Brevibacterium paucivorans sp. nov., from human clinical specimens

Phenotypic and genomic characteristics of Brevibacterium zhoupengii sp. nov., a novel halotolerant actinomycete isolated from bat feces

Two strictly aerobic, Gram-staining-positive, non-spore-forming, regular rod-shaped (approximately 0.7 × 1.9 mm) bacteria (HY170^T and HY001) were isolated from bat feces collected from Chongzuo city, Guangxi province (22°20′54″N, 106°49′20″E, July 2011) and Chuxiong Yi Autonomous Prefecture, Yunnan province (25°09′10″N, 102°04′39″E, October 2013) of South China, respectively. Optimal growth is obtained at 25–28°C (range, 4–32°C) on BHI-5% sheep blood plate with pH 7.5 (range, 5.0–10.0) in the presence of 0.5–1.0% NaCl (w/v) (range, 0–15% NaCl [w/v]). The phylogenetic and phylogenomic trees based respectively on the 16S rRNA gene and 845 core gene sequences revealed that the two strains formed a distinct lineage within the genus Brevibacterium, most closely related to B. aurantiacum NCDO 739^T (16S rRNA similarity, both 98.5%; dDDH, 46.7–46.8%; ANI, 91.9–92.1%). Strain HY170^T contained MK-8(H₂), diphosphatidylglycerol (DPG) and phosphatidylglycerol (PG), galactose and ribose as the predominant menaquinone, major polar lipids, and main sugars in the cell wall teichoic acids, respectively. The meso-diaminopimelic acid (meso-DAP) was the diagnostic diamino acid of the peptidoglycan found in strain HY170^T. Anteiso-C_15:0 and anteiso-C_17:0 were the major fatty acids (> 10%) of strains HY170^T and HY001, with anteiso-C_17:1A predominant in strain HY170^T but absent in strain HY001. Mining the genomes revealed the presence of secondary metabolite biosynthesis gene clusters encoding for non-alpha poly-amino acids (NAPAA), ectoine, siderophore, and terpene. Based on results from the phylogenetic, chemotaxonomic and phenotypic analyses, the two strains could be classified as a novel species of the genus Brevibacterium, for which the name Brevibacterium zhoupengii sp. nov. is proposed (type strain HY170^T = CGMCC 1.18600^T = JCM 34230^T).

Brevibacterium rongguiense sp. nov., isolated from freshwater sediment

A Gram stain-positive, non-spore-forming, non-motile and rod-shaped actinomycete, strain 5221^T, was isolated from the sediment of a river collected at Ronggui in the Pearl River Delta, PR China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain formed a distinct lineage within the genus Brevibacterium and had the highest sequence similarity to Brevibacterium pityocampae Tp12^T (96.7 %), followed by Brevibacterium daeguense 2C6-41^T (96.5 %), Brevibacterium samyangense SST-8^T (96.0 %) and Brevibacterium ravenspurgense 20^T (95.9 %). The results of chemotaxonomic analyses, including detecting anteiso-C_15 : 0, anteiso-C_17 : 0, and C_16 : 0 as the major cellular fatty acids, diphosphatidylglycerol, phosphatidylglycerol and three phosphoglycolipids as the polar lipids, MK-8(H₂) as the major menaquinone, and a DNA G+C content of 72.4 mol%, supported that strain 5221^T is a member of the genus Brevibacterium. Furthermore, low sequence similarities of 16S rRNA gene sequences, differences in fatty acid compositions and differential physiological characteristics such as enzyme activity and carbon sources utilization ability distinguished the isolate from its close relatives. Therefore, strain 5221^T represents a novel species of the genus Brevibacterium, for which the name Brevibacterium rongguiense sp. nov. is proposed, with the type strain 5221^T (=GDMCC 1.1766^T=KACC 21700^T).

