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Lopez AE, Mayoral J, Cianciotto NP. Complete Genome Sequence of Legionella cardiaca Strain H63 T, Isolated from a Case of Native Valve Endocarditis. Microbiol Resour Announc 2023; 12:e0017523. [PMID: 37310280 PMCID: PMC10353460 DOI: 10.1128/mra.00175-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/30/2023] [Indexed: 06/14/2023] Open
Abstract
We report the complete genome sequence of Legionella cardiaca strain H63T, which had been isolated from aortic valve tissue from a patient with native endocarditis. The genome assembly contains a single 3,477,232-bp contig, with a G+C content of 38.59%, and is predicted to encode 2,948 proteins.
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Affiliation(s)
- Alberto E. Lopez
- Department of Microbiology and Immunology, Northwestern University Medical School, Chicago, Illinois, USA
| | - Joshua Mayoral
- Department of Microbiology and Immunology, Northwestern University Medical School, Chicago, Illinois, USA
| | - Nicholas P. Cianciotto
- Department of Microbiology and Immunology, Northwestern University Medical School, Chicago, Illinois, USA
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Hassler HB, Probert B, Moore C, Lawson E, Jackson RW, Russell BT, Richards VP. Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies. MICROBIOME 2022; 10:104. [PMID: 35799218 PMCID: PMC9264627 DOI: 10.1186/s40168-022-01295-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 05/23/2022] [Indexed: 05/02/2023]
Abstract
BACKGROUND The 16S rRNA gene is used extensively in bacterial phylogenetics, in species delineation, and now widely in microbiome studies. However, the gene suffers from intragenomic heterogeneity, and reports of recombination and an unreliable phylogenetic signal are accumulating. Here, we compare core gene phylogenies to phylogenies constructed using core gene concatenations to estimate the strength of signal for the 16S rRNA gene, its hypervariable regions, and all core genes at the intra- and inter-genus levels. Specifically, we perform four intra-genus analyses (Clostridium, n = 65; Legionella, n = 47; Staphylococcus, n = 36; and Campylobacter, n = 17) and one inter-genus analysis [41 core genera of the human gut microbiome (31 families, 17 orders, and 12 classes), n = 82]. RESULTS At both taxonomic levels, the 16S rRNA gene was recombinant and subject to horizontal gene transfer. At the intra-genus level, the gene showed one of the lowest levels of concordance with the core genome phylogeny (50.7% average). Concordance for hypervariable regions was lower still, with entropy masking providing little to no benefit. A major factor influencing concordance was SNP count, which showed a positive logarithmic association. Using this relationship, we determined that 690 ± 110 SNPs were required for 80% concordance (average 16S rRNA gene SNP count was 254). We also found a wide range in 16S-23S-5S rRNA operon copy number among genomes (1-27). At the inter-genus level, concordance for the whole 16S rRNA gene was markedly higher (73.8% - 10th out of 49 loci); however, the most concordant hypervariable regions (V4, V3-V4, and V1-V2) ranked in the third quartile (62.5 to 60.0%). CONCLUSIONS Ramifications of a poor phylogenetic performance for the 16S rRNA gene are far reaching. For example, in addition to incorrect species/strain delineation and phylogenetic inference, it has the potential to confound community diversity metrics if phylogenetic information is incorporated - for example, with popular approaches such as Faith's phylogenetic diversity and UniFrac. Our results highlight the problematic nature of these approaches and their use (along with entropy masking) is discouraged. Lastly, the wide range in 16S rRNA gene copy number among genomes also has a strong potential to confound diversity metrics. Video Abstract.
