High Prevalence and Mechanism Associated With Extended Spectrum Beta-Lactamase-Positive Phenotype in Laribacter hongkongensis

In this study, we reported the prevalence and mechanism associated with the extended-spectrum beta-lactamase (ESBL)-positive phenotype in Laribacter hongkongensis isolated from patients and fish. Using the inhibition zone enhancement test, 20 (95.2%) of the 21 patient strains and 8 (57.1%) of the 14 fish strains were tested ESBL-positive. However, ESBL genes, including SHV, TEM, CTX-M, GES, and PER, were not detected in all of these 28 L. hongkongensis isolates. No ESBL gene could be detected in either the complete genome of L. hongkongensis HLHK9 or the draft genome of PW3643. PCR and DNA sequencing revealed that all the 35 L. hongkongensis isolates (showing both ESBL-positive and ESBL-negative phenotypes) were positive for the ampC gene. When the AmpC deletion mutant, HLHK9ΔampC, was subject to the zone enhancement test, the difference of zone size between ceftazidime/clavulanate and ceftazidime was less than 5 mm. When boronic acid was added to the antibiotic disks, none of the 28 “ESBL-positive” isolates showed a ≥ 5 mm enhancement of inhibition zone size diameter between ceftazidime/clavulanate and ceftazidime and between cefotaxime/clavulanate and cefotaxime. A high prevalence (80%) of ESBL-positive phenotype is present in L. hongkongensis. Overall, our results suggested that the ESBL-positive phenotype in L. hongkongensis results from the expression of the intrinsic AmpC beta-lactamase. Confirmatory tests should be performed before issuing laboratory reports for L. hongkongensis isolates that are tested ESBL-positive by disk diffusion clavulanate inhibition test.

Comparative evaluation of a laboratory-developed real-time PCR assay and RealStar® Adenovirus PCR Kit for quantitative detection of human adenovirus

Background

Human adenoviruses are common causes of community-acquired respiratory tract and enteric infections. Severe disseminated infections with high mortality rates may be seen in immunocompromised individuals. An accurate and cost-effective quantitative assay is essential not only for laboratory diagnosis of adenoviral infections, but also for monitoring of response to antiviral treatment. The diagnostic performance of an in-house quantitative polymerase chain reaction assay was compared to a commercial system.

Methods

The analytical sensitivity, specificity, linearity, precision and accuracy of an in-house adenovirus quantitative polymerase chain reaction assay were evaluated against the RealStar® Adenovirus PCR Kit (Altona Diagnostics GmbH, Hamburg, Germany), using 122 clinical specimens and 18 proficiency testing samples.

Results

Linear regression analysis of the quantitative results by the in-house assay showed the dynamic range from 2.60 to 9 log₁₀ (plasma) and 2.94 to 9 log₁₀ (viral transport medium) copies/mL, with the coefficient of determination (R²) of 0.996 and 0.998, respectively. A dilution series demonstrated the limits of detection and lower limits of quantification for plasma were 2.06 log₁₀ and 2.60 log₁₀ copies/mL and those for viral transport medium were 2.31 log₁₀ and 2.94 log₁₀ copies/mL respectively. The precision of the in-house assay was highly reproducible among runs with coefficients of variance ranging from 0.07 to 3.21% for plasma and 0.17% to 2.11% for viral transport medium. A comparison of 52 matched samples showed an excellent correlation between the quantitative viral loads measured by the in-house assay and the RealStar® Adenovirus PCR Kit (R² = 0.984), with an average bias of − 0.16 log₁₀ copies/mL.

Conclusions

The in-house adenovirus assay is a sensitive and reliable assay with lower cost for the detection and quantification of adenoviral DNA when compared to the RealStar® Adenovirus PCR Kit.

Electronic supplementary material

The online version of this article (10.1186/s12985-018-1059-7) contains supplementary material, which is available to authorized users.

Comparative evaluation of a laboratory developed real-time PCR assay and the RealStar® HHV-6 PCR Kit for quantitative detection of human herpesvirus 6

BACKGROUND

HHV-6 reactivation in immunocompromised patients is common and may be associated with serious morbidity and mortality; therefore, early detection and initiation of therapy might be of benefit. Real-time PCR assays allow for early identification of HHV-6 reactivation to assist in providing a timely response. Thus, we compared the performance of an in-house developed HHV-6 quantitative PCR assay with a commercially available kit, the RealStar^® HHV-6 PCR Kit.