Analysis of the complete genome sequence of Brevibacterium frigoritolerans ZB201705 isolated from drought- and salt-stressed rhizosphere soil of maize

Purpose

To analyze the complete genome sequence of the Brevibacterium frigoritolerans ZB201705, a Brevibacterium strain was isolated from the maize rhizosphere in drought- and salt-stressed soil, and the activity of the strain under simulated drought and high salt conditions was assessed.

Methods

We used a combination of the PacBio RS and Illumina sequencing platforms to obtain the complete genome sequence of B. frigoritolerans ZB201705.

Results

The genome consists of 5,475,560 bp in a linear chromosome with no gaps, 4,391 protein-coding sequences, 39 ribosomal RNAs, and 81 transfer RNAs. The genome analysis revealed many putative gene clusters involved in defense mechanisms. In addition, an activity analysis of the strain under high-salt and simulated drought conditions helped clarify its potential tolerance to these abiotic stresses.

Conclusions

Our data revealed the complete genome sequence of the new isolated strain, and showed that it produces many proteins involved in drought and salt stress responses, suggesting that B. frigoritolerans ZB201705 may be a potential factor to increase crop yield under abiotic stresses. The information provided here on the genome of B. frigoritolerans ZB201705 provides valuable insight into rhizobacteria-mediated plant salt and drought tolerance and rhizobacteria-based solutions for agriculture under abiotic stress.

Antibiotic resistance genes in the Actinobacteria phylum

The Actinobacteria phylum is one of the oldest bacterial phyla that have a significant role in medicine and biotechnology. There are a lot of genera in this phylum that are causing various types of infections in humans, animals, and plants. As well as antimicrobial agents that are used in medicine for infections treatment or prevention of infections, they have been discovered of various genera in this phylum. To date, resistance to antibiotics is rising in different regions of the world and this is a global health threat. The main purpose of this review is the molecular evolution of antibiotic resistance in the Actinobacteria phylum.

Brevibacterium paucivorans bacteremia: case report and review of the literature

Background

Brevibacteria are obligate aerobic gram-positive rods that are associated with milk products and are also found on human skin. Brevibacterium has been reported as a rare cause of catheter related blood steam infection mainly in immunocompromised hosts such as malignancies or AIDS patients.

Case presentation

A 94-year old woman, which had a past history of diabetes mellitus and chronic heart failure, presented with high fever associated with decreased oral intake and appetite loss and was admitted to our institute. A physical examination at the time of presentation was unremarkable. On day 2, both blood cultures collected on admission became positive with coryneform organism within 24 h without Staphylococci and Brevibacterium species were identified by Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Subsequently, genetic investigation by 16S ribosomal RNA analysis was performed in order to identify the organism. Finally, the result identified this pathogen as Brevibacterium paucivorans with 99.5% homology on the Ez taxon database.

The patient was started empirically on meropenem and teicoplanin for broad-spectrum antibiotic coverage. The patient’s fever finally abated and labs were also improved. On day 14, the antibiotic therapy was discontinued. The site of infections was unknown. We hereby report a case of Brevibacterium paicivorans bacteremia in an immunocompetent patient and review cases of Brevibacterium specises bacteremia previously reported. This is the first case of B. paucivorans bacteremia as far as we could search.

Conclusion

Physicians and microbiologists should be aware that Brevibacteria are uncommon but important agents which could cause opportunistic infections in immunocompetent.

The expanding spectrum of human infections caused by Kocuria species: a case report and literature review

Although not previously known to cause human infections, Kocuria species have now emerged as human pathogens, mostly in compromised hosts with severe underlying disease. Recently, there has been an increasing incidence of different types of Kocuria infections reported, most likely due to the adoption of better identification methods. Here, we report a case of peritonitis caused by Kocuria rosea in a diabetic nephropathy patient who was on continuous ambulatory peritoneal dialysis. Sepsis and peritonitis caused by K. rosea in our case yielded two identical Kocuria isolates from the peritoneal dialysate fluid within a period of three days. The infection was subsequently resolved by antibiotic treatment and catheter removal. In addition to reporting this case, we herein review the literature concerning the emergence of Kocuria as a significant human pathogen. The majority of cases were device-related, acquired in the hospital or endogenous, and different Kocuria species appear to share a common etiology of peritonitis. The overall disease burden associated with Kocuria appears to be high, and the treatment guidelines for diseases associated with Kocuria have not yet been clearly defined.

