A Case of Catabacter hongkongensis and Alistipes indistinctus Isolated from Blood Cultures of a Patient with Acute Appendicitis

Catabacter hongkongensis is an anaerobic gram-positive coccobacillus that was first isolated in Hong Kong. It is infectious and causes high mortality in patients with rare but underlying diseases. Alistipes indistinctus is an anaerobic gram-negative coccobacillus. This bacterium is a common member of the human intestinal microbiota. We report a case of C. hongkongensis and A. indistinctus isolated from blood cultures of a patient with acute appendicitis. A 35-year-old female patient with no specific medical history was admitted to the hospital due to abdominal pain, vomiting, nausea, and diarrhea experienced on the day before admission. On admission, laboratory tests revealed leukocytosis, neutropenia, and elevated C–reactive protein and procalcitonin levels. Following an abdominal computed tomography showing acute appendicitis with suspected perforation, emergency surgery was performed. Growth was observed in two anaerobic blood culture bottles after four days. After further culturing of the bacteria on Brucella Blood Agar, two types of bacteria were obtained. The two bacterial isolates, one gram-positive and one gram-negative, were unable to be identified using matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Thus, 16S rRNA gene sequence analysis was performed, resulting in identification of the bacteria as C. hongkongensis and A. indistinctus. The patient was administered antibiotics and discharged two days after surgery. Although MALDI-TOF MS enables fast and accurate identification of bacteria, C. hongkongensis and A. indistinctus were not listed in the spectral library, and 16S rRNA gene sequence analysis was useful for identifying the two bacteria.

Species identification on 43 clinical non-tuberculosis Mycobacteria isolates from Gansu Province, China / 中国人兽共患病学报

To understand pathogen spectrum of nontuberculosis Mycobacteria (NTM) and the dominant NTM in Gansu Province and provide the scientific basis for the effective prevention and treatment of NTM diseases,875 Mycobacteria isolates were collected from 2012 to 2014 in Lanzhou Pulmonary Hospital,NTM species were identified by means of PNB/TCH differentiate medium and 16S rRNA gene sequence analysis respectively.Forty-six isolats of NTM were identied from 875 PNB/TCH.Then with 16S rRNA gene sequence analysis,the NTM strains were identified to 3 strains of Nocadia and 43 strains of NTM,including M.intracellulare,M.kansasii,M.avium,M.senegalense,M.gordonae,M.szulgai,M.peregrinumand M.fortuitum.Among them,there were 31 strains of M.intracellulare,which accounted for 72.09％ of the total number of NTM strains.The dominant nontuberculosis Mycobacteria in Gansu Province were mainly M.intracellulare.The application of molecular biology can rapidly and accurately identify the species of nontuberculosis Mycobacteria,and can provide relevant evidence for clinical diagnosis and therapy.

Comparison of the Vitek 2, API 20A, and 16s rRNA Gene Sequencing for the Identification of Anaerobic Bacteria / 대한임상미생물학회지

BACKGROUND: Recently, genotypic identification of anaerobes is emerging as an alternative to the phenotypic method. In this study, we evaluated the performance of Vitek 2, API 20A and 16s rRNA gene sequencing for the identification of anaerobic bacteria. METHODS: A total of 35 anaerobe reference strains were identified using Vitek 2, API 20A and 16s rRNA gene sequencing. We evaluated the performance of three methods on the basis of the accurate identification rates. RESULTS: The Vitek 2, API 20A and 16s rRNA gene sequencing identified 54.3, 15.4, and 94.3% of test strains correctly at the species level and identified 77.1, 42.3, and 100% at the genus level, respectively. Results of the McNemar's test showed that there was a significant difference between each of the three identification methods in species level identification (P value<0.05). CONCLUSION: 16s rRNA gene sequencing showed better performance than Vitek 2 or API 20A for anaerobic bacteria. Considering its excellent performance, 16s rRNA gene sequencing may be useful for accurate identification of anaerobic bacteria that cannot be correctly identified by phenotypic methods.