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Affiliation(s)
- Hayley B. Hassler
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC 29634 USA
| | - Brett Probert
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC 29634 USA
| | - Carson Moore
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC 29634 USA
| | - Elizabeth Lawson
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC 29634 USA
| | | | - Brook T. Russell
- School of Mathematical and Statistical Sciences, Clemson University, Clemson, SC 29634 USA
| | - Vincent P. Richards
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC 29634 USA
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Travel-related epidemiological studies of legionellosis in Federation of Bosnia and Herzegovina. HEALTH AND TECHNOLOGY 2021. [DOI: 10.1007/s12553-021-00584-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Checa J, Carbonell I, Manero N, Martí I. Comparative study of Legiolert with ISO 11731-1998 standard method-conclusions from a Public Health Laboratory. J Microbiol Methods 2021; 186:106242. [PMID: 34019935 DOI: 10.1016/j.mimet.2021.106242] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/16/2021] [Accepted: 05/16/2021] [Indexed: 11/18/2022]
Abstract
BACKGROUND Legionella pneumophila (L. pneumophila) is responsible for 96% of Legionnaires' disease (LD) and 10% of all worldwide pneumonia cases. Legiolert™, a liquid culture method for most probable number (MPN) enumeration of L. pneumophila, was developed by IDEXX Laboratories. The method detects all serogroups of L. pneumophila in potable and non-potable water samples. OBJECTIVE The goal of this study is to establish that Legiolert is a suitable alternative method to meet testing requirements in Spain for the enumeration of Legionella in water samples. METHODOLOGY The laboratory analyzed 118 environmental water samples from the Barcelona region (56 potable and 62 non-potable) in parallel by the Standard method for detection and enumeration of Legionella (ISO 11731:1998) and by Legiolert. Comparison of the recovery of the alternative method (Legiolert) and the Standard was made using ISO 17994:2014 and McNemar's binomial test statistical methods. RESULTS 44 samples were positive for Legionella (36 potable and 8 non-potable). Legiolert and the Standard method detected a similar percentage of positive samples, with Legiolert being slightly higher (31 vs 30%) and detecting higher concentrations of Legionella within the samples. ISO 17994:2014 analysis of the potable water samples found Legiolert was more sensitive than the Standard at detecting Legionella, even when complete Legionella species (L. spp.) results were considered for both methods. The two methods also demonstrated equivalent detection of L. spp. according to the McNemar's test. The comparison is significantly more in favor of Legiolert when only L. pneumophila results are considered. Each confirmation run with material extracted from positive Legiolert wells contained L. pneumophila, giving the method a specificity of 100%. Although statistical results for non-potable waters are not included because of the low number of samples, the two methods trended towards equivalence. CONCLUSIONS Relative to the Standard method, Legiolert has a greater sensitivity and selectivity, and appears to have higher recovery for L. pneumophila, and equivalent recovery when L. spp. is included in the comparison. Legiolert also has high specificity. The procedural advantages of Legiolert allow laboratories to save on resources, costs, and time and consequently to test more frequently. In conclusion, the study finds IDEXX Legiolert a suitable alternative to ISO 11731:1998.
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Affiliation(s)
- Javier Checa
- Public Health Laboratory of L'Hospitalet. Health Service, L'Hospitalet City Council, Cobalt Building. Cobalt street, 57-59, 2nd floor, 08907 L'Hospitalet de Llobregat, Barcelona, Spain.
| | - Iago Carbonell
- Public Health Laboratory of L'Hospitalet. Health Service, L'Hospitalet City Council, Cobalt Building. Cobalt street, 57-59, 2nd floor, 08907 L'Hospitalet de Llobregat, Barcelona, Spain.
| | - Neus Manero
- Public Health Laboratory of L'Hospitalet. Health Service, L'Hospitalet City Council, Cobalt Building. Cobalt street, 57-59, 2nd floor, 08907 L'Hospitalet de Llobregat, Barcelona, Spain.
| | - Inés Martí
- Public Health Laboratory of L'Hospitalet. Health Service, L'Hospitalet City Council, Cobalt Building. Cobalt street, 57-59, 2nd floor, 08907 L'Hospitalet de Llobregat, Barcelona, Spain.
