{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T03:14:15Z","timestamp":1789614855626,"version":"build-2803163510"},"reference-count":34,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,5,15]],"date-time":"2023-05-15T00:00:00Z","timestamp":1684108800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"<jats:p>Sequence-based typing (SBT) of <jats:italic>Legionella pneumophila<\/jats:italic> is a valuable tool in epidemiological studies and outbreak investigations of Legionnaires\u2019 disease. In the <jats:italic>L. pneumophila<\/jats:italic> SBT scheme, <jats:italic>mompS2<\/jats:italic> is one of seven genes that determine the sequence type (ST). The <jats:italic>Legionella<\/jats:italic> genome typically contains two copies of <jats:italic>mompS (mompS1<\/jats:italic> and <jats:italic>mompS2).<\/jats:italic> When they are non-identical it can be challenging to determine the <jats:italic>mompS2<\/jats:italic> allele, and subsequently the ST, from Illumina short-reads. In our collection of 233 <jats:italic>L. pneumophila<\/jats:italic> genomes, there were 62 STs, 18 of which carried non-identical <jats:italic>mompS<\/jats:italic> copies. Using short-reads, the <jats:italic>mompS2<\/jats:italic> allele was misassembled or untypeable in several STs. Genomes belonging to ST154 and ST574, which carried <jats:italic>mompS1<\/jats:italic> allele 7 and <jats:italic>mompS2<\/jats:italic> allele 15, were assigned an incorrect <jats:italic>mompS2<\/jats:italic> allele and\/or <jats:italic>mompS<\/jats:italic> gene copy number when short-read assembled. For other isolates, mainly those carrying non-identical <jats:italic>mompS<\/jats:italic> copies, short-read assemblers occasionally failed to resolve the structure of the <jats:italic>mompS-<\/jats:italic>region, also resulting in untypeability from the short-read data. In this study, we wanted to understand the challenges we observed with calling the <jats:italic>mompS<\/jats:italic>2 allele from short-reads, assess if other short-read methods were able to resolve the <jats:italic>mompS<\/jats:italic>-region, and investigate the possibility of using long-reads to obtain the <jats:italic>mompS<\/jats:italic> alleles, and thereby perform <jats:italic>L. pneumophila<\/jats:italic> SBT from long-reads only. We found that the choice of short-read assembler had a major impact on resolving the <jats:italic>mompS<\/jats:italic>-region and thus SBT from short-reads, but no method consistently solved the <jats:italic>mompS2<\/jats:italic> allele. By using Oxford Nanopore Technology (ONT) sequencing together with Trycycler and Medaka for long-read assembly and polishing we were able to resolve the <jats:italic>mompS<\/jats:italic> copies and correctly identify the <jats:italic>mompS2<\/jats:italic> allele, in accordance with Sanger sequencing\/EQA results for all tested isolates (n=35). The remaining six genes of the SBT profile could also be determined from the ONT-only reads. The STs called from ONT-only assemblies were also consistent with hybrid-assemblies of Illumina and ONT reads. We therefore propose ONT sequencing as an alternative method to perform <jats:italic>L. pneumophila<\/jats:italic> SBT to overcome the <jats:italic>mompS<\/jats:italic> challenge observed with short-reads. To facilitate this, we have developed ONTmompS (<jats:ext-link>https:\/\/github.com\/marithetland\/ONTmompS<\/jats:ext-link>), an <jats:italic>in silico<\/jats:italic> approach to determine <jats:italic>L. pneumophila<\/jats:italic> ST from long-read or hybrid assemblies.<\/jats:p>","DOI":"10.3389\/fcimb.2023.1176182","type":"journal-article","created":{"date-parts":[[2023,5,15]],"date-time":"2023-05-15T14:54:04Z","timestamp":1684162444000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":4,"title":["Long-read sequencing for reliably calling the mompS allele in Legionella pneumophila sequence-based typing"],"prefix":"10.3389","volume":"13","author":[{"given":"Anne Vatland","family":"Kr\u00f8vel","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marit A. 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