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Schully KL, Voegtly LJ, Rice GK, Drumm H, Fitzpatrick MC, Malagon F, Shea A, Dong M, Oduro G, Robberts FJL, Dartey PKA, Owusu-Ofori A, Clark DV, Cer RZ, Bishop-Lilly KA. Phylogenetic and phenotypic characterization of Burkholderia pseudomallei isolates from Ghana reveals a novel sequence type and common phenotypes. Front Microbiol 2024; 15:1401259. [PMID: 39044950 PMCID: PMC11264198 DOI: 10.3389/fmicb.2024.1401259] [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: 03/15/2024] [Accepted: 06/13/2024] [Indexed: 07/25/2024] Open
Abstract
Melioidosis is a potentially severe disease caused by the gram-negative soil-dwelling bacterium called Burkholderia pseudomallei. The true breadth of the distribution of this tropical pathogen is starting to emerge with environmental and clinical isolates frequently characterized in new countries and regions. Even so, isolates, clinical cases, and genetic data from the continent of Africa remain scant. We previously confirmed the presence of B. pseudomallei in the environment of Ghana, unmasking a new area of endemicity for this pathogen. Here, we describe the genetic characteristics of isolates obtained from that environmental survey. Twenty-one isolates were subjected to whole genome sequencing and found to represent three discrete sequence types (ST), one of which was novel, and designated ST2058. Phylogenetic analysis places this novel isolate within a B. pseudomallei clade that includes genomes derived from the Americas, although it is closely related to a sub-clade that includes isolates from Africa. Importantly, phenotypic characterization demonstrates common features including API 20NE profiles and B. pseudomallei CPS to support existing diagnostics, and susceptibility to standard of care antibiotics often used in the clinical management of melioidosis. These findings add to our knowledge about the presence and distribution of B. pseudomallei in Africa and represent the first published genomes out of Ghana.
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Affiliation(s)
- Kevin L. Schully
- Austere Environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Command-Frederick, Ft. Detrick, MD, United States
| | - Logan J. Voegtly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command-Frederick, Ft. Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Gregory K. Rice
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command-Frederick, Ft. Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Hannah Drumm
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command-Frederick, Ft. Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Maren C. Fitzpatrick
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command-Frederick, Ft. Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Francisco Malagon
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command-Frederick, Ft. Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - April Shea
- National Strategic Research Institute, Omaha, NE, United States
| | - Ming Dong
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), The Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | | | | | | | - Alex Owusu-Ofori
- Komfo Anokye Teaching Hospital, Kumasi, Ghana
- Department of Clinical Microbiology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Danielle V. Clark
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), The Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Regina Z. Cer
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command-Frederick, Ft. Detrick, MD, United States
| | - Kimberly A. Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command-Frederick, Ft. Detrick, MD, United States
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Mosavari N, Bashashati M, Dehghanpour M, Abdolvand M, Heshmatinia F, Sabouri F, Dashtipour S, Hosseini SM, Najafpour R, Baradaran‐Seyed Z. Tracking melioidosis in Iran: Utilizing abattoir-based surveillance as a One Health approach. Vet Med Sci 2024; 10:e1503. [PMID: 38923363 PMCID: PMC11198021 DOI: 10.1002/vms3.1503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 05/19/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Burkholderia pseudomallei, an environmental saprophyte bacterium, causes melioidosis in humans and animals. It was first discovered in Iran between 1967 and 1976 in small ruminants, equines, environments and humans. No subsequent studies have been conducted to determine the existence and prevalence of this pathogen in the country. OBJECTIVES The present study aims to monitor the presence of B. pseudomallei in the ruminant population of the Golestan province of Iran, which largely depends on pastures. The ruminants can serve as sentinels to indicate the presence of the bacteria in the environment and its potential impact on human health in the One Health triad. METHODS Liver and lung abscesses from domestic sheep, cattle and goats in three industrial and three conventional slaughterhouses were sampled and analysed using 23S ribosomal DNA polymerase chain reaction (rDNA PCR) with primers CVMP 23-1 and CVP-23-2 for B. pseudomallei, Burkholderia cepacia and Burkholderia vietnamiensis, as well as B. pseudomallei-specific TTS1 real-time PCR, along with microbiological and biochemical assays. RESULTS Out of the 97 animals sampled, only 14 (15%) tested positive for 23S rDNA PCR. However, the follow-up evaluation using TTS1 real-time PCR and microbiological and biochemical assays did not confirm the presence of B. pseudomallei in the samples. CONCLUSIONS Although B. pseudomallei was not detected in the current survey, conducting abattoir-based surveillance of ruminants is a cost-effective One Health approach to monitor pathogenic Burkholderia. Developing standards of clinical and laboratory good practices for Burkholderia infections is crucial for One Health surveillance.
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Affiliation(s)
- Nader Mosavari
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO)KarajIran
| | - Mohsen Bashashati
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO)KarajIran
| | - Mahdi Dehghanpour
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO)KarajIran
| | | | - Faezeh Heshmatinia
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO)KarajIran
| | - Fereshteh Sabouri
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO)KarajIran
| | - Shojaat Dashtipour
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO)KarajIran
| | - Saeid Mohammad Hosseini
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO)KarajIran
| | - Reza Najafpour
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO)KarajIran
| | - Zahra Baradaran‐Seyed
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO)KarajIran
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Anggraini D, Siregar FM, Rosdiana D, Kemal RA, Yovi I, Triani ZD, Jasmin N, Dwijelita N, Webb JR, Mayo M, Kaestli M, Currie BJ. Epidemiology and genetic diversity of Burkholderia pseudomallei from Riau Province, Indonesia. PLoS Negl Trop Dis 2024; 18:e0012195. [PMID: 38805481 PMCID: PMC11161056 DOI: 10.1371/journal.pntd.0012195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 06/07/2024] [Accepted: 05/06/2024] [Indexed: 05/30/2024] Open
Abstract
Melioidosis is a bacterial infection caused by Burkholderia pseudomallei, that is common in tropical and subtropical countries including Southeast Asia and Northern Australia. The magnitude of undiagnosed and untreated melioidosis across the country remains unclear. Given its proximity to regions with high infection rates, Riau Province on Sumatera Island is anticipated to have endemic melioidosis. This study reports retrospectively collected data on 68 culture-confirmed melioidosis cases from two hospitals in Riau Province between January 1, 2009, and December 31, 2021, with full clinical data available on 41 cases. We also describe whole genome sequencing and genotypic analysis of six isolates of B. pseudomallei. The mean age of the melioidosis patients was 49.1 (SD 11.5) years, 85% were male and the most common risk factor was diabetes mellitus (78%). Pulmonary infection was the most common presentation (39%), and overall mortality was 41%. Lung as a focal infection (aOR: 6.43; 95% CI: 1.13-36.59, p = 0.036) and bacteremia (aOR: 15.21; 95% CI: 2.59-89.31, p = 0.003) were significantly associated with death. Multilocus sequence typing analysis conducted on six B.pseudomallei genomes identified three sequence types (STs), namely novel ST1794 (n = 3), ST46 (n = 2), and ST289 (n = 1). A phylogenetic tree of Riau B. pseudomallei whole genome sequences with a global dataset of genomes clearly distinguished the genomes of B. pseudomallei in Indonesia from the ancestral Australian clade and classified them within the Asian clade. This study expands the known presence of B. pseudomallei within Indonesia and confirms that Indonesian B. pseudomallei are genetically linked to those in the rest of Southeast Asia. It is anticipated that melioidosis will be found in other locations across Indonesia as laboratory capacities improve and standardized protocols for detecting and confirming suspected cases of melioidosis are more widely implemented.
