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Basak S, Subramanian B, Thirumurugan R, Saleena LM. PHB Production by Bacillus megaterium LSRB 0103 Using Cornstarch and Urea. Curr Microbiol 2024; 81:139. [PMID: 38613599 DOI: 10.1007/s00284-024-03667-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 03/16/2024] [Indexed: 04/15/2024]
Abstract
Polyhydroxybutyrates (PHBs) are biopolymers that are good green alternative for synthetic carbon-based polymers, and are also one of the most researched members of the Polyhydroxyalkanoates (PHA) family. In this study, a gram-positive bacterial strain Bacillus megaterium LSRB 0103 was isolated from Pallikaranai Marshland, Chennai, India. Primary screening using Sudan Black dye revealed the presence of intracellular PHB granules. Minimal Davis Media (MDM) which was used or PHB production gave a yield of 0.7107 g/L. Subsequently, using response surface methodology (RSM), a central composite design (CCD) model was designed for media optimization having cornstarch, urea, and pH as independent variables. The findings of the CCD model were fitted into a second-order polynomial equation. The RSM model predicted the maximum PHB yield of 0.93 g/L, at these independent variable levels, cornstarch, 5 g/L; urea, 2.1 g/L; and pH 7.0; while the experimental PHB yield was 0.94 g/L, with a percentage error of 1.1%. This study is the first-time report of production of PHB by Bacillus megaterium using cornstarch and urea as substrate.
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Affiliation(s)
- Souvik Basak
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Kanchipuram, Chennai, Tamil Nadu, 603203, India
| | - Bhargavi Subramanian
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Kanchipuram, Chennai, Tamil Nadu, 603203, India
| | - Rithanya Thirumurugan
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Kanchipuram, Chennai, Tamil Nadu, 603203, India
| | - Lilly M Saleena
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Kanchipuram, Chennai, Tamil Nadu, 603203, India.
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Pakdeerat S, Boonklang P, Angchagun K, Chomkatekaew C, Apichaidejudom N, Dokket Y, Faosap A, Wongsuwan G, Wuthiekanun V, Aramrueung P, Khamnoi P, Thananchai H, Siriboon S, Chamnan P, Peacock SJ, Day NPJ, Thomson NR, Uttamapinant C, Wongpalee SP, Chewapreecha C. Benchmarking CRISPR-BP34 for point-of-care melioidosis detection in low-income and middle-income countries: a molecular diagnostics study. THE LANCET. MICROBE 2024; 5:e379-e389. [PMID: 38493790 PMCID: PMC10990966 DOI: 10.1016/s2666-5247(23)00378-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 10/17/2023] [Accepted: 11/16/2023] [Indexed: 03/19/2024]
Abstract
BACKGROUND Melioidosis is a neglected but often fatal tropical disease. The disease has broad clinical manifestations, which makes diagnosis challenging and time consuming. To improve diagnosis, we aimed to evaluate the performance of the CRISPR-Cas12a system (CRISPR-BP34) to detect Burkholderia pseudomallei DNA across clinical specimens from patients suspected to have melioidosis. METHODS We conducted a prospective, observational cohort study of adult patients (aged ≥18 years) with melioidosis at Sunpasitthiprasong Hospital, a tertiary care hospital in Thailand. Participants were eligible for inclusion if they had culture-confirmed B pseudomallei infection from any clinical samples. Data were collected from patient clinical records and follow-up telephone calls. Routine clinical samples (blood, urine, respiratory secretion, pus, and other body fluids) were collected for culture. We documented time taken for diagnosis, and mortality at day 28 of follow-up. We also performed CRISPR-BP34 detection on clinical specimens collected from 330 patients with suspected melioidosis and compared its performance with the current gold-standard culture-based method. Discordant results were validated by three independent qualitative PCR tests. This study is registered with the Thai Clinical Trial Registry, TCTR20190322003. FINDINGS Between Oct 1, 2019, and Dec 31, 2022, 876 patients with culture-confirmed melioidosis were admitted or referred to Sunpasitthiprasong Hospital, 433 of whom were alive at diagnosis and were enrolled in this study. Median time from sample collection to diagnosis by culture was 4·0 days (IQR 3·0-5·0) among all patients with known survival status at day 28, which resulted in delayed treatment. 199 (23%) of 876 patients died before diagnosis and 114 (26%) of 433 patients in follow-up were treated, but died within 28 days of admission. To test the CRISPR-BP34 assay, we enrolled and collected clinical samples from 114 patients with melioidosis and 216 patients without melioidosis between May 26 and Dec 31, 2022. Application of CRISPR-BP34 reduced the median sample-to-diagnosis time to 1·1 days (IQR 0·7-1·5) for blood samples, 2·3 h (IQR 2·3-2·4) for urine, and 3·3 h (3·1-3·4) for respiratory secretion, pus, and other body fluids. The overall sensitivity of CRISPR-BP34 was 93·0% (106 of 114 samples [95% CI 86·6-96·9]) compared with 66·7% (76 of 114 samples [57·2-75·2]) for culture. The overall specificity of CRISPR-BP34 was 96·8% (209 of 216 samples [95% CI 93·4-98·7]), compared with 100% (216 of 216 samples [98·3-100·0]) for culture. INTERPRETATION The sensitivity, specificity, speed, and window of clinical intervention offered by CRISPR-BP34 support its prospective use as a point-of-care diagnostic tool for melioidosis. Future development should be focused on scalability and cost reduction. FUNDING Chiang Mai University Thailand and Wellcome Trust UK.
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Affiliation(s)
- Sukripong Pakdeerat
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Phumrapee Boonklang
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Kesorn Angchagun
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Chalita Chomkatekaew
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Navaporn Apichaidejudom
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Yaowaret Dokket
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Areeya Faosap
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Gumphol Wongsuwan
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Vanaporn Wuthiekanun
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Panatda Aramrueung
- Central Laboratory, Sunpasitthiprasong Hospital, Ubon Ratchathani, Thailand
| | - Phadungkiat Khamnoi
- Diagnostic Laboratory, Maharaj Nakorn Chiang Mai Hospital, Chiang Mai, Thailand
| | - Hathairat Thananchai
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Suwattiya Siriboon
- Department of Infectious Medicine, Sunpasitthiprasong Hospital, Ubon Ratchathani, Thailand
| | - Parinya Chamnan
- Cardiometabolic Research Group, Department of Social Medicine, Sunpasitthiprasong Hospital, Ubon Ratchathani, Thailand
| | | | - Nicholas P J Day
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nicholas R Thomson
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Chayasith Uttamapinant
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Rayong, Thailand
| | - Somsakul Pop Wongpalee
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.
| | - Claire Chewapreecha
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK.
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Abnaroodheleh F, Mosavari N, Pourbakhsh SA, Tadayon K, Jamshidian M. Identification of Burkholderia mallei Isolates with Polymerase Chain Reaction-Restriction Fragment Length Polymorphism. ARCHIVES OF RAZI INSTITUTE 2023; 78:1305-1312. [PMID: 38226390 PMCID: PMC10787924 DOI: 10.32592/ari.2023.78.4.1305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 06/14/2021] [Indexed: 01/17/2024]
Abstract
Burkholderia mallei is the main cause of glanders as a dangerous contagious zoonosis disease that is mostly observed in single-hoofed animals, especially horses. Modern molecular techniques have been recently employed to improve epidemiology for identifying and searching for strains of this bacterium at different times and locations. Due to the unknown number of circulating strains and lack of preventive methods, glanders is still observed in the form of epidemics. The present study aimed to evaluate six field isolates plus two laboratory strains of Borkolderia mallei and Burkholderia pseudomallei using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. All the isolates and strains were microbially cultured in the glycerol nutrient and glycerol agar media. The individually grown colonies of the bacterium were used in the biochemical tests. The DNA of isolates was extracted by boiling, and the PCR-RFLP test was conducted on their genome. Finally, the bacterium was injected into guinea pigs to induce the Straus reaction. The biochemical assays (or bioassays) confirmed the isolates as Burkholderia mallei. The PCR-RFLP assay demonstrated a product for Burkholderia mallei with a length of 650 bp. Nevertheless, 250 and 400 bp were produced for Burkholderia pseudomallei. The swollen scrotum pointed to the occurrence of the Straus reaction. The PCR-RFLP is a proper differential diagnosis technique for B. mallei; moreover, it is a suitable method for differentiating between Burkholderia mallei and Burkholderia pseudomallei. This technique can detect Burkholderia mallei in a short time with high precision and sensitivity.
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Affiliation(s)
- F Abnaroodheleh
- Veterinary Department, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - N Mosavari
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - S A Pourbakhsh
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - K Tadayon
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - M Jamshidian
- Veterinary Department, Science and Research Branch, Islamic Azad University, Tehran, Iran
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Zhang JX, Xu JH, Yuan B, Wang XD, Mao XH, Wang JL, Zhang XLL, Yuan Y. Detection of Burkholderia pseudomallei with CRISPR-Cas12a based on specific sequence tags. Front Public Health 2023; 11:1153352. [PMID: 37250090 PMCID: PMC10211466 DOI: 10.3389/fpubh.2023.1153352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 04/07/2023] [Indexed: 05/31/2023] Open
Abstract
Melioidosis is a bacterial infection caused by Burkholderia pseudomallei (B. pseudomallei), posing a significant threat to public health. Rapid and accurate detection of B. pseudomallei is crucial for preventing and controlling melioidosis. However, identifying B. pseudomallei is challenging due to its high similarity to other species in the same genus. To address this issue, this study proposed a dual-target method that can specifically identify B. pseudomallei in less than 40 min. We analyzed 1722 B. pseudomallei genomes to construct large-scale pan-genomes and selected specific sequence tags in their core genomes that effectively distinguish B. pseudomallei from its closely related species. Specifically, we selected two specific tags, LC1 and LC2, which we combined with the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR associated proteins (Cas12a) system and recombinase polymerase amplification (RPA) pre-amplification. Our analysis showed that the dual-target RPA-CRISPR/Cas12a assay has a sensitivity of approximately 0.2 copies/reaction and 10 fg genomic DNA for LC1, and 2 copies/reaction and 20 fg genomic DNA for LC2. Additionally, our method can accurately and rapidly detect B. pseudomallei in human blood and moist soil samples using the specific sequence tags mentioned above. In conclusion, the dual-target RPA-CRISPR/Cas12a method is a valuable tool for the rapid and accurate identification of B. pseudomallei in clinical and environmental samples, aiding in the prevention and control of melioidosis.
