Pseudobacteraemia in a patient with neutropenic fever caused by a novel paenibacillus species: Paenibacillus hongkongensis sp. nov

Comparative genomic analysis of Cohnella hashimotonis sp. nov. isolated from the International Space Station

A single strain from the family Paenibacillaceae was isolated from the wall behind the Waste Hygiene Compartment aboard the International Space Station (ISS) in April 2018, as part of the Microbial Tracking mission series. This strain was identified as a gram-positive, rod-shaped, oxidase-positive, catalase-negative motile bacterium in the genus Cohnella, designated as F6_2S_P_1^T. The 16S sequence of the F6_2S_P_1^T strain places it in a clade with C. rhizosphaerae and C. ginsengisoli, which were originally isolated from plant tissue or rhizosphere environments. The closest 16S and gyrB matches to strain F6_2S_P_1^T are to C. rhizosphaerae with 98.84 and 93.99% sequence similarity, while a core single-copy gene phylogeny from all publicly available Cohnella genomes places it as more closely related to C. ginsengisoli. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values to any described Cohnella species are <89 and <22%, respectively. The major fatty acids for strain F6_2S_P_1^T are anteiso-C_15:0 (51.7%), iso-C_16:0 (23.1%), and iso-C_15:0 (10.5%), and it is able to metabolize a wide range of carbon compounds. Given the results of the ANI and dDDH analyses, this ISS strain is a novel species within the genus Cohnella for which we propose the name Cohnella hashimotonis, with the type strain F6_2S_P_1^T (=NRRL B-65657^T and DSMZ 115098^T). Because no closely related Cohnella genomes were available, this study generated the whole-genome sequences (WGSs) of the type strains for C. rhizosphaerae and C. ginsengisoli. Phylogenetic and pangenomic analysis reveals that F6_2S_P_1^T, C. rhizosphaerae, and C. ginsengisoli, along with two uncharacterized Cohnella strains, possess a shared set of 332 gene clusters which are not shared with any other WGS of Cohnella species, and form a distinct clade branching off from C. nanjingensis. Functional traits were predicted for the genomes of strain F6_2S_P_1^T and other members of this clade.

Paenibacillus spp. isolated from human and environmental samples in Spain: detection of 11 new species

One hundred thirty-six isolates, 88 human and 48 environmental, that met the requirements to belong to the genus Paenibacillus were identified using a polyphasic taxonomic approach known as 16S rRNA plus phenotypic traits. Thirty-seven Paenibacillus species were identified; some had not been previously reported from clinical samples. The main species were P. pabuli (13 isolates), P. provencensis (11), P. phoenicis (9) and P. lautus (8). P. pabuli (11/13) and P. provencensis (8/11) were mainly environmental isolates, while P. phoenicis (9/9) and P. lautus (6/8) were mainly human isolates. Despite the difficulties in assigning to human Paenibacillus isolates a role as a pathogen or contaminant, here 25% of the isolates were involved in true infections, especially in those cases that affected abscesses, wound exudates, ocular infections and diverse fluids. In addition, 15 isolates were identified as 11 'Candidatus' to a new species, all of them from human specimens except one that was obtained from laboratory air. The antimicrobial susceptibility testing showed 95.6% of isolates were resistant to ampicillin, 44% were resistant to cotrimoxazole, 20 to 30% were resistant to cefotaxime and vancomycin and 13% were resistant to rifampicin and erythromycin.

Non-contiguous-Finished Genome Sequence and Description of Paenibacillus camerounensis sp. nov

Strain G4(T) was isolated from the stool sample of a wild gorilla (Gorilla gorilla gorilla) from Cameroon. It is a facultative anaerobic, Gram-negative, rod-shaped bacterium. This strain exhibits a 16S rRNA nucleotide sequence similarity of 97.48% with Paenibacillus typhae, the phylogenetically closest species with standing nomenclature. Moreover, the strain G4(T) presents some phenotypic differences when compared to other Paenibacillus species and shows a low MALDI-TOF Mass Spectrometry score that does not allow any identification. Thus, it is likely that this strain represents a new species. Here, we describe the characteristics of this organism, complete genome sequence, and annotation. The 6,933,847 bp size genome (1 chromosome but no plasmid) contains 5972 protein-coding genes and 54 RNAs genes, including 44 tRNA genes. In addition, digital DNA-DNA hybridization values for the genome of the strain G4(T) against the closest Paenibacillus genomes range between 19.7 and 22.1, once again confirming its new status as a new species. On the basis of these polyphasic data, consisting of phenotypic and genomic analyses, we propose the creation of Paenibacillus camerounensis sp. nov. that contains the strain G4(T).

A Case of Paenibacillus pasadenensis Bacteremia in a Patient with Acute Respiratory Distress Syndrome after Microsurgical Clipping

We report the first case of bacteremia by a novel Paenibacillus species, Paenibacillus pasadenensis, from a 55-year-old male patient with acute respiratory distress syndrome, following a microsurgical clipping procedure of a ruptured intracranial aneurysm. The bacterium was identified using 16S rRNA gene sequencing analysis, which was applied because current conventional methods employed in the clinical microbiology laboratory proved unsuccessful. Since this bacterium was first identified in 2006 and has never been reported elsewhere, we believe this report can provide practitioners with useful insight on the pathogenicity of this species.