METHOD

The analytical sensitivity, analytical specificity, linearity, precision and accuracy of the in-house developed HHV-6 qPCR assay were evaluated. The diagnostic performance of the in-house HHV-6 qPCR assay was compared with the RealStar^® HHV-6 PCR Kit, using 72 clinical specimens and 17 proficiency testing samples.

RESULTS

Linear regression analysis of the quantitative results showed a dynamic range from 2 to 10 log₁₀ copies/ml and a coefficient of determination (R²) of 0.999 for the in-house assay. A dilution series demonstrated a limit of detection and a limit of quantification of 1.7 log₁₀ and 2 log₁₀ copies/ml, respectively. The precision of the assay was highly reproducible among runs with coefficients of variance (CV) ranging from 0.27% to 4.37%. A comparison of 27 matched samples showed an excellent correlation between the quantitative viral loads measured by the in-house HHV-6 qPCR assay and the RealStar^® HHV-6 PCR Kit (R²=0.926; P<0.0001), with an average bias of -0.24 log₁₀ copies/ml.

CONCLUSIONS

The in-house developed HHV-6 qPCR method is a sensitive and reliable assay with lower cost for the detection and quantification of HHV-6 DNA when compared to the RealStar^® HHV-6 PCR Kit.

Streptococcus hongkongensis sp. nov., isolated from a patient with an infected puncture wound and from a marine flatfish

A bacterium, HKU30T, was isolated from the infected tissue of a patient with wound infection after puncture by a fish fin. Cells are facultative anaerobic, non-spore-forming, non-motile, Gram-positive cocci arranged in chains. Colonies were non-haemolytic. The strain was catalase, oxidase, urease and Voges–Proskauer test negative. It reacted with Lancefield’s group G antisera and was resistant to optochin. It grew on bile aesculin agar and in 5 % NaCl. It was unidentified by three commercial identification systems. 16S rRNA gene sequence analysis indicated that the bacterium shared 98.2, 97.7, 97.4 and 97.1 % nucleotide identities with Streptococcus iniae , Streptococcus pseudoporcinus , Streptococcus parauberis and Streptococcus uberis , respectively. The DNA G+C content was 35.6±0.9 mol% (mean±sd). In view of the occupational exposure of the patient, an epidemiological study was performed to isolate the bacterium from marine fish. Two strains, with similar phenotypic and genotypic characteristics to those of HKU30T, were isolated from a three-lined tongue sole (Cynoglossus abbreviatus) and an olive flounder (Paralichthys olivaceus) respectively. Phylogenetic analysis of four additional housekeeping genes, groEL, gyrB, sodA and rpoB, showed that the three isolates formed a distinct branch among known species of the genus Streptococcus , being most closely related to S. parauberis (CCUG 39954T). DNA–DNA hybridization demonstrated ≤53.8 % DNA relatedness between the three isolates and related species of the genus Streptococcus . A novel species, Streptococcus hongkongensis sp. nov., is proposed. The type strain is HKU30T ( = DSM 26014T = CECT 8154T).

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.

Guidelines for interpretation of 16S rRNA gene sequence-based results for identification of medically important aerobic Gram-positive bacteria

This study is believed to be the first to provide guidelines for facilitating interpretation of results based on full and 527 bp 16S rRNA gene sequencing and MicroSeq databases used for identifying medically important aerobic Gram-positive bacteria. Overall, full and 527 bp 16S rRNA gene sequencing can identify 24 and 40 % of medically important Gram-positive cocci (GPC), and 21 and 34 % of medically important Gram-positive rods (GPR) confidently to the species level, whereas the full-MicroSeq and 500-MicroSeq databases can identify 15 and 34 % of medically important GPC and 14 and 25 % of medically important GPR confidently to the species level. Among staphylococci, streptococci, enterococci, mycobacteria, corynebacteria, nocardia and members of Bacillus and related taxa (Paenibacillus, Brevibacillus, Geobacillus and Virgibacillus), the methods and databases are least useful for identification of staphylococci and nocardia. Only 0–2 and 2–13 % of staphylococci, and 0 and 0–10 % of nocardia, can be confidently and doubtfully identified, respectively. However, these methods and databases are most useful for identification of Bacillus and related taxa, with 36–56 and 11–14 % of Bacillus and related taxa confidently and doubtfully identified, respectively. A total of 15 medically important GPC and 18 medically important GPR that should be confidently identified by full 16S rRNA gene sequencing are not included in the full-MicroSeq database. A total of 9 medically important GPC and 21 medically important GPR that should be confidently identified by 527 bp 16S rRNA gene sequencing are not included in the 500-MicroSeq database. 16S rRNA gene sequence results of Gram-positive bacteria should be interpreted with basic phenotypic tests results. Additional biochemical tests or sequencing of additional gene loci are often required for definitive identification. To improve the usefulness of the MicroSeq databases, bacterial species that can be confidently identified by 16S rRNA gene sequencing but are not found in the MicroSeq databases should be included.