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Affiliation(s)
- Dewi Anggraini
- Department of Microbiology, Faculty of Medicine, Universitas Riau, Pekanbaru, Indonesia
- Arifin Achmad General Hospital, Riau Province, Pekanbaru, Indonesia
- Eka Hospital Pekanbaru, Pekanbaru, Indonesia
| | - Fajri Marindra Siregar
- Arifin Achmad General Hospital, Riau Province, Pekanbaru, Indonesia
- Department of Biochemistry, Faculty of Medicine, Universitas Riau, Pekanbaru, Indonesia
| | - Dani Rosdiana
- Arifin Achmad General Hospital, Riau Province, Pekanbaru, Indonesia
- Department of Internal Medicine, Faculty of Medicine, Universitas Riau, Pekanbaru, Indonesia
| | - Rahmat Azhari Kemal
- Arifin Achmad General Hospital, Riau Province, Pekanbaru, Indonesia
- Department of Medical Biology, Faculty of Medicine, Universitas Riau, Pekanbaru, Indonesia
| | - Indra Yovi
- Arifin Achmad General Hospital, Riau Province, Pekanbaru, Indonesia
- Eka Hospital Pekanbaru, Pekanbaru, Indonesia
- Department of Pulmonology, Faculty of Medicine, Universitas Riau, Pekanbaru, Indonesia
| | | | - Novira Jasmin
- Department of Microbiology, Faculty of Medicine, Universitas Riau, Pekanbaru, Indonesia
| | - Norsila Dwijelita
- Department of Microbiology, Faculty of Medicine, Universitas Riau, Pekanbaru, Indonesia
| | - Jessica R. Webb
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Mark Mayo
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Mirjam Kaestli
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Bart J. Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- Department of Infectious Diseases, Royal Darwin Hospital, Darwin, Northern Territory, Australia
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Yadav PK, Singh S, Paul M, Kumar S, Ponmariappan S, Thavaselvam D. Development of a novel sequence based real-time PCR assay for specific and sensitive detection of Burkholderia pseudomallei in clinical and environmental matrices. Ann Clin Microbiol Antimicrob 2024; 23:30. [PMID: 38600514 PMCID: PMC11007888 DOI: 10.1186/s12941-024-00693-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 03/29/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND Melioidosis, caused by the category B biothreat agent Burkholderia pseudomallei, is a disease with a high mortality rate and requires an immediate culture-independent diagnosis for effective disease management. In this study, we developed a highly sensitive qPCR assay for specific detection of Burkholderia pseudomallei and melioidosis disease diagnosis based on a novel target sequence. METHODS An extensive in-silico analysis was done to identify a novel and highly conserved sequence for developing a qPCR assay. The specificity of the developed assay was analyzed with 65 different bacterial cultures, and the analytical sensitivity of the assay was determined with the purified genomic DNA of B. pseudomallei. The applicability of the assay for B. pseudomallei detection in clinical and environmental matrices was evaluated by spiking B. pseudomallei cells in the blood, urine, soil, and water along with suitable internal controls. RESULTS A novel 85-nucleotide-long sequence was identified using in-silico tools and employed for the development of the highly sensitive and specific quantitative real-time PCR assay S664. The assay S664 was found to be highly specific when evaluated with 65 different bacterial cultures related and non-related to B. pseudomallei. The assay was found to be highly sensitive, with a detection limit of 3 B. pseudomallei genome equivalent copies per qPCR reaction. The detection limit in clinical matrices was found to be 5 × 102 CFU/mL for both human blood and urine. In environmental matrices, the detection limit was found to be 5 × 101 CFU/mL of river water and 2 × 103 CFU/gm of paddy field soil. CONCLUSIONS The findings of the present study suggest that the developed assay S664 along with suitable internal controls has a huge diagnostic potential and can be successfully employed for specific, sensitive, and rapid molecular detection of B. pseudomallei in various clinical and environmental matrices.
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Affiliation(s)
- Pranjal Kumar Yadav
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India
| | - Suchetna Singh
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India
| | - Moumita Paul
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India
| | - Sanjay Kumar
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India.
| | - S Ponmariappan
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India
| | - Duraipandian Thavaselvam
- O/o DGLS, Defence Research and Development Organization, Ministry of Defence, SSPL Campus, Timarpur, New Delhi, 110 054, 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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Burtnick MN, Dance DAB, Vongsouvath M, Newton PN, Dittrich S, Sendouangphachanh A, Woods K, Davong V, Kenna DTD, Saiprom N, Sengyee S, Hantrakun V, Wuthiekanun V, Limmathurotsakul D, Chantratita N, Brett PJ. Identification of Burkholderia cepacia strains that express a Burkholderia pseudomallei-like capsular polysaccharide. Microbiol Spectr 2024; 12:e0332123. [PMID: 38299821 PMCID: PMC10913486 DOI: 10.1128/spectrum.03321-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/10/2023] [Indexed: 02/02/2024] Open
Abstract
Burkholderia pseudomallei and Burkholderia cepacia are Gram-negative, soil-dwelling bacteria that are found in a wide variety of environmental niches. While B. pseudomallei is the causative agent of melioidosis in humans and animals, members of the B. cepacia complex typically only cause disease in immunocompromised hosts. In this study, we report the identification of B. cepacia strains isolated from either patients or soil in Laos and Thailand that express a B. pseudomallei-like 6-deoxyheptan capsular polysaccharide (CPS). These B. cepacia strains were initially identified based on their positive reactivity in a latex agglutination assay that uses the CPS-specific monoclonal antibody (mAb) 4B11. Mass spectrometry and recA sequencing confirmed the identity of these isolates as B. cepacia (formerly genomovar I). Total carbohydrates extracted from B. cepacia cell pellets reacted with B. pseudomallei CPS-specific mAbs MCA147, 3C5, and 4C4, but did not react with the B. pseudomallei lipopolysaccharide-specific mAb Pp-PS-W. Whole genome sequencing of the B. cepacia isolates revealed the presence of genes demonstrating significant homology to those comprising the B. pseudomallei CPS biosynthetic gene cluster. Collectively, our results provide compelling evidence that B. cepacia strains expressing the same CPS as B. pseudomallei co-exist in the environment alongside B. pseudomallei. Since CPS is a target that is often used for presumptive identification of B. pseudomallei, it is possible that the occurrence of these unique B. cepacia strains may complicate the diagnosis of melioidosis.IMPORTANCEBurkholderia pseudomallei, the etiologic agent of melioidosis, is an important cause of morbidity and mortality in tropical and subtropical regions worldwide. The 6-deoxyheptan capsular polysaccharide (CPS) expressed by this bacterial pathogen is a promising target antigen that is useful for rapidly diagnosing melioidosis. Using assays incorporating CPS-specific monoclonal antibodies, we identified both clinical and environmental isolates of Burkholderia cepacia that express the same CPS antigen as B. pseudomallei. Because of this, it is important that staff working in melioidosis-endemic areas are aware that these strains co-exist in the same niches as B. pseudomallei and do not solely rely on CPS-based assays such as latex-agglutination, AMD Plus Rapid Tests, or immunofluorescence tests for the definitive identification of B. pseudomallei isolates.
