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Buchta C, Aberle SW, Allerberger F, Benka B, Görzer I, Griesmacher A, Hübl W, Huf W, Kapiotis S, Müller MM, Neuwirth E, Puchhammer-Stöckl E, Weseslindtner L, Camp JV. Performance of SARS-CoV-2 nucleic acid amplification testing in Austria as measured by external quality assessment schemes during 3 years of the COVID-19 pandemic: an observational retrospective study. Lancet Microbe 2023; 4:e1015-e1023. [PMID: 37979591 DOI: 10.1016/s2666-5247(23)00286-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 11/20/2023]
Abstract
BACKGROUND The aim of external quality assessment (EQA) schemes is to evaluate the analytical performance of laboratories and test systems in a near-to-real-life setting. This monitoring service provides feedback to participant laboratories and serves as a control measure for the epidemiological assessment of the regional incidence of a pathogen, particularly during epidemics. Using data from EQA schemes implemented as a result of the intensive effort to monitor SARS-CoV-2 infections in Austria, we aimed to identify factors that explained the variation in laboratory performance for SARS-CoV-2 detection over the course of the COVID-19 pandemic. METHODS For this observational study, we retrospectively analysed 6308 reverse transcriptase quantitative PCR (RT-qPCR) test results reported by 191 laboratories on 71 samples during 14 rounds of three SARS-CoV-2 pathogen detection EQA schemes in Austria between May 18, 2020, and Feb 20, 2023. We calculated the overall rates of false and true-negative, false and true-positive, and inconclusive results. We then assessed laboratory performance by estimating the sensitivity by testing whether significant variation in the odds of obtaining a true-positive result could be explained by virus concentration, laboratory type, or assay format. We also assessed whether laboratory performance changed over time. FINDINGS 4371 (93·7%) of 4663 qPCR test results were true-positive, 241 (5·2%) were false-negative, and 51 (1·1%) were inconclusive. The mean per-sample sensitivity was 99·7% in samples with high virus concentrations (1383 [99·4%] true-positive, three [0·2%] false-negative, and five [0·4%] inconclusive results for 1391 tests in which the sample cycle threshold was ≤32), whereas detection rates were lower in samples with low virus concentrations (mean per-sample sensitivity 92·5%; 2988 [91·3%] true-positive, 238 [7·3%] false-negative, and 46 [1·4%] inconclusive results for 3272 tests in which the cycle threshold was >32). Of the 1645 results expected to be negative, 1561 (94·9%) were correctly reported as negative, 10 (0·6%) were incorrectly reported as positive, and 74 (4·5%) were reported as inconclusive. Notably, the overall performance of the tests did not change significantly over time. The odds of reporting a correct result were 2·94 (95% CI 1·75-4·96) times higher for a medical laboratory than for a non-medical laboratory, and 4·60 (2·91-7·41) times greater for automated test systems than for manual test systems. Automated test systems within medical laboratories had the highest sensitivity when compared with systems requiring manual intervention in both medical and non-medical laboratories. INTERPRETATION High rates of false-negativity in all PCR analyses evaluated in comprehensive, multiple, and repeated EQA schemes outline a clear path for improvement in the future. The performance of some laboratories (eg, non-medical laboratories or those using non-automated test systems) should receive additional scrutiny-for example, by requiring additional EQA schemes for certification or accreditation-if the aggregated data from EQA rounds suggest lower sensitivity than that recorded by others. This strategy will provide assurances that epidemiological data as a whole are reliable when testing on such a large scale. Although performance did not improve over time, we cannot exclude extenuating circumstances-such as shortages and weakened supply chains-that could have prevented laboratories from seeking alternative methods to improve performance. FUNDING None.
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Affiliation(s)
- Christoph Buchta
- Austrian Association for Quality Assurance and Standardization of Medical and Diagnostic Tests (ÖQUASTA), Vienna, Austria.
| | - Stephan W Aberle
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | | | - Bernhard Benka
- Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Irene Görzer
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Andrea Griesmacher
- Austrian Association for Quality Assurance and Standardization of Medical and Diagnostic Tests (ÖQUASTA), Vienna, Austria; Central Institute for Medical and Chemical Laboratory Diagnosis, Innsbruck University Hospital, Innsbruck, Austria
| | - Wolfgang Hübl
- Austrian Association for Quality Assurance and Standardization of Medical and Diagnostic Tests (ÖQUASTA), Vienna, Austria; Department of Laboratory Medicine, Klinik Ottakring, Vienna, Austria
| | - Wolfgang Huf
- Karl Landsteiner Institute for Clinical Risk Management, Vienna, Austria
| | - Stylianos Kapiotis
- Austrian Association for Quality Assurance and Standardization of Medical and Diagnostic Tests (ÖQUASTA), Vienna, Austria; LABCON Medizinische Laboratorien, Vienna, Austria
| | - Mathias M Müller
- Austrian Association for Quality Assurance and Standardization of Medical and Diagnostic Tests (ÖQUASTA), Vienna, Austria
| | - Erich Neuwirth
- Faculty of Computer Science, University of Vienna, Vienna, Austria
| | | | | | - Jeremy V Camp
- Center for Virology, Medical University of Vienna, Vienna, Austria.
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2
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Jesumirhewe C, Cabal-Rosel A, Allerberger F, Springer B, Ruppitsch W. Genetic characterization of Escherichia coli and Klebsiella spp. from humans and poultry in Nigeria. Access Microbiol 2023; 5:acmi000509.v4. [PMID: 37601433 PMCID: PMC10436014 DOI: 10.1099/acmi.0.000509.v4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 05/31/2023] [Indexed: 08/22/2023] Open
Abstract
The emergence of antibiotic resistance in livestock, especially food-producing animals, is of major public health importance as a result of the possibility of these bacteria entering the food chain. In this study, the genetic characteristics of antibiotic-resistant Escherichia coli and Klebsiella spp. isolates from humans and poultry in Edo state, Nigeria, were investigated. In April 2017, 45 Klebsiella spp. and 46 E. coli isolates were obtained from urine, clinical wounds, nasal and chicken faecal samples. Isolates were recovered and identified as previously described. Species identification was achieved by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry and ribosomal multilocus sequence typing. Antimicrobial susceptibility testing was carried out using the Kirby-Bauer method for 12 antibiotics. A double disc synergy test was used to screen for extended-spectrum beta-lactamse (ESBL) production. Whole genome sequencing was performed for strain characterization of the isolates. Thirteen Klebsiella spp. isolates yielded positive results by the ESBL phenotypic test and harboured ESBL genes. Of the 46 E. coli isolates, 21 human and 13 poultry isolates were resistant to at least one of the tested antibiotics. Four human E. coli isolates harboured ESBL genes and revealed positive results when applying ESBL double disc synergy tests. ESBL genes in the Klebsiella spp. and E. coli isolates include bla CTX-M-15 and bla SHV-28. Whole genome-based core gene multilocus sequence typing of the Klebsiella spp. and E. coli isolates revealed a close relatedness among the isolates. An integrated 'One Health' surveillance system is required to monitor transmission of antimicrobial resistance in Nigeria.
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Affiliation(s)
- Christiana Jesumirhewe
- Department of Pharmaceutical Microbiology, College of Pharmacy, Igbinedion University, Okada, Edo state, Nigeria
| | - Adriana Cabal-Rosel
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Franz Allerberger
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Burkhard Springer
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Werner Ruppitsch
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
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3
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Buchta C, Zeichhardt H, Aberle SW, Camp JV, Görzer I, Weseslindtner L, Puchhammer-Stöckl E, Huf W, Benka B, Allerberger F, Mielke M, Griesmacher A, Müller MM, Schellenberg I, Kammel M. Design of external quality assessment schemes and definition of the roles of their providers in future epidemics. Lancet Microbe 2023; 4:e552-e562. [PMID: 37156257 PMCID: PMC10162712 DOI: 10.1016/s2666-5247(23)00072-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 05/10/2023]
Abstract
During an epidemic, individual test results form the basis of epidemiological indicators such as case numbers or incidence. Therefore, the accuracy of measures derived from these indicators depends on the reliability of individual results. In the COVID-19 pandemic, monitoring and evaluating the performance of the unprecedented number of testing facilities in operation, and novel testing systems in use, was urgently needed. External quality assessment (EQA) schemes are unique sources of data reporting on testing performance, and their providers are recognised contacts and support for test facilities (for technical-analytical topics) and health authorities (for planning the monitoring of infection diagnostics). To identify information provided by SARS-CoV-2 genome detection EQA schemes that is relevant for public health microbiology, we reviewed the current literature published in PubMed between January, 2020, and July, 2022. We derived recommendations for EQA providers and their schemes for best practices to monitor pathogen-detection performance in future epidemics. We also showed laboratories, test facilities, and health authorities the information and benefits they can derive from EQA data, and from the non-EQA services of their providers.
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Affiliation(s)
- Christoph Buchta
- Austrian Association for Quality Assurance and Standardization of Medical and Diagnostic Tests, Vienna, Austria; European Organisation for External Quality Assurance Providers in Laboratory Medicine, Geneva, Switzerland.
| | - Heinz Zeichhardt
- INSTAND eV Society for Promoting Quality Assurance in Medical Laboratories, Düsseldorf, Germany; IQVD GmbH, Institut für Qualitätssicherung in der Virusdiagnostik, Berlin, Germany; GBD Gesellschaft für Biotechnologische Diagnostik, Berlin, Germany
| | - Stephan W Aberle
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Jeremy V Camp
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Irene Görzer
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | | | | | - Wolfgang Huf
- Karl Landsteiner Institute for Clinical Risk Management, Vienna, Austria
| | - Bernhard Benka
- Austrian Agency for Health and Food Safety, Vienna, Austria
| | | | - Martin Mielke
- Department for Infectious Diseases, Robert Koch-Institute, Berlin, Germany
| | - Andrea Griesmacher
- Austrian Association for Quality Assurance and Standardization of Medical and Diagnostic Tests, Vienna, Austria
| | - Mathias M Müller
- Austrian Association for Quality Assurance and Standardization of Medical and Diagnostic Tests, Vienna, Austria
| | - Ingo Schellenberg
- INSTAND eV Society for Promoting Quality Assurance in Medical Laboratories, Düsseldorf, Germany
| | - Martin Kammel
- INSTAND eV Society for Promoting Quality Assurance in Medical Laboratories, Düsseldorf, Germany; IQVD GmbH, Institut für Qualitätssicherung in der Virusdiagnostik, Berlin, Germany; GBD Gesellschaft für Biotechnologische Diagnostik, Berlin, Germany
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4
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Munk P, Brinch C, Møller FD, Petersen TN, Hendriksen RS, Seyfarth AM, Kjeldgaard JS, Svendsen CA, van Bunnik B, Berglund F, Larsson DGJ, Koopmans M, Woolhouse M, Aarestrup FM, Gibb K, Coventry K, Collignon P, Cassar S, Allerberger F, Begum A, Hossain ZZ, Worrell C, Vandenberg O, Pieters I, Victorien DT, Gutierrez ADS, Soria F, Grujić VR, Mazalica N, Rahube TO, Tagliati CA, Rodrigues D, Oliveira G, de Souza LCR, Ivanov I, Juste BI, Oumar T, Sopheak T, Vuthy Y, Ngandjio A, Nzouankeu A, Olivier ZAAJ, Yost CK, Kumar P, Brar SK, Tabo DA, Adell AD, Paredes-Osses E, Martinez MC, Cuadros-Orellana S, Ke C, Zheng H, Baisheng L, Lau LT, Chung T, Jiao X, Yu Y, JiaYong Z, Morales JFB, Valencia MF, Donado-Godoy P, Coulibaly KJ, Hrenovic J, Jergović M, Karpíšková R, Deogratias ZN, Elsborg B, Hansen LT, Jensen PE, Abouelnaga M, Salem MF, Koolmeister M, Legesse M, Eguale T, Heikinheimo A, Le Guyader S, Schaeffer J, Villacis JE, Sanneh B, Malania L, Nitsche A, Brinkmann A, Schubert S, Hesse S, Berendonk TU, Saba CKS, Mohammed J, Feglo PK, Banu RA, Kotzamanidis C, Lytras E, Lickes SA, Kocsis B, Solymosi N, Thorsteinsdottir TR, Hatha AM, Ballal M, Bangera SR, Fani F, Alebouyeh M, Morris D, O’Connor L, Cormican M, Moran-Gilad J, Battisti A, Diaconu EL, Corno G, Di Cesare A, Alba P, Hisatsune J, Yu L, Kuroda M, Sugai M, Kayama S, Shakenova Z, Kiiyukia C, Ng’eno E, Raka L, Jamil K, Fakhraldeen SA, Alaati T, Bērziņš A, Avsejenko J, Kokina K, Streikisa M, Bartkevics V, Matar GM, Daoud Z, Pereckienė A, Butrimaite-Ambrozeviciene C, Penny C, Bastaraud A, Rasolofoarison T, Collard JM, Samison LH, Andrianarivelo MR, Banda DL, Amin A, Rajandas H, Parimannan S, Spiteri D, Haber MV, Santchurn SJ, Vujacic A, Djurovic D, Bouchrif B, Karraouan B, Vubil DC, Pal P, Schmitt H, van Passel M, Jeunen GJ, Gemmell N, Chambers ST, Mendoza FP, Huete-Pιrez J, Vilchez S, Ahmed AO, Adisa IR, Odetokun IA, Fashae K, Sørgaard AM, Wester AL, Ryrfors P, Holmstad R, Mohsin M, Hasan R, Shakoor S, Gustafson NW, Schill CH, Rojas MLZ, Velasquez JE, Magtibay BB, Catangcatang K, Sibulo R, Yauce FC, Wasyl D, Manaia C, Rocha J, Martins J, Álvaro P, Di Yoong Wen D, Shin H, Hur HG, Yoon S, Bosevska G, Kochubovski M, Cojocaru R, Burduniuc O, Hong PY, Perry MR, Gassama A, Radosavljevic V, Tay MYF, Zuniga-Montanez R, Wuertz S, Gavačová D, Pastuchová K, Truska P, Trkov M, Keddy K, Esterhuyse K, Song MJ, Quintela-Baluja M, Lopez MG, Cerdà-Cuéllar M, Perera RRDP, Bandara NKBKRGW, Premasiri HI, Pathirage S, Charlemagne K, Rutgersson C, Norrgren L, Örn S, Boss R, Van der Heijden T, Hong YP, Kumburu HH, Mdegela RH, Hounmanou YMG, Chonsin K, Suthienkul O, Thamlikitkul V, de Roda Husman AM, Bidjada B, Njanpop-Lafourcade BM, Nikiema-Pessinaba SC, Levent B, Kurekci C, Ejobi F, Kalule JB, Thomsen J, Obaidi O, Jassim LM, Moore A, Leonard A, Graham DW, Bunce JT, Zhang L, Gaze WH, Lefor B, Capone D, Sozzi E, Brown J, Meschke JS, Sobsey MD, Davis M, Beck NK, Sukapanpatharam P, Truong P, Lilienthal R, Kang S, Wittum TE, Rigamonti N, Baklayan P, Van CD, Tran DMN, Do Phuc N, Kwenda G, Larsson DGJ, Koopmans M, Woolhouse M, Aarestrup FM. Author Correction: Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance. Nat Commun 2023; 14:178. [PMID: 36635285 PMCID: PMC9837105 DOI: 10.1038/s41467-023-35890-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Patrick Munk
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Christian Brinch
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Frederik Duus Møller
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Thomas N. Petersen
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Rene S. Hendriksen
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Anne Mette Seyfarth
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Jette S. Kjeldgaard
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Christina Aaby Svendsen
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Bram van Bunnik
- grid.4305.20000 0004 1936 7988Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK
| | - Fanny Berglund
- grid.8761.80000 0000 9919 9582Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | | | - D. G. Joakim Larsson
- grid.8761.80000 0000 9919 9582Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Marion Koopmans
- grid.5645.2000000040459992XDepartment of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Mark Woolhouse
- grid.4305.20000 0004 1936 7988Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK
| | - Frank M. Aarestrup
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
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5
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Amman F, Markt R, Endler L, Hupfauf S, Agerer B, Schedl A, Richter L, Zechmeister M, Bicher M, Heiler G, Triska P, Thornton M, Penz T, Senekowitsch M, Laine J, Keszei Z, Klimek P, Nägele F, Mayr M, Daleiden B, Steinlechner M, Niederstätter H, Heidinger P, Rauch W, Scheffknecht C, Vogl G, Weichlinger G, Wagner AO, Slipko K, Masseron A, Radu E, Allerberger F, Popper N, Bock C, Schmid D, Oberacher H, Kreuzinger N, Insam H, Bergthaler A. Viral variant-resolved wastewater surveillance of SARS-CoV-2 at national scale. Nat Biotechnol 2022; 40:1814-1822. [PMID: 35851376 DOI: 10.1038/s41587-022-01387-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 06/07/2022] [Indexed: 01/14/2023]
Abstract
SARS-CoV-2 surveillance by wastewater-based epidemiology is poised to provide a complementary approach to sequencing individual cases. However, robust quantification of variants and de novo detection of emerging variants remains challenging for existing strategies. We deep sequenced 3,413 wastewater samples representing 94 municipal catchments, covering >59% of the population of Austria, from December 2020 to February 2022. Our system of variant quantification in sewage pipeline designed for robustness (termed VaQuERo) enabled us to deduce the spatiotemporal abundance of predefined variants from complex wastewater samples. These results were validated against epidemiological records of >311,000 individual cases. Furthermore, we describe elevated viral genetic diversity during the Delta variant period, provide a framework to predict emerging variants and measure the reproductive advantage of variants of concern by calculating variant-specific reproduction numbers from wastewater. Together, this study demonstrates the power of national-scale WBE to support public health and promises particular value for countries without extensive individual monitoring.