Surgical site abscess caused by Lactobacillus fermentum identified by 16S ribosomal RNA gene sequencing

We report the first case of surgical site abscess caused by Lactobacillus fermentum from a 53-year-old woman with squamous cell carcinoma of the esophagus after transthoracic esophagectomy and neoadjuvant chemoirradiation. 16S rRNA gene sequencing is a useful tool to better characterize the epidemiology and clinical significance of L. fermentum.

Catabacter hongkongensis gen. nov., sp. nov., isolated from blood cultures of patients from Hong Kong and Canada

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 HKU16T) 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 degrees 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 HKU16T 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.

Usefulness of the MicroSeq 500 16S rDNA bacterial identification system for identification of anaerobic Gram positive bacilli isolated from blood cultures

Using full 16S ribosomal RNA (rRNA) gene sequencing as the gold standard, 20 non-duplicating anaerobic Gram positive bacilli isolated from blood cultures were analysed by the MicroSeq 500 16S rDNA bacterial identification system. The MicroSeq system successfully identified 13 of the 20 isolates. Four and three isolates were misidentified at the genus and species level, respectively. Although the MicroSeq 500 16S rDNA bacterial identification system is better than three commercially available identification systems also evaluated, its database needs to be expanded for accurate identification of anaerobic Gram positive bacilli.

Clinical isolates of Streptococcus iniae from Asia are more mucoid and β-hemolytic than those from North America

Streptococcus iniae, a widely distributed fish pathogen, is known to cause rare cases of human infection. We describe 2 cases of invasive S. iniae infection, one with septic arthritis complicating chronic gout and the other with bacteremic cellulitis. Both patients were Chinese and have been regularly handling fresh fish for cooking. Both isolates were unidentified or misidentified by 3 commercially available identification system and were only identified by 16S rRNA gene sequencing. When compared with a clinical isolate of S. iniae from Canada, their colonies were larger, more beta-hemolytic, and microcoid. Although bacteremic cellulitis has been described as the most common infection associated with S. iniae, the bacterium has not been reported to cause exacerbations of gouty arthritis previously. Clinical laboratories should be aware of the possibility of different colony morphology of S. iniae from Asia. More accurate identification of nongroupable beta-hemolytic streptococci, especially from patients with epidemiologic linkage to fresh fish, may uncover more cases of S. iniae infection. The Asian population and handlers of fresh fish should be informed of the risk of acquiring S. iniae infection.

Bacteraemia caused by Anaerotruncus colihominis and emended description of the species

BACKGROUND

Anaerotruncus colihomonis is a newly described bacterial genus and species isolated from the stool specimens of children. Its clinical significance, however, is unknown.

AIMS

To describe a case of A colihominis bacteraemia identified by 16S ribosomal RNA (rRNA) gene sequencing and provide an emended description of the species.

METHODS

An unidentified anaerobic bacillus (strain HKU19) that stains Gram negative was subjected to characterisation by 16S rRNA gene sequencing, G+C content determination and electron microscopy.

RESULTS

Strain HKU19 was isolated from the blood culture of a 78-year-old woman with nosocomial bacteraemia. It was found to be an anaerobic, non-motile, pleomorphic, thin bacillus that stains Gram negative. It produces Indole and utilises glucose and mannose. Identifying the strain to the species level was not possible by conventional phenotypic tests and commercial identification systems. The G+C content of strain HKU19 was found to be 53.43 mol%. A similarity of 99.3% nucleotide identities was found between the 16S rRNA gene sequence of strain HKU19 and that of A colihominis WAL 14 565(T), which was isolated from a human faecal specimen. In contrast with the original description of A colihominis, HKU19 was found to produce occasional oval, terminal spores, although the other phenotypic characteristics matched. Spores were also occasionally observed when the two previously reported strains were re-examined.