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Affiliation(s)
- Jia-Xin Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jian-Hao Xu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Bing Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiao-Dong Wang
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Xu-hu Mao
- Department of Clinical Microbiology and Immunology, The Third Military Medical University, Chongqing, China
| | - Jing-Lin Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiang-Li-Lan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yuan Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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Aung NM, Su KK, Chantratita N, Tribuddharat C. Workflow for Identification of <i>Burkholderia pseudomallei</i> Clinical Isolates in Myanmar. Jpn J Infect Dis 2022; 76:106-112. [PMID: 36450576 DOI: 10.7883/yoken.jjid.2022.508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Burkholderia pseudomallei, the highly infectious and causative organism of melioidosis, was first identified in Myanmar in 1911. B. pseudomallei was identified in Myanmar because of its genetic relatedness to Burkholderia species. In this study, we identified two isolates of Burkholderia cenocepacia, two Acinetobacter baumannii complexes, and 18 clinical isolates of B. pseudomallei using Vitek 2. These isolates were first screened using a latex agglutination test, which showed positive results in 20 of the 22 isolates. All isolates were cultured on Ashdown՚s agar and further tested using molecular methods. Specific PCR for type III secretion system (TTSs) gene clusters indicated 19 B. pseudomallei isolates out of 22 isolates. Furthermore, 16S rRNA and recA gene sequencing were used as the gold standard methods and yielded the same results. RapID NF Plus detected 16 B. pseudomallei out of 22 isolates. Vitek 2 and RapID NF Plus should be considered key tools in the diagnosis of melioidosis and surveillance of B. pseudomallei in Myanmar; however, accurate identification must be confirmed by TTS1 PCR. This study evaluated the presumptive workflow for the investigation of B. pseudomallei infections using different methods and options, in line with the available equipment.
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Affiliation(s)
- Nay Myo Aung
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand
| | - Khine Khine Su
- Department of Microbiology, Defense Services Medical Academy, Myanmar
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Thailand
| | - Chanwit Tribuddharat
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand
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6
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Genotyping of Burkholderia pseudomallei Isolated From Patients in South-Western Coastal Region of India. Curr Microbiol 2022; 79:226. [PMID: 35731378 DOI: 10.1007/s00284-022-02905-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 05/16/2022] [Indexed: 11/03/2022]
Abstract
Burkholderia pseudomallei is the causative agent of melioidosis. Various tools have been used to determine the genetic diversity in B. pseudomallei isolates. In this study, Random Amplified Polymorphic DNA (RAPD)-PCR and flagellin gene (fliC) based PCR-Restriction Fragment Length Polymorphism (RFLP) were used to genotype Indian clinical B. pseudomallei isolates. A total of 89 clinical isolates could be grouped in 6 groups (A through F) by RAPD-PCR analysis. Some of the isolates in various groups had identical banding pattern suggesting them to be epidemiologically related. The RAPD groups also correlated with MLST sequence types suggesting the utility of this easy to do typing method. The PCR- RFLP analysis suggested Type III to be the predominant type which is different from other RFLP types reported from Southeast Asia. In conclusion, the results of this study show that RAPD-PCR, a simple genotyping method, may be used for analyzing the B. pseudomallei isolates and also establish epidemiological relevant relatedness among them. The results of fliC PCR-RFLP further suggest the Indian isolates are different from other Southeast Asian isolates.
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7
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McLaughlin HP, Gulvik CA, Sue D. In silico analyses of penicillin binding proteins in Burkholderia pseudomallei uncovers SNPs with utility for phylogeography, species differentiation, and sequence typing. PLoS Negl Trop Dis 2022; 16:e0009882. [PMID: 35417451 PMCID: PMC9037935 DOI: 10.1371/journal.pntd.0009882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 04/25/2022] [Accepted: 03/15/2022] [Indexed: 11/26/2022] Open
Abstract
Burkholderia pseudomallei causes melioidosis. Sequence typing this pathogen can reveal geographical origin and uncover epidemiological associations. Here, we describe B. pseudomallei genes encoding putative penicillin binding proteins (PBPs) and investigate their utility for determining phylogeography and differentiating closely related species. We performed in silico analysis to characterize 10 PBP homologs in B. pseudomallei 1026b. As PBP active site mutations can confer β-lactam resistance in Gram-negative bacteria, PBP sequences in two resistant B. pseudomallei strains were examined for similar alterations. Sequence alignments revealed single amino acid polymorphisms (SAAPs) unique to the multidrug resistant strain Bp1651 in the transpeptidase domains of two PBPs, but not directly within the active sites. Using BLASTn analyses of complete assembled genomes in the NCBI database, we determined genes encoding PBPs were conserved among B. pseudomallei (n = 101) and Burkholderia mallei (n = 26) strains. Within these genes, single nucleotide polymorphisms (SNPs) useful for predicting geographic origin of B. pseudomallei were uncovered. SNPs unique to B. mallei were also identified. Based on 11 SNPs identified in two genes encoding predicted PBP-3s, a dual-locus sequence typing (DLST) scheme was developed. The robustness of this typing scheme was assessed using 1,523 RefSeq genomes from B. pseudomallei (n = 1,442) and B. mallei (n = 81) strains, resulting in 32 sequence types (STs). Compared to multi-locus sequence typing (MLST), the DLST scheme demonstrated less resolution to support the continental separation of Australian B. pseudomallei strains. However, several STs were unique to strains originating from a specific country or region. The phylogeography of Western Hemisphere B. pseudomallei strains was more highly resolved by DLST compared to internal transcribed spacer (ITS) typing, and all B. mallei strains formed a single ST. Conserved genes encoding PBPs in B. pseudomallei are useful for strain typing, can enhance predictions of geographic origin, and differentiate strains of closely related Burkholderia species. Burkholderia pseudomallei causes the life-threatening disease melioidosis and is considered a biological threat and select agent by the United States government. This soil-dwelling bacterium is commonly found in regions of southeast Asia and northern Australia, but it is also detected in other tropical and sub-tropical areas around the world. With a predicted global burden of 165,000 annual cases and mortality rate that can exceed 40% without prompt and appropriate antibiotic treatment, understanding the epidemiology of melioidosis and mechanisms of antibiotic resistance in B. pseudomallei can benefit public health and safety. Recently, we identified ten conserved genes encoding putative penicillin binding proteins (PBPs) in B. pseudomallei. Here, we examined B. pseudomallei PBP sequences for amino acid mutations that may contribute to β-lactam resistance. We also uncovered nucleotide mutations with utility to predict the geographical origin of B. pseudomallei strains and to differentiate closely related Burkholderia species. Based on 11 informative single nucleotide polymorphisms in two genes each encoding a PBP-3, we developed a simple, targeted dual-locus typing approach.
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Affiliation(s)
- Heather P. McLaughlin
- Biodefense Research and Development Laboratory, Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
| | - Christopher A. Gulvik
- Zoonoses and Select Agent Laboratory, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - David Sue
- Biodefense Research and Development Laboratory, Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
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Chieng R. Melioidosis. WIKIJOURNAL OF MEDICINE 2022. [DOI: 10.15347/wjm/2022.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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16S rDNA and ITS Sequence Diversity of Burkholderia mallei Isolated from Glanders-Affected Horses and Mules in India (2013-2019). Curr Microbiol 2021; 79:31. [PMID: 34921617 DOI: 10.1007/s00284-021-02701-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 11/11/2021] [Indexed: 10/19/2022]
Abstract
Glanders is a highly contagious and fatal infection of equids caused by the bacteria known as Burkholderia mallei. It is one of the notifiable equine diseases and is still present in Asia, South America and Africa. In India, glanders re-emerged in 2006, and thereafter, increasing numbers of cases were reported in different regions of the country. Between 2013 and 2019, 39 B. mallei were isolated from glanders-affected horses (n = 30) and mules (n = 9) from seven states of India such as Uttar Pradesh, Haryana, Delhi, Himachal Pradesh, Gujarat, Maharashtra and Tamil Nadu. In this study, the phylogenetic relationships of these isolates were assessed by sequence analysis of 16S rDNA gene and ITS region. Purified PCR-amplified products of 16S rDNA gene and ITS region were sequenced, aligned and phylogenetic trees were constructed using MEGA 11 software. Additionally, B. mallei 16S rDNA (n = 36) and ITS (n = 18) sequences available in the GenBank were also included for analysis to determine the diversity of older B. mallei isolates with recent Indian isolates. Both the phylogeny showed that the majority of the recent isolates from India are closely related to each other, but are genetically diverse from older isolates that originated from India. Nucleotide substitutions were also observed in a single and double position in 12 recent and two old Indian isolates. The study also indicates that similar B. mallei strains were responsible for glanders outbreaks in different states (Uttar Pradesh- Himachal Pradesh and Uttar Pradesh- Haryana) and this is due to the migration of infected animals from one state to another state. This study implies that 16S rDNA and ITS region may be used for molecular characterization of B. mallei associated with glanders in resource-limited settings.
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Kapustina Ž, Medžiūnė J, Alzbutas G, Rokaitis I, Matjošaitis K, Mackevičius G, Žeimytė S, Karpus L, Lubys A. High-resolution microbiome analysis enabled by linking of 16S rRNA gene sequences with adjacent genomic contexts. Microb Genom 2021; 7. [PMID: 34473015 PMCID: PMC8715429 DOI: 10.1099/mgen.0.000624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Sequence-based characterization of bacterial communities has long been a hostage of limitations of both 16S rRNA gene and whole metagenome sequencing. Neither approach is universally applicable, and the main efforts to resolve constraints have been devoted to improvement of computational prediction tools. Here, we present semi-targeted 16S rRNA sequencing (st16S-seq), a method designed for sequencing V1-V2 regions of the 16S rRNA gene along with the genomic locus upstream of the gene. By in silico analysis of 13 570 bacterial genome assemblies, we show that genome-linked 16S rRNA sequencing is superior to individual hypervariable regions or full-length gene sequences in terms of classification accuracy and identification of gene copy numbers. Using mock communities and soil samples we experimentally validate st16S-seq and benchmark it against the established microbial classification techniques. We show that st16S-seq delivers accurate estimation of 16S rRNA gene copy numbers, enables taxonomic resolution at the species level and closely approximates community structures obtainable by whole metagenome sequencing.
