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Journal of Clinical Microbiology, February 2007, p. 395-401, Vol. 45, No. 2
0095-1137/07/$08.00+0     doi:10.1128/JCM.01831-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Catabacter hongkongensis gen. nov., sp. nov., Isolated from Blood Cultures of Patients from Hong Kong and Canada

Susanna K. P. Lau,^1,2,3 Alan McNabb,⁴ Gibson K. S. Woo,¹ Linda Hoang,^4,5 Ami M. Y. Fung,¹ Liliane M. W. Chung,¹ Patrick C. Y. Woo,^1,2,3* and Kwok-Yung Yuen^1,2,3

Department of Microbiology,¹ Research Center of Infection and Immunology, The University of Hong Kong,² State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, Hong Kong,³ Laboratory Services, British Columbia Centre for Disease Control,⁴ Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada⁵

Received 4 September 2006/ Returned for modification 13 October 2006/ Accepted 7 November 2006

Top Abstract Introduction Materials and Methods Results Discussion References

 
Four bacterial isolates were recovered from the blood cultures of four patients, two of whom were from Hong Kong and two of whom were from Canada. The two Hong Kong strains were isolated from a 48-year-old man with intestinal obstruction and secondary sepsis (strain HKU16^T) and from a 39-year-old man with acute appendicitis (strain HKU17), while the two Canadian strains were isolated from a 74-year-old man with biliary sepsis (strain CA1) and from a 66-year-old woman with metastatic carcinoma and sepsis (strain CA2). While the first three patients survived, the last patient died 2 weeks after the episode of bacteremia. All four isolates are strictly anaerobic, nonsporulating, gram-positive coccobacilli that were unidentified by conventional phenotypic tests and commercial identification systems. They grow on sheep blood agar as nonhemolytic pinpoint colonies after 48 h of incubation at 37°C in an anaerobic environment. All are catalase positive and motile, with flagella. They produce acid from arabinose, glucose, mannose, and xylose. They do not produce indole or reduce nitrate. They are sensitive to penicillin, vancomycin, and metronidazole but resistant to cefotaxime. 16S rRNA gene sequence analysis showed 16.0%, 16.8%, and 21.0% base differences from Clostridium propionicum, Clostridium neopropionicum, and Atopobium minutum, respectively. The G+C content of strain HKU16^T is 40.2% ± 2.2%. Based on their phylogenetic affiliation, unique G+C content, and phenotypic characteristics, we propose a new genus and species, Catabacter hongkongensis gen. nov., sp. nov., to describe the bacterium, for which HKU16 is the type strain, and suggest that it be assigned to a new family, Catabacteriaceae. The gastrointestinal tract was probably the source of the bacterium for at least three of the four patients. The isolation of a catalase-positive, motile, nonsporulating, anaerobic gram-positive bacillus in clinical laboratories should raise the possibility of C. hongkongensis. Further studies should be performed to ascertain the epidemiology and other disease associations of this bacterium.

Top Abstract Introduction Materials and Methods Results Discussion References

 
Medically important anaerobic gram-positive bacilli are a heterogeneous group of bacteria that include members of the genera Clostridium, Actinomyces, Bifidobacterium, Eggerthella, Eubacterium, Lactobacillus, and Propionibacterium. The genus classification of these bacteria is traditionally based on phenotypic characteristics, such as spore formation, biochemical profiles, and analyses of cell wall fatty acids and metabolic end products. However, analyses of cell wall fatty acids and metabolic end products by gas-liquid chromatography are often limited by the lack of special equipment and expertise in most clinical microbiology laboratories and the limited database. Based on 16S rRNA gene analysis as a new standard for classification of bacteria (17, 18), many of these bacteria have undergone taxonomic revisions, with new genera and species being introduced (8, 9, 12, 15, 23-26). For example, Eubacterium lentum has been reclassified under a new genus as Eggerthella lenta in the family Coriobacteriaceae by its phylogenetic position and high G+C content (9). Two novel species under the new genus, i.e., Eggerthella hongkongensis and Eggerthella sinensis, were also subsequently identified using 16S rRNA gene analysis (12).

