1
|
Stephens CRA, McAmmond BM, Van Hamme JD, Otter KA, Reudink MW, Bottos EM. Analysis of bacterial communities associated with Mountain Chickadees ( Poecile gambeli) across urban and rural habitats. Can J Microbiol 2021; 67:572-583. [PMID: 33656947 DOI: 10.1139/cjm-2020-0320] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Host-associated microbial communities play important roles in wildlife health, but these dynamics can be influenced by environmental factors. Urbanization has numerous effects on wildlife; however, the degree to which wildlife-associated bacterial communities and potential bacterial pathogens vary across urban-rural/native habitat gradients remains largely unknown. We used 16S rRNA gene amplicon sequencing to examine bacterial communities found on Mountain Chickadee (Poecile gambeli) feathers and nests in urban and rural habitats. The feathers and nests in urban and rural sites had similar abundances of major bacterial phyla and dominant genera with pathogenic members. However, richness of bacterial communities and potential pathogens on birds were higher in urban habitats, and potential pathogens accounted for some of the differences in bacterial occurrence between urban and rural environments. We predicted habitat using potential pathogen occurrence with a 90% success rate for feather bacteria, and a 72.2% success rate for nest bacteria, suggesting an influence of urban environments on the presence of potential pathogens. We additionally observed similarities in bacterial communities between nests and their occupants, suggesting bacterial transmission between them. These findings improve our understanding of the bacterial communities associated with urban wildlife and suggest that urbanization impacts the composition of wildlife-associated bacterial communities.
Collapse
Affiliation(s)
- Colton R A Stephens
- Department of Biological Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, BC V2C 0C8, Canada
| | - Breanne M McAmmond
- Department of Biological Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, BC V2C 0C8, Canada
| | - Jonathan D Van Hamme
- Department of Biological Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, BC V2C 0C8, Canada
| | - Ken A Otter
- Natural Resources and Environmental Studies, University of Northern British Columbia, 3333 University Way, Prince George, BC V2N 4Z9, Canada
| | - Matthew W Reudink
- Department of Biological Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, BC V2C 0C8, Canada
| | - Eric M Bottos
- Department of Biological Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, BC V2C 0C8, Canada
| |
Collapse
|
2
|
Jahan NA, Godden SM, Royster E, Schoenfuss TC, Gebhart C, Timmerman J, Fink RC. Evaluation of the matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) system in the detection of mastitis pathogens from bovine milk samples. J Microbiol Methods 2021; 182:106168. [PMID: 33600875 DOI: 10.1016/j.mimet.2021.106168] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 12/08/2020] [Accepted: 01/18/2021] [Indexed: 10/22/2022]
Abstract
MALDI-TOF is a chemistry analytical tool that has recently been deployed in the identification of microorganisms isolated from nosocomial environments. Its use in diagnostics has been extremely advantageous in terms of cost effectiveness, sample preparation easiness, turn-around time and result analysis accessibility. In the dairy industry, where mastitis causes great financial losses, a rapid diagnostic method such as MALDI-TOF could assist in the control and prevention program of mastitis, in addition to the sanitation and safety level of the dairy farms and processing facility. However, the diagnostic strengths and limitations of this test method require further understanding. In the present study, we prospectively compared MALDI-TOF MS to conventional 16S rDNA sequencing method for the identification of pathogens recovered from milk associated with clinical and subclinical bovine mastitis cases. Initially, 810 bacterial isolates were collected from raw milk samples over a period of three months. However, only the isolates (481) having both 16S rDNA sequencing and MALDI-TOF identification were included in the final phase of the study. Among the 481 milk isolates, a total of 26 genera (12 g-postive and 14 g-negative), including 71 different species, were taxonomically charecterized by 16S rDNA at the species level. Comparatively, MALDI-TOF identified 17 genera (9 g-positive and 8 g-negative) and 33 differernt species. Overall, 445 (93%) were putatively identified to the genus level by MALDI-TOF MS and 355 (74%) were identified to the species level, but no reliable identification was obtained for 16 (3.3%), and 20 (4.2%) discordant results were identified. Future studies may help to overcome the limitations of the MALDI database and additional sample preparation steps might help to reduce the number of discordances in identification. In conclusion, our results show that MALDI-TOF MS is a fast and reliable technique which has the potential to replace conventional identification methods for common mastitis pathogens, routinely isolated from raw milk. Thus it's adoption will strengthen the capacity, quality, and possibly the scope of diagnostic services to support the dairy industry.
