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Kanatani JI, Isobe J, Norimoto S, Kimata K, Mitsui C, Amemura-Maekawa J, Kura F, Sata T, Watahiki M. Prevalence of Legionella species isolated from shower water in public bath facilities in Toyama Prefecture, Japan. J Infect Chemother 2017; 23:265-270. [PMID: 28188095 DOI: 10.1016/j.jiac.2017.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 01/04/2017] [Accepted: 01/14/2017] [Indexed: 11/20/2022]
Abstract
AIMS We investigated the prevalence of Legionella spp. isolated from shower water in public bath facilities in Toyama Prefecture, Japan. In addition, we analyzed the genetic diversity among Legionella pneumophila isolates from shower water as well as the genetic relationship between isolates from shower water and from stock strains previously analyzed from sputum specimens. METHODS The isolates were characterized using serogrouping, 16S rRNA gene sequencing, and sequence-based typing. RESULTS Legionella spp. were isolated from 31/91 (34.1%) samples derived from 17/37 (45.9%) bath facilities. Isolates from shower water and bath water in each public bath facility were serologically or genetically different, indicating that we need to isolate several L. pneumophila colonies from both bath and shower water to identify public bath facilities as sources of legionellosis. The 61 L. pneumophila isolates from shower water were classified into 39 sequence types (STs) (index of discrimination = 0.974), including 19 new STs. Among the 39 STs, 12 STs match clinical isolates in the European Working Group for Legionella Infections database. Notably, ST505 L. pneumophila SG 1, a strain frequently isolated from patients with legionellosis and from bath water in this area, was isolated from shower water. CONCLUSIONS Pathogenic L. pneumophila strains including ST505 strain were widely distributed in shower water in public bath facilities, with genetic diversity showing several different origins. This study highlights the need to isolate several L. pneumophila colonies from both bath water and shower water to identify public bath facilities as infection sources in legionellosis cases.
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Affiliation(s)
- Jun-Ichi Kanatani
- Department of Bacteriology, Toyama Institute of Health, 17-1 Nakataikoyama, Imizu-City, Toyama 939-0363, Japan.
| | - Junko Isobe
- Department of Bacteriology, Toyama Institute of Health, 17-1 Nakataikoyama, Imizu-City, Toyama 939-0363, Japan
| | - Shiho Norimoto
- Department of Bacteriology, Toyama Institute of Health, 17-1 Nakataikoyama, Imizu-City, Toyama 939-0363, Japan
| | - Keiko Kimata
- Department of Bacteriology, Toyama Institute of Health, 17-1 Nakataikoyama, Imizu-City, Toyama 939-0363, Japan
| | - Chieko Mitsui
- Department of Bacteriology, Toyama Institute of Health, 17-1 Nakataikoyama, Imizu-City, Toyama 939-0363, Japan
| | - Junko Amemura-Maekawa
- Department of Bacteriology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Fumiaki Kura
- Department of Bacteriology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Tetsutaro Sata
- Department of Bacteriology, Toyama Institute of Health, 17-1 Nakataikoyama, Imizu-City, Toyama 939-0363, Japan
| | - Masanori Watahiki
- Department of Bacteriology, Toyama Institute of Health, 17-1 Nakataikoyama, Imizu-City, Toyama 939-0363, Japan
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Geographical and Temporal Structures of Legionella pneumophila Sequence Types in Comunitat Valenciana (Spain), 1998 to 2013. Appl Environ Microbiol 2015; 81:7106-13. [PMID: 26231651 DOI: 10.1128/aem.02196-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 07/28/2015] [Indexed: 01/08/2023] Open
Abstract
Legionella pneumophila is an accidental human pathogen associated with aerosol formation in water-related sources. High recombination rates make Legionella populations genetically diverse, and nearly 2,000 different sequence types (STs) have been described to date for this environmental pathogen. The spatial distribution of STs is extremely heterogeneous, with some variants being present worldwide and others being detected at only a local scale. Similarly, some STs have been associated with disease outbreaks, such as ST578 or ST23. Spain is among the European countries with the highest incidences of reported legionellosis cases, and specifically, Comunitat Valenciana (CV) is the second most affected area in the country. In this work, we aimed at studying the overall diversity of Legionella pneumophila populations found in the period from 1998 to 2013 in 79 localities encompassing 23 regions within CV. To do so, we performed sequence-based typing (SBT) on 1,088 L. pneumophila strains detected in the area from both environmental and clinical sources. A comparison with the genetic structuring detected in a global data set that included 20 European and 7 non-European countries was performed. Our results reveal a level of diversity in CV that can be considered representative of the diversity found in other countries worldwide.
