Phylogenomics and systematics in Pseudomonas

© 2015 Gomila, Peña, Mulet, Lalucat and García-Valdés. The genus Pseudomonas currently contains 144 species, making it the genus of Gram-negative bacteria that contains the largest number of species. Currently, multilocus sequence analysis (MLSA) is the preferred method for establishing the phylogeny between species and genera. Four partial gene sequences of housekeeping genes (16S rRNA, gyrB, rpoB, and rpoD) were obtained from 112 complete or draft genomes of strains related to the genus Pseudomonas that were available in databases. These genes were analyzed together with the corresponding sequences of 133 Pseudomonas type strains of validly published species to assess their correct phylogenetic assignations. We confirmed that 30% of the sequenced genomes of non-type strains were not correctly assigned at the species level in the accepted taxonomy of the genus and that 20% of the strains were not identified at the species level. Most of these strains had been isolated and classified several years ago, and their taxonomic status has not been updated by modern techniques. MLSA was also compared with indices based on the analysis of whole-genome sequences that have been proposed for species delineation, such as tetranucleotide usage patterns (TETRA), average nucleotide identity (ANIm, based on MUMmer and ANIb, based on BLAST) and genome-to-genome distance (GGDC). TETRA was useful for discriminating Pseudomonas from other genera, whereas ANIb and GGDC clearly separated strains of different species. ANIb showed the strongest correlation with MLSA. The correct species classification is a prerequisite for most diversity and evolutionary studies. This work highlights the necessity for complete genomic sequences of type strains to build a phylogenomic taxonomy and that all new genome sequences submitted to databases should be correctly assigned to species to avoid taxonomic inconsistencies.Financial support was obtained from the Spanish MINECO through projects CGL2011-24318 and Consolider CSD2009-00006, as well as funds for competitive research groups from the Government of the Balearic Islands (the last two funds with FEDER cofunding). MG and AP were supported by a postdoctoral contract from the University of the Balearic IslandsPeer Reviewe

Identification and diversity of multiresistant Corynebacterium striatum clinical isolates by MALDI-TOF mass spectrometry and by a multigene sequencing approach

<p>Abstract</p> <p>Background</p> <p>The genus <it>Corynebacterium </it>is composed of Gram-positive bacteria that are widely distributed throughout the environment; these bacteria are also part of the normal microbiota of human skin and mucous membranes. Multiple studies have shown that species of this genus, including <it>C. striatum</it>, become pathogenic to humans under special conditions. Our aim was to determine the characteristics of clinical multiresistant strains of <it>C. striatum </it>that were isolated in our geographical region, to determine their diversity, and to compare them with the type strain and with related species. We studied fifty-two strains of <it>C. striatum </it>isolated from different hospitals from Mallorca, Spain, mainly from the Hospital Joan March in Bunyola, Mallorca. Most of the strains were isolated from sputum cultures of respiratory samples from patients with chronic obstructive pulmonary disease. To gain further insight into the genetic diversity of the strains, we analysed several housekeeping genes and other genes associated with antibiotic resistance. Strains were also characterised phenotypically by their antibiotic resistance profiles and by MALDI-TOF mass spectrometry analysis.</p> <p>Results</p> <p>The ITS1 region, <it>gyrA </it>and <it>rpoB </it>were chosen as the appropriate genes in the <it>C. striatum </it>genome to study the genetic diversity of <it>C. striatum </it>species and to discriminate between strains. After analysing these three genes, four sequence types (ST2, ST4, ST1 and ST11) were found to be the most abundant. Splits tree analysis of the strains demonstrated that these clinical isolates did not share any alleles with the type strain of the species. Recombination was detected within all of the <it>C. striatum </it>isolates, and different clonal populations were detected within the samples.</p> <p>Conclusions</p> <p>Our results demonstrate that the isolates were best identified using gene-based molecular methods; using these methods, the isolated strains were determined to be different from the type strain of <it>C. striatum</it>. The ITS1 region and the <it>gyrA </it>and <it>rpoB </it>genes were selected because of their variability and were the most useful tools for discriminating between strains. The phenotype and antibiotype characteristics of the strains did not seem suitable for typing purposes. MALDI-TOF mass spectrometry can be a useful method for identifying and discriminating between <it>C. striatum </it>strains.</p

Respiratory infection by Corynebacterium striatum: Epidemiological and clinical determinants