CONCLUSIONS

Although the source of the bacteraemia in the patient cannot be determined, this report suggests that A colihominis is of clinical significance. Spore formation is proposed as an emended description of A colihominis.

Life-threatening invasive Helcococcus kunzii infections in intravenous-drug users and ermA-mediated erythromycin resistance

We report the first two cases of life-threatening invasive Helcococcus kunzii infection, with primary bacteremia and empyema thoracis, respectively. Gram smears of both H. kunzii isolates showed a mixture of gram-positive and gram-negative cocci. The isolate from the first patient, resistant to erythromycin and clindamycin, possessed an ermA gene.

Differential sensitivities of severe acute respiratory syndrome (SARS) coronavirus spike polypeptide enzyme-linked immunosorbent assay (ELISA) and SARS coronavirus nucleocapsid protein ELISA for serodiagnosis of SARS coronavirus pneumonia

The use of recombinant severe acute respiratory syndrome-coronavirus (SARS-CoV) nucleocapsid protein (N) enzyme-linked immunosorbent assay (ELISA)-based antibody and antigen tests for diagnosis of SARS-CoV infections have been widely reported. However, no recombinant SARS-CoV spike protein (S)-based ELISA is currently available. In this article, we describe the problems and solutions of setting up the recombinant SARS-CoV S-based ELISA for antibody detection. The SARS-CoV S-based immunoglobulin M (IgM) and IgG ELISAs were evaluated and compared with the corresponding N-based ELISA for serodiagnosis of SARS-CoV pneumonia, using sera from 148 healthy blood donors who donated blood 3 years ago as controls and 95 SARS-CoV pneumonia patients in Hong Kong. Results obtained by the recombinant S (rS)-based IgG ELISA using the regenerated S prepared by dialysis with decreasing concentrations of urea or direct addition of different coating buffers, followed by addition of different regeneration buffer, identified 4 M urea and 1 M sarcosine for plate coating and no regeneration buffer as the most optimal conditions for antibody detection. The specificities of the S-based ELISA for IgG and IgM detection were 98.6% and 93.9%, with corresponding sensitivities of 58.9% and 74.7%, respectively. The sensitivity of the rN IgG ELISA (94.7%) is significantly higher than that of the rS IgG ELISA (P < 0.001), whereas the sensitivity of the rS IgM ELISA is significantly higher than that of the rN IgM ELISA (55.2%) (P < 0.01). An ELISA for detection of IgM against S and N could be more sensitive than one that detects IgM against N alone for serodiagnosis of SARS-CoV pneumonia.

Clostridium bacteraemia characterised by 16S ribosomal RNA gene sequencing

BACKGROUND

Owing to problems in accurate species identification of the diverse genus clostridium, the epidemiology and pathogenicity of many species are not fully understood. Moreover, previous studies on clostridium bacteraemia have been limited and relied only on phenotypic species identification.

AIMS

To characterise the epidemiology, disease spectrum, and outcome of clostridium bacteraemia using 16S ribosomal RNA (rRNA) gene sequencing.

METHOD

During a four year period (1998-2001), all cases of clostridium bacteraemia were prospectively studied and all "non-perfringens" clostridium isolates identified to the species level by 16S rRNA gene sequencing.

RESULTS

Fifty one blood culture isolates were identified as Clostridium perfringens and 17 belonged to 11 other clostridium species. The first case of C disporicum infection and two cases of clostridium bacteraemia in children with intussusception were also described. Of the 68 clostridium isolates from 68 different patients, 38 were associated with clinically relevant bacteraemia. The gastrointestinal and hepatobiliary tracts were common sites of both underlying disease and portal of entry in these patients. Clostridium perfringens accounted for 79% of all clinically relevant bacteraemia, with the remainder caused by a diversity of species. The attributable mortality rate of clinically relevant clostridium bacteraemia was 29%. Younger age and underlying gastrointestinal/hepatobiliary tract disease were associated with mortality (p < 0.05).

CONCLUSIONS

Patients with clinically relevant clostridium bacteraemia should be investigated for the presence of underlying disease processes in the gastrointestinal or hepatobiliary tracts. 16S rRNA gene analysis will continue to be useful in further understanding the pathogenicity of various clostridium species.

