Genome-Based Taxonomy of Species in the Pseudomonas syringae and Pseudomonas lutea Phylogenetic Groups and Proposal of Pseudomonas maioricensis sp. nov., Isolated from Agricultural Soil.

Species in the phylogenetic group Pseudomonas syringae are considered the most relevant plant pathogenic bacteria, but their taxonomy is still controversial. Twenty named species are validated in the current taxonomy of this group and in recent years many strains have been genome-sequenced, putative new species have been proposed and an update in the taxonomy is needed. A taxonomic study based on the core-genome phylogeny, genomic indices (ANI and GGDC) and gene content (phyletic pattern and Jaccard index) have been applied to clarify the taxonomy of the group. A phylogenomic analysis demonstrates that at least 50 phylogenomic species can be delineated within the group and that many strains whose genomes have been deposited in the databases are not correctly classified at the species level. Other species names, like "Pseudomonas coronafaciens", have been proposed but are not validated yet. One of the putative new species is taxonomically described, and the name Pseudomonas maioricensis sp. nov. is proposed. The taxonomies of Pseudomonas avellanae and Pseudomonas viridiflava are discussed in detail as case studies. Correct strain identification is a prerequisite for many studies, and therefore, criteria are given to facilitate identification.

CMR-based right ventricular strain analysis in cardiac amyloidosis and its potential as a supportive diagnostic feature.

Background: Right ventricular (RV) strain has provided valuable prognostic information for patients with cardiac amyloidosis (CA). However, the extent to which RV strain and strain rate can differentiate CA is not yet clinically established. CA underdiagnosis delays treatment strategies and exacerbates patient prognosis. Aims: Evaluation of cardiac magnetic resonance (CMR) quantified RV global and regional strain of CA and HCM patients along with CA subtypes. Methods: CMR feature tracking attained longitudinal, radial and circumferential global and regional strain in 47 control subjects (CTRL), 43 CA-, 20 hypertrophic cardiomyopathy- (HCM) patients. CA patients were subdivided in 21 transthyretin-related amyloidosis (ATTR) and 20 acquired immunoglobulin light chain (AL) patients. Strain data and baseline clinical parameters were statistically analysed with respect to diagnostic performance and discriminatory power between the different clinical entities. Results: Effective differentiation of CA from HCM patients was achieved utilizing global longitudinal (GLS: 16.5 ± 3.9% vs. -21.3 ± 6.7%, p = 0.032), radial (GRS: 11.7 ± 5.3% vs. 16.5 ± 7.1%, p < 0.001) and circumferential (GCS: -7.6 ± 4.0% vs. -9.4 ± 4.4%, p = 0.015) right ventricular strain. Highest strain-based hypertrophic phenotype differentiation was attained using GRS (AUC = 0.86). Binomial regression found right ventricular ejection fraction (RV-EF) (p = 0.017) to be a significant predictor of CA-HCM differentiation. CA subtypes had comparable cardiac strains. Conclusion: CMR-derived RV global strains and various regional longitudinal strains provide discriminative radiological features for CA-HCM differentiation. However, in terms of feasibility, cine-derived RV-EF quantification may suffice for efficient differential diagnostic support.

Stutzerimonas decontaminans sp. nov. isolated from marine polluted sediments.

