Laribacter hongkongensis gen. nov., sp. nov., a Novel Gram-Negative Bacterium Isolated from a Cirrhotic Patient with Bacteremia and Empyema

Abstract

A bacterium was isolated from the blood and empyema of a cirrhotic patient. The cells were facultatively anaerobic, nonsporulating, gram-negative, seagull shaped or spiral rods. The bacterium grows on sheep blood agar as nonhemolytic, gray colonies 1 mm in diameter after 24 h of incubation at 37°C in ambient air. Growth also occurs on MacConkey agar and at 25 and 42°C but not at 4, 44, and 50°C. The bacterium can grow in 1 or 2% but not 3, 4, or 5% NaCl. No enhancement of growth is observed with 5% CO 2 . The organism is aflagellated and nonmotile at both 25 and 37°C. It is oxidase, catalase, urease, and arginine dihydrolase positive, and it reduces nitrate. It does not ferment, oxidize, or assimilate any sugar tested. 16S rRNA gene sequencing showed that there are 91 base differences (6.2%), 112 base differences (7.7%), and 116 base differences (8.2%) between the bacterium and Microvirgula aerodenitrificans, Vogesella indigofera, and Chromobacterium species, respectively. The G؉C content (mean and standard deviation) is 68.0% ؎ 2.43%, and the genomic size is about 3 Mb. Based on phylogenetic affiliation, the bacterium belongs to the Neisseriaceae family of the ␤-subclass of Proteobacteria. For these reasons, a new genus and species, Laribacter hongkongensis gen. nov., sp. nov., is proposed, for which HKU1 is the type strain. Further studies should be performed to ascertain the potential of this bacterium to become an emerging pathogen.Since the discovery of PCR and DNA sequencing, comparison of the gene sequences of bacterial species has shown that the 16S rRNA gene is highly conserved within a species and among species of the same genus and hence can be used as the new gold standard for the identification of bacteria to the species level. Using this new standard, phylogenetic trees based on base differences between species can be constructed, and bacteria can be classified and reclassified into new genera (7,8). Furthermore, noncultivable organisms and organisms with ambiguous biochemical profiles can be classified and identified (10, 11). Recently, this technique was used for the identification of a strain of Mycobacterium neoaurum with ambiguous biochemical and whole-cell fatty acid profiles isolated from a patient with acute lymphoblastic leukemia (18), a strain of Escherichia coli with an ambiguous biochemical profile isolated from a bone marrow transplant recipient (16), a strain of Enterobacter cloacae with an ambiguous biochemical profile isolated from a renal transplant recipient (14), a strain of tube coagulase-negative Staphylococcus aureus isolated from a patient with refractory anemia with excessive blasts in transformation (19), a strain of Arcobacter cryaerophilus isolated from a traffic accident victim (13), and a noncultivable strain of Pseudomonas veronii from a patient with a pseudotumor (3).In this study, we report the isolation of a bacterial strain from the blood and empyema of a cirrhotic patient. The strain, named HKU1, exhibited phenotypic characteristics that do not fit into the patter...

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

“…With the whole genome sequencing data of more than 100 bacteria and archaea available, it has been noted that there are relatively small interoperon heterogeneities for 16S rDNAs. In our experience in 16S rDNA sequencing, both for the known species and novel genera and species, direct sequencing of the PCR products has always been successful (16,(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)30). In this study, when we first amplified the 16S rDNA of HKU15 T and sequenced the PCR product directly, it was repeatedly observed that the 5' end of the PCR product could not be sequenced clearly, with the presence of multiple peaks.…”

“…Bacterial DNA extraction was performed according to our previous publications (24,30). Briefly, 80 µl of NaOH (0.05 M) was added to 20 µl of bacterial cells suspended in distilled water and the mixture was incubated at 60 C for 45 min, followed by addition of 6 µl of Tris-HCl (pH 7.0), achieving a final pH of 8.0.…”

Uruburuella suis gen. nov., sp. nov., isolated from clinical specimens of pigs

“…In recent years, other genera, e.g. Laribacter (Yuen et al, 2001) and Microvirgula (Patureau et al, 1998), have been described and assigned to the family Neisseriaceae.Organisms within the family Neisseriaceae can be isolated from a range of environmental sources (Moss & Bryant, 1982) as well as from different human and animal mucosal surfaces (Kuhn, 1981;Snell, 1984). Only two species, Neisseria gonorrhoeae and Neisseria meningitidis, are wellestablished human pathogens (Morse & Knapp, 1991).…”

“…In recent years, other genera, e.g. Laribacter (Yuen et al, 2001) and Microvirgula (Patureau et al, 1998), have been described and assigned to the family Neisseriaceae.…”

Two-dimensional gel electrophoresis in bacterial proteomics

“…For example, protein expression in Gram-negative bacterium Laribacter hongkongensis cultured at 20°C and 37°C were compared using 2-DE . L. hongkongensis is a recently discovered β-Proteobacterium that is associated with community-acquired gasteroenteritis and traveler's diarrhea (Yuen et al, 2001;Woo et al, 2004;Woo et al, 2005). It can inhabit in the intestines of freshwater fish, frogs and humans, and can also grow independently in freshwater environments (Woo et al, 2004;Teng et al, 2005;Lau et al, 2007;Ni et al, 2007;Lau et al, 2009).…”