Proposal of Helicobacter higonensis sp. nov. isolated from a human clinical specimen, and emended description of Helicobacter valdiviensis Collado, 2014.

We have previously isolated a gram-negative microaerophilic strain, PAGU2000T from a patient presenting with a fever in Kumamoto Prefecture, Japan. The present study aimed to comprehensively analyze the taxonomy of the isolated strain using a polyphasic approach. The 16S rRNA gene sequence analysis indicated that the strain was a member of enterohepatic Helicobacter. The strain PAGU2000T shared a 97.5% 16S rRNA gene nucleotide identity with Helicobacter valdiviensis, and this taxonomic position was confirmed by phylogenetic analysis of the GyrA amino acid sequences. The proposed strain PAGU2000T has a 1.482 Mbp chromosome with a DNA G + C content of 31.3 mol% and encodes 1520 predicted coding sequences. The average nucleotide identity between the strain PAGU2000T and type strain of H. valdiviensis was 70.3%, which was lower than the recommended threshold of 95% for species delineation. The strain PAGU2000T was a motile, non-spore-forming, and spiral-shaped bacterium, exhibiting catalase and oxidase activities but not urease and nitrate reduction. This study demonstrates that the isolate represents a novel species within enterohepatic Helicobacter, for which the name Helicobacter higonensis is proposed (type strain: PAGU2000T = GTC 16811T = LMG 33095T). In this study, we describe the phenotypic and morphological features of this strain and propose an emended description of some biochemical traits of H. valdiviensis.

Statin, Ezetimibe, or Fibrate Initiation and Subsequent Use for the Primary and Secondary Prevention of Cardiovascular Diseases among Japanese Patients Aged ≥55 Years: A Nationwide Cohort Study.

The use of lipid-modifying agents (LMAs) other than statins has rarely been reported in real clinical settings. We aimed to compare the initiation and subsequent use of LMA classes for prevention of cardiovascular diseases. Using the national claims database, this retrospective cohort study was conducted on patients aged ≥55 years who initiated to use statins, ezetimibe, or fibrates between Fiscal Years (FYs) 2014 and 2017 as the first pharmacotherapy for dyslipidemia in Japan. A permissible gap for defining persistence was set as the median days of supply of a class to an individual. Kaplan-Meier estimates were calculated for rates. Cohorts for primary prevention without/with risk and secondary prevention comprised 1307438, 908378, and 503059 initiators for statins; 44116, 34206, and 11373 for ezetimibe; and 124511, 96380, and 27751 for fibrates. The persistence rates declined shortly after the therapy initiation regardless of the classes, which was approximately 50% at 1 year for any class for primary prevention without risk. A notable sex difference in terms of persistence rates was observed only for statins of secondary prevention. The restarting rates were similar between prevention settings: approximately 50-60% for statins and 30-40% for ezetimibe and fibrates 1 year after first discontinuation. For ezetimibe and fibrates, approximately 10% of initiators were added or switched to statins within 1 year of initiation. Collectively, any class tended to be discontinued early and some restarted; however, there were some unique classes. The findings are useful for improvement of dyslipidemia therapy.

Siderophore-producing Pantoea ferrattrahens sp. nov. isolated from a clinical specimen and Pantoea ferramans sp. nov. isolated from soil at the bottom of a pond.

Two Gram-negative facultative anaerobes were isolated from a sepsis patient with pancreatic cancer (strain PAGU 2156T ) and soil at the bottom of a pond (strain PAGU 2198T ), respectively. These two strains formed haloes around the colonies on chrome azurol S agar plates, indicating the production of siderophores. Two isolates assigned to the genus Pantoea based on the 16S rRNA gene were differentiated from established species by using polymorphic taxonomies. Phylogenetic analysis using four housekeeping genes (gyrB, rpoB, atpD, and infB) showed that strain PAGU 2156T is closely related to Pantoea cypripedii LMG 2657T (89.9%) or Pantoea septica LMG 5345T (95.7%). Meanwhile, strain PAGU 2198T formed a single clade with Pantoea rodasii DSM 26611T (93.6%) and Pantoea rwandensis DSM 105076T (93.3%). The average nucleotide identity values obtained from the draft genome assembly showed ≤90.2% between strain PAGU 2156T and closely related species and ≤81.5% between strain PAGU 2198T and closely related species. Based on various phenotypes, biochemical properties, and whole-cell fatty acid composition compared with related species, it was concluded that each strain should be classified as a new species of the genus Pantoea. In this manuscript, Pantoea ferrattrahens sp. nov. and Pantoea ferramans sp. nov. with strain PAGU 2156T (=NBRC 115930T = CCUG 76757T ) and strain PAGU 2198T (=NBRC 114265T = CCUG 75151T ) are proposed as each type strain.