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Sequence types diversity of Legionella pneumophila isolates from environmental water sources in Guangzhou and Jiangmen, China. INFECTION GENETICS AND EVOLUTION 2015; 29:35-41. [DOI: 10.1016/j.meegid.2014.10.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 10/17/2014] [Accepted: 10/25/2014] [Indexed: 11/18/2022]
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Costa J, Teixeira PG, d'Avó AF, Júnior CS, Veríssimo A. Intragenic recombination has a critical role on the evolution of Legionella pneumophila virulence-related effector sidJ. PLoS One 2014; 9:e109840. [PMID: 25299187 PMCID: PMC4192588 DOI: 10.1371/journal.pone.0109840] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 08/14/2014] [Indexed: 12/31/2022] Open
Abstract
SidJ is a Dot/Icm effector involved in the trafficking or retention of ER-derived vesicles to Legionella pneumophila vacuoles whose mutation causes an observable growth defect, both in macrophage and amoeba hosts. Given the crucial role of this effector in L. pneumophila virulence we investigated the mechanisms shaping its molecular evolution. The alignment of SidJ sequences revealed several alleles with amino acid variations that may influence the protein properties. The identification of HGT events and the detection of balancing selection operating on sidJ evolution emerge as a clear result. Evidence suggests that intragenic recombination is an important strategy in the evolutionary adaptive process playing an active role on sidJ genetic plasticity. This pattern of evolution is in accordance with the life style of L. pneumophila as a broad host-range pathogen by preventing host-specialization and contributing to the resilience of the species.
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Affiliation(s)
- Joana Costa
- Department of Life Sciences, University of Coimbra, Coimbra, Portugal
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Paulo Gonçalves Teixeira
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ana Filipa d'Avó
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Célio Santos Júnior
- Department of Molecular Biology and Evolutionary Genetics, Federal University of São Carlos (UFSCar), São Paulo, Brazil
| | - António Veríssimo
- Department of Life Sciences, University of Coimbra, Coimbra, Portugal
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- * E-mail:
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Luiz DP, Santos Júnior CD, Bonetti AM, Brandeburgo MAM. Tollip or not Tollip: what are the evolving questions behind it? PLoS One 2014; 9:e97219. [PMID: 24828816 PMCID: PMC4020778 DOI: 10.1371/journal.pone.0097219] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 04/16/2014] [Indexed: 11/17/2022] Open
Abstract
Tollip plays an important role in the interleukin-1 receptor IL-1R and Toll pathways. As a modulator of the immune pathway, it indirectly controls the amount of antimicrobial peptides. This could indicate a vital step in maintaining animal immune systems and preventing infection. Evolutionary questions are crucial to understanding the conservation and functioning of the biochemical pathways like the Tollip-mediated one. Through an analysis of 36 sequences of the Tollip protein from different animal taxa, downloaded from Kyoto Encyclopedia of Genes and Genomes (KEGG) databank, we inferred diverse evolutionary parameters, such as molecular selection and structure conservation, by analyzing residue by residue, beyond the canonical parameters to this type of study, as maximum likelihood trees. We found that Tollip presented different trends in its evolving history. In primates, the protein is becoming more unstable, just the opposite is observed in the arthropod group. The most interesting finding was the concentration of positively selected residues at amino terminal ends. Some observed topological incongruences in maximum likelihood trees of complete and curated Tollip data sets could be explained through horizontal transfers, evidenced by recombination detection. These results suggest that there is more to be researched and understood about this protein.