Non-contiguous finished genome sequence and description of Paenibacillus gorillae sp. nov

Strain G1(T) sp. nov. is the type strain of Paenibacillus gorillae a newly proposed species within the genus Paenibacillus. This strain, whose genome is described here, was isolated in France from the fecal sample of a wild western lowland gorilla from Cameroon. P. gorillae is a facultative anaerobic, Gram-negative, rod-shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 6,257,967 bp long genome (one chromosome but no plasmid) contains 5,856 protein-coding and 62 RNAs genes, including 60 tRNA genes.

Anaerospora hongkongensisGen. Nov. Sp. Nov., a Novel Genus and Species with Ribosomal DNA Operon Heterogeneity Isolated from an Intravenous Drug Abuser with Pseudobacteremia

A bacterium was isolated from the blood culture of an intravenous drug abuser with pseudobacteremia. The cells were strictly anaerobic, straight or slightly curved, sporulating, Gram-negative rods. It grew on sheep blood agar as non-hemolytic, pinpoint colonies after 48 hr of incubation at 37 C in an anaerobic environment. It was motile but did not produce catalase or cytochrome oxidase. 16S ribosomal DNA (rDNA) sequencing revealed three different copies of 16S rDNA sequences. More than 90% of the differences among them were due to differences in the lengths of the sequences. Phylogenetically, the bacterium is clustered with Dendrosporobacter, Sporomusa, and Propionispora, the other three genera of anaerobic, sporulating, Gram-negative rods. There were 8.6-11.1% differences between the 16S rDNA sequences of the bacterium and that of D. quercicolus, 4.7-15.1% differences between the 16S rDNA sequences of it and those of S. acidovorans, S. aerivorans, S. malonica, S. ovata, S. paucivorans, S. silvacetica, S. spaeroides, and S. termitida, and 7.6-13.1% differences between the 16S rDNA sequences of it and those of P. hippei and P. vibrioides. The G+C content of the bacterium (mean +/- SD) was 46.8 +/- 3.2%. For these reasons, a new genus and species, Anaerospora hongkongensis gen. nov. sp. nov., is proposed, for which HKU15T is the type strain.

Detecting the dormant: a review of recent advances in molecular techniques for assessing the viability of bacterial endospores

Due to their contribution to gastrointestinal and pulmonary disease, their ability to produce various deadly exotoxins, and their resistance to extreme temperature, pressure, radiation, and common chemical disinfecting agents, bacterial endospores of the Firmicutes phylum are a major concern for public and environmental health. In addition, the hardy and dormant nature of endospores renders them a particularly significant threat to the integrity of robotic extraterrestrial life-detection investigations. To prevent the contamination of critical surfaces with seemingly ubiquitous bacterial endospores, clean rooms maintained at exceedingly stringent cleanliness levels (i.e., fewer than 100,000 airborne particles per ft(3)) are used for surgical procedures, pharmaceutical processing and packaging, and fabrication and assembly of medical devices and spacecraft components. However, numerous spore-forming bacterial species have been reported to withstand typical clean room bioreduction strategies (e.g., UV lights, maintained humidity, paucity of available nutrients), which highlights the need for rapid and reliable molecular methods for detecting, enumerating, and monitoring the incidence of viable endospores. Robust means of evaluating and tracking spore burden not only provide much needed information pertaining to endospore ecophysiology in different environmental niches but also empower decontamination and bioreduction strategies aimed at sustaining the reliability and integrity of clean room environments. An overview of recent molecular advances in detecting and enumerating viable endospores, as well as the expanding phylogenetic diversity of pathogenic and clean room-associated spore-forming bacteria, ensues.

Cohnella cellulosilytica sp. nov., isolated from buffalo faeces

A cellulose-degrading bacterium, strain FCN3-3T, was isolated from buffalo faeces collected in Nakhonnayok province, Thailand. The strain was characterized based on its phenotypic and genotypic characteristics. Strain FCN3-3T was a Gram-positive, aerobic, spore-forming, rod-shaped bacterium. It contained meso-diaminopimelic acid in cell-wall peptidoglycan. The major menaquinone was MK-7. Anteiso-C15 : 0 (52.5 %), iso-C16 : 0 (18.9 %) and C16 : 0 (9.1 %) were the predominant cellular fatty acids, and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and lysyl-phosphatidylglycerol were the major phospholipids. The DNA G+C content was 58.0 mol%. Phylogenetic analysis using 16S rRNA gene sequences showed that strain FCN3-3T was affiliated to the genus Cohnella and was closely related to Cohnella phaseoli GSPC1T, Cohnella luojiensis HY-22RT and Cohnella hongkongensis HKU3T, with 97.2, 96.8 and 96.3 % sequence similarity, respectively. Strain FCN3-3T could be clearly distinguished from all known species of the genus Cohnella by its physiological and biochemical characteristics as well as its phylogenetic position and level of DNA–DNA relatedness. Therefore, the strain represents a novel species of the genus Cohnella , for which the name Cohnella cellulosilytica sp. nov. is proposed; the type strain is FCN3-3T ( = KCTC 13645T = TISTR 1996T = PCU 323T).