Bacteremia due to Clostridium hathewayi in a patient with acute appendicitis

Clostridium hathewayi is a newly described Clostridium species isolated from the feces of healthy human individuals, but its clinical significance is not known. We describe a case of human infection associated with C. hathewayi. The bacterium (strain HKU18) was isolated from the blood culture of a 39-year-old patient with acute gangrenous appendicitis complicated by septic shock. The cells were strictly anaerobic, nonmotile rods that stained gram negative. Conventional phenotypic tests and commercial identification systems failed to identify HKU18 to the species level. 16S rRNA gene analysis showed 1.4% nucleotide difference between the sequence of HKU18 and that of C. hathewayi, indicating that HKU18 was a strain of C. hathewayi. The patient responded to appendectomy and antibiotic treatment. 16S rRNA gene sequencing would be useful in further characterizing the clinical disease spectrum of C. hathewayi.

Eggerthella hongkongensis sp. nov. and eggerthella sinensis sp. nov., two novel Eggerthella species, account for half of the cases of Eggerthella bacteremia

Eggerthella, one of the human gut flora, was rarely reported to cause bacteremia in the literature. We describe the application of 16S ribosomal RNA gene sequencing in defining the epidemiology and clinical significance of Eggerthella bacteremia during a 4-year period. Among 55 clinically significant blood culture isolates of anaerobic Gram-positive bacilli, 5 were identified as E. lenta and 5 belonged to 2 novel Eggerthella species, proposed as E. hongkongensis and E. sinensis, respectively. The 10 patients with Eggerthella bacteremia were adults, and 9 had underlying diseases. In all cases, the source of the bacteremia was likely from endogenous flora. Septic shock was a complication in 4 patients, and 3 patients died. The present study suggests that Eggerthella bacteremia is much more common than expected and is associated with significant morbidity and mortality. Moreover, the 2 novel species account for half of the cases of Eggerthella bacteremia.

Detection of specific antibodies to severe acute respiratory syndrome (SARS) coronavirus nucleocapsid protein for serodiagnosis of SARS coronavirus pneumonia

We report the evaluation of recombinant severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) nucleocapsid protein enzyme-linked immunosorbent assay (ELISA)-based antibody tests for serodiagnosis of SARS-CoV pneumonia and compare the sensitivities and specificities of this ELISA for detection of immunoglobulin G (IgG), IgM, IgA, and their combinations with serum samples from 149 healthy blood donors who donated blood 3 years ago as controls and 106 SARS-CoV pneumonia patients in Hong Kong. The specificities of the ELISA for IgG, IgM, and IgA detection were 95.3, 96.6, and 96.6%, respectively, with corresponding sensitivities of 94.3, 59.4, and 60.4%, respectively. The present ELISA appears to be a sensitive test for serodiagnosis of SARS-CoV pneumonia, is much more economical and less labor-intensive than the indirect immunofluorescence assay, and does not require cultivation of SARS-CoV.

Phenotypic and molecular characterization of erythromycin resistance in four isolates of Streptococcus-like gram-positive cocci causing bacteremia

Among nine patients with bacteremia caused by Granulicatella or Gemella in a 6-year period (July 1995 to June 2001), three had bacteremia caused by erythromycin-resistant Granulicatella adiacens and one had bacteremia caused by erythromycin-resistant Gemella haemolysans. All four isolates possessed mef genes, whereas none possessed ermT, ermTR, or ermB genes.

"Streptococcus milleri" endocarditis caused by Streptococcus anginosus

Unlike other viridans streptococci, members of the "Streptococcus milleri group" are often associated with abscess formation, but are only rare causes of infective endocarditis. Although it has been shown that almost all S. intermedius isolates and most S. constellatus isolates, but only 19% of S. anginosus isolates, were associated with abscess formation, no report has addressed the relative importance of the 3 species of the "S. milleri group" in infective endocarditis. During a 5-year period (April 1997 through March 2002), 6 cases of "S. milleri" endocarditis (out of 377 cases of infective endocarditis), that fulfil the Duke's criteria for the diagnosis of infective endocarditis, were encountered. All 6 "S. milleri" isolates were identified as S. anginosus by 16S ribosomal RNA (rRNA) gene sequencing. Three patients had underlying chronic rheumatic heart disease and 1 was an IV drug abuser. Five had monomicrobial bacteremia, and 1 had polymicrobial (S. anginosus, S. mitis, Granulicatella adiacens, and Slackia exigua) bacteremia. Two patients died. None of the 6 isolates were identified by the Vitek system (GPI) or the API system (20 STREP) at >95% confidence. All 6 isolates were sensitive to penicillin G (MIC 0.008-0.064 microg/mL), cefalothin, erythromycin, clindamycin, and vancomycin. Accurate identification to the species level, by 16S rRNA gene sequencing, in cases of bacteremia caused by members of the "S. milleri group", would have direct implication on the underlying disease process, hence guiding diagnosis and treatment. Infective endocarditis should be actively looked for in cases of monomicrobial S. anginosus bacteremia, especially if the organism is recovered in multiple blood cultures.

