scholarly journals Introduction and adaptation of an emerging pathogen to olive trees in Italy

2021 ◽  
Vol 7 (12) ◽  
Author(s):  
Anne Sicard ◽  
Maria Saponari ◽  
Mathieu Vanhove ◽  
Andreina I. Castillo ◽  
Annalisa Giampetruzzi ◽  
...  
Keyword(s):  
Central America ◽  
Type Species ◽  
Invasive Plant ◽  
Content Type ◽  
Link Type ◽  
Political Crises ◽  
Relevant Today ◽  
Wide Range ◽  
Olive Quick Decline Syndrome ◽  
Olive Trees

The invasive plant pathogen Xylella fastidiosa currently threatens European flora through the loss of economically and culturally important host plants. This emerging vector-borne bacterium, native to the Americas, causes several important diseases in a wide range of plants including crops, ornamentals, and trees. Previously absent from Europe, and considered a quarantine pathogen, X. fastidiosa was first detected in Apulia, Italy in 2013 associated with a devastating disease of olive trees (Olive Quick Decline Syndrome, OQDS). OQDS has led to significant economic, environmental, cultural, as well as political crises. Although the biology of X. fastidiosa diseases have been studied for over a century, there is still no information on the determinants of specificity between bacterial genotypes and host plant species, which is particularly relevant today as X. fastidiosa is expanding in the naive European landscape. We analysed the genomes of 79 X . fastidiosa samples from diseased olive trees across the affected area in Italy as well as genomes of the most genetically closely related strains from Central America. We provided insights into the ecological and evolutionary emergence of this pathogen in Italy. We first showed that the outbreak in Apulia is due to a single introduction from Central America that we estimated to have occurred in 2008 [95 % HPD: 1930–2016]. By using a combination of population genomic approaches and evolutionary genomics methods, we further identified a short list of genes that could play a major role in the adaptation of X. fastidiosa to this new environment. We finally provided experimental evidence for the adaptation of the strain to this new environment.

Usitatibacter rugosus gen. nov., sp. nov. and Usitatibacter palustris sp. nov., novel members of Usitatibacteraceae fam. nov. within the order Nitrosomonadales isolated from soil

2021 ◽  
Author(s):  
Selma Vieira ◽  
Katharina J. Huber ◽  
Meina Neumann-Schaal ◽  
Alicia Geppert ◽  
Manja Luckner ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Content Type ◽  
Link Type ◽  
Wide Range

Members of the metabolically diverse order Nitrosomonadales inhabit a wide range of environments. Two strains affiliated with this order were isolated from soils in Germany and characterized by a polyphasic approach. Cells of strains 0125_3T and Swamp67T are Gram-negative rods, non-motile, non-spore-forming, non-capsulated and divide by binary fission. They tested catalase-negative, but positive for cytochrome c-oxidase. Both strains form small white colonies on agar plates and grow aerobically and chemoorganotrophically on SSE/HD 1 : 10 medium, preferably utilizing organic acids and proteinaceous substrates. Strains 0125_3T and Swamp67T are mesophilic and grow optimally without NaCl addition at slightly alkaline conditions. Major fatty acids are C16 : 1  ω7c, C16 : 0 and C14 : 0. The major polar lipids are diphosphatidylglycerol, phosphatidylethanolamine and phosphatidyglycerol. The predominant respiratory quinone is Q-8. The G+C content for 0125_3T and Swamp67T was 67 and 66.1 %, respectively. The 16S rRNA gene analysis indicated that the closest relatives (<91 % sequence similarity) of strain 0125_3T were Nitrosospira multiformis ATCC 25196T, Methyloversatilis universalis FAM5T and Denitratisoma oestradiolicum AcBE2-1T, while Nitrosospira multiformis ATCC 25196T, Nitrosospira tenuis Nv1T and Nitrosospira lacus APG3T were closest to strain Swamp67T. The two novel strains shared 97.4 % 16S rRNA gene sequence similarity with one another and show low average nucleotide identity of their genomes (83.8 %). Based on the phenotypic, chemotaxonomic, genomic and phylogenetic analysis, we propose the two novel species Usitatibacter rugosus sp. nov (type strain 0125_3T=DSM 104443T=LMG 29998T=CECT 9241T) and Usitatibacter palustris sp. nov. (type strain Swamp67T=DSM 104440T=LMG 29997T=CECT 9242T) of the novel genus Usitatibacter gen. nov., within the novel family Usitatibacteraceae fam. nov.