Isolation and characterisation of aerobic endospore forming Bacilli from sugarcane rhizosphere for the selection of strains with agriculture potentialities

Eighteen aerobic endospore forming strains were isolated from sugarcane rhizosphere in N-free medium. A phenotypic description and analysis of the 5' end hypervariable region sequences of 16S rRNA revealed a high diversity of Bacillus and related genera. Isolates were identified, and four genera were obtained: seven strains belonged to Bacillus (Bacillaceae family), four belonged to Paenibacillus, six belonged to Brevibacillus and one strain was identified as Cohnella (Paenibacillaceae family). Four Brevibacillus strains showed in vitro inhibitory activity against plant pathogens fungi Curvularia and Fusarium. Seventy-four percent of the isolated bacteria grew on pectin as the only carbon source, showing polygalacturonase activity. Pectate lyase activity was detected for the first time in a Brevibacillus genus strain. All isolates showed endoglucanase activity. Calcium phosphate solubilisation was positive in 83.3% of the isolates, with higher values than those reported for Bacillus inorganic phosphate solubilising strains. High ethylene plant hormone secretion in the culture medium was detected in 22% of the bacteria. This is the first report of ethylene secretion in Paenibacillaceae isolates. Indole-3-acetic acid production was found in a Brevibacillus genus isolate. It was reported for the first time the presence of Cohnella genus strain on sugarcane rhizosphere bearing plant growth promoting traits. The sugarcane isolate Brevibacillus B65 was identified as a plant growth inoculant because it showed wider spectra of plant stimulation capabilities, including an antifungal effect, extracellular hydrolases secretion, inorganic phosphate solubilisation and plant hormone liberation. In this work, sugarcane was shown to be a suitable niche for finding aerobic endospore forming 'Bacilli' with agriculture biotechnological purposes.

Detection and differentiation of bacterial spores in a mineral matrix by Fourier transform infrared spectroscopy (FTIR) and chemometrical data treatment

BACKGROUND

Fourier transform infrared spectroscopy (FTIR) has been used as analytical tool in chemistry for many years. In addition, FTIR can also be applied as a rapid and non-invasive method to detect and identify microorganisms. The specific and fingerprint-like spectra allow - under optimal conditions - discrimination down to the species level. The aim of this study was to develop a fast and reproducible non-molecular method to differentiate pure samples of Bacillus spores originating from different species as well as to identify spores in a simple matrix, such as the clay mineral, bentonite.

RESULTS

We investigated spores from pure cultures of seven different Bacillus species by FTIR in reflection or transmission mode followed by chemometrical data treatment. All species investigated (B. atrophaeus, B. brevis, B. circulans, B. lentus, B. megaterium, B. subtilis, B. thuringiensis) are typical aerobic soil-borne spore formers. Additionally, a solid matrix (bentonite) and mixtures of benonite with spores of B. megaterium at various wt/wt ratios were included in the study. Both hierarchical cluster analysis and principal component analysis of the spectra along with multidimensional scaling allowed the discrimination of different species and spore-matrix-mixtures.

CONCLUSIONS

Our results show that FTIR spectroscopy is a fast method for species-level discrimination of Bacillus spores. Spores were still detectable in the presence of the clay mineral bentonite. Even a tenfold excess of bentonite (corresponding to 2.1 × 1010 colony forming units per gram of mineral matrix) still resulted in an unambiguous identification of B. megaterium spores.

In silico analysis of 16S rRNA gene sequencing based methods for identification of medically important aerobic Gram-negative bacteria

This study provides guidelines on the usefulness of full and 527 bp 16S rRNA gene sequencing and Microseq databases for identifying medically important aerobic Gram-negative bacteria. Overall, full and 527 bp 16S rRNA gene sequencing can identify 26.1 % and 32.6 %, respectively, of medically important aerobic Gram-negative bacteria confidently to the species level, whereas the full-MicroSeq and 500-MicroSeq databases can identify 15.2 % and 26.1 %, respectively, of medically important aerobic Gram-negative bacteria confidently to the species level. Among the major groups of aerobic Gram-negative bacteria, the methods and databases are least useful for identification of Aeromonas, Bordetella and Bartonella species. None of the Aeromonas species can be confidently or doubtfully identified, whereas only 0 % and 0-33.3 % of Bordetella species and 0-10 % and 0-10 % of Bartonella species can be confidently and doubtfully identified, respectively. On the other hand, these methods and databases are most useful for identification of members of the families Pasteurellaceae and Legionellaceae and Campylobacter species: 29.6-59.3 % and 7.4-18.5 % of members of Pasteurellaceae, 36-52 % and 12-24 % of members of Legionellaceae, and 26.7-60 % and 0-13.3 % of Campylobacter species can be confidently and doubtfully identified, respectively. Thirty-nine medically important aerobic Gram-negative bacteria that should be confidently identified by full 16S rRNA gene sequencing are not included in the full-MicroSeq database. Twenty-three medically important aerobic Gram-negative bacteria that should be confidently identified by 527 bp 16S rRNA gene sequencing are not included in the 500-MicroSeq database. Compared with results of our previous studies on anaerobic and Gram-positive bacteria, full and 527 bp 16S rRNA gene sequencing are able to confidently identify significantly more anaerobic Gram-positive and Gram-negative bacteria than aerobic Gram-positive and Gram-negative bacteria.

