Genomic characterization and assessment of pathogenic potential of Legionella spp. isolates from environmental monitoring

Abstract

Several species in the genus Legionella are known to cause an acute pneumonia when the aerosols containing the bacteria from man-made water systems are inhaled. The disease is usually caused by Legionella pneumophila, but other species have been implicated in the infection. The disease is frequently manifested as an outbreak, which means several people are affected when exposed to the common source of Legionella contamination. Therefor environmental surveillance which includes isolation and identification of Legionella is performed routinely. However, usually no molecular or genome-based methods are employed in further characterization of the isolates during routine environmental monitoring. During several years of such monitoring, isolates from different geographical locations were collected and 39 of them were sequenced by hybrid de novo approach utilizing short and long sequencing reads. In addition, the isolates were typed by standard culture and MALDI-TOF method. The sequencing reads were assembled and annotated to produce high-quality genomes. By employing discriminatory genome typing, four potential new species in the Legionella genus were identified, which are yet to be biochemically and morphologically characterized. Moreover, functional annotations concerning virulence and antimicrobial resistance were performed on the sequenced genomes. The study contributes to the knowledge on little-known non-pneumophila species present in man-made water systems and establishes support for future genetic relatedness studies as well as understanding of their pathogenic potential.

Legionella pneumophila Presence in Dental Unit Waterlines: A Cultural and Molecular Investigation in the West Bank, Palestine

“…A comparison with the international 16S rRNA and the sequenced L. pneumophila from DUWL in the West Bank showed that L. pneumophila was clearly identified and distinguished from other species. L. pneumophila is forming a distinct clade, allowing the design of species-specific primers and probes [2,45,49,50]. This demonestrates the higher discriminatory power and effective resolution of using L. pneumophila-specific primer in this study.…”

Characterization of a Novel Species of Legionella Isolated from a Healthcare Facility: Legionella resiliens sp. nov

“…The FEZ-1 gene is also associated with the resistance of carbapenem, cephalosporin, and penam antibiotics. Despite that, they are not conventionally used for legionellosis treatment, and the same resistance has already been reported for L. gormanii and L. anisa [ 81 , 82 ].…”

Genome characterisation and comparative analysis of Schaalia dentiphila sp. nov. and its subspecies, S. dentiphila subsp. denticola subsp. nov., from the human oral cavity

“…Specifically, strain NCTC 9931 demonstrated overlaps of 1,845, 1,512, and 1,776 orthologous gene clusters with strain C24, Schaalia meyeri DSM 20733 T , and Schaalia odontolytica NCTC 9935 T , respectively. Singletons were found to be most abundant in Schaalia odontolytica NCTC 9935 T [155], followed by strain NCTC 9931 [86], Schaalia meyeri DSM 20733 T [106], and strain C24 [ 67 ] (Table S3). When juxtaposed, strains NCTC 9931 and C24 exhibited 51 and 36 exclusive unique gene clusters, respectively, underscoring their evolutionary and functional disparities.…”

“…However, a consensus on the protein sequence identity threshold for pangenome analysis remains elusive. While many studies default to a 50% blastp threshold [ 64 – 67 ], our analyses (both BPGA and Roary) employed a stringent 95% blastp threshold [ 54 , 68 ], which ensures that only sequences with very high similarity are deemed homologous. Given the close evolutionary ties and subtle differences expected between NCTC 9931 and C24, a higher threshold may help in discerning highly conserved core genes from accessory and unique genes, minimizing false positives [ 68 , 69 ].…”