Strains 19SMN4T and ST27MN3 were isolated from marine sediments after enrichment with 2-methylnaphthalene and were classified as Pseudomonas stutzeri genomovar 4. Four other strains, BG 2, HT20, HT24, and A7, were isolated from sulphide-oxidizing bioreactors or activated sludge affiliated with the same clade in the 16S rRNA phylogenetic tree. P. stutzeri has been recently reclassified as a new genus, Stutzerimonas, and a preliminary analysis indicated that the strains in this study were distinct from any classified Stutzerimonas and are considered representatives of phylogenomic species 4 (pgs4). Strains 19SMN4T and ST27MN3 were extensively characterized with phenotypic, chemotaxonomic, genomic and phylogenomic data. Strain 19SMN4T had a well-characterized naphthalene degradative plasmid that has been compared with other plasmids, while in strain ST27MN3, the naphthalene degradative genes were detected in the chromosome sequence. Phylogenomic analysis of the core gene sequences showed that strains 19SMN4T and ST27MN3 shared 3,995 genes and were closely related to members of the species "Stutzerimonas songnenensis" and Stutzerimonas perfectomarina, as well as to the Stutzerimonas phylogenomic species, pgs9, pgs16 and pgs24. The aggregate average nucleotide identity (ANI) indicated that strains 19SMN4T and ST27MN3 belonged to the same genomic species, whereas the genomic indices with their closest-related type strains were below the accepted species threshold (95 %). We therefore conclude that strains 19SMN4T and ST27MN3 represent a novel species of Stutzerimonas, for which the name Stutzerimonas decontaminans is proposed; the type strain is 19SMN4T (=CCUG44593T = DSM6084T = LMG18521T).

Cardiovascular Magnetic Resonance Imaging-Based Right Atrial Strain Analysis of Cardiac Amyloidosis.

Background: Cardiac amyloidosis (CA) manifests in a hypertrophic phenotype with a poor prognosis, making differentiation from hypertrophic cardiomyopathy (HCM) challenging and delaying early treatment. The extent to which magnetic resonance imaging (MRI) quantifies the right atrial strain (RAS) and strain rate (RASR), providing valuable diagnostic information, is not yet clinically established. Aims: This study assesses diagnostic differences in the longitudinal RAS and RASR between CA and HCM patients, control subjects (CTRL) and CA subtypes in addition to the impact of atrial fibrillation (AF) on the right atrial function in CA patients. The RAS and RASR of tricuspid regurgitation (TR) patients are used to assess the potential for diagnostic overlap. Methods: RAS and RASR quantification was conducted via MRI feature-tracking for biopsy-confirmed CA patients with subtypes identified. Strain parameters were compared for CTRL, HCM and TR patients. Post hoc testing identified intergroup differences. Results: In total, 41 CA patients were compared to 47 CTRL, 20 HCM and 31 TR patients. Reservoir (R), conduit and booster RAS and RASRs allow for significant differentiation (p < 0.001) between CA and HCM patients (R: 10.6 ± 14.3% vs. R: 33.5 ± 16.3%) and CTRL (R: 44.6 ± 15.7%). Booster and reservoir RAS and RASRs qualified as reliable diagnostic tests (AUC > 0.8). CA patients with AF, in contrast to sinus rhythm, demonstrated a significantly impaired reservoir RAS and RASR and booster RASR. The discriminative power of RAS for CA vs. TR was insufficient (R: 10.6% ± 14.3% vs. 7.0% ± 6.0%, p = 0.069). Differentiation between 21 transthyretin and 20 light-chain amyloidosis subtypes was not achievable (R: 0.7% ± 1.0% vs. 0.7% ± 1.0%, p = 0.827). Conclusion: The MRI-derived RAS and RASR are impaired in CA patients and may support noninvasive differentiation between CA, HCM and CTRL.

A Machine Learning Challenge: Detection of Cardiac Amyloidosis Based on Bi-Atrial and Right Ventricular Strain and Cardiac Function.