Cohnella xylanilytica sp. nov. and Cohnella terrae sp. nov., xylanolytic bacteria from soil

Two xylan-degrading bacteria, strains MX15-2T and MX21-2T, were isolated from soils collected in Nan province, Thailand. Cells were Gram-reaction-positive, facultatively anaerobic, spore-forming and rod-shaped. They contained meso-diaminopimelic acid in the cell-wall peptidoglycan. The major menaquinone was MK-7. iso-C16 : 0 and anteiso-C15 : 0 were the predominant cellular fatty acids. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and lysyl-phosphatidylglycerol were the major polar lipids. The genomic DNA G+C contents of strains MX15-2T and MX21-2T were 63.0 and 65.1 mol%, respectively. Phylogenetic analysis using 16S rRNA gene sequences showed that strains MX15-2T and MX21-2T were affiliated with the genus Cohnella and were closely related to Cohnella thermotolerans CCUG 47242T, with 96.5 and 95.6 % sequence similarity, respectively. The strains could be clearly distinguished from each other and from all known species of the genus Cohnella based on their physiological and biochemical characteristics as well as their phylogenetic positions and levels of DNA–DNA hybridization. Therefore, these two strains represent novel species of the genus Cohnella, for which the names Cohnella xylanilytica sp. nov. (type strain MX15-2T =KCTC 22294T =PCU 309T =TISTR 1891T) and Cohnella terrae sp. nov. (type strain MX21-2T =KCTC 22295T =PCU 310T =TISTR 1892T) are proposed.

Cohnella thailandensis sp. nov., a xylanolytic bacterium from Thai soil

A xylanolytic bacterium, strain S1-3T, was isolated from soil collected in Nan province, Thailand. It was characterized taxonomically based on phenotypic characteristics and 16S rRNA gene sequence comparison. The strain was a Gram-stain-positive, facultatively anaerobic, spore-forming, rod-shaped bacterium. It contained meso-diaminopimelic acid in the cell-wall peptidoglycan. The major menaquinone was MK-7. Iso-C16 : 0 (39.5 %) and anteiso-C15 : 0 (26.8 %) were predominant cellular fatty acids. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and lysyl-phosphatidylglycerol were the major polar lipids. The DNA G+C content was 53.3 mol%. Phylogenetic analysis using 16S rRNA gene sequences showed that strain S1-3T was affiliated to the genus Cohnella, and was closely related to Cohnella ginsengisoli GR21-5T and Cohnella thermotolerans CCUG 47242T with 95.7 and 95.3 % sequence similarity, respectively. Strain S1-3T could be clearly distinguished from related species of the genus Cohnella by its physiological and biochemical characteristics as well as by its phylogenetic position. Therefore, the strain represents a novel species of the genus Cohnella, for which the name Cohnella thailandensis sp. nov. is proposed. The type strain is S1-3T (=KCTC 22296T =TISTR 1890T =PCU 306T).

Spore-forming Bacilli and Clostridia in human disease

Many Gram-positive spore-forming bacteria in the Firmicute phylum are important members of the human commensal microbiota, which, in rare cases, cause opportunistic infections. Other spore-formers, however, have evolved to become dedicated pathogens that can cause a striking variety of diseases. Despite variations in disease presentation, the etiologic agent is often the spore, with bacterially produced toxins playing a central role in the pathophysiology of infection. This review will focus on the specific diseases caused by spores of the Clostridia and Bacilli.

Cohnella fontinalis sp. nov., a xylanolytic bacterium isolated from fresh water

A novel xylan-degrading bacterium, YT-1101T, was isolated from fresh water. The isolate was a Gram-reaction-negative, aerobic, motile, endospore-forming and rod-shaped bacterium. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain YT-1101T belonged to the genus Cohnella, sharing sequence similarities of less than 94 % with the type species. The genomic G+C content was 58.6 mol%. The predominant menaquinone was MK-7. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and iso-C15 : 0. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. On the basis of morphological, physiological and phylogenetic properties, strain YT-1101T represents a novel species of the genus Cohnella, for which the name Cohnella fontinalis sp. nov. is proposed. The type strain is YT-1101T (=NBRC 104957T =DSM 21753T).

Paenibacillus larvae Bacteremia in injection drug users

Paenibacillus larvae causes American foulbrood in honey bees. We describe P. larvae bacteremia in 5 injection drug users who had self-injected honey-prepared methadone proven to contain P. larvae spores. That such preparations may be contaminated with spores of this organism is not well known among pharmacists, physicians, and addicts.