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Affiliation(s)
- Denis Prudencio Luiz
- Genetics Laboratory, Genetics and Biochemistry Institute, Federal University of Uberlandia - UFU, Uberlândia, Minas Gerais, Brazil
| | - Célio Dias Santos Júnior
- Genetics Laboratory, Genetics and Biochemistry Institute, Federal University of Uberlandia - UFU, Uberlândia, Minas Gerais, Brazil
| | - Ana Maria Bonetti
- Genetics Laboratory, Genetics and Biochemistry Institute, Federal University of Uberlandia - UFU, Uberlândia, Minas Gerais, Brazil
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Underwood AP, Jones G, Mentasti M, Fry NK, Harrison TG. Comparison of the Legionella pneumophila population structure as determined by sequence-based typing and whole genome sequencing. BMC Microbiol 2013; 13:302. [PMID: 24364868 PMCID: PMC3877988 DOI: 10.1186/1471-2180-13-302] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 12/16/2013] [Indexed: 01/07/2023] Open
Abstract
Background Legionella pneumophila is an opportunistic pathogen of humans where the source of infection is usually from contaminated man-made water systems. When an outbreak of Legionnaires’ disease caused by L. pneumophila occurs, it is necessary to discover the source of infection. A seven allele sequence-based typing scheme (SBT) has been very successful in providing the means to attribute outbreaks of L. pneumophila to a particular source or sources. Particular sequence types described by this scheme are known to exhibit specific phenotypes. For instance some types are seen often in clinical cases but are rarely isolated from the environment and vice versa. Of those causing human disease some types are thought to be more likely to cause more severe disease. It is possible that the genetic basis for these differences are vertically inherited and associated with particular genetic lineages within the population. In order to provide a framework within which to test this hypothesis and others relating to the population biology of L. pneumophila, a set of genomes covering the known diversity of the organism is required. Results Firstly, this study describes a means to group L. pneumophila strains into pragmatic clusters, using a methodology that takes into consideration the genetic forces operating on the population. These clusters can be used as a standardised nomenclature, so those wishing to describe a group of strains can do so. Secondly, the clusters generated from the first part of the study were used to select strains rationally for whole genome sequencing (WGS). The data generated was used to compare phylogenies derived from SBT and WGS. In general the SBT sequence type (ST) accurately reflects the whole genome-based genotype. Where there are exceptions and recombination has resulted in the ST no longer reflecting the genetic lineage described by the whole genome sequence, the clustering technique employed detects these sequence types as being admixed, indicating their mixed inheritance. Conclusions We conclude that SBT is usually a good proxy for the genetic lineage described by the whole genome, and therefore utility of SBT is still suitable until the technology and economics of high throughput sequencing reach the point where routine WGS of L. pneumophila isolates for outbreak investigation is feasible.
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Affiliation(s)
- Anthony P Underwood
- Bioinformatics Unit, Microbiology Services (Colindale), Public Health England, 61 Colindale Avenue, London, NW9 5EQ, UK.