In this study, we report the isolation and characterization of four bacterial isolates from the blood cultures of four patients. Two of the isolates (strains HKU16^T and HKU17) were recovered from two patients in Hong Kong, one with intestinal obstruction and secondary sepsis and the other with acute appendicitis. The other two isolates (strains CA1 and CA2) were recovered from two patients in Canada, one of whom developed biliary sepsis after stent removal and the other of whom had metastatic carcinoma of the lung and sepsis syndrome. The four isolates exhibited similar phenotypic characteristics that do not fit into the pattern for any known genus and species. Based on 16S rRNA gene analysis and the unique phenotypic characteristics, we propose a novel genus and species, Catabacter hongkongensis gen. nov., sp. nov., to describe this bacterium.

Top Abstract Introduction Materials and Methods Results Discussion References

 
Patients and microbiological methods. The BACTEC 9240 blood culture system (Becton Dickinson, MD) was used. Bacterial strains were identified by standard conventional methods (7, 14). Flagellum staining was performed by the method described by Kodaka et al. (10). Testing for spores was performed by malachite green staining and phase-contrast microscopy. In addition, a Vitek system (ANI; bioMerieux Vitek), an ATB expression system (ID32A; bioMerieux Vitek), and an API system (20A; bioMerieux Vitek) were used for the identification of the bacterial isolates in this study. Antibiotic susceptibility tests were performed by Etest, and results were interpreted according to the CLSI (formerly NCCLS) criteria for anaerobic bacteria (16). All tests were performed in triplicate with freshly prepared media on separate occasions.

Scanning electron microscopy. Scanning electron microscopy was performed as described previously (27, 28). Polycarbonate membranes (Nuclepore) with a pore size of 5 µm were used.

Bacterial DNA extraction, PCR, and sequencing of 16S rRNA genes. Bacterial DNA extraction, PCR amplification, and DNA sequencing of the 16S rRNA genes were performed according to previous published protocols (11, 25, 26). LPW57 (5'-AGTTTGATCCTGGCTCAG-3') and LPW205 (5'-CTTGTTACGACTTCACCC-3') (Gibco BRL, Rockville, MD) were used as the PCR primers. Both strands of the PCR products were sequenced twice, using the PCR primers (LPW57 and LPW205) and additional sequencing primers, LPW284 (5'-GTTTACAACCCGAAGGCC-3') and LPW306 (5'-TGAGATGTTGGGTTAAGT-3'), designed from the first round of sequencing results.

Phylogenetic characterization. The sequences of the PCR products were compared with known 16S rRNA gene sequences in GenBank by multiple sequence alignment using the CLUSTAL W program (22). Their phylogenetic relationships to other closely related gram-positive rods were determined using Clustal X, version 1.81 (6), and the neighbor-joining method in GrowTree (Genetics Computer Group, Inc., San Diego, CA). A total of 1,311 nucleotide positions were included in the analysis.

G+C content determination. The G+C content of the genomic DNA of HKU16^T was determined by thermal denaturation, as described previously (27, 28). The melting temperature (T_m) of the DNA was defined as the temperature at 50% hyperchronicity. The G+C content of the genomic DNA was calculated by the following formula: (G+C)% = 2.44T_m – 169.

Nucleotide sequence accession number. The 16S rRNA gene sequence of HKU16^T has been lodged within the GenBank sequence database under accession no. AY574991.