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Affiliation(s)
- Žana Kapustina
- Thermo Fisher Scientific Baltics, V. A. Graičiūno str. 8, Vilnius 02241, Lithuania.,Institute of Biosciences, Life Sciences Center, Vilnius University, Saulėtekio al. 7, Vilnius 10257, Lithuania
| | - Justina Medžiūnė
- Thermo Fisher Scientific Baltics, V. A. Graičiūno str. 8, Vilnius 02241, Lithuania.,Institute of Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 24, Vilnius 03225, Lithuania
| | - Gediminas Alzbutas
- Thermo Fisher Scientific Baltics, V. A. Graičiūno str. 8, Vilnius 02241, Lithuania
| | | | - Karolis Matjošaitis
- Thermo Fisher Scientific Baltics, V. A. Graičiūno str. 8, Vilnius 02241, Lithuania
| | - Gytis Mackevičius
- Thermo Fisher Scientific Baltics, V. A. Graičiūno str. 8, Vilnius 02241, Lithuania
| | - Simona Žeimytė
- Thermo Fisher Scientific Baltics, V. A. Graičiūno str. 8, Vilnius 02241, Lithuania
| | - Laurynas Karpus
- Biomatter Designs, Žirmūnų str. 139A, Vilnius 09120, Lithuania
| | - Arvydas Lubys
- Thermo Fisher Scientific Baltics, V. A. Graičiūno str. 8, Vilnius 02241, Lithuania
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Persistence of endothelial thrombomodulin in a patient with infectious purpura fulminans treated with protein C concentrate. Blood Adv 2019; 2:2917-2921. [PMID: 30396911 DOI: 10.1182/bloodadvances.2018024430] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/11/2018] [Indexed: 12/26/2022] Open
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Khakhum N, Bharaj P, Myers JN, Tapia D, Walker DH, Endsley JJ, Torres AG. Evaluation of Burkholderia mallei ΔtonB Δhcp1 (CLH001) as a live attenuated vaccine in murine models of glanders and melioidosis. PLoS Negl Trop Dis 2019; 13:e0007578. [PMID: 31306423 PMCID: PMC6658008 DOI: 10.1371/journal.pntd.0007578] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 07/25/2019] [Accepted: 06/25/2019] [Indexed: 01/01/2023] Open
Abstract
Background Glanders caused by Burkholderia mallei is a re-emerging zoonotic disease affecting solipeds and humans. Furthermore, B. mallei is genetically related to B. pseudomallei, which is the causative agent of melioidosis. Both facultative intracellular bacteria are classified as tier 1 select biothreat agents. Our previous study with a B. mallei ΔtonB Δhcp1 (CLH001) live-attenuated vaccine demonstrated that it is attenuated, safe and protective against B. mallei wild-type strains in the susceptible BALB/c mouse model. Methodology/Principal finding In our current work, we evaluated the protective efficacy of CLH001 against glanders and melioidosis in the more disease-resistant C57BL/6 mouse strain. The humoral as well as cellular immune responses were also examined. We found that CLH001-immunized mice showed 100% survival against intranasal and aerosol challenge with B. mallei ATCC 23344. Moreover, this vaccine also afforded significant cross-protection against B. pseudomallei K96243, with low level bacterial burden detected in organs. Immunization with a prime and boost regimen of CLH001 induced significantly greater levels of total and subclasses of IgG, and generated antigen-specific splenocyte production of IFN-γ and IL-17A. Interestingly, protection induced by CLH001 is primarily dependent on humoral immunity, while CD4+ and CD8+ T cells played a less critical protective role. Conclusions/Significance Our data indicate that CLH001 serves as an effective live attenuated vaccine to prevent glanders and melioidosis. The quantity and quality of antibody responses as well as improving cell-mediated immune responses following vaccination need to be further investigated prior to advancement to preclinical studies. Glanders (caused by Burkholderia. mallei) and melioidosis (caused by B. pseudomallei) are severe infectious diseases of concern worldwide because of the rising number of cases and mortality rate. The low infectious doses of these two pathogens along with their amenability for aerosolization are factors that could be exploited as potential biothreat agents. Once the diseases have developed in humans and animals, intrinsic resistance to broad classes of antibiotics becomes a challenge for treatment and increases the risk for relapse. The progress in vaccine development demonstrates that live attenuated vaccine strains are the most effective in protection and providing long-lasting immune responses against both diseases. Our data indicate that the B. mallei double mutant (ΔtonB Δhcp1) strain CLH001, is a feasible vaccine candidate to prevent glanders and melioidosis, especially for biodefense and public health purposes.
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Affiliation(s)
- Nittaya Khakhum
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Preeti Bharaj
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Julia N. Myers
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Daniel Tapia
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - David H. Walker
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Janice J. Endsley
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Alfredo G. Torres
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
- * E-mail:
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The reemergence of glanders as a zoonotic and occupational infection in Iran and neighboring countries. ACTA ACUST UNITED AC 2019. [DOI: 10.1097/mrm.0000000000000165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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14
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Das A, Behera BK, Acharya S, Paria P, Chakraborty HJ, Parida PK, Das BK. Genetic diversity and multiple antibiotic resistance index study of bacterial pathogen, Klebsiella pneumoniae strains isolated from diseased Indian major carps. Folia Microbiol (Praha) 2019; 64:875-887. [PMID: 31020632 DOI: 10.1007/s12223-019-00701-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 03/25/2019] [Indexed: 12/17/2022]
Abstract
Intensive fish farming systems have led to increase in disease incidence, due to higher stocking density, high organic matter levels, and poor quality of the aquatic environment. Diseased fish samples showing hemorrhages and reddish lesions were collected from different freshwater fish farms located at three different districts of West Bengal, India (Burdwan, North 24 Parganas, and Nadia). The present study was conducted to evaluate the genetic diversity of ten different Klebsiella pneumoniae strains isolated from different infected freshwater fish samples based on 16S rRNA gene sequence analysis. Primarily, Klebsiella-specific media was used for the isolation and characterization of Klebsiella pneumoniae. Further, through a biochemical test, all the strains were confirmed as K. pneumoniae. PCR analysis of 16S-23S internal transcribed spacer (PCR ribotyping) was carried out to study the species variation within different Klebsiella pneumoniae isolates. For all the isolates, a conserved PCR ribotype pattern was observed while differing from other bacterial species. Phylogenetic study showed the high degree of homology with diverse source of other strains. The multiple antibiotic resistance (MAR) values of the present study for the isolates were found to be 0.468. MAR value above 0.2 indicates that the source of isolation was highly contaminated with antibiotics. Based on the 16S rRNA gene sequence analysis, the present study revealed the genetic diversity of Klebsiella pneumoniae isolated from the different diseased fish farms of West Bengal. All the strains were found to be hypermucoviscous and multidrug-resistant, thus making it pathogenic towards the host organisms. Further, the study revealed a high prevalence of K. pneumoniae in aquaculture farms, representing a risk towards successful aquaculture.
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Affiliation(s)
- A Das
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, 700120, India.,Department of Zoology, Vidyasagar University, Medinipur, West Bengal, 721102, India
| | - B K Behera
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, 700120, India.
| | - S Acharya
- Department of Zoology, Vidyasagar University, Medinipur, West Bengal, 721102, India
| | - P Paria
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, 700120, India
| | - H J Chakraborty
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, 700120, India
| | - P K Parida
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, 700120, India
| | - B K Das
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, 700120, India
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Volpe-Chaves CE, Rodrigues ACS, Lacerda MLGG, de Oliveira CTF, Castilho SB, Franciscato C, Santos ICDO, Assef APDC, Roever L, de Oliveira SMDVL, Paniago AMM. Melioidosis, an emerging infectious disease in the Midwest Brazil: A case report. Medicine (Baltimore) 2019; 98:e15235. [PMID: 31008955 PMCID: PMC6494395 DOI: 10.1097/md.0000000000015235] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
RATIONALE Melioidosis is an emerging infectious disease in Brazil and caused by Burkholderia pseudomallei, with high morbidity and mortality rates. A total of 28 melioidosis cases were reported in Brazil until 2015. The majority of melioidosis cases were reported in the Northwest region of Brazil and such cases were not previously detected in the Midwest region of Brazil. PATIENT CONCERNS A 42-year-old man was admitted with a non-productive cough, dyspnea, myalgia, diffuse abdominal pain. Pulmonary auscultation revealed a vesicular murmur, snoring sounds, and the presence of basal crackling rales in the left hemithorax. The patient evolved with several respiratory failures and he was diagnosed as the first case of community-acquired pneumonia with sepsis caused by B pseudomallei in Mato Grosso do Sul, Midwest state of Brazil. DIAGNOSIS The cell isolates were subjected to 16S rRNA gene sequencing to confirm the bacterial species. INTERVENTIONS Administration of trimethoprim/sulfamethoxazole and meropenem stabilized the clinical condition of the patient. Subsequently upon discharge, the patient was also treated with trimethoprim/sulfametothoxazole for a year. OUTCOME We reported the first case of community-acquired pneumonia with sepsis caused by B pseudomallei in Mato Grosso do Sul, Midwest state of Brazil and the patient survived. LESSONS The emergence of melioidosis in the Midwest region is being neglected and underestimated and melioidosis must be considered of the differential diagnosis in community infections.
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Affiliation(s)
- Cláudia Elizabeth Volpe-Chaves
- Graduate Program in Infectious and Parasitic Diseases of Federal University of Mato Grosso do Sul
- Regional Hospital of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul
| | - Ana Cláudia Souza Rodrigues
- Graduate Program on Health and Development in West Central Region of Federal University of Mato Grosso do Sul
- UNIDERP – Medical School
| | | | | | | | - Caroline Franciscato
- Graduate Program in Infectious and Parasitic Diseases of Federal University of Mato Grosso do Sul
| | | | | | - Leonardo Roever
- Federal University of Uberlandia, Department of Clinical Research, Brazil
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McLaughlin HP, Sue D. Rapid antimicrobial susceptibility testing and β-lactam-induced cell morphology changes of Gram-negative biological threat pathogens by optical screening. BMC Microbiol 2018; 18:218. [PMID: 30563467 PMCID: PMC6299660 DOI: 10.1186/s12866-018-1347-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 11/16/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND For Yersinia pestis, Burkholderia pseudomallei, and Burkholderia mallei, conventional broth microdilution (BMD) is considered the gold standard for antimicrobial susceptibility testing (AST) and, depending on the species, requires an incubation period of 16-20 h, or 24-48 h according to the Clinical and Laboratory Standards Institute (CLSI) guidelines. After a diagnosis of plague, melioidosis or glanders during an outbreak or after an exposure event, the timely distribution of appropriate antibiotics for treatment or post-exposure prophylaxis of affected populations could reduce mortality rates. RESULTS Herein, we developed and evaluated a rapid, automated susceptibility test for these Gram-negative bacterial pathogens based on time-lapse imaging of cells incubating in BMD microtitre drug panels using an optical screening instrument (oCelloScope). In real-time, the instrument screened each inoculated well containing broth with various concentrations of antibiotics published by CLSI for primary testing: ciprofloxacin (CIP), doxycycline (DOX) and gentamicin (GEN) for Y. pestis; imipenem (IPM), ceftazidime (CAZ) and DOX for B. mallei; and IPM, DOX, CAZ, amoxicillin-clavulanic acid (AMC) and trimethoprim-sulfamethoxazole (SXT) for B. pseudomallei. Based on automated growth kinetic data, the time required to accurately determine susceptibility decreased by ≥70% for Y. pestis and ≥ 50% for B. mallei and B. pseudomallei compared to the times required for conventional BMD testing. Susceptibility to GEN, IPM and DOX could be determined in as early as three to six hours. In the presence of CAZ, susceptibility based on instrument-derived growth values could not be determined for the majority of B. pseudomallei and B. mallei strains tested. Time-lapse video imaging of these cultures revealed that the formation of filaments in the presence of this cephalosporin at inhibitory concentrations was detected as growth. Other β-lactam-induced cell morphology changes, such as the formation of spheroplasts and rapid cell lysis, were also observed and appear to be strain- and antibiotic concentration-dependent. CONCLUSIONS A rapid, functional AST was developed and real-time video footage captured β-lactam-induced morphologies of wild-type B. mallei and B. pseudomallei strains in broth. Optical screening reduced the time to results required for AST of three Gram-negative biothreat pathogens using clinically relevant, first-line antibiotics compared to conventional BMD.