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Affiliation(s)
- Mary N. Burtnick
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - David A. B. Dance
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Manivanh Vongsouvath
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | - Paul N. Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Sabine Dittrich
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Deggendorf Institut of Technology, European Campus Rottal Inn, Pfarrkirchen, Germany
| | - Amphone Sendouangphachanh
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | - Kate Woods
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | - Viengmon Davong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | - Dervla T. D. Kenna
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Public Health Microbiology Division, Specialised Microbiology & Laboratories Directorate, UK Health Security Agency, London, United Kingdom
| | - Natnaree Saiprom
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sineenart Sengyee
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Viriya Hantrakun
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Vanaporn Wuthiekanun
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Direk Limmathurotsakul
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Paul J. Brett
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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7
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Fungwithaya P, Boonhoh W, Sontigun N, Hayakijkosol O, Klangbud WK, Wongtawan T. Seroprevalence of melioidosis and its association with blood profiles and pathogens in sheltered dogs in southern Thailand. Vet World 2024; 17:705-711. [PMID: 38680143 PMCID: PMC11045522 DOI: 10.14202/vetworld.2024.705-711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/04/2024] [Indexed: 05/01/2024] Open
Abstract
Background and Aims Melioidosis is a notable zoonotic disease in Thailand that can affect both humans and animals. Although dogs are one of the most popular pets worldwide, there is a remarkable lack of information on the prevalence and knowledge of canine melioidosis. This study aimed to estimate the seroprevalence of melioidosis in sheltered dogs and its relationship with the blood profile and blood pathogens. Materials and Methods Melioidosis in 156 dogs was analyzed using an indirect hemagglutination assay. Hematology and serum biochemistry tests were performed using an automated system. Blood pathogens (e.g., Ehrlichia, Anaplasma, Hepatozoon, and Babesia) were diagnosed using conventional polymerase chain reaction. Results The seroprevalence rates of canine melioidosis and blood pathogen infection were 5.77% (9/156) and 50.64% (79/156), respectively. Seropositive dogs generally have higher lymphocyte counts and aspartate aminotransferase levels but lower total white blood cell, neutrophil, and platelet (PLT) counts than seronegative dogs. No statistically significant difference (p > 0.05) was observed between the seropositive and seronegative dogs' hematology and serum biochemistry findings. Neither the correlation between melioidosis and blood pathogen infection nor the association between melioidosis and thrombocytopenia was statistically significant (p > 0.05). Remarkably, dogs that had coinfections with both melioidosis and blood pathogens demonstrated a significantly reduced PLTcount (49,167 ± 7,167) compared with dogs that tested positive for melioidosis but negative for blood pathogens (139,333 ± 29,913) (p < 0.01). Conclusion In southern Thailand, the prevalence of canine melioidosis was low but the prevalence of blood pathogens was high. Coinfection with blood pathogens can significantly reduce PLT counts, which may have a potentially serious impact. Future research should focus on conducting seroprevalence studies in the general dog population.
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Affiliation(s)
- Punpichaya Fungwithaya
- Office of Administrative Interdisciplinary Program on Agricultural Technology, School of Agricultural Technology, King Mongkut’s Institute of Technology Ladkrabang, Bangkok 10520 Thailand
| | - Worakan Boonhoh
- Akkhraratchakumari Veterinary College, Walailak University, Nakhon Si Thammarat 80160, Thailand
- Centre for One Health, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Narin Sontigun
- Akkhraratchakumari Veterinary College, Walailak University, Nakhon Si Thammarat 80160, Thailand
- Centre for One Health, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Orachun Hayakijkosol
- Division of Tropical Health and Medicine, College of Public Health, Medical and Veterinary Sciences, James Cook University, Queensland, Australia
| | - Wiyada Kwanhian Klangbud
- Centre of Excellence Research for Melioidosis and Microorganisms, Walailak University, Nakhon Si Thammarat 80160, Thailand
- Department of Medical Technology, School of Allied Health, Sciences, Walailak University, Nakhon Si Thammarat 80161, Thailand
| | - Tuempong Wongtawan
- Akkhraratchakumari Veterinary College, Walailak University, Nakhon Si Thammarat 80160, Thailand
- Centre for One Health, Walailak University, Nakhon Si Thammarat 80160, Thailand
- Centre of Excellence Research for Melioidosis and Microorganisms, Walailak University, Nakhon Si Thammarat 80160, Thailand
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8
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Yadav PK, Paul M, Singh S, Kumar S, Ponmariappan S, Thavaselvam D. Development of a Novel Internally Controlled HrpB1 Gene-Based Real-Time qPCR Assay for Detection of Burkholderia pseudomallei. Mol Diagn Ther 2024; 28:101-112. [PMID: 38085447 DOI: 10.1007/s40291-023-00686-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2023] [Indexed: 01/14/2024]
Abstract
BACKGROUND Melioidosis, caused by category B bioterrorism agent Burkholderia pseudomallei, is a seasonal disease of tropical and subtropical regions with a high mortality rate. An early and culture-independent detection of B. pseudomallei is required for the appropriate disease management and prevention. The present study is designed to identify novel and unique sequences of B. pseudomallei and development of quantitative polymerase chain reaction (qPCR) assay. METHODS A novel B. pseudomallei-specific target sequence was identified by in silico analysis for the qPCR assay development. The specificity of the developed assay was assessed using purified DNA of 65 different bacterial cultures, and the sensitivity was estimated using a cloned target gene. Further, a type III secretion protein HrpB1 (HrpB1) gene-based duplex qPCR assay incorporating suitable extraction and amplification control was developed, and its viability was assessed in different clinical and environmental matrices for the detection of B. pseudomallei. RESULTS In this study, an 80-nucleotide-long B. pseudomallei-specific region within the gene HrpB1 was identified by computational analysis. The developed HrpB1-based qPCR assay was highly specific for B. pseudomallei detection when evaluated with 65 different bacterial cultures. The sensitivity of the qPCR assay with the HrpB1-recombinant plasmid was found to be five copies per qPCR reaction. The assay's detection limit was found to be 5 × 102 CFU/mL for human blood and urine, 5 × 101 CFU/mL in river water, and 2 × 103 CFU/gm in paddy field soil. CONCLUSION The results of the study showed the applicability of a novel HrpB1-based qPCR assay for sensitive and specific detection of B. pseudomallei in diverse clinical and environmental samples.
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Affiliation(s)
- Pranjal Kumar Yadav
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India
| | - Moumita Paul
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India
| | - Suchetna Singh
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India
| | - Sanjay Kumar
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India.
| | - S Ponmariappan
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India
| | - Duraipandian Thavaselvam
- O/o Director General Life Science (DGLS), Defence Research and Development Organization, Ministry of Defence, SSPL Campus, Timarpur, New Delhi, 110 054, India.
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9
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Noparatvarakorn C, Jakkul W, Seng R, Tandhavanant S, Ottiwet O, Janon R, Saikong W, Chantratita N. Optimization and prospective evaluation of sensitive real-time PCR assays with an internal control for the diagnosis of melioidosis in Thailand. Microbiol Spectr 2023; 11:e0103923. [PMID: 37819125 PMCID: PMC10715024 DOI: 10.1128/spectrum.01039-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 08/18/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE Melioidosis is a serious infectious disease caused by Burkholderia pseudomallei, an environmental Gram-negative bacterium. Early detection of B. pseudomallei infection is crucial for successful antibiotic treatment and reducing mortality rates associated with melioidosis. Bacteria culture is currently used to identify B. pseudomallei in clinical samples, but the method is slow. Therefore, there is a need for more accurate and sensitive molecular-based diagnostic methods that can detect B. pseudomallei in all sample types, including samples from blood. We developed an optimal DNA extraction method for B. pseudomallei from plasma samples and used an internal control for real-time PCR. We evaluated six PCR target genes and identified the most effective target for the early detection of B. pseudomallei infection in patients. To prevent delays in the treatment of melioidosis that can lead to fatal outcomes, we recommend implementing this new approach for routine early detection of B. pseudomallei in clinical settings.