Top Abstract Introduction Materials and Methods Results Discussion References

 
Patients. (i) Case 1. A 48-year-old Chinese man was admitted to the hospital in Hong Kong in 1999 because of fever, repeated vomiting, abdominal distension, and constipation for 2 days. He had end-stage renal disease of unknown etiology. He had been on hemodialysis for 11 years after discontinuation of continuous ambulatory peritoneal dialysis as a result of tuberculous peritonitis. Since the episode of tuberculous peritonitis, he had had recurrent episodes of intestinal obstruction, which were treated conservatively. On admission, he was dehydrated and had generalized abdominal distension and hyperactive bowel sounds. An abdominal radiograph revealed a dilated small bowel with multiple air-fluid levels in the central abdomen. The large bowel was air filled with fecal matter. A diagnosis of incomplete small-bowel obstruction and secondary sepsis was made. Blood culture was performed, and intravenous cefuroxime and metronidazole treatment was commenced. On day 3 postincubation, the anaerobic blood culture bottle turned positive for a gram-positive bacillus (strain HKU16^T). His fever responded to intravenous antibiotics, and the intestinal obstruction resolved with conservative treatment. He was discharged after 19 days of hospitalization.

(ii) Case 2. A 39-year-old Chinese man was admitted to the hospital in Hong Kong in 2003 because of central colicky abdominal pain radiating to the right lower quadrant for 1 day. He also complained of vomiting, fever, chills, and rigor. His past medical history was unremarkable. Examination of his abdomen revealed tenderness, guarding, and rebound tenderness over the right lower quadrant. Blood cultures were performed. A clinical diagnosis of acute appendicitis was made, and empirical intravenous cefuroxime and metronidazole treatment was commenced. Emergency laparoscopic appendectomy was performed. At operation, an acutely inflamed appendix with perforation near the base was found, with a small amount of surrounding purulent fluid. Histology of the appendix showed transmural inflammation with marked neutrophil infiltration and local peritonitis. On day 3 postincubation, the anaerobic blood culture bottle turned positive for a gram-positive bacillus (strain HKU17). He recovered uneventfully after the operation and was discharged with oral antibiotics 2 days after admission.

(iii) Case 3. A 74-year-old man was admitted to the hospital in British Columbia, Canada, for removal of a biliary stent in 2004. He had a 4-year history of plasmacytoma complicated by biliary obstruction, which was managed by a combination of radiation therapy and multiple biliary stenting, with the last replacement done in 2002. He was afebrile on admission but developed fever in the evening after complete removal of the biliary stent. Blood cultures were performed, which recovered an anaerobic, gram-positive bacillus (strain CA1). Empirical oral ciprofloxacin treatment was commenced. His fever subsided, and he was discharged home with no subsequent complications.

(iv) Case 4. A 66-year-old female was admitted to the hospital in British Columbia, Canada, because of fever and sepsis syndrome. She was under palliative care for metastatic carcinoma of the lung. Blood cultures were obtained, and the patient was started empirically on cefuroxime and ciprofloxacin. On day 5 postincubation, the anaerobic blood culture bottle turned positive for a gram-positive bacillus with variable staining (strain CA2). The patient died 2 weeks after admission.

Phenotypic characteristics. HKU16^T, HKU17, CA1, and CA2 exhibit similar phenotypic characteristics. They are all nonsporulating, gram-positive coccobacilli. They are motile, with flagella (Fig. 1a). They grow on sheep blood agar as nonhemolytic pinpoint colonies after 48 h of incubation at 37°C in an anaerobic environment. They do not grow in aerobic or microaerophilic environments. They produce catalase when tested with 15% H₂O₂ but do not produce indole or reduce nitrate. Their biochemical profiles are shown in Table 1. They all produce acid from arabinose, glucose, mannose, and xylose. The two isolates from Canada differ from the two isolates from Hong Kong by being negative for glycerol fermentation and positive for rhamnose fermentation and leucine arylamidase. All four isolates were "unidentified" by all three commercially available identification systems used. The code profile for the four isolates by the ATB expression system (ID32A) was 0012000010. The code profile for HKU16^T and HKU17 by the API system (20A) was 40415042, and that for CA1 and CA2 was 40414052. All four isolates were susceptible to bile and kanamycin but resistant to colistin. The MICs of cefotaxime, vancomycin, and metronidazole for all four strains were >32 µg/ml, 2 µg/ml, and <0.016 µg/ml, respectively. The MICs of penicillin were 0.75 µg/ml for strain HKU16^T, 0.5 µg/ml for strain HKU17, and 4 µg/ml for strains CA1 and CA2.