Statin persistence and adherence among older initiators: A nationwide cohort study using the national health insurance claims database in Japan.

PURPOSE: This study clarifies the reality of persistence and adherence to statins in older Japanese people who initiated statin use and compares it between primary and secondary prevention cohorts. METHODS: The nationwide study using the national claims database targeted statin initiators aged ≥55 years from FY2014 to FY2017 in Japan. Persistence and adherence to statins were analyzed overall and according to subgroups based on sex, age stratum, and prevention cohorts. Permissible gap of median days that statins were supplied per prescription to an individual was employed. Persistence rates were estimated as Kaplan-Meier estimates. Poor adherence during persistence was evaluated and defined as <0.8 of the proportion of days covered. RESULTS: Of 3 675 949 initiators, approximately 80% initiated statin use with strong variants. The persistence rate at 1 year was 0.61. Poor adherence to statins during persistence was 8.0% in all patients and this value gradually improved with increasing age. Persistence rate and adherence were lower for the primary prevention cohort than for the secondary prevention cohort, and a notable sex difference was observed for the secondary prevention cohort, which was lower in females but was almost never and slightly observed in the primary prevention cohorts without and with high-risk factors, respectively. CONCLUSIONS: Many statin initiators discontinued statins shortly following statin initiation but adherence while on statin therapy was good. Attentively watching older patients not to discontinue statins and listening to their reasons for discontinuation are required, especially for initiators in primary prevention and females in secondary prevention.

Helicobacter kumamotonensis sp. nov., isolated from human clinical specimens.

A Gram-stain-negative, spiral bacterium (PAGU 1991T) was isolated from the blood of a patient with diffuse large B-cell lymphoma. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate was very closely related to Helicobacter equorum LMG 23362T (99.1 % similarity), originally isolated from a faecal sample from a healthy horse. PAGU 1991T was also very closely related to PAGU 1750 in our strain library (=CCUG 41437) with 99.7 % similarity. Additional phylogenetic analyses based on the 23S rRNA gene sequence and GyrA amino acid sequence further supported the close relationship between the two human isolates (PAGU 1991T and PAGU 1750) and the horse strain. However, a phylogenetic analysis based on 16S rRNA showed that the two human isolates formed a lineage that was distinct from the horse strain (less than 99.2 % similarity). In silico whole-genome comparisons based on digital DNA-DNA hybridization, average nucleotide identity based on blast and orthologous average nucleotide identity using usearch between the two human isolates and the type strain of H. equorum showed values of less than 52.40, 93.47, and 93.50 %, respectively, whereas those between the two human isolates were 75.8, 97.2, and 97.2 %, respectively. These data clearly demonstrated that the two human isolates formed a single species, distinct from H. equorum. Morphologically, the human isolates could be distinguished by the type of flagella; the human isolates showed a bipolar sheathed flagellum, whereas that of H. equorum was monopolar. Biochemically, the human isolate was characterized by growth at 42 °C under microaerobic conditions and nitrate reduction unability. We conclude that the two human isolates, obtained from geographically and temporally distinct sources, were a novel species, for which we propose the name Helicobacter kumamotonensis sp. nov., with the type strain PAGU 1991T (=GTC 16810T=CCUG 75774T).

Two new ɑ-pyrone derivatives from the endophytic Diaporthe sp. ECN371.