BACKGROUND: This study challenges state-of-the-art cardiac amyloidosis (CA) diagnostics by feeding multi-chamber strain and cardiac function into supervised machine (SVM) learning algorithms. METHODS: Forty-three CA (32 males; 79 years (IQR 71; 85)), 20 patients with hypertrophic cardiomyopathy (HCM, 10 males; 63.9 years (±7.4)) and 44 healthy controls (CTRL, 23 males; 56.3 years (IQR 52.5; 62.9)) received cardiovascular magnetic resonance imaging. Left atrial, right atrial and right ventricular strain parameters and cardiac function generated a 41-feature matrix for decision tree (DT), k-nearest neighbor (KNN), SVM linear and SVM radial basis function (RBF) kernel algorithm processing. A 10-feature principal component analysis (PCA) was conducted using SVM linear and RBF. RESULTS: Forty-one features resulted in diagnostic accuracies of 87.9% (AUC = 0.960) for SVM linear, 90.9% (0.996; Precision = 94%; Sensitivity = 100%; F1-Score = 97%) using RBF kernel, 84.9% (0.970) for KNN, and 78.8% (0.787) for DT. The 10-feature PCA achieved 78.9% (0.962) via linear SVM and 81.8% (0.996) via RBF SVM. Explained variance presented bi-atrial longitudinal strain and left and right atrial ejection fraction as valuable CA predictors. CONCLUSION: SVM RBF kernel achieved competitive diagnostic accuracies under supervised conditions. Machine learning of multi-chamber cardiac strain and function may offer novel perspectives for non-contrast clinical decision-support systems in CA diagnostics.

Genome-Based Taxonomy of the Genus Stutzerimonas and Proposal of S. frequens sp. nov. and S. degradans sp. nov. and Emended Descriptions of S. perfectomarina and S. chloritidismutans.

Stutzerimonas is a recently proposed genus within the Pseudomonadaceae comprising strains in the formerly phylogenetic group of Pseudomonas stutzeri. At least sixteen named species have to be included in the genus, together with 22 genomovars of Stutzerimonas stutzeri. To clarify the taxonomy of Stutzerimonas, a core-genome phylogeny of 200 strains in the genus was inferred and monophyletic strains with average nucleotide identities (ANIb) with values equal to or higher than 95 were grouped in the same phylogenomic species. A total of 45 phylogenomic species within the genus Stutzerimonas were detected in the present study. Sixteen phylogenomic species correspond to already named species, although three of them are not yet validated and two are proposed in the present study. A synonymy was detected between P. kunmingensis and S. chloritidismutans, both members of phylogenomic species 3, with a prevalence of the S. chloritidismutans name. The correspondence of the phylogenomic species to the genome taxonomy database classification (GTDB taxonomy) is discussed. Combining phylogenomic and phenotypic data, two novel species are described (Stutzerimonas frequens and Stutzerimonas degradans) and two species descriptions are emended (Stutzerimonas perfectomarina and Stutzerimonas chloritidismutans).

Past, present and future of the boundaries of the Pseudomonas genus: Proposal of Stutzerimonas gen. Nov.

Pseudomonas is one the best studied bacterial genera, and it is the genus with the highest number of species among the gram-negative bacteria. Pseudomonas spp. are widely distributed and play relevant ecological roles; several species are commensal or pathogenic to humans, animals and plants. The main aim of the present minireview is the discussion of how the Pseudomonas taxonomy has evolved with the development of bacterial taxonomy since the first description of the genus in 1894. We discuss how the successive implementation of novel methodologies has influenced the taxonomy of the genus and, vice versa, how the taxonomic studies developed in Pseudomonas have introduced novel tools and concepts to bacterial taxonomy. Current phylogenomic analyses of the family Pseudomonadaceae demonstrate that a considerable number of named Pseudomonas spp. are not monophyletic with P. aeruginosa, the type species of the genus, and that a reorganization of several genera can be foreseen. Phylogenomics of Pseudomonas, Azomonas and Azotobacter within the Pseudomonadaceae is presented as a case study. Five new genus names are delineated to accommodate five well-defined phylogenetic branches that are supported by the shared genes in each group, and two of them can be differentiated by physiological and ecological properties: the recently described genus Halopseudomonas and the genus Stutzerimonas proposed in the present study. Five former Pseudomonas species are transferred to Halopseudomonas and 10 species to Stutzerimonas.

Left-Ventricular Reference Myocardial Strain Assessed by Cardiovascular Magnetic Resonance Feature Tracking and fSENC-Impact of Temporal Resolution and Cardiac Muscle Mass.