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Affiliation(s)
- Heather P. McLaughlin
- Laboratory of Preparedness and Response Branch, Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, MS-H17-5, Atlanta, GA 30333 USA
| | - David Sue
- Laboratory of Preparedness and Response Branch, Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, MS-H17-5, Atlanta, GA 30333 USA
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Walper SA, Lasarte Aragonés G, Sapsford KE, Brown CW, Rowland CE, Breger JC, Medintz IL. Detecting Biothreat Agents: From Current Diagnostics to Developing Sensor Technologies. ACS Sens 2018; 3:1894-2024. [PMID: 30080029 DOI: 10.1021/acssensors.8b00420] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Although a fundamental understanding of the pathogenicity of most biothreat agents has been elucidated and available treatments have increased substantially over the past decades, they still represent a significant public health threat in this age of (bio)terrorism, indiscriminate warfare, pollution, climate change, unchecked population growth, and globalization. The key step to almost all prevention, protection, prophylaxis, post-exposure treatment, and mitigation of any bioagent is early detection. Here, we review available methods for detecting bioagents including pathogenic bacteria and viruses along with their toxins. An introduction placing this subject in the historical context of previous naturally occurring outbreaks and efforts to weaponize selected agents is first provided along with definitions and relevant considerations. An overview of the detection technologies that find use in this endeavor along with how they provide data or transduce signal within a sensing configuration follows. Current "gold" standards for biothreat detection/diagnostics along with a listing of relevant FDA approved in vitro diagnostic devices is then discussed to provide an overview of the current state of the art. Given the 2014 outbreak of Ebola virus in Western Africa and the recent 2016 spread of Zika virus in the Americas, discussion of what constitutes a public health emergency and how new in vitro diagnostic devices are authorized for emergency use in the U.S. are also included. The majority of the Review is then subdivided around the sensing of bacterial, viral, and toxin biothreats with each including an overview of the major agents in that class, a detailed cross-section of different sensing methods in development based on assay format or analytical technique, and some discussion of related microfluidic lab-on-a-chip/point-of-care devices. Finally, an outlook is given on how this field will develop from the perspective of the biosensing technology itself and the new emerging threats they may face.
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Affiliation(s)
- Scott A. Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Guillermo Lasarte Aragonés
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University Fairfax, Virginia 22030, United States
| | - Kim E. Sapsford
- OMPT/CDRH/OIR/DMD Bacterial Respiratory and Medical Countermeasures Branch, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Carl W. Brown
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University Fairfax, Virginia 22030, United States
| | - Clare E. Rowland
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- National Research Council, Washington, D.C. 20036, United States
| | - Joyce C. Breger
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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Abstract
Burkholderia pseudomallei is a Gram-negative environmental bacterium and the aetiological agent of melioidosis, a life-threatening infection that is estimated to account for ∼89,000 deaths per year worldwide. Diabetes mellitus is a major risk factor for melioidosis, and the global diabetes pandemic could increase the number of fatalities caused by melioidosis. Melioidosis is endemic across tropical areas, especially in southeast Asia and northern Australia. Disease manifestations can range from acute septicaemia to chronic infection, as the facultative intracellular lifestyle and virulence factors of B. pseudomallei promote survival and persistence of the pathogen within a broad range of cells, and the bacteria can manipulate the host's immune responses and signalling pathways to escape surveillance. The majority of patients present with sepsis, but specific clinical presentations and their severity vary depending on the route of bacterial entry (skin penetration, inhalation or ingestion), host immune function and bacterial strain and load. Diagnosis is based on clinical and epidemiological features as well as bacterial culture. Treatment requires long-term intravenous and oral antibiotic courses. Delays in treatment due to difficulties in clinical recognition and laboratory diagnosis often lead to poor outcomes and mortality can exceed 40% in some regions. Research into B. pseudomallei is increasing, owing to the biothreat potential of this pathogen and increasing awareness of the disease and its burden; however, better diagnostic tests are needed to improve early confirmation of diagnosis, which would enable better therapeutic efficacy and survival.
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Affiliation(s)
- W Joost Wiersinga
- Department of Medicine, Division of Infectious Diseases, Academic Medical Center, Meibergdreef 9, Rm. G2-132, 1105 AZ Amsterdam, The Netherlands
- Centre for Experimental and Molecular Medicine, Academic Medical Center, Amsterdam, The Netherlands
| | - Harjeet S Virk
- Centre for Experimental and Molecular Medicine, Academic Medical Center, Amsterdam, The Netherlands
| | - Alfredo G Torres
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Bart J Currie
- Menzies School of Health Research, Charles Darwin University and Royal Darwin Hospital, Darwin, Australia
| | - Sharon J Peacock
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - David A B Dance
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Lao-Oxford-Mahosot Hospital Wellcome Trust Research Unit, Vientiane, Lao People's Democratic Republic
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Direk Limmathurotsakul
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Department of Tropical Hygiene and Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
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Bugrysheva JV, Sue D, Gee JE, Elrod MG, Hoffmaster AR, Randall LB, Chirakul S, Tuanyok A, Schweizer HP, Weigel LM. Antibiotic Resistance Markers in Burkholderia pseudomallei Strain Bp1651 Identified by Genome Sequence Analysis. Antimicrob Agents Chemother 2017; 61:e00010-17. [PMID: 28396541 PMCID: PMC5444168 DOI: 10.1128/aac.00010-17] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 03/31/2017] [Indexed: 12/30/2022] Open
Abstract
Burkholderia pseudomallei Bp1651 is resistant to several classes of antibiotics that are usually effective for treatment of melioidosis, including tetracyclines, sulfonamides, and β-lactams such as penicillins (amoxicillin-clavulanic acid), cephalosporins (ceftazidime), and carbapenems (imipenem and meropenem). We sequenced, assembled, and annotated the Bp1651 genome and analyzed the sequence using comparative genomic analyses with susceptible strains, keyword searches of the annotation, publicly available antimicrobial resistance prediction tools, and published reports. More than 100 genes in the Bp1651 sequence were identified as potentially contributing to antimicrobial resistance. Most notably, we identified three previously uncharacterized point mutations in penA, which codes for a class A β-lactamase and was previously implicated in resistance to β-lactam antibiotics. The mutations result in amino acid changes T147A, D240G, and V261I. When individually introduced into select agent-excluded B. pseudomallei strain Bp82, D240G was found to contribute to ceftazidime resistance and T147A contributed to amoxicillin-clavulanic acid and imipenem resistance. This study provides the first evidence that mutations in penA may alter susceptibility to carbapenems in B. pseudomallei Another mutation of interest was a point mutation affecting the dihydrofolate reductase gene folA, which likely explains the trimethoprim resistance of this strain. Bp1651 was susceptible to aminoglycosides likely because of a frameshift in the amrB gene, the transporter subunit of the AmrAB-OprA efflux pump. These findings expand the role of penA to include resistance to carbapenems and may assist in the development of molecular diagnostics that predict antimicrobial resistance and provide guidance for treatment of melioidosis.
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Affiliation(s)
| | - David Sue
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jay E Gee
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Mindy G Elrod
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Linnell B Randall
- Department of Molecular Genetics and Microbiology, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Sunisa Chirakul
- Department of Molecular Genetics and Microbiology, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Apichai Tuanyok
- Department of Molecular Genetics and Microbiology, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Herbert P Schweizer
- Department of Molecular Genetics and Microbiology, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Linda M Weigel
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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20
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Accidental Occupational Exposure to Burkholderia pseudomallei in South Korea Did Not Result in Melioidosis. Infect Control Hosp Epidemiol 2017; 38:886-888. [PMID: 28414016 DOI: 10.1017/ice.2017.65] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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21
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Suttisunhakul V, Pumpuang A, Ekchariyawat P, Wuthiekanun V, Elrod MG, Turner P, Currie BJ, Phetsouvanh R, Dance DAB, Limmathurotsakul D, Peacock SJ, Chantratita N. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the identification of Burkholderia pseudomallei from Asia and Australia and differentiation between Burkholderia species. PLoS One 2017; 12:e0175294. [PMID: 28384252 PMCID: PMC5383291 DOI: 10.1371/journal.pone.0175294] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 03/23/2017] [Indexed: 11/21/2022] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is increasingly used for rapid bacterial identification. Studies of Burkholderia pseudomallei identification have involved small isolate numbers drawn from a restricted geographic region. There is a need to expand the reference database and evaluate B. pseudomallei from a wider geographic distribution that more fully captures the extensive genetic diversity of this species. Here, we describe the evaluation of over 650 isolates. Main spectral profiles (MSP) for 26 isolates of B. pseudomallei (N = 5) and other Burkholderia species (N = 21) were added to the Biotyper database. MALDI-TOF MS was then performed on 581 B. pseudomallei, 19 B. mallei, 6 B. thailandensis and 23 isolates representing a range of other bacterial species. B. pseudomallei originated from northeast and east Thailand (N = 524), Laos (N = 12), Cambodia (N = 14), Hong Kong (N = 4) and Australia (N = 27). All 581 B. pseudomallei were correctly identified, with 100% sensitivity and specificity. Accurate identification required a minimum inoculum of 5 x 107 CFU/ml, and identification could be performed on spiked blood cultures after 24 hours of incubation. Comparison between a dendrogram constructed from MALDI-TOF MS main spectrum profiles and a phylogenetic tree based on recA gene sequencing demonstrated that MALDI-TOF MS distinguished between B. pseudomallei and B. mallei, while the recA tree did not. MALDI-TOF MS is an accurate method for the identification of B. pseudomallei, and discriminates between this and other related Burkholderia species.
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Affiliation(s)
- Vichaya Suttisunhakul
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Apinya Pumpuang
- Department of Clinical Pathology, Faculty of Medicine, Navamindradhiraj University, Bangkok, Thailand
| | - Peeraya Ekchariyawat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Vanaporn Wuthiekanun
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Mindy G. Elrod
- Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Zoonotic and Emerging Infectious Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, United States of America
| | - Paul Turner
- Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Bart J. Currie
- Department of Infectious Diseases, Royal Darwin Hospital, Darwin, Northern Territory, Australia; Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Rattanaphone Phetsouvanh
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic; Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - David A. B. Dance
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic; Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Direk Limmathurotsakul
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sharon J. Peacock
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- * E-mail:
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22
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Lowe CW, Satterfield BA, Nelson DB, Thiriot JD, Heder MJ, March JK, Drake DS, Lew CS, Bunnell AJ, Moore ES, O'Neill KL, Robison RA. A Quadruplex Real-Time PCR Assay for the Rapid Detection and Differentiation of the Most Relevant Members of the B. pseudomallei Complex: B. mallei, B. pseudomallei, and B. thailandensis. PLoS One 2016; 11:e0164006. [PMID: 27736903 PMCID: PMC5063335 DOI: 10.1371/journal.pone.0164006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 09/19/2016] [Indexed: 11/24/2022] Open
Abstract
The Burkholderia pseudomallei complex classically consisted of B. mallei, B. pseudomallei, and B. thailandensis, but has now expanded to include B. oklahomensis, B. humptydooensis, and three unassigned Burkholderia clades. Methods for detecting and differentiating the B. pseudomallei complex has been the topic of recent research due to phenotypic and genotypic similarities of these species. B. mallei and B. pseudomallei are recognized as CDC Tier 1 select agents, and are the causative agents of glanders and melioidosis, respectively. Although B. thailandensis and B. oklahomensis are generally avirulent, both display similar phenotypic characteristics to that of B. pseudomallei. B. humptydooensis and the Burkholderia clades are genetically similar to the B. pseudomallei complex, and are not associated with disease. Optimal identification of these species remains problematic, and PCR-based methods can resolve issues with B. pseudomallei complex detection and differentiation. Currently, no PCR assay is available that detects the major species of the B. pseudomallei complex. A real-time PCR assay in a multiplex single-tube format was developed to simultaneously detect and differentiate B. mallei, B. pseudomallei, and B. thailandensis, and a common sequence found in B. pseudomallei, B. mallei, B. thailandensis, and B. oklahomensis. A total of 309 Burkholderia isolates and 5 other bacterial species were evaluated. The assay was 100% sensitive and specific, demonstrated sensitivity beyond culture and GC methods for the isolates tested, and is completed in about an hour with a detection limit between 2.6pg and 48.9pg of gDNA. Bioinformatic analyses also showed the assay is likely 100% specific and sensitive for all 84 fully sequenced B. pseudomallei, B. mallei, B. thailandensis, and B. oklahomensis strains currently available in GenBank. For these reasons, this assay could be a rapid and sensitive tool in the detection and differentiation for those species of the B. pseudomallei complex with recognized clinical and practical significance.