Diaportholides A (1) and B (2), two polyketides with ɑ-pyrone moieties, were isolated from the cultures of an endophytic Diaporthe sp. ECN371 isolated from Orixa japonica, together with four known polyketides, phomopsolide B (3), phomopsolidones A (4) and B (5), and 5-[(1R)-1-hydroxyethyl]-γ-oxo-2-furanbutanoic acid (6). The structures of 1 and 2 were determined by extensive analysis of NMR and MS spectroscopic data. Furthermore, the structure of 2 was confirmed by analyzing the single-crystal X-ray diffraction data. The luciferase reporter gene assay revealed that among all isolated compounds (1-6), 3, a known ɑ-pyrone derivative, exhibited agonistic activity against the peroxisome proliferator-activated receptor ɑ, which is an important regulator of lipid metabolism in humans.

Chryseobacterium lecithinasegens sp. nov., a siderophore-producing bacterium isolated from soil at the bottom of a pond.

Bacterial strain PAGU 2197T, which was isolated from soil collected from the bottom of a pond in Japan, is characterized in this study. Cells of strain PAGU 2197T were aerobic, Gram-negative, short rod-shaped, non-motile, flexirubin-producing, oxidase-positive, catalase-positive and lecithinase-negative. A phylogenetic study based on 16S rRNA gene sequences and multilocus sequence analysis (gyrB, rpoB and rpoD) indicated that strain PAGU 2197T belongs to the genus Chryseobacterium and is a member of an independent lineage including Chryseobacterium tructae CCUG 60111T (sequence similarity, 95.9 %), Chryseobacterium lactis CCUG 60566T (93.4 %) and Chryseobacterium viscerum CCUG 60103T (91.6 %). The average nucleotide identity values were 80.83-85.04 %. Because average nucleotide identity values of 95-96 % exceed the 70 % DNA-DNA hybridization cutoff value for species discrimination, strain PAGU 2197T represents a novel species in the genus Chryseobacterium. The genome of strain PAGU 2197T was 4 967 738 bp with a G+C content of 35.5 mol%. The sole respiratory quinone of strain PAGU 2197T was MK-6; the major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3OH, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and summed feature 9 (iso-C17 : 1 ω9c and/or C16 : 0 10-methyl); and the major polar lipids were phosphoglycolipids and phosphatidylethanolamine. These results indicate that strain PAGU 2197T should be classified as representing a novel species in the genus Chryseobacterium, for which the name Chryseobacterium lecithinasegens sp. nov. is proposed, with strain PAGU 2197T (=NBRC 114264T=CCUG 75150T) as the type strain.

Draft Genome Sequence of Paraclostridium bifermentans subsp. muricolitidis Strain PAGU 1678T, Which Exacerbates Pathosis in a Mouse Model of Ulcerative Colitis.

Paraclostridium bifermentans subsp. muricolitidis strain PAGU 1678T was isolated from rat feces and has the ability to exacerbate pathosis in a mouse model of ulcerative colitis. Here, we report the draft genome sequence of the 3,471,060-bp chromosome of strain PAGU 1678T.

Overexpression of the MexXY Multidrug Efflux System Correlates with Deficient Pyoverdine Production in Pseudomonas aeruginosa.

Multidrug-resistant Pseudomonas aeruginosa poses a serious problem due to hospital- and healthcare-associated infections. A major drug resistance mechanism of P. aeruginosa involves active efflux via resistance nodulation cell division (RND)-type multidrug efflux pumps of which MexXY is increasingly recognized as a primary determinant of aminoglycoside resistance in P. aeruginosa. MexXY overexpression is often observed in drug-resistant P. aeruginosa clinical isolates. MexXY deficiency increased pyoverdine production in all four P. aeruginosa strains we tested. MexXY-overproducing multidrug-resistant P. aeruginosa PA7 exhibited the greatest effect among the strains. Complementation with a MexXY-expressing plasmid restored low-level pyoverdine production in a MexXY-deficient P. aeruginosa mutant from PA7, indicating that MexXY expression decreases pyoverdine production. Because P. aeruginosa produces pyoverdine to acquire iron, MexXY-deficient mutants might be more susceptible to iron deficiency than MexXY-producing strains or might require extra iron. High-risk clones of multidrug-resistant P. aeruginosa reportedly tend to be MexXY overproducers but defective pyoverdine producers. This study suggests that P. aeruginosa reduces production of a virulence factor after acquiring a drug resistance factor.

