Browsing by Author "Cormican, Martin"
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- Emergence of ST131 carrying carbapenemase genes, European Union/European Economic Area, August 2012 to May 2024Publication . Kohlenberg, Anke; Svartström, Olov; Apfalter, Petra; Hartl, Rainer; Bogaerts, Pierre; Huang, Te-Din; Chudejova, Katerina; Malisova, Lucia; Eisfeld, Jessica; Sandfort, Mirco; Hammerum, Anette M.; Roer, Louise; Räisänen, Kati; Dortet, Laurent; Bonnin, Rémy A.; Tóth, Ákos; Tóth, Kinga; Clarke, Christina; Cormican, Martin; Griškevičius, Algirdas; Khonyongwa, Kirstin; Meo, Marie; Niedre-Otomere, Baiba; Vangravs, Reinis; Hendrickx, Antoni Pa; Notermans, Daan W; Samuelsen, Ørjan; Caniça, Manuela; Manageiro, Vera; Müller, Vilhelm; Mäkitalo, Barbro; Kramar, Urška; Pirs, Mateja; Palm, Daniel; Monnet, Dominique L.; Alm, Erik; Linkevicius, MariusAnalysis of 594 isolates of sequence type (ST)131 and its single locus variants carrying carbapenemase genes from 17 European Union/European Economic Area countries revealed acquisition of 18 carbapenemase variants, mainly in ST131 clades A and C. Most frequent were (n = 230) and (n = 224), detected in 14 and 12 countries, respectively. Isolates carrying have increased rapidly since 2021. The increasing detection of carbapenemase genes in the high-risk lineage ST131 is a public health concern.
- Rapid cross-border emergence of NDM-5-producing Escherichia coli in the European Union/European Economic Area, 2012 to June 2022Publication . Linkevicius, Marius; Bonnin, Rémy A.; Alm, Erik; Svartström, Olov; Apfalter, Petra; Hartl, Rainer; Hasman, Henrik; Roer, Louise; Räisänen, Kati; Dortet, Laurent; Pfennigwerth, Niels; Hans, Jörg B.; Tóth, Ákos; Buzgó, Lilla; Cormican, Martin; Delappe, Niall; Monaco, Monica; Giufrè, Maria; Hendrickx, Antoni P.A.; Samuelsen, Ørjan; Pöntinen, Anna K.; Caniça, Manuela; Manageiro, Vera; Oteo-Iglesias, Jesús; Pérez-Vázquez, María; Westmo, Karin; Mäkitalo, Barbro; Palm, Daniel; Monnet, Dominique L.; Kohlenberg, AnkeWhole genome sequencing data of 874 Escherichia coli isolates carrying bla NDM-5 from 13 European Union/European Economic Area countries between 2012 and June 2022 showed the predominance of sequence types ST167, ST405, ST410, ST361 and ST648, and an increasing frequency of detection. Nearly a third (30.6%) of these isolates were associated with infections and more than half (58.2%) were predicted to be multidrug-resistant. Further spread of E. coli carrying bla NDM-5 would leave limited treatment options for serious E. coli infections.
- Retrospective validation of whole genome sequencing-enhanced surveillance of listeriosis in Europe, 2010 to 2015Publication . Van Walle, Ivo; Björkman, Jonas Torgny; Cormican, Martin; Dallman, Timothy; Mossong, Joël; Moura, Alexandra; Pietzka, Ariane; Ruppitsch, Werner; Takkinen, Johanna; European Listeria Wgs Typing GroupBackground and aim: The trend in reported case counts of invasive Listeria monocytogenes (Lm), a potentially severe food-borne disease, has been increasing since 2008. In 2015, 2,224 cases were reported in the European Union/European Economic Area (EU/ EEA). We aimed to validate the microbiological and epidemiological aspects of an envisaged EU/EEAwide surveillance system enhanced by routine whole genome sequencing (WGS). Methods: WGS and core genome multilocus sequence typing (cgMLST) were performed on isolates from 2,726 cases from 27 EU/ EEA countries from 2010–15. Results: Quality controls for contamination, mixed Lm cultures and sequence quality classified nearly all isolates with a minimum average coverage of the genome of 55x as acceptable for analysis. Assessment of the cgMLST variation between six different pipelines revealed slightly less variation associated with assembly-based analysis compared to reads-based analysis. Epidemiological concordance, based on 152 isolates from 19 confirmed outbreaks and a cluster cutoff of seven allelic differences, was good (sensitivity > 95% for two cgMLST schemes of 1,748 and 1,701 loci each; PPV 58–68%). The proportion of sporadic cases was slightly below 50%. Of remaining isolates, around one third were in clusters involving more than one country, often spanning several years. Detection of multi-country clusters was on average several months earlier when pooling the data at EU/EEA level, compared with first detection at national level. Conclusions: These findings provide a good basis for comprehensive EU/EEA-wide, WGS-enhanced surveillance of listeriosis. Time limits should not be used for hypothesis generation during outbreak investigations, but should be for analytical studies.