Brevibacterium siliguriense sp. nov., a facultatively oligotrophic bacterium isolated from river water

A Gram-positive-staining, rod-shaped, facultatively oligotrophic bacterial strain, designated MB18(T), was isolated from a water sample collected from the River Mahananda at Siliguri (26° 44' 23.20' N, 88° 25' 22.89' E), West-Bengal, India. On the basis of 16S rRNA gene sequence similarity, the closest relative of this strain was Brevibacterium epidermidis NCDO 2286(T) (96 % similarity). The DNA G+C content of strain MB18(T) was 64.6 mol%. Chemotaxonomic data [MK-8(H(2)) as the major menaquinone, galactose as the sole cell-wall sugar, meso-diaminopimelic acid as the diagnostic cell-wall diamino acid, phosphatidylglycerol and diphosphatidylglycerol as constituents of the polar lipids, anteiso-C(15 : 0), anteiso-C(17 : 0) and iso-C(15 : 0) as the major fatty acids] supported the affiliation of strain MB18(T) to the genus Brevibacterium. The results of DNA G+C content, 16S rRNA gene sequence analysis and biochemical and physiological analyses allowed genotypic and phenotypic differentiation of strain MB18(T) from its nearest neighbour B. epidermidis. The isolate therefore represents a novel species, for which the name Brevibacterium siliguriense sp. nov. is proposed; the type strain is MB18(T) ( = DSM 23676(T) = LMG 25772(T)).

Brevibacterium sandarakinum sp. nov., isolated from a wall of an indoor environment

A Gram-stain-positive, rod-shaped, non-endospore-forming, orange-pigmented (coloured) actinobacterium (01-Je-003T) was isolated from the wall of an indoor environment primarily colonized with moulds. On the basis of 16S rRNA gene sequence similarity studies, strain 01-Je-003Twas shown to belong to the genusBrevibacteriumand was most similar to the type strains ofBrevibacterium picturae(98.8 % similarity),Brevibacterium marinum(97.3 %) andBrevibacterium aurantiacum(97.2 %). Chemotaxonomic data [predominant quinone menaquinone MK-8(H2); polar lipid profile consisting of major compounds diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid; characteristic cell-wall diamino acidmeso-diaminopimelic acid; polyamine pattern showing major compounds putrescine and cadaverine; major fatty acids anteiso-C15 : 0and anteiso-C17 : 0] supported the affiliation of strain 01-Je-003Tto the genusBrevibacterium. The results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 01-Je-003Tfrom the two most closely related species,B. picturaeandB. marinum. Strain 01-Je-003Ttherefore represents a novel species, for which the nameBrevibacterium sandarakinumsp. nov. is proposed, with the type strain 01-Je-003T(=DSM 22082T=CCM 7649T).

Brevibacterium pityocampae sp. nov., isolated from caterpillars of Thaumetopoea pityocampa (Lepidoptera, Thaumetopoeidae)

This work deals with the taxonomic study of a bacterium, strain Tp12T, isolated from caterpillars of the pine processionary moth (Thaumetopoea pityocampaDenis & Schiffermüller, 1775; Lepidoptera, Thaumetopoeidae). The isolate was assigned to the genusBrevibacteriumon the basis of a polyphasic taxonomic study, including morphological and biochemical characteristics, 16S rRNA gene sequence analysis, fatty acid analysis and DNA G+C content. The highest 16S rRNA gene sequence similarity to this isolate was approximately 96 %, with the type strains ofBrevibacterium albumandBrevibacterium samyangense. Cellular fatty acids of the isolate are of the branched type, with the major components being anteiso-C15 : 0and anteiso-C17 : 0. The DNA G+C content was 69.8 mol%. Although the strain was related toB. albumandB. samyangenseaccording to 16S rRNA gene sequence analysis, it differed from any known species ofBrevibacterium. Based on this evidence, the novel speciesBrevibacterium pityocampaesp. nov. is proposed, with strain Tp12T(=DSM 21720T=NCCB 100255T) as the type strain.