Idification and structural characterisation of a catecholate-type siderophore produced by Stenotrophomonas maltophilia K279a

Microbiology ◽  
2021 ◽  
Vol 167 (7) ◽  
Author(s):  
Atsushi Hisatomi ◽  
Yuh Shiwa ◽  
Nobuyuki Fujita ◽  
Hiroyuki Koshino ◽  
Naoto Tanaka
Keyword(s):  
Stenotrophomonas Maltophilia ◽  
Type Species ◽  
Monomer Unit ◽  
Reversed Phase ◽  
Negative Bacterium ◽  
Content Type ◽  
Structural Characterisation ◽  
Link Type ◽  
Wide Range ◽  
C Nmr

Siderophores are produced by several bacteria that utilise iron in various environments. Elucidating the structure of a specific siderophore may have valuable applications in drug development. Stenotrophomonas maltophilia , a Gram-negative bacterium that inhabits a wide range of environments and can cause pneumonia, produces siderophores. However, the structure was unknown, and therefore, in this study, we aimed to elucidate it. We purified siderophores from cultures of S. maltophilia K279a using preparative reversed-phase HPLC. The structure was analysed through LC-MS and 1H and 13C NMR. The results demonstrated that S. maltophilia K279a produces 2,3-dihydroxybenzoylserine (DHBS), a monomer unit of enterobactin. We suggested the uptake of Iron(III) by the DHBS complex. DHBS production by S. maltophilia K279a could be attributed to an incomplete enterobactin pathway. Drugs targeting DHBS synthesis could prevent S. maltophilia infection.

scholarly journals Lysinibacillus acetophenoni sp. nov., a solvent-tolerant bacterium isolated from acetophenone

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1741-1748 ◽  
Author(s):  
M. Azmatunnisa ◽  
K. Rahul ◽  
K. V. N. S. Lakshmi ◽  
Ch. Sasikala ◽  
Ch. V. Ramana
Keyword(s):  
Cell Wall ◽  
Type Species ◽  
Optimal Growth ◽  
Log P ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Wide Range ◽  
Solvent Tolerant ◽  
Micro Organisms

A Gram-stain-positive, solvent-tolerating, aerobic, rod-shaped bacterium that formed terminal endospores was isolated from the organic solvent acetophenone. The strain, designated JC23T, was oxidase- and catalase-positive. The strain grew in the presence of a wide range of organic solvents with partition coefficients (log p values) between 1 and 4, which are exceptionally toxic to micro-organisms. Based on 16S rRNA gene sequence analysis, strain JC23T was identified as belonging to the genus Lysinibacillus and was most closely related to Lysinibacillus manganicus Mn1-7T (98.5 % similarity), L. massiliensis 440831T (97.2 %) and L. chungkukjangi 2RL3-2T (96.8 %). DNA–DNA relatedness of strain JC23T with the type strains of the closest species was <39 %. Strain JC23T grew chemo-organoheterotrophically with optimal growth at pH 7 (range pH 6–9) and at 35 °C (range 25–40 °C). The DNA G+C content was 41 mol%. Major cellular fatty acids of strain JC23T were iso-C15 : 0, iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The cell-wall peptidoglycan type was determined to be A4α (l-Lys–d-Asp), which is in agreement with the cell-wall characteristics of the genus Lysinibacillus . The predominant quinone system was MK-7. Polar lipids of strain JC23T included diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids, β-gentiobiosyldiacylglycerol, two unidentified phospholipids and two unidentified lipids. On the basis of our morphological, physiological, genetic, phylogenetic and chemotaxonomic analyses, we conclude that strain JC23T should be assigned to a novel species of the genus Lysinibacillus , for which the name Lysinibacillus acetophenoni sp. nov. is proposed. The type strain is strain JC23T ( = CCUG 57911T = KCTC 13605T = NBRC 105754T = DSM 23394T).

