{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T07:19:46Z","timestamp":1790752786630,"version":"4.1.0"},"reference-count":69,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2023,2,10]],"date-time":"2023-02-10T00:00:00Z","timestamp":1675987200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["HO-930\/5-1\/2"],"award-info":[{"award-number":["HO-930\/5-1\/2"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["STE 838\/12-1"],"award-info":[{"award-number":["STE 838\/12-1"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Hildegard-Elisabeth Foundation","award":["HO-930\/5-1\/2"],"award-info":[{"award-number":["HO-930\/5-1\/2"]}]},{"name":"Hildegard-Elisabeth Foundation","award":["STE 838\/12-1"],"award-info":[{"award-number":["STE 838\/12-1"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Legionella pneumophila is an environmental bacterium and clinical pathogen that causes many life-threating outbreaks of an atypical pneumonia called Legionnaires\u2019 disease (LD). Studies of this pathogen have focused mainly on Europe and the United States. A shortage in L. pneumophila data is clearly observed for developing countries. To reduce this knowledge gap, L. pneumophila isolates were studied in two widely different geographical areas, i.e., the West Bank and Germany. For this study, we sequenced and compared the whole genome of 38 clinical and environmental isolates of L. pneumophila covering different MLVA-8(12) genotypes in the two areas. Sequencing was conducted using the Illumina HiSeq 2500 platform. In addition, two isolates (A194 and H3) were sequenced using a Pacific Biosciences (PacBio) RSII platform to generate complete reference genomes from each of the geographical areas. Genome sequences from 55 L. pneumophila strains, including 17 reference strains, were aligned with the genome sequence of the closest strain (L. pneumophila strain Alcoy). A whole genome phylogeny based on single nucleotide polymorphisms (SNPs) was created using the ParSNP software v 1.0. The reference genomes obtained for isolates A194 and H3 consisted of circular chromosomes of 3,467,904 bp and 3,691,263 bp, respectively. An average of 36,418 SNPs (min. 8569, max. 70,708 SNPs) against our reference strain L. pneumophila str. Alcoy, and 2367 core-genes were identified among the fifty-five strains. An analysis of the genomic population structure by SNP comparison divided the fifty-five L. pneumophila strains into six branches. Individual isolates in sub-lineages in these branches differed by less than 120 SNPs if they had the same MLVA genotype and were isolated from the same location. A bioinformatics analysis identified the genomic islands (GIs) for horizontal gene transfer and mobile genetic elements, demonstrating that L. pneumophila showed high genome plasticity. Four L. pneumophila isolates (H3, A29, A129 and L10-091) contained well-defined plasmids. On average, only about half of the plasmid genes could be matched to proteins in databases. In silico phage findings suggested that 43 strains contained at least one phage. However, none of them were found to be complete. BLASTp analysis of proteins from the type IV secretion Dot\/Icm system showed those proteins highly conserved, with less than 25% structural differences in the new L. pneumophila isolates. Overall, we demonstrated that whole genome sequencing provides a molecular surveillance tool for L. pneumophila at the highest conceivable discriminatory level, i.e., two to eight SNPs were observed for isolates from the same location but several years apart.<\/jats:p>","DOI":"10.3390\/microorganisms11020449","type":"journal-article","created":{"date-parts":[[2023,2,10]],"date-time":"2023-02-10T03:52:49Z","timestamp":1676001169000},"page":"449","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Comparative Genomics of Legionella pneumophila Isolates from the West Bank and Germany Support Molecular Epidemiology of Legionnaires\u2019 Disease"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4327-6168","authenticated-orcid":false,"given":"Ashraf R.","family":"Zayed","sequence":"first","affiliation":[{"name":"Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus P.O. Box 7, Palestine"},{"name":"Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany"},{"name":"Microbiology Research Laboratory, Faculty of Medicine, Al-Quds University, Abu-Dies, East Jerusalem 9993100, Palestine"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dina M.","family":"Bitar","sequence":"additional","affiliation":[{"name":"Microbiology Research Laboratory, Faculty of Medicine, Al-Quds University, Abu-Dies, East Jerusalem 9993100, Palestine"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9197-6305","authenticated-orcid":false,"given":"Michael","family":"Steinert","sequence":"additional","affiliation":[{"name":"Institut f\u00fcr Mikrobiologie, Technische Universit\u00e4t Braunschweig, 38106 Braunschweig, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christian","family":"L\u00fcck","sequence":"additional","affiliation":[{"name":"Medical Faculty Carl Gustav Carus, Institute for Virology, Technische Universit\u00e4t Dresden, 01307 Dresden, Germany"},{"name":"Medical Faculty Carl Gustav Carus, Institute for Medical Microbiology and Hygiene, Technische Universit\u00e4t Dresden, 01307 Dresden, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cathrin","family":"Spr\u00f6er","sequence":"additional","affiliation":[{"name":"Leibniz Institute-German Collections of Microorganisms and Cell Cultures DSMZ GmbH, 38124 Braunschweig, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ingrid","family":"Brettar","sequence":"additional","affiliation":[{"name":"Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany"},{"name":"Hildegard-Elisabeth Foundation, 66271 Saarbr\u00fccken, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manfred G.","family":"H\u00f6fle","sequence":"additional","affiliation":[{"name":"Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany"},{"name":"Hildegard-Elisabeth Foundation, 66271 Saarbr\u00fccken, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8420-8161","authenticated-orcid":false,"given":"Boyke","family":"Bunk","sequence":"additional","affiliation":[{"name":"Leibniz Institute-German Collections of Microorganisms and Cell Cultures DSMZ GmbH, 38124 Braunschweig, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,2,10]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1128\/CMR.15.3.506-526.2002","article-title":"Legionella and Legionnaires\u2019 disease: 25 years of investigation","volume":"15","author":"Fields","year":"2002","journal-title":"Clin. 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