Identities of Arthrobacter spp. and Arthrobacter-like bacteria encountered in human clinical specimens

After the initial description of Arthrobacter spp. isolated from clinical specimens in the mid-1990s, very few further reports on Arthrobacter spp. have appeared in the clinical microbiology literature. The aim of the present study was to elucidate the distribution of Arthrobacter spp. and Arthrobacter-like bacteria encountered in clinical specimens by studying 50 consecutively isolated or received strains of large-colony-forming, whiteish-grayish, non-cheese-like-smelling, nonfermentative gram-positive rods by applying phenotypic methods as well as 16S rRNA gene sequencing. We observed a very heterogenous distribution, with the 50 strains belonging to 20 different taxa and each of 13 strains as a single representative of its particular taxon. Thirty-eight strains represented true Arthrobacter strains, 7 strains belonged to the genus Brevibacterium, 2 were Microbacterium species, and each of 3 single strains was a member of the rarely encountered genera Pseudoclavibacter, Leucobacter, and Brachybacterium, respectively. A. cumminsii (n = 14) and A. oxydans (n = 11) were the most frequently found species. The present report describes the first three A. aurescens strains isolated from human clinical specimens. Comprehensive antimicrobial susceptibility data are given for the 38 Arthrobacter isolates.

Description of Wautersiella falsenii gen. nov., sp. nov., to accommodate clinical isolates phenotypically resembling members of the genera Chryseobacterium and Empedobacter

A total of 26 isolates of non-fermenting, Gram-negative rods, obtained between 1980 and 2004 by various clinical laboratories in Belgium, with phenotypic characteristics resembling those of members of the genera Chryseobacterium and Empedobacter (indole-positive) and a biochemical profile resembling that of CDC group II-h, but urease-positive, were collected at the Université Catholique de Louvain Microbiology Laboratory, Belgium. The 16S rRNA gene sequences were determined for most of the isolates and showed 94–95 % similarity with the type strain of Empedobacter brevis as the closest relative, indicating that these isolates might belong to a separate genus. Furthermore, the 16S rRNA gene sequences of the isolates were similar, but two clusters (genomovars) could be distinguished. The sequence similarities were 99.5–100 % for the 14 isolates of genomovar 1 and 99.4–100 % for the 12 isolates of genomovar 2. The similarity between the two clusters was 98.3–99.5 %. The presence of two clearly different groups was corroborated by using tRNA intergenic length polymorphism analysis, which also enabled differentiation of the novel species from all other species studied thus far using this technique. DNA–DNA hybridization results excluded a close relatedness to Empedobacter brevis. The DNA G+C contents of the reference strains of genomovars 1 and 2 were 33.8±0.4 and 34.4±0.2 mol%, respectively. The name Wautersiella falsenii gen. nov., sp. nov., is proposed for this group, comprising two closely related genomovars. The type strain of the species and reference strain for genomovar 1 is NF 993T (=CCUG 51536T=CIP 108861T), which was isolated from a surgical wound. The reference strain for genomovar 2 is NF 770 (=CCUG 51537=CIP 108860), which was isolated from blood.