scholarly journals Lipopolysaccharide core type diversity in the Escherichia coli species in association with phylogeny, virulence gene repertoire and distribution of type VI secretion systems

2021 ◽  
Vol 7 (9) ◽  
Author(s):  
Sébastien O. Leclercq ◽  
Maxime Branger ◽  
David G. E. Smith ◽  
Pierre Germon
Keyword(s):  
Escherichia Coli ◽  
Type Species ◽  
Virulence Gene ◽  
Uneven Distribution ◽  
Gene Repertoire ◽  
Content Type ◽  
E Coli ◽  
Link Type ◽  
Wide Range ◽  
K 12

Escherichia coli is a very versatile species for which diversity has been explored from various perspectives highlighting, for example, phylogenetic groupings and pathovars, as well as a wide range of O serotypes. The highly variable O-antigen, the most external part of the lipopolysaccharide (LPS) component of the outer membrane of E. coli , is linked to the innermost lipid A through the core region of LPS of which five different structures, denominated K-12, R1, R2, R3 and R4, have been characterized so far. The aim of the present study was to analyse the prevalence of these LPS core types in the E. coli species and explore their distribution in the different E. coli phylogenetic groups and in relationship with the virulence gene repertoire. Results indicated an uneven distribution of core types between the different phylogroups, with phylogroup A strains being the most diverse in terms of LPS core types, while phylogroups B1, D and E strains were dominated by the R3 type, and phylogroups B2 and C strains were dominated by the R1 type. Strains carrying the LEE virulence operon were mostly of the R3 type whatever the phylogroup while, within phylogroup B2, strains carrying a K-12 core all belonged to the complex STc131, one of the major clones of extraintestinal pathogenic E. coli (ExPEC) strains. The origin of this uneven distribution is discussed but remains to be fully explained, as well as the consequences of carrying a specific core type on the wider aspects of bacterial phenotype.

scholarly journals Bifidobacterium aesculapii sp. nov., from the faeces of the baby common marmoset (Callithrix jacchus)

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2819-2827 ◽  
Author(s):  
M. Modesto ◽  
S. Michelini ◽  
I. Stefanini ◽  
A. Ferrara ◽  
S. Tacconi ◽  
...  
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Callithrix Jacchus ◽  
Rrna Gene ◽  
Positive Staining ◽  
Gene Sequences ◽  
Common Marmosets ◽  
Content Type ◽  
Link Type ◽  
Wide Range

Six Gram-positive-staining, microaerophilic, non-spore-forming, fructose-6-phosphate phosphoketolase-positive bacterial strains with a peculiar morphology were isolated from faecal samples of baby common marmosets (Callithrix jacchus). Cells of these strains showed a morphology not reported previously for a bifidobacterial species, which resembled a coiled snake, always coiled or ring shaped or forming a ‘Y’ shape. Strains MRM 3/1T and MRM 4/2 were chosen as representative strains and characterized further. The bacteria utilized a wide range of carbohydrates and produced urease. Glucose was fermented to acetate and lactate. Strain MRM 3/1T showed a peptidoglycan type unique among members of the genus Bifidobacterium . The DNA base composition was 64.7 mol% G+C. Almost-complete 16S rRNA, hsp60, clpC and rpoB gene sequences were obtained and phylogenetic relationships were determined. Comparative analysis of 16S rRNA gene sequences showed that strains MRM 3/1T and MRM 4/2 had the highest similarities to Bifidobacterium scardovii DSM 13734T (94.6 %) and Bifidobacterium stellenboschense DSM 23968T (94.5 %). Analysis of hsp60 showed that both strains were closely related to B. stellenboschense DSM 23968T (97.5 % similarity); however, despite this high degree of similarity, our isolates could be distinguished from B. stellenboschense DSM 23968T by low levels of DNA–DNA relatedness (30.4 % with MRM 3/1T). Strains MRM 3/1T and MRM 4/2 were located in an actinobacterial cluster and were more closely related to the genus Bifidobacterium than to other genera in the family Bifidobacteriaceae . On the basis of these results, strains MRM 3/1T and MRM 4/2 represent a novel species within the genus Bifidobacterium , for which the name Bifidobacterium aesculapii sp. nov. is proposed; the type strain is MRM 3/1T ( = DSM 26737T = JCM 18761T).