Fusobacterium watanabei sp. nov. As additional species within the genus Fusobacerium, isolated from human clinical specimens.

Eight spindle-shaped bacteria were isolated from clinical samples in Japan and investigated for their taxonomic position. Phylogenetic trees (based on 16S rRNA, rpoB, zinc protease, and gyrB gene sequence comparisons) showed distinct clustering of eight strains with the type strain of Fusobacterium nucleatum and its closely related species. In silico whole genome comparison analysis based on average nucleotide index based on BLAST (ANIb) and digital DNA-DNA hybridization (dDDH) data between our clinical isolates (PAGU 1795, PAGU 1796T, and PAGU 1797) and the type strain of the closely related species showed values of less than 92.4% and 49.5%, respectively. On the basis of its phylogenetic and genomic distinctiveness together with differential phenotypic properties and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) characteristic signal patterns, we propose Fusobacterium watanabei sp. nov., with the type strain PAGU 1796T (= GTC 21791T = CCUG 74246T).

Muyocopronones A and B: azaphilones from the endophytic fungus Muyocopron laterale.

Two new azaphilones, namely muyocopronones A (1) and B (2), were isolated from the cultures of an endophytic fungus Muyocopron laterale ECN279. Their structures were elucidated by extensive spectroscopic analysis. Their absolute configurations were determined using the modified Mosher's method and through comparisons of experimental and calculated electronic circular dichroism data. In addition, muyocopronone B (2) was found to exhibit a weak antibacterial activity against some Gram-positive bacteria.

Correction to: Sesquiterpenes with new carbon skeletons from the basidiomycete Phlebia tremellosa.

The article Sesquiterpenes with new carbon skeletons from the basidiomycete Phlebia tremellosa, written by Ken ichi Nakashima, Junko Tomida, Takao Hirai, Yoshiaki Kawamura and Makoto Inoue was originally published Online First without Open Access.

Absolute configurations of talaromycones A and B, α-diversonolic ester, and aspergillusone B from endophytic Talaromyces sp. ECN211.

Talaromycones A (1) and B (2), new xanthenediones, were isolated from the cultures of Talaromyces sp. ECN211, an endophytic fungus, along with α-diversonolic ester (3), aspergillusone B (4), glauconic acid (5), and rosellisin (6). The planar structures of 1 and 2 were elucidated by extensive spectroscopic analyses. Furthermore, the absolute configurations of 1-4 were determined by single-crystal X-ray diffraction and electronic circular dichroism spectroscopy (ECD). In addition, the crystallographic data for 5 were updated for the first time in over 50 years.

Paraconiothins A-J: Sesquiterpenoids from the Endophytic Fungus Paraconiothyrium brasiliense ECN258.

Paraconiothins A-J (1-10), 10 new sesquiterpenoids, as well as five known sesquiterpenoids, were isolated from the cultures of the endophytic fungus Paraconiothyrium brasiliense ECN-258. The structures of the sesquiterpenoids were elucidated by extensive spectroscopic analysis. Furthermore, the absolute structures of 7 and 8 were determined by comparing their experimental and computed electronic circular dichroism data. Paraconiothins A-G (1-7) were eremophilane sesquiterpenoids, while paraconiothins H-J (8-10) had new or rare carbon frameworks that are possibly biosynthesized by a pathway involving the rearrangement of eremophilane sesquiterpenoids. Paraconiothins C (3) and I (9) exhibited an inhibitory effect on the liver X receptor α at a concentration of 50 µM.

13-(2-Methylbenzyl) Berberine Is a More Potent Inhibitor of MexXY-Dependent Aminoglycoside Resistance than Berberine.