Brevibacterium samyangense sp. nov., an actinomycete isolated from a beach sediment

A novel actinomycete, strain SST-8T, was isolated from sand sediment of Samyang Beach in Jeju, Korea, and subjected to a polyphasic taxonomic study. The organism, which produced opaque, circular, yellow colonies, with a coryneform morphology, showed the following chemotaxonomic characteristics:meso-diaminopimelic acid as the diamino acid in the peptidoglycan, MK-8(H2) as the major menaquinone, phosphatidylglycerol as the only polar lipid, anteiso-C15 : 0and anteiso-C17 : 0as major fatty acids and a DNA G+C content of 70.7 mol%. The combination of morphological and chemotaxonomic features supported its classification in the genusBrevibacterium. Phylogenetic analyses, based on 16S rRNA gene sequence studies, showed that strain SST-8Tformed an intermediate branch between theBrevibacterium luteolum/Brevibacterium otitidisandBrevibacterium mcbrellneri/Brevibacterium paucivoransclusters. Sequence similarity calculations based on a neighbour-joining analysis revealed that the closest relatives of strain SST-8Twere the type strains ofB. paucivorans(96.6 %),B. luteolum(96.5 %),B. mcbrellneri(96.3 %),Brevibacterium avium(96.0 %) andB. otitidis(95.9 %). Based on a broad set of phenotypic and genetic data, it was evident that the strain represents a novel species of the genusBrevibacterium. The nameBrevibacterium samyangensesp. nov. is proposed, with SST-8T(=NRRL B-41420T=KCCM 42316T) as the type strain.

Distribution of nocardia species in clinical samples and their routine rapid identification in the laboratory

Eighty-six Nocardia strains isolated from clinical samples in Belgium were identified by 16S rRNA gene sequencing. Eighty-three (96%) strains belonged to only six Nocardia species: N. farcinica (38 [44%]), N. nova (19 [22%]), N. cyriacigeorgica (13 [15%]), N. brasiliensis (6 [6.9%]), N. abscessus (5 [5.8%]), and N. paucivorans (2 [2.3%]). A gallery of nine conventional and enzymatic tests was developed for the rapid identification of the most common species isolated during this survey. Pyrrolidonyl aminopeptidase, gamma-glutamyl aminopeptidase, alpha-mannosidase, and alpha-glucosidase were found to be highly discriminating and could be used to develop an identification scheme.

Industrial importance of the genus Brevibacterium

The genus Brevibacterium has long been difficult for taxonomists to classify due to its close morphological similarity to other genera. Since it was proposed in 1953, the genus has often been redefined. The genus is best known for its important role in the ripening of certain cheeses (B. linens) and for its supposed over-production of L: -amino acids. Other interesting industrial applications, including the production of ectoine, have recently been proposed. The general characteristics, the occurrence and the recent taxonomy of Brevibacterium are reviewed here. Furthermore, known and potential industrial applications for Brevibacterium species are briefly discussed.

Brevibacterium celere sp. nov., isolated from degraded thallus of a brown alga

Two whitish yellow, Gram-positive, non-motile, aerobic bacteria were isolated from enrichment culture during degradation of the thallus of the brown alga Fucus evanescens. The bacteria studied were chemo-organotrophic, mesophilic and grew well on nutrient media containing up to 15 % (w/v) NaCl. The DNA G+C content was 61 mol%. The two isolates exhibited a conspecific DNA-DNA relatedness value of 98 %, indicating that they belong to the same species. A comparative analysis of 16S rRNA gene sequences revealed that strain KMM 3637(T) formed a distinct phyletic lineage in the genus Brevibacterium (family Brevibacteriaceae, class Actinobacteria) and showed the highest sequence similarity (about 97 %) to Brevibacterium casei. DNA-DNA hybridization experiments demonstrated 45 % binding with the DNA of B. casei DSM 20657(T). Physiological and chemotaxonomic characteristics (meso-diaminopimelic acid in the peptidoglycan, major cellular fatty acids 15 : 0ai and 17 : 0ai) of the bacteria studied were consistent with the genomic and phylogenetic data. On the basis of the results of this study, a novel species, Brevibacterium celere sp. nov., is proposed. The type strain is KMM 3637(T) (=DSM 15453(T)=ATCC BAA-809(T)).