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Sánchez-Busó L, Coscollá M, Pinto-Carbó M, Catalán V, González-Candelas F. Genetic Characterization of Legionella pneumophila Isolated from a Common Watershed in Comunidad Valenciana, Spain. PLoS One 2013; 8:e61564. [PMID: 23634210 PMCID: PMC3636276 DOI: 10.1371/journal.pone.0061564] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 03/11/2013] [Indexed: 11/19/2022] Open
Abstract
Legionella pneumophila infects humans to produce legionellosis and Pontiac fever only from environmental sources. In order to establish control measures and study the sources of outbreaks it is essential to know extent and distribution of strain variants of this bacterium in the environment. Sporadic and outbreak-related cases of legionellosis have been historically frequent in the Comunidad Valenciana region (CV, Spain), with a high prevalence in its Southeastern-most part (BV). Environmental investigations for the detection of Legionella pneumophila are performed in this area routinely. We present a population genetics study of 87 L. pneumophila strains isolated in 13 different localities of the BV area irrigated from the same watershed and compare them to a dataset of 46 strains isolated in different points of the whole CV. Our goal was to compare environmental genetic variation at two different geographic scales, at county and regional levels. Genetic diversity, recombination and population structure were analyzed with Sequence-Based Typing data and three intergenic regions. The results obtained reveal a low, but detectable, level of genetic differentiation between both datasets, mainly, but not only, attributed to the occurrence of unusual variants of the neuA locus present in the BV populations. This differentiation is still detectable when the 10 loci considered are analyzed independently, despite the relatively high incidence of the most common genetic variant in this species, sequence type 1 (ST-1). However, when the genetic data are considered without their associated geographic information, four major groups could be inferred at the genetic level which did not show any correlation with sampling locations. The overall results indicate that the population structure of these environmental samples results from the joint action of a global, widespread ST-1 along with genetic differentiation at shorter geographic distances, which in this case are related to the common watershed for the BV localities.
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Affiliation(s)
- Leonor Sánchez-Busó
- Genomics and Health Joint Unit CSISP (FISABIO)-University of Valencia/Cavanilles Institute, Valencia, Spain
- CIBER Epidemiology and Public Health, Valencia, Spain
| | - Mireia Coscollá
- Tuberculosis Research Unit, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Marta Pinto-Carbó
- Genomics and Health Joint Unit CSISP (FISABIO)-University of Valencia/Cavanilles Institute, Valencia, Spain
| | | | - Fernando González-Candelas
- Genomics and Health Joint Unit CSISP (FISABIO)-University of Valencia/Cavanilles Institute, Valencia, Spain
- CIBER Epidemiology and Public Health, Valencia, Spain
- * E-mail:
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Ng KW, Pointing SB, Dvornyk V. Patterns of nucleotide diversity of the ldpA circadian gene in closely related species of cyanobacteria from extreme cold deserts. Appl Environ Microbiol 2013; 79:1516-22. [PMID: 23263969 PMCID: PMC3591978 DOI: 10.1128/aem.03439-12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 12/14/2012] [Indexed: 11/20/2022] Open
Abstract
In the circadian system of cyanobacteria, the ldpA gene is a component of the input to the clock. We comparatively analyzed nucleotide polymorphism of this gene in populations of two closely related species of cyanobacteria (denoted as Synechococcus species S1 and S2, respectively) from extreme cold deserts in Antarctica, the Canadian Arctic, and Tibet. Although both species manifested similarly high haplotype diversities (0.990 and 0.809, respectively), the nucleotide diversity differed significantly (0.0091 in S1 and 0.0037 in S2). The populations of species S2 were more differentiated (F(ST) = 0.2242) compared to those of species S1 (F(ST) between 0.0296 and 0.1188). An analysis of positive selection with several tests yielded highly significant values (P < 0.01) for both species. On the other hand, these results may be somewhat compromised by fluctuating population sizes of the species. The apparent selection pressure coupled with the pronounced demographic factors, such as population expansion, small effective population size, and genetic drift, may thus result in the observed significant interpopulation differentiation and subsequent speciation of cyanobacteria.