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Affiliation(s)
- Fabian Amman
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Institute of Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Rudolf Markt
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Lukas Endler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Institute of Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Sebastian Hupfauf
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Benedikt Agerer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Anna Schedl
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Institute of Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Lukas Richter
- Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | | | - Martin Bicher
- dwh GmbH, Vienna, Austria.,Institute for Information Systems Engineering, Technische Universität Wien, Vienna, Austria
| | - Georg Heiler
- Complexity Science Hub, Vienna, Austria.,Institute of Information Systems Engineering, Technische Universität Wien, Vienna, Austria
| | - Petr Triska
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Institute of Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Matthew Thornton
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Institute of Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Thomas Penz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Martin Senekowitsch
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jan Laine
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Zsofia Keszei
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Peter Klimek
- Complexity Science Hub, Vienna, Austria.,Section for Science of Complex Systems, Medical University of Vienna, Vienna, Austria
| | - Fabiana Nägele
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Markus Mayr
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Beatrice Daleiden
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Innsbruck, Austria
| | - Martin Steinlechner
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Innsbruck, Austria
| | - Harald Niederstätter
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Innsbruck, Austria
| | - Petra Heidinger
- Austrian Centre of Industrial Biotechnology GmbH, Graz, Austria
| | - Wolfgang Rauch
- Department of Infrastructure, Universität Innsbruck, Innsbruck, Austria
| | | | - Gunther Vogl
- Institut für Lebensmittelsicherheit, Veterinärmedizin und Umwelt des Landes Kärnten, Klagenfurt am Wörthersee, Austria
| | - Günther Weichlinger
- Abteilung 12 - Wasserwirtschaft, Amt der Kärntner Landesregierung, Klagenfurt am Wörthersee, Austria
| | | | - Katarzyna Slipko
- Institute for Water Quality and Resource Management, Technische Universität Wien, Vienna, Austria
| | - Amandine Masseron
- Institute for Water Quality and Resource Management, Technische Universität Wien, Vienna, Austria
| | - Elena Radu
- Institute for Water Quality and Resource Management, Technische Universität Wien, Vienna, Austria.,Ştefan S. Nicolau Institute of Virology, Bucharest, Romania
| | | | - Niki Popper
- dwh GmbH, Vienna, Austria.,Institute for Information Systems Engineering, Technische Universität Wien, Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Institute of Artificial Intelligence, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Daniela Schmid
- Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Herbert Oberacher
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Innsbruck, Austria
| | - Norbert Kreuzinger
- Institute for Water Quality and Resource Management, Technische Universität Wien, Vienna, Austria
| | - Heribert Insam
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Andreas Bergthaler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria. .,Institute of Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria.
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6
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Tschiderer L, Seekircher L, Richter L, von Laer D, Lass-Flörl C, Forer L, Schönherr S, Krammer F, Embacher-Aichhorn S, Tilg H, Weiss G, Allerberger F, Willeit P. Ultra-rapid rollout vaccination with BNT162b2 to reduce SARS-CoV-2 infections in the general population. iScience 2022; 25:105380. [PMID: 36373097 PMCID: PMC9639213 DOI: 10.1016/j.isci.2022.105380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 08/30/2022] [Accepted: 10/12/2022] [Indexed: 11/09/2022] Open
Abstract
This study aimed to determine the impact of ultra-rapid rollout vaccination on incidence of SARS-CoV-2 infection. Vaccination with BNT162b2 was provided to 66.9% of eligible residents of the Schwaz district in Tyrol, Austria, within six days per dose (first dose: 11–16 March 2021, second dose: 8–13 April 2021). Of 11,955 individuals enrolled at nine vaccination centers (median age 44.6 years; 51.3% female), 71 had incident SARS-CoV-2 over a six-month follow-up. Incidence rates per 100,000 person-weeks were 92.3 (95% confidence interval [CI]: 70.8–120.2) at weeks 1–5 and 6.4 (3.9–10.4) at ≥6 weeks after dose 1. In these two periods, effectiveness of the vaccination campaign to reduce incident SARS-CoV-2 was 58.6% (50.8%–65.2%) and 91.1% (89.6%–92.3%) in study participants and 28.3% (23.1%–33.0%) and 64.0% (61.7%–66.1%) in the Schwaz district, compared with districts with slower vaccination rollout. Therefore, the vaccination campaign in the Schwaz district illustrates the impact of accelerated vaccination rollout in controlling the pandemic. This study accompanied an ultra-rapid rollout vaccination campaign in Austria 66.9% of eligible residents of the Schwaz district received BNT162b2 within 6 days Over six months, SARS-CoV-2 incidence rate was 22.8 per 100.000 person-weeks Effectiveness of the vaccination campaign was 91.1% at ≥6 weeks after the 1st dose
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Affiliation(s)
- Lena Tschiderer
- Institute of Health Economics, Medical University of Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria
| | - Lisa Seekircher
- Institute of Health Economics, Medical University of Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria
| | - Lukas Richter
- Institute of Infectious Disease Epidemiology, Austrian Agency for Health and Food Safety, 1220 Vienna, Austria
| | - Dorothee von Laer
- Institute of Virology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Cornelia Lass-Flörl
- Department of Hygiene and Medical Microbiology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Lukas Forer
- Institute of Genetic Epidemiology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Sebastian Schönherr
- Institute of Genetic Epidemiology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Florian Krammer
- Department of Microbiology and Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029-5674, USA
| | | | - Herbert Tilg
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology and Metabolism, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Günter Weiss
- Department of Internal Medicine II, Infectious Diseases, Immunology, Pneumology and Rheumatology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Franz Allerberger
- Institute of Infectious Disease Epidemiology, Austrian Agency for Health and Food Safety, 1220 Vienna, Austria
| | - Peter Willeit
- Institute of Health Economics, Medical University of Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria
- Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
- Corresponding author
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7
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Cabal A, Rab G, Daza-Prieto B, Stöger A, Peischl N, Chakeri A, Mo SS, Bock H, Fuchs K, Sucher J, Rathammer K, Hasenberger P, Stadtbauer S, Caniça M, Strauß P, Allerberger F, Wögerbauer M, Ruppitsch W. Characterizing Antimicrobial Resistance in Clinically Relevant Bacteria Isolated at the Human/Animal/Environment Interface Using Whole-Genome Sequencing in Austria. Int J Mol Sci 2022; 23:ijms231911276. [PMID: 36232576 PMCID: PMC9570485 DOI: 10.3390/ijms231911276] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial resistance (AMR) is a public health issue attributed to the misuse of antibiotics in human and veterinary medicine. Since AMR surveillance requires a One Health approach, we sampled nine interconnected compartments at a hydrological open-air lab (HOAL) in Austria to obtain six bacterial species included in the WHO priority list of antibiotic-resistant bacteria (ARB). Whole genome sequencing-based typing included core genome multilocus sequence typing (cgMLST). Genetic and phenotypic characterization of AMR was performed for all isolates. Eighty-nine clinically-relevant bacteria were obtained from eight compartments including 49 E. coli, 27 E. faecalis, 7 K. pneumoniae and 6 E. faecium. Clusters of isolates from the same species obtained in different sample collection dates were detected. Of the isolates, 29.2% were resistant to at least one antimicrobial. E. coli and E. faecalis isolates from different compartments had acquired antimicrobial resistance genes (ARGs) associated with veterinary drugs such as aminoglycosides and tetracyclines, some of which were carried in conjugative and mobilizable plasmids. Three multidrug resistant (MDR) E. coli isolates were found in samples from field drainage and wastewater. Early detection of ARGs and ARB in natural and farm-related environments can identify hotspots of AMR and help prevent its emergence and dissemination along the food/feed chain.
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Affiliation(s)
- Adriana Cabal
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
- Correspondence:
| | - Gerhard Rab
- Institute of Hydraulic Engineering and Water Resources Management, Technical University of Vienna, 1040 Vienna, Austria
- Institute for Land and Water Management Research, Federal Agency for Water Management, 3252 Petzenkirchen, Austria
| | - Beatriz Daza-Prieto
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
- Institute of Chemical, Environmental and Bioscience Engineering, 1060 Vienna, Austria
| | - Anna Stöger
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
| | - Nadine Peischl
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
| | - Ali Chakeri
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
- Center for Public Health, Medical University Vienna, 1090 Vienna, Austria
| | - Solveig Sølverød Mo
- Section for Food Safety and Animal Health Research, Department of Animal Health, Welfare and Food Safety, Norwegian Veterinary Institute, 1433 Ås, Norway
| | - Harald Bock
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
| | - Klemens Fuchs
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
| | - Jasmin Sucher
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
| | - Krista Rathammer
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
| | | | - Silke Stadtbauer
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
| | - Manuela Caniça
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, 1600-609 Lisbon, Portugal
| | - Peter Strauß
- Institute for Land and Water Management Research, Federal Agency for Water Management, 3252 Petzenkirchen, Austria
| | | | | | - Werner Ruppitsch
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
- Department of Biotechnology, University of Natural Resources and Life Sciences, 1180 Vienna, Austria
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8
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Schaeffer J, Lippert K, Pleininger S, Stöger A, Hasenberger P, Stadlbauer S, Heger F, Eigentler A, Geusau A, Indra A, Allerberger F, Ruppitsch W. Association of Phylogenomic Relatedness among Neisseria gonorrhoeae Strains with Antimicrobial Resistance, Austria, 2016-2020. Emerg Infect Dis 2022; 28:1694-1698. [PMID: 35876744 PMCID: PMC9328923 DOI: 10.3201/eid2808.220071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We investigated genomic determinants of antimicrobial resistance in 1,318 Neisseria gonorrhoeae strains isolated in Austria during 2016–2020. Sequence type (ST) 9363 and ST11422 isolates had high rates of azithromycin resistance, and ST7363 isolates correlated with cephalosporin resistance. These results underline the benefit of genomic surveillance for antimicrobial resistance monitoring.
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9
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Finsterwalder SK, Loncaric I, Cabal A, Szostak MP, Barf LM, Marz M, Allerberger F, Burgener IA, Tichy A, Feßler AT, Schwarz S, Monecke S, Ehricht R, Ruppitsch W, Spergser J, Künzel F. Dogs as carriers of virulent and resistant genotypes of Clostridioides difficile. Zoonoses Public Health 2022; 69:673-681. [PMID: 35546073 PMCID: PMC9544694 DOI: 10.1111/zph.12956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/19/2022] [Accepted: 04/25/2022] [Indexed: 11/29/2022]
Abstract
While previous research on zoonotic transmission of community-acquired Clostridioides difficile infection (CA-CDI) focused on food-producing animals, the present study aimed to investigate whether dogs are carriers of resistant and/or virulent C. difficile strains. Rectal swabs were collected from 323 dogs and 38 C. difficile isolates (11.8%) were obtained. Isolates were characterized by antimicrobial susceptibility testing, whole-genome sequencing (WGS) and a DNA hybridization assay. Multilocus sequence typing (MLST), core genome MLST (cgMLST) and screening for virulence and antimicrobial resistance genes were performed based on WGS. Minimum inhibitory concentrations for erythromycin, clindamycin, tetracycline, vancomycin and metronidazole were determined by E-test. Out of 38 C. difficile isolates, 28 (73.7%) carried genes for toxins. The majority of isolates belonged to MLST sequence types (STs) of clade I and one to clade V. Several isolates belonged to STs previously associated with human CA-CDI. However, cgMLST showed low genetic relatedness between the isolates of this study and C. difficile strains isolated from humans in Austria for which genome sequences were publicly available. Four isolates (10.5%) displayed resistance to three of the tested antimicrobial agents. Isolates exhibited resistance to erythromycin, clindamycin, tetracycline and metronidazole. These phenotypic resistances were supported by the presence of the resistance genes erm(B), cfr(C) and tet(M). All isolates were susceptible to vancomycin. Our results indicate that dogs may carry virulent and antimicrobial-resistant C. difficile strains.
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Affiliation(s)
- S K Finsterwalder
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna, Austria.,Clinical Unit of Internal Medicine Small Animals, University of Veterinary Medicine Vienna, Vienna, Austria
| | - I Loncaric
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - A Cabal
- AGES - Austrian Agency for Health and Food Safety, Vienna, Austria
| | - M P Szostak
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - L M Barf
- Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany.,Max Planck Institute for Science of Human History, Jena, Germany
| | - M Marz
- Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany.,FLI Leibniz Institute for Age Research, Jena, Germany.,InfectoGnostics Research Campus Jena, Jena, Germany
| | - F Allerberger
- AGES - Austrian Agency for Health and Food Safety, Vienna, Austria
| | - I A Burgener
- Clinical Unit of Internal Medicine Small Animals, University of Veterinary Medicine Vienna, Vienna, Austria
| | - A Tichy
- Department of Biomedical Science, University of Veterinary Medicine Vienna, Vienna, Austria
| | - A T Feßler
- Department of Veterinary Medicine, Centre of Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany.,Department of Veterinary Medicine, Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - S Schwarz
- Department of Veterinary Medicine, Centre of Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany.,Department of Veterinary Medicine, Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - S Monecke
- InfectoGnostics Research Campus Jena, Jena, Germany.,Leibniz Institute of Photonic Technology (IPHT), Jena, Germany.,Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinik Dresden, Dresden, Germany
| | - R Ehricht
- InfectoGnostics Research Campus Jena, Jena, Germany.,Leibniz Institute of Photonic Technology (IPHT), Jena, Germany.,Institute of Physical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - W Ruppitsch
- AGES - Austrian Agency for Health and Food Safety, Vienna, Austria
| | - J Spergser
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - F Künzel
- Clinical Unit of Internal Medicine Small Animals, University of Veterinary Medicine Vienna, Vienna, Austria
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10
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Bakran-Lebl K, Pree S, Brenner T, Daroglou E, Eigner B, Griesbacher A, Gunczy J, Hufnagl P, Jäger S, Jerrentrup H, Klocker L, Paill W, Petermann JS, Barogh BS, Schwerte T, Suchentrunk C, Wieser C, Wortha LN, Zechmeister T, Zezula D, Zimmermann K, Zittra C, Allerberger F, Fuehrer HP. First Nationwide Monitoring Program for the Detection of Potentially Invasive Mosquito Species in Austria. Insects 2022; 13:insects13030276. [PMID: 35323574 PMCID: PMC8949374 DOI: 10.3390/insects13030276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 02/04/2023]
Abstract
Simple Summary In the last years several alien mosquito species have been introduced into Austria. Those species pose a threat, as they—especially the Asian tiger mosquito (Aedes albopictus)—can transmit many pathogens. The aim of this study is a nationwide overview on the situation of alien mosquitoes in Austria. Using traps representing ideal breeding sites for those mosquitoes, we collected, counted and identified the species of the mosquito eggs laid in the traps. The Asian tiger mosquito was found at two sites, once in Tyrol, where this species has been reported before, and for the first time in the province of Lower Austria. The Asian bush mosquito (Aedes japonicus) was widespread and abundant in Austria. Although it was found in all provinces, the Asian bush mosquito was more often found in the South than the North and more eggs were collected in urban/industrial/transport areas than in (mostly) natural areas. Further, more eggs from the Asian bush mosquito were found in samples collected at higher daily mean temperatures, and fewer eggs in samples collected at higher daily maximum wind speeds. The results of this study will help to better understand the risk from alien mosquitoes to human health in Austria and will be useful to show future changes in the distribution of those species. Abstract In Austria, only fragmented information on the occurrence of alien and potentially invasive mosquito species exists. The aim of this study is a nationwide overview on the situation of those mosquitoes in Austria. Using a nationwide uniform protocol for the first time, mosquito eggs were sampled with ovitraps at 45 locations in Austria at weekly intervals from May to October 2020. The sampled eggs were counted and the species were identified by genetic analysis. The Asian tiger mosquito Aedes albopictus was found at two sites, once in Tyrol, where this species has been reported before, and for the first time in the province of Lower Austria, at a motorway rest stop. The Asian bush mosquito Aedes japonicus was widespread in Austria. It was found in all provinces and was the most abundant species in the ovitraps by far. Aedes japonicus was more abundant in the South than in the North and more eggs were found in habitats with artificial surfaces than in (semi-) natural areas. Further, the number of Ae. japonicus eggs increased with higher ambient temperature and decreased with higher wind speed. The results of this study will contribute to a better estimation of the risk of mosquito-borne disease in Austria and will be a useful baseline for a future documentation of changes in the distribution of those species.
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Affiliation(s)
- Karin Bakran-Lebl
- Institute for Medical Microbiology & Hygiene, AGES—Austrian Agency for Health and Food Safety Ltd., 1096 Vienna, Austria; (P.H.); (F.A.)
- Institute of Parasitology, Vetmeduni Vienna, 1210 Vienna, Austria; (S.P.); (B.E.); (B.S.B.); (L.N.W.); (H.-P.F.)
