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.

253 J at 0.2†Hz, LD pumped cryogenic helium gas cooled Yb:YAG ceramics laser.

A 253 J with 26 ns at 0.2 Hz laser performance was demonstrated using a LD pumped cryogenically cooled Yb:YAG ceramics laser amplifier. A high energy storage of 344 J was achieved with a stored energy density of 0.58 J/cm3 using a 1 kJ output multidirectional-pumping system. High energy-extraction efficiency of 56.5% was achieved with high energy fluence of 4.63 J /cm2. To the best of our knowledge, this is the highest output energy obtained with a repetitive nanosecond pulse by LD pumped solid-state laser. This paper presented a design of 1 kJ amplifier based on experimentally proven numerical data.

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.

Comparative evaluation of nasopharyngeal swab and saliva specimens for the molecular detection of SARS-CoV-2 RNA in Japanese patients with COVID-19.

Considering the issues of shortage of medical resources and the invasiveness and infection risk involved in the collection of nasopharyngeal swab specimens, there is a need for an effective alternative test specimen for SARS-CoV-2 RNA detection. Here, we investigated suitability of saliva as a non-invasively obtained specimen for molecular detection of SARS-CoV-2 RNA in Japanese patients with COVID-19. In total, 28 paired clinical specimens of saliva and nasopharyngeal swabs were collected from 12 patients at various time points after symptom onset. Each specimen was assayed using reverse transcription real-time polymerase chain reaction (rRT-PCR) on the BD MAX open system using primers and probes targeting the N-gene. The saliva and nasopharyngeal swab specimens showed 19 and 15 positive results, respectively. No invalid (PCR inhibition) result was observed for any specimen. The qualitative results of each specimen obtained in the period immediately after symptom onset were similar. Three convalescent patients presented saliva-positive results, whereas their nasopharyngeal swabs were negative at four different time points, suggesting that saliva may be superior to nasopharyngeal swabs in terms of obtaining stable assay result of SARS-CoV-2. In conclusion, our results suggest that saliva can potentially serve as an alternative to nasopharyngeal swabs as a specimen for SARS-CoV-2 rRT-PCR. As saliva can be collected by patients themselves, it may be an effective way to overcome the shortage of personal protective equipment and specimen sampling tools.

Roseobacter cerasinus sp. nov., isolated from a fish farm.

An obligate aerobic and bacteriochlorophyll a-containing bacterium, designated strain AI77T, was isolated from a fish farm in Uwa Sea, Japan. Cells were Gram-stain-negative, coccoid- to oval-shaped, and showed no motility. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain AI77T is a member of the genus Roseobacter and closely related to Roseobacter ponti MM-7T (97.8 %), Roseobacter denitrificans OCh 114T (97.3 %) and Roseobacter litoralis OCh 149T (97.3 %). The G+C content of strain AI77T was 61.0 mol%. The average amino acid identity values of the genome in strain AI77T with those in R. denitrificans OCh 114T and R. litoralis OCh 149T were 73.26 % (SD 16.46) and 72.63 % (SD 16.76), respectively. The digital DNA-DNA hybridization values of strain AI77T with the type strains R. denitrificans OCh 114T and R. litoralis OCh 149T were 18.70 and 18.50 %, respectively. The dominant fatty acids (>10 % of total fatty acids) of AI77T were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and saturated fatty acid C16 : 0. The sole respiratory quinone was ubiquinone-10. The predominant polar lipids were phosphatidylcholine, phosphatidylglycerol and diphosphatidylglycerol. Based on the genetic and phenotypic data obtained herein, we conclude that strain AI77T represents a new species of the genus Roseobacter, for which we propose the name Roseobacter cerasinus sp. nov.; the type strain is AI77T (=DSM 110091T=NBRC 114115T).

Gluconobacter aidae sp. nov., an acetic acid bacterium isolated from tropical fruits in Thailand.

Two bacterial strains, isolates AC10T and AC20, which were reported in a previous study on the diversity of acetic acid bacteria in Thailand, were subjected to a taxonomic study. The phylogenetic analysis based on the 16S rRNA gene sequences showed that the two isolates were located closely to the type strains of Gluconobacter oxydans and Gluconobacter roseus. However, the two isolates formed a separate cluster from the type strains of the two species. The genomic DNA of isolate AC10T was sequenced. The assembled genomes of the isolate were analysed for average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH). The results showed that the highest ANI and dDDH values between isolate AC10T and G. oxydans DSM 3503T were 91.15 and 68.2 %, which are lower than the suggested values for species delineation. The genome-based tree was reconstructed and the phylogenetic lineage based on genome sequences showed that the lineage of isolate AC10T was distinct from G. oxydans DSM 3503T and its related species. The two isolates were distinguished from G. oxydans and their relatives by their phenotypic characteristics and MALDI-TOF profiles. Therefore, the two isolates, AC10T (=BCC 15749T=TBRC 11329T=NBRC 103576T) and AC20 (=BCC 15759=TBRC 11330=NBRC 103579), can be assigned to an independent species within the genus Gluconobacter, and the name Gluconobacter aidae sp. nov. is proposed for the two isolates.