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Affiliation(s)
- Ka Wai Ng
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, People's Republic of China
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Costa J, d'Avó AF, da Costa MS, Veríssimo A. Molecular evolution of key genes for type II secretion in Legionella pneumophila. Environ Microbiol 2011; 14:2017-33. [PMID: 22118294 DOI: 10.1111/j.1462-2920.2011.02646.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Given the role of type II protein secretion system (T2S) in the ecology and pathogenesis of Legionella pneumophila, it is possible that this system is a target for adaptive evolution. The population genetic structure of L.pneumophila was inferred from the partial sequences of rpoB and from the complete sequence of three T2S structural components (lspD, lspE and pilD) and from two T2S effectors critical for intracellular infection of protozoa (proA and srnA) of 37 strains isolated from natural and man-made environments and disease-related from worldwide sources. A phylogenetic analysis was obtained for the concatenated alignment and for each individual locus. Seven main groups were identified containing the same L.pneumophila strains, suggesting an ancient divergence for each cluster and indicating that the operating selective pressures have equally affected the evolution of the five genes. Although linkage disequilibrium analysis indicate a clonal nature for population structure in this sample, our results indicate that recombination is a common phenomenon among T2S-related genes on this species, as 24 of the 37 L.pneumophila isolates contained at least one locus in which recombination was identified. Furthermore, neutral selection acting on the analysed T2S-related genes emerged as a clear result, namely on T2S effectors, ProA and SrnA, indicating that they are probably implicated in conserved virulence mechanisms through legionellae hosts.
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Affiliation(s)
- Joana Costa
- Centro de Neurociências e Biologia Celular, Universidade de Coimbra, 3004-517 Coimbra, Portugal
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Gomez-Valero L, Rusniok C, Jarraud S, Vacherie B, Rouy Z, Barbe V, Medigue C, Etienne J, Buchrieser C. Extensive recombination events and horizontal gene transfer shaped the Legionella pneumophila genomes. BMC Genomics 2011; 12:536. [PMID: 22044686 PMCID: PMC3218107 DOI: 10.1186/1471-2164-12-536] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 11/01/2011] [Indexed: 02/06/2023] Open
Abstract
Background Legionella pneumophila is an intracellular pathogen of environmental protozoa. When humans inhale contaminated aerosols this bacterium may cause a severe pneumonia called Legionnaires' disease. Despite the abundance of dozens of Legionella species in aquatic reservoirs, the vast majority of human disease is caused by a single serogroup (Sg) of a single species, namely L. pneumophila Sg1. To get further insights into genome dynamics and evolution of Sg1 strains, we sequenced strains Lorraine and HL 0604 1035 (Sg1) and compared them to the available sequences of Sg1 strains Paris, Lens, Corby and Philadelphia, resulting in a comprehensive multigenome analysis. Results We show that L. pneumophila Sg1 has a highly conserved and syntenic core genome that comprises the many eukaryotic like proteins and a conserved repertoire of over 200 Dot/Icm type IV secreted substrates. However, recombination events and horizontal gene transfer are frequent. In particular the analyses of the distribution of nucleotide polymorphisms suggests that large chromosomal fragments of over 200 kbs are exchanged between L. pneumophila strains and contribute to the genome dynamics in the natural population. The many secretion systems present might be implicated in exchange of these fragments by conjugal transfer. Plasmids also play a role in genome diversification and are exchanged among strains and circulate between different Legionella species. Conclusion Horizontal gene transfer among bacteria and from eukaryotes to L. pneumophila as well as recombination between strains allows different clones to evolve into predominant disease clones and others to replace them subsequently within relatively short periods of time.