Cohnella yongneupensis sp. nov. and Cohnella ginsengisoli sp. nov., isolated from two different soils

Two aerobic, Gram-positive, rod-shaped bacterial strains, 5YN10-14T and GR21-5T, were isolated from the Yongneup wetland and ginseng soil in Korea, respectively. The two strains formed ellipsoidal or oval spores positioned centrally or paracentrally in swollen sporangia. On the basis of 16S rRNA gene sequence analysis, these strains were related to members of the genus Cohnella. 16S rRNA gene sequence similarity between strains 5YN10-14T and GR21-5T was 95.9 %. Strains 5YN10-14T and GR21-5T showed, respectively, 94.3 and 95.2 % 16S rRNA gene sequence similarity to Cohnella thermotolerans CCUG 47242T, 94.6 and 94.4 % to Cohnella hongkongensis HKU3T, 94.7 and 94.7 % to Cohnella laeviribosi RI-39T, and 95.4 and 94.8 % to Cohnella phaseoli GSPC1T. The major fatty acids of strain 5YN10-14T were anteiso-C15 : 0 (51.1 %), iso-C16 : 0 (18.5 %) and C16 : 0 (13.2 %), and the major fatty acids of strain GR21-5T were anteiso-C15 : 0 (48.9 %), iso-C16 : 0 (15.0 %) and iso-C15 : 0 (12.2 %). The two strains contained menaquinone with seven isoprene units (MK-7) as the predominant quinone, and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as major polar lipids; however, strain 5YN10-14T also contained lysylphosphatidylglycerol as a major polar lipid, whereas strain GR21-5T had an unknown aminophospholipid as another major polar lipid. The DNA G+C contents of strains 5YN10-14T and GR21-5T were 58.8 and 61.3 mol%, respectively. Based on the results of the phylogenetic and phenotypic data presented, it was concluded that the two strains represent two novel species of the genus Cohnella, for which the names Cohnella yongneupensis sp. nov. (type strain 5YN10-14T=KACC 11768T=DSM 18998T) and Cohnella ginsengisoli sp. nov. (type strain GR21-5T=KACC 11771T=DSM 18997T) are proposed.

Cohnella phaseoli sp. nov., isolated from root nodules of Phaseolus coccineus in Spain, and emended description of the genus Cohnella

A bacterial strain designated GSPC1 T was isolated from root nodules of Phaseolus coccineus in Segovia (Spain). The 16S rRNA gene sequence of this strain showed 95.9 and 94.7 % sequence similarity, respectively, with those of the type strains of Cohnella hongkongensis and Cohnella thermotolerans. Strain GSPC1 T presented phenotypic, chemotaxonomic and molecular differences with respect to Cohnella species which indicated that it belonged to a different species. The isolate was a Gram-positive, aerobic, sporulated rod, motile by means of peritrichous flagella. The strain was catalase-positive and showed weak oxidase activity. It grew in the presence of 2 % NaCl. MK-7 was the predominant menaquinone. anteiso-C15:0, iso-C15:0, iso-C16: 0 and C16:0 were the major fatty acids. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The G+C content was 60.3 mol%. The results of this study suggest that isolate GSPC1 T should be classified within a novel Cohnella species, for which the name Cohnella phaseoli sp. nov. is proposed, with strain GSPC1T (=LMG 24086T =DSM 19269T) as the type strain.

Saccharibacillus sacchari gen. nov., sp. nov., isolated from sugar cane

A bacterial strain designated GR21T was isolated from apoplastic fluid of Saccharum officinarum (sugar cane). Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate forms a separate branch within the family 'Paenibacillaceae', with Paenibacillus as the closest related genus. Within this genus, the closest related species is Paenibacillus xylanilyticus, with 93.4 % similarity to the sequence of the type strain. The isolate has Gram-variable, facultatively anaerobic, rod-shaped cells, motile by polar and subpolar flagella. Round, non-ornamented, central or subterminal spores are formed in unswollen sporangia. The strain is catalase-positive and oxidase-negative on nutrient agar medium. Cellulose and aesculin were hydrolysed, whereas xylan, starch and gelatin were not. Growth was supported by many carbohydrates as carbon sources. Strain GR21T displayed a lipid profile consisting of diphosphatidylglycerol, phosphatidylglycerol, an unknown aminophospholipid, two unknown glycolipids and an unknown phosphoglycolipid. MK-7 was the predominant menaquinone and anteiso-C15: 0 was the major fatty acid. The DNA G+C content was 57.8 mol%. Phylogenetic and phenotypic analyses, including assimilation of carbon sources and exoenzyme production commonly used for classification within the family 'Paenibacillaceae', showed that strain GR21T belongs to a new genus within this family, for which the name Saccharibacillus sacchari gen. nov., sp. nov. is proposed. The type strain of Saccharibacillus sacchari is GR21T (=LMG 24085T =DSM 19268T).