scholarly journals Antibiofilm activity in the culture supernatant of a marine Pseudomonas sp. bacterium

Microbiology ◽  
2020 ◽  
Vol 166 (3) ◽  
pp. 239-252 ◽  
Author(s):  
Ibtissem Doghri ◽  
Florence Brian-Jaisson ◽  
Marianne Graber ◽  
Alexis Bazire ◽  
Alain Dufour ◽  
...  
Keyword(s):  
Marine Bacteria ◽  
Type Species ◽  
Culture Supernatant ◽  
Heterotrophic Bacteria ◽  
Bioactive Metabolites ◽  
Antibiofilm Activity ◽  
Human Pathogens ◽  
Content Type ◽  
Link Type ◽  
Wide Range

In the marine environment, most solid surfaces are covered by microbial biofilms, mainly composed of bacteria and diatoms. The negative effects of biofilms on materials and equipment are numerous and pose a major problem for industry and human activities. Since marine micro-organisms are an important source of bioactive metabolites, it is possible that they synthesize natural ecofriendly molecules that inhibit the adhesion of organisms. In this work, the antibiofilm potential of marine bacteria was investigated using Flavobacterium sp. II2003 as a target. This strain is potentially a pioneer strain of bacteria that was previously selected from marine biofilms for its strong biofilm-forming ability. The culture supernatants of 86 marine heterotrophic bacteria were tested for their ability to inhibit Flavobacterium sp. II2003 biofilm formation and the Pseudomonas sp. IV2006 strain was identified as producing a strong antibiofilm activity. The Pseudomonas sp. IV2006 culture supernatant (SNIV2006) inhibited Flavobacterium sp. II2003 adhesion without killing the bacteria or inhibiting its growth. Moreover, SNIV2006 had no effect on the Flavobacterium sp. II2003 cell surface hydrophilic/hydrophobic and general Lewis acid–base characteristics, but modified the surface properties of glass, making it on the whole more hydrophilic and more alkaline and significantly reducing bacterial cell adhesion. The glass-coating molecules produced by Pseudomonas sp. IV2006 were found to probably be polysaccharides, whereas the antibiofilm molecules contained in SNIV2006 and acting during the 2 h adhesion step on glass and polystyrene surfaces would be proteinaceous. Finally, SNIV2006 exhibited a broad spectrum of antibiofilm activity on other marine bacteria such as Flavobacterium species that are pathogenic for fish, and human pathogens in both the medical environment, such as Staphylococcus aureus and Pseudomonas aeruginosa , and in the food industry, such as Yersinia enterocolitica . Thus, a wide range of applications could be envisaged for the SNIV2006 compounds, both in aquaculture and human health.

scholarly journals Comparative genomics of global optrA-carrying Enterococcus faecalis uncovers a common chromosomal hotspot for optrA acquisition within a diversity of core and accessory genomes

2020 ◽  
Vol 6 (6) ◽  
Author(s):  
Ana R. Freitas ◽  
Ana P. Tedim ◽  
Carla Novais ◽  
Val F. Lanza ◽  
Luísa Peixe
Keyword(s):  
Enterococcus Faecalis ◽  
Type Species ◽  
De Novo ◽  
Integration Site ◽  
Medium Size ◽  
Phylogenetic Structure ◽  
Content Type ◽  
Link Type ◽  
Healthy Humans ◽  
Wide Range

