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- Volume 25, Issue 20, 21/May/2020
Eurosurveillance - Volume 25, Issue 20, 21 May 2020
Volume 25, Issue 20, 2020
- Editorial
- Rapid communication
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Cross-border spread of blaNDM-1- and blaOXA-48-positive Klebsiella pneumoniae: a European collaborative analysis of whole genome sequencing and epidemiological data, 2014 to 2019
Catherine Ludden , Felix Lötsch , Erik Alm , Narender Kumar , Karin Johansson , Barbara Albiger , Te-Din Huang , Olivier Denis , Anette M Hammerum , Henrik Hasman , Jari Jalava , Kati Räisänen , Laurent Dortet , Agnès B Jousset , Sören Gatermann , Sebastian Haller , Martin Cormican , Wendy Brennan , Maria Del Grosso , Monica Monaco , Leo Schouls , Ørjan Samuelsen , Mateja Pirš , Tjaša Cerar , Jésus Oteo-Iglesias , Maria Pérez-Vázquez , Karin Sjöström , Petra Edquist , Katie L Hopkins , Marc J Struelens , Daniel Palm , Dominique L Monnet and Anke KohlenbergAnalysis of sequencing data for 143 blaNDM-1- and blaOXA-48-positive Klebsiella pneumoniae isolates from 13 European national collections and the public domain resulted in the identification of 15 previously undetected multi-country transmission clusters. For 10 clusters, cases had prior travel/hospitalisation history in countries outside of the European Union including Egypt, Iran, Morocco, Russia, Serbia, Tunisia and Turkey. These findings highlight the benefit of European whole genome sequencing-based surveillance and data sharing for control of antimicrobial resistance.
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- Research
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Multilevel genome typing: genomics-guided scalable resolution typing of microbial pathogens
BackgroundBoth long- and short-term epidemiology are fundamental to disease control and require accurate bacterial typing. Genomic data resulting from implementation of whole genome sequencing in many public health laboratories can potentially provide highly sensitive and accurate descriptions of strain relatedness. Previous typing efforts using these data have mainly focussed on outbreak detection.
AimWe aimed to develop multilevel genome typing (MGT), using consecutive multilocus sequence typing (MLST) schemes of increasing sizes, stepping up from seven-gene MLST to core genome MLST, to allow examination of genetic relatedness at multiple resolution levels.
MethodsThe system was applied to Salmonellaenterica serovar Typhimurium. The MLST scheme used at each step (MGT level), defined a given MGT-level specific sequence type (ST). The list of STs generated from all of these increasing MGT levels, was named a genome type (GT). Using MGT, we typed 9,096 previously characterised isolates with publicly available data.
ResultsOur approach could identify previously described S. Typhimurium populations, such as the DT104 multidrug resistance lineage (GT 19-2-11) and two invasive lineages of African isolates (GT 313-2-3 and 313-2-752). Further, we showed that MGT-derived clusters can accurately distinguish five outbreaks from each other and five background isolates.
ConclusionMGT provides a universal and stable nomenclature at multiple resolutions for S. Typhimurium strains and could be implemented as an internationally standardised strain identification system. While established so far only for S. Typhimurium, the results here suggest that MGT could form the basis for typing systems in other similar microorganisms.
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- Outbreaks
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Large community-acquired Legionnaires’ disease outbreak caused by Legionella pneumophila serogroup 1, Italy, July to August 2018
Marino Faccini , Antonio Giampiero Russo , Maira Bonini , Sara Tunesi , Rossella Murtas , Monica Sandrini , Sabrina Senatore , Anna Lamberti , Giorgio Ciconali , Serafina Cammarata , Eros Barrese , Valentina Ceriotti , Sonia Vitaliti , Marina Foti , Gabriella Gentili , Elisabetta Graziano , Emerico Panciroli , Marco Bosio , Maria Gramegna , Danilo Cereda , Carlo Federico Perno , Ester Mazzola , Daniela Campisi , Gianuario Aulicino , Silvana Castaldi , Antonietta Girolamo , Maria Grazia Caporali , Maria Scaturro , Maria Cristina Rota and Maria Luisa RicciIn July 2018, a large outbreak of Legionnaires’ disease (LD) caused by Legionella pneumophila serogroup 1 (Lp1) occurred in Bresso, Italy. Fifty-two cases were diagnosed, including five deaths. We performed an epidemiological investigation and prepared a map of the places cases visited during the incubation period. All sites identified as potential sources were investigated and sampled. Association between heavy rainfall and LD cases was evaluated in a case-crossover study. We also performed a case–control study and an aerosol dispersion investigation model. Lp1 was isolated from 22 of 598 analysed water samples; four clinical isolates were typed using monoclonal antibodies and sequence-based typing. Four Lp1 human strains were ST23, of which two were Philadelphia and two were France-Allentown subgroup. Lp1 ST23 France-Allentown was isolated only from a public fountain. In the case-crossover study, extreme precipitation 5–6 days before symptom onset was associated with increased LD risk. The aerosol dispersion model showed that the fountain matched the case distribution best. The case–control study demonstrated a significant eightfold increase in risk for cases residing near the public fountain. The three studies and the matching of clinical and environmental Lp1 strains identified the fountain as the source responsible for the epidemic.
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Volumes & issues
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Volume 29 (2024)
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Volume 28 (2023)
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Volume 27 (2022)
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Volume 26 (2021)
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Volume 25 (2020)
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Volume 24 (2019)
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Volume 23 (2018)
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Volume 22 (2017)
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Volume 21 (2016)
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Volume 20 (2015)
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Volume 19 (2014)
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Volume 18 (2013)
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Volume 17 (2012)
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Volume 16 (2011)
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Volume 15 (2010)
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Volume 14 (2009)
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Volume 13 (2008)
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Volume 12 (2007)
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Volume 11 (2006)
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Volume 10 (2005)
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Volume 9 (2004)
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Volume 8 (2003)
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Volume 7 (2002)
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Volume 6 (2001)
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Volume 5 (2000)
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Volume 4 (1999)
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Volume 3 (1998)
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Volume 2 (1997)
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Volume 1 (1996)
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Volume 0 (1995)
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Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR
Victor M Corman , Olfert Landt , Marco Kaiser , Richard Molenkamp , Adam Meijer , Daniel KW Chu , Tobias Bleicker , Sebastian Brünink , Julia Schneider , Marie Luisa Schmidt , Daphne GJC Mulders , Bart L Haagmans , Bas van der Veer , Sharon van den Brink , Lisa Wijsman , Gabriel Goderski , Jean-Louis Romette , Joanna Ellis , Maria Zambon , Malik Peiris , Herman Goossens , Chantal Reusken , Marion PG Koopmans and Christian Drosten
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