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Affiliation(s)
- Chawitar Noparatvarakorn
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Wallop Jakkul
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rathanin Seng
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sarunporn Tandhavanant
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Orawan Ottiwet
- Department of Medical Technology and Clinical Pathology, Mukdahan Hospital, Mukdahan, Thailand
| | - Rachan Janon
- Department of Medicine, Mukdahan Hospital, Mukdahan, Thailand
| | | | - 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
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10
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Yao J, Zhang Z, Tian S, Luo N, Tan J, Zhang Y, Gu S, Xia Q. Synchronous detection of Burkholderia pseudomallei and its ceftazidime resistance mutation based on RNase-HII hydrolysis combined with lateral flow strip assay. Microbiol Spectr 2023; 11:e0112523. [PMID: 37815337 PMCID: PMC10714834 DOI: 10.1128/spectrum.01125-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 08/19/2023] [Indexed: 10/11/2023] Open
Abstract
IMPORTANCE This study focused on the development of a reaction system using rhPCR to amplify a specific gene, ORF2, of B. pseudomallei and to identify the P174L mutation associated with increased drug resistance to ceftazidime (CAZ). The system incorporated universal primer probes and a simple temperature cycle reaction. The amplified products were then analyzed using lateral flow strip assay (LFSA) for strain identification and mutation interpretation. The developed system provides a reliable basis for diagnosing melioidosis and selecting appropriate drugs. Its potential impact is particularly significant in resource-limited settings where access to advanced diagnostic techniques is limited. This platform stands out for its simplicity, convenience, sensitivity, specificity, and portability. It shows promise as a point-of-care testing method for detecting single nucleotide polymorphism in genes associated with other diseases. By leveraging the advantages of this platform, researchers and healthcare professionals can potentially expand its use beyond melioidosis and apply it to the rapid detection of genetic variations in other disease-related genes.
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Affiliation(s)
- Juan Yao
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China
- Nanobiosensing and Microfluidic Point-of-Care Testing Key Laboratory of LuZhou, Luzhou, Sichuan, China
| | - Zhang Zhang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China
- Department of Neurosurgery, Neurology Center, The First Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Shen Tian
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China
| | - Nini Luo
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China
| | - Jun Tan
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China
| | - Yue Zhang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China
| | - Shuo Gu
- Department of Neurosurgery, Neurology Center, The First Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Qianfeng Xia
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China
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11
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Jilani MSA, Farook S, Bhattacharjee A, Barai L, Ahsan CR, Haq JA, Tuanyok A. Phylogeographic characterization of Burkholderia pseudomallei isolated from Bangladesh. PLoS Negl Trop Dis 2023; 17:e0011823. [PMID: 38060593 PMCID: PMC10729972 DOI: 10.1371/journal.pntd.0011823] [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: 07/13/2022] [Revised: 12/19/2023] [Accepted: 11/27/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Burkholderia pseudomallei possesses a diverse set of genes which encode a vast array of biological functions reflecting its clinical, ecological and phenotypic diversity. Strain variation is linked to geographic location as well as pattern of land uses. This soil-dwelling Gram-negative pathogen causes melioidosis, a tropical disease endemic in northern Australia and Southeast Asian regions including Bangladesh. Phylogeographic analyses of B. pseudomallei isolates by molecular typing techniques could be used to examine the diversity of this organism as well as to track melioidosis epidemics. METHODS In this study, 22 B. pseudomallei isolates, of which 20 clinical and two soil isolates were analyzed, utilizing Real-time PCR assay and multilocus sequence typing (MLST). The sequences were then submitted to PubMLST database for analysis and construction of phylogenetic tree. FINDINGS A total of 12 different sequence types (STs) that includes four novel STs were identified for the first time. Strains having STs 1005, 1007 and 56 were the most widespread STs frequently isolated in Bangladesh. ST 1005, ST 56, ST 1007 and ST 211 have been detected not only in Bangladesh but are also present in many Southeast Asian countries. SIGNIFICANCE ST 1005 was detected in both soil and clinical samples of Gazipur. Most prevalent, ST 56 has been previously reported from Myanmar, Thailand, Cambodia and Vietnam, confirming the persistence of the genotype over the entire continent. Further large-scale study is necessary to find out the magnitude of the infection and its different reservoirs in the environment along with phylogeographic association.
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Affiliation(s)
| | - Saika Farook
- Department of Microbiology, Ibrahim Medical College, Dhaka, Bangladesh
| | - Arittra Bhattacharjee
- Bioinformatics Division, National Institute of Biotechnology, Savar, Dhaka, Bangladesh
| | - Lovely Barai
- Department of Microbiology, BIRDEM General Hospital, Dhaka, Bangladesh
| | | | | | - Apichai Tuanyok
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America
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12
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Guterres H, Gusmao C, Pinheiro M, Martins J, Odio G, Maia C, da Conceicao V, Soares M, Osorio C, da Silva ES, Tilman A, Givney R, Oakley T, Yan J, Toto L, Amaral E, James R, Buising K, Mayo M, Kaestli M, Webb JR, Baird RW, Currie BJ, Francis JR, Muhi S. Melioidosis in Timor-Leste: First Case Description and Phylogenetic Analysis. Open Forum Infect Dis 2023; 10:ofad405. [PMID: 37577114 PMCID: PMC10414804 DOI: 10.1093/ofid/ofad405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/24/2023] [Indexed: 08/15/2023] Open
Abstract
Burkholderia pseudomallei, the causative agent of melioidosis, has not yet been reported in Timor-Leste, a sovereign state northwest of Australia. In the context of improved access to diagnostic resources and expanding clinical networks in the Australasian region, we report the first 3 cases of culture-confirmed melioidosis in Timor-Leste. These cases describe a broad range of typical presentations, including sepsis, pneumonia, multifocal abscesses, and cutaneous infection. Phylogenetic analysis revealed that the Timor-Leste isolates belong to the Australasian clade of B. pseudomallei, rather than the Asian clade, consistent with the phylogeographic separation across the Wallace Line. This study underscores an urgent need to increase awareness of this pathogen in Timor-Leste and establish diagnostic laboratories with improved culture capacity in regional hospitals. Clinical suspicion should prompt appropriate sampling and communication with laboratory staff to target diagnostic testing. Local antimicrobial guidelines have recently been revised to include recommendations for empiric treatment of severe sepsis.