- Correspondence:
| | - Stefanie Pree
- Institute of Parasitology, Vetmeduni Vienna, 1210 Vienna, Austria; (S.P.); (B.E.); (B.S.B.); (L.N.W.); (H.-P.F.)
| | - Thomas Brenner
- GEBL—Gelsenbekaempfung in den Leithaauen, 2452 Mannersdorf, Austria;
| | - Eleni Daroglou
- Verein Biologische Gelsenregulierung March-Thaya Auen, 2273 Hohenau an der March, Austria; (E.D.); (H.J.)
| | - Barbara Eigner
- Institute of Parasitology, Vetmeduni Vienna, 1210 Vienna, Austria; (S.P.); (B.E.); (B.S.B.); (L.N.W.); (H.-P.F.)
| | - Antonia Griesbacher
- Data, Statistics & Risk Assessment, AGES—Austrian Agency for Health and Food Safety Ltd., 8010 Graz, Austria;
| | - Johanna Gunczy
- Universalmuseum Joanneum, Studienzentrum Naturkunde, 8045 Graz, Austria; (J.G.); (W.P.)
| | - Peter Hufnagl
- Institute for Medical Microbiology & Hygiene, AGES—Austrian Agency for Health and Food Safety Ltd., 1096 Vienna, Austria; (P.H.); (F.A.)
| | - Stefanie Jäger
- Department of Zoology, University of Innsbruck, 6020 Innsbruck, Austria; (S.J.); (T.S.)
| | - Hans Jerrentrup
- Verein Biologische Gelsenregulierung March-Thaya Auen, 2273 Hohenau an der March, Austria; (E.D.); (H.J.)
| | | | - Wolfgang Paill
- Universalmuseum Joanneum, Studienzentrum Naturkunde, 8045 Graz, Austria; (J.G.); (W.P.)
| | - Jana S. Petermann
- Environment and Biodiversity, University of Salzburg, 5020 Salzburg, Austria; (J.S.P.); (D.Z.)
| | - Bita Shahi Barogh
- Institute of Parasitology, Vetmeduni Vienna, 1210 Vienna, Austria; (S.P.); (B.E.); (B.S.B.); (L.N.W.); (H.-P.F.)
| | - Thorsten Schwerte
- Department of Zoology, University of Innsbruck, 6020 Innsbruck, Austria; (S.J.); (T.S.)
| | | | | | - Licha N. Wortha
- Institute of Parasitology, Vetmeduni Vienna, 1210 Vienna, Austria; (S.P.); (B.E.); (B.S.B.); (L.N.W.); (H.-P.F.)
| | | | - David Zezula
- Environment and Biodiversity, University of Salzburg, 5020 Salzburg, Austria; (J.S.P.); (D.Z.)
| | | | - Carina Zittra
- Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Vienna, Austria;
| | - Franz Allerberger
- Institute for Medical Microbiology & Hygiene, AGES—Austrian Agency for Health and Food Safety Ltd., 1096 Vienna, Austria; (P.H.); (F.A.)
| | - Hans-Peter Fuehrer
- Institute of Parasitology, Vetmeduni Vienna, 1210 Vienna, Austria; (S.P.); (B.E.); (B.S.B.); (L.N.W.); (H.-P.F.)
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11
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Posautz A, Szostak MP, Cabal Rosel A, Allerberger F, Stöger A, Rab G, Feßler AT, Spergser J, Kübber-Heiss A, Schwarz S, Forsythe SJ, Ruppitsch W, Loncaric I. Outbreak of Cronobacter turicensis in European brown hares (Lepus europaeus). Lett Appl Microbiol 2022; 74:1008-1015. [PMID: 35263446 DOI: 10.1111/lam.13685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/21/2022] [Accepted: 02/24/2022] [Indexed: 11/30/2022]
Abstract
This is the first report of acute deaths in five European brown hares (Lepus europaeus) attributed to mucoid and necrotizing typhlocolitis caused by genetically different Cronobacter (C.) turicensis strains in northeastern Austria. As this opportunistic pathogen is mainly known for causing disease in immunocompromised humans and neonates, this previously unrecognized potential for a spillover from a wildlife reservoir to humans warrants further attention.
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Affiliation(s)
| | | | | | | | - Anna Stöger
- Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Gerhard Rab
- Institute of Hydraulic Engineering and Water Resources Management, University of Technology Vienna, Austria.,Institute for Land and Water Management Research, Federal Agency for Water Management, Petzenkirchen, Austria
| | - Andrea T Feßler
- Freie Universität Berlin, Berlin, Germany; Veterinary Centre for Resistance Research (TZR), Department of Veterinary Medicine, Freie Universität Berlin, 14163, Berlin, Germany
| | | | | | - Stefan Schwarz
- Freie Universität Berlin, Berlin, Germany; Veterinary Centre for Resistance Research (TZR), Department of Veterinary Medicine, Freie Universität Berlin, 14163, Berlin, Germany
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12
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Jesumirhewe C, Springer B, Allerberger F, Ruppitsch W. Genetic Characterization of Antibiotic Resistant Enterobacteriaceae Isolates From Bovine Animals and the Environment in Nigeria. Front Microbiol 2022; 13:793541. [PMID: 35283848 PMCID: PMC8916115 DOI: 10.3389/fmicb.2022.793541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/10/2022] [Indexed: 11/30/2022] Open
Abstract
There is a link between antibiotic resistance in humans, livestock and the environment. This study was carried out to characterize antibiotic resistant bovine and environmental Enterobacteriaceae isolates from Edo state, Nigeria. A total of 109 consecutive isolates of Enterobacteriaceae were isolated from March–May 2015 from 150 fecal samples of healthy bovine animals from three farms at slaughter in Edo state Nigeria. Similarly, 43 Enterobacteriaceae isolates were also obtained from a total of 100 environmental samples from different sources. Isolates were recovered and identified from samples using standard microbiological techniques. Recovered isolates were pre-identified by the Microbact Gram-Negative identification system and confirmed with Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry and ribosomal multilocus sequence typing (rMLST). Antibiotic susceptibility testing was carried out by Kirby-Bauer method for 14 antibiotics. Whole genome sequencing (WGS) was carried out for isolate characterization and identification of resistance determinants. Out of 109 animal and 43 environmental Enterobacteriaceae isolates, 18 (17%) and 8 (19%) isolates based on selection criteria showed antibiotic resistance and were further investigated by whole genome sequencing (WGS). Resistance genes were detected in all (100%) of the resistant bovine and environmental Enterobacteriaceae isolates. The resistance determinants included β-lactamase genes, aminoglycoside modifying enzymes, qnr genes, sulfonamide, tetracycline and trimethoprim resistance genes, respectively. Out of the 18 and 8 resistant animal and environmental isolates 3 (17%) and 2 (25%) were multidrug resistant (MDR) and had resistance determinants which included efflux genes, regulatory systems modulating antibiotic efflux and antibiotic target alteration genes. Our study shows the dissemination of antibiotic resistance especially MDR strains among Nigerian bovine and environmental Enterobacteriaceae isolates. The presence of these resistant strains in animals and the environment constitute a serious health concern indicated by the difficult treatment options of the infections caused by these organisms. To the best of our knowledge we report the first detailed genomic characterization of antibiotic resistance in bovine and environmental Enterobacteriaceae isolates for Nigeria.
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Affiliation(s)
- Christiana Jesumirhewe
- Department of Pharmaceutical Microbiology, Prof Dora Akunyili College of Pharmacy, Igbinedion University, Okada, Nigeria
- *Correspondence: Christiana Jesumirhewe,
| | - Burkhard Springer
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Franz Allerberger
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Werner Ruppitsch
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
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13
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Bakran-Lebl K, Jerrentrup H, Daroglou E, Pfitzner WP, Fuehrer HP, Allerberger F. First records of Aedes pulcritarsis (Rondani, 1872) (Diptera: Culicidae) in Austria. Parasitol Res 2022; 121:765-768. [PMID: 35032218 PMCID: PMC8800895 DOI: 10.1007/s00436-022-07430-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 01/05/2022] [Indexed: 11/25/2022]
Abstract
Aedes pulcritarsis is a tree-hole breeding species with its main distribution in the Mediterranean area. Within the scope of two independent monitoring programmes, this mosquito species was detected for the first time in Austria, in the province of Lower Austria (2018, districts Mistelbach and Gaenserndorf; 2020, district Bruck an der Leitha). As the climatic and habitat situation in Central Europe seems to be generally suitable for this species, the most likely explanation for the species not being recorded previously is that it might have been overlooked in the past due to its specialized breeding habitat. However, further research on the distribution of Ae. pulcritarsis in Austria would be needed to support this hypothesis. The results from this study will contribute to the investigation of the northern distribution limit of Ae. pulcritarsis in Europe and possible changes thereof.
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Affiliation(s)
- Karin Bakran-Lebl
- Institute for Medical Microbiology & Hygiene, AGES - Austrian Agency for Health and Food Safety Ltd, Währinger Straße 25A, 1090, Vienna, Austria. .,Institute of Parasitology, Vetmeduni Vienna, Veterinaerplatz 1, 1210, Vienna, Austria.
| | - Hans Jerrentrup
- Verein Biologische Gelsenregulierung March-Thaya Auen, Rathausplatz 1, 2273, Hohenau an der March, Austria
| | - Eleni Daroglou
- Verein Biologische Gelsenregulierung March-Thaya Auen, Rathausplatz 1, 2273, Hohenau an der March, Austria
| | - Wolf Peter Pfitzner
- KABS - Kommunale Aktionsgemeinschaft Zur Bekämpfung Der Schnakenplage E.V, 67346, Speyer, Germany
| | - Hans-Peter Fuehrer
- Institute of Parasitology, Vetmeduni Vienna, Veterinaerplatz 1, 1210, Vienna, Austria
| | - Franz Allerberger
- Institute for Medical Microbiology & Hygiene, AGES - Austrian Agency for Health and Food Safety Ltd, Währinger Straße 25A, 1090, Vienna, Austria
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14
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Markt R, Endler L, Amman F, Schedl A, Penz T, Büchel-Marxer M, Grünbacher D, Mayr M, Peer E, Pedrazzini M, Rauch W, Wagner AO, Allerberger F, Bergthaler A, Insam H. Detection and abundance of SARS-CoV-2 in wastewater in Liechtenstein, and the estimation of prevalence and impact of the B.1.1.7 variant. J Water Health 2022; 20:114-125. [PMID: 35100159 DOI: 10.2166/wh.2021.180] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The new coronavirus 2 (SARS-CoV-2) is known to be also shed through feces, which makes wastewater-based surveillance possible, independent of symptomatic cases and unbiased by any testing strategies and frequencies. We investigated the entire population of the Principality of Liechtenstein with samples from the wastewater treatment plant Bendern (serving all 39,000 inhabitants). Twenty-four-hour composite samples were taken once or twice a week over a period of 6 months from September 2020 to March 2021. Viral RNA was concentrated using the PEG centrifugation method followed by reverse transcription quantitative PCR. The aim of this research was to assess the suitability of SARS-CoV-2 fragments to relate the viral wastewater signal to the incidences and assess the impact of the emerging B.1.1.7. variant. The viral load in the wastewater peaked at almost 9 × 108 viral fragments per person equivalent (PE) and day on October 25, and showed a second peak on December 22 reaching a viral load of approximately 2 × 108 PE-1d-1. Individual testing showed a lag of 4 days and a distinct underestimation of cases at the first peak when testing frequency was low. The wastewater signal showed an immediate response to the implementation of non-pharmaceutical interventions. The new virus variant B.1.1.7. was first detected in wastewater on December 23, while it was first observed with individual testing on January 13, 2021. Further, our data indicate that the emergence of new virus variant may change the wastewater signal, probably due to different shedding patterns, which should be considered in future models.
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Affiliation(s)
- R Markt
- Department of Microbiology, Universität Innsbruck, Technikerstraße 25d, Innsbruck 6020, Austria E-mail:
| | - L Endler
- Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, Vienna 1090, Austria
| | - F Amman
- Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, Vienna 1090, Austria
| | - A Schedl
- Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, Vienna 1090, Austria
| | - T Penz
- Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, Vienna 1090, Austria
| | - M Büchel-Marxer
- Ministry of Social Affairs and Culture, Peter-Kaiser-Platz 1, Vaduz 9490, Principality of Liechtenstein
| | - D Grünbacher
- Unit of Environmental Engineering, Department of Infrastructure, Universität Innsbruck, Technikerstraße 13, Innsbruck 6020, Austria
| | - M Mayr
- Department of Microbiology, Universität Innsbruck, Technikerstraße 25d, Innsbruck 6020, Austria E-mail:
| | - E Peer
- Department of Microbiology, Universität Innsbruck, Technikerstraße 25d, Innsbruck 6020, Austria E-mail:
| | - M Pedrazzini
- Ministry of Social Affairs and Culture, Peter-Kaiser-Platz 1, Vaduz 9490, Principality of Liechtenstein
| | - W Rauch
- Unit of Environmental Engineering, Department of Infrastructure, Universität Innsbruck, Technikerstraße 13, Innsbruck 6020, Austria
| | - A O Wagner
- Department of Microbiology, Universität Innsbruck, Technikerstraße 25d, Innsbruck 6020, Austria E-mail:
| | - F Allerberger
- Austrian Agency for Health and Food Safety (AGES), Vienna 1220, Austria
| | - A Bergthaler
- Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, Vienna 1090, Austria
| | - H Insam
- Department of Microbiology, Universität Innsbruck, Technikerstraße 25d, Innsbruck 6020, Austria E-mail:
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15
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Steiner V, Rosel AC, Ruppitsch W, Allerberger F, Carranza Valencia A, Markovic M, Luckschander-Zeller N, Szostak MP, Spergser J, Loncaric I, Künzel F. The First Bacterial Endocarditis Due to Achromobacter xylosoxidans in a Dog. Pathogens 2021; 10:pathogens10121580. [PMID: 34959535 PMCID: PMC8709460 DOI: 10.3390/pathogens10121580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/21/2021] [Accepted: 11/30/2021] [Indexed: 12/04/2022] Open
Abstract
Infectious endocarditis (IE) in dogs is often associated with a high mortality rate as diagnostic work-up as well as antibiotic treatment might be challenging. The present case describes bacteremia in a dog caused by Achromobacter xylosoxidans, leading to an infectious endocarditis. Achromobacter xylosoxidans (A. xylosoxidans) is an aerobic Gram-negative rod-shaped bacterium, which has been associated with multiple nosocomial opportunistic diseases in human medicine. One such manifestation of A. xylosoxidans infection is endocarditis. A. xylosoxidans infections are challenging to treat due to the reduced effectiveness of a wide range of antimicrobial agents. To date, only a few case reports of infections with A. xylosoxidans in animals have been described. This is the first case report of A. xylosoxidans endocarditis in a dog. Whole-genome sequencing was performed to determine the sequencing type and to gain more information about this bacterium regarding its intrinsic resistance genes. With this case report, we seek to increase awareness of A. xylosoxidans as an opportunistic nosocomial pathogen in dogs and to provide a short summary regarding the current state of general knowledge and known resistance patterns.
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Affiliation(s)
- Verena Steiner
- Department for Companion Animals and Horses, Clinical Unit of Internal Medic and Small Animals, University of Veterinary Medicine, 1210 Vienna, Austria; (A.C.V.); (M.M.); (N.L.-Z.); (F.K.)
- Correspondence:
| | - Adriana Cabal Rosel
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, 1090 Vienna, Austria; (A.C.R.); (W.R.); (F.A.)
| | - Werner Ruppitsch
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, 1090 Vienna, Austria; (A.C.R.); (W.R.); (F.A.)
| | - Franz Allerberger
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, 1090 Vienna, Austria; (A.C.R.); (W.R.); (F.A.)
| | - Alejandra Carranza Valencia
- Department for Companion Animals and Horses, Clinical Unit of Internal Medic and Small Animals, University of Veterinary Medicine, 1210 Vienna, Austria; (A.C.V.); (M.M.); (N.L.-Z.); (F.K.)
| | - Mato Markovic
- Department for Companion Animals and Horses, Clinical Unit of Internal Medic and Small Animals, University of Veterinary Medicine, 1210 Vienna, Austria; (A.C.V.); (M.M.); (N.L.-Z.); (F.K.)
| | - Nicole Luckschander-Zeller
- Department for Companion Animals and Horses, Clinical Unit of Internal Medic and Small Animals, University of Veterinary Medicine, 1210 Vienna, Austria; (A.C.V.); (M.M.); (N.L.-Z.); (F.K.)
| | - Michael P. Szostak
- Institute of Microbiology, University of Veterinary Medicine, 1210 Vienna, Austria; (M.P.S.); (J.S.); (I.L.)
| | - Joachim Spergser
- Institute of Microbiology, University of Veterinary Medicine, 1210 Vienna, Austria; (M.P.S.); (J.S.); (I.L.)
| | - Igor Loncaric
- Institute of Microbiology, University of Veterinary Medicine, 1210 Vienna, Austria; (M.P.S.); (J.S.); (I.L.)
| | - Frank Künzel
- Department for Companion Animals and Horses, Clinical Unit of Internal Medic and Small Animals, University of Veterinary Medicine, 1210 Vienna, Austria; (A.C.V.); (M.M.); (N.L.-Z.); (F.K.)