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Affiliation(s)
- Laura Gomez-Valero
- Institut Pasteur, Biologie des Bactéries Intracellulaires, 75724, Paris, France
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Costa J, Tiago I, Da Costa MS, Veríssimo A. Molecular evolution of Legionella pneumophila dotA gene, the contribution of natural environmental strains. Environ Microbiol 2011; 12:2711-29. [PMID: 20482739 DOI: 10.1111/j.1462-2920.2010.02240.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Given the role of DotA protein in establishing successful infections and the diversity of host cells interacting with Legionella pneumophila in nature, it is possible that this gene product is a target for adaptive evolution. We investigated the influence of L. pneumophila isolates from natural environments with the molecular evolution of this crucial virulence-related gene. The population genetic structure of L. pneumophila was inferred from the partial sequences of rpoB and dotA of 303 worldwide strains. The topology of the two inferred trees was not congruent and in the inferred dotA tree the vast majority of the natural environmental isolates were clustered in a discrete group. The Ka/Ks ratio demonstrated that this group, contrary to all others, has been under strong diversifying selection. The alignment of all DotA sequences allowed the identification of several alleles and the amino acid variations were not randomly distributed. Moreover, from these results we can conclude that dotA from L. pneumophila clinical and man-made environmental strains belong to a sub-set of all genotypes existing in nature. A split graph analysis showed evidence of a network-like organization and several intergenic recombination events were detected within L. pneumophila strains resulting in mosaic genes in which different gene segments exhibited different evolutionary histories. We have determined that the allelic diversity of dotA is predominantly found in L. pneumophila isolates from natural environments, suggesting that niche-specific selection pressures have been operating on this gene. Indeed, the high level of dotA allelic diversity may reflect fitness variation in the persistence of those strains in distinct environmental niches and/or tropism to various protozoan hosts.
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Affiliation(s)
- Joana Costa
- Centro de Neurociências e Biologia Celular, Universidade de Coimbra, 3004-517 Coimbra, Portugal
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Insertion sequences as highly resolutive genomic markers for sequence type 1 Legionella pneumophila Paris. J Clin Microbiol 2010; 49:315-24. [PMID: 20980561 DOI: 10.1128/jcm.01261-10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The causative agent of legionellosis, Legionella pneumophila, colonizes all natural and human-made water networks, thus constituting the source of contaminated aerosols responsible for airborne human infections. Efficient control of infections, especially during epidemics, necessitates the fastest and most resolutive identification possible of the bacterial source for subsequent disinfection of reservoirs. We thus compared recognized typing approaches for Legionella with a method based on characterization of insertion sequence (IS) content. A total of 86 clinical or environmental isolates of L. pneumophila, including 84 Paris isolates, sampled from 25 clinical investigations in France between 2001 and 2007, were obtained from the Legionella National Reference Center. All strains were typed by monoclonal antibody subgrouping, sequence-based typing, pulsed-field gel electrophoresis, and restriction fragment length polymorphism based on the presence or absence of IS elements. We identified six different types of IS elements in L. pneumophila Paris and used them as genomic markers in hybridization experiments. One IS type, ISLpn11, revealed a high discriminatory power. Simpson's index of discrimination, calculated from the distribution of IS elements, was higher than that obtained with the other typing methods used for L. pneumophila Paris. Moreover, specific ISLpn11 copies were found only in strains isolated from particular cities. In more than half of the cases, each clinical isolate had an ISLpn11 profile that was recovered in at least one environmental isolate from the same geographical location, suggesting that our method could identify the infection source. Phylogenetic analysis suggests a clonal expansion for the L. pneumophila Paris strain.