Aims: Cardiac strain parameters are increasingly measured to overcome shortcomings of ejection fraction. For broad clinical use, this study provides reference values for the two strain assessment methods feature tracking (FT) and fast strain-encoded (fSENC) cardiovascular magnetic resonance (CMR) imaging, including the child/adolescent group and systematically evaluates the influence of temporal resolution and muscle mass on strain. Methods and Results: Global longitudinal (GLS), circumferential (GCS), and radial (GRS) strain values in 181 participants (54% women, 11-70 years) without cardiac illness were assessed with FT (CVI42® software). GLS and GCS were also analyzed using fSENC (MyoStrain® software) in a subgroup of 84 participants (60% women). Fourteen patients suffering hypertrophic cardiomyopathy (HCM) were examined with both techniques. CMR examinations were done on a 3.0T MR-system. FT-GLS, FT-GCS, and FT-GRS were -16.9 ± 1.8%, -19.2 ± 2.1% and 34.2 ± 6.1%. fSENC-GLS was higher at -20.3 ± 1.8% (p < 0.001). fSENC-GCS was comparable at-19.7 ± 1.8% (p = 0.06). All values were lower in men (p < 0.001). Cardiac muscle mass correlated (p < 0.001) with FT-GLS (r = 0.433), FT-GCS (r = 0.483) as well as FT-GRS (r = -0.464) and acts as partial mediator for sex differences. FT-GCS, FT-GRS and fSENC-GLS correlated weakly with age. FT strain values were significantly lower at lower cine temporal resolutions, represented by heart rates (r = -0.301, -0.379, 0.385) and 28 or 45 cardiac phases per cardiac cycle (0.3-1.9% differences). All values were lower in HCM patients than in matched controls (p < 0.01). Cut-off values were -15.0% (FT-GLS), -19.3% (FT-GCS), 32.7% (FT-GRS), -17.2% (fSENC-GLS), and -17.7% (fSENC-GCS). Conclusion: The analysis of reference values highlights the influence of gender, temporal resolution, cardiac muscle mass and age on myocardial strain values.

In Silico Analysis of the Enzymes Involved in Haloarchaeal Denitrification.

During the last century, anthropogenic activities such as fertilization have led to an increase in pollution in many ecosystems by nitrogen compounds. Consequently, researchers aim to reduce nitrogen pollutants following different strategies. Some haloarchaea, owing to their denitrifier metabolism, have been proposed as good model organisms for the removal of not only nitrate, nitrite, and ammonium, but also (per)chlorates and bromate in brines and saline wastewater. Bacterial denitrification has been extensively described at the physiological, biochemical, and genetic levels. However, their haloarchaea counterparts remain poorly described. In previous work the model structure of nitric oxide reductase was analysed. In this study, a bioinformatic analysis of the sequences and the structural models of the nitrate, nitrite and nitrous oxide reductases has been described for the first time in the haloarchaeon model Haloferax mediterranei. The main residues involved in the catalytic mechanism and in the coordination of the metal centres have been explored to shed light on their structural characterization and classification. These results set the basis for understanding the molecular mechanism for haloarchaeal denitrification, necessary for the use and optimization of these microorganisms in bioremediation of saline environments among other potential applications including bioremediation of industrial waters.

Pseudomonas arcuscaelestis sp. nov., isolated from rainbow trout and water.