Collapse
Affiliation(s)
- Nusrat A Jahan
- Department of Biology, St. Cloud State University, Saint Cloud, MN, USA
| | - Sandra M Godden
- College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Erin Royster
- College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Tonya C Schoenfuss
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN, USA
| | - Connie Gebhart
- College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Jennifer Timmerman
- College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Ryan C Fink
- Department of Biology, St. Cloud State University, Saint Cloud, MN, USA,.
| |
Collapse
|
3
|
Baccari O, Elleuch J, Barkallah M, Boukedi H, Ayed NB, Hammami A, Fendri I, Abdelkafi S. Development of a new TaqMan-based PCR assay for the specific detection and quantification of Simkania negevensis. Mol Cell Probes 2020; 53:101645. [PMID: 32745685 DOI: 10.1016/j.mcp.2020.101645] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/02/2020] [Accepted: 07/30/2020] [Indexed: 02/07/2023]
Abstract
Simkania negevensis is an emerging Chlamydia-like bacterium related to human respiratory diseases. An early and accurate detection of this pathogen could be useful to monitor the potential infectious risks and to set suitable outbreak control measures. In Tunisia, distribution and abundance of S. negevensis remain until now largely unknown. In the present work, a qPCR assay, targeting the 16S rRNA gene, for fast detection and quantification of S. negevensis was developed and validated. A high specificity for S. negevensis detection displaying no cross-reaction with the closely related Chlamydia spp. or the other tested microorganisms was noticed. qPCR assay performance was considered very satisfying with detection limits of 5 DNA copies per reaction. qPCR assay validation was performed by screening 37 clinical specimens and 35 water samples. S. negevensis wasn't detected in respiratory samples, but it was found in four cases of water samples. We suggest that the qPCR assay developed in this study could be considered sufficiently characterized to initiate the quantification of S. negevensis in environmental samples.
Collapse
Affiliation(s)
- Olfa Baccari
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, Sfax, Tunisia
| | - Jihen Elleuch
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, Sfax, Tunisia.
| | - Mohamed Barkallah
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, Sfax, Tunisia
| | - Hanen Boukedi
- Laboratory of Biopesticides, Biotechnology Center of Sfax, University of Sfax, Sfax, Tunisia
| | - Nourelhouda Ben Ayed
- Laboratory of Microbiology, Faculty of Medicine of Sfax, Habib Bourguiba University Hospital, University of Sfax, Tunisia
| | - Adnene Hammami
- Laboratory of Microbiology, Faculty of Medicine of Sfax, Habib Bourguiba University Hospital, University of Sfax, Tunisia
| | - Imen Fendri
- Laboratory of Plant Biotechnology Applied to the Improvement of Cultures, Faculty of Science of Sfax, Tunisia
| | - Slim Abdelkafi
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, Sfax, Tunisia
| |
Collapse
|
4
|
Chong YK, Ho CC, Leung SY, Lau SK, Woo PC. Clinical Mass Spectrometry in the Bioinformatics Era: A Hitchhiker's Guide. Comput Struct Biotechnol J 2018; 16:316-334. [PMID: 30237866 PMCID: PMC6138949 DOI: 10.1016/j.csbj.2018.08.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 08/20/2018] [Accepted: 08/21/2018] [Indexed: 02/06/2023] Open
Abstract
Mass spectrometry (MS) is a sensitive, specific and versatile analytical technique in the clinical laboratory that has recently undergone rapid development. From initial use in metabolic profiling, it has matured into applications including clinical toxicology assays, target hormone and metabolite quantitation, and more recently, rapid microbial identification and antimicrobial resistance detection by matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). In this mini-review, we first succinctly outline the basics of clinical mass spectrometry. Examples of hard ionization (electron ionization) and soft ionization (electrospray ionization, MALDI) are presented to demonstrate their clinical applications. Next, a conceptual discourse on mass selection and determination is presented: quadrupole mass filter, time-of-flight mass spectrometer and the Orbitrap; and MS/MS (tandem-in-space, tandem-in-time and data acquisition), illustrated with clinical examples. Current applications in (1) bacterial and fungal identification, antimicrobial susceptibility testing and phylogenetic classification, (2) general unknown urine toxicology screening and expanded new-born metabolic screening and (3) clinical metabolic profiling by gas chromatography are outlined. Finally, major limitations of MS-based techniques, including the technical challenges of matrix effect and isobaric interference; and novel challenges in the post-genomic era, such as protein molecular variants, are critically discussed from the perspective of service laboratories. Computer technology and structural biology have played important roles in the maturation of this field. MS-based techniques have the potential to replace current analytical techniques, and existing expertise and instrument will undergo rapid evolution. Significant automation and adaptation to regulatory requirements are underway. Mass spectrometry is unleashing its potentials in clinical laboratories.