Extended drip infusion of peripheral parental nutrition containing amino acids might be associated with Bacillus cereus bloodstream infection.

In some Japanese hospitals, patients using infusion bags for parenteral nutrition containing amino acids have developed Bacillus cereus bloodstream infections. We considered that proliferation of contaminated B cereus in the bag during prolonged drip infusion might be one of the causes of infection. This study indicated that 8 h is the maximum appropriate drip infusion time for peripheral parental nutrition containing amino acids to prevent B cereus bloodstream infections.

Litoreibacter roseus sp. nov., a novel bacteriochlorophyll a-containing bacterium.

A strictly aerobic, bacteriochlorophyll (BChl) a-containing alphaproteobacterium, designated strain K6T, was isolated from seawater around an aquaculture site in the Uwa Sea in Japan. The novel strain grew optimally at 30 °C at pH 7.0-7.5 and in the presence of 2.0 % (w/v) NaCl. The nonmotile and coccoid or rod-shaped cells formed pink-pigmented colonies on agar plates containing organic compounds. Cells showed an in vivo absorption maximum at 870 nm in the near-infrared region, indicating the presence of BChl a in the light-harvesting 1 complex. The new bacterial strain was Gram-stain-negative and oxidase- and catalase-positive. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain K6T was closely related to species in the genus Litoreibacter. The closest phylogenetic relatives of strain K6T were Litoreibacter ponti GJSW-31T (98.56 % sequence similarity), Litoreibacter janthinus KMM 3842T (97.63 %) and Litoreibacter albidus KMM 3851T (96.88 %). The G+C content of the genomic DNA was 58.26 mol%. The average nucleotide identity value of strain K6T with the type strain of L. ponti was 77.16 % (SD 4.79 %). The digital DNA-DNA hybridization value of strain K6T with the type strain of L. ponti was 19.40 %. The respiratory quinone was ubiquinone-10. The major cellular fatty acids were C18 : 1 ω7c, C16 : 0 and 11-methyl C18 : 1 ω7c. The dominant polar lipids were phosphatidylcholine and phosphatidylglycerol. On the basis of the genetic and phenotypic data obtained in the present study, we propose a new species in the genus Litoreibacter: Litoreibacter roseus sp. nov., whose type strain is K6T (=DSM 110109T=NBRC 114114T). Strain K6T represents the first confirmed species that produces BChl a within the genus Litoreibacter.

Reclassification of Flexibacter tractuosus NBRC 15981T as Marivirga harenae sp. nov. in the family Flammeovirgaceae.

Flexibacter tractuosa [Lewin, 1969] was reclassified as Marivirga tractuosa. Flexibacter tractuosus NBRC 15981T was reclassified herein by using a polyphasic taxonomic approach. Cells of the strain were strictly aerobic, Gram-stain-negative, slender rods, which were motile by gliding. The major respiratory quinone was menaquinone-7 and the predominant (>5 %) cellular fatty acids were iso-C15 : 0, iso-G-C15 : 1, C16 : 1ω7c and iso-C17 : 0 3-OH. The polar lipid pattern indicated the presence of a phosphatidylethanolamine, several unidentified aminolipids, glycolipids and five unidentified polar lipids. The G+C content of the genomic DNA was 35.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain NBRC 15981T clustered with members of the genus Marivirga in the family Flammeovirgaceae of the phylum Bacteroidetes. Levels of DNA-DNA relatedness were less than 16 % between strain NBRC 15981T and the two closely related species, Marivirga sericea NBRC 15983T and Marivirga tractuosa NBRC 15989T. Strain NBRC 15981T could be differentiated from these type strains in the genus Marivirga based on the polar lipid pattern and the activity of α-chymotrypsin, as well as by α-glucosidase and ß-glucosidase activity. On the basis of these results, NBRC 15981T is proposed as representing a novel species of the genus Marivirga, named Marivirga harenae sp. nov. The type strain is JK11T (=NBRC 15981T=NCIMB 1429T).

Achromobacter aloeverae sp. nov., isolated from the root of Aloe vera (L.) Burm.f.