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De Giglio O, Fasano F, Diella G, Lopuzzo M, Napoli C, Apollonio F, Brigida S, Calia C, Campanale C, Marzella A, Pousis C, Rutigliano S, Triggiano F, Caggiano G, Montagna MT. Legionella and legionellosis in touristic-recreational facilities: Influence of climate factors and geostatistical analysis in Southern Italy (2001-2017). ENVIRONMENTAL RESEARCH 2019; 178:108721. [PMID: 31541805 DOI: 10.1016/j.envres.2019.108721] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 09/02/2019] [Accepted: 09/03/2019] [Indexed: 06/10/2023]
Abstract
Legionella is the causative agent of Legionnaires' disease, a flu-like illness normally acquired following inhalation or aspiration of contaminated water aerosols. Our recent studies revealed that climatic parameters can increase the number of reported cases of community-acquired Legionnaires' disease. Here, we evaluated the presence of Legionella in water networks and the distribution of Legionnaires' disease cases associated with touristic-recreational facilities in the Apulia region (southern Italy) during the period 2001-2017 using geostatistical and climatic analyses. Geostatistical analysis data revealed that the area with the highest concentration of Legionella in water systems also had the greatest number of cases of Legionnaires' disease associated with touristic-recreational facilities. Climatic analysis showed that higher daily temperature excursion (difference between maximum and minimum temperature) on the day of sampling was more often associated with Legionella-positive samples than Legionella-negative samples. In addition, our data highlighted an increased risk of Legionnaires' disease with increases in precipitation and average temperature and with decreases in daily temperature excursion (difference between maximum and minimum temperature over the course of 24 h in the days of incubation period of disease) and minimum temperature. Healthcare professionals should be aware of this phenomenon and be particularly vigilant for cases of community-acquired pneumonia during such climatic conditions and among the tourist population. The innovative geo-statistical approach used in this study could be applied in other contexts when evaluating the effects of climatic conditions on the incidence of Legionella infections.
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Affiliation(s)
- Osvalda De Giglio
- Department of Biomedical Science and Human Oncology, University of Bari "Aldo Moro", Piazza G. Cesare 11, 70124, Bari, Italy.
| | - Fabrizio Fasano
- Department of Biomedical Science and Human Oncology, University of Bari "Aldo Moro", Piazza G. Cesare 11, 70124, Bari, Italy.
| | - Giusy Diella
- Department of Biomedical Science and Human Oncology, University of Bari "Aldo Moro", Piazza G. Cesare 11, 70124, Bari, Italy.
| | - Marco Lopuzzo
- Department of Biomedical Science and Human Oncology, University of Bari "Aldo Moro", Piazza G. Cesare 11, 70124, Bari, Italy.
| | - Christian Napoli
- Department of Medical Surgical Sciences and Translational Medicine, "Sapienza" University of Rome, Via di Grottarossa 1035/1039, 00189, Rome, Italy.
| | - Francesca Apollonio
- Department of Biomedical Science and Human Oncology, University of Bari "Aldo Moro", Piazza G. Cesare 11, 70124, Bari, Italy.
| | - Silvia Brigida
- Water Research Institute-Italian National Research Council, Bari, Italy.
| | - Carla Calia
- Department of Biomedical Science and Human Oncology, University of Bari "Aldo Moro", Piazza G. Cesare 11, 70124, Bari, Italy.
| | - Carmen Campanale
- Department of Biomedical Science and Human Oncology, University of Bari "Aldo Moro", Piazza G. Cesare 11, 70124, Bari, Italy.
| | - Angelo Marzella
- Department of Biomedical Science and Human Oncology, University of Bari "Aldo Moro", Piazza G. Cesare 11, 70124, Bari, Italy.
| | - Chrysovalentinos Pousis
- Department of Biomedical Science and Human Oncology, University of Bari "Aldo Moro", Piazza G. Cesare 11, 70124, Bari, Italy.
| | - Serafina Rutigliano
- Department of Biomedical Science and Human Oncology, University of Bari "Aldo Moro", Piazza G. Cesare 11, 70124, Bari, Italy.
| | - Francesco Triggiano
- Department of Biomedical Science and Human Oncology, University of Bari "Aldo Moro", Piazza G. Cesare 11, 70124, Bari, Italy.
| | - Giuseppina Caggiano
- Department of Biomedical Science and Human Oncology, University of Bari "Aldo Moro", Piazza G. Cesare 11, 70124, Bari, Italy.
| | - Maria Teresa Montagna
- Department of Biomedical Science and Human Oncology, University of Bari "Aldo Moro", Piazza G. Cesare 11, 70124, Bari, Italy.