Collapse
Affiliation(s)
- Yeow-Kuan Chong
- Hospital Authority Toxicology Reference Laboratory, Department of Pathology, Princess Margaret Hospital (PMH), Kowloon, Hong Kong
- Chemical Pathology and Medical Genetics, Department of Pathology, Princess Margaret Hospital (PMH), Kowloon, Hong Kong
| | - Chi-Chun Ho
- Division of Chemical Pathology, Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital (PYNEH), Hong Kong
- Division of Clinical Biochemistry, Department of Pathology, Queen Mary Hospital (QMH), Hong Kong
- Centre for Genomic Sciences, The University of Hong Kong, Hong Kong
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Shui-Yee Leung
- Department of Ocean Science, School of Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Susanna K.P. Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Hong Kong
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong
| | - Patrick C.Y. Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Hong Kong
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong
| |
Collapse
|
5
|
Detection of 16S rRNA and KPC Genes from Complex Matrix Utilizing a Molecular Inversion Probe Assay for Next-Generation Sequencing. Sci Rep 2018; 8:2028. [PMID: 29391471 PMCID: PMC5794912 DOI: 10.1038/s41598-018-19501-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 12/27/2017] [Indexed: 11/08/2022] Open
Abstract
Targeted sequencing promises to bring next-generation sequencing (NGS) into routine clinical use for infectious disease diagnostics. In this context, upfront processing techniques, including pathogen signature enrichment, must amplify multiple targets of interest for NGS to be relevant when applied to patient samples with limited volumes. Here, we demonstrate an optimized molecular inversion probe (MIP) assay targeting multiple variable regions within the 16S ribosomal gene for the identification of biothreat and ESKAPE pathogens in a process that significantly reduces complexity, labor, and processing time. Probes targeting the Klebsiella pneumoniae carbapenemase (KPC) antibiotic resistance (AR) gene were also included to demonstrate the ability to concurrently identify etiologic agent and ascertain valuable secondary genetic information. Our assay captured gene sequences in 100% of mock clinical samples prepared from flagged positive blood culture bottles. Using a simplified processing and adjudication method for mapped sequencing reads, genus and species level concordance was 100% and 80%, respectively. In addition, sensitivity and specificity for KPC gene detection was 100%. Our MIP assay produced sequenceable amplicons for the identification of etiologic agents and the detection of AR genes directly from blood culture bottles in a simplified single tube assay.