Two Gram-staining-negative, strictly aerobic, rod-shaped bacteria, designated strains AVA-1T and AVA-2, were isolated from the root of Aloe vera (L.) Brum.f. derived from Chachoengsao Province, Thailand. The strains contained cytochrome oxidase and catalase activities. They grew in 4 % (w/v) NaCl, at a pH range of 6.0-9.0 (optimally at pH 7) and at 20-42 °C (optimally at 30-37 °C). The major isoprenoid quinone was ubiquinone with eight isoprene units (Q-8). The major fatty acids were C16 : 0 and C17 : 0 cyclo. On the basis of 16S rRNA gene sequence analysis, the strains represent a species belonging to the genus Achromobacter and are closely related to Achromobacter xylosoxidans NBRC 15126T (98.80 %), Achromobacter insolitus LMG 6003T (98.64 %), Achromobacter aminicus LMG 26690T (98.59 %), Achromobacter pulmonis LMG 26696T (98.58 %) and Achromobacter insuavis LMG 26845T (98.58 %). The DNA G+C content of strain AVA-1T was 66.5 mol%. The novel strains had low DNA-DNA relatedness values with related type strains. On the basis of the phenotypic and genotypic data obtained, the strains clearly represent a novel species, for which the name Achromobacter aloeverae sp. nov. is proposed. The type strain is strain AVA-1T (=LMG 29108T=NBRC 111463T=PCU 352T=TISTR 2383T).

Roseomonas elaeocarpi sp. nov., isolated from olive (Elaeocarpus hygrophilus Kurz.) phyllosphere.

An aerobic, Gram-stain-negative, coccobacillus-shaped, non-endospore-forming, pink-pigmented bacterium, designated PN2T, was isolated from an olive leaf. The strain grew at 15-35 °C with an optimum temperature for growth at 30 °C, and at pH 5.0-7.5 with an optimum pH for growth at 6.0. Growth was observed in the presence of up to 1.02 % (w/v) NaCl. The major fatty acids were C19 : 0 cyclo ω8c, C16 : 0 and C18 : 1ω7c. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, unknown aminolipids, an unknown phospholipid and an unknown lipid. The respiratory quinone was ubiquinone-10. The DNA G+C content of strain PN2T was 70.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain PN2T was closely related to members of the genus Roseomonas and shared highest similarity with Roseomonas mucosa ATCC BAA-692T (96.5 %), Roseomonas gilardii subsp. gilardii ATCC 49956T (96.2 %) and Roseomonas gilardii subsp. rosea ATCC BAA-691T (96.2 %). Furthermore, the DNA-DNA relatedness value between strain PN2T and the closest related species R. mucosa ATCC BAA-692T was 27 %. These data allowed the phenotypic and genotypic differentiation of strain PN2T from its closest phylogenetic neighbour (R. mucosa ATCC BAA-692T). Based on phenotypic and genotypic characteristics, strain PN2T is classified as representing a novel species of the genus Roseomonas for which the name Roseomonas elaeocarpi sp. nov. is proposed. The type strain is PN2T ( = BCC 44864T = NBRC 107871T).

Aureicoccus marinus gen. nov., sp. nov., a member of the family Flavobacteriaceae, isolated from seawater.

A coccoid and amorphous-shaped, non-gliding, proteorhodopsin-containing, yellow bacterium, designated strain SG-18(T), was isolated from seawater in the western North Pacific Ocean near Japan. The strain was Gram-stain-negative, obligately aerobic, heterotrophic and oxidase-positive. It hydrolysed aesculin but not DNA, urea, gelatin or agar. Growth occurred in the presence of 1-5 % NaCl, with optimum growth at 2 % NaCl. The strain grew at 15-37 °C with an optimum temperature of 25-30 °C. The DNA G+C content of the genomic DNA of strain SG-18(T) was 47.0 mol% (HPLC). The predominant isoprenoid quinone was MK-6, and major cellular fatty acids were iso-C15 : 1 G, iso-C15 : 0, iso-C15 : 0 3-OH. Phylogenetic trees generated by using 16S rRNA gene sequences revealed that strain SG-18(T) belonged to the family Flavobacteriaceae and showed 92.7 % sequence similarity to the most closely related species, Croceitalea eckloniae DOKDO 025(T). On the basis of phenotypic and phylogenetic features, strain SG-18(T) is classified as representing a novel species of a new genus within the family Flavobacteriaceae, for which the name Aureicoccus marinus gen. nov., sp. nov. is proposed. The type strain of the type species is SG-18(T) ( = NBRC 108814(T) = KCTC 23967(T)).

Roseomonas musae sp. nov., a new bacterium isolated from a banana phyllosphere.