Paenibacillus provencensis sp. nov., isolated from human cerebrospinal fluid, and Paenibacillus urinalis sp. nov., isolated from human urine

Gram-negative, spore-forming rods were isolated from a human urine sample (strain 5402403(T)) and a human cerebrospinal fluid sample (strain 4401170(T)). Based on genotypic characteristics, these strains belonged to the genus Paenibacillus and were closely related. Phylogenetic analysis based on 16S rRNA gene sequence comparison showed that they clustered with Paenibacillus massiliensis 2301065(T) (95.9 and 94.3 % 16S rRNA gene sequence similarity, respectively, for strains 5402403(T) and 4401170(T)), Paenibacillus illinoisensis NRRL NRS-61356(T) (90.6 and 93.8 %), Paenibacillus xylanilyticus XIL14(T) (95.3 and 95.4 %), Paenibacillus barcinonensis BP-23(T) (94.3 and 94.0 %), Paenibacillus pabuli NCIMB 12781(T) (89.1 and 92.3 %) and Paenibacillus amylolyticus NRRL NRS-290(T) (94.2 and 93.8 %). The predominant fatty acids were 15 : 0 anteiso (49.0 and 55.3 %, respectively, for strains 5402403(T) and 4401170(T)), 16 : 0 iso (15.4 and 13.5 %), 16 : 0 (7.6 and 3.6 %), 15 : 0 (6.3 and 2.8 %), 17 : 0 anteiso (5.7 and 7.5 %), 14 : 0 iso (4.1 and 2.7 %) and 15 : 0 iso (4.1 and 3.4 %). 16S rRNA gene sequence similarity between strain 4401170(T) and strain 5402403(T) was 98.4 %, but the DNA-DNA reassociation rate between the two strains was 53.2 %. So, considering the recommendations of the ad hoc committee, they do not belong to the same species. On the basis of phenotypic data and genotypic inference, it is proposed that the strains should be assigned to the novel species Paenibacillus urinalis sp. nov. (type strain 5402403(T) =CIP 109357(T) =CCUG 53521(T)) and Paenibacillus provencensis sp. nov. (type strain 4401170(T) =CIP 109358(T) =CCUG 53519(T)).

Case report: Paenibacillus thiaminolyticus: a new cause of human infection, inducing bacteremia in a patient on hemodialysis

Paenibacilli are gram-positive, aerobic bacteria that are related to Bacilli but differ in the DNA encoding their 16S rRNA. Until recently, these organisms were not known to cause human disease. There are now several reports of human infection caused by a few members of this genus, most commonly by P. alvei. We report a human infection in a patient with a permacath for chronic hemodialysis who was found to have bacteremia caused by P. thiaminolyticus, which is an environmental bacterium that has never been found to cause human disease. We identified this bacterium by biochemical tests, cloning, sequencing the genomic DNA encoding its 16S rRNA, growth characteristics, and electron microscopic studies. This constitutes the first report of a human infection caused by this organism.

Molecular subtyping and characterization of psychrotolerant endospore-forming bacteria in two New York State fluid milk processing systems

Psychrotolerant endospore-forming bacteria Bacillus and Paenibacillus spp. are important spoilage organisms in fluid milk. A recently developed rpoB subtyping method was applied to characterize the diversity and phylogenetic relationships among Bacillus and related sporeformers associated with milk processing systems. Milk samples representing the processing continuum from raw milk to pasteurized products were collected from two fluid milk processing plants, held at 6 degrees C up to the code date that had been established by each processing plant (i.e., either 18 or 21 days), and plated for bacterial enumeration throughout storage. Bacterial colonies selected to represent the visible diversity in colony morphology on enumeration plates were examined further. Among 385 bacterial isolates characterized, 35% were Bacillus spp., and 65% were Paenibacillus spp. A total of 92 rpoB allelic types were identified among these isolates, indicating considerable diversity among endospore-forming spoilage organisms present in fluid milk systems. Of the 92 allelic types identified, 19 were isolated from samples collected from both processing plants. The same rpoB allelic types were frequently identified in paired raw milk and packaged product samples, indicating that Bacillus and Paenibacillus spp. can enter dairy processing systems through raw milk. Certain subtypes were found exclusively in pasteurized samples, including those that were temporally independent, suggesting the possibility of in-plant sources for these spoilage organisms, including through the persistence of selected subtypes in processing plants. Development of effective control strategies for the diverse array of psychrotolerant endospore-forming organisms that currently limit the shelf lives of high-temperature short-time fluid milk products will require comprehensive, integrated efforts along the entire milk processing continuum.