Collapse
|
6
|
Molecular identification of cestodes and nematodes by cox1 gene real-time PCR and sequencing. Diagn Microbiol Infect Dis 2017; 89:185-190. [PMID: 28865743 DOI: 10.1016/j.diagmicrobio.2017.07.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 07/24/2017] [Accepted: 07/24/2017] [Indexed: 11/22/2022]
Abstract
Unlike bacteria and fungi, identification of helminths by gene sequencing is not well-standardized. No "pan-cestode" or "pan-nematode" PCR primers are available. In this study, we designed 2 pairs of PCR primers for amplifying the cox1 genes of cestodes and nematodes respectively and validated their usefulness for real-time PCR and sequencing identification using clinical samples with cestodes and nematodes collected from a variety of animals and human in 7 countries in Asia, Europe and Africa. The detection limits of the cox1 real-time PCR assays for cestodes and nematodes were 10 copies/reaction of extracted DNA, corresponding to CT values of 33 and 31 respectively. Real-time PCR using the 2 pairs of primers and probes showed positive results for all 20 clinical samples of cestodes and nematodes. Using phenotypic identification results as the reference standard, DNA sequencing successfully identified all the 5 cestodes and 7 nematodes with cox1 gene sequences available in GenBank, with all these names appearing as the best match of the cox1 gene sequences of the corresponding clinical samples. The percentage nucleotide identities between the cox1 gene sequences of the samples and those of the corresponding best match sequences in GenBank were 98-100%. For the remaining 5 cestodes and 3 nematodes, the corresponding cox1 gene sequences were not available in GenBank. cox1 gene sequencing is discriminative enough for accurately identifying most of the cestodes and nematodes in the present study. Further expansion of the cox1 gene sequence database will enable accurate identification of more cestodes and nematodes.
Collapse
|
7
|
Chen JH, Cheng VC, She KK, Yam WC, Yuen KY. Application of a dual target PCR-high resolution melting (HRM) method for rapid nontuberculous mycobacteria identification. J Microbiol Methods 2016; 132:1-3. [PMID: 27838538 DOI: 10.1016/j.mimet.2016.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/08/2016] [Accepted: 11/08/2016] [Indexed: 11/25/2022]
Abstract
Species differentiation of nontuberculous mycobacteria (NTM) has long been a difficult task in clinical laboratories. This study demonstrated and evaluated a simple and cost-effective method using the real-time PCR with high-resolution melting (PCR-HRM) analysis technique, which could differentiate at least 14 different medically related NTM.
Collapse
Affiliation(s)
- Jonathan Hk Chen
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Vincent Cc Cheng
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong Special Administrative Region; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Kevin Kk She
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Wing-Cheong Yam
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Kwok-Yung Yuen
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong Special Administrative Region; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong Special Administrative Region.
| |
Collapse
|
8
|
Chen JHK, Cheng VCC, Wong OY, Wong SCY, So SYC, Yam WC, Yuen KY. The importance of matrix-assisted laser desorption ionization-time of flight mass spectrometry for correct identification of Clostridium difficile isolated from chromID C. difficile chromogenic agar. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2016; 50:723-726. [PMID: 26860352 DOI: 10.1016/j.jmii.2015.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 12/10/2015] [Accepted: 12/16/2015] [Indexed: 01/05/2023]
Abstract
The clinical workflow of using chromogenic agar and matrix-assisted laser desorption ionization time-of-fight mass spectrometry (MALDI-TOF MS) for Clostridium difficile identification was evaluated. The addition of MALDI-TOF MS identification after the chromID C. difficile chromogenic agar culture could significantly improve the diagnostic accuracy of C. difficile.
Collapse
Affiliation(s)
- Jonathan H K Chen
- Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, China
| | - Vincent C C Cheng
- Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, China; Infection Control Team, Queen Mary Hospital, Hong Kong Special Administrative Region, China
| | - Oi-Ying Wong
- Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, China
| | - Sally C Y Wong
- Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, China
| | - Simon Y C So
- Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, China
| | - Wing-Cheong Yam
- Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, China; Infection Control Team, Queen Mary Hospital, Hong Kong Special Administrative Region, China
| | - Kwok-Yung Yuen
- Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, China; Carol Yu Centre for Infection, University of Hong Kong, Hong Kong Special Administrative Region, China.