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Affiliation(s)
- Chinn-Woan Lowe
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - Benjamin A. Satterfield
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - Daniel B. Nelson
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - Joseph D. Thiriot
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - Michael J. Heder
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - Jordon K. March
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - David S. Drake
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - Cynthia S. Lew
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - Annette J. Bunnell
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - Emily S. Moore
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - Kim L. O'Neill
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
| | - Richard A. Robison
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, United States of America
- * E-mail:
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Identification and Analysis of Informative Single Nucleotide Polymorphisms in 16S rRNA Gene Sequences of the Bacillus cereus Group. J Clin Microbiol 2016; 54:2749-2756. [PMID: 27582514 DOI: 10.1128/jcm.01267-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 08/17/2016] [Indexed: 01/22/2023] Open
Abstract
Analysis of 16S rRNA genes is important for phylogenetic classification of known and novel bacterial genera and species and for detection of uncultivable bacteria. PCR amplification of 16S rRNA genes with universal primers produces a mixture of amplicons from all rRNA operons in the genome, and the sequence data generally yield a consensus sequence. Here we describe valuable data that are missing from consensus sequences, variable effects on sequence data generated from nonidentical 16S rRNA amplicons, and the appearance of data displayed by different software programs. These effects are illustrated by analysis of 16S rRNA genes from 50 strains of the Bacillus cereus group, i.e., Bacillus anthracis, Bacillus cereus, Bacillus mycoides, and Bacillus thuringiensis These species have 11 to 14 rRNA operons, and sequence variability occurs among the multiple 16S rRNA genes. A single nucleotide polymorphism (SNP) previously reported to be specific to B. anthracis was detected in some B. cereus strains. However, a different SNP, at position 1139, was identified as being specific to B. anthracis, which is a biothreat agent with high mortality rates. Compared with visual analysis of the electropherograms, basecaller software frequently missed gene sequence variations or could not identify variant bases due to overlapping basecalls. Accurate detection of 16S rRNA gene sequences that include intragenomic variations can improve discrimination among closely related species, improve the utility of 16S rRNA databases, and facilitate rapid bacterial identification by targeted DNA sequence analysis or by whole-genome sequencing performed by clinical or reference laboratories.
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Senthilraj R, Prasad GS, Janakiraman K. Sequence-based identification of microbial contaminants in non-parenteral products. BRAZ J PHARM SCI 2016. [DOI: 10.1590/s1984-82502016000200011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
ABSTRACT Phenotypic profiles for microbial identification are unusual for rare, slow-growing and fastidious microorganisms. In the last decade, as a result of the widespread use of PCR and DNA sequencing, 16S rRNA sequencing has played a pivotal role in the accurate identification of microorganisms and the discovery of novel isolates in microbiology laboratories. The 16S rRNA region is universally distributed among microorganisms and is species-specific. Accordingly, the aim of our study was the genotypic identification of microorganisms isolated from non-parenteral pharmaceutical formulations. DNA was separated from five isolates obtained from the formulations. The target regions of the rRNA genes were amplified by PCR and sequenced using suitable primers. The sequence data were analyzed and aligned in the order of increasing genetic distance to relevant sequences against a library database to achieve an identity match. The DNA sequences of the phylogenetic tree results confirmed the identity of the isolates as Bacillus tequilensis, B. subtilis, Staphylococcus haemolyticus and B. amyloliqueficians. It can be concluded that 16S rRNA sequence-based identification reduces the time by circumventing biochemical tests and also increases specificity and accuracy.
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Drobish AM, Emery BD, Whitney AM, Lauer AC, Metcalfe MG, McQuiston JR. Oblitimonas alkaliphila gen. nov., sp. nov., in the family Pseudomonadaceae, recovered from a historical collection of previously unidentified clinical strains. Int J Syst Evol Microbiol 2016; 66:3063-3070. [PMID: 27169721 DOI: 10.1099/ijsem.0.001147] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Eight Gram-stain-negative bacteria (B4199T, C6819, C6918, D2441, D3318, E1086, E1148 and E5571) were identified during a retrospective study of unidentified strains from a historical collection held in the Special Bacteriology Reference Laboratory at the Centers for Disease Control and Prevention. The strains were isolated from eight patients: five female, two male and one not specified. No ages were indicated for the patients. The sources were urine (3), leg tissue (2), foot wound, lung tissue and deep liver. The strains originated from seven different states across the USA [Colorado, Connecticut (2), Indiana, North Carolina, Oregon and Pennsylvania]. The strains grew at 10-42 °C, were non-motile, alkalitolerant, slightly halophilic, microaerophilic, and catalase- and oxidase-positive. The DNA G+C content was 47.3-47.6 mol%. The major cellular fatty acids were tetradecanoic acid (C14 : 0), hexadecanoic acid (C16 : 0) and 11-octadecenoic acid (C18 : 1ω7c). Polar lipids detected were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and unknown phospholipids; the only respiratory quinone detected was the ubiquinone Q-9 (100 %). 16S rRNA gene sequence analysis produced results with 95.6 % similarity to Pseudomonas caeni DSM 24390T and 95.2 % similarity to Thiopseudomonas denitrificans X2T. The results of the biochemical, chemotaxonomic and phylogenetic analyses between the study strains and some related type strains indicated that these strains represent a novel species of a new genus within the family Pseudomonadaceae, for which the name Oblitimonas alkaliphila gen. nov., sp. nov. is proposed. The type strain is B4199T (=DSM 100830T=CCUG 67636T).
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Affiliation(s)
- Adam M Drobish
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Brian D Emery
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Anne M Whitney
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ana C Lauer
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Maureen G Metcalfe
- Infectious Diseases Pathology Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - John R McQuiston
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Humrighouse BW, Emery BD, Kelly AJ, Metcalfe MG, Mbizo J, McQuiston JR. Haematospirillum jordaniae gen. nov., sp. nov., isolated from human blood samples. Antonie van Leeuwenhoek 2016; 109:493-500. [PMID: 26857139 DOI: 10.1007/s10482-016-0654-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 01/15/2016] [Indexed: 10/22/2022]
Abstract
A Gram-negative, aerobic, motile, spiral-shaped bacterium, strain H5569(T), was isolated from a human blood sample. Phenotypic and molecular characteristics of the isolate were investigated. Optimal growth was found to occur at 35 °C under aerobic conditions on Heart Infusion Agar supplemented with 5 % rabbit blood. The major fatty acids present in the cells were identified as C16:0, C16:1ω7c and C18:1ω7c. The predominant respiratory quinone was found to be ubiquinone-Q10. The G+C content of genomic DNA for strain H5569(T) was found to be 49.9 %. Based on 16S rRNA gene sequence analysis results, 13 additional isolates were also analysed in this study. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the organism, represented by strain H5569(T), forms a distinct lineage within the family Rhodospirillaceae, closely related to two Novispirillum itersonii subspecies (93.9-94.1 %) and two Caenispirillum sp. (91.2-91.6 %). Based on these results, the isolate H5569(T) is concluded to represent a new genus and species for which the name Haematospirillum jordaniae gen. nov., sp. nov. is proposed. The type strain is H5569(T) (=DSM(T) 28903 = CCUG 66838(T)).
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Affiliation(s)
- B W Humrighouse
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, USA.
| | - B D Emery
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, USA
| | - A J Kelly
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, USA
| | - M G Metcalfe
- Infectious Diseases Pathology Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, USA
| | - J Mbizo
- Department of Public Health, Clinical and Health Sciences, College of Science, Engineering and Health, University of West Florida, Pensacola, USA
| | - J R McQuiston
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, USA
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Hoffmaster AR, AuCoin D, Baccam P, Baggett HC, Baird R, Bhengsri S, Blaney DD, Brett PJ, Brooks TJG, Brown KA, Chantratita N, Cheng AC, Dance DAB, Decuypere S, Defenbaugh D, Gee JE, Houghton R, Jorakate P, Lertmemongkolchai G, Limmathurotsakul D, Merlin TL, Mukhopadhyay C, Norton R, Peacock SJ, Rolim DB, Simpson AJ, Steinmetz I, Stoddard RA, Stokes MM, Sue D, Tuanyok A, Whistler T, Wuthiekanun V, Walke HT. Melioidosis diagnostic workshop, 2013. Emerg Infect Dis 2015; 21. [PMID: 25626057 PMCID: PMC4313648 DOI: 10.3201/eid2102.141045] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Melioidosis is a severe disease that can be difficult to diagnose because of its diverse clinical manifestations and a lack of adequate diagnostic capabilities for suspected cases. There is broad interest in improving detection and diagnosis of this disease not only in melioidosis-endemic regions but also outside these regions because melioidosis may be underreported and poses a potential bioterrorism challenge for public health authorities. Therefore, a workshop of academic, government, and private sector personnel from around the world was convened to discuss the current state of melioidosis diagnostics, diagnostic needs, and future directions.
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Monecke S, Friedrichs A, Pöhlmann C, Hochauf K, Gunzer F, Wiesner D, Sickert W, Steinmetz I, Scholz H, Ehricht R, Schmoock G, Jacobs E. An imported case of melioidosis presenting as pyelonephritis/urosepsis. JMM Case Rep 2015. [DOI: 10.1099/jmmcr.0.000073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Stefan Monecke
- Alere Technologies GmbH, Löbstedter Strasse 103-105, D-07749 Jena, Germany
- Institute for Medical Microbiology and Hygiene, Technische Universität Dresden, Fetscherstrasse 74, D-01307 Dresden, Germany
| | - Anette Friedrichs
- Department of Internal Medicine I, University Hospital Schleswig-Holstein, Campus Kiel, Schittenhelmstrasse12, D-24105 Kiel, Germany
| | - Christoph Pöhlmann
- Department of Laboratory Medicine, Robert-Bosch-Hospital, Auerbachstraße 110, D-70376 Stuttgart, Germany
| | - Kristina Hochauf
- Institute for Medical Microbiology and Hygiene, Technische Universität Dresden, Fetscherstrasse 74, D-01307 Dresden, Germany
| | - Florian Gunzer
- Institute for Medical Microbiology and Hygiene, Technische Universität Dresden, Fetscherstrasse 74, D-01307 Dresden, Germany
| | - Diana Wiesner
- Deaconesses' Hospital Dessau, Gropiusallee 3, D-06846 Dessau-Roßlau, Germany
| | | | - Ivo Steinmetz
- Friedrich-Loeffler-Institute for Medical Microbiology, University of Greifswald, Lutherstrasse 6, D-17489 Greifswald, Germany
| | - Holger Scholz
- Bundeswehr Institute of Microbiology, Neuherbergstrasse 11, D-80937 Munich, Germany
- German Center for Infection Research (DZIF), Munich, Germany
| | - Ralf Ehricht
- Alere Technologies GmbH, Löbstedter Strasse 103-105, D-07749 Jena, Germany
| | - Gernot Schmoock
- Friedrich Loeffler Institute, Institute of Bacterial Infections and Zoonoses, Naumburger Strasse 96a, D-07743 Jena, Germany
| | - Enno Jacobs
- Institute for Medical Microbiology and Hygiene, Technische Universität Dresden, Fetscherstrasse 74, D-01307 Dresden, Germany
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Jang HR, Lee CW, Ok SJ, Kim MJ, Bae MJ, Song S, Yi J, Kim KH. Melioidosis presenting as a mycotic aneurysm in a Korean patient, diagnosed by 16S rRNA sequencing and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Int J Infect Dis 2015. [PMID: 26216763 DOI: 10.1016/j.ijid.2015.07.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
A case of melioidosis with a mycotic aneurysm is reported. The blood and tissue isolates were identified as three different species of Burkholderia using the automated identification systems, VITEK 2 and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The isolate was confirmed as Burkholderia pseudomallei by 16S rRNA sequencing. The typical features of the Gram staining of colonies and 16S rRNA sequencing can be useful to identify B. pseudomallei.
