Development of two quantitative PCR assays for the detection of emerging opportunistic human pathogens belonging to the genus Phytobacter in routine diagnostics.

The genus Phytobacter (fam. Enterobacteriaceae) includes species like Phytobacter diazotrophicus and Phytobacter ursingii, which have emerged as opportunistic human pathogens, particularly affecting vulnerable populations such as pre-term infants and immunocompromised patients. Traditional biochemical and molecular methods have struggled to accurately identify Phytobacter species in clinical diagnostics.

Fire blight cases in Almaty Region of Kazakhstan in the proximity of wild apple distribution area.

Fire blight caused by reached Kazakhstan in 2008. Here, the disease poses a threat not only to agricultural production of apples and pears, but also to the forests of wild , the progenitor of most domesticated apple varieties worldwide. In the period 2019-2021, the spread of fire blight in the growth area of wild apples was limited by the weather conditions.

Dissemination of NDM-producing bacteria in Southern Brazil.

Background: The dissemination of NDM-1 carbapenemases (New Delhi Metallo-β-lactamase) is a global public health problem, mainly in developing countries. The aim of this study was to characterize the spread of NDM-producing bacteria in the Southern Brazilian states analyzing epidemiological, molecular, and antimicrobial susceptibility aspects.

Methods: A total of 10,684 carbapenem-resistant isolates of Enterobacterales, Pseudomonas spp.

Comparative genomics to examine the endophytic potential of Pantoea agglomerans DAPP-PG 734.

Pantoea agglomerans DAPP-PG 734 was isolated as endophyte from knots (tumors) caused by Pseudomonas savastanoi pv. savastanoi DAPP-PG 722 in olive trees. To understand the plant pathogen-endophyte interaction on a genomic level, the whole genome of P.

Resolving taxonomic confusion: establishing the genus Phytobacter on the list of clinically relevant Enterobacteriaceae.

Although many clinically significant strains belonging to the family Enterobacteriaceae fall into a restricted number of genera and species, there is still a substantial number of isolates that elude this classification and for which proper identification remains challenging. With the current improvements in the field of genomics, it is not only possible to generate high-quality data to accurately identify individual nosocomial isolates at the species level and understand their pathogenic potential but also to analyse retrospectively the genome sequence databases to identify past recurrences of a specific organism, particularly those originally published under an incorrect or outdated taxonomy. We propose a general use of this approach to classify further clinically relevant taxa, i.

from Intestine of Confers Colonization-Resistance against Using Flagellin (FliC) as an Inhibition Factor.

Symbiotic microorganisms in the intestinal tract can influence the general fitness of their hosts and contribute to protecting them against invading pathogens. In this study, we obtained isolate SCO41 from the gut of free-living nematode that displayed strong colonization-resistance against invading biocontrol bacterium B16. The colonization-resistance phenotype was found to be mediated by a 37-kDa extracellular protein that was identified as flagellin (FliC).

Complete Genome and Plasmid Sequence Data of Three Strains of pv. , the Bacterium Responsible for Bacterial Blight of Hazelnut.

pv. is the causal agent of bacterial blight of hazelnut. The bacterium has been listed as an A2 quarantine pathogen in Europe since 1978 and on the regulated non-quarantine pest list since 2019.

Synergistic interaction between the type III secretion system of the endophytic bacterium Pantoea agglomerans DAPP-PG 734 and the virulence of the causal agent of olive knot Pseudomonas savastanoi pv. savastanoi DAPP-PG 722.

The endophytic bacterium Pantoea agglomerans DAPP-PG 734 was previously isolated from olive knots caused by infection with Pseudomonas savastanoi pv. savastanoi DAPP-PG 722. Whole-genome analysis of this P.

Microbial communities in floodplain ecosystems in relation to altered flow regimes and experimental flooding.

River floodplains are spatially diverse ecosystems that respond quickly to flow variations and disturbance. However, it remains unclear how flow alteration and hydrological disturbance impacts the structure and biodiversity of complex microbial communities in these ecosystems. Here, we examined the spatial and seasonal dynamics of microbial communities in aquatic (benthic) and terrestrial habitats of three hydrologically contrasting (natural flow, residual flow, hydropeaking flow) floodplain systems.

Broad diversity of bacteria degrading 17ß-estradiol-3-sulfate isolated from river sediment and biofilm at a wastewater treatment plant discharge.

Conjugated estrogens, such as 17β-estradiol-3-sulfate (E2-3S), can be released into aquatic environments through wastewater treatment plants (WWTP). There, they are microbiologically degraded into free estrogens, which can have harmful effects on aquatic wildlife. Here, the degradation of E2-3S in environmental samples taken upstream, downstream and at the effluent of a WWTP was assessed.

Environmental parameters and microbial community profiles as indication towards microbial activities and diversity in aquaponic system compartments.

Background: An aquaponic system couples cultivation of plants and fish in the same aqueous medium. The system consists of interconnected compartments for fish rearing and plant production, as well as for water filtration, with all compartments hosting diverse microbial communities, which interact within the system. Due to the design, function and operation mode of the individual compartments, each of them exhibits unique biotic and abiotic conditions.

Complete or High-Quality Draft Genome Sequences of Six Xanthomonas hortorum Strains Sequenced with Short- and Long-Read Technologies.