© 2014 The Authors. The increasing prevalence of advanced chronic respiratory disease, with frequent exposure to broad-spectrum antibiotics for repeated and prolonged hospitalizations, favours the emergence of nosocomial respiratory infection by Gram-positive bacteria, such as outbreaks of Corynebacterium striatum. There is little evidence about patterns of respiratory infection, transmission and adaptive ability of this pathogen. Seventy-two C. striatum isolates from 51 advanced respiratory patients, mainly chronic obstructive pulmonary disease, were studied during 38 months. Patients were 74.8 ± 8.6 years old and 81.9% were men, who had required an average of 2.2 hospitalizations and 63.5 days in the hospital in the previous year. Of 49 isolates from 42 patients we were able to identify 12 clones by multilocus sequence analysis (MLSA), nine phenotypic variants and 22 antibiotic susceptibility patterns, and we determined their clinical and epidemiological determinants. MLSA allows identification of the existence of nosocomial outbreaks by transmission of the same or different clones, the persistence of the same clone in the environment or in patient airways for months. The study showed the high variability and adaptive capacity of the isolates, the antibiotic multidrug-resistance in all of them, and their contribution to a high morbidity and mortality (41%) during the study period.This work was supported by the General Board for Research, Technological Development and Innovation of the Department of Finance and Innovation of the Autonomous Community of the Balearic Islands (Direcció General de Recerca, Desenvolupament Tecnològic i Innovació, de la Conselleria d'Hisenda i Innovació, de la Comunitat Autònoma de les Illes Balears). This work was supported also by funding from Spanish MINECO through Consolider CSD2009-00006. Margarita Gomila was supported by a postdoctoral contract from the University of the Balearic Islands, with funds from the Spanish Ministry of Education, Culture and Sports through the International Excellence Campus ProgrammePeer Reviewe

Cupriavidus pampae sp. nov., a novel herbicidedegrading bacterium isolated from agricultural soil

A bacterial consortium able to degrade the herbicide 4-(2,4-dichlorophenoxy) butyric acid (2,4-DB) was obtained from an agricultural soil of the Argentinean Humid Pampa region which has a history of long-term herbicide use. Four bacterial strains were isolated from the consortium and identified as members of the genera Cupriavidus, Labrys and Pseudomonas. A polyphasic systematic analysis was carried out on strain CPDB6T, the member of the 2,4-DB-degrading consortium able to degrade 2,4-DB as a sole carbon and energy source. The Gram-negative, rod-shaped, motile, non-sporulating, non-fermenting bacterium was shown to belong to the genus Cupriavidus on the basis of 16S rRNA gene sequence analyses. Strain CPDB6T did not reduce nitrate, which differentiated it from the type species of the genus, Cupriavidus necator; it did not grow in 0.5–4.5 % NaCl, although most species of Cupriavidus are able to grow at NaCl concentrations as high as 1.5 %; and it was able to deamidate acetamide, which differentiated it from all other species of Cupriavidus. DNA–DNA hybridization data revealed low levels of genomic DNA similarity (less than 30 %) between strain CPDB6T and the type strains of Cupriavidus species with validly published names. The major cellular fatty acids detected were cis-9-hexadecenoic (16 : 1ω7c) and hexadecanoic (16 : 0) acids. On the basis of phenotypic and genotypic characterizations, strain CPDB6T was recognized as a representative of a novel species within the genus Cupriavidus. The name Cupriavidus pampae sp. nov. is proposed, with strain CPDB6T (=CCUG 55948T=CCM-A-29:1289T) as the type strain.Fil: Cuadrado, Virginia. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Microbiología Industrial y Biotecnología; ArgentinaFil: Gomila, Margarita. Universidad de las Islas Baleares; España. Consejo Superior de Investigaciones Cientificas. Instituto Mediterraneo de Estudios Avanzados; EspañaFil: Merini, Luciano Jose. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Microbiología Industrial y Biotecnología; ArgentinaFil: Giulietti, Ana Maria. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Microbiología Industrial y Biotecnología; ArgentinaFil: Moore, Edward R. B.. University of Gothenburg; Suecia. Sahlgrenska University Hospital. Department of Clinical Bacteriology; Sueci

Rethinking the Xylella fastidiosa scenario in the Balearic Islands: what epidemiological, phylogenetic and dendrochronological data tell us