Brevibacterium picturae sp. nov., isolated from a damaged mural painting at the Saint-Catherine chapel (Castle Herberstein, Austria)

Three strains showing highly similar (GTG)5-PCR patterns were isolated from a heavily damaged mural painting at the Saint-Catherine chapel (Castle Herberstein, Austria). On the basis of 16S rRNA gene sequence similarity, the strains were attributed to Brevibacterium, with Brevibacterium casei (96·7 %), Brevibacterium iodinum (96·7 %) and Brevibacterium linens (96·6 %) as the closest related species. Chemotaxonomic data [peptidoglycan contains meso-diaminopimelic acid; mycolic acids absent; MK-8(H2) as the major menaquinone; polar lipids phosphatidylglycerol and diphosphatidylglycerol present; anteiso-C15 : 0 and anteiso-C17 : 0 as major fatty acids] supported the affiliation of the strains to the genus Brevibacterium. Additional physiological and biochemical tests confirmed the taxonomic position of the strains and allowed phenotypic differentiation from Brevibacterium species with validly published names. The isolates from the mural painting, therefore, represent a novel species, for which the name Brevibacterium picturae sp. nov. is proposed, with LMG 22061T (=DSM 16132T) as the type strain.

Identification of a novel Brevibacterium species isolated from humans and description of Brevibacterium sanguinis sp. nov

Six coryneforms isolated from blood and dialysate fluid were phenotypically similar to Brevibacterium casei, but 16S rRNA gene sequencing and DNA-DNA hybridization indicate that they belong to a new species for which the name Brevibacterium sanguinis is proposed.

Development of a 16S rRNA primer for the detection of Brevibacterium spp

AIM

To develop a PCR method for the rapid identification of the genus Brevibacterium.

METHODS AND RESULTS

Genus-specific primers were designed by aligning and comparing the 16S sequence of all Brevibacterium spp. with closely related genera. The primer set was tested with all validly described Brevibacterium spp. and their closest neighbours.

SIGNIFICANCE

Until today brevibacteria could only be identified with laborious and time-consuming phenotypic characterization. The primer from this study offers a rapid alternative to the detection of Brevibacterium spp. Brevibacteria have been isolated from food, blood, ear discharge, from a wound and from an intravascular catheter.

Management of long-term catheter-related Brevibacterium bacteraemia

Brevibacterium has been reported as a rare cause of implanted-device infection. In two cases of recurrent Brevibacterium casei bacteraemia associated with infection of surgically implanted intravascular devices, relapse occurred 2 and 5 months, respectively, after completion of therapy with vancomycin via the infected catheter. A second intravenous antibiotic therapy course by the antibiotic-lock technique led to bacteriological cure in one patient. Molecular typing results demonstrated that the recurrent bacteraemia was caused by the same strain. Implanted-device removal may be necessary, in addition to appropriate antibiotics, for successful management of such infections.

Brevibacterium lutescens sp. nov., from human and environmental samples

Three strains of coryneform rods isolated from clinical samples and one of environmental origin exhibited phenotypic and chemotaxonomic properties characteristic of the genus Brevibacterium and their 16S rRNA gene sequences were closely related (98.5-99.0 %) to that of Brevibacterium otitidis. However, DNA-DNA hybridization of one strain (CF87(T)) showed only 59.6 % relatedness to the type strain of B. otitidis, DSM 10718(T), and 75-82 % relatedness to the three other strains. The four strains could be differentiated from B. otitidis by cellular fatty acid composition and some phenotypic characteristics. These findings suggest that the four strains belong to a novel species, for which the name Brevibacterium lutescens sp. nov. is proposed. The type strain of B. lutescens is CF87(T) (=DSM 15022(T)=CCUG 46604(T)).