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16
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van Prehn J, Reigadas E, Vogelzang EH, Bouza E, Hristea A, Guery B, Krutova M, Norén T, Allerberger F, Coia JE, Goorhuis A, van Rossen TM, Ooijevaar RE, Burns K, Scharvik Olesen BR, Tschudin-Sutter S, Wilcox MH, Vehreschild MJGT, Fitzpatrick F, Kuijper EJ. European Society of Clinical Microbiology and Infectious Diseases: 2021 update on the treatment guidance document for Clostridioides difficile infection in adults. Clin Microbiol Infect 2021; 27 Suppl 2:S1-S21. [PMID: 34678515 DOI: 10.1016/j.cmi.2021.09.038] [Citation(s) in RCA: 194] [Impact Index Per Article: 64.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 09/23/2021] [Accepted: 09/30/2021] [Indexed: 12/13/2022]
Abstract
SCOPE In 2009, the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) published the first treatment guidance document for Clostridioides difficile infection (CDI). This document was updated in 2014. The growing literature on CDI antimicrobial treatment and novel treatment approaches, such as faecal microbiota transplantation (FMT) and toxin-binding monoclonal antibodies, prompted the ESCMID study group on C. difficile (ESGCD) to update the 2014 treatment guidance document for CDI in adults. METHODS AND QUESTIONS Key questions on CDI treatment were formulated by the guideline committee and included: What is the best treatment for initial, severe, severe-complicated, refractory, recurrent and multiple recurrent CDI? What is the best treatment when no oral therapy is possible? Can prognostic factors identify patients at risk for severe and recurrent CDI and is there a place for CDI prophylaxis? Outcome measures for treatment strategy were: clinical cure, recurrence and sustained cure. For studies on surgical interventions and severe-complicated CDI the outcome was mortality. Appraisal of available literature and drafting of recommendations was performed by the guideline drafting group. The total body of evidence for the recommendations on CDI treatment consists of the literature described in the previous guidelines, supplemented with a systematic literature search on randomized clinical trials and observational studies from 2012 and onwards. The Grades of Recommendation Assessment, Development and Evaluation (GRADE) system was used to grade the strength of our recommendations and the quality of the evidence. The guideline committee was invited to comment on the recommendations. The guideline draft was sent to external experts and a patients' representative for review. Full ESCMID endorsement was obtained after a public consultation procedure. RECOMMENDATIONS Important changes compared with previous guideline include but are not limited to: metronidazole is no longer recommended for treatment of CDI when fidaxomicin or vancomycin are available, fidaxomicin is the preferred agent for treatment of initial CDI and the first recurrence of CDI when available and feasible, FMT or bezlotoxumab in addition to standard of care antibiotics (SoC) are preferred for treatment of a second or further recurrence of CDI, bezlotoxumab in addition to SoC is recommended for the first recurrence of CDI when fidaxomicin was used to manage the initial CDI episode, and bezlotoxumab is considered as an ancillary treatment to vancomycin for a CDI episode with high risk of recurrence when fidaxomicin is not available. Contrary to the previous guideline, in the current guideline emphasis is placed on risk for recurrence as a factor that determines treatment strategy for the individual patient, rather than the disease severity.
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Affiliation(s)
- Joffrey van Prehn
- Department of Medical Microbiology, Centre for Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Elena Reigadas
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Erik H Vogelzang
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Center, Location VUmc, Amsterdam, the Netherlands
| | - Emilio Bouza
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Adriana Hristea
- University of Medicine and Pharmacy Carol Davila, National Institute for Infectious Diseases Prof Dr Matei Bals, Romania
| | - Benoit Guery
- Infectious Diseases Specialist, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Marcela Krutova
- Department of Medical Microbiology, Charles University in Prague and Motol University Hospital, Czech Republic
| | - Torbjorn Norén
- Faculty of Medicine and Health, Department of Laboratory Medicine, National Reference Laboratory for Clostridioides difficile, Clinical Microbiology, Örebro University Hospital, Örebro, Sweden
| | | | - John E Coia
- Department of Clinical Microbiology, Hospital South West Jutland and Department of Regional Health Research IRS, University of Southern Denmark, Esbjerg, Denmark
| | - Abraham Goorhuis
- Department of Infectious Diseases, Amsterdam University Medical Centers, Academic Medical Center, Amsterdam, the Netherlands
| | - Tessel M van Rossen
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Center, Location VUmc, Amsterdam, the Netherlands
| | - Rogier E Ooijevaar
- Department of Gastroenterology, Amsterdam University Medical Center, Location VUmc, Amsterdam, the Netherlands
| | - Karen Burns
- Departments of Clinical Microbiology, Beaumont Hospital & Royal College of Surgeons in Ireland, Dublin, Ireland
| | | | - Sarah Tschudin-Sutter
- Department of Infectious Diseases and Infection Control, University Hospital Basel, University Basel, Universitatsspital, Basel, Switzerland
| | - Mark H Wilcox
- Department of Microbiology, Old Medical, School Leeds General Infirmary, Leeds Teaching Hospitals & University of Leeds, Leeds, United Kingdom
| | - Maria J G T Vehreschild
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany; Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Fidelma Fitzpatrick
- Department of Clinical Microbiology, Beaumont Hospital, Dublin, Ireland; Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Ed J Kuijper
- Department of Medical Microbiology, Centre for Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands; National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands.
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17
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Cabal A, Schmid D, Hell M, Chakeri A, Mustafa-Korninger E, Wojna A, Stöger A, Möst J, Leitner E, Hyden P, Rattei T, Habington A, Wiedermann U, Allerberger F, Ruppitsch W. Isolate-Based Surveillance of Bordetella pertussis, Austria, 2018-2020. Emerg Infect Dis 2021; 27:862-871. [PMID: 33622477 PMCID: PMC7920692 DOI: 10.3201/eid2703.202314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Pertussis is a vaccine-preventable disease, and its recent resurgence might be attributable to the emergence of strains that differ genetically from the vaccine strain. We describe a novel pertussis isolate-based surveillance system and a core genome multilocus sequence typing scheme to assess Bordetella pertussis genetic variability and investigate the increased incidence of pertussis in Austria. During 2018–2020, we obtained 123 B. pertussis isolates and typed them with the new scheme (2,983 targets and preliminary cluster threshold of <6 alleles). B. pertussis isolates in Austria differed genetically from the vaccine strain, both in their core genomes and in their vaccine antigen genes; 31.7% of the isolates were pertactin-deficient. We detected 8 clusters, 1 of them with pertactin-deficient isolates and possibly part of a local outbreak. National expansion of the isolate-based surveillance system is needed to implement pertussis-control strategies.
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18
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Yusuf E, Allerberger F. Infectious disease serology in 2021. Clin Microbiol Infect 2021; 27:1204-1206. [PMID: 34197934 DOI: 10.1016/j.cmi.2021.06.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/11/2021] [Accepted: 06/12/2021] [Indexed: 11/29/2022]
Affiliation(s)
- Erlangga Yusuf
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, the Netherlands.
| | - Franz Allerberger
- Division of Public Health, Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
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19
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Bakran-Lebl K, Camp JV, Kolodziejek J, Weidinger P, Hufnagl P, Cabal Rosel A, Zwickelstorfer A, Allerberger F, Nowotny N. Diversity of West Nile and Usutu virus strains in mosquitoes at an international airport in Austria. Transbound Emerg Dis 2021; 69:2096-2109. [PMID: 34169666 PMCID: PMC9540796 DOI: 10.1111/tbed.14198] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/21/2021] [Indexed: 11/27/2022]
Abstract
Increased globalization and international transportation have resulted in the inadvertent introduction of exotic mosquitoes and new mosquito‐borne diseases. International airports are among the possible points of entry for mosquitoes and their pathogens. We established a mosquito and mosquito‐borne diseases monitoring programme at the largest international airport in Austria and report the results for the first two years, 2018 and 2019. This included weekly monitoring and sampling of adult mosquitoes, and screening them for the presence of viral nucleic acids by standard molecular diagnostic techniques. Additionally, we surveyed the avian community at the airport, as birds are potentially amplifying hosts. In 2018, West Nile virus (WNV) was detected in 14 pools and Usutu virus (USUV) was detected in another 14 pools of mosquitoes (minimum infection rate [MIR] of 6.8 for each virus). Of these 28 pools, 26 consisted of female Culex pipiens/torrentium, and two contained male Culex sp. mosquitoes. Cx. pipiens/torrentium mosquitoes were the most frequently captured mosquito species at the airport. The detected WNV strains belonged to five sub‐clusters within the sub‐lineage 2d‐1, and all detected USUV strains were grouped to at least seven sub‐clusters among the cluster Europe 2; all strains were previously shown to be endemic in Austria. In 2019, all mosquito pools were negative for any viral nucleic acids tested. Our study suggests that airports may serve as foci of arbovirus activity, particularly during epidemic years, and should be considered when designing mosquito control and arbovirus monitoring programmes.
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Affiliation(s)
- Karin Bakran-Lebl
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Vienna, Austria
| | - Jeremy V Camp
- Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Jolanta Kolodziejek
- Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Pia Weidinger
- Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Peter Hufnagl
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Vienna, Austria
| | - Adriana Cabal Rosel
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Vienna, Austria
| | | | - Franz Allerberger
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Vienna, Austria
| | - Norbert Nowotny
- Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria.,Department of Basic Medical Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Healthcare City, Dubai, United Arab Emirates
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20
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Halbedel S, Wilking H, Holzer A, Kleta S, Fischer MA, Lüth S, Pietzka A, Huhulescu S, Lachmann R, Krings A, Ruppitsch W, Leclercq A, Kamphausen R, Meincke M, Wagner-Wiening C, Contzen M, Kraemer IB, Al Dahouk S, Allerberger F, Stark K, Flieger A. Large Nationwide Outbreak of Invasive Listeriosis Associated with Blood Sausage, Germany, 2018-2019. Emerg Infect Dis 2021; 26:1456-1464. [PMID: 32568037 PMCID: PMC7323541 DOI: 10.3201/eid2607.200225] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Invasive listeriosis is a severe foodborne infection in humans and is difficult to control. Listeriosis incidence is increasing worldwide, but some countries have implemented molecular surveillance programs to improve recognition and management of listeriosis outbreaks. In Germany, routine whole-genome sequencing, core genome multilocus sequence typing, and single nucleotide polymorphism calling are used for subtyping of Listeria monocytogenes isolates from listeriosis cases and suspected foods. During 2018–2019, an unusually large cluster of L. monocytogenes isolates was identified, including 134 highly clonal, benzalkonium-resistant sequence type 6 isolates collected from 112 notified listeriosis cases. The outbreak was one of the largest reported in Europe during the past 25 years. Epidemiologic investigations identified blood sausage contaminated with L. monocytogenes highly related to clinical isolates; withdrawal of the product from the market ended the outbreak. We describe how epidemiologic investigations and complementary molecular typing of food isolates helped identify the outbreak vehicle.
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21
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Allerberger F. Training in clinical microbiology and infectious diseases in Europe. Clin Microbiol Infect 2021; 27:1575. [PMID: 34116203 DOI: 10.1016/j.cmi.2021.05.044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/22/2021] [Accepted: 05/25/2021] [Indexed: 01/03/2023]
Affiliation(s)
- Franz Allerberger
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Austria.
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22
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Grünzweil OM, Palmer L, Cabal A, Szostak MP, Ruppitsch W, Kornschober C, Korus M, Misic D, Bernreiter-Hofer T, Korath ADJ, Feßler AT, Allerberger F, Schwarz S, Spergser J, Müller E, Braun SD, Monecke S, Ehricht R, Walzer C, Smodlaka H, Loncaric I. Presence of β-Lactamase-producing Enterobacterales and Salmonella Isolates in Marine Mammals. Int J Mol Sci 2021; 22:ijms22115905. [PMID: 34072783 PMCID: PMC8199236 DOI: 10.3390/ijms22115905] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 02/07/2023] Open
Abstract
Marine mammals have been described as sentinels of the health of marine ecosystems. Therefore, the aim of this study was to investigate (i) the presence of extended-spectrum β-lactamase (ESBL)- and AmpC-producing Enterobacterales, which comprise several bacterial families important to the healthcare sector, as well as (ii) the presence of Salmonella in these coastal animals. The antimicrobial resistance pheno- and genotypes, as well as biocide susceptibility of Enterobacterales isolated from stranded marine mammals, were determined prior to their rehabilitation. All E. coli isolates (n = 27) were screened for virulence genes via DNA-based microarray, and twelve selected E. coli isolates were analyzed by whole-genome sequencing. Seventy-one percent of the Enterobacterales isolates exhibited a multidrug-resistant (MDR) pheno- and genotype. The gene blaCMY (n = 51) was the predominant β-lactamase gene. In addition, blaTEM-1 (n = 38), blaSHV-33 (n = 8), blaCTX-M-15 (n = 7), blaOXA-1 (n = 7), blaSHV-11 (n = 3), and blaDHA-1 (n = 2) were detected. The most prevalent non-β-lactamase genes were sul2 (n = 38), strA (n = 34), strB (n = 34), and tet(A) (n = 34). Escherichia coli isolates belonging to the pandemic sequence types (STs) ST38, ST167, and ST648 were identified. Among Salmonella isolates (n = 18), S. Havana was the most prevalent serotype. The present study revealed a high prevalence of MDR bacteria and the presence of pandemic high-risk clones, both of which are indicators of anthropogenic antimicrobial pollution, in marine mammals.
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Affiliation(s)
- Olivia M. Grünzweil
- Institute of Microbiology, University of Veterinary Medicine, 1210 Vienna, Austria; (O.M.G.); (M.P.S.); (T.B.-H.); (A.D.J.K.); (J.S.)
| | - Lauren Palmer
- Marine Mammal Care Center, Los Angeles, CA 90731, USA;
| | - Adriana Cabal
- Austrian Agency for Health and Food Safety (AGES), Institute of Medical Microbiology and Hygiene, 1090 Vienna, Austria; (A.C.); (W.R.); (F.A.)
| | - Michael P. Szostak
- Institute of Microbiology, University of Veterinary Medicine, 1210 Vienna, Austria; (O.M.G.); (M.P.S.); (T.B.-H.); (A.D.J.K.); (J.S.)
| | - Werner Ruppitsch
- Austrian Agency for Health and Food Safety (AGES), Institute of Medical Microbiology and Hygiene, 1090 Vienna, Austria; (A.C.); (W.R.); (F.A.)
| | - Christian Kornschober
- Austrian Agency for Health and Food Safety (AGES), National Reference Centre for Salmonella, 8010 Graz, Austria;
| | - Maciej Korus
- Department of Functional Food Products Development, Faculty of Biotechnology and Food Science, Wroclaw University of Environmental and Life Sciences, 51-630 Wroclaw, Poland; (M.K.); (D.M.)
| | - Dusan Misic
- Department of Functional Food Products Development, Faculty of Biotechnology and Food Science, Wroclaw University of Environmental and Life Sciences, 51-630 Wroclaw, Poland; (M.K.); (D.M.)
| | - Tanja Bernreiter-Hofer
- Institute of Microbiology, University of Veterinary Medicine, 1210 Vienna, Austria; (O.M.G.); (M.P.S.); (T.B.-H.); (A.D.J.K.); (J.S.)
- Department for Farm Animals and Veterinary Public Health, University Clinic for Swine, University of Veterinary Medicine, 1210 Vienna, Austria
| | - Anna D. J. Korath
- Institute of Microbiology, University of Veterinary Medicine, 1210 Vienna, Austria; (O.M.G.); (M.P.S.); (T.B.-H.); (A.D.J.K.); (J.S.)
| | - Andrea T. Feßler
- Centre for Infection Medicine, Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, 14163 Berlin, Germany; (A.T.F.); (S.S.)
| | - Franz Allerberger
- Austrian Agency for Health and Food Safety (AGES), Institute of Medical Microbiology and Hygiene, 1090 Vienna, Austria; (A.C.); (W.R.); (F.A.)
| | - Stefan Schwarz
- Centre for Infection Medicine, Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, 14163 Berlin, Germany; (A.T.F.); (S.S.)
| | - Joachim Spergser
- Institute of Microbiology, University of Veterinary Medicine, 1210 Vienna, Austria; (O.M.G.); (M.P.S.); (T.B.-H.); (A.D.J.K.); (J.S.)
| | - Elke Müller
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (E.M.); (S.D.B.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Sascha D. Braun
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (E.M.); (S.D.B.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Stefan Monecke
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (E.M.); (S.D.B.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
- Institute for Medical Microbiology and Hygiene, Technical University of Dresden, 01307 Dresden, Germany
| | - Ralf Ehricht
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (E.M.); (S.D.B.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
- Institute of Physical Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Chris Walzer
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, 1160 Vienna, Austria;
- Health Program, Wildlife Conservation Society, Bronx, New York City, NY 10460, USA
| | - Hrvoje Smodlaka
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA 91766-1854, USA;
| | - Igor Loncaric
- Institute of Microbiology, University of Veterinary Medicine, 1210 Vienna, Austria; (O.M.G.); (M.P.S.); (T.B.-H.); (A.D.J.K.); (J.S.)