Comparison of Two Kinds of Automated Microbial Identification System Used in the Identification of Brucella / 现代检验医学杂志

Objective To compare Vitek2 Compact and Walkaway 40 in the identification of Brucella.Methods Used Vitek2 Compact and Walkaway 40 automated microbial identification system to identify clinical isolates and compared with the de-tection of 16S rRNA gene sequences analysis.Results The clinical isolates was identified as Bergeyella zoohelcum or Moraxella by Walkaway 40 and as Brucella melitensis by Vitek2 Compact.16S RNA sequence analysis of the isolate,the se-quence was identical to the sequences of 16S rRNA of Brucella,which excluded the possibility of B.zoohelam and Moraxel-la .Determined that the isolate was B.melitensis.Conclusion Vitek 2 Compact can accurately identified Brucella.Use molec-ular methods to corroborate when the isolates was identified as Brucella by Vitek 2 Compact,this method can greatly im-prove the detection rate of brucellosis and reduce the possibility of misdiagnosis.Walkaway 40 cannot accurately identified Brucella,Misidentification of Brucella can result in wrong treatment of the patient and let the staff in the risk of laboratory-acquired infection.Recommend laboratory should be cautious reporting in the identified B.zoohelam or Moraxella by Walk-away 40 and use Vitek2 Compact or molecular methods for review.

Identification and characterization of rhizospheric microbial diversity by 16S ribosomal RNA gene sequencing

In the present study, samples of rhizosphere and root nodules were collected from different areas of Pakistan to isolate plant growth promoting rhizobacteria. Identification of bacterial isolates was made by 16S rRNA gene sequence analysis and taxonomical confirmation on EzTaxon Server. The identified bacterial strains were belonged to 5 genera i.e. Ensifer, Bacillus, Pseudomona, Leclercia and Rhizobium. Phylogenetic analysis inferred from 16S rRNA gene sequences showed the evolutionary relationship of bacterial strains with the respective genera. Based on phylogenetic analysis, some candidate novel species were also identified. The bacterial strains were also characterized for morphological, physiological, biochemical tests and glucose dehydrogenase (gdh) gene that involved in the phosphate solublization using cofactor pyrroloquinolone quinone (PQQ). Seven rhizoshperic and 3 root nodulating stains are positive for gdh gene. Furthermore, this study confirms a novel association between microbes and their hosts like field grown crops, leguminous and non-leguminous plants. It was concluded that a diverse group of bacterial population exist in the rhizosphere and root nodules that might be useful in evaluating the mechanisms behind plant microbial interactions and strains QAU-63 and QAU-68 have sequence similarity of 97 and 95% which might be declared as novel after further taxonomic characterization.

Characterization of cellulase producing Bacillus and Paenibacillus strains from Thai soils.

Seventeen strains of cellulase producing bacteria were isolated from soil samples collected in Nan province, Thailand. They exhibited cellulase activity as a clear zone surrounded their colonies grown on carboxymethyl cellulose (CMC) agar medium ranged from 0.63 to 2.95 cm in diameter. Their hydrolysis capacity values were 1.65 - 7.55. The bacteria isolated were divided into 2 groups and belonged to genus Bacillus and Paenibacillus based on their phenotypic characteristics and chemotaxonomic characteristics such as meso-diaminopimelic in cell wall peptidoglycan and menaquinones of MK-7. Bacillus strains, P3-1 and P4-6 in Group I, produced maximum cellulase at 0.015 U ml-1. Their optimal pH and temperature for enzyme production and enzyme activity were 7.0 and 50 oC, respectively. The strains P3-1 and P4-6 were closely related to Bacillus velesensis LMG 22478T (100% similarity) whereas representative strain, S10-4 in Group II, was closely related to P. cellulositrophicus KCTC 13135T (98.7% similarity) based on 16S rRNA gene sequence. On the basis of their phenotypic, chemotaxonomic characteristics and phylogenetic analysis of 16S rRNA gene sequence, the strains P3-1 and P4-6 were identified as B. velesensis and the strain S10-4 was a novel species in the genus Paenibacillus.