Trabajo presentado en la 2nd European conference on Xylella fastidiosa (how research can support solutions), celebrada en Ajaccio el 29 y 30 de octubre de 2019.The emergence of Xylella fastidiosa(Xf) in Europe has been dealt as relatively recent introductions from the American continent. While this seems accurate for highly virulent genotypes such as thestrain currently causing the quick olive decline syndrome in Apulia since ca. 2013, less virulent Xf genotypes might have gone undetected for a long time, being confused with drought or fungal disease symptoms under Mediterranean climatic conditions. Indeed, the current widespread incidence and severity of the Pierce’s disease (PD) and Almond Leaf Scorch Disease (ALSD) in Mallorca Island can only be understood in this context of a 20-year introduction scenario. Our current epidemiological, phylogenetic anddendrochronological data onXf strains belonging to subsp. fastidiosaST1, and Xf subsp. multiplexST81, causing Pierce’s disease (PD) and ALSD, respectively, strongly suggest that they were overlooked for decades. Both subspecies were very likely transported from California to Mallorca with infected almond scions around 1995 and subsequently spread throughout the island by the local vector Philaenus spumarius. Our phylogenetic analysis based on WGS of isolates of both subspecies from Mallorca supports their Californian origin. Congruent with this, Xf DNA was consistently detected in the growing rings of infected almond trees from 2006 to the present and occasionally as far back as 1998. In the main focus in Son Carrió more than 50% of the almond trees diedand 90% of trees showed symptoms compatible with ALSD in 2012, but the aetiology of this problem was attributed to fungal trunk diseases, drought or field abandonment. We hypothesise that during the last 20 years, Xf subsp. multiplexST81 isolates have adapted to wild olive trees, widespread on the island, causing a mild dieback, and later on reaching the island of Menorca very likely on infected P. spumariustransported as a hitchhiker on ships moving between the islands.This research was funded by project E-RTA2017-00004-C06 from AEI-INIA Spain and FEDER and received financial support from the Ministry of Agriculture, Fishery and Food (Dirección General de la Sanidad de la Producción Agrària) of Spain and from ‘Govern de les Illes Balears’

Influence of immigration on tuberculosis transmission patterns in Castellón, Spain (2004–2007)

Objetivo Describir los patrones de transmisión de la tuberculosis en Castellón en un periodo de importantes cambios demográficos. Métodos Estudio prospectivo descriptivo de los pacientes con cultivo positivo en la provincia de Castellón entre 2004 y2007. Se describen los pacientes por año y nacionalidad, y se cotejan con los casos declarados a la Dirección General de Salud Pública (DGSP). Se estudia la población con patrón molecular disponible por RFLP (restriction fragment length polymorphism) y se analizan las variables de los pacientes agrupados (clusters) a partir de los datos de la DGSP y del Programa de Gestión del Laboratorio. Resultados Según la DGSP, la tasa global de tuberculosis por 100.000 habitantes en la provincia de Castellón fue de 15,7 en 2004, 19,9 en 2005, 18,2 en 2006 y 17,5 en 2007. En nuestro laboratorio se identificaron las cepas de 301 pacientes, que suponen el 77% (301/390) de los casos declarados y el 94% (301/321) aquellos con cultivo positivo. El porcentaje de tuberculosis en extranjeros aumentó hasta superar el 50% en 2007. Se disponía de estudio molecular en el 95% de los casos (286), con un 58% de españoles y un 42% de extranjeros. El porcentaje de agregación fue del 40%, con un 30% de clusters mixtos. Según el estudio convencional de contactos, el 85% de los pacientes en cluster habían sido considerados casos aislados. Conclusiones El aumento de la tasa de tuberculosis en Castellón se debe, principalmente, al creciente número de los casos en extranjeros. Disponer del estudio molecular de todos los pacientes con cultivo positivo nos ha permitido analizar cómo y dónde se transmite la tuberculosis. El 40% de los pacientes se agruparon en clusters, y eran mixtos un tercio de ellos, lo que indica una elevada integración de los inmigrantes.Background This study aimed to identify tuberculosis transmission patterns in Castellón in a period of major demographic changes. Methods A prospective study of patients with positive culture in the province of Castellon over a 4-year period (2004–2007) was carried out. Cases were described by year and nationality and were compared with those reported to the Department of Public Health. We studied the population with available molecular patterns, identified through restriction fragment length polymorphism (RFLP) and analyzed the variables from patient clusters, based on data collected in surveys of the Department of Health and the Laboratory Management Program. Results According to data from the Department of Public Health, the overall rate of tuberculosis per 100,000 inhabitants in the province of Castellón was 15.7 in 2004, 19.9 in 2005, 18.2 in 2006 and 17.5 in 2007. In our laboratory, strains were identified from 301 patients, representing 77% (301/390) of reported cases and 94% (301/321) of reported cases with a positive culture. The percentage of tuberculosis among foreigners increased with age, exceeding 50% in 2007. Molecular studies were available in 95% of patients (286); 58% were Spanish and 42% were foreigners, of whom 54% were Romanians. The cluster percentage was 40%, with 30% of mixed clusters. According to conventional contact studies, 85% of patients in clusters had been considered isolated cases. Conclusions The increased rate of tuberculosis in Castellón was mainly due to the increasing number of cases among foreigners, mostly Romanians. The availability of molecular studies in all patients with a positive culture allowed us to analyze how and where tuberculosis is transmitted in our province. Forty percent of the patients were grouped into clusters; of these, mixed clusters accounted for one third, indicating the high integration of immigrants in our area