Cells of strains P66T, V1 and W15Feb18 are Gram-stain-negative short rods and motile by one polar flagellum. Strain P66T was isolated from rainbow trout (Oncorhynchus mykiss) cultivated at a fish farm in Turkey. Strain V1 was isolated from sand of an intertidal shore on the Galicia coast in Spain and strain W15Feb18 was isolated from water collected at the Woluwe River in Belgium. Based on 16S rRNA sequence similarity values, the strains were grouped under the genus Pseudomonas and the Pseudomonas putida phylogenetic group of species. The DNA G+C content ranged from 58.5 to 58.9 mol%. The strains were characterized phenotypically by the API 20NE and Biolog GEN III tests, and chemotaxonomically by their whole-cell MALDI-TOF MS protein profiles and fatty acid contents. The absence of the hydrolysis of gelatin and the assimilation of arabinose, mannose and mannitol differentiated these strains from the closest species, Pseudomonas alkylphenolica. The major fatty acid components were C16:0 (29.91-31.68 %) and summed feature 3 (36.44-37.55 %). Multilocus sequence analysis with four and 83 housekeeping gene sequences and a core proteome analysis showed that these strains formed a phylogenetic cluster in the P. putida group of species. Genome comparisons by the average nucleotide identity based on blast and the Genome-to-Genome Distance Calculator demonstrated that the three strains belonged to the same genomic species and were distant from any known species, with similarity values lower than the thresholds established for species in the genus Pseudomonas. These data permitted us to conclude that strains P66T, V1 and W15Feb18 belong to a novel species in the genus Pseudomonas, for which the name Pseudomonas arcuscaelestis sp. nov. is proposed. The type strain is P66T (=CECT 30176T=CCUG 74872T). The other strains have been deposited in the CECT with the corresponding collection numbers: V1 (=CECT 30356) and W15Feb18 (=CECT 30355).

Pseudomonas lalucatii sp. nov. isolated from Vallgornera, a karstic cave in Mallorca, Western Mediterranean.

Caves are extreme underground environments colonized by oligotrophic bacterial communities that influence mineral transformations. The identification at the species level is important and this study aims to the taxonomic characterisation of four bacterial strains previously isolated from rock surfaces and water samples from a karstic cave located on Mallorca (Spain) that were assigned to the genus Pseudomonas according to 16S rRNA nucleotide sequence analysis. Sequence analysis of the RNA polymerase sigma factor gene (rpoD) allocated these strains to the P. fluorescens lineage within the P. anguilliseptica phylogenetic group, close to the P. benzenivorans type strain. A polyphasic taxonomic approach included phenotypic characterization, fatty acid composition analysis, and whole-cell protein profiling, together with phylogenomic data. The results supported the proposal of a new species in the Pseudomonas genus. Characteristic fatty acid methyl esters of members of the Pseudomonas genus were present (C16:0, C10:0 3-OH, C12:0 2-OH and C12:0 3-OH) and the C12:1 3OH content differentiated these strains from P. benzenivorans. The genomic G + C mol% content of the four sequenced genomes was 66.9%. The average nucleotide indices based on BLAST analysis and the calculation of genome-to-genome distance with respect to their closest relative were lower than 88% and 30%, respectively. These data confirm that the four isolates, R1b-4, R1b-52A, A2bC-1 and R1b-54T, represent a new species, for which the name Pseudomonas lalucatii is proposed, with strain R1b-54T as the type strain (=CCUG 74754T = CECT 30179T). This is the first species in the P. anguilliseptica group isolated from this extreme habitat.

Pseudomonas anatoliensis sp. nov and Pseudomonas iridis sp. nov. isolated from fish.

In a study carried out between 2013 and 2018 in fish farms in Turkey, several putative novel species were isolated. The 16S rRNA nucleotide sequences of fourteen strains of Gram-negative rods, which were isolated from asymptomatic and symptomatic rainbow trouts (Onchorhynchus mykiss), placed them under the genus Pseudomonas. The similarity values of the concatenated nucleotide sequences of the rpoD, rpoB, gyrB and 16S rRNA genes clustered these isolates into the P. fluorescens phylogenetic group of species and into the Pseudomonas koreensis subgroup, close to Pseudomonas helmanticensis and Pseudomonas baetica. An isolate of a totally different origin, strain CCUG 67011, clustered with these isolates. Phenotypic characterization, together with the chemotaxonomic data, whole-cell MALDI-TOF MS and fatty acids methyl esters analyses were performed. The DNA G + C content was 58.7 mol% for isolate P9T and 58.8 mol% for isolate P42T. The phylogenomic analysis and whole genome nucleotide sequences of four of these isolates confirmed that the isolates P9T, P25 and P141, represent a novel species for which the name Pseudomonas anatoliensis sp. nov. is proposed, with P9T as the type strain (=CCUG 74755T = CECT 3172T). The isolates P1, P2, P10, P27, P30, P24a, P42T, P117, P139, P152 and CCUG 67011 represent another novel sècies, for which the name Pseudomonas iridis sp. nov. is proposed, with P42T as the type strain (=CCUG 74870T = CECT 3174T).