Linezolid-resistant Enterococcus faecalis (LREfs) carrying optrA are increasingly reported globally from multiple sources, but we lack a comprehensive analysis of human and animal optrA-LREfs strains. To assess if optrA is dispersed in isolates with varied genetic backgrounds or with common genetic features, we investigated the phylogenetic structure, genetic content [antimicrobial resistance (AMR), virulence, prophages, plasmidome] and optrA-containing platforms of 27 publicly available optrA-positive E. faecalis genomes from different hosts in seven countries. At the genome-level analysis, an in-house database with 64 virulence genes was tested for the first time. Our analysis showed a diversity of clones and adaptive gene sequences related to a wide range of genera from Firmicutes . Phylogenies of core and accessory genomes were not congruent, and at least PAI-associated and prophage genes contribute to such differences. Epidemiologically unrelated clones (ST21, ST476-like and ST489) obtained from human clinical and animal hosts in different continents over eight years (2010–2017) could be phylogenetically related (3–126 SNPs difference). optrA was located on the chromosome within a Tn6674-like element (n=10) or on medium-size plasmids (30–60 kb; n=14) belonging to main plasmid families (RepA_N/Inc18/Rep_3). In most cases, the immediate gene vicinity of optrA was generally identical in chromosomal (Tn6674) or plasmid (impB-fexA-optrA) backbones. Tn6674 was always inserted into the same ∆radC integration site and embedded in a 32 kb chromosomal platform common to strains from different origins (patients, healthy humans, and animals) in Europe, Africa, and Asia during 2012–2017. This platform is conserved among hundreds of E. faecalis genomes and proposed as a chromosomal hotspot for optrA integration. The finding of optrA in strains sharing common adaptive features and genetic backgrounds across different hosts and countries suggests the occurrence of common and independent genetic events occurring in distant regions and might explain the easy de novo generation of optrA-positive strains. It also anticipates a dramatic increase of optrA carriage and spread with a serious impact on the efficacy of linezolid for the treatment of Gram-positive infections.

Mesorhizobium shonense sp. nov., Mesorhizobium hawassense sp. nov. and Mesorhizobium abyssinicae sp. nov., isolated from root nodules of different agroforestry legume trees

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1746-1753 ◽  
Author(s):  
Tulu Degefu ◽  
Endalkachew Wolde-meskel ◽  
Binbin Liu ◽  
Ilse Cleenwerck ◽  
Anne Willems ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Novel Species ◽  
Root Nodules ◽  
Housekeeping Genes ◽  
Content Type ◽  
Link Type ◽  
Wide Range ◽  
Type Strains

A total of 18 strains, representing members of the genus Mesorhizobium , obtained from root nodules of woody legumes growing in Ethiopia, have been previously shown, by multilocus sequence analysis (MLSA) of five housekeeping genes, to form three novel genospecies. In the present study, the phylogenetic relationship between representative strains of these three genospecies and the type strains of their closest phylogenetic neighbours Mesorhizobium plurifarium , Mesorhizobium amorphae , Mesorhizobium septentrionale and Mesorhizobium huakuii was further evaluated using a polyphasic taxonomic approach. In line with our earlier MLSA of other housekeeping genes, the phylogenetic trees derived from the atpD and glnII genes grouped the test strains into three well-supported, distinct lineages that exclude all defined species of the genus Mesorhizobium . The DNA–DNA relatedness between the representative strains of genospecies I–III and the type strains of their closest phylogenetic neighbours was low (≤59 %). They differed from each other and from their closest phylogenetic neighbours by the presence/absence of several fatty acids, or by large differences in the relative amounts of particular fatty acids. While showing distinctive features, they were generally able to utilize a wide range of substrates as sole carbon and nitrogen sources. The strains belonging to genospecies I, II and III therefore represent novel species for which we propose the names Mesorhizobium shonense sp. nov., Mesorhizobium hawassense sp. nov. and Mesorhizobium abyssinicae sp. nov. The isolates AC39aT ( = LMG 26966T = HAMBI 3295T), AC99bT ( = LMG 26968T = HAMBI 3301T) and AC98cT ( = LMG 26967T = HAMBI 3306T) are proposed as type strains for the respective novel species.