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Affiliation(s)
| | - Celia Gusmao
- National Hospital Guido Valadares, Dili, Timor-Leste
| | | | - Joana Martins
- National Hospital Guido Valadares, Dili, Timor-Leste
| | - Gustavo Odio
- National Hospital Guido Valadares, Dili, Timor-Leste
| | | | - Virginia da Conceicao
- National Health Laboratory, Dili, Timor-Leste
- Menzies School of Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Messias Soares
- National Health Laboratory, Dili, Timor-Leste
- Menzies School of Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | | | | | | | - Rodney Givney
- Menzies School of Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Tessa Oakley
- Menzies School of Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Jennifer Yan
- Menzies School of Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Lucia Toto
- Menzies School of Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Elfiana Amaral
- Menzies School of Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Rodney James
- Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Kirsty Buising
- Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Mark Mayo
- Menzies School of Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Mirjam Kaestli
- Menzies School of Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Jessica R Webb
- Menzies School of Research, Charles Darwin University, Darwin, Northern Territory, Australia
- Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Robert W Baird
- Territory Pathology, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Bart J Currie
- Menzies School of Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Joshua R Francis
- Menzies School of Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Stephen Muhi
- Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
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13
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Assig K, Lichtenegger S, Bui LNH, Mosbacher B, Vu ATN, Erhart D, Trinh TT, Steinmetz I. Rational design of an acidic erythritol (ACER) medium for the enhanced isolation of the environmental pathogen Burkholderia pseudomallei from soil samples. Front Microbiol 2023; 14:1213818. [PMID: 37469425 PMCID: PMC10353019 DOI: 10.3389/fmicb.2023.1213818] [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: 04/28/2023] [Accepted: 06/07/2023] [Indexed: 07/21/2023] Open
Abstract
The soil bacterium Burkholderia pseudomallei causes melioidosis, a potentially fatal and greatly underdiagnosed tropical disease. Detection of B. pseudomallei in the environment is important to trace the source of infections, define risk areas for melioidosis and increase the clinical awareness. Although B. pseudomallei polymerase chain reaction (PCR)-based environmental detection provides important information, the culture of the pathogen remains essential but is still a methodological challenge. B. pseudomallei can catabolize erythritol, a metabolic pathway, which is otherwise rarely encountered among bacteria. We recently demonstrated that replacing threonine with erythritol as a single carbon source in the pH-neutral threonine-basal salt solution (TBSS-C50) historically used improved the isolation of B. pseudomallei from rice paddy soils. However, further culture medium parameters for an optimized recovery of B. pseudomallei strains from soils are still ill-defined. We, therefore, aimed to design a new erythritol-based medium by systematically optimizing parameters such as pH, buffer capacity, salt and nutrient composition. A key finding of our study is the enhanced erythritol-based growth of B. pseudomallei under acidic medium conditions. Our experiments with B. pseudomallei strains from different geographical origin led to the development of a phosphate-buffered acidic erythritol (ACER) medium with a pH of 6.3, higher erythritol concentration of 1.2%, supplemented vitamins and nitrate. This highly selective medium composition shortened the lag phase of B. pseudomallei cultures and greatly increased growth densities compared to TBSS-C50 and TBSS-C50-based erythritol medium. The ACER medium led to the highest enrichments of B. pseudomallei as determined from culture supernatants by quantitative PCR in a comparative validation with soil samples from the central part of Vietnam. Consequently, the median recovery of B. pseudomallei colony forming units on Ashdown's agar from ACER subcultures was 5.4 times higher compared to TBSS-C50-based erythritol medium (p = 0.005) and 30.7 times higher than TBSS-C50 (p < 0.001). In conclusion, our newly developed ACER medium significantly improves the isolation of viable B. pseudomallei from soils and, thereby, has the potential to reduce the rate of false-negative environmental cultures in melioidosis risk areas.
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Affiliation(s)
- Karoline Assig
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria
| | - Sabine Lichtenegger
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria
| | - Linh N. H. Bui
- Institute of Microbiology and Biotechnology, Vietnam National University, Hanoi, Vietnam
| | - Bettina Mosbacher
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria
| | - Anh T. N. Vu
- Institute of Microbiology and Biotechnology, Vietnam National University, Hanoi, Vietnam
| | - Daniel Erhart
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria
| | - Trung T. Trinh
- Institute of Microbiology and Biotechnology, Vietnam National University, Hanoi, Vietnam
| | - Ivo Steinmetz
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria
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14
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Kaewrakmuk J, Chusri S, Hortiwakul T, Kawila S, Patungkaro W, Jariyapradub B, Limvorapan P, Chiewchanyont B, Thananchai H, Duangsonk K, Tuanyok A. Under-Reporting Cases and Deaths from Melioidosis: A Retrospective Finding in Songkhla and Phatthalung Province of Southern Thailand, 2014-2020. Trop Med Infect Dis 2023; 8:tropicalmed8050286. [PMID: 37235334 DOI: 10.3390/tropicalmed8050286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/14/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
Melioidosis, caused by Burkholderia pseudomallei, is a notifiable disease associated with a high mortality rate in Thailand. The disease is highly endemic in northeast Thailand, while its prevalence in other parts of the country is poorly documented. This study aimed at improving the surveillance system for melioidosis in southern Thailand, where the disease was believed to be underreported. Two adjacent southern provinces, Songkhla and Phatthalung, were selected as the model provinces to study melioidosis. There were 473 individuals diagnosed with culture-confirmed melioidosis by clinical microbiology laboratories at four tertiary care hospitals in both provinces from January 2014 to December 2020. The median age was 54 years (IQR 41.5-64), 284 (60%) of the patients were adults ≥50 years of age, and 337 (71.2%) were male. We retrospectively analyzed 455 patients treated at either Songklanarind Hospital, Hatyai Hospital, Songkhla Provincial Hospital, or Phatthalung Provincial Hospital, of whom 181 (39.8%) patients died. The median duration from admission to death was five days (IQR 2-17). Of the 455 patients, 272 (57.5%) had at least one clinical risk factor, and 188 (39.8%) had diabetes. Two major clinical manifestations, bacteremia and pneumonia, occurred in 274 (58.1%) and 166 (35.2%) patients, respectively. In most cases, 298 (75%) out of 395 local patients were associated with rainfall. Over the seven years of the study, the average annual incidence was 2.87 cases per 100,000 population (95% CI, 2.10 to 3.64). This study has confirmed that these two provinces of southern Thailand are endemic to melioidosis; even though the incidence rate is much lower than that of the Northeast, the mortality rate is comparably high.
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Affiliation(s)
- Jedsada Kaewrakmuk
- Faculty of Medical Technology, Prince of Songkla University, Hatyai, Songkhla 90110, Thailand
- Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Sarunyou Chusri
- Faculty of Medicine, Prince of Songkla University, Hatyai, Songkhla 90110, Thailand
| | - Thanaporn Hortiwakul
- Faculty of Medicine, Prince of Songkla University, Hatyai, Songkhla 90110, Thailand
| | - Soontara Kawila
- Faculty of Medicine, Prince of Songkla University, Hatyai, Songkhla 90110, Thailand
| | | | | | | | | | | | - Kwanjit Duangsonk
- Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Apichai Tuanyok
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL 32608, USA
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15
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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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16
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Noparatvarakorn C, Sengyee S, Yarasai A, Phunpang R, Dulsuk A, Ottiwet O, Janon R, Morakot C, Burtnick MN, Brett PJ, West TE, Chantratita N. Prospective Analysis of Antibody Diagnostic Tests and TTS1 Real-Time PCR for Diagnosis of Melioidosis in Areas Where It Is Endemic. J Clin Microbiol 2023; 61:e0160522. [PMID: 36877019 PMCID: PMC10035309 DOI: 10.1128/jcm.01605-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/02/2023] [Indexed: 03/07/2023] Open
Abstract
Melioidosis is a tropical infectious disease caused by Burkholderia pseudomallei. Melioidosis is associated with diverse clinical manifestations and high mortality. Early diagnosis is needed for appropriate treatment, but it takes several days to obtain bacterial culture results. We previously developed a rapid immunochromatography test (ICT) based on hemolysin coregulated protein 1 (Hcp1) and two enzyme-linked immunosorbent assays (ELISAs) based on Hcp1 (Hcp1-ELISA) and O-polysaccharide (OPS-ELISA) for serodiagnosis of melioidosis. This study prospectively validated the diagnostic accuracy of the Hcp1-ICT in suspected melioidosis cases and determined its potential use for identifying occult melioidosis cases. Patients were enrolled and grouped by culture results, including 55 melioidosis cases, 49 other infection patients, and 69 patients with no pathogen detected. The results of the Hcp1-ICT were compared with culture, a real-time PCR test based on type 3 secretion system 1 genes (TTS1-PCR), and ELISAs. Patients in the no-pathogen-detected group were followed for subsequent culture results. Using bacterial culture as a gold standard, the sensitivity and specificity of Hcp1-ICT were 74.5% and 89.8%, respectively. The sensitivity and specificity of TTS1-PCR were 78.2% and 100%, respectively. The diagnostic accuracy was markedly improved if the Hcp1-ICT results were combined with TTS1-PCR results (sensitivity and specificity were 98.2% and 89.8%, respectively). Among patients with initially negative cultures, Hcp1-ICT was positive in 16/73 (21.9%). Five of the 16 patients (31.3%) were subsequently confirmed to have melioidosis by repeat culture. The combined Hcp1-ICT and TTS1-PCR test results are useful for diagnosis, and Hcp1-ICT may help identify occult cases of melioidosis.