We report the genome sequences of six species-level clade members, pathovars taraxaci, pelargonii, cynarae, and gardneri (complete genome sequences) and pathovars carotae and vitians (high-quality draft genome sequences). Both short- and long-read sequencing technologies were used.

Isolation and Identification of Actinomycetes Strains from Switzerland and their Biotechnological Potential.

Actinomycetes strains isolated from different habitats in Switzerland were investigated for production of antibacterial and antitumoral compounds. Based on partial 16S rRNA gene sequences, the isolated strains were identified to genus level. as the largest genus of was isolated the most frequently.

sp. nov., a novel endophytic, N fixing, plant growth promoting isolated from oil palm ().

A novel strain S29 with high nitrogen fixing ability was isolated from surface-sterilized leaf tissues of oil palm () growing in Science Park II, Singapore. On the basis of 16S rRNA gene analysis and multilocus sequence typing with the and genes, strain S29 was a member of the genus , with ATCC 27989 and LS 8 as its closest relatives. Unique biochemical features that differentiated strain S29 from its closest relatives were the ability to utilize melibiose, -cyclodextrin, glycogen, adonital, d-arabitol, -inositol and xylitol.

Updated Genome Sequence and Annotation for the Full Genome of Pseudomonas protegens CHA0.

Minor differences in the previously obtained genome of CHA0 were detected after resequencing the strain. Based on this, the genome size slightly increased. Additionally, we performed a manual annotation of genes involved in biocontrol and insect pathogenicity.

High-Quality Draft Genome Sequence of Pseudomonas reidholzensis Strain CCOS 865.

We have sequenced and assembled the genome of Pseudomonas reidholzensis CCOS 865, which was isolated in 2014 from forest soil. Members of the genus Pseudomonas play important roles in environmental systems and are utilized in many biotechnological processes. The genome of this species may provide an important resource for the discovery of novel enzyme activities.

High-Quality Draft Genome Sequence of Pseudomonas wadenswilerensis CCOS 864.

Pseudomonas wadenswilerensis CCOS 864 was isolated in 2014 from forest soil. The organism belongs taxonomically to the Pseudomonas putida group, members of which have been well studied for their potential in biotechnological applications. We present here the draft genome sequence of P.

Molecular investigation of isolates from a multistate polymicrobial outbreak associated with contaminated total parenteral nutrition in Brazil.

Background: Between November 2013 and June 2014, 56 cases of bacteremia (15 deaths) associated with the use of Total Parenteral Nutrition (TPN) and/or calcium gluconate (CG) were reported in four Brazilian states.

Methods: We analyzed 73 bacterial isolates from four states: 45 from blood, 25 from TPN and three from CG, originally identified as Acinetobacter baumannii, Rhizobium radiobacter, Pantoea sp. or Enterobacteriaceae using molecular methods.

Genome-based population structure analysis of the strawberry plant pathogen Xanthomonas fragariae reveals two distinct groups that evolved independently before its species description.

Xanthomonas fragariae is a quarantine organism in Europe, causing angular leaf spots on strawberry plants. It is spreading worldwide in strawberry-producing regions due to import of plant material through trade and human activities. In order to resolve the population structure at the strain level, we have employed high-resolution molecular typing tools on a comprehensive strain collection representing global and temporal distribution of the pathogen.

Emended description of the genus Phytobacter, its type species Phytobacter diazotrophicus (Zhang 2008) and description of Phytobacter ursingii sp. nov.

The species Phytobacter diazotrophicus and the associated genus Phytobacter were originally described by Zhanget al. [Arch Microbiol189 (2008), 431-439] on the basis of few endophytic nitrogen-fixing bacteria isolated from wild rice (Oryza rufipogon) in China. In this study, we demonstrate that a number of clinical isolates that were either described in the literature, preserved in culture collections, or obtained during a 2013 multi-state sepsis outbreak in Brazil also belong to the same genus.

Role of the type VI secretion systems during disease interactions of Erwinia amylovora with its plant host.

Background: Type VI secretion systems (T6SS) are widespread among Gram-negative bacteria and have a potential role as essential virulence factors or to maintain symbiotic interactions. Three T6SS gene clusters were identified in the genome of E. amylovora CFBP 1430, of which T6SS-1 and T6SS-3 represent complete T6SS machineries, while T6SS-2 is reduced in its gene content.

Pathogen recognition in compatible plant-microbe interactions.

Microbial infections in plant leaves remain a major challenge in agriculture. Hence an understanding of disease mechanisms at the molecular level is of paramount importance for identifying possible intervention points for their control. Whole-transcriptome changes during early disease stages in susceptible plant species are less well-documented than those of resistant ones.

sp. nov., a cosmopolitan epiphyte originally isolated from pome fruit trees.

A survey to obtain potential antagonists of pome fruit tree diseases yielded two yellow epiphytic bacterial isolates morphologically similar to , but showing no biocontrol activity. Whole-cell MALDI-TOF mass spectrometry and analysis of 16S rRNA gene and sequences suggested the possibility of a novel species with a phylogenetic position in either the genus or the genus . Multi-locus sequence analysis (MLSA) placed the two strains in the genus and supported their classification as a novel species.