Chryseobacterium frigidisoli sp. nov., a psychrotolerant species of the family Flavobacteriaceae isolated from sandy permafrost from a glacier forefield

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2666-2671 ◽  
Author(s):  
Felizitas Bajerski ◽  
Lars Ganzert ◽  
Kai Mangelsdorf ◽  
Lisa Padur ◽  
André Lipski ◽  
...  
Keyword(s):  
Type Species ◽  
Carbon Sources ◽  
Dry Weight ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Content Type ◽  
Optimum Growth Temperature ◽  
Glacier Forefield ◽  
Link Type ◽  
Wide Range

During diversity studies of the glacier forefields of the Larsemann Hills, East Antarctica, a novel psychrotolerant, non-motile Gram-negative, shiny yellow, rod-shaped, aerobic bacterium, designated strain PB4T was isolated from a soil sample. Strain PB4T produces indole from tryptophan and hydrolyses casein. It grows between 0 and 25 °C with an optimum growth temperature of 20 °C. A wide range of substrates are used as sole carbon sources and acid is produced from numerous carbohydrates. The major menaquinone is MK-6. Identified polar lipids are ethanolamines and ornithine lipids. Major fatty acids (>10 %) are iso-C15 : 0 (13.0 %) and iso-2OH-C15 : 0 (51.2 %). G+C content is 33.7 mol%. The polyamine pattern is composed of sym-homospermidine (25.1 µmol g−1 dry weight), minor amounts of cadaverine (0.2 µmol g−1 dry weight) and spermidine (0.4 µmol g−1 dry weight) and traces of putrescine and spermine (<0.1 µmol g−1 dry weight). Strain PB4T had highest 16S rRNA gene similarities with the type strains of Chryseobacterium humi (97.0 %) and Chryseobacterium marinum (96.5 %). Considering phenotypic and genotypic characterization, strain PB4T represents a novel species in the genus Chryseobacterium (family Flavobacteriaceae ), for which the name Chryseobacterium frigidisoli sp. nov. is proposed. The type strain is PB4T ( = DSM 26000T = LMG 27025T).

scholarly journals Corynebacterium striatum thrombophlebitis: a nosocomial multidrug-resistant disease?

2021 ◽  
Vol 3 (12) ◽  
Author(s):  
Julie Tang ◽  
Dimitri Kornblum ◽  
Nagisa Godefroy ◽  
Gentiane Monsel ◽  
Jérome Robert ◽  
...  
Keyword(s):  
Type Species ◽  
Bacterial Load ◽  
Anticoagulation Therapy ◽  
Specific Treatment ◽  
Multidrug Resistant ◽  
Septic Thrombophlebitis ◽  
Content Type ◽  
Link Type ◽  
Wide Range ◽  
Corynebacterium Striatum

Introduction. Corynebacterium striatum is a non-Diphteriae commensal bacterium with a wide range of pathogenicity. The identification of multidrug-resistant (MDR) C. striatum is concerning because drug susceptibility testing is not usually performed in microbiology laboratories. There is no consensus yet on the treatment of septic thrombophlebitis in this situation. Case report. We report here the first case of a quinquagenarian patient with a history of AIDS and fungic endocarditis, who was diagnosed with a nosocomial thrombophlebitis in the right jugular vein caused by C. striatum . Bitherapy with daptomycin for 12 days and linezolid for 23 days was combined with a therapeutic anticoagulant. The follow-up included weekly cervical ultrasound controls. The efficiency of the treatment and the stability of the lesions allowed us to alleviate the medication with a prophylactic dose of anticoagulant. The patient was discharged from hospital and showed no signs of recurrence after 12 months. Conclusion. The lack of consensus relative to the management of septic thrombophlebitis precludes the validation of a specific treatment for the condition. Our results suggest that a combination that includes removal of the medical device is needed. A total of 6 weeks of antibiotherapy should be applied, starting with 2 weeks of vancomycin or a combination of antibiotitherapy with daptomycin in order to reduce the bacterial load and avoid resistance. Six weeks of anticoagulation therapy is effective.

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