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Affiliation(s)
- Hee Ryeong Jang
- Department of Internal Medicine, Pusan National University Hospital, 179 Gudeok-ro, Seogu, Busan 602-739, Republic of Korea
| | - Chung Won Lee
- Department of Thoracic and Cardiovascular Surgery, Pusan National University Hospital, Seogu, Busan, Republic of Korea
| | - Soon Jung Ok
- Department of Laboratory Medicine, Pusan National University Hospital, Seogu, Busan, Republic of Korea
| | - Min Ji Kim
- Department of Internal Medicine, Pusan National University Hospital, 179 Gudeok-ro, Seogu, Busan 602-739, Republic of Korea
| | - Mi Ju Bae
- Department of Thoracic and Cardiovascular Surgery, Pusan National University Hospital, Seogu, Busan, Republic of Korea
| | - Seunghwan Song
- Department of Thoracic and Cardiovascular Surgery, Pusan National University Hospital, Seogu, Busan, Republic of Korea
| | - Jongyoun Yi
- Department of Laboratory Medicine, Pusan National University Hospital, Seogu, Busan, Republic of Korea; Biomedical Research Institute, Pusan National University Hospital, Seogu, Busan, Republic of Korea
| | - Kye-Hyung Kim
- Department of Internal Medicine, Pusan National University Hospital, 179 Gudeok-ro, Seogu, Busan 602-739, Republic of Korea; Biomedical Research Institute, Pusan National University Hospital, Seogu, Busan, Republic of Korea.
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30
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Rosengarten D, Block C, Hidalgo-Grass C, Temper V, Gross I, Budin-Mizrahi A, Berkman N, Benenson S. Cluster of Pseudoinfections withBurkholderia cepaciaAssociated with a Contaminated Washer-Disinfector in a Bronchoscopy Unit. Infect Control Hosp Epidemiol 2015; 31:769-71. [DOI: 10.1086/653611] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In December 2008, bronchoalveolar lavage fluid samples obtained from 3 patients were positive forBurkholderia cepaciacomplex on culture. Samples obtained from bronchoscopes and rinse-water samples obtained from the washer-disinfector were found to be positive forB. cepaciacomplex. The cause of this pseudo-outbreak was that the washer-disinfector was installed without the required antibacterial filter.
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Prakash A, Thavaselvam D, Kumar A, Kumar A, Arora S, Tiwari S, Barua A, Sathyaseelan K. Isolation, identification and characterization of Burkholderia pseudomallei from soil of coastal region of India. SPRINGERPLUS 2014; 3:438. [PMID: 25187882 PMCID: PMC4152474 DOI: 10.1186/2193-1801-3-438] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 08/07/2014] [Indexed: 11/17/2022]
Abstract
Melioidosis is an emerging infectious disease caused by a free living soil dwelling Gram-negative bacterium Burkholderia pseudomallei. The disease is endemic to most parts of Southeast Asia and northern Australia and the organism has been isolated from moist soil and water. In India clinical cases are recently reported from the states of Tamilnadu, Kerala, Karnataka, Maharashtra, Orissa, Assam, West Bengal, Pondicherry and Tripura. This study is aimed to confirm the prevalence of this important bacterial species in soil samples collected from coastal areas of Tamilnadu. Forty five soil samples from five different sites were collected from Parangipettai, Tamilnadu and screened for the presence of B. pseudomallei. The study confirmed 4 isolates as B. pseudomallei with the help of conventional bacteriological methods and molecular methods that include; 16S rDNA sequencing, B. pseudomallei specific PCR, fliC gene RFLP and MALDI-TOF mass spectrometry based bacterial identification. This study reveals the prevalence and distribution of B. pseudomallei in the soil environment in coastal areas of southern India and further necessitates studies from other parts of the country. It will also be helpful to understand the distribution of B. pseudomallei and to access its epidemiological importance.
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Affiliation(s)
- Archana Prakash
- Division of Microbiology, Defence Research & Development Establishment, Jhansi Road, Gwalior, 474 002 India
| | - Duraipandian Thavaselvam
- Division of Microbiology, Defence Research & Development Establishment, Jhansi Road, Gwalior, 474 002 India
| | - Ashu Kumar
- Division of Microbiology, Defence Research & Development Establishment, Jhansi Road, Gwalior, 474 002 India
| | - Ajith Kumar
- Centre for Advanced Studies in Marine Biology, Annamalai University, Parangipettai, Tamil Nadu India
| | - Sonia Arora
- Division of Microbiology, Defence Research & Development Establishment, Jhansi Road, Gwalior, 474 002 India
| | - Sapana Tiwari
- Division of Microbiology, Defence Research & Development Establishment, Jhansi Road, Gwalior, 474 002 India
| | - Anita Barua
- Division of Microbiology, Defence Research & Development Establishment, Jhansi Road, Gwalior, 474 002 India
| | - Kannusamy Sathyaseelan
- Division of Microbiology, Defence Research & Development Establishment, Jhansi Road, Gwalior, 474 002 India
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Frickmann H, Neubauer H, Loderstaedt U, Derschum H, Hagen RM. rpsU-based discrimination within the genus Burkholderia. Eur J Microbiol Immunol (Bp) 2014; 4:106-16. [PMID: 24883196 DOI: 10.1556/eujmi.4.2014.2.3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 04/08/2014] [Indexed: 11/19/2022] Open
Abstract
Sequencing of the gene rpsU reliably delineates saprophytic Burkholderia (B.) thailandensis from highly pathogenic B. mallei and B. pseudomallei. We analyzed the suitability of this technique for the delineation of the B. pseudomallei complex from other Burkholderia species. Both newly recorded and previously deposited sequences of well-characterized or reference strains (n = 84) of Azoarcus spp., B. ambifaria, B. anthina, B. caledonica, B. caribensis, B. caryophylli, B. cenocepacia, B. cepacia, B. cocovenenans, B. dolosa, B. fungorum, B. gladioli, B. glathei, B. glumae, B. graminis, B. hospita, B. kururensis, B. mallei, B. multivorans, B. phenazinium, B. phenoliruptrix, B. phymatum, B. phytofirmans, B. plantarii, B. pseudomallei, B. pyrrocinia, B. stabilis, B. thailandensis, B. ubonensis, B. vietnamiensis, B. xenovorans, not further defined Burkholderia spp., and the outliers Cupriavidus metallidurans, Laribacter hongkongensis, Pandorea norimbergensis, and Ralstonia pickettii were included in a multiple sequence analysis. Multiple sequence alignments led to the delineation of four major clusters, rpsU-I to rpsU-IV, with a sequence homology >92%. The B. pseudomallei complex formed the complex rpsU-II. Several Burkholderia species showed 100% sequence homology. This procedure is useful for the molecular confirmation or exclusion of glanders or melioidosis from primary patient material. Further discrimination within the Burkholderia genus requires other molecular approaches.
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Prevalence and molecular characterization of pertactin-deficient Bordetella pertussis in the United States. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2013; 21:119-25. [PMID: 24256623 DOI: 10.1128/cvi.00717-13] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Pertussis has shown a striking resurgence in the United States, with a return to record numbers of reported cases as last observed in the 1950s. Bordetella pertussis isolates lacking pertactin, a key antigen component of the acellular pertussis vaccine, have been observed, suggesting that B. pertussis is losing pertactin in response to vaccine immunity. Screening of 1,300 isolates from outbreak and surveillance studies (historical isolates collected from 1935 up to 2009, isolates from the 2010 California pertussis outbreak, U.S. isolates from routine surveillance between 2010-2012, and isolates from the 2012 Washington pertussis outbreak) by conventional PCR and later by Western blotting and prn sequencing analyses ultimately identified 306 pertactin-deficient isolates. Of these pertactin-deficient strains, 276 were identified as having an IS481 in the prn gene (prnIS481 positive). The first prnIS481-positive isolate was found in 1994, and the next prnIS481-positive isolates were not detected until 2010. The prevalence of pertactin-deficient isolates increased substantially to more than 50% of collected isolates in 2012. Sequence analysis of pertactin-deficient isolates revealed various types of mutations in the prn gene, including two deletions, single nucleotide substitutions resulting in a stop codon, an inversion in the promoter, and a single nucleotide insertion resulting in a frameshift mutation. All but one mutation type were found in prn2 alleles. CDC 013 was a predominant pulsed-field gel electrophoresis (PFGE) profile in the pertactin-positive isolates (203/994) but was found in only 5% (16/306) of the pertactin-deficient isolates. Interestingly, PFGE profiles CDC 002 and CDC 237 represented 55% (167/306) of the identified pertactin-deficient isolates. These results indicate that there has been a recent dramatic increase in pertactin-deficient B. pertussis isolates throughout the United States.
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Mechergui A, Achour W, Hassen AB. Intraspecific 16S rRNA gene diversity among clinical isolates of Neisseria species. APMIS 2013; 122:437-42. [PMID: 24020769 DOI: 10.1111/apm.12164] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 07/19/2013] [Indexed: 12/01/2022]
Abstract
In the present work, nearly the entire 16S rRNA gene sequences of 46 clinical samples of Neisseria spp. were determined, and the aligned sequences were analyzed to investigate the diversity of 16S rRNA genes in each commensal Neisseria species. Two 16S rRNA types were identified in two Neisseria sicca strains, three 16S rRNA types in five Neisseria macacae strains, fourteen 16S rRNA types in twenty Neisseria flavescens isolates, and fourteen 16S rRNA types in nineteen Neisseria mucosa isolates. The number of nucleotides that were different between 16S rRNA sequences within specie ranged from 1 to 15. We found high intraspecific sequence variation in 16S rRNA genes of Neisseria spp. strains.