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Affiliation(s)
- Chawitar Noparatvarakorn
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sineenart Sengyee
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Atchara Yarasai
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rungnapa Phunpang
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Adul Dulsuk
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Orawan Ottiwet
- Department of Medical Technology and Clinical Pathology, Mukdahan Hospital, Mukdahan, Thailand
| | - Rachan Janon
- Department of Medicine, Mukdahan Hospital, Mukdahan, Thailand
| | - Chumpol Morakot
- Department of Medicine, Mukdahan Hospital, Mukdahan, Thailand
| | - Mary N. Burtnick
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA
| | - Paul J. Brett
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA
| | - T. Eoin West
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Division of Pulmonary, Critical Care & Sleep Medicine, Harborview Medical Center, University of Washington, Seattle, Washington, USA
| | - 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
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17
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Somprasong N, Hagen JP, Sahl JW, Webb JR, Hall CM, Currie BJ, Wagner DM, Keim P, Schweizer HP. A conserved active site PenA β-lactamase Ambler motif specific for Burkholderia pseudomallei/B. mallei is likely responsible for intrinsic amoxicillin-clavulanic acid sensitivity and facilitates a simple diagnostic PCR assay for melioidosis. Int J Antimicrob Agents 2023; 61:106714. [PMID: 36640845 DOI: 10.1016/j.ijantimicag.2023.106714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 11/23/2022] [Accepted: 12/31/2022] [Indexed: 01/13/2023]
Abstract
Burkholderia pseudomallei is a soil- and water-dwelling Gram-negative bacterium that causes melioidosis in humans and animals. Amoxicillin-clavulanic acid (AMC) susceptibility has been hailed as an integral part of the screening algorithm for identification of B. pseudomallei, but the molecular basis for the inherent AMC susceptibility of this bacterium remains undefined. This study showed that B. pseudomallei (and the closely-related B. mallei) wild-type strains are the only Burkholderia spp. that contain a 70STSK73 PenA Ambler motif. This motif was present in >99.5% of 1820 analysed B. pseudomallei strains and 100% of 83 analysed B. mallei strains, and is proposed as the likely cause for their inherent AMC sensitivity. The authors developed a polymerase chain reaction (PCR) assay that specifically amplifies the penA70ST(S/F)K73-containing region from B. pseudomallei and B. mallei, but not from the remaining B. pseudomallei complex species or the 70STFK73 region from the closely-related penB of B. cepacia complex species. The abundance and purity of the 193-bp PCR fragment from putative B. pseudomallei isolates from clinical and environmental samples is likely sufficient for reliable confirmation of the presence of B. pseudomallei. The PCR assay is designed to be especially suited for use in resource-constrained areas. While not further explored in this study, the assay may allow diagnosis of putative B. mallei in culture isolates from animal and human samples.
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Affiliation(s)
- Nawarat Somprasong
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA
| | - Johannah P Hagen
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA
| | - Jason W Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Jessica R Webb
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia; Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Carina M Hall
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA
| | - Bart J Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia; Department of Infectious Diseases and Northern Territory Medical Programme, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - David M Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Paul Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Herbert P Schweizer
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA.
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18
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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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19
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Chong YM, Chan YF, Jamaluddin MFH, Hasan MS, Pang YK, Ponnampalavanar S, Syed Omar SF, Sam IC. Rhinovirus/enterovirus was the most common respiratory virus detected in adults with severe acute respiratory infections pre-COVID-19 in Kuala Lumpur, Malaysia. PLoS One 2022; 17:e0273697. [PMID: 36054088 PMCID: PMC9439195 DOI: 10.1371/journal.pone.0273697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 08/14/2022] [Indexed: 02/01/2023] Open
Abstract
Background Severe acute respiratory infections (SARI) pose a great global burden. The contribution of respiratory viruses to adult SARI is relatively understudied in Asia. We aimed to determine viral aetiology of adult SARI patients in Kuala Lumpur, Malaysia. Methods The prevalence of 20 common (mainly viral) respiratory pathogens, and MERS-CoV, SARS-CoV and 5 bacterial select agents was investigated from May 2017 to October 2019 in 489 SARI adult patients in Kuala Lumpur, Malaysia, using molecular assays (Luminex NxTAG-RPP kit and qPCR assays). Viral metagenomics analysis was performed on 105 negative samples. Results Viral respiratory pathogens were detected by PCR in 279 cases (57.1%), including 10 (2.0%) additional detections by metagenomics analysis. The most detected viruses were rhinovirus/enterovirus (RV/EV) (49.1%) and influenza virus (7.4%). Three melioidosis cases were detected but no SARS-CoV, MERS-CoV or other bacterial select agents. Bacterial/viral co-detections and viral co-detections were found in 44 (9.0%) and 27 (5.5%) cases respectively, mostly involving RV/EV. Independent predictors of critical disease were male gender, chronic lung disease, lack of runny nose and positive blood culture with a significant bacterial pathogen. Asthma and sore throat were associated with increased risk of RV/EV detection, while among RV/EV cases, males and those with neurological disease were at increased risk of critical disease. Conclusions Prior to the COVID-19 pandemic, the high prevalence of respiratory viruses in adults with SARI was mainly attributed to RV/EV. Continued surveillance of respiratory virus trends contributes to effective diagnostic, prevention, and treatment strategies.
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Affiliation(s)
- Yoong Min Chong
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Yoke Fun Chan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- * E-mail: (YFC); (ICS)
| | | | - M. Shahnaz Hasan
- Department of Anesthesiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Yong Kek Pang
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | | | | | - I-Ching Sam
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- * E-mail: (YFC); (ICS)
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20
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Wongpalee SP, Thananchai H, Chewapreecha C, Roslund HB, Chomkatekaew C, Tananupak W, Boonklang P, Pakdeerat S, Seng R, Chantratita N, Takarn P, Khamnoi P. Highly specific and sensitive detection of Burkholderia pseudomallei genomic DNA by CRISPR-Cas12a. PLoS Negl Trop Dis 2022; 16:e0010659. [PMID: 36037185 PMCID: PMC9423629 DOI: 10.1371/journal.pntd.0010659] [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: 03/27/2022] [Accepted: 07/12/2022] [Indexed: 11/18/2022] Open
Abstract
Detection of Burkholderia pseudomallei, a causative bacterium for melioidosis, remains a challenging undertaking due to long assay time, laboratory requirements, and the lack of specificity and sensitivity of many current assays. In this study, we are presenting a novel method that circumvents those issues by utilizing CRISPR-Cas12a coupled with isothermal amplification to identify B. pseudomallei DNA from clinical isolates. Through in silico search for conserved CRISPR-Cas12a target sites, we engineered the CRISPR-Cas12a to contain a highly specific spacer to B. pseudomallei, named crBP34. The crBP34-based detection assay can detect as few as 40 copies of B. pseudomallei genomic DNA while discriminating against other tested common pathogens. When coupled with a lateral flow dipstick, the assay readout can be simply performed without the loss of sensitivity and does not require expensive equipment. This crBP34-based detection assay provides high sensitivity, specificity and simple detection method for B. pseudomallei DNA. Direct use of this assay on clinical samples may require further optimization as these samples are complexed with high level of human DNA. Melioidosis is a fatal infectious disease caused by a Gram-negative bacterium called Burkholderia pseudomallei. The bacteria can be found in many parts of the world, especially in the tropical and subtropical regions. Infection displays a variety of symptoms such as pneumonia, organ abscess and septicemia. The latter can lead to death within 24–48 hours if not properly diagnosed and treated. Rapid and accurate diagnosis, consequently, are essential for saving patients’ lives. Currently, culturing B. pseudomallei is a gold standard diagnostic method, but the assay turnaround time is 2–4 days, and the result could be of low sensitivity. Other detection methods such as real-time PCR and serological assays are limited by availability of equipment and by low specificity in endemic areas, respectively. For these reasons, in this study we developed a specific, sensitive and rapid detection assay for B. pseudomallei DNA, that is based on CRISPR-Cas12a system. The CRISPR-Cas12a is a protein-RNA complex that recognizes DNA. The RNA can be reprogramed to guide the detection of any DNA of interest, which in our case B. pseudomallei genomic DNA. Our data showed that this assay exhibited a 100% specificity to B. pseudomallei while discriminating against 10 other pathogens and human. The assay can detect B. pseudomallei DNA in less than one hour and does not require sophisticated equipment.