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Coscollá M, Comas I, González-Candelas F. Quantifying Nonvertical Inheritance in the Evolution of Legionella pneumophila. Mol Biol Evol 2010; 28:985-1001. [PMID: 20961962 DOI: 10.1093/molbev/msq278] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Mireia Coscollá
- Unidad Mixta de Investigación Genómica y Salud CSISP-UV/Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Valencia, Spain
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Vandersmissen L, De Buck E, Saels V, Coil DA, Anné J. ALegionella pneumophilacollagen-like protein encoded by a gene with a variable number of tandem repeats is involved in the adherence and invasion of host cells. FEMS Microbiol Lett 2010; 306:168-76. [DOI: 10.1111/j.1574-6968.2010.01951.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Coil DA, Vandersmissen L, Ginevra C, Jarraud S, Lammertyn E, Anné J. Intragenic tandem repeat variation between Legionella pneumophila strains. BMC Microbiol 2008; 8:218. [PMID: 19077205 PMCID: PMC2639597 DOI: 10.1186/1471-2180-8-218] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2008] [Accepted: 12/10/2008] [Indexed: 11/30/2022] Open
Abstract
Background Bacterial genomes harbour a large number of tandem repeats, yet the possible phenotypic effects of those found within the coding region of genes are only beginning to be examined. Evidence exists from other organisms that these repeats can be involved in the evolution of new genes, gene regulation, adaptation, resistance to environmental stresses, and avoidance of the immune system. Results In this study, we have investigated the presence and variability in copy number of intragenic tandemly repeated sequences in the genome of Legionella pneumophila, the etiological agent of a severe pneumonia known as Legionnaires' disease. Within the genome of the Philadelphia strain, we have identified 26 intragenic tandem repeat sequences using conservative selection criteria. Of these, seven were "polymorphic" in terms of repeat copy number between a large number of L. pneumophila serogroup 1 strains. These strains were collected from a wide variety of environments and patients in several geographical regions. Within this panel of strains, all but one of these seven genes exhibited statistically different patterns in repeat copy number between samples from different origins (environmental, clinical, and hot springs). Conclusion These results support the hypothesis that intragenic tandem repeats could play a role in virulence and adaptation to different environments. While tandem repeats are an increasingly popular focus of molecular typing studies in prokaryotes, including in L. pneumophila, this study is the first examining the difference in tandem repeat distribution as a function of clinical or environmental origin.
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Affiliation(s)
- David A Coil
- Laboratory of Bacteriology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
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Edwards MT, Fry NK, Harrison TG. Clonal population structure of Legionella pneumophila inferred from allelic profiling. Microbiology (Reading) 2008; 154:852-864. [DOI: 10.1099/mic.0.2007/012336-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Martin T. Edwards
- Statistics, Modelling and Bioinformatics Department, Health Protection Agency Centre for Infections, London, UK
- Respiratory and Systemic Infection Laboratory, Health Protection Agency Centre for Infections, London, UK
| | - Norman K. Fry
- Respiratory and Systemic Infection Laboratory, Health Protection Agency Centre for Infections, London, UK
| | - Timothy G. Harrison
- Respiratory and Systemic Infection Laboratory, Health Protection Agency Centre for Infections, London, UK
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Coscollá M, González-Candelas F. Population structure and recombination in environmental isolates of Legionella pneumophila. Environ Microbiol 2007; 9:643-56. [PMID: 17298365 DOI: 10.1111/j.1462-2920.2006.01184.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Legionella pneumophila is a water-borne bacteria responsible for most cases of legionellosis, an emerging disease with an increasing incidence in industrialized countries. Although early analysis based on multilocus enzyme electrophoresis (MLEE) described the population structure of this species as clonal, more recent reports have suggested that recombination also contributes to shaping variation across its genome. We report here the results of analysing the nucleotide sequences of 19 loci in 31 environmental samples of L. pneumophila from a small Spanish region (near Alcoi, province of Alicante) where legionellosis has become almost endemic. We analysed the six loci currently incorporated to the sequence-based typing scheme developed by European Working Group for Legionella Infections (EWGLI) for L. pneumophila and 13 intergenic regions, for which we developed primers anchored in flanking, conserved genes. Our results show that recombination among natural isolates of this species is a common phenomenon, as 20 of the 31 isolates contained at least one locus in which recombination was revealed by at least three different methods. The mapping of the recombination events on the maximum likelihood tree of the concatenate sequence of the 19 loci indicated that at least nine independent recombination events might explain the observed distribution of recombinant loci among isolates. In consequence, we have shown that recombination in L. pneumophila is much more frequent than previously considered and that it does not seem to be restricted to already described pathogenicity islands or other genome constituents which provide it with a high plasticity.
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Affiliation(s)
- Mireia Coscollá
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Departament de Genètica, Universitat de València, 46071 València, Spain
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