Population Genomics of<i>Legionella longbeachae</i>and Hidden Complexities of Infection Source Attribution

Bacigalupe, Rodrigo; Lindsay, Diane; Edwards, Giles; Fitzgerald, J. Ross

doi:10.3201/eid2305.161165

Cited by 17 publications

(25 citation statements)

References 33 publications

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“…Interestingly, comparative analysis of the plasmid sequences with those previously identified in other Legionella spp., showed that the 122-kb plasmid (CP025493) contained a 40,243-bp fragment of the L. longbeachae NSW150 plasmid, providing further evidence of gene transfer across Legionella spp. through mosaic plasmids, as first suggested by Bacigalupe et al ( 7 ).…”

Section: Genome Announcementmentioning

confidence: 81%

Complete Genome Sequence of Legionella sainthelensi Isolated from a Patient with Legionnaires’ Disease

et al. 2018

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Section: Genome Announcementmentioning

confidence: 81%

Complete Genome Sequence of Legionella sainthelensi Isolated from a Patient with Legionnaires’ Disease

et al. 2018

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“…Some reasons may explain the discrepancy. On one hand, L. longbeachae is commonly isolated from compost and potting mixes ( 7 ). The composition of commercial potting mix used in different countries is different ( 8 ).…”

Section: Case Reportmentioning

confidence: 99%

Epileptic Seizure after Use of Moxifloxacin in Man with Legionella longbeachae Pneumonia

Wang¹,

Li²,

Chen³

et al. 2020

Emerg. Infect. Dis.

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Legionellosis caused by Legionella longbeachae is diagnosed mainly by PCR. We report a case of L. longbeachae infection in mainland China, which was diagnosed by metagenomic next-generation sequencing, in a man who developed an epileptic seizure after using moxifloxacin. Metagenomic next-generation sequencing may be a useful tool to detect Legionella spp.

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“…The recent emergence of L. longbeachae as an important cause of LD in Europe and the UK [15], particularly a 2013 outbreak in Scotland [16], prompted concerted efforts in genomic sequencing. This has resulted in a substantial increase in the amount of available genomic data with a large-scale sequencing project of 64 clinical and environmental isolates being reported in 2017 [17]. The availability of a much larger amount of sequence data has revealed further complexity in the L. longbeachae genome; variation is driven largely by extensive intra-species horizontal gene transfer and recombination, and there is evidence that there is inter-species gene transfer via plasmids that are the result of recombination between various plasmids of the different Legionella species.…”

Section: Introductionmentioning

confidence: 99%

“…The availability of a much larger amount of sequence data has revealed further complexity in the L. longbeachae genome; variation is driven largely by extensive intra-species horizontal gene transfer and recombination, and there is evidence that there is inter-species gene transfer via plasmids that are the result of recombination between various plasmids of the different Legionella species. [17]. Two more complete genomes have also been sequenced, including for the ATCC type strain from one of the first reported cases of LD caused by L. longbeachae in Long Beach, California in 1980 (GenBank: FDAARGOS_201; [18]) and one we have obtained from a NZ patient hospitalised with LD in 2014 (F1157CHC; GenBank NZ_CP020894; [19]) that was sequenced as part of this study.…”

Section: Introductionmentioning

confidence: 99%

“…Although the available genomic data to date have provided valuable information about the biology [10] and genetic diversity [17] of L. longbeachae , there is scope for further large-scale genomic sequencing in order to more fully assess genetic relationships, determine changes over time and define regions that are important for virulence and pathogenesis. Given the clinical significance of L. longbeachae in NZ, particularly the sg1 strain, we have obtained the genome sequence of 54 sg1 clinical isolates, including one complete NZ reference genome [19] and its associated epigenomic data.…”

Section: Introductionmentioning

confidence: 99%

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Characterising the methylome of Legionella longbeachae serogroup 1 clinical isolates and assessing geo-temporal genetic diversity

Slow

Anderson

Murdoch

et al. 2020

Preprint

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Legionella longbeachae is an environmental bacterium that is commonly found in soil and composted plant material. In New Zealand (NZ) it is the most clinically significant Legionella species causing around two-thirds of all notified cases of Legionnaires’ disease. Here we report the sequencing and analysis of the geo-temporal genetic diversity of 54 L. longbeachae serogroup 1 (sg1) clinical isolates that were derived from cases from around NZ over a 22-year period, including one complete genome and its associated methylome.Our complete genome consisted of a 4.1 Mb chromosome and a 108 kb plasmid. The genome was highly methylated with two known epigenetic modifications, m4C and m6A, occurring in particular sequence motifs within the genome. Phylogenetic analysis demonstrated the 54 sg1 isolates belonged to two main clades that last shared a common ancestor between 108 BCE and 1608 CE. These isolates also showed diversity at the genome-structural level, with large-scale arrangements occurring in some regions of the chromosome and evidence of extensive chromosomal and plasmid recombination. This includes the presence of plasmids derived from recombination and horizontal gene transfer between various Legionella species, indicating there has been both intra-species and inter-species gene flow. However, because similar plasmids were found among isolates within each clade, plasmid recombination events may pre-empt the emergence of new L. longbeachae strains.Our high-quality reference genome and extensive genetic diversity data will serve as a platform for future work linking genetic, epigenetic and functional diversity in this globally important emerging environmental pathogen.Author SummaryLegionnaires’ disease is a serious, sometimes fatal pneumonia caused by bacteria of the genus Legionella. In New Zealand, the species that causes the majority of disease is Legionella longbeachae. Although the analyses of pathogenic bacterial genomes is an important tool for unravelling evolutionary relationships and identifying genes and pathways that are associated with their disease-causing ability, until recently genomic data for L. longbeachae has been sparse. Here, we conducted a large-scale genomic analysis of 54 L. longbeachae isolates that had been obtained from people hospitalised with Legionnaires’ disease between 1993 and 2015 from 8 regions around New Zealand. Based on our genome analysis the isolates could be divided into two main groups that persisted over time and last shared a common ancestor up to 1700 years ago. Analysis of the bacterial chromosome revealed areas of high modification through the addition of methyl groups and these were associated with particular DNA sequence motifs. We also found there have been large-scale rearrangements in some regions of the chromosome, producing variability between the different L. longbeacahe strains, as well as evidence of gene-flow between the various Legionella species via the exchange of plasmid DNA.

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Population Genomics ofLegionella longbeachaeand Hidden Complexities of Infection Source Attribution

Cited by 17 publications

References 33 publications

Complete Genome Sequence of Legionella sainthelensi Isolated from a Patient with Legionnaires’ Disease

Complete Genome Sequence of Legionella sainthelensi Isolated from a Patient with Legionnaires’ Disease

Epileptic Seizure after Use of Moxifloxacin in Man with Legionella longbeachae Pneumonia

Characterising the methylome of Legionella longbeachae serogroup 1 clinical isolates and assessing geo-temporal genetic diversity

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