- Correspondence: ; Tel.: +43-125-077-2115
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23
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Yelagandula R, Bykov A, Vogt A, Heinen R, Özkan E, Strobl MM, Baar JC, Uzunova K, Hajdusits B, Kordic D, Suljic E, Kurtovic-Kozaric A, Izetbegovic S, Schaeffer J, Hufnagl P, Zoufaly A, Seitz T, Födinger M, Allerberger F, Stark A, Cochella L, Elling U. Multiplexed detection of SARS-CoV-2 and other respiratory infections in high throughput by SARSeq. Nat Commun 2021; 12:3132. [PMID: 34035246 PMCID: PMC8149640 DOI: 10.1038/s41467-021-22664-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/23/2021] [Indexed: 12/14/2022] Open
Abstract
The COVID-19 pandemic has demonstrated the need for massively-parallel, cost-effective tests monitoring viral spread. Here we present SARSeq, saliva analysis by RNA sequencing, a method to detect SARS-CoV-2 and other respiratory viruses on tens of thousands of samples in parallel. SARSeq relies on next generation sequencing of multiple amplicons generated in a multiplexed RT-PCR reaction. Two-dimensional, unique dual indexing, using four indices per sample, enables unambiguous and scalable assignment of reads to individual samples. We calibrate SARSeq on SARS-CoV-2 synthetic RNA, virions, and hundreds of human samples of various types. Robustness and sensitivity were virtually identical to quantitative RT-PCR. Double-blinded benchmarking to gold standard quantitative-RT-PCR performed by human diagnostics laboratories confirms this high sensitivity. SARSeq can be used to detect Influenza A and B viruses and human rhinovirus in parallel, and can be expanded for detection of other pathogens. Thus, SARSeq is ideally suited for differential diagnostic of infections during a pandemic. Massively parallel but cost-effective testing is essential to monitor the spread of pathogenic agents. Here the authors present SARSseq, which uses a dual indexing strategy in a multiplexed RT-PCR reaction to diagnose SARS-CoV-2 at scale.
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Affiliation(s)
- Ramesh Yelagandula
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Aleksandr Bykov
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Alexander Vogt
- Vienna Biocenter Core Facilities GmbH (VBCF), Vienna, Austria
| | - Robert Heinen
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria.,Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Gregor Mendel Institute (GMI), Vienna BioCenter (VBC), Vienna, Austria
| | - Ezgi Özkan
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Marcus Martin Strobl
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Juliane Christina Baar
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Kristina Uzunova
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria.,Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Gregor Mendel Institute (GMI), Vienna BioCenter (VBC), Vienna, Austria
| | - Bence Hajdusits
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Darja Kordic
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Erna Suljic
- Clinical Center of the University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | | | - Sebija Izetbegovic
- Clinical Center of the University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Justine Schaeffer
- Österreichische Agentur für Gesundheit und Ernährungssicherheit (AGES), Vienna, Austria.,EUPHEM Fellowship, European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Peter Hufnagl
- Österreichische Agentur für Gesundheit und Ernährungssicherheit (AGES), Vienna, Austria
| | - Alexander Zoufaly
- Department for Infectious Diseases, Clinic Favoriten, Vienna, Austria.,Faculty of Medicine, Sigmund Freud Private University, Vienna, Austria
| | - Tamara Seitz
- Department for Infectious Diseases, Clinic Favoriten, Vienna, Austria
| | | | - Manuela Födinger
- Faculty of Medicine, Sigmund Freud Private University, Vienna, Austria.,Institute of Laboratory Diagnostics, Clinic Favoriten, Vienna, Austria
| | - Franz Allerberger
- Österreichische Agentur für Gesundheit und Ernährungssicherheit (AGES), Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Luisa Cochella
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
| | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria.
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24
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Seitz T, Schindler S, Winkelmeyer P, Zach B, Wenisch C, Zoufaly A, Allerberger F. Evaluation of rapid antigen tests based on saliva for the detection of SARS-CoV-2. J Med Virol 2021; 93:4161-4162. [PMID: 33788280 PMCID: PMC8251355 DOI: 10.1002/jmv.26983] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/03/2021] [Accepted: 03/29/2021] [Indexed: 11/10/2022]
Affiliation(s)
- Tamara Seitz
- Department of Infectious Diseases and Tropical Medicine, Clinic Favoriten, Vienna, Austria
| | | | | | - Bernhard Zach
- Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Christoph Wenisch
- Department of Infectious Diseases and Tropical Medicine, Clinic Favoriten, Vienna, Austria
| | - Alexander Zoufaly
- Department of Infectious Diseases and Tropical Medicine, Clinic Favoriten, Vienna, Austria
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25
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Fischer MA, Wamp S, Fruth A, Allerberger F, Flieger A, Halbedel S. Population structure-guided profiling of antibiotic resistance patterns in clinical Listeria monocytogenes isolates from Germany identifies pbpB3 alleles associated with low levels of cephalosporin resistance. Emerg Microbes Infect 2021; 9:1804-1813. [PMID: 32691687 PMCID: PMC7473133 DOI: 10.1080/22221751.2020.1799722] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Numbers of listeriosis illnesses have been increasing in Germany and the European Union during the last decade. In addition, reports on the occurrence of antibiotic resistance in Listeria monocytogenes in clinical and environmental isolates are accumulating. The susceptibility towards 14 antibiotics was tested in a selection of clinical L. monocytogenes isolates to get a more precise picture of the development and manifestation of antibiotic resistance in the L. monocytogenes population. Based on the population structure determined by core genome multi locus sequence typing (cgMLST) 544 out of 1220 sequenced strains collected in Germany between 2009 and 2019 were selected to cover the phylogenetic diversity observed in the clinical L. monocytogenes population. All isolates tested were susceptible towards ampicillin, penicillin and co-trimoxazole – the most relevant antibiotics in the treatment of listeriosis. Resistance to daptomycin and ciprofloxacin was observed in 493 (91%) and in 71 (13%) of 544 isolates, respectively. While all tested strains showed resistance towards ceftriaxone, their resistance levels varied widely between 4 mg/L and >128 mg/L. An allelic variation of the penicillin binding protein gene pbpB3 was identified as the cause of this difference in ceftriaxone resistance levels. This study is the first population structure-guided analysis of antimicrobial resistance in recent clinical isolates and confirms the importance of penicillin binding protein B3 (PBP B3) for the high level of intrinsic cephalosporin resistance of L. monocytogenes on a population-wide scale.
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Affiliation(s)
- Martin A Fischer
- FG11 Division of Enteropathogenic bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
| | - Sabrina Wamp
- FG11 Division of Enteropathogenic bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
| | - Angelika Fruth
- FG11 Division of Enteropathogenic bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
| | | | - Antje Flieger
- FG11 Division of Enteropathogenic bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany.,German Consultant Laboratory for Listeria, Robert Koch Institute, Wernigerode, Germany
| | - Sven Halbedel
- FG11 Division of Enteropathogenic bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany.,German Consultant Laboratory for Listeria, Robert Koch Institute, Wernigerode, Germany
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26
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Pilz S, Chakeri A, Ioannidis JP, Richter L, Theiler-Schwetz V, Trummer C, Krause R, Allerberger F. SARS-CoV-2 re-infection risk in Austria. Eur J Clin Invest 2021; 51:e13520. [PMID: 33583018 PMCID: PMC7988582 DOI: 10.1111/eci.13520] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND A key question concerning coronavirus disease 2019 (COVID-19) is how effective and long lasting immunity against this disease is in individuals who were previously infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We aimed to evaluate the risk of SARS-CoV-2 re-infections in the general population in Austria. METHODS This is a retrospective observational study using national SARS-CoV-2 infection data from the Austrian epidemiological reporting system. As the primary outcome, we aim to compare the odds of SARS-CoV-2 re-infections of COVID-19 survivors of the first wave (February to April 30, 2020) versus the odds of first infections in the remainder general population by tracking polymerase chain reaction (PCR)-confirmed infections of both groups during the second wave from September 1 to November 30, 2020. Re-infection counts are tentative, since it cannot be excluded that the positive PCR in the first and/or second wave might have been a false positive. RESULTS We recorded 40 tentative re-infections in 14 840 COVID-19 survivors of the first wave (0.27%) and 253 581 infections in 8 885 640 individuals of the remaining general population (2.85%) translating into an odds ratio (95% confidence interval) of 0.09 (0.07 to 0.13). CONCLUSIONS We observed a relatively low re-infection rate of SARS-CoV-2 in Austria. Protection against SARS-CoV-2 after natural infection is comparable with the highest available estimates on vaccine efficacies. Further well-designed research on this issue is urgently needed for improving evidence-based decisions on public health measures and vaccination strategies.
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Affiliation(s)
- Stefan Pilz
- Division of Endocrinology and Diabetology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Ali Chakeri
- Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - John Pa Ioannidis
- Departments of Medicine, Epidemiology and Population Health, Biomedical Data Science, and Statistics and Meta-Research Innovation Center at Stanford (METRICS), Stanford University, Stanford, CA, USA
| | - Lukas Richter
- Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Verena Theiler-Schwetz
- Division of Endocrinology and Diabetology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Christian Trummer
- Division of Endocrinology and Diabetology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Robert Krause
- Section of Infectious Diseases and Tropical Medicine, Medical University of Graz, Graz, Austria
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27
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Agerer B, Koblischke M, Gudipati V, Montaño-Gutierrez LF, Smyth M, Popa A, Genger JW, Endler L, Florian DM, Mühlgrabner V, Graninger M, Aberle SW, Husa AM, Shaw LE, Lercher A, Gattinger P, Torralba-Gombau R, Trapin D, Penz T, Barreca D, Fae I, Wenda S, Traugott M, Walder G, Pickl WF, Thiel V, Allerberger F, Stockinger H, Puchhammer-Stöckl E, Weninger W, Fischer G, Hoepler W, Pawelka E, Zoufaly A, Valenta R, Bock C, Paster W, Geyeregger R, Farlik M, Halbritter F, Huppa JB, Aberle JH, Bergthaler A. SARS-CoV-2 mutations in MHC-I-restricted epitopes evade CD8 + T cell responses. Sci Immunol 2021; 6:6/57/eabg6461. [PMID: 33664060 PMCID: PMC8224398 DOI: 10.1126/sciimmunol.abg6461] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 02/27/2021] [Indexed: 12/26/2022]
Abstract
CD8+ T cell immunity to SARS-CoV-2 has been implicated in COVID-19 severity and virus control. Here, we identified nonsynonymous mutations in MHC-I-restricted CD8+ T cell epitopes after deep sequencing of 747 SARS-CoV-2 virus isolates. Mutant peptides exhibited diminished or abrogated MHC-I binding in a cell-free in vitro assay. Reduced MHC-I binding of mutant peptides was associated with decreased proliferation, IFN-γ production and cytotoxic activity of CD8+ T cells isolated from HLA-matched COVID-19 patients. Single cell RNA sequencing of ex vivo expanded, tetramer-sorted CD8+ T cells from COVID-19 patients further revealed qualitative differences in the transcriptional response to mutant peptides. Our findings highlight the capacity of SARS-CoV-2 to subvert CD8+ T cell surveillance through point mutations in MHC-I-restricted viral epitopes.
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Affiliation(s)
- Benedikt Agerer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Venugopal Gudipati
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | | | - Mark Smyth
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alexandra Popa
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jakob-Wendelin Genger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Lukas Endler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - David M Florian
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Vanessa Mühlgrabner
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | | | - Stephan W Aberle
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Anna-Maria Husa
- St. Anna Children´s Cancer Research Institute (CCRI), Vienna, Austria
| | - Lisa Ellen Shaw
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Alexander Lercher
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Pia Gattinger
- Department of Pathophysiology and Allergy Research, Division of Immunopathology, Medical University of Vienna, Vienna, Austria
| | - Ricard Torralba-Gombau
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Doris Trapin
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Thomas Penz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Daniele Barreca
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Ingrid Fae
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria
| | - Sabine Wenda
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria
| | | | - Gernot Walder
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Winfried F Pickl
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria.,Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Volker Thiel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | | | - Hannes Stockinger
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | | | - Wolfgang Weninger
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Gottfried Fischer
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | | | - Erich Pawelka
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria
| | - Alexander Zoufaly
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria
| | - Rudolf Valenta
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria.,Department of Pathophysiology and Allergy Research, Division of Immunopathology, Medical University of Vienna, Vienna, Austria.,Karl Landsteiner University of Health Sciences, Krems, Austria.,Laboratory for Immunopathology, Department of Clinical Immunology and Allergy, First Moscow State Medical University Sechenov, Moscow, Russia.,NRC Institute of Immunology FMBA of Russia, Moscow, Russia
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Wolfgang Paster
- St. Anna Children´s Cancer Research Institute (CCRI), Vienna, Austria
| | - René Geyeregger
- St. Anna Children´s Cancer Research Institute (CCRI), Vienna, Austria
| | - Matthias Farlik
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | | | - Johannes B Huppa
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Judith H Aberle
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Andreas Bergthaler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
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28
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Schaeffer J, Revilla-Fernández S, Hofer E, Posch R, Stoeger A, Leth C, Schmoll F, Djordjevic V, Lakicevic B, Matovic K, Hufnagl P, Indra A, Allerberger F, Ruppitsch W. Tracking the Origin of Austrian Human Brucellosis Cases Using Whole Genome Sequencing. Front Med (Lausanne) 2021; 8:635547. [PMID: 33718408 PMCID: PMC7943447 DOI: 10.3389/fmed.2021.635547] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/04/2021] [Indexed: 11/13/2022] Open
Abstract
Brucellosis is a zoonotic disease caused by Brucella spp. and a major concern for livestock. Most human cases are caused by B. melitensis and clinical presentation is usually a mild febrile illness. However, treatment failure is frequent and more severe complications can occur. In Austria, every human brucellosis is investigated to determine whether it was imported from endemic areas or is the sign of an undetected autochthonous transmission. For this study, 21 B. melitensis strains isolated in Austria between 2005 and 2019 were collected, 17 strains from 15 different patients and four strains from cattle. Whole genome sequencing combined with core-genome MLST analysis was used to characterize these strains. A cluster of seven isolates from 2018 (three human and four cattle isolates) was identified, with fewer than two allelic differences. They corresponded to the only Austrian B. melitensis outbreak that happened over the past 15 years. The other 12 Austrian brucellosis cases were single cases, and geographical origins were available for 8/12. Genomic data was used to locate probable geographical origins and compared with the results of the epidemiological investigations. Austrian strains were compared with 67 published B. melitensis sequences available on NCBI. The result of genomic analysis matched for 7/8 cases with documented conclusion of the epidemiological investigation. Genome analysis also pointed to the geographical origin for three of the four cases with missing epidemiological data. Strains from six cases were grouped together (<40 allelic differences) with 4/6 cases imported from the Balkans. Additional B. melitensis isolates from Serbian animals were analyzed and grouped with this branch, suggesting frequent importation from Balkan countries to Austria. Overall, this study highlights the specificities of human brucellosis in Austria. It also underlines the value of whole genome sequencing as a tool to investigate brucellosis cases, allowing to identify and investigate outbreaks but also to support epidemiological investigation of imported cases. However, the reliability of such methods depends on the number of strains for comparison, which can be challenging in low incidence countries. Increasing the availability of published sequences with documented geographical origins would help establishing genomic-based methods for investigating brucellosis cases.
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Affiliation(s)
- Justine Schaeffer
- Institute for Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety (AGES), Vienna, Austria.,EUPHEM Fellowship, European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Sandra Revilla-Fernández
- Institute for Veterinary Disease Control Mödling, Austrian Agency for Health and Food Safety (AGES), Mödling, Austria
| | - Erwin Hofer
- Institute for Veterinary Disease Control Mödling, Austrian Agency for Health and Food Safety (AGES), Mödling, Austria
| | - Romana Posch
- Institute for Veterinary Disease Control Mödling, Austrian Agency for Health and Food Safety (AGES), Mödling, Austria
| | - Anna Stoeger
- Institute for Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Christoph Leth
- Institute for Veterinary Disease Control Mödling, Austrian Agency for Health and Food Safety (AGES), Mödling, Austria
| | - Friedrich Schmoll
- Institute for Veterinary Disease Control Mödling, Austrian Agency for Health and Food Safety (AGES), Mödling, Austria
| | - Vesna Djordjevic
- Department of Microbiology and Molecular Biology, Institute of Meat Hygiene and Technology, Belgrade, Serbia
| | - Brankica Lakicevic
- Department of Microbiology and Molecular Biology, Institute of Meat Hygiene and Technology, Belgrade, Serbia
| | - Kazimir Matovic
- Department for Laboratory Diagnostic, Veterinary Specialized Institute, Kraljevo, Serbia
| | - Peter Hufnagl
- Institute for Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Alexander Indra
- Institute for Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Franz Allerberger
- Institute for Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Werner Ruppitsch
- Institute for Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
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29
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Laferl H, Kelani H, Seitz T, Holzer B, Zimpernik I, Steinrigl A, Schmoll F, Wenisch C, Allerberger F. An approach to lifting self-isolation for health care workers with prolonged shedding of SARS-CoV-2 RNA. Infection 2021; 49:95-101. [PMID: 33025521 PMCID: PMC7538033 DOI: 10.1007/s15010-020-01530-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 09/16/2020] [Indexed: 12/23/2022]
Abstract
PURPOSE According to the European Public Health Authority guidance for ending isolation in the context of COVID-19, a convalescent healthcare worker (HCW) can end their isolation at home and resume work upon clinical improvement and two negative RT-PCR tests from respiratory specimens obtained at 24-h intervals at least 8 days after the onset of symptoms. However, convalescent HCWs may shed SARS-CoV-2 viral RNA for prolonged periods. METHODS 40 healthy HCWs off work because of ongoing positive RT-PCR results in combined nasopharyngeal (NP) and oropharyngeal (OP) swabs following SARS-CoV-2 infection were invited to participate in this study. These HCWs had been in self-isolation because of a PCR-confirmed SARS-CoV-2 infection. NP and OP swabs as well as a blood sample were collected from each participant. RT-PCR and virus isolation was performed with each swab sample and serum neutralization test as well as two different ELISA tests were performed on all serum samples. RESULTS No viable virions could be detected in any of 29 nasopharyngeal and 29 oropharyngeal swabs taken from 15 long-time carriers. We found SARSCoV- 2 RNA in 14/29 nasopharyngeal and 10/29 oropharyngeal swabs obtained from screening 15 HCWs with previous COVID-19 up to 55 days after symptom onset. Six (40%) of the 15 initially positive HCWs converted to negative and later reverted to positive again according to their medical records. All but one HCW, a healthy volunteer banned from work, showed the presence of neutralizing antibodies in concomitantly taken blood samples. Late threshold cycle (Ct) values in RT-PCR [mean 37.4; median 37.3; range 30.8-41.7] and the lack of virus growth in cell culture indicate that despite the positive PCR results no infectivity remained. CONCLUSION We recommend lifting isolation if the RT-PCR Ct-value of a naso- or oropharyngeal swab sample is over 30. Positive results obtained from genes targeted with Ct-values > 30 correspond to non-viable/noninfectious particles that are still detected by RT-PCR. In case of Ct-values lower than 30, a blood sample from the patient should be tested for the presence of neutralizing antibodies. If positive, non-infectiousness can also be assumed.