Pseudooutbreak of Acinetobacter spp. Bacteriuria Confirmed by 16S rRNA Gene Sequence Analysis / 감염과화학요법

BACKGROUND: Acinetobacter spp. is increasingly implicated in hospital-acquired infections. We experienced a pseudooutbreak of Bordetella bronchiseptica bacteriuria identified with biochemical tests, that was later identified as Acinetobacter spp. by using 16S rRNA gene sequence analysis. MATERIALS AND METHODS: Five in-ward patients were found to have B. bronchiseptica bacteriuria without symptoms of urinary tract infection between September 23 and 26 of 2005. We conducted pulsed field gel electrophoresis (PFGE) of the bacteria and epidemiological investigation of this pseudooutbreak. In addition, 16S rRNA gene sequence analysis was performed for the verification of the strains. RESULTS: All 5 isolates were identified as B. bronchiseptica with similar antibiogram by VITEK system. There was no evidence of any symptom or sign of urinary tract infection. The source of this pseudooutbreak was not detected even after performing environmental culture and interviews with healthcare workers. We could not get the appropriate results from the first PFGE with XbaI restriction enzyme. B. bronchiseptica is an unusual organism in human so we conducted 16S rRNA gene sequence analysis for verification. The analysis of 16S rRNA gene sequence with 5 isolates demonstrated 99-100% similarity to a sequence of Acinetobacter spp. (AU1523). According to the results of 16S rRNA gene sequence analysis, we performed the second PFGE with SmaI restriction enzyme, which showed indistinguishable pattern among the all 5 isolates. CONCLUSION: This investigation suggests that the combined method of 16s rRNA gene sequence analysis and PFGE would be helpful for investigation of outbreak caused by unusual organisms

Pseudooutbreak of Acinetobacter spp. Bacteriuria Confirmed by 16S rRNA Gene Sequence Analysis / 감염과화학요법

BACKGROUND: Acinetobacter spp. is increasingly implicated in hospital-acquired infections. We experienced a pseudooutbreak of Bordetella bronchiseptica bacteriuria identified with biochemical tests, that was later identified as Acinetobacter spp. by using 16S rRNA gene sequence analysis. MATERIALS AND METHODS: Five in-ward patients were found to have B. bronchiseptica bacteriuria without symptoms of urinary tract infection between September 23 and 26 of 2005. We conducted pulsed field gel electrophoresis (PFGE) of the bacteria and epidemiological investigation of this pseudooutbreak. In addition, 16S rRNA gene sequence analysis was performed for the verification of the strains. RESULTS: All 5 isolates were identified as B. bronchiseptica with similar antibiogram by VITEK system. There was no evidence of any symptom or sign of urinary tract infection. The source of this pseudooutbreak was not detected even after performing environmental culture and interviews with healthcare workers. We could not get the appropriate results from the first PFGE with XbaI restriction enzyme. B. bronchiseptica is an unusual organism in human so we conducted 16S rRNA gene sequence analysis for verification. The analysis of 16S rRNA gene sequence with 5 isolates demonstrated 99-100% similarity to a sequence of Acinetobacter spp. (AU1523). According to the results of 16S rRNA gene sequence analysis, we performed the second PFGE with SmaI restriction enzyme, which showed indistinguishable pattern among the all 5 isolates. CONCLUSION: This investigation suggests that the combined method of 16s rRNA gene sequence analysis and PFGE would be helpful for investigation of outbreak caused by unusual organisms

Isolation and 16S rRNA Gene Sequence Analysis of a Thermotolerant Halophilic Bacterium / 微生物学通报

A strain of thermotolerant halophilic bacteria YJ0238 was isolated from the salt well at 47℃ in the Kangning countryside where was located at the side of Lancang River in the Tibet Autonomous Region. Some physiological and biochemical properties were characterized.16S rRNA gene sequence of YJ0238 was amplified by PCR,and its nucleotide sequence was determined. Based on it’s physiological and biochemical properties,homology and phylogenetic analysis of 16S rRNA gene sequence,strain YJ0238 was identified as a subspecies of the species Idiomarina zobellii. The GenBank accession number of the 16S rRNA gene sequence of strain YJ0238 is EF693953. Until now,there were few reports on the study of high-temperature and high-salt microbial in domestics. The results of this study will provide research material and information for further studies in this area.