Tracking Spore-Forming Bacterial Contaminants in Fluid Milk-Processing Systems

The presence of psychrotolerant Bacillus species and related spore formers (e.g., Paenibacillus spp.) in milk has emerged as a key biological obstacle in extending the shelf life of high-temperature, short-time pasteurized fluid milk beyond 14 d. A recently developed rpoB DNA sequence-based subtyping method was applied to characterize spoilage bacteria present in raw milk supplies for 2 processing plants, and to assess transmission of these organisms into pasteurized products. Thirty-nine raw milk samples and 11 pasteurized product samples were collected to represent the processing continuum from incoming truck loads of raw milk to packaged products. Milk samples were held at 6 degrees C for up to 16 d and plated for bacterial enumeration at various times throughout storage. Among the 88 bacterial isolates characterized, a total of 31 rpoB allelic types representing Bacillus and Paenibacillus spp. were identified, including 5 allelic types found in both raw milk and finished product samples. The presence of the same bacterial subtypes in raw and commercially pasteurized milk samples suggests that the raw milk supply represents an important source of these spoilage bacteria. Extension of the shelf life of high-temperature, short-time pasteurized fluid milk products will require elimination of these organisms from milk-processing systems.

Cohnella thermotolerans gen. nov., sp. nov., and classification of ‘Paenibacillus hongkongensis’ as Cohnella hongkongensis sp. nov

A Gram-positive, rod-shaped, endospore-forming organism, strain CCUG 47242T, was isolated from a sample of industrial starch production in Sweden. 16S rRNA gene sequence analysis demonstrated that this isolate was moderately related to species of the genus Paenibacillus, with <94·4 % sequence similarity to all other hitherto described Paenibacillus species. Strain CCUG 47242T showed the greatest sequence similarity (96·5 %) to ‘Paenibacillus hongkongensis’ HKU3, a strain with a name that has not yet been validly published. Chemotaxonomic data [major menaquinone, MK-7 (98 %); major polar lipids, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, lysyl-phosphatidylglycerol, two unknown phospholipids, four unknown aminophospholipids; major fatty acids, iso-C16 : 0 and anteiso-C15 : 0] showed some significant differences when compared with the type species of the genus Paenibacillus, Paenibacillus polymyxa. Physiological and biochemical tests allowed clear phenotypic differentiation of strain CCUG 47242T from strain HKU3. On the basis of 16S rRNA gene sequence analysis, in combination with chemotaxonomic data, strains CCUG 47242T and HKU3 represent two novel species of a new genus of endospore-forming bacteria for which we propose the names Cohnella thermotolerans gen. nov., sp. nov. (type strain CCUG 47242T=CIP 108492T=DSM 17683T) and Cohnella hongkongensis sp. nov. (type strain HKU3T=CCUG 49571T=CIP 107898T=DSM 17642T).

Alkanindiges hongkongensis sp. nov. A novel Alkanindiges species isolated from a patient with parotid abscess

A bacterium was isolated from the abscess pus of a 72-year-old patient with Warthin's tumor and parotid abscess. The cells were aerobic, non-motile, Gram-negative but difficult to be destained, non-sporulating, coccobacillus. The bacterium grew poorly on sheep blood agar and MacConkey agar as non-hemolytic colonies of 0.5 mm in diameter after 24h of incubation at 37 degrees C in ambient air. Growth was enhanced by Tween 80. It produces catalase but not cytochrome oxidase. Sequencing of the cloned 16S rRNA PCR products of the bacterium revealed three different 16S rRNA gene sequences, with 12 - 31 bp differences among them. Phylogenetic analysis showed that the bacterium is closely related to Alkanindiges illinoisensis, with 5.0 - 5.9% differences between the 16S rRNA gene sequence of the bacterium and that of A. illinoisensis. Tryptophan auxotrophic strain of Acinetobacter trpE27 transformed with DNA extracted from the bacterium was unable to grow on tryptophan deficient medium, indicating that the bacterium was not a strain of Acinetobacter. The G+C content of the bacterium (mean +/-SD) was 46.9+4.3%. A new species, Alkanindiges hongkongensis sp. nov., is proposed, for which HKU9T is the type strain. Isolates with "small colonies" that are apparently Acinetobacter-like species should be carefully identified. Growth enhancement with aliphatic hydrocarbons should be looked for and 16S rRNA gene sequencing performed in order to find more potential cases of Alkanindiges infections, as well as to define the epidemiology, clinical spectrum, and outcome of infections associated with this genus.

Bacteremia in a patient with colonic carcinoma caused by a novel Sedimentibacter species: Sedimentibacter hongkongensis sp. nov

A bacterium was isolated from the blood culture of a 91-year-old patient with colonic carcinoma. The cells were strict anaerobic, motile, Gram-negative, sporulating, straight, or slightly curved rods. The bacterium grew on agar using the BACTEC anaerobic blood culture broth or buffered charcoal yeast extract agar as pinpoint colonies after 72 h of incubation at 37 degrees C in anaerobic conditions. It did not grow on blood agar, chocolate agar, MacConkey agar, nutrient agar or broth, brain heart infusion agar or broth, Brucella agar, or cooked meat medium. It produces catalase but not cytochrome oxidase. 16S rRNA gene sequencing and phylogenetic analysis showed that it is closely related to Sedimentibacter hydroxybenzoicus and Sedimentibacter saalensis, with 10.5% and 11.9% differences between the 16S rRNA gene sequence of the bacterium and those of S. hydroxybenzoicus and S. saalensis respectively. A new species, Sedimentibacter hongkongenesis sp. nov., is proposed, for which HKU2(T) is the type strain.