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FIG. 1. Flagellum stain (a) of Catabacter hongkongensis. The bacterium is a gram-positive coccobacillus with a tuft of flagella inserted on one side (arrows). (b) Scanning electron micrograph of Catabacter hongkongensis. The bacterium is short and straight and tapered at both ends. Cells vary in length from 0.71 to 1.12 µm and in diameter from 0.36 to 0.48 µm (mean, 0.96 µm by 0.42 µm; n = 20). Bar, 0.5 µm.

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TABLE 1. Biochemical profiles of the four blood culture isolates by the Vitek system (ANI), ATB expression system (ID32A), and API system (20A)

Scanning electron microscopy. A scanning electron micrograph of strain HKU16^T is shown in Fig. 1b. The bacterial cells are short straight rods tapered at both ends, with a tuft of flagella inserted on one side.

Molecular characterization by 16S rRNA gene sequencing and phylogenetic characterization. PCRs to amplify the 16S rRNA genes of all four isolates showed bands of about 1,400 bp. The 16S rRNA gene sequences were identical. There was a 16.0% difference in the 16S rRNA gene sequences of the four isolates from that of Clostridium propionicum (GenBank accession no. X77841), a 16.8% difference from that of Clostridium neopropionicum (GenBank accession no. 76746), a 21.0% difference from that of Atopobium minutum (GenBank accession no. X67148), a 21.9% difference from that of Eggerthella lenta (GenBank accession no. AF292375), a 22.2% difference from that of Bifidobacterium dentium (GenBank accession no. D86183), a 21.7% difference from that of Propionibacterium acnes (GenBank accession no. AB097215), and a 21.8% difference from that of Actinomyces odontolyticus (GenBank accession no. AJ234047) (Fig. 2). Although the four sequences had >99% identity to "Ruminococcus sp." strain CCUG 37327 (GenBank accession no. AJ318864), a ruminococcus-like organism from a human clinical source in the United Kingdom, the true identity of this "Ruminococcus sp." has not been validated or published. Moreover, this "Ruminococcus sp." possessed a phylogenetic position distant from the known Ruminococcus species, suggesting that it is unlikely to belong to the genus Ruminococcus and may have been misidentified, since our present four isolates formed small, short bacilli which may be mistaken as cocci (Fig. 2). Based on phylogenetic affiliation, the four isolates form a distinct lineage among the anaerobic gram-positive bacilli and are only peripherally associated with clusters I, III, and XIVb of the clostridia (2). We propose that they be assigned a novel genus and species, Catabacter hongkongensis, under a new family, Catabacteriaceae. The name "Catabacter," which did not exist previously, was constructed as an arbitrary name as an abbreviation for "catalase-positive bacterium" in order to avoid an unusually long genus name.

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FIG. 2. Phylogenetic tree showing the relationships of Catabacter hongkongensis gen. nov., sp. nov., to related anaerobic gram-positive bacteria. The tree was constructed by using the neighbor-joining method, with Bacteroides fragilis as the root. Bootstrap values were calculated from 1,000 trees. Bar, estimated number of substitutions per 100 bases, using the Jukes-Cantor correction. Names and accession numbers are given as cited in the GenBank database.

G+C content determination. The G+C content of strain HKU16^T (mean ± standard deviation) was 40.2% ± 2.2%.