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Affiliation(s)
- Somsakul Pop Wongpalee
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- * E-mail:
| | - Hathairat Thananchai
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Claire Chewapreecha
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Henrik B. Roslund
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Chalita Chomkatekaew
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Warunya Tananupak
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Phumrapee Boonklang
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sukritpong Pakdeerat
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rathanin Seng
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Piyawan Takarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Phadungkiat Khamnoi
- Microbiology Unit, Diagnostic Laboratory, Maharaj Nakorn Chiang Mai Hospital, Chiang Mai, Thailand
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21
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Hall CM, Romero-Alvarez D, Martz M, Santana-Propper E, Versluis L, Jiménez L, Alkishe A, Busch JD, Maness T, Stewart J, Sidwa T, Gee JE, Elrod MG, Weiner Z, Hoffmaster AR, Sahl JW, Salzer JS, Peterson AT, Kieffer A, Wagner DM. Low risk of acquiring melioidosis from the environment in the continental United States. PLoS One 2022; 17:e0270997. [PMID: 35905049 PMCID: PMC9337633 DOI: 10.1371/journal.pone.0270997] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/21/2022] [Indexed: 11/29/2022] Open
Abstract
Melioidosis is an underreported human disease of tropical and sub-tropical regions caused by the saprophyte Burkholderia pseudomallei. Although most global melioidosis cases are reported from tropical regions in Southeast Asia and northern Australia, there are multiple occurrences from sub-tropical regions, including the United States (U.S.). Most melioidosis cases reported from the continental U.S. are the result of acquiring the disease during travel to endemic regions or from contaminated imported materials. Only two human melioidosis cases from the continental U.S. have likely acquired B. pseudomallei directly from local environments and these cases lived only ~7 km from each other in rural Texas. In this study, we assessed the risk of acquiring melioidosis from the environment within the continental U.S. by surveying for B. pseudomallei in the environment in Texas where these two human melioidosis cases likely acquired their infections. We sampled the environment near the homes of the two cases and at additional sampling locations in surrounding counties in Texas that were selected based on ecological niche modeling. B. pseudomallei was not detected at the residences of these two cases or in the surrounding region. These negative data are important to demonstrate that B. pseudomallei is rare in the environment in the U.S. even at locations where locally acquired human cases likely have occurred, documenting the low risk of acquiring B. pseudomallei infection from the environment in the continental U.S.
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Affiliation(s)
- Carina M. Hall
- Pathogen Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Daniel Romero-Alvarez
- University of Kansas, Lawrence, Kansas, United States of America
- OneHealth Research Group, Facultad de Medicina, Universidad de las Américas, Quito, Ecuador
| | - Madison Martz
- Pathogen Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Ella Santana-Propper
- Pathogen Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Lora Versluis
- Pathogen Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Laura Jiménez
- University of Kansas, Lawrence, Kansas, United States of America
| | | | - Joseph D. Busch
- Pathogen Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Trevor Maness
- Texas Department of State Health Services, San Antonio, Texas, United States of America
| | - Jonathan Stewart
- Texas Department of State Health Services, San Antonio, Texas, United States of America
| | - Tom Sidwa
- Texas Department of State Health Services, Austin, Texas, United States of America
| | - Jay E. Gee
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Mindy G. Elrod
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Zachary Weiner
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Alex R. Hoffmaster
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jason W. Sahl
- Pathogen Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Johanna S. Salzer
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | | | - Amanda Kieffer
- Texas Department of State Health Services, San Antonio, Texas, United States of America
| | - David M. Wagner
- Pathogen Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- * E-mail:
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22
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Shaw T, Assig K, Tellapragada C, Wagner GE, Choudhary M, Göhler A, Eshwara VK, Steinmetz I, Mukhopadhyay C. Environmental Factors Associated With Soil Prevalence of the Melioidosis Pathogen Burkholderia pseudomallei: A Longitudinal Seasonal Study From South West India. Front Microbiol 2022; 13:902996. [PMID: 35847064 PMCID: PMC9283100 DOI: 10.3389/fmicb.2022.902996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Melioidosis is a seasonal infectious disease in tropical and subtropical areas caused by the soil bacterium Burkholderia pseudomallei. In many parts of the world, including South West India, most cases of human infections are reported during times of heavy rainfall, but the underlying causes of this phenomenon are not fully understood. India is among the countries with the highest predicted melioidosis burden globally, but there is very little information on the environmental distribution of B. pseudomallei and its determining factors. The present study aimed (i) to investigate the prevalence of B. pseudomallei in soil in South West India, (ii) determine geochemical factors associated with B. pseudomallei presence and (iii) look for potential seasonal patterns of B. pseudomallei soil abundance. Environmental samplings were performed in two regions during the monsoon and post-monsoon season and summer from July 2016 to November 2018. We applied direct quantitative real time PCR (qPCR) together with culture protocols to overcome the insufficient sensitivity of solely culture-based B. pseudomallei detection from soil. A total of 1,704 soil samples from 20 different agricultural sites were screened for the presence of B. pseudomallei. Direct qPCR detected B. pseudomallei in all 20 sites and in 30.2% (517/1,704) of all soil samples, whereas only two samples from two sites were culture-positive. B. pseudomallei DNA-positive samples were negatively associated with the concentration of iron, manganese and nitrogen in a binomial logistic regression model. The highest number of B. pseudomallei-positive samples (42.6%, p < 0.0001) and the highest B. pseudomallei loads in positive samples [median 4.45 × 103 genome equivalents (GE)/g, p < 0.0001] were observed during the monsoon season and eventually declined to 18.9% and a median of 1.47 × 103 GE/g in summer. In conclusion, our study from South West India shows a wide environmental distribution of B. pseudomallei, but also considerable differences in the abundance between sites and within single sites. Our results support the hypothesis that nutrient-depleted habitats promote the presence of B. pseudomallei. Most importantly, the highest B. pseudomallei abundance in soil is seen during the rainy season, when melioidosis cases occur.