Gemella bacteraemia characterised by 16S ribosomal RNA gene sequencing

AIMS

To define epidemiology, clinical disease, and outcome of gemella bacteraemia by 16S rRNA gene sequencing. To examine the usefulness of the Vitek, API, and ATB systems in identifying two gemella species.

METHODS

All alpha haemolytic streptococci other than Streptococcus pneumoniae isolated from blood cultures during a six year period were identified by conventional biochemical methods, the Vitek system, and the API system. 16S rRNA gene sequencing was performed on all isolates identified by both kits as gemella with >or= 95% confidence or by either kit as any bacterial species with < 95% confidence. The ATB expression system was used to identify the two isolates that were defined as gemella species by 16S rRNA gene sequencing.

RESULTS

Of the 302 alpha haemolytic streptococci other than S pneumoniae isolated, one was identified as Gemella morbillorum, and another as Gemella haemolysans by 16S rRNA gene sequencing. The patient with monomicrobial G morbillorum bacteraemia was a 66 year old man with community acquired infective endocarditis with septic thromboemboli. The patient with G haemolysans bacteraemia was a 41 year old woman with hospital acquired polymicrobial bacteraemia during the neutropenic period of an autologous bone marrow transplant for non-Hodgkin's lymphoma, the first case of its kind in the English literature. The API and ATB expression systems only identified the second strain as G haemolysans at 94% and 99% confidence, respectively, whereas the Vitek system identified none of the two strains correctly at > 70% confidence.

CONCLUSIONS

Gemella bacteraemia is uncommon. 16S rRNA gene sequencing is the method of choice for identification of gemella and gemella-like isolates.

Usefulness of the MicroSeq 500 16S ribosomal DNA-based bacterial identification system for identification of clinically significant bacterial isolates with ambiguous biochemical profiles

Due to the inadequate automation in the amplification and sequencing procedures, the use of 16S rRNA gene sequence-based methods in clinical microbiology laboratories is largely limited to identification of strains that are difficult to identify by phenotypic methods. In this study, using conventional full-sequence 16S rRNA gene sequencing as the "gold standard," we evaluated the usefulness of the MicroSeq 500 16S ribosomal DNA (rDNA)-based bacterial identification system, which involves amplification and sequencing of the first 527-bp fragment of the 16S rRNA genes of bacterial strains and analysis of the sequences using the database of the system, for identification of clinically significant bacterial isolates with ambiguous biochemical profiles. Among 37 clinically significant bacterial strains that showed ambiguous biochemical profiles, representing 37 nonduplicating aerobic gram-positive and gram-negative, anaerobic, and Mycobacterium species, the MicroSeq 500 16S rDNA-based bacterial identification system was successful in identifying 30 (81.1%) of them. Five (13.5%) isolates were misidentified at the genus level (Granulicatella adiacens was misidentified as Abiotrophia defectiva, Helcococcus kunzii was misidentified as Clostridium hastiforme, Olsenella uli was misidentified as Atopobium rimae, Leptotrichia buccalis was misidentified as Fusobacterium mortiferum, and Bergeyella zoohelcum was misidentified as Rimerella anatipestifer), and two (5.4%) were misidentified at the species level (Actinomyces odontolyticus was misidentified as Actinomyces meyeri and Arcobacter cryaerophilus was misidentified as Arcobacter butzleri). When the same 527-bp DNA sequences of these seven isolates were compared to the known 16S rRNA gene sequences in the GenBank, five yielded the correct identity, with good discrimination between the best and second best match sequences, meaning that the reason for misidentification in these five isolates was due to a lack of the 16S rRNA gene sequences of these bacteria in the database of the MicroSeq 500 16S rDNA-based bacterial identification system. In conclusion, the MicroSeq 500 16S rDNA-based bacterial identification system is useful for identification of most clinically important bacterial strains with ambiguous biochemical profiles, but the database of the MicroSeq 500 16S rDNA-based bacterial identification system has to be expanded in order to encompass the rarely encountered bacterial species and achieve better accuracy in bacterial identification.

Actinomyces hongkongensis sp. nov. – A Novel Actinomyces species Isolated from a Patient with Pelvic Actinomycosis

A bacterium was isolated from the pus of a patient with pelvic actinomycosis. The cells were strictly anaerobic, straight, non-sporulating, Gram-positive rods. It grows on sheep blood agar as non-haemolytic, pinpoint colonies after 24 hours of incubation at 37 degrees C in anaerobic environment. It is non-motile and does not produce catalase. 16S ribosomal RNA (rRNA) gene sequencing showed that there were 6.6% difference between the 16S rRNA gene sequence of the bacterium that of Actinomyces marimammalium (GenBank Accession no. AJ276405), a new species described in 2001, isolated from two seals and a porpoise. For these reasons a new species, Actinomyces hongkongensis sp. nov., is proposed, for which HKU8(T) is the type strain. Further studies should be performed to ascertain the potential of this bacterium to become an important cause of actinomycosis.