Diversity of pathogenic Pseudomonas isolated from citrus in Tunisia.

The damages observed in Tunisian citrus orchards have prompted studies on the Pseudomonas spp. responsible for blast and black pit. Prospective orchards between 2015 and 2017 showed that the diseases rapidly spread geographically and to new cultivars. A screening of Pseudomonas spp. isolated from symptomatic trees revealed their wide diversity according to phylogenetic analysis of their housekeeping rpoD and cts genes. The majority of strains were affiliated to Pseudomonas syringae pv. syringae (Phylogroup PG02b), previously described in Tunisia. However, they exhibited various BOX-PCR fingerprints and were not clonal. This work demonstrated, for the first time in Tunisia, the involvement of Pseudomonas cerasi (PG02a) and Pseudomonas congelans (PG02c). The latter did not show significant pathogenicity on citrus, but was pathogenic on cantaloupe and active for ice nucleation that could play a role in the disease. A comparative phylogenetic study of citrus pathogens from Iran, Montenegro and Tunisia revealed that P. syringae (PG02b) strains are closely related but again not clonal. Interestingly P. cerasi (PG02a) was isolated in two countries and seems to outspread. However, its role in the diseases is not fully understood and it should be monitored in future studies. The diversity of pathogenic Pseudomonas spp. and the extension of the diseases highlight that they have become complex and synergistic. It opens questions about which factors favor diseases and how to fight against them efficiently and with sustainable means.

Pseudomonas Species Diversity Along the Danube River Assessed by rpoD Gene Sequence and MALDI-TOF MS Analyses of Cultivated Strains.

A collection of 611 Pseudomonas isolated from 14 sampling sites along the Danube River were identified previously by MALDI-TOF MS with the VITEK MS system and were grouped in 53 clusters by their main protein profiles. The strains were identified in the present study at the phylospecies level by rpoD gene sequencing. Partial sequences of the rpoD gene of 190 isolates representatives of all clusters were analyzed. Strains in the same MALDI-TOF cluster were grouped in the same phylospecies when they shared a minimum 95% similarity in their rpoD sequences. The sequenced strains were assigned to 34 known species (108 strains) and to 32 possible new species (82 strains). The 611 strains were identified at the phylospecies level combining both methods. Most strains were assigned to phylospecies in the Pseudomonas putida phylogenetic group of species. Special attention was given to 14 multidrug resistant strains that could not be assigned to any known Pseudomonas species and were considered environmental reservoir of antibiotic resistance genes. Coverage indices and rarefaction curves demonstrated that at least 50% of the Pseudomonas species in the Danube River able to grow in the isolation conditions have been identified at the species level. Main objectives were the confirmation of the correlation between the protein profile clusters detected by MALDI-TOF MS and the phylogeny of Pseudomonas strains based on the rpoD gene sequence, the assessment of the higher species discriminative power of the rpoD gene sequence, as well as the estimation of the high diversity of Pseudomonas ssp. along the Danube river. This study highlights the Pseudomonas species diversity in freshwater ecosystems and the usefulness of the combination of MALDI-TOF mass spectrometry for the dereplication of large sets of strains and the rpoD gene sequences for rapid and accurate identifications at the species level.

Pseudomonas sivasensis sp. nov. isolated from farm fisheries in Turkey.