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White RC, Cianciotto NP. Assessing the impact, genomics and evolution of type II secretion across a large, medically important genus: the Legionella type II secretion paradigm. Microb Genom 2019; 5. [PMID: 31166887 PMCID: PMC6617341 DOI: 10.1099/mgen.0.000273] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The type II secretion system (T2SS) plays a major role in promoting bacterial survival in the environment and in human hosts. One of the best characterized T2SS is that of Legionella pneumophila, the agent of Legionnaires’ disease. Secreting at least 25 proteins, including degradative enzymes, eukaryotic-like proteins and novel effectors, this T2SS contributes to the ability of L. pneumophila to grow at low temperatures, infect amoebal and macrophage hosts, damage lung tissue, evade the immune system, and undergo sliding motility. The genes encoding the T2SS are conserved across the genus Legionella, which includes 62 species and >30 pathogens in addition to L. pneumophila. The vast majority of effectors associated with L. pneumophila are shared by a large number of Legionella species, hinting at a critical role for them in the ecology of Legionella as a whole. However, no other species has the same repertoire as L. pneumophila, with, as a general rule, phylogenetically more closely related species sharing similar sets of effectors. T2SS effectors that are involved in infection of a eukaryotic host(s) are more prevalent throughout Legionella, indicating that they are under stronger selective pressure. The Legionella T2SS apparatus is closest to that of Aquicella (another parasite of amoebae), and a significant number of L. pneumophila effectors have their closest homologues in Aquicella. Thus, the T2SS of L. pneumophila probably originated within the order Legionellales, with some of its effectors having arisen within that Aquicella-like progenitor, while other effectors derived from the amoebal host, mimiviruses, fungi and less closely related bacteria.
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Affiliation(s)
- Richard C White
- 1 Department of Microbiology and Immunology, Northwestern University Medical School, Chicago, IL 60611, USA
| | - Nicholas P Cianciotto
- 1 Department of Microbiology and Immunology, Northwestern University Medical School, Chicago, IL 60611, USA
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Wu HY, Yan H, Zheng ML, Sun MM, Wang Q, Hu CM, Zhan XY, Yuan MG, Qu PH, Hu CH. Legionella qingyii sp. nov., isolated from water samples in China. Int J Syst Evol Microbiol 2019; 69:2017-2022. [PMID: 31063123 DOI: 10.1099/ijsem.0.003421] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three Legionella-like strains, designed km488T, km489 and km521, were isolated from freshwater samples in China. Cells were Gram-stain-negative, rod-shaped and non-spore-forming. Growth was observed on BCYEα agar, but not on BCYEα agar without l-cysteine, chocolate agar with PolyViteX or Columbia blood agar. The major fatty acids (>5 %) of strains km488T, km489 and km521 were C16 : 0, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The mip gene sequences (574 nt) showed the isolates were almost identical with more than 99.7 % sequence similarities, and closely matched to L. gormanii ATCC 33297T with 95.4-95.6 % sequence similarities. Phylogenetic analyses based on concatenated gene (16S rRNA, mip, rpoB and rnpB) sequences indicated that the isolates formed a distinct cluster along with L. gormanii within the genus Legionella. Matrix-assisted laser desorption ionization time-of-flight analyses also demonstrated a clear separation between the isolates and other closely and distantly related Legionella species. DNA-DNA hybridization studies demonstrated that the isolates were closely related (92.0 -95.0 % DNA-DNA relatedness) but differentiated from their phylogenetic neighbours (<70 % DNA-DNA relatedness). The whole genome of km488T was sequenced, and showed a G+C content of 37.8 mol%. Based on the findings from this polyphasic taxonomic study, the isolates are considered to represent a single novel species, for which the name Legionella qingyii sp. nov. is proposed. The type strain is km488T (KCTC 15636T=CCTCC AB 2018025T=NRBC 113223T).