Enterococcus cecorum empyema thoracis successfully treated with cefotaxime

We report the first case of Enterococcus cecorum empyema thoracis and spontaneous bacterial peritonitis in a 44-year-old man with underlying cirrhosis. The patient responded to cefotaxime (MIC, 0.25 microg/ml) treatment and drainage of the empyema. Susceptibility of E. cecorum to expanded-spectrum cephalosporins could be due to its production of types of penicillin-binding proteins similar to those produced by Streptococcus species rather than to those produced by Enterococcus species (as predicted by phylogenetic analysis of the 16S rRNA gene sequences).

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.

Seronegative bacteremic melioidosis caused by Burkholderia pseudomallei with ambiguous biochemical profile: clinical importance of accurate identification by 16S rRNA gene and groEL gene sequencing

An aerobic gram-negative bacterium was isolated from the blood and sputum of an 84-year-old, chair-bound nursing home resident with acute bacteremic pneumonia. Although the phenotypic characteristics suggested that the bacterium could be Burkholderia pseudomallei, the Vitek 1 system (GNI+), which can successfully identify 99% of B. pseudomallei strains, showed that the bacterium was "unidentified." Immunoglobulin G against the lipopolysaccharide (LPS) of B. pseudomallei, as detected by an LPS-based enzyme-linked immunosorbent assay with 95% sensitivity, was negative in both the acute-phase and convalescent-phase sera. Sequencing of the groEL gene showed that the isolate was B. pseudomallei. Proper identification of the bacterium in this study is crucial, since there would be a radical difference in the duration of antimicrobial therapy.

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.

Diagnosis of pelvic actinomycosis by 16S ribosomal RNA gene sequencing and its clinical significance

Traditional ways of identification of anaerobic Gram-positive non-sporulating bacilli by isolation of the organism and studying it phenotypically by elucidation of its morphologic and biochemical characteristics and metabolic end products are associated with a need for special equipment and expertise, and strains that are "unidentified" because of ambiguous biochemical profiles. In this study, an anaerobic Gram-positive non-sporulating bacterium was isolated from the intrauterine contraceptive device of a 36-year old woman with pyosalpinx. The Vitek system (ANI) showed that it was 99% Propionibacterium granulosum; whereas the API system (20A) showed that it was 78% Actinomyces meyeri/odontolyticus. The 16S ribosomal RNA gene of the strain was amplified and sequenced. There was 0 base difference between the isolate and A. odontolyticus (GenBank Accession no. AJ234047), indicating the isolate most closely resembled a strain of A. odontolyticus. Identification of the organism in this study was important because the duration of antibiotic therapy would be entirely different. In the present case, identification of the bacterium as A. odontolyticus inferred that the patient suffered from an intermediate form of pelvic actinomycosis. A prolonged course of antibiotics would be more desirable, as the relapse rate of actinomycosis after a short course of antibiotics is high.

Identification by 16S rRNA gene sequencing of Lactobacillus salivarius bacteremic cholecystitis

An anaerobic, nonsporulating, gram-positive bacterium was isolated from blood and bile pus cultures of a 70-year-old man with bacteremic acute cholecystitis. The API 20A system showed that it was 70% Actinomyces naeslundii and 30% Bifidobacterium species, whereas the Vitek ANI system and the ATB ID32A Expression system showed that it was "unidentified." The 16S rRNA gene of the strain was amplified and sequenced. There were 3 base differences between the nucleotide sequence of the isolate and that of Lactobacillus salivarius subsp. salivarius or L. salivarius subsp. salicinius, indicating that the isolate was a strain of L. salivarius. The patient responded to cholecystectomy and a 2-week course of antibiotic treatment. Identification of the organism in the present study was important because the duration of antibiotic therapy would have been entirely different depending on the organism. If the bacterium had been identified as Actinomyces, penicillin for 6 months would have been the regimen of choice. However, it was Lactobacillus, and a 2-week course of antibiotic was sufficient.