We previously showed that berberine attenuates MexXY efflux-dependent aminoglycoside resistance in Pseudomonas aeruginosa. Here, we aimed to synthesize berberine derivatives with higher MexXY inhibitory activities. We synthesized 11 berberine derivatives, of which 13-(2-methylbenzyl) berberine (13-o-MBB) but not its regiomers showed the most promising MexXY inhibitory activity. 13-o-MBB reduced the minimum inhibitory concentrations (MICs) of various aminoglycosides 4- to 128 fold for a highly multidrug resistant P. aeruginosa strain. Moreover, 13-o-MBB significantly reduced the MICs of gentamicin and amikacin in Achromobacter xylosoxidans and Burkholderia cepacia. The fractional inhibitory concentration indices indicated that 13-o-MBB acted synergistically with aminoglycosides in only MexXY-positive P. aeruginosa strains. Time-kill curves showed that 13-o-MBB or higher concentrations of berberine increased the bactericidal activity of gentamicin by inhibiting MexXY in P. aeruginosa. Our findings indicate that 13-o-MBB inhibits MexXY-dependent aminoglycoside drug resistance more strongly than berberine and that 13-o-MBB is a useful inhibitor of aminoglycoside drug resistance due to MexXY.

Draft Genome Sequences of Two Veillonella tobetsuensis Clinical Isolates from Intraoperative Bronchial Fluids of Elderly Patients with Pulmonary Carcinoma.

To date, Veillonella tobetsuensis has been known as an oral anaerobe and a facilitator of early-stage oral biofilm development with streptococci. Here, we report the draft genome sequences of 2 strains of V. tobetsuensis first isolated from intraoperative bronchial fluids of elderly patients with pulmonary carcinoma.

Profiling of microbiota in liquid baby formula consumed with an artificial nipple.

It is suspected that oral bacteria are transferred to the liquid baby formula through the artificial nipple and multiply in the bottle after feeding. In the present study, in order to understand the influence of bacteria on liquid baby formula after feeding, the transfer of oral bacteria through artificial nipples and their survival in liquid baby formula were examined immediately after drinking as well as after storage at 4°C for 3 h. Four healthy human subjects (20-23 years old) were asked to drink liquid baby formula (Aptamil®, ca. 50 mL) from baby bottles using artificial nipples. Samples of the liquid baby formula (immediately after drinking and 3 h later) were inoculated onto blood agar plates and incubated anaerobically at 37°C for 7 days. Salivary samples from each subject and 6 newborn infants were also cultured. Genomic DNA was extracted from individual colonies, and bacterial species were identified by 16S rRNA gene sequencing. The mean amounts of bacteria (CFU/mL) were (3.2 ± 3.0) ×104 and (3.4 ± 3.3) ×104 immediately after drinking and 3 h later, respectively. Streptococcus (41.6 and 40.5%), Actinomyces (24.3 and 21.5%) and Veillonella (16.2 and 11.0%) were recovered from the samples immediately after drinking and 3 h later, respectively. On the other hand, Streptococcus (38.9%), Actinomyces (17.1%), Neisseria (9.1%), Prevotella (6.9%), Rothia (6.9%) and Gemella (5.1%) were predominant in the saliva of adult subjects, and Streptococcus (65.2%), Staphylococcus (18.5%), Gemella (8.2%) and Rothia (5.4%) were predominant in the saliva of infant subjects. From these findings, oral bacteria, e.g., Streptococcus, Gemella and Rothia, were found to transfer into the liquid baby formula through artificial nipples, and the bacterial composition in the remaining liquid baby formula was found to resemble that of human saliva. The bacterial levels were similar between immediately after drinking and when stored at 4°C for 3 h, suggesting that the remaining liquid baby formula may be preserved in a refrigerator for a specified amount of time.

Spodiobacter cordis gen. nov. sp. nov., a member of the family Flavobacteriaceae isolated from patients with infective endocarditis.