Top Abstract Introduction Materials and Methods Results Discussion References

 
In this study, we report the isolation of a novel anaerobic gram-positive bacillus from the blood cultures of four patients, two from Hong Kong and two from Canada. The bacterium was likely to be clinically significant in all four patients, as evidenced by its isolation from blood in pure culture and the patients' systemic responses to the bacteremia. The isolation of the bacterium from patients in both Asia and North America suggests that it is widely distributed. The historical failure to recognize this new genus and species is likely a reflection of the difficulties in accurately identifying anaerobic gram-positive bacilli. While spore formation may not be obvious in isolates primarily recovered from clinical specimens, analysis of cell wall fatty acids and metabolic end products by gas-liquid chromatography requires special equipment and expertise, which are generally not available in clinical microbiology laboratories. Therefore, many of the anaerobic gram-positive bacilli in clinical laboratories are not identified even to the genus level. Application of 16S rRNA gene analysis of suspected isolates is likely to uncover more strains of C. hongkongensis and to help to better define its epidemiology, clinical disease associations, and pathogenicity. The presence of C. hongkongensis in Asia, America, and probably Europe implies that it is a bacterium of global importance. The possibility of C. hongkongensis should be considered when a catalase-positive, motile, nonsporulating, anaerobic gram-positive bacillus is encountered. Since C. hongkongensis demonstrates variable susceptibility to penicillin (MICs range from 0.5 to 4 µg/ml), metronidazole should be considered the drug of choice for C. hongkongensis infections.

While there were no localizing symptoms or signs in the last patient, we speculate that the source of the bacteremia in the first three patients was the gastrointestinal tract. It has been documented for both animals and humans that intestinal obstruction (present in case 1) promotes gastrointestinal tract translocation of bacteria (5, 13, 20). Acute appendicitis (present in case 2) is also recognized as being associated with anaerobic bacteremia as a result of bacterial translocation through inflamed intestinal mucosa (1). Moreover, it is well known that biliary sepsis (present in case 3) is usually due to ascending infection by bacteria from the gut through the ampulla of Vater. In fact, many other nonsporulating anaerobic gram-positive bacilli, including Bifidobacterium, Eggerthella, Eubacterium, and Lactobacillus, are common flora of the human gastrointestinal tract. Further studies should be carried out to determine if Catabacter hongkongensis is also one of our normal gut commensals.

C. hongkongensis exhibited phenotypic and genotypic characteristics that are very different from those of other closely related medically important bacterial genera (Table 2). Members of the genus Clostridium produce spores. However, C. hongkongensis, like members of the Eubacterium, Eggerthella, Bifidobacterium, Propionibacterium, and Actinomyces genera, is nonsporulating. Most Clostridium species and C. hongkongensis are motile, whereas members of Eubacterium have variable motility and those of Eggerthella, Bifidobacterium, Propionibacterium, and Actinomyces are nonmotile. C. hongkongensis, Eubacterium, Eggerthella, and Bifidobacterium are obligately anaerobic, whereas some members of the Clostridium, Propionibacterium, and Actinomyces genera are aerotolerant. C. hongkongensis, some members of the Eggerthella and Propionibacterium genera, and Actinomyces viscosus produce catalase, but members of the Clostridium, Eubacterium, and Bifidobacterium genera do not. C. hongkongensis and members of Eubacterium, Eggerthella, Bifidobacterium, and Actinomyces do not produce indole, but some members of Clostridium and Propionibacterium produce indole. C. hongkongensis and Bifidobacterium do not reduce nitrate, but some members of the Clostridium, Eubacterium, Eggerthella, Propionibacterium, and Actinomyces genera reduce nitrate. Genotypically, members of the genus Eubacterium have low G+C contents of 30 to 40 mol%, HKU16^T has a G+C content of about 40%, members of the Eggerthella, Bifidobacterium, Propionibacterium, and Actinomyces genera have high G+C contents of over 55%, and those of the genus Clostridium have highly variable G+C contents of 26 to 56%. Furthermore, the 16S rRNA genes of C. hongkongensis exhibited >16% nucleotide differences from the 16S rRNA genes of all previously described bacteria. Phylogenetic analysis showed that C. hongkongensis isolates form a distinct lineage among the anaerobic gram-positive rods and are only peripherally associated with clusters I, III, and XIVb of the clostridia (2) (Fig. 2). Although it is closest to C. propionicum, a species that has never been reported to be associated with human infection, it is well discerned from the clade. Lactobacillus and Eubacterium, which are also associated phylogenetically with clusters I and XIVb of the clostridia, are classified under different families, i.e., Lactobacillaceae and Eubacteriaceae, respectively, because of their distinct phenotypic and genotypic characteristics. Therefore, the deep branch of C. hongkongensis in phylogenetic analysis, together with its unique phenotypic characteristics, is representative of a novel genus, and we propose that it be assigned to a new family, Catabacteriaceae.