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Affiliation(s)
- Hai-Yan Wu
- 1School of KingMed Laboratory, Guangzhou Medical University, Guangzhou, 510330, PR China
| | - Hui Yan
- 2Guangzhou KingMed Center for Clinical Laboratory, Guangzhou, 510330, PR China
| | - Min-Ling Zheng
- 3Department of Clinical Laboratory, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, 51006, PR China
| | - Ming-Ming Sun
- 2Guangzhou KingMed Center for Clinical Laboratory, Guangzhou, 510330, PR China
| | - Qun Wang
- 2Guangzhou KingMed Center for Clinical Laboratory, Guangzhou, 510330, PR China
| | - Chang-Ming Hu
- 2Guangzhou KingMed Center for Clinical Laboratory, Guangzhou, 510330, PR China
| | - Xiao-Yong Zhan
- 2Guangzhou KingMed Center for Clinical Laboratory, Guangzhou, 510330, PR China
| | - Mu-Ge Yuan
- 1School of KingMed Laboratory, Guangzhou Medical University, Guangzhou, 510330, PR China
| | - Ping-Hua Qu
- 3Department of Clinical Laboratory, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, 51006, PR China
| | - Chao-Hui Hu
- 2Guangzhou KingMed Center for Clinical Laboratory, Guangzhou, 510330, PR China.,1School of KingMed Laboratory, Guangzhou Medical University, Guangzhou, 510330, PR China
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Llewellyn AC, Lucas CE, Roberts SE, Brown EW, Nayak BS, Raphael BH, Winchell JM. Distribution of Legionella and bacterial community composition among regionally diverse US cooling towers. PLoS One 2017; 12:e0189937. [PMID: 29261791 PMCID: PMC5738086 DOI: 10.1371/journal.pone.0189937] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 12/05/2017] [Indexed: 11/19/2022] Open
Abstract
Cooling towers (CTs) are a leading source of outbreaks of Legionnaires' disease (LD), a severe form of pneumonia caused by inhalation of aerosols containing Legionella bacteria. Accordingly, proper maintenance of CTs is vital for the prevention of LD. The aim of this study was to determine the distribution of Legionella in a subset of regionally diverse US CTs and characterize the associated microbial communities. Between July and September of 2016, we obtained aliquots from water samples collected for routine Legionella testing from 196 CTs located in eight of the nine continental US climate regions. After screening for Legionella by PCR, positive samples were cultured and the resulting Legionella isolates were further characterized. Overall, 84% (164) were PCR-positive, including samples from every region studied. Of the PCR-positive samples, Legionella spp were isolated from 47% (78), L. pneumophila was isolated from 32% (53), and L. pneumophila serogroup 1 (Lp1) was isolated from 24% (40). Overall, 144 unique Legionella isolates were identified; 53% (76) of these were Legionella pneumophila. Of the 76 L. pneumophila isolates, 51% (39) were Lp1. Legionella were isolated from CTs in seven of the eight US regions examined. 16S rRNA amplicon sequencing was used to compare the bacterial communities of CT waters with and without detectable Legionella as well as the microbiomes of waters from different climate regions. Interestingly, the microbial communities were homogenous across climate regions. When a subset of seven CTs sampled in April and July were compared, there was no association with changes in corresponding CT microbiomes over time in the samples that became culture-positive for Legionella. Legionella species and Lp1 were detected frequently among the samples examined in this first large-scale study of Legionella in US CTs. Our findings highlight that, under the right conditions, there is the potential for CT-related LD outbreaks to occur throughout the US.
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Affiliation(s)
- Anna C. Llewellyn
- Laboratory Leadership Service, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
- Pneumonia Response and Surveillance Laboratory, Respiratory Disease Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Claressa E. Lucas
- Pneumonia Response and Surveillance Laboratory, Respiratory Disease Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Sarah E. Roberts
- Pneumonia Response and Surveillance Laboratory, Respiratory Disease Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Ellen W. Brown
- Pneumonia Response and Surveillance Laboratory, Respiratory Disease Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Bina S. Nayak
- Water Quality Division, Pinellas County Utilities, Largo, FL, United States of America
| | - Brian H. Raphael
- Pneumonia Response and Surveillance Laboratory, Respiratory Disease Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Jonas M. Winchell
- Pneumonia Response and Surveillance Laboratory, Respiratory Disease Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
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