Draft genome sequence of Pseudomonas stutzeri strain B1SMN1, a nitrogen-fixing and naphthalene-degrading strain isolated from wastewater

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Haloargentinum marplatensis gen. nov., sp. nov., a novel extremely halophilic bacterium isolated from salted-ripened anchovy (Engraulis anchoita)

A facultative aerobic, Gram-negative, motile, non-endospore forming and extremely halophilic bacterium, strain 11aii⊺, isolated from salted-ripened anchovy, was examined using a polyphasic approach to characterize and clarify its phylogenetic and taxonomic position. Sequences of the 16S rRNA gene revealed close relationships to species of the genera Lentibacillus and Virgibacillus (94.2% similarity). The organism grew optimally in the presence of 20-35 % NaCl. The major fatty acids of strain 11aii⊺ were C16:0 (42.1%) and anteiso-C15:0 (31.2%) and also presented iso-C16:0 (11.0%), anteiso-C17:0 (10.4%) and C18:0 (5.2%). Based on data presented here, strain 11aii⊺ is considered to represent a novel genus and species, for which the name Haloargentinum marplatensis gen. nov. sp. nov. is proposed with the strain 11aii⊺ as type strain.Fil: Perez, Silvina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata; Argentina. Universidad Nacional de Mar del Plata. Facultad de Ingeniería. Departamento de Ingeniería Química; Argentina. Universidad Nacional de Mar del Plata. Facultad de Ingeniería. Departamento de Ingeniería Química. Grupo de Investigación en Preservación y Calidad de Alimentos; ArgentinaFil: Gomila, Margarita. Universitat de les Illes Balears; EspañaFil: Murialdo, Silvia Elena. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata; Argentina. Universidad Nacional de Mar del Plata. Facultad de Ingeniería. Departamento de Ingeniería Química; Argentina. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas; Argentina. Universidad Nacional de Mar del Plata. Facultad de Ingeniería. Departamento de Ingeniería Química. Grupo de Ingeniería Bioquímica; ArgentinaFil: Ameztoy, Irene Mabel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata; Argentina. Universidad Nacional de Mar del Plata. Facultad de Ingeniería. Departamento de Ingeniería Química. Grupo de Investigación en Preservación y Calidad de Alimentos; ArgentinaFil: Gonzalez Escalona, Narjol. Center For Food Safety And Applied Nutrition; Estados UnidosFil: Ramirez, Elida Elvia. Universidad Nacional de Mar del Plata. Facultad de Ingeniería. Departamento de Ingeniería Química. Grupo de Investigación en Preservación y Calidad de Alimentos; ArgentinaFil: Yeannes, Maria Isabel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata; Argentina. Universidad Nacional de Mar del Plata. Facultad de Ingeniería. Departamento de Ingeniería Química; Argentina. Universidad Nacional de Mar del Plata. Facultad de Ingeniería. Departamento de Ingeniería Química. Grupo de Investigación en Preservación y Calidad de Alimentos; Argentin

Do Klebsiella pneumoniae environmental strains maintain clinically relevant genomic and phenotypic traits?

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Achromobacter marplatensis sp. nov., isolated from a pentachlorophenol contaminated soil

A polyphasic taxonomic approach was applied to the study of a Gram-negative bacterium (B2T) isolated from soil by selective enrichment with pentachlorophenol. 16S rRNA gene sequence analysis of strain B2T showed that the strain belongs to the genus Achromobacter within the Betaproteobacteria. The 16S rRNA gene sequence displayed more than 99 % similarity to the sequences of the type strains of all species of Achromobacter, with the highest sequence similarity to those of Achromobacter spanius CCM 7183T and A. piechaudii CCM 2986T (99.8 %). On the basis of phylogenetic analysis, genomic DNA&ndash;DNA relatedness and phenotypic characteristics, including chemotaxonomic (cellular fatty acid profile) analysis, a novel species is proposed, Achromobacter marplatensis sp. nov., with the type strain B2T ( = CCM 7608T = CCUG 56371T = CECT 7342T)