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Affiliation(s)
- H Laferl
- 4th Medical Department with Infectious Diseases and Tropical Medicine, Kaiser Franz Josef Hospital, 1100, Vienna, Austria.
| | - H Kelani
- 4th Medical Department with Infectious Diseases and Tropical Medicine, Kaiser Franz Josef Hospital, 1100, Vienna, Austria
| | - T Seitz
- 4th Medical Department with Infectious Diseases and Tropical Medicine, Kaiser Franz Josef Hospital, 1100, Vienna, Austria
| | - B Holzer
- Austrian Agency for Health and Food Safety (AGES), Institute for Veterinary Disease Control Mödling, 2340, Mödling, Austria
| | - I Zimpernik
- Austrian Agency for Health and Food Safety (AGES), Institute for Veterinary Disease Control Mödling, 2340, Mödling, Austria
| | - A Steinrigl
- Austrian Agency for Health and Food Safety (AGES), Institute for Veterinary Disease Control Mödling, 2340, Mödling, Austria
| | - F Schmoll
- Austrian Agency for Health and Food Safety (AGES), Institute for Veterinary Disease Control Mödling, 2340, Mödling, Austria
| | - C Wenisch
- 4th Medical Department with Infectious Diseases and Tropical Medicine, Kaiser Franz Josef Hospital, 1100, Vienna, Austria
| | - F Allerberger
- Austrian Agency for Health and Food Safety (AGES), Institute for Veterinary Disease Control Mödling, 2340, Mödling, Austria
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30
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Schittek GA, Köstenberger M, Allerberger F, Schaden E. Web-based survey of the importance and effectiveness of personal protective equipment during the COVID-19 pandemic. Intensive Crit Care Nurs 2020; 63:102996. [PMID: 33342653 PMCID: PMC7713545 DOI: 10.1016/j.iccn.2020.102996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/24/2020] [Accepted: 11/24/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Gregor A Schittek
- Division of General Anaesthesiology, Emergency- and Intensive Care Medicine, University Hospital of Graz, Austria.
| | | | - Franz Allerberger
- Division of Public Health at the Austrian Agency for Health and Food Safety, Spargelfeldstraße 191, 1220 Vienna, Austria
| | - Eva Schaden
- Department of Anaesthesia, Intensive Care Medicine and Pain Medicine, Währinger Gürtel 18-20, 1090 Vienna, Austria; Ludwig Boltzmann Institute for Digital Health and Patient Safety, Medical University of Vienna, Spitalgasse 23, Bauteil 86, 2. Stock, 1090 Vienna, Austria
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31
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Popa A, Genger JW, Nicholson MD, Penz T, Schmid D, Aberle SW, Agerer B, Lercher A, Endler L, Colaço H, Smyth M, Schuster M, Grau ML, Martínez-Jiménez F, Pich O, Borena W, Pawelka E, Keszei Z, Senekowitsch M, Laine J, Aberle JH, Redlberger-Fritz M, Karolyi M, Zoufaly A, Maritschnik S, Borkovec M, Hufnagl P, Nairz M, Weiss G, Wolfinger MT, von Laer D, Superti-Furga G, Lopez-Bigas N, Puchhammer-Stöckl E, Allerberger F, Michor F, Bock C, Bergthaler A. Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2. Sci Transl Med 2020; 12:eabe2555. [PMID: 33229462 PMCID: PMC7857414 DOI: 10.1126/scitranslmed.abe2555] [Citation(s) in RCA: 154] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/16/2020] [Indexed: 12/17/2022]
Abstract
Superspreading events shaped the coronavirus disease 2019 (COVID-19) pandemic, and their rapid identification and containment are essential for disease control. Here, we provide a national-scale analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) superspreading during the first wave of infections in Austria, a country that played a major role in initial virus transmissions in Europe. Capitalizing on Austria's well-developed epidemiological surveillance system, we identified major SARS-CoV-2 clusters during the first wave of infections and performed deep whole-genome sequencing of more than 500 virus samples. Phylogenetic-epidemiological analysis enabled the reconstruction of superspreading events and charts a map of tourism-related viral spread originating from Austria in spring 2020. Moreover, we exploited epidemiologically well-defined clusters to quantify SARS-CoV-2 mutational dynamics, including the observation of low-frequency mutations that progressed to fixation within the infection chain. Time-resolved virus sequencing unveiled viral mutation dynamics within individuals with COVID-19, and epidemiologically validated infector-infectee pairs enabled us to determine an average transmission bottleneck size of 103 SARS-CoV-2 particles. In conclusion, this study illustrates the power of combining epidemiological analysis with deep viral genome sequencing to unravel the spread of SARS-CoV-2 and to gain fundamental insights into mutational dynamics and transmission properties.
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Affiliation(s)
- Alexandra Popa
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Jakob-Wendelin Genger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Michael D Nicholson
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Thomas Penz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Daniela Schmid
- Austrian Agency for Health and Food Safety (AGES), 1220 Vienna, Austria
| | - Stephan W Aberle
- Center for Virology, Medical University of Vienna, 1090 Vienna, Austria
| | - Benedikt Agerer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Alexander Lercher
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Lukas Endler
- Bioinformatics and Biostatistics Platform, Department of Biomedical Sciences, University of Veterinary Medicine, 1210 Vienna, Austria
| | - Henrique Colaço
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Mark Smyth
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Michael Schuster
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Miguel L Grau
- Institute for Research in Biomedicine (IRB), 08028 Barcelona, Spain
| | | | - Oriol Pich
- Institute for Research in Biomedicine (IRB), 08028 Barcelona, Spain
| | - Wegene Borena
- Institute of Virology, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Erich Pawelka
- Department of Medicine IV, Kaiser Franz Josef Hospital, 1100 Vienna, Austria
| | - Zsofia Keszei
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Martin Senekowitsch
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Jan Laine
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Judith H Aberle
- Center for Virology, Medical University of Vienna, 1090 Vienna, Austria
| | | | - Mario Karolyi
- Department of Medicine IV, Kaiser Franz Josef Hospital, 1100 Vienna, Austria
| | - Alexander Zoufaly
- Department of Medicine IV, Kaiser Franz Josef Hospital, 1100 Vienna, Austria
| | | | - Martin Borkovec
- Austrian Agency for Health and Food Safety (AGES), 1220 Vienna, Austria
| | - Peter Hufnagl
- Austrian Agency for Health and Food Safety (AGES), 1220 Vienna, Austria
| | - Manfred Nairz
- Department of Internal Medicine II, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Günter Weiss
- Department of Internal Medicine II, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Michael T Wolfinger
- Department of Theoretical Chemistry, University of Vienna, 1090 Vienna, Austria
- Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, 1090 Vienna, Austria
| | - Dorothee von Laer
- Institute of Virology, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine (IRB), 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | | | - Franz Allerberger
- Austrian Agency for Health and Food Safety (AGES), 1220 Vienna, Austria
| | - Franziska Michor
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ludwig Center at Harvard, Boston, MA, USA
- Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Andreas Bergthaler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria.
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Lepuschitz S, Hauser K, Schriebl A, Schlagenhaufen C, Stöger A, Chakeri A, Vötsch K, Pekard-Amenitsch S, Springer B, Allerberger F, Ruppitsch W. Fecal Klebsiella pneumoniae Carriage Is Intermittent and of High Clonal Diversity. Front Microbiol 2020; 11:581081. [PMID: 33324367 PMCID: PMC7721676 DOI: 10.3389/fmicb.2020.581081] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/29/2020] [Indexed: 12/27/2022] Open
Abstract
The Klebsiella pneumoniae complex comprises several closely related entities, which are ubiquitous in the natural environment, including in plants, animals, and humans. K. pneumoniae is the major species within this complex. K. pneumoniae strains are opportunistic pathogens and a common cause of healthcare-associated infections. K. pneumoniae can colonize the human gastrointestinal tract, which may become a reservoir for infection. The aim of this study was to investigate the fecal K. pneumoniae carriage in six healthy individuals during a 1 year period. Stool samples were obtained once a week. Using direct and pre-enriched cultures streaked on ampicillin-supplemented agar plates, up to eight individual colonies per positive sample were selected for further characterization. Whole genome sequencing (WGS) was performed for strain characterization. Sequence type (ST), core genome complex type (CT), K and O serotypes, virulence traits, antibiotic resistance profiles, and plasmids were extracted from WGS data. In total, 80 K. pneumoniae isolates were obtained from 48 positive cultures of 278 stool samples from five of the six test subjects. The samples of the five colonized volunteers yielded at most two, three, four (two persons), and five different strains, respectively. These 80 K. pneumoniae isolates belonged to 60 STs, including nine new STs; they were of 70 CTs, yielded 48 K serotypes, 11 O serotypes, and 39 wzc and 51 wzi alleles. Four of the five subjects harbored serotypes K20 and K47, as well as STs ST37, ST101, ST1265, and ST20, which had previously been linked to high-risk K. pneumoniae clones. In total, 25 genes conferring antibiotic resistance and 42 virulence genes were detected among all 80 isolates. Plasmids of 15 different types were found among 65 of the isolates. Fecal carriage of individual strains was of short duration: 70 strains were found on a single sampling day only, and 5 strains were isolated in samples collected over two consecutive weeks. Two of the five colonized individuals—working colleagues having meals together—shared identical K. pneumoniae types four times during the study period. Our findings point toward the potential role of food as a reservoir for K. pneumoniae in humans.
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Affiliation(s)
- Sarah Lepuschitz
- Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Graz, Austria
| | - Kathrin Hauser
- Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Graz, Austria
| | - Agnes Schriebl
- Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Graz, Austria
| | - Claudia Schlagenhaufen
- Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Graz, Austria
| | - Anna Stöger
- Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Graz, Austria
| | - Ali Chakeri
- Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Graz, Austria
| | - Kornelia Vötsch
- Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Graz, Austria
| | - Shiva Pekard-Amenitsch
- Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Graz, Austria
| | - Burkhard Springer
- Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Graz, Austria
| | - Franz Allerberger
- Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Graz, Austria
| | - Werner Ruppitsch
- Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Graz, Austria
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Kerschner H, Rosel AC, Hartl R, Hyden P, Stoeger A, Ruppitsch W, Allerberger F, Apfalter P. Oxazolidinone Resistance Mediated by optrA in Clinical Enterococcus faecalis Isolates in Upper Austria: First Report and Characterization by Whole Genome Sequencing. Microb Drug Resist 2020; 27:685-690. [PMID: 33090061 DOI: 10.1089/mdr.2020.0098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The genetic mechanisms associated with acquisition of linezolid (LZD) resistance are diverse, including point mutations in the V domain of the 23S rRNA and the 50S ribosomal proteins as well as cfr, optrA, and/or poxtA genes, which may be plasmid- or chromosomally encoded. The aim of this study was to investigate through Whole Genome Sequencing (WGS)-based typing the presence and location of genes and point mutations associated with LZD resistance in two Enterococcus faecalis isolates from Upper Austrian patients. The isolates were retrieved during screening by LZD disk diffusion test of a total of 911 clinical E. faecalis isolates in 2017. The two E. faecalis isolates had LZD minimum inhibitory concentrations of 8 and 32 mg/L and were optrA-positive (ST476 and ST585). Bioinformatic analysis revealed the presence of optrA located in the chromosome of both isolates. One isolate carried the optrA gene in the transposon 6674, previously reported as chromosomally encoded, and the second isolate in fragments originating from the integrative plasmid pEF10748. Additional mechanisms of LZD resistance on the 23S rRNA and the 50S ribosomal proteins were detected. None of the patients reported travels to geographical areas with high LZD resistance or previous LZD treatments. This is the first report of optrA carrying E. faecalis, including characterization by WGS from Austria. LZD resistance in a low-prevalence setting is of concern and should be further monitored.
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Affiliation(s)
- Heidrun Kerschner
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections (NRZ), Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Linz, Austria
| | - Adriana Cabal Rosel
- AGES-Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Vienna, Austria
| | - Rainer Hartl
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections (NRZ), Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Linz, Austria
| | - Patrick Hyden
- CUBE, Division of Computational Systems Biology, University of Vienna, Vienna, Austria
| | - Anna Stoeger
- AGES-Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Vienna, Austria
| | - Werner Ruppitsch
- AGES-Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Vienna, Austria
| | - Franz Allerberger
- AGES-Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Vienna, Austria
| | - Petra Apfalter
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections (NRZ), Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Linz, Austria
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Lachmann R, Halbedel S, Adler M, Becker N, Allerberger F, Holzer A, Boone I, Falkenhorst G, Kleta S, Al Dahouk S, Stark K, Luber P, Flieger A, Wilking H. Nationwide outbreak of invasive listeriosis associated with consumption of meat products in health care facilities, Germany, 2014-2019. Clin Microbiol Infect 2020; 27:1035.e1-1035.e5. [PMID: 32979571 DOI: 10.1016/j.cmi.2020.09.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/27/2020] [Accepted: 09/11/2020] [Indexed: 12/16/2022]
Abstract
OBJECTIVES Invasive listeriosis is a severe foodborne infection caused by Listeria(L.)monocytogenes. The aim of this investigation was to verify and describe a molecular cluster of listeriosis patients and identify factors leading to this outbreak. METHODS Whole genome sequencing and core genome multilocus sequence typing were used for subtyping L. monocytogenes isolates from listeriosis cases and food samples in Germany. Patient interviews and investigational tracing of foodstuffs offered in health-care facilities (HCF), where some of the cases occurred, were conducted. RESULTS We identified a German-wide listeriosis outbreak with 39 genetically related cases occurring between 2014 and 2019. Three patients died as a result of listeriosis. After identification of HCF in different regions of Germany for at least 13 cases as places of exposure, investigational tracing of food supplies in six prioritized HCF revealed meat products from one company (X) as a commonality. Subsequently the outbreak strain was analysed in six isolates from ready-to-eat meat products and one isolate from the production environment of company X. No further Sigma1 cases were detected after recall of the meat products from the market and closure of company X (as of August 2020). CONCLUSIONS Interdisciplinary efforts including whole genome sequencing, epidemiological investigations in patients and investigational tracing of foods were essential to identify the source of infections, and thereby prevent further illnesses and deaths. This outbreak underlines the vulnerability of hospitalized patients for foodborne diseases, such as listeriosis. Food producers and HCF should minimize the risk of microbiological hazards when producing, selecting and preparing food for patients.
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Affiliation(s)
- Raskit Lachmann
- FG35 Division of Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Berlin, Germany.
| | - Sven Halbedel
- FG11 Division of Enteropathogenic Bacteria and Legionella, Consultant Laboratory for Listeria, Robert Koch Institute, Wernigerode, Germany
| | - Marlen Adler
- German Federal Institute for Risk Assessment, Berlin, Germany
| | - Natalie Becker
- Federal Office of Consumer Protection and Food Safety, Berlin, Germany
| | | | - Alexandra Holzer
- FG35 Division of Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Berlin, Germany
| | - Idesbald Boone
- FG35 Division of Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Berlin, Germany
| | - Gerhard Falkenhorst
- FG35 Division of Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Berlin, Germany
| | - Sylvia Kleta
- German Federal Institute for Risk Assessment, Berlin, Germany
| | | | - Klaus Stark
- FG35 Division of Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Berlin, Germany
| | - Petra Luber
- Federal Office of Consumer Protection and Food Safety, Berlin, Germany
| | - Antje Flieger
- FG11 Division of Enteropathogenic Bacteria and Legionella, Consultant Laboratory for Listeria, Robert Koch Institute, Wernigerode, Germany
| | - Hendrik Wilking
- FG35 Division of Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Berlin, Germany
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Cabal A, Allerberger F, Huhulescu S, Kornschober C, Springer B, Schlagenhaufen C, Wassermann-Neuhold M, Fötschl H, Pless P, Krause R, Lennkh A, Murer A, Ruppitsch W, Pietzka A. Listeriosis outbreak likely due to contaminated liver pâté consumed in a tavern, Austria, December 2018. ACTA ACUST UNITED AC 2020; 24. [PMID: 31576804 PMCID: PMC6774228 DOI: 10.2807/1560-7917.es.2019.24.39.1900274] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In late December 2018, an outbreak of listeriosis occurred after a group of 32 individuals celebrated in a tavern in Styria, Austria; traditional Austrian food (e.g. meat, meat products and cheese) was served. After the celebration, 11 individuals developed gastrointestinal symptoms, including one case with severe sepsis. Cases had consumed mixed platters with several meat products and pâtés originating from a local production facility (company X). Human, food and environmental samples taken from the tavern and company X were tested for L. monocytogenes. Whole genome sequence-based typing detected a novel L. monocytogenes strain of serotype IVb, sequence type 4 and CT7652 in 15 samples; 12 human, two food and one environmental sample from company X with an allelic difference of 0 to 1. Active case finding identified two further cases who had not visited the tavern but tested positive for the outbreak strain. In total, 13 cases (seven females and six males; age range: 4–84 years) were identified. Liver pâté produced by company X was identified as the likely source of the outbreak. Control measures were implemented and since the end of December 2018, no more cases were detected.