| |
Collapse
|
9
|
Chen JHK, She KKK, Wong OY, Teng JLL, Yam WC, Lau SKP, Woo PCY, Cheng VCC, Yuen KY. Use of MALDI Biotyper plus ClinProTools mass spectra analysis for correct identification ofStreptococcus pneumoniaeandStreptococcus mitis/oralis. J Clin Pathol 2015; 68:652-6. [DOI: 10.1136/jclinpath-2014-202818] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 04/22/2015] [Indexed: 12/23/2022]
|
10
|
Srinivasan R, Karaoz U, Volegova M, MacKichan J, Kato-Maeda M, Miller S, Nadarajan R, Brodie EL, Lynch SV. Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens. PLoS One 2015; 10:e0117617. [PMID: 25658760 PMCID: PMC4319838 DOI: 10.1371/journal.pone.0117617] [Citation(s) in RCA: 210] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 12/29/2014] [Indexed: 01/06/2023] Open
Abstract
According to World Health Organization statistics of 2011, infectious diseases remain in the top five causes of mortality worldwide. However, despite sophisticated research tools for microbial detection, rapid and accurate molecular diagnostics for identification of infection in humans have not been extensively adopted. Time-consuming culture-based methods remain to the forefront of clinical microbial detection. The 16S rRNA gene, a molecular marker for identification of bacterial species, is ubiquitous to members of this domain and, thanks to ever-expanding databases of sequence information, a useful tool for bacterial identification. In this study, we assembled an extensive repository of clinical isolates (n = 617), representing 30 medically important pathogenic species and originally identified using traditional culture-based or non-16S molecular methods. This strain repository was used to systematically evaluate the ability of 16S rRNA for species level identification. To enable the most accurate species level classification based on the paucity of sequence data accumulated in public databases, we built a Naïve Bayes classifier representing a diverse set of high-quality sequences from medically important bacterial organisms. We show that for species identification, a model-based approach is superior to an alignment based method. Overall, between 16S gene based and clinical identities, our study shows a genus-level concordance rate of 96% and a species-level concordance rate of 87.5%. We point to multiple cases of probable clinical misidentification with traditional culture based identification across a wide range of gram-negative rods and gram-positive cocci as well as common gram-negative cocci.
Collapse
Affiliation(s)
- Ramya Srinivasan
- University of California San Francisco, Department of Medicine, Gastroenterology Division, 513 Parnassus Ave, San Francisco, CA 94143–0538, United States of America
| | - Ulas Karaoz
- Lawrence Berkeley National Laboratory, Earth Sciences Division, 1 Cyclotron Rd., MS70A-3317, Berkeley, CA 94720, United States of America
| | - Marina Volegova
- University of California, Berkeley, CA 94720, United States of America
| | - Joanna MacKichan
- School of Biological Sciences, Victoria University of Wellington, 34 Kenepuru Drive, Porirua, Wellington, New Zealand
| | - Midori Kato-Maeda
- San Francisco General Hospital, Department of Medicine, Bldg 100, San Francisco, CA 94110, United States of America
| | - Steve Miller
- University of California San Francisco, Clinical Microbiology Laboratory, 185 Berry Street, Suite 290, San Francisco, CA 94107, United States of America
| | - Rohan Nadarajan
- University of California San Francisco, Clinical Microbiology Laboratory, 185 Berry Street, Suite 290, San Francisco, CA 94107, United States of America
| | - Eoin L. Brodie
- Lawrence Berkeley National Laboratory, Earth Sciences Division, 1 Cyclotron Rd., MS70A-3317, Berkeley, CA 94720, United States of America
| | - Susan V. Lynch
- University of California San Francisco, Department of Medicine, Gastroenterology Division, 513 Parnassus Ave, San Francisco, CA 94143–0538, United States of America
- * E-mail:
| |
Collapse
|
11
|
|
12
|
Draft Genome Sequence of Clostridium butyricum Strain NOR 33234, Isolated from an Elderly Patient with Diarrhea. GENOME ANNOUNCEMENTS 2014; 2:2/6/e01356-14. [PMID: 25540356 PMCID: PMC4276834 DOI: 10.1128/genomea.01356-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Clostridium butyricum is one of the species frequently present in patients’ stool samples. However, the identification of this species is sometimes difficult. Here, we present the draft genome of Clostridium butyricum NOR 33234, which was isolated from a patient with suspected Clostridium difficile infection-associated diarrhea and resembles Clostridium clostridioforme in biochemical tests.
Collapse
|
13
|
Gürtler V, Subrahmanyam G, Shekar M, Maiti B, Karunasagar I. Bacterial Typing and Identification By Genomic Analysis of 16S–23S rRNA Intergenic Transcribed Spacer (ITS) Sequences. METHODS IN MICROBIOLOGY 2014. [DOI: 10.1016/bs.mim.2014.07.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|