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Affiliation(s)
- Arij Mechergui
- Service des Laboratoires, Centre National de Greffe de Moelle Osseuse de Tunis, Faculté de Médecine de Tunis, Tunis, Tunisia
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Li D, March J, Bills T, Holt B, Wilson C, Lowe W, Tolley H, Lee M, Robison R. Gas chromatography-mass spectrometry method for rapid identification and differentiation of Burkholderia pseudomallei
and Burkholderia mallei
from each other, Burkholderia thailandensis
and several members of the Burkholderia cepacia
complex. J Appl Microbiol 2013; 115:1159-71. [DOI: 10.1111/jam.12310] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 07/07/2013] [Accepted: 07/18/2013] [Indexed: 10/26/2022]
Affiliation(s)
- D. Li
- Department of Chemistry and Biochemistry; Brigham Young University; Provo UT USA
| | - J.K. March
- Department of Microbiology and Molecular Biology; Brigham Young University; Provo UT USA
| | - T.M. Bills
- Department of Microbiology and Molecular Biology; Brigham Young University; Provo UT USA
| | - B.C. Holt
- Department of Statistics; Brigham Young University; Provo UT USA
| | - C.E. Wilson
- Department of Chemistry and Biochemistry; Brigham Young University; Provo UT USA
| | - W. Lowe
- Department of Microbiology and Molecular Biology; Brigham Young University; Provo UT USA
| | - H.D. Tolley
- Department of Statistics; Brigham Young University; Provo UT USA
| | - M.L. Lee
- Department of Chemistry and Biochemistry; Brigham Young University; Provo UT USA
| | - R.A. Robison
- Department of Microbiology and Molecular Biology; Brigham Young University; Provo UT USA
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36
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Ciervo A, Mattei R, Cassone A. Melioidosis in an Italian Tourist Injured by the Tsunami in Thailand. J Chemother 2013; 18:443-4. [PMID: 17024805 DOI: 10.1179/joc.2006.18.4.443] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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37
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Hellberg RS, Martin KG, Keys AL, Haney CJ, Shen Y, Smiley RD. 16S rRNA partial gene sequencing for the differentiation and molecular subtyping of Listeria species. Food Microbiol 2013; 36:231-40. [PMID: 24010602 DOI: 10.1016/j.fm.2013.06.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 05/24/2013] [Accepted: 06/04/2013] [Indexed: 01/22/2023]
Abstract
Use of 16S rRNA partial gene sequencing within the regulatory workflow could greatly reduce the time and labor needed for confirmation and subtyping of Listeria monocytogenes. The goal of this study was to build a 16S rRNA partial gene reference library for Listeria spp. and investigate the potential for 16S rRNA molecular subtyping. A total of 86 isolates of Listeria representing L. innocua, L. seeligeri, L. welshimeri, and L. monocytogenes were obtained for use in building the custom library. Seven non-Listeria species and three additional strains of Listeria were obtained for use in exclusivity and food spiking tests. Isolates were sequenced for the partial 16S rRNA gene using the MicroSeq ID 500 Bacterial Identification Kit (Applied Biosystems). High-quality sequences were obtained for 84 of the custom library isolates and 23 unique 16S sequence types were discovered for use in molecular subtyping. All of the exclusivity strains were negative for Listeria and the three Listeria strains used in food spiking were consistently recovered and correctly identified at the species level. The spiking results also allowed for differentiation beyond the species level, as 87% of replicates for one strain and 100% of replicates for the other two strains consistently matched the same 16S type.
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Affiliation(s)
- Rosalee S Hellberg
- Chapman University, School of Earth and Environmental Sciences, Food Science and Nutrition, Orange, CA 92866, USA.
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38
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Ritter JM, Sanchez S, Jones TL, Zaki SR, Drew CP. Neurologic melioidosis in an imported pigtail macaque (Macaca nemestrina). Vet Pathol 2013; 50:1139-44. [PMID: 23576240 DOI: 10.1177/0300985813485249] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Burkholderia pseudomallei is the cause of melioidosis in humans and other animals. Disease occurs predominately in Asia and Australia. It is rare in North America, and affected people and animals typically have a history of travel to (in human cases) or importation from (in animal cases) endemic areas. We describe the gross and histopathologic features and the microbiologic, molecular, and immunohistochemical diagnoses of a case of acute meningoencephalomyelitis and focal pneumonia caused by B. pseudomallei infection in a pigtail macaque that was imported from Indonesia to the United States for research purposes. This bacterium has been classified as a Tier 1 overlap select agent and toxin; therefore, recognition of pathologic features, along with accurate and timely confirmatory diagnostic testing, in naturally infected research animals is imperative to protect animals and personnel in the laboratory animal setting.
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Affiliation(s)
- J M Ritter
- Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop G 32, Atlanta, GA 30333, USA.
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39
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SESWITA ZILDA DEWI, HARMAYANI ENI, WIDADA JAKA, ASMARA WIDYA, IRIANTO EKO, PATANTIS GINTUNG, NURI FAWZYA YUSRO. Optimization of Culture Conditions to Produce Thermostable Keratinolytic Protease of Brevibacillus thermoruber LII, Isolated from the Padang Cermin Hot Spring, Lampung, Indonesia. MICROBIOLOGY INDONESIA 2012. [DOI: 10.5454/mi.6.4.8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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40
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Hellberg RS, Haney CJ, Shen Y, Cheng CM, Williams-Hill DM, Martin WB. Development of a custom 16S rRNA gene library for the identification and molecular subtyping of Salmonella enterica. J Microbiol Methods 2012; 91:448-58. [DOI: 10.1016/j.mimet.2012.09.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 09/17/2012] [Indexed: 10/27/2022]
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41
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Pushalkar S, Ji X, Li Y, Estilo C, Yegnanarayana R, Singh B, Li X, Saxena D. Comparison of oral microbiota in tumor and non-tumor tissues of patients with oral squamous cell carcinoma. BMC Microbiol 2012; 12:144. [PMID: 22817758 PMCID: PMC3507910 DOI: 10.1186/1471-2180-12-144] [Citation(s) in RCA: 216] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 07/20/2012] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Bacterial infections have been linked to malignancies due to their ability to induce chronic inflammation. We investigated the association of oral bacteria in oral squamous cell carcinoma (OSCC/tumor) tissues and compared with adjacent non-tumor mucosa sampled 5 cm distant from the same patient (n = 10). By using culture-independent 16S rRNA approaches, denaturing gradient gel electrophoresis (DGGE) and cloning and sequencing, we assessed the total bacterial diversity in these clinical samples. RESULTS DGGE fingerprints showed variations in the band intensity profiles within non-tumor and tumor tissues of the same patient and among the two groups. The clonal analysis indicated that from a total of 1200 sequences characterized, 80 bacterial species/phylotypes were detected representing six phyla, Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, Actinobacteria and uncultivated TM7 in non-tumor and tumor libraries. In combined library, 12 classes, 16 order, 26 families and 40 genera were observed. Bacterial species, Streptococcus sp. oral taxon 058, Peptostreptococcus stomatis, Streptococcus salivarius, Streptococcus gordonii, Gemella haemolysans, Gemella morbillorum, Johnsonella ignava and Streptococcus parasanguinis I were highly associated with tumor site where as Granulicatella adiacens was prevalent at non-tumor site. Streptococcus intermedius was present in 70% of both non-tumor and tumor sites. CONCLUSIONS The underlying changes in the bacterial diversity in the oral mucosal tissues from non-tumor and tumor sites of OSCC subjects indicated a shift in bacterial colonization. These most prevalent or unique bacterial species/phylotypes present in tumor tissues may be associated with OSCC and needs to be further investigated with a larger sample size.
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Affiliation(s)
- Smruti Pushalkar
- Department of Basic Sciences and Craniofacial Biology, New York University College of Dentistry, 345 E, 24th Street, Room 921B, New York, NY, 10010, USA
| | - Xiaojie Ji
- Department of Basic Sciences and Craniofacial Biology, New York University College of Dentistry, 345 E, 24th Street, Room 921B, New York, NY, 10010, USA
- Department of Chemical and Biological Sciences, Polytechnic Institute of NYU, New York, NY, USA
| | - Yihong Li
- Department of Basic Sciences and Craniofacial Biology, New York University College of Dentistry, 345 E, 24th Street, Room 921B, New York, NY, 10010, USA
| | - Cherry Estilo
- Dental Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Ramanathan Yegnanarayana
- Laboratory of Epithelial Cancer Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Bhuvanesh Singh
- Laboratory of Epithelial Cancer Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Xin Li
- Department of Basic Sciences and Craniofacial Biology, New York University College of Dentistry, 345 E, 24th Street, Room 921B, New York, NY, 10010, USA
| | - Deepak Saxena
- Department of Basic Sciences and Craniofacial Biology, New York University College of Dentistry, 345 E, 24th Street, Room 921B, New York, NY, 10010, USA
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42
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Frickmann H, Chantratita N, Gauthier YP, Neubauer H, Hagen RM. DISCRIMINATION OF Burkholderia mallei/pseudomallei FROM Burkholderia thailandensis BY SEQUENCE COMPARISON OF A FRAGMENT OF THE RIBOSOMAL PROTEIN S21 (RPSU) GENE. Eur J Microbiol Immunol (Bp) 2012; 2:148-156. [PMID: 23227305 DOI: 10.1556/eujmi.2.2012.2.8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Discrimination of Burkholderia (B.) pseudomallei and B. mallei from environmental B. thailandensis is challenging. We describe a discrimination method based on sequence comparison of the ribosomal protein S21 (rpsU) gene.The rpsU gene was sequenced in ten B. pseudomallei, six B. mallei, one B. thailandensis reference strains, six isolates of B. pseudomallei, and 37 of B. thailandensis. Further rpsU sequences of six B. pseudomallei, three B. mallei, and one B. thailandensis were identified via NCBI GenBank. Three to four variable base-positions were identified within a 120-base-pair fragment, allowing discrimination of the B. pseudomallei/mallei-cluster from B. thailandensis, whose sequences clustered identically. All B. mallei and three B. pseudomallei sequences were identical, while 17/22 B. pseudomallei strains differed in one nucleotide (78A>C). Sequences of the rpsU fragment of 'out-stander' reference strains of B. cepacia, B. gladioli, B. plantarii, and B. vietnamensis clustered differently.Sequence comparison of the described rpsU gene fragment can be used as a supplementary diagnostic procedure for the discrimination of B. mallei/pseudomallei from B. thailandensis as well as from other species of the genus Burkholderia, keeping in mind that it does not allow for a differentiation between B. mallei and B. pseudomallei.
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Affiliation(s)
- H Frickmann
- Department of Tropical Medicine at the Bernhard Nocht Institute, German Armed Forces Hospital Hamburg, Germany ; Institute for Medical Microbiology, Virology and Hygiene, University of Rostock Hospital, Rostock, Germany
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43
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Livovsky DM, Leibowitz D, Hidalgo-Grass C, Temper V, Salameh S, Korem M. Bordetella holmesii meningitis in an asplenic patient with systemic lupus erythematosus. J Med Microbiol 2012; 61:1165-1167. [PMID: 22556329 DOI: 10.1099/jmm.0.038208-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Bordetella holmesii is a slow-growing, Gram-negative, non-oxidizing bacillus with colonies that produce a brown soluble pigment and was originally described by Weyant et al. (1995) as CDC nonoxidizer group 2 (NO-2). It has recently been shown that B. holmesii may be isolated from nasopharyngeal specimens of up to 20% of patients with pertussis-like symptoms. However, invasive B. holmesii has rarely been reported and in the vast majority of cases the patients were immune deficient, mostly as a result of splenectomy or functional asplenia. Clinical presentations have included endocarditis, pneumonia, cellulitis, suppurative arthritis, pyelonephritis and septicaemia but no previous reports have documented meningitis secondary to this organism. Here we report what we believe to be the first clinical description of an adult with B. holmesii meningitis and bacteraemia with a brief review of published cases.