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Affiliation(s)
- Adriana Cabal
- European Public Health Microbiology Training Programme (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden.,Institute for Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna/Graz, Austria
| | - Franz Allerberger
- Institute for Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna/Graz, Austria
| | - Steliana Huhulescu
- Institute for Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna/Graz, Austria
| | - Christian Kornschober
- Institute for Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna/Graz, Austria
| | - Burkhard Springer
- Institute for Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna/Graz, Austria
| | - Claudia Schlagenhaufen
- Institute for Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna/Graz, Austria
| | | | - Harald Fötschl
- Department - Health and Nursing Management, Styrian Provincial Government, Graz, Austria
| | - Peter Pless
- Department - Health and Nursing Management, Styrian Provincial Government, Graz, Austria
| | - Robert Krause
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Anna Lennkh
- Institute for Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna/Graz, Austria
| | - Andrea Murer
- Institute for Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna/Graz, Austria
| | - Werner Ruppitsch
- Institute for Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna/Graz, Austria
| | - Ariane Pietzka
- Institute for Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna/Graz, Austria
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Kreidl P, Schmid D, Maritschnik S, Richter L, Borena W, Genger JW, Popa A, Penz T, Bock C, Bergthaler A, Allerberger F. Emergence of coronavirus disease 2019 (COVID-19) in Austria. Wien Klin Wochenschr 2020; 132:645-652. [PMID: 32816114 PMCID: PMC7439636 DOI: 10.1007/s00508-020-01723-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/23/2020] [Indexed: 01/08/2023]
Abstract
This is a report on the first identified cases of coronavirus disease 2019 (COVID-19) in Austria. The first documented case was a person who stayed in Kühtai, Tyrol, from 24 to 26 January 2020, and had been infected by a Chinese instructor in Starnberg (Germany) between 20 and 22 January. This counts as a German case since her diagnosis was eventually made in Munich (Germany) on 28 January. On 25 February, two cases imported from Italy were diagnosed in Innsbruck but again no secondary cases were identified in Austria. The first three infections of Austrian inhabitants were detected on 27 February in Vienna. The two resulting clusters finally included 6 (source of initial infection unknown) and 61 cases. Most likely, Italy was the source of the latter cluster. On 12 March the first fatal case of COVID-19 in Austria was reported, a 69-year-old Viennese who died in a Vienna hospital after returning from a cruise ship tour in Italy. On 6 March three autochthonously acquired cases were reported in the Tyrol, all related to the ski resort Ischgl. Of the first 14 Islandic COVID-19 cases infected in Ischgl, 11 had already returned to Iceland on 29 February. We consider that the incriminated barkeeper, who tested PCR positive on 7 March, was neither the primary case nor a superspreader. In our opinion, undetected transmission of SARS-CoV‑2 had been ongoing in Ischgl prior to the first laboratory confirmed cases. Our data also underline that the introduction of SARS-CoV‑2 into Austria was not one single event.
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Affiliation(s)
- Peter Kreidl
- Österreichische Agentur für Gesundheit und Ernährungssicherheit (AGES), Spargelfeldstr. 191, 1220, Vienna, Austria.,Institut für Hygiene und Medizinische Mikrobiologie, Schöpfstr. 41, 6020, Innsbruck, Austria
| | - Daniela Schmid
- Österreichische Agentur für Gesundheit und Ernährungssicherheit (AGES), Spargelfeldstr. 191, 1220, Vienna, Austria
| | - Sabine Maritschnik
- Österreichische Agentur für Gesundheit und Ernährungssicherheit (AGES), Spargelfeldstr. 191, 1220, Vienna, Austria
| | - Lukas Richter
- Österreichische Agentur für Gesundheit und Ernährungssicherheit (AGES), Spargelfeldstr. 191, 1220, Vienna, Austria
| | - Wegene Borena
- Institut für Virologie, Schöpfstr. 41, 6020, Innsbruck, Austria
| | - Jakob-Wendelin Genger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Alexandra Popa
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Thomas Penz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Andreas Bergthaler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Franz Allerberger
- Österreichische Agentur für Gesundheit und Ernährungssicherheit (AGES), Spargelfeldstr. 191, 1220, Vienna, Austria. .,Institut für Hygiene und Medizinische Mikrobiologie, Schöpfstr. 41, 6020, Innsbruck, Austria.
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Jesumirhewe C, Springer B, Allerberger F, Ruppitsch W. Whole genome sequencing of extended-spectrum β-lactamase genes in Enterobacteriaceae isolates from Nigeria. PLoS One 2020; 15:e0231146. [PMID: 32287306 PMCID: PMC7156064 DOI: 10.1371/journal.pone.0231146] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 03/17/2020] [Indexed: 01/22/2023] Open
Abstract
Extended Spectrum β-lactamase (ESBL)-producing Enterobacteriaceae are of major concern as they are implicated in multidrug resistant nosocomial infections. They are listed on a recently published global priority list of antibiotic-resistant bacteria by the World Health Organization which raises concern in both healthcare and community settings. This study aimed at determining the frequency of ESBL genes in multidrug resistant human clinical Enterobacteriaceae isolates from Edo state Nigeria and to characterize the resistance mechanisms using whole genome sequencing. A total of 217 consecutive clinical isolates of Enterobacteriaceae, selection based on inclusion criteria, were collected from March-May 2015 from three medical microbiology laboratories of hospitals in Edo state Nigeria. All isolates were analyzed using matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry. Antibiotic susceptibility testing was performed by Kirby-Bauer method and minimum inhibitory concentration (MIC) determination by E-test method. Double disc synergy test was used to screen for the production of ESBL. Whole genome sequencing (WGS) was performed for isolate characterization and identification of resistance determinants. Out of 217 consecutive clinical Enterobacteriaceae isolates, 148 (68.2%) were multi-drug resistant. Of these multi-drug resistant isolates, 60 (40.5%) were positive for the ESBL phenotypic test and carried ESBL genes. CTX-M-15 was the predominant ESBL found, among 93.3% (n = 56/60). Thirty-two plasmid incompatibility groups and 28 known and two new sequence types were identified among the ESBL isolates. The high occurrence of CTX-M-15 with associated resistant determinants in multidrug resistant Enterobacteriaceae harboring different plasmid incompatibility groups and sequence types calls for the need of continuous monitoring of this resistance threat to reduce its public health impact. To our knowledge, this study presents the first genomic characterization of ESBL production mediated by blaCTX-M-15 in human clinical isolates of Enterobacter hormaechei, Citrobacter werkmanii and Atlantibacter hermannii from Nigeria.
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Affiliation(s)
- Christiana Jesumirhewe
- Department of Pharmaceutical Microbiology, Prof Dora Akunyili College of Pharmacy, Igbinedion University, Okada, Nigeria
- * E-mail:
| | - Burkhard Springer
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Franz Allerberger
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Werner Ruppitsch
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
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Duscher GG, Hodžić A, Hufnagl P, Wille-Piazzai W, Schötta AM, Markowicz MA, Estrada-Peña A, Stanek G, Allerberger F. Adult Hyalomma marginatum tick positive for Rickettsia aeschlimannii in Austria, October 2018. ACTA ACUST UNITED AC 2019; 23. [PMID: 30621821 PMCID: PMC6280420 DOI: 10.2807/1560-7917.es.2018.23.48.1800595] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report on a non-indigenous adult Hyalomma marginatum tick in Austria carrying the human pathogenic Rickettsia aeschlimannii; presumably introduced as a nymph via migratory birds and completed the moulting within the same year. It was negative for Crimean-Congo haemorrhagic fever virus, but the finding of R. aeschlimannii represents a potential threat for humans due to its zoonotic character. Awareness of invasive tick species and carried pathogens should be improved in central and northern Europe.
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Affiliation(s)
| | - Adnan Hodžić
- Institute of Parasitology, University of Veterinary Medicine Vienna, Austria
| | - Peter Hufnagl
- Institute for Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety Vienna, Austria
| | | | | | | | | | - Gerold Stanek
- Institute for Hygiene and Applied Immunology, Medical University of Vienna, Austria
| | - Franz Allerberger
- Institute for Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety Vienna, Austria
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Cabal A, Pietzka A, Huhulescu S, Allerberger F, Ruppitsch W, Schmid D. Isolate-Based Surveillance of Listeria monocytogenes by Whole Genome Sequencing in Austria. Front Microbiol 2019; 10:2282. [PMID: 31632381 PMCID: PMC6779813 DOI: 10.3389/fmicb.2019.02282] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 09/18/2019] [Indexed: 11/18/2022] Open
Abstract
Listeria monocytogenes (L. monocytogenes) is a ubiquitous organism that can easily enter the food chain. Infection with L. monocytogenes can cause invasive listeriosis. Since 2014, in Austria, L. monocytogenes isolates from human and food/food-associated samples have been provided on a mandatory basis by food producers and laboratories to the National Reference Laboratory. Since 2017, isolates undergo routinely whole genome sequencing (WGS) and core genome Multilocus Sequence Typing (cgMLST) for cluster analyses. Aims of this study were to characterize isolates and clusters of 2017 by using WGS data and to assess the usefulness of this isolate-based surveillance for generating hypotheses on sources of invasive listeriosis in real-time. WGS data from 31 human and 1744 non-human isolates originating from 2017, were eligible for the study. A cgMLST-cluster was defined as two or more isolates differing by ≤10 alleles. We extracted the sequence types (STs) from the WGS data and analyzed the food subcategories meat, fish, vegetable and diary for associations with the ten most prevalent STs among food, through calculating prevalence ratios (PR) with 95% confidence intervals (CI). The three most frequent STs among the human isolates were ST1 (7/31; 22.6%), ST155 (4/31; 12.9%) and ST451 (3/31; 9.7%) and among the non-human isolates ST451 (614/1744; 35.2%), ST8 (173/1744, 10.0%) and ST9 (117/1744; 6.7%). We found ST21 associated with vegetables (PR: 11.39, 95% CI: 8.32–15.59), ST121 and ST155 with fish (PR: 7.05, 95% CI: 4.88–10.17, PR: 3.29, 95% CI: 1.86–5.82), and ST511, ST7 and ST451 with dairy products (PR: 8.55, 95% CI: 6.65–10.99; PR: 5.05, 95% CI: 3.83–6.66, PR: 3.03, 95% CI: 2.02–4.55). We identified 132 cgMLST-clusters. Six clusters contained human isolates (ST155, ST1, ST101, ST177, ST37 and ST7) and for five of those cgMLST-based cluster analyses solely was able to hypothesize the source: an Austrian meat processing company, two Austrian cheese manufacturers and two vegetable processing companies, one based in Austria and the other in Belgium. Determining routinely STs in food isolates by WGS allows to associate STs with food products. Real-time WGS of L. monocytogenes isolates provided mandatorily, proved to be useful in promptly generating hypotheses on sources of invasive listeriosis.
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Affiliation(s)
- Adriana Cabal
- Austrian National Reference Centre for Listeria, Austrian Agency for Health and Food Safety, Vienna, Austria.,European Public Health Microbiology Training Programme (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Ariane Pietzka
- Austrian National Reference Centre for Listeria, Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Steliana Huhulescu
- Austrian National Reference Centre for Listeria, Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Franz Allerberger
- Austrian National Reference Centre for Listeria, Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Werner Ruppitsch
- Austrian National Reference Centre for Listeria, Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Daniela Schmid
- Austrian National Reference Centre for Listeria, Austrian Agency for Health and Food Safety, Vienna, Austria
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Kerschner H, Cabal A, Hartl R, Machherndl-Spandl S, Allerberger F, Ruppitsch W, Apfalter P. Hospital outbreak caused by linezolid resistant Enterococcus faecium in Upper Austria. Antimicrob Resist Infect Control 2019; 8:150. [PMID: 31516698 PMCID: PMC6732827 DOI: 10.1186/s13756-019-0598-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 08/15/2019] [Indexed: 12/13/2022] Open
Abstract
Background Enterococcus faecium is part of the human gastrointestinal flora but may act as opportunistic pathogen. Environmental persistence, high colonization capability and diverse intrinsic and acquired resistance mechanisms make it especially successful in nosocomial high-risk settings. In March 2014, an outbreak of Linezolid resistant Enterococcus faecium (LREfm) was observed at the hematooncology department of a tertiary care center in Upper Austria. Methods We report on the outbreak investigation together with the whole genome sequencing (WGS)-based typing results including also non-outbreak LREfm and susceptible isolates. Results The 54 investigated isolates could be divided in six clusters based on cgMLST. Cluster one comprised LREfm isolates of genotype ST117 and CT24, which was identified as the causative clone of the outbreak. In addition, the detection of four other clusters comprising isolates originating from hematooncology patients but also at other hospitals, pointed to LREfm transmission between local healthcare facilities. LREfm patients (n = 36) were typically at risk for acquisition of nosocomial pathogens because of immunosuppression, frequent hospitalization and antibiotic therapies. Seven of these 36 patients developed LREfm infection but were successfully treated. After termination of the initial outbreak, sporadic cases occurred despite a bundle of applied outbreak control interventions. Conclusions WGS proved to be an effective tool to differentiate several LREfm clusters in an outbreak. Active screening for LREfm is important in a high-risk setting such as hematooncology, where multiple introductions are possible and occur despite intensified infection control measures. Electronic supplementary material The online version of this article (10.1186/s13756-019-0598-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Heidrun Kerschner
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections, Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Fadingerstrasse 1, 4020 Linz, Austria
| | - Adriana Cabal
- AGES - Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Waehringerstrasse 25a, 1090 Vienna, Austria.,3European Public Health Microbiology Training Programme (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Rainer Hartl
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections, Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Fadingerstrasse 1, 4020 Linz, Austria
| | - Sigrid Machherndl-Spandl
- Department of Internal Medicine 1, Ordensklinikum Linz Elisabethinen, Fadingerstrasse 1, 4020 Linz, Austria
| | - Franz Allerberger
- AGES - Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Waehringerstrasse 25a, 1090 Vienna, Austria
| | - Werner Ruppitsch
- AGES - Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Waehringerstrasse 25a, 1090 Vienna, Austria
| | - Petra Apfalter
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections, Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Fadingerstrasse 1, 4020 Linz, Austria
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Taus K, Schmoll F, El-Khatib Z, Auer H, Holzmann H, Aberle S, Pekard-Amenitsch S, Monschein S, Sattler T, Steinparzer R, Allerberger F, Schmid D. Occupational swine exposure and Hepatitis E virus, Leptospira, Ascaris suum seropositivity and MRSA colonization in Austrian veterinarians, 2017-2018-A cross-sectional study. Zoonoses Public Health 2019; 66:842-851. [PMID: 31419070 PMCID: PMC6851874 DOI: 10.1111/zph.12633] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 06/07/2019] [Accepted: 06/23/2019] [Indexed: 12/16/2022]
Abstract
We investigated the prevalence of Hepatitis E Virus (HEV), Leptospira and Ascaris suum (A. suum) seropositivity, and of nasal methicillin-resistant Staphylococcus aureus (MRSA) colonization among Austrian practising veterinarians, and assessed the association with occupational swine livestock exposure. The 261 participants completed a questionnaire on demographics, intensity of occupational swine livestock contact and glove use during handling animals and their secretions. Participants' blood samples were tested for HEV, Leptospira and A. suum seropositivity and nasal swabs cultured for MRSA. We compared swine veterinarians (defined as >3 swine livestock visits/week) to non-swine veterinarians (≤3 swine livestock visits/week) with regard to the outcomes through calculating prevalence ratio (PR) and 95% confidence interval (CI). Furthermore, the relationship between occupational swine livestock contact and the study outcomes was examined by age (</≥55 years) and glove usage. The prevalence of nasal MRSA colonization was 13.4% (95% CI: 9.3-17.6), of HEV seropositivity 20.8% (95% CI: 15.8-25.7) and A. suum seropositivity 44% (95% CI: 37.7-50.2). The highest anti-leptospiral antibodies titres were 1:200 (L. hebdomadis) and 1:100 (L. autumnalis, L. caicola) found in three non-swine veterinarians. Compared to non-swine veterinarians, swine veterinarians were 1.9 (95% CI: 1.0-3.4) and 1.5 (95%CI: 1.0-2.3) times more likely HEV seropositive and A. suum seropositive, respectively, and 4.8 (95%CI: 2.5; 9.3) times more likely nasally colonized with MRSA. Among glove-using veterinarians, occupational swine contact was no longer a determinant for HEV seropositivity (PR 1.6; 95% CI: 0.8-2.9). Similar was found for A. suum seropositivity, which was no longer associated with occupational swine livestock contact in the subgroup of glove using, ≥55-year-old veterinarians (PR: 1.07; 95% CI: 0.4-3.3). Our findings indicate that >3 occupational swine livestock visits per week is associated with HEV and A. suum seropositivity and nasal MRSA colonization and that glove use may play a putative preventive role in acquiring HEV and A. suum. Further analytical epidemiological studies have to prove the causality of these associations.