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TABLE 2. Comparison of characteristics of Catabacter hongkongensis and those of medically important, closely related anaerobic gram-positive rods

The production of catalase in C. hongkongensis may explain the relative aerotolerance of the bacterium. In aerobic and facultative bacteria, DNA damage by oxygen radicals generated under oxygen exposure is prevented by the dismutation of O₂^– to H₂O₂ by superoxide dismutase and the elimination of H₂O₂ by catalase and peroxidase (3, 4). On the other hand, the sensitivity to oxygen exposure of anaerobes has been attributed to the lack of these protective mechanisms against oxidative stress. Nevertheless, some anaerobes are more aerotolerant than others. For Bacteroides fragilis, one of the most aerotolerant species, it has been shown that the production of catalase plays a role in the protection against oxidative stress (19). Moreover, it was found that clinical isolates of B. fragilis were more aerotolerant than fecal isolates, suggesting that aerotolerance may be an important virulence factor (21). C. hongkongensis isolates were able to survive in the presence of oxygen for 72 to 96 h on chocolate agar incubated in 5% CO₂, in contrast to only 12 h for a strain of the strict anaerobe Prevotella melaninogenica (data not shown). Further studies will be needed to clarify the role of catalase production in the oxidative stress response and virulence of C. hongkongensis.

Description of Catabacter hongkongensis gen. nov., sp. nov. Catabacter (Ca.ta.bac'ter. arbitrary name; N.L. cata- [abbreviation for catalase positive], derived from Gr. kata, down; N.L. masc. n. bacter, rod; N.L. masc. n. Catabacter, catalase-positive rod); hongkongensis (hong.kong.en'sis. N.L. fem. adj. in honor of Hong Kong, the place where the type strain was isolated).

Cells are obligately anaerobic, gram-positive coccobacilli or short, straight rods. The bacterium grows on sheep blood agar as nonhemolytic pinpoint colonies after 48 h of incubation at 37°C in an anaerobic environment. It does not grow in aerobic or microaerophilic environments. The organism does not produce spores but is motile, with flagella. It produces catalase but does not produce indole or reduce nitrate. It produces acid from arabinose, glucose, mannose, and xylose (Table 1). The moles percent G+C content of the DNA of the type strain, HKU16, is 40.2% ± 2.2%. The organism was isolated from the blood cultures of three patients with acute gastrointestinal compromises and one with acute sepsis. The type strain of C. hongkongensis is strain HKU16.

 
This work was partly supported by the University Development Fund, a University Research Grant Council grant (HKU 7236/02 M), a Committee for Research and Conference grant, The University of Hong Kong, and the William Benter Infectious Disease Fund.

We thank Hans G. Trüper (Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Germany) for advice on the nomenclature of the novel bacterial genus and species, Pam Kibsey (Fraser Health, Royal Columbian Hospital, New Westminster, British Columbia, Canada) for providing the case information on the Canadian isolates, and Kathy Adie and Nancy Kopp (Laboratory Services, British Columbia Center for Disease Control, Vancouver, British Columbia, Canada) for their expert technical assistance.

 
* Corresponding author. Mailing address: Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong, Hong Kong. Phone: (852) 28554892. Fax: (852) 28551241. E-mail for Patrick C. Y. Woo: pcywoo{at}hkucc.hku.hk. E-mail for Kwok-Yung Yuen: hkumicro{at}hkucc.hku.hk.

Published ahead of print on 22 November 2006.

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Journal of Clinical Microbiology, February 2007, p. 395-401, Vol. 45, No. 2
0095-1137/07/$08.00+0     doi:10.1128/JCM.01831-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

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