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Affiliation(s)
- Dan M Livovsky
- Hadassah-Hebrew University Medical Center, Mount-Scopus Campus, Jerusalem 91240, Israel
| | - David Leibowitz
- Hadassah-Hebrew University Medical Center, Mount-Scopus Campus, Jerusalem 91240, Israel
| | - Carlos Hidalgo-Grass
- Hadassah-Hebrew University Medical Center, Ein-Karem Campus, Jerusalem 91240, Israel
| | - Violeta Temper
- Hadassah-Hebrew University Medical Center, Ein-Karem Campus, Jerusalem 91240, Israel
| | - Shaden Salameh
- Hadassah-Hebrew University Medical Center, Mount-Scopus Campus, Jerusalem 91240, Israel
| | - Maya Korem
- Hadassah-Hebrew University Medical Center, Mount-Scopus Campus, Jerusalem 91240, Israel
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44
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MALLE DOMINGGUS, PICARIMA JUNUS, CHARA HUWAE LAURY, RAHMAWATI INDRA, PURBOWASITO WAHYU. ISOLATION AND IDENTIFICATION OF A THERMOSTABLE AMYLASE-PRODUCING BACTERIUM FROM HATUASA HOTSPRING. MICROBIOLOGY INDONESIA 2012. [DOI: 10.5454/mi.6.2.5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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45
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Kim BK, Cho MS, Kim MH, Choi HJ, Kang MJ, Shim HS, Ahn TY, Kim J, Park DS. Rapid and Specific Detection of Burkholderia glumae in Rice Seed by Real-Time Bio-PCR Using Species-Specific Primers Based on an rhs Family Gene. PLANT DISEASE 2012; 96:577-580. [PMID: 30727429 DOI: 10.1094/pdis-03-11-0235] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this study, we developed a reliable, quick, and accurate quantitative polymerase chain reaction (qPCR) assay to detect grain rot caused by Burkholderia glumae in rice seed. The control of bacterial grain rot is difficult, and the only practical methods for disease management rely on the use of pathogen-free seed, appropriate culture practices, and resistant cultivars. Therefore, the specific detection of this pathogen in seed is essential for effective control of the disease. However, other Burkholderia spp. are also detected by currently available molecular and serological methods. In this study, we exploited the available genome sequence information in public databases to develop specific PCR primers for accurate diagnosis of B. glumae. An SYBR Green real-time PCR primer set was designed based on the rhs family gene (YD repeat protein) of B. glumae BGR1 because these genes are structurally diverse. The specificity of the primers was evaluated using purified DNA from 5 isolates of B. glumae, 6 different species of Burkholderia, and 18 other reference pathogenic bacteria. The assay was able to detect at least one genome equivalent of cloned amplified target DNA using purified DNA or 1 CFU per reaction when using calibrated cell suspension. This method is rapid and reliable and has great potential for analyzing large numbers of samples.
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Affiliation(s)
- Byoung Kyu Kim
- National Academy of Agricultural Science, Rural Development Administration, 441-707 Suwon, Republic of Korea
| | - Min Seok Cho
- National Academy of Agricultural Science, Rural Development Administration, 441-707 Suwon, Republic of Korea
| | - Myeong Ho Kim
- National Academy of Agricultural Science, Rural Development Administration, 441-707 Suwon, Republic of Korea
| | - Hyeon Jin Choi
- National Academy of Agricultural Science, Rural Development Administration, 441-707 Suwon, Republic of Korea
| | - Man Jung Kang
- National Academy of Agricultural Science, Rural Development Administration, 441-707 Suwon, Republic of Korea
| | - Hong Sik Shim
- National Academy of Agricultural Science, Rural Development Administration, 441-707 Suwon, Republic of Korea
| | - Tae-Young Ahn
- Department of Microbiology, Dankook University, 330-71, Cheonan, Republic of Korea
| | - Jaisoo Kim
- Department of Life Science, Kyonggi University, Suwon 443-760, Republic of Korea
| | - Dong Suk Park
- National Academy of Agricultural Science, Rural Development Administration, 441-707 Suwon, Republic of Korea
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46
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Comparison of TaqMan PCR assays for detection of the melioidosis agent Burkholderia pseudomallei in clinical specimens. J Clin Microbiol 2012; 50:2059-62. [PMID: 22442327 DOI: 10.1128/jcm.06737-11] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Melioidosis is an emerging infectious disease caused by the soil bacterium Burkholderia pseudomallei. In diagnostic and forensic settings, molecular detection assays need not only high sensitivity with low limits of detection but also high specificity. In a direct comparison of published and newly developed TaqMan PCR assays, we found the TTS1-orf2 assay to be superior in detecting B. pseudomallei directly from clinical specimens. The YLF/BTFC multiplex assay (targeting the Yersinia-like fimbrial/Burkholderia thailandensis-like flagellum and chemotaxis region) also showed high diagnostic sensitivity and provides additional information on possible geographic origin.
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47
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Wernery U, Wernery R, Joseph M, Al-Salloom F, Johnson B, Kinne J, Jose S, Jose S, Tappendorf B, Hornstra H, Scholz HC. Natural Burkholderia mallei infection in Dromedary, Bahrain. Emerg Infect Dis 2012; 17:1277-9. [PMID: 21762586 PMCID: PMC3381376 DOI: 10.3201/eid1707.110222] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
We confirm a natural infection of dromedaries with glanders. Multilocus variable number tandem repeat analysis of a Burkholderia mallei strain isolated from a diseased dromedary in Bahrain revealed close genetic proximity to strain Dubai 7, which caused an outbreak of glanders in horses in the United Arab Emirates in 2004.
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Affiliation(s)
- Ulrich Wernery
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates
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48
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Liguori AP, Warrington SD, Ginther JL, Pearson T, Bowers J, Glass MB, Mayo M, Wuthiekanun V, Engelthaler D, Peacock SJ, Currie BJ, Wagner DM, Keim P, Tuanyok A. Diversity of 16S-23S rDNA internal transcribed spacer (ITS) reveals phylogenetic relationships in Burkholderia pseudomallei and its near-neighbors. PLoS One 2011; 6:e29323. [PMID: 22195045 PMCID: PMC3237603 DOI: 10.1371/journal.pone.0029323] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Accepted: 11/24/2011] [Indexed: 11/19/2022] Open
Abstract
Length polymorphisms within the 16S-23S ribosomal DNA internal transcribed spacer (ITS) have been described as stable genetic markers for studying bacterial phylogenetics. In this study, we used these genetic markers to investigate phylogenetic relationships in Burkholderia pseudomallei and its near-relative species. B. pseudomallei is known as one of the most genetically recombined bacterial species. In silico analysis of multiple B. pseudomallei genomes revealed approximately four homologous rRNA operons and ITS length polymorphisms therein. We characterized ITS distribution using PCR and analyzed via a high-throughput capillary electrophoresis in 1,191 B. pseudomallei strains. Three major ITS types were identified, two of which were commonly found in most B. pseudomallei strains from the endemic areas, whereas the third one was significantly correlated with worldwide sporadic strains. Interestingly, mixtures of the two common ITS types were observed within the same strains, and at a greater incidence in Thailand than Australia suggesting that genetic recombination causes the ITS variation within species, with greater recombination frequency in Thailand. In addition, the B. mallei ITS type was common to B. pseudomallei, providing further support that B. mallei is a clone of B. pseudomallei. Other B. pseudomallei near-neighbors possessed unique and monomorphic ITS types. Our data shed light on evolutionary patterns of B. pseudomallei and its near relative species.
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Affiliation(s)
- Andrew P. Liguori
- Department of Biological Sciences, Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Stephanie D. Warrington
- Department of Biological Sciences, Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jennifer L. Ginther
- Department of Biological Sciences, Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Talima Pearson
- Department of Biological Sciences, Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jolene Bowers
- Division of Pathogen Genomics, The Translational Genomics Research Institute North, Flagstaff, Arizona, United States of America
| | - Mindy B. Glass
- Bacterial Zoonoses Branch, Division of Foodborne, Bacterial and Mycotic Diseases, National Center for Zoonotic, Vector-Borne and Enteric Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, United States of America
| | - Mark Mayo
- Charles Darwin University, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | | | - David Engelthaler
- Division of Pathogen Genomics, The Translational Genomics Research Institute North, Flagstaff, Arizona, United States of America
| | | | - Bart J. Currie
- Charles Darwin University, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - David M. Wagner
- Department of Biological Sciences, Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Paul Keim
- Department of Biological Sciences, Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Apichai Tuanyok
- Department of Biological Sciences, Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
- * E-mail:
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49
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Proteomics analyses of the opportunistic pathogen Burkholderia vietnamiensis using protein fractionations and mass spectrometry. J Biomed Biotechnol 2011; 2011:701928. [PMID: 22187530 PMCID: PMC3237022 DOI: 10.1155/2011/701928] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 08/27/2011] [Accepted: 08/27/2011] [Indexed: 01/14/2023] Open
Abstract
The main objectives of this work were to obtain a more extensive coverage of the Burkholderia vietnamiensis proteome than previously reported and to identify virulence factors using tandem mass spectrometry. The proteome of B. vietnamiensis was precipitated into four fractions to as extracellular, intracellular, cell surface and cell wall proteins. Two different approaches were used to analyze the proteins. The first was a gel-based method where 1D SDS-PAGE was used for separation of the proteins prior to reverse phase liquid chromatography tandem mass spectrometry (LC-MS/MS). The second method used MudPIT analysis (Multi dimensional Protein Identification Technique), where proteins are digested and separated using cation exchange and reversed phase separations before the MS/MS analysis (LC/LC-MS/MS). Overall, gel-based LC-MS/MS analysis resulted in more protein identifications than the MudPIT analysis. Combination of the results lead to identification of more than 1200 proteins, approximately 16% of the proteins coded from the annotated genome of Burkholderia species. Several virulence factors were detected including flagellin, porin, peroxiredoxin and zinc proteases.
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50
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Hesstvedt L, Wilhelmsen M, Mengshoel AT, Dyrhol-Riise AM. Two Norwegian patients with melioidosis presenting with bacteraemia and splenic and prostatic abscesses. J Travel Med 2011; 18:418-21. [PMID: 22017720 DOI: 10.1111/j.1708-8305.2011.00550.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Infections caused by Burkholderia pseudomallei are rare in nonendemic areas, such as Scandinavia. We report the first two cases of melioidosis in Norway presenting with bacteraemia and splenic and prostatic abscesses, respectively.
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Affiliation(s)
- Liv Hesstvedt
- Department of Infectious Diseases, Oslo University Hospital, Ullevål, Oslo, Norway.
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