A Gram-negative, coccobacilli, non-spore forming and non-motile bacterium, designated PN1(T), was isolated from a banana leaf collected in Mattra island, Thailand. This isolate was observed to grow optimally at 30 °C and pH 7.0, and to grow with 0-3 % NaCl. Comparative 16S rRNA gene sequence analysis showed that strain PN1(T) is closely related to members of the genus Roseomonas, exhibiting the highest 16S rRNA gene sequence similarity to Roseomonas aestuarii JC17(T) (96.5 %). The DNA G + C content of strain PN1(T) was determined to be 69.7 mol %. Based on physiological and biochemical tests, and genotypic differences between strain PN1(T) and the validly named species of the genus Roseomonas, it is proposed that the strain be classified as a new species of Roseomonas for which the name Roseomonas musae sp. nov. is proposed. The type strain is PN1(T) (= BCC 44863(T) = NBRC 107870(T)).

Nonlabens marinus [corrected] sp. nov., a novel member of the Flavobacteriaceae isolated from the Pacific Ocean.

Two aerobic, Gram-negative, orange pigmented and irregular rod-shaped bacteria, designated S1-05 and S1-08(T), were isolated from seawater from the Pacific Ocean. Phylogenetic analysis based on their 16S rRNA gene sequences revealed that the novel isolates could be affiliated with the genus Nonlabens of the family Flavobacteriaceae. The strains S1-05 and S1-08(T) shared 100 % pairwise sequences similarity with each other and showed less than 96.8 % similarity with the cultivated members of the genus Nonlabens. The novel isolates are phenotypically and physiologically different from strains described previously. The strains were found to be non-motile, oxidase positive, catalase positive and hydrolyzed gelatin and aesculin. The G+C contents of the DNA were determined to 41.4 and 41.7 mol% and MK-6 the predominant menaquinone. Anteiso-C15:0 and iso-C15:0 were found to be the major two cellular fatty acids. On the basis of polyphasic taxonomic studies, it was concluded that strains S1-05 and S1-08(T) represent a novel species within the genus Nonlabens, for which the name Nonlabens marina sp. nov. is proposed. The type strain of N. marina is S1-08(T) (=KCTC 23432(T) = NBRC 107738(T)).

Preventing surgical-site infections after colorectal surgery.

Surgical-site infection (SSI) is a major contributor to patient mortality rates and health care costs. Due to the high risk of bacterial contamination, colorectal surgery is associated with a particularly high risk of postoperative infection. The surveillance reported here was conducted at Aichi Medical University Hospital on 304 patients who underwent elective colorectal resection--total or partial--from June 2006 to May 2009. To determine risk factors for SSI, multivariate analysis was used. Forty-six (15.1%) patients were diagnosed with SSI. Patients who received cefotiam for prophylaxis showed the highest incidence of SSI (26.6%), and patients who were administered flomoxef showed the lowest incidence (8.1%). Patients who developed SSI were more likely to intraoperative blood loss (308.1 ± 29.8 vs. 153.9 ± 12.2; p < 0.05), longer postoperative antimicrobial administration (5.3 ± 2.2 vs. 4.5 ± 1.5; p < 0.05), and longer operative time (3.3 ± 1.6 vs. 2.7 ± 1.2; p < 0.05). Intraoperative bleeding, antimicrobial choices to cover both anaerobic and aerobic bacteria, and length of antimicrobial administration were independently predictive of SSI development according to multivariate logistic regression analysis. These results suggest that the degree of operative invasion and anaerobic bacteria contribute to SSI following colorectal surgery.

Salinirepens amamiensis gen. nov., sp. nov., a member of the family Cryomorphaceae isolated from seawater, and emended descriptions of the genera Fluviicola and Wandonia.

The taxonomic position of bacterial strain AM11-6(T), isolated from seawater in Japan, was determined by using a polyphasic taxonomic approach. The strain was a strictly aerobic and Gram-staining-negative slender rod, motile by gliding. The major respiratory quinone was menaquinone-6 and the predominant cellular fatty acids were iso-C(15 : 0), iso-C(17 : 0) 3-OH, C(14 : 0) and iso-C(15 : 1) G. The polar lipid pattern indicated the presence of an unidentified phospholipid, several glycolipids and an unidentified polar lipid. The G+C content of the genomic DNA was 36.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AM11-6(T) clustered with members of the genera Wandonia and Fluviicola in the family Cryomorphaceae of the phylum Bacteroidetes. The strain required NaCl and MgCl(2) for growth and could be differentiated from members of other genera in the family Cryomorphaceae by fatty acid composition and other phenotypic characters. On the basis of these results, we describe the novel genus and species, Salinirepens amamiensis gen. nov., sp. nov. The type strain of Salinirepens amamiensis is AM11-6(T) (= NBRC 101268(T) = NCIMB 14607(T)). Emended descriptions of the genera Fluviicola and Wandonia are also proposed.