue Pt 4, Page(s) 786–796

Abstract: Tick-borne encephalitis virus (TBEV) is a member of the family Flaviviridae. It is transmitted by Ixodes spp. ticks in a cycle involving rodents and small mammals. TBEV has three subtypes: European, Siberian and Far Eastern. The virus causes thousands of ...

Abstract	Tick-borne encephalitis virus (TBEV) is a member of the family Flaviviridae. It is transmitted by Ixodes spp. ticks in a cycle involving rodents and small mammals. TBEV has three subtypes: European, Siberian and Far Eastern. The virus causes thousands of cases of meningoencephalitis in Europe annually, with an increasing trend. The increase may be attributed to a complex network of elements, including climatic, environmental and socio-economic factors. In an attempt to understand the evolutionary history and dispersal of TBEV, to existing genetic data we add two novel complete ORF sequences of TBEV strains from northern Europe and the completion of the genome of four others. Moreover, we provide a unique measure for the natural rate of evolution of TBEV by studying two isolations from the same forest on an island in Åland archipelago 44 years apart. For all isolates, we analysed the phylogeny, rate of evolution and probable time of radiation of the different TBEV strains. The results show that the two lineages of TBEV in different Ixodes species have evolved independently for approximately 3300 years. Notably, rapid radiation of TBEV-Eur occurred approximately 300 years ago, without the large-scale geographical clustering observed previously for the Siberian subtype. The measurements from the natural rate of evolution correlated with the estimates done by phylogenetic programs, demonstrating their robustness.
MeSH term(s)	Animals ; Base Sequence ; Encephalitis Viruses, Tick-Borne/genetics ; Encephalitis, Tick-Borne/epidemiology ; Encephalitis, Tick-Borne/virology ; Estonia/epidemiology ; Europe/epidemiology ; Evolution, Molecular ; Female ; Finland/epidemiology ; Genetic Variation/genetics ; Humans ; Ixodes/virology ; Male ; Mice ; Molecular Epidemiology ; Molecular Sequence Data ; Phylogeny
Language	English
Publishing date	2011-12-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	219316-4
ISSN	1465-2099 ; 0022-1317
ISSN (online)	1465-2099
ISSN	0022-1317
DOI	10.1099/vir.0.035766-0
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