Two gram-negative, catalase-negative, oxidase-positive strains (PAGU 1467T and PAGU 1468) isolated from patients with infective endocarditis were investigated to determine their taxonomic status. 16S rRNA gene sequence analysis indicated that the two strains were members of the Bergeyella-Chryseobacterium-Riemerella branch of the family Flavobacteriaceae. Strains PAGU 1467T and PAGU 1468 were highly related to each other (98.8% 16S rRNA gene sequence similarity). Phylogenetically closely-related species to PAGU 1467T comprised Bergeyella zoohelcum (95.0% 16S rRNA gene sequence similarity), Riemerella anatipestifer (94.3%) and Cloacibacterium normanense (94.3%). The major fatty acids of the two isolates were iso-C15:0 , iso-C17:0 3-OH and iso-C15:0 3-OH. The presence of C16:0 3-OH and iso-C15:0 2-OH allowed these isolates to be distinguished from B. zoohelcum. Menaquinone MK-6 was the only respiratory quinone in these organisms; this is a consistent characteristic of the family Flavobacteriaceae. The guanine-plus-cytosine content of the genomic DNA was 42.0%, which is higher than that of other close phylogenetic relatives. On the basis of their phenotypic properties and genetic distinctiveness, isolates PAGU 1467T and PAGU 1468 were classified within the novel genus Spodiobacter, as Spodiobacter cordis gen. nov., sp. nov., which is also the type species. The type strain of S. cordis is PAGU 1467T ( = CCUG 65564T = NBRC 109998T ).

Sesquiterpenes with new carbon skeletons from the basidiomycete Phlebia tremellosa.

Three new sesquiterpenes, phlebidiol, phlebioic acid, and phlebiolide, as well as the known compound tremetriol, were isolated from cultures of the basidiomycete Phlebia tremellosa. The structures of all isolated compounds were established by extensive spectroscopic analyses, including those involving extensive two-dimensional nuclear magnetic resonance. The absolute configurations of phlebidiol, phlebioic acid, and phlebiolide were determined by comparisons of experimental and calculated electronic circular dichroism spectra. Phlebidiol and phlebioic acid have previously unreported carbon skeletons, for which we propose the skeletal names "seco-sterpurane" and "phlebiane," respectively. Phlebiolide is also the second published example of a merulane sesquiterpene.

Description of Paraclostridium bifermentans subsp. muricolitidis subsp. nov., emended description of Paraclostridium bifermentans (Sasi Jyothsna et al., 2016), and creation of Paraclostridium bifermentans subsp. bifermentans subsp. nov.

Taxonomic studies of strain PAGU 1678T , an obligately anaerobic, gram-positive, spore-forming bacterium isolated from biobreeding rat feces, were performed. This strain has been demonstrated to have the ability to exacerbate pathosis in a mouse model of dextran sulfate sodium-induced ulcerative colitis. Phylogenetic analysis based on the 16S rRNA gene showed high homology with Paraclostridium bifermentans. To clarify the correct taxonomic position of strain PAGU 1678T , a comparative taxonomic study using P. bifermentans PAGU 2008T (═JCM 1386T ) and the closely related bacterial species P. benzoelyticum PAGU 2068T (═LMG 28745T ) was carried out. Despite the close similarity of 16S rRNA gene sequences, DNA-DNA hybridization between strain PAGU 1678T and P. bifermentans PAGU 2008T was 60.03% on average, average nucleotide identity was 96.17%, and it was shown to have different genomic sequences. Biochemically, strain PAGU 1678T could be differentiated from P. bifermentans PAGU 2008T by H2 S production. Furthermore, strain PAGU 1678T was characterized by the presence of two phospholipids with different polarity on polar lipid analysis. In addition, strain PAGU 1678T differed from P. bifermentans PAGU 2008T in findings on whole-cell protein analysis and matrix-assisted laser desorption/ionization-time of flight mass spectrometry. On the basis of these biochemical and genetic characteristics, a novel subspecies of P. bifermentans with the name Paraclostridium bifermentans subsp. muricolitidis subsp. nov. is here proposed, with PAGU 1678T (═CCUG 72489T ═NBRC 113386T ) as the type strain, which automatically creates P. bifermentans subsp. bifermentans subsp. nov. JCM 1386T (═ATCC 638T ═DSM 14991T ).