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Affiliation(s)
- Karin Taus
- Austrian Agency for Health and Food Safety (AGES), Vienna, Austria.,European Programme for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | | | - Ziad El-Khatib
- Austrian Agency for Health and Food Safety (AGES), Vienna, Austria.,Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Herbert Auer
- Institute for Specific Prophylaxis and Tropical medicine, Centre for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Heidemarie Holzmann
- Clinical Institute of Virology, Medical University of Vienna, Vienna, Austria
| | - Stephan Aberle
- Clinical Institute of Virology, Medical University of Vienna, Vienna, Austria
| | | | | | - Tatjana Sattler
- Austrian Agency for Health and Food Safety (AGES), Mödling, Austria.,Clinic for Ruminants and Swine, University Leipzig, Leipzig, Germany
| | | | | | - Daniela Schmid
- Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
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Lepuschitz S, Ruppitsch W, Pekard-Amenitsch S, Forsythe SJ, Cormican M, Mach RL, Piérard D, Allerberger F. Multicenter Study of Cronobacter sakazakii Infections in Humans, Europe, 2017. Emerg Infect Dis 2019; 25:515-522. [PMID: 30789137 PMCID: PMC6390735 DOI: 10.3201/eid2503.181652] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Cronobacter sakazakii has been documented as a cause of life-threating infections, predominantly in neonates. We conducted a multicenter study to assess the occurrence of C. sakazakii across Europe and the extent of clonality for outbreak detection. National coordinators representing 24 countries in Europe were requested to submit all human C. sakazakii isolates collected during 2017 to a study center in Austria. Testing at the center included species identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, subtyping by whole-genome sequencing (WGS), and determination of antimicrobial resistance. Eleven countries sent 77 isolates, including 36 isolates from 2017 and 41 historical isolates. Fifty-nine isolates were confirmed as C. sakazakii by WGS, highlighting the challenge of correctly identifying Cronobacter spp. WGS-based typing revealed high strain diversity, indicating absence of multinational outbreaks in 2017, but identified 4 previously unpublished historical outbreaks. WGS is the recommended method for accurate identification, typing, and detection of this pathogen.
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Adeoshun FG, Ruppitsch W, Allerberger F, Ayeni FA. Prevalence and Antimicrobial Properties of Lactic Acid Bacteria in Nigerian Women During the Menstrual Cycle. Pol J Microbiol 2019; 68:203-209. [PMID: 31250590 PMCID: PMC7256855 DOI: 10.33073/pjm-2019-020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/31/2019] [Accepted: 02/01/2019] [Indexed: 11/27/2022] Open
Abstract
The composition of vagina lactic acid bacteria (LAB) differs within the different ethnic group. This study is aimed at determining the prevalence of LAB with their antimicrobial properties in Nigerian women’s vagina during different stages of the menstrual cycle. Microorganisms were isolated from vaginal swabs of ten Nigerian women during different stages of the menstrual cycle and identified by partial sequencing of the 16S rRNA gene. The antimicrobial properties of the LAB were tested against the multidrug-resistant uropathogens. The prevalence of LAB was higher during ovulation period while during menstruation period, it declined. Twenty-five LAB isolates were identified as three species, namely: Lactobacillus plantarum (15), Lactobacillus fermentum (9), Lactobacillus brevis (1) and one acetic acid bacteria – Acetobacter pasteurianus. The LAB had antimicrobial activities against the three uropathogens with zones of inhibition from 8 to 22 mm. The presence of LAB inhibits the growth of Staphylococcus sp. GF01 also in the co-culture. High LAB counts were found during ovulation period with L. plantarum as a dominant species while during menstruation, there was a decrease in the LAB counts. The isolated LAB has antimicrobial properties against the urogenital pathogens tested thus exhibiting their potential protective role against uropathogens.
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Affiliation(s)
- Folashade Grace Adeoshun
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan , Ibadan, Oyo State , Nigeria
| | - Werner Ruppitsch
- Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene , Vienna , Austria
| | - Franz Allerberger
- Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene , Vienna , Austria
| | - Funmilola Abidemi Ayeni
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan , Ibadan, Oyo State , Nigeria
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45
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Loncaric I, Lepuschitz S, Ruppitsch W, Trstan A, Andreadis T, Bouchlis N, Marbach H, Schauer B, Szostak MP, Feßler AT, Künzel F, Licka T, Springer B, Allerberger F, Monecke S, Ehricht R, Schwarz S, Spergser J. Increased genetic diversity of methicillin-resistant Staphylococcus aureus (MRSA) isolated from companion animals. Vet Microbiol 2019; 235:118-126. [PMID: 31282369 DOI: 10.1016/j.vetmic.2019.06.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/13/2019] [Accepted: 06/14/2019] [Indexed: 12/11/2022]
Abstract
The aim of the present study was to investigate the diversity of methicillin-resistant Staphylococcus aureus (MRSA) that originated from Austrian companion animals during the last five-year period. A total of 90 non-repetitive MRSA isolates were obtained during diagnostic activities from autumn 2013 to autumn 2018. They originated from horses (n = 62), cats (n = 13), dogs (n = 10), rabbits (n = 2), a domestic canary, a zoo-kept hammer-headed bat (Hypsignathus monstrosus) and a semi-captive northern bald ibis (Geronticus eremita). Antimicrobial susceptibility testing was performed. All isolates were mecA-positive and mecC-negative. The isolates were genotyped by SCCmec, spa and dru typing, Multiple-Locus Variable number of tandem repeat Analyses (MLVA), S. aureus DNA microarray, and whole-genome sequencing (WGS). Eight sequence types (STs - ST398, ST5275 (new ST), ST225, ST8, ST22, ST152, ST1, and ST45), three SCCmec types (II, IV, and V), sixteen spa types (t003, t008, t011, t015, t032, t034, t1381, t1928, t1985, t223, t334, t355, t430, t6447, t6867, and t7105), fourteen dru types (dt10a, dt10az, dt10q, dt10r, dt11a, dt5e, dt6j, dt9a, dt9ak, dt9g, and four new types dt8as, dt7ak, dt4j, dt14n), and thirty-five MLVA types were detected. WGS-based core genome MLST (cgMLST) displayed five main clusters. Compared to the time period 2004-2013, the results of the present study show not only a higher diversity among the MRSA isolates within the population of Austrian companion animals, but also the introduction of new clones. Although ST398 isolates remained predominant, mainly due to high presence of this lineage among horses, increasing isolation rates of human-associated MRSA clones were observed in cats and dogs.
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Affiliation(s)
- Igor Loncaric
- Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria.
| | - Sarah Lepuschitz
- Austrian Agency for Health and Food Safety (AGES), Institute of Medical Microbiology and Hygiene, Vienna, Austria
| | - Werner Ruppitsch
- Austrian Agency for Health and Food Safety (AGES), Institute of Medical Microbiology and Hygiene, Vienna, Austria
| | - Alan Trstan
- Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria
| | - Thomas Andreadis
- Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria
| | - Nikolaos Bouchlis
- Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria
| | - Helene Marbach
- Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria
| | - Bernhard Schauer
- Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria
| | - Michael P Szostak
- Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria
| | - Andrea T Feßler
- Institute of Microbiology and Epizootics, Centre of Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Frank Künzel
- Clinical Unit of Internal Medicine Small Animals, University of Veterinary Medicine, Vienna, Austria
| | - Theresia Licka
- Clinical Unit of Equine Surgery, University of Veterinary Medicine, Vienna, Austria
| | - Burkhard Springer
- Austrian Agency for Health and Food Safety (AGES), Institute of Medical Microbiology and Hygiene, Vienna, Austria
| | - Franz Allerberger
- Austrian Agency for Health and Food Safety (AGES), Institute of Medical Microbiology and Hygiene, Vienna, Austria
| | - Stefan Monecke
- InfectoGnostics research campus, Jena, Germany; Leibniz Institute of Photonic Technology (IPHT), Jena, Germany; Institute for Medical Microbiology and Hygiene, Technical University of Dresden, Dresden, Germany
| | - Ralf Ehricht
- InfectoGnostics research campus, Jena, Germany; Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre of Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Joachim Spergser
- Institute of Microbiology and Epizootics, Centre of Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
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Pietzka A, Allerberger F, Murer A, Lennkh A, Stöger A, Cabal Rosel A, Huhulescu S, Maritschnik S, Springer B, Lepuschitz S, Ruppitsch W, Schmid D. Whole Genome Sequencing Based Surveillance of L. monocytogenes for Early Detection and Investigations of Listeriosis Outbreaks. Front Public Health 2019; 7:139. [PMID: 31214559 PMCID: PMC6557975 DOI: 10.3389/fpubh.2019.00139] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 05/16/2019] [Indexed: 02/01/2023] Open
Abstract
In Austria, all laboratories are legally obligated to forward human and food/environmental L. monocytogenes isolates to the National Reference Laboratory/Center (NRL) for Listeria. Two invasive human isolates of L. monocytogenes serotype 1/2a of the same pulsed-field gel electrophoresis (PFGE) pattern, previously unknown in Austria, were cultured for the first time in January 2016. Five further human isolates, obtained from patients with invasive listeriosis between April 2016 and September 2017, showed this PFGE pattern. In Austria the NRL started to use whole-genome sequencing (WGS) based typing in 2016, using a core genome MLST (cgMLST) scheme developed by Ruppitsch et al. 2015, which contains 1701 target genes. Sequence data are submitted to a publicly available nomenclature server (Ridom GmbH, Münster, Germany) for allocation of the core genome complex type (CT). The seven invasive human isolates differed from each other with zero to two alleles and were allocated to CT1234 (declared as outbreak strain). Among the Austrian strain collection of about 6,000 cgMLST-characterized non-human isolates (i.e., food/environmental isolates) 90 isolates shared CT1234. Out of these, 83 isolates were traced back to one meat processing-company. They differed from the outbreak strain by up to seven alleles; one isolate originated from the company's industrial slicer. The remaining seven CT1234-isolates were obtained from food products of four other companies (five fish-products, one ready-to-eat dumpling and one deer-meat) and differed from the outbreak strain by six to eleven alleles. The outbreak described shows the considerable potential of WGS to identify the source of a listeriosis outbreak. Compared to PFGE analysis, WGS-based typing has higher discriminatory power, yields better data accuracy, and allows higher laboratory through-put at lower cost. Utilization of WGS-based typing results of human and food/ environmental L. monocytogenes isolates by appropriate public health analysts and epidemiologists is indispensable to support a successful outbreak investigation.
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Affiliation(s)
- Ariane Pietzka
- AGES - Austrian Agency for Health and Food Safety, Graz, Austria
| | | | - Andrea Murer
- AGES - Austrian Agency for Health and Food Safety, Graz, Austria
| | - Anna Lennkh
- AGES - Austrian Agency for Health and Food Safety, Graz, Austria
| | - Anna Stöger
- AGES - Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Adriana Cabal Rosel
- AGES - Austrian Agency for Health and Food Safety, Vienna, Austria
- European Public Health Microbiology training programme (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | | | | | | | - Sarah Lepuschitz
- AGES - Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Werner Ruppitsch
- AGES - Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Daniela Schmid
- AGES - Austrian Agency for Health and Food Safety, Vienna, Austria
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47
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Pisazka V, Duscher G, Hodžić A, Reider N, Allerberger F. Alpha-gal allergy after a tick bite in Austria. Wien Klin Wochenschr 2019; 131:385-388. [PMID: 31087152 PMCID: PMC6702184 DOI: 10.1007/s00508-019-1506-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 04/26/2019] [Indexed: 11/20/2022]
Abstract
Tick bites can cause the alpha-gal syndrome, which is characterized by delayed anaphylactic reactions mainly to red meat and offal due to IgE antibodies against mammalian galactose-alpha-1.3-galactose carbohydrate (alpha-gal). Ixodes ricinus bites are considered the primary cause of IgE antibody responses specific for alpha-gal in Europe. This article reports on a 51-year-old Austrian male who acquired a tick bite in Austria in spring 2017, which, within 48 h, resulted in prolonged inflammation of the skin area around the bite. The patient experienced an allergic reaction 3 months later approximately 8 h after eating a medium rare steak for dinner. The symptoms included an itchy rash on both sides of the torso and on both arms which persisted for several hours. In spring 2018, the patient suffered another tick bite. The patient’s skin reaction was similar to that of the previous year. In the following months, the patient experienced five episodes of severe allergic reactions, each during the night after having eaten beef for dinner. The symptoms included pruritic urticarial rash involving the entire body along with swollen hands, diarrhea, vomiting and in some episodes even shortness of breath. At the request of the patient, specific IgE antibodies against alpha-gal were determined, revealing a highly positive result (>100 kU/l). This brief report aims to raise awareness that recurrent delayed anaphylactic reactions to food can develop after tick bites.
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Affiliation(s)
- Veronika Pisazka
- Austrian Agency for Health and Food Safety (AGES), Spargelfeldstraße 191, 1220, Vienna, Austria
| | - Georg Duscher
- Institute of Parasitology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Adnan Hodžić
- Institute of Parasitology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Norbert Reider
- Department of Dermatology, Venereology and Allergy, Medical University Innsbruck, Innsbruck, Austria
| | - Franz Allerberger
- Austrian Agency for Health and Food Safety (AGES), Spargelfeldstraße 191, 1220, Vienna, Austria.
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Lepuschitz S, Schill S, Stoeger A, Pekard-Amenitsch S, Huhulescu S, Inreiter N, Hartl R, Kerschner H, Sorschag S, Springer B, Brisse S, Allerberger F, Mach RL, Ruppitsch W. Whole genome sequencing reveals resemblance between ESBL-producing and carbapenem resistant Klebsiella pneumoniae isolates from Austrian rivers and clinical isolates from hospitals. Sci Total Environ 2019; 662:227-235. [PMID: 30690357 DOI: 10.1016/j.scitotenv.2019.01.179] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 01/14/2019] [Accepted: 01/14/2019] [Indexed: 06/09/2023]
Abstract
In 2016, the Austrian Agency for Health and Food Safety started a pilot project to investigate antimicrobial resistance in surface water. Here we report on the characterisation of carbapenem resistant and ESBL-producing K. pneumoniae isolates from Austrian river water samples compared to 95 clinical isolates recently obtained in Austrian hospitals. Ten water samples were taken from four main rivers, collected upstream and downstream of major cities in 2016. For subtyping and comparison, public core genome multi locus sequence typing (cgMLST) schemes were used. The presence of AMR genes, virulence genes and plasmids was extracted from whole genome sequence (WGS) data. In total three ESBL-producing strains and two carbapenem resistant strains were isolated. WGS based comparison of these five water isolates to 95 clinical isolates identified three clusters. Cluster 1 (ST11) and cluster 2 (ST985) consisted of doublets of carbapenem resistant strains (one water and one clinical isolate each). Cluster 3 (ST405) consisted of three ESBL-producing strains isolated from one water sample and two clinical specimens. The cities, in which patient isolates of cluster 2 and 3 were collected, were in concordance with the water sampling locations downstream from these cities. The genetic concordance between isolates from river water samples and patient isolates raises concerns regarding the release of wastewater treatment plant effluents into surface water. From a public health perspective these findings demand attention and strategies are required to minimize the spread of multiresistant strains to the environment.
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Affiliation(s)
- Sarah Lepuschitz
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Vienna, Austria; TU Wien, Research Area of Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering, Vienna, Austria.
| | - Simone Schill
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Vienna, Austria
| | - Anna Stoeger
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Vienna, Austria
| | - Shiva Pekard-Amenitsch
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Vienna, Austria
| | - Steliana Huhulescu
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Vienna, Austria
| | - Norbert Inreiter
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Vienna, Austria
| | - Rainer Hartl
- Ordensklinikum Linz Elisabethinen, Institute of Hygiene, Microbiology and Tropical Medicine, National Reference Centre for Nosocomial Infections and Antimicrobial Resistance, Linz, Austria
| | - Heidrun Kerschner
- Ordensklinikum Linz Elisabethinen, Institute of Hygiene, Microbiology and Tropical Medicine, National Reference Centre for Nosocomial Infections and Antimicrobial Resistance, Linz, Austria
| | - Sieglinde Sorschag
- Department of Hospital Hygiene and Infectious Diseases, Community-Hospital Klagenfurt am Wörthersee, Klagenfurt, Austria
| | - Burkhard Springer
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Vienna, Austria
| | - Sylvain Brisse
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Franz Allerberger
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Vienna, Austria
| | - Robert L Mach
- TU Wien, Research Area of Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering, Vienna, Austria
| | - Werner Ruppitsch
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Vienna, Austria; University of Natural Resources and Life Sciences, Department of Biotechnology, Vienna, Austria
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Affiliation(s)
- M M G Leeflang
- Amsterdam UMC, University of Amsterdam, Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam Public Health, Amsterdam, Netherlands
| | - F Allerberger
- Division of Public Health, Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
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Cabal A, Schmid D, Lepuschitz S, Stöger A, Blaschitz M, Allerberger F, Ruppitsch W, Hell M. Nosocomial outbreak of Streptococcus pyogenes puerperal sepsis. Clin Microbiol Infect 2019; 25:521-523. [DOI: 10.1016/j.cmi.2018.11.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/14/2018] [Accepted: 11/30/2018] [Indexed: 10/27/2022]
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