A study of 91 isolates from fish farms in Turkey showed that isolates P7T, P11, P24b, P29, P72, P73 and P158 belonged to the genus Pseudomonas according to 16S rRNA nucleotide sequence analysis. The analysis of the sequences of the RNA polymerase sigma factor gene (rpoD) located these strains in the Pseudomonas fluorescens lineage of species within the P. fluorescens subgroup, close to the cluster composed of the species Pseudomonas grimontii, Pseudomonas marginalis and Pseudomonas panacis. Based on similarities in the 16S rRNA and rpoD gene sequences of three previously isolated strains from other origins (CCUG 57209, CCUG 62357 and W5.2-93) linked them to the same cluster. A polyphasic taxonomic approach including phenotypic characterization, fatty acid composition, and multilocus sequence analysis, together with whole-cell MALDI-TOF data, corroborated this assumption. The genome G+C mol% contents were 59.48 and 59.71, respectively. The average nucleotide indices based on BLAST analysis and the genome-to-genome distance calculation for the P7T and CCUG 57209 strains with their closest relative, P. grimontii, were 88.16-88.29% and 38.10-38.20%, respectively. These data confirm that isolates P7T, P11, P24b, P29, P72, P73, P158, CCUG 57209, CCUG 62357 and W5.2-93 represent a new species for which the name Pseudomonas sivasensis is proposed, with P7T as a type strain (=CCUG 74260T= and CECT30107T).

Genomics in Bacterial Taxonomy: Impact on the Genus Pseudomonas.

The introduction of genomics is profoundly changing current bacterial taxonomy. Phylogenomics provides accurate methods for delineating species and allows us to infer the phylogeny of higher taxonomic ranks as well as those at the subspecies level. We present as a model the currently accepted taxonomy of the genus Pseudomonas and how it can be modified when new taxonomic methodologies are applied. A phylogeny of the species in the genus deduced from analyses of gene sequences or by whole genome comparison with different algorithms allows three main conclusions: (i) several named species are synonymous and have to be reorganized in a single genomic species; (ii) many strains assigned to known species have to be proposed as new genomic species within the genus; and (iii) the main phylogenetic groups defined by 4-, 100- and 120-gene multilocus sequence analyses are concordant with the groupings in the whole genome analyses. Moreover, the boundaries of the genus Pseudomonas are also discussed based on phylogenomic analyses in relation to other genera in the family Pseudomonadaceae. The new technologies will result in a substantial increase in the number of species and probably split the current genus into several genera or subgenera, although these classifications have to be supported by a polyphasic taxonomic approach.

Pseudomonas nosocomialis sp. nov., isolated from clinical specimens.

Strains A31/70T, CCUG 58779 and SD129 were Gram-stain-negative, short rods, motile by one polar flagellum and isolated from clinical specimens in Botswana, Sweden and Spain, respectively. The 16S rRNA sequence similarity values grouped them in the Pseudomonas stutzeri phylogenetic group of species. The DNA G+C content ranged from 65.5 to 65.7 mol%. The strains were characterized phenotypically by the API 20NE and Biolog GEN III tests, and chemotaxonomically by their whole-cell MALDI-TOF MS protein profiles and by their fatty acid contents. The absence of the arginine dihydrolase and the hydrolysis of gelatin differentiated these strains from the closest species, Pseudomonas azotifigens. The major fatty acid contents were summed feature 8 (38.6 %), C16 : 0 (22.6 %), summed feature 3 (20.5 %) and C12 : 0 (8.4 %). Multilocus sequence analysis with three housekeeping gene sequences (rpoD, gyrB and 16S rRNA) together with whole-genome comparisons indicated that these strains cluster together in the phylogenetic analysis and their similarity values were lower than the thresholds established for species in the genus Pseudomonas. These results permit us to conclude that strains A31/70T, CCUG 58779 and SD129 belong to a novel species in the genus Pseudomonas for which the name Pseudomonas nosocomialis sp. nov. is proposed. The type strain is A31/70T (=CECT 9981T=CCUG 73638T).