Abstract
Legionella pneumophila serogroup 1 (Lp1) sequence type (ST) 23 is one of the most commonly detected STs in Italy where it currently causes all investigated outbreaks. ST23 has caused both epidemic and sporadic cases between 1995 and 2018 and was analysed at genomic level and compared with ST23 isolated in other countries to determine possible similarities and differences. A core genome multi-locus sequence typing (cgMLST), based on a previously described set of 1,521 core genes, and single-nucleotide polymorphisms (SNPs) approaches were applied to an ST23 collection including genomes from Italy, France, Denmark and Scotland. DNAs were automatically extracted, libraries prepared using NextEra library kit and MiSeq sequencing performed. Overall, 63 among clinical and environmental Italian Lp1 isolates and a further seven and 11 ST23 from Denmark and Scotland, respectively, were sequenced, and pangenome analysed. Both cgMLST and SNPs analyses showed very few loci and SNP variations in ST23 genomes. All the ST23 causing outbreaks and sporadic cases in Italy and elsewhere, were phylogenetically related independent of year, town or country of isolation. Distances among the ST23s were further shortened when SNPs due to horizontal gene transfers were removed. The Lp1 ST23 isolated in Italy have kept their monophyletic origin, but they are phylogenetically close also to ST23 from other countries. The ST23 are quite widespread in Italy, and a thorough epidemiological investigation is compelled to determine sources of infection when this ST is identified in both LD sporadic cases and outbreaks.
Highlights
Legionnaires’ disease (LD) is a severe pneumonia caused by bacteria belonging to the Legionella genus with the most cases due to Legionella pneumophila serogroup 1 (Lp1) (Gomez-Valero & Buchrieser, 2019)
Based on the previously published core genome multi-locus sequence typing (cgMLST) scheme (Moran-Gilad et al, 2015), cgMLST profiles were determined on the basis of the set of 1,362 cgMLST targets shared by the 44 genomes which had caused outbreaks in Italy, including 29 from Bresso, five from Rome, seven from Cesano Maderno, and three from Lazise, and a minimum spanning tree was constructed (Fig 1)
This study demonstrated that the ST23 responsible for the two outbreaks occurred in Bresso in 2014 and 2018 were genetically very similar
Summary
Legionnaires’ disease (LD) is a severe pneumonia caused by bacteria belonging to the Legionella genus with the most cases due to Legionella pneumophila serogroup 1 (Lp1) (Gomez-Valero & Buchrieser, 2019). In Europe between 2018 and 2019, the LD incidence was 2.2 per 100,000 inhabitants, showing an increasing trend compared with previous years (European Centre for Disease Prevention and Control, 2020). According to the ECDC surveillance atlas of 2019, Italy reported the highest incidence equal to 5,29 per 100,000 inhabitants and the highest number of LD cases in the EU (n = 3,143). In 2020, the number of cases decreased by 35% compared with 2019, but Italy still had the highest number of reported cases in the EU. The decline might be correlated with the COVID-19 pandemic which led to travel restrictions (fewer travel-associated cases), worldwide government instigated lockdowns and to wearing masks in public areas. The decline might be correlated with the COVID-19 pandemic which led to travel restrictions (fewer travel-associated cases), worldwide government instigated lockdowns and to wearing masks in public areas. (https://atlas.ecdc.europa.eu/public/index.aspx)
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