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Affiliation(s)
- Tushar Shaw
- Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
- Faculty of Life and Allied Health Sciences, Ramaiah University of Applied Sciences, Bengaluru, India
| | - Karoline Assig
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
- Friedrich Loeffler Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Chaitanya Tellapragada
- Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Gabriel E. Wagner
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Madhu Choudhary
- ICAR-Central Soil Salinity Research Institute (CSSRI), Karnal, India
| | - André Göhler
- German Federal Institute for Risk Assessment, Berlin, Germany
| | - Vandana Kalwaje Eshwara
- Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
- Centre for Antimicrobial Resistance and Education, Manipal Academy of Higher Education, Manipal, India
| | - Ivo Steinmetz
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
- Friedrich Loeffler Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
- *Correspondence: Ivo Steinmetz,
| | - Chiranjay Mukhopadhyay
- Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
- Centre for Emerging and Tropical Diseases, Manipal Academy of Higher Education, Manipal, India
- Chiranjay Mukhopadhyay,
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23
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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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24
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On the Environmental Presence of Burkholderia pseudomallei in South-Central Ghana. Appl Environ Microbiol 2022; 88:e0060022. [PMID: 35652663 DOI: 10.1128/aem.00600-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Burkholderia pseudomallei is a Gram-negative soil saprophyte with the potential to cause melioidosis, an opportunistic disease with a high mortality potential. Periodic case reports of melioidosis in or imported from Africa occur in the literature dating back decades. Furthermore, statistical models suggest Western sub-Saharan Africa as a high-risk zone for the presence of B. pseudomallei. A recent case report from the United Kingdom of a returning traveler from Ghana highlights the need for environmental studies in Ghana. We examined 100 soil samples from a rice farm in south-central Ghana. Soil was subjected to selective enrichment culture for B. pseudomallei using threonine-basal salt solution with colistin (TBSS-C50) and erythritol medium, as described in the literature. Bacterial cultures were identified with standard biochemical tests, a rapid antigen detection assay, and real-time PCR specific for B. pseudomallei. Of the 100 soil samples, 55% yielded cultures consistent with B. pseudomallei on Ashdown's agar as well as by capsular polysaccharide antigen production. This is the first confirmatory report of culture-confirmed B. pseudomallei in the environment of Ghana. Our study emphasizes the need for further exploration of the burden of human melioidosis in Ghana. We recommend that local clinicians familiarize themselves with the diagnosis and clinical management of melioidosis, while laboratories develop capacity for the safe isolation and identification of B. pseudomallei. IMPORTANCE We present the first confirmation of the presence of B. pseudomallei in the environment of Ghana. This study will bring attention to a disease with the potential to cause significant morbidity and mortality in Ghana, but which has gone completely unrecognized until this point. Furthermore, this work would encourage local clinicians to familiarize themselves with the diagnosis and clinical management of melioidosis and laboratories to develop capacity for the safe isolation and identification of B. pseudomallei.
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Bhaskaran P, Prasad V, Gopinathan A, Shaw T, Sivadas S, Jayakumar C, Chowdhury S, Dravid A, Mukhopadhyay C, Kumar A. Burkholderia pseudomallei in Environment of Adolescent Siblings with Melioidosis, Kerala, India, 2019. Emerg Infect Dis 2022; 28:1246-1249. [PMID: 35608830 PMCID: PMC9155894 DOI: 10.3201/eid2806.211526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In 2019, Burkholderia pseudomallei was isolated from the backyard of 2 siblings with melioidosis in Kerala, India. This finding highlights the value of healthcare providers being aware of risk for melioidosis in febrile patients, of residents taking precautions when outside, and of increasing environmental surveillance for B. pseudomallei in this region.
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Currie BJ, Woerle C, Mayo M, Meumann EM, Baird RW. What is the role of lateral flow immunoassay for the diagnosis of melioidosis? Open Forum Infect Dis 2022; 9:ofac149. [PMID: 35493111 PMCID: PMC9043003 DOI: 10.1093/ofid/ofac149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 03/19/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Culture of Burkholderia pseudomallei remains the gold standard for diagnosis of melioidosis but is not possible in many resource-limited settings where melioidosis is endemic. Direct identification of B. pseudomallei antigen in clinical samples has been developed using a lateral flow immunoassay (LFA) targeting B. pseudomallei capsular polysaccharide.
Methods
We summarised the findings from the 8 studies to date of the Active Melioidosis Detect (AMD) LFA and compared these with our results from 232 patients with culture-confirmed melioidosis. We have also optimised the methodology for testing different clinical samples.
Results
Sensitivity and specificity for different samples was broadly similar in our study to those published from Thailand, India, Laos and Malaysia. 130/232 (56%) of our melioidosis patients were positive on one or more AMD tests: 27% for serum (rising to 39% in those with bacteremic melioidosis and 68% in those with septic shock); 63% for urine (72% in bacteremic melioidosis and 90% in septic shock); 85% in sputum that was culture positive; and 83% in pus that was culture positive. Heating sputum and pus samples increased sensitivity. Faint false positive urine bands seen on earlier AMD versions were not seen when re-tested using the most recent version, AMD-Plus.
Conclusions
While sensitivity of melioidosis LFA is low overall for blood samples, there is potential for use as a rapid diagnostic; testing serum and urine from those with severe sepsis who may have melioidosis and testing sputum and pus samples from clinically relevant scenarios. Prospective studies of patients with sepsis and other clinical presentations resembling melioidosis are required to ascertain if the specificity of AMD-PLUS is adequate to enable diagnosis of melioidosis with a high positive predictive value.
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Affiliation(s)
- Bart J Currie
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- Department of Infectious Diseases and Pathology and Northern Territory Medical Program, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Celeste Woerle
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Mark Mayo
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Ella M Meumann
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- Department of Infectious Diseases and Pathology and Northern Territory Medical Program, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Robert W Baird
- Department of Infectious Diseases and Pathology and Northern Territory Medical Program, Royal Darwin Hospital, Darwin, Northern Territory, Australia
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Gassiep I, Bauer MJ, Page M, Harris PNA, Norton R. Comparative evaluation of Panther Fusion and real-time PCR for detection of Burkholderia pseudomallei in spiked human blood. Access Microbiol 2022; 4:000333. [PMID: 35693467 PMCID: PMC9175970 DOI: 10.1099/acmi.0.000333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/24/2022] [Indexed: 12/26/2022] Open
Abstract
Introduction. Melioidosis is an infection that most commonly presents with bacteraemia. Culture-based laboratory methods can result in a significant delay to organism identification. Molecular diagnostic techniques have a high sensitivity and rapid time to diagnosis. A decreased time to diagnosis is likely to improve patient outcomes. Aim. To compare the Panther Fusion automated molecular instrument to an in-house method for the detection of Burkholderia pseudomallei directly from spiked human whole-blood samples. Results. The in-house method detected 11/12 (92 %) samples with a B. pseudomallei concentration of 2.5–4.5×102 c.f.u. ml−1. The Panther was less reliable, detecting only 8/14 (75 %) samples with a similar bacterial concentration. The Panther was able to detect 12/12 (100 %) spiked blood culture-positive samples. Conclusion. The direct detection of B. pseudomallei from patient blood on presentation to a healthcare facility will significantly decrease time to diagnosis. We describe an in-house real-time PCR method with the lowest reported limit of detection to date. Due to lower sensitivity, the Panther Fusion would be best used as a diagnostic method directly from a positive blood culture.
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Affiliation(s)
- Ian Gassiep
- Pathology Queensland, Royal Brisbane and Women’s Hospital, Herston, Queensland, Australia
- Department of Infectious Diseases, Mater Hospital Brisbane, South Brisbane, Queensland, Australia
- University of Queensland Centre for Clinical Research, Royal Brisbane and Woman’s Hospital, Herston, Queensland, Australia
| | - Michelle J. Bauer
- University of Queensland Centre for Clinical Research, Royal Brisbane and Woman’s Hospital, Herston, Queensland, Australia
| | - Melissa Page
- Pathology Queensland, Royal Brisbane and Women’s Hospital, Herston, Queensland, Australia
| | - Patrick N. A. Harris
- Pathology Queensland, Royal Brisbane and Women’s Hospital, Herston, Queensland, Australia
- University of Queensland Centre for Clinical Research, Royal Brisbane and Woman’s Hospital, Herston, Queensland, Australia
| | - Robert Norton
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
- Pathology Queensland, Townsville University Hospital, Townsville, Queensland, Australia
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Wang X, Wang L, Zhu H, Wang C, Zhu X. Reliable detection of Burkholderia pseudomallei using multiple cross displacement amplification label-based biosensor. BMC Microbiol 2022; 22:72. [PMID: 35272632 PMCID: PMC8908694 DOI: 10.1186/s12866-022-02485-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 02/28/2022] [Indexed: 11/16/2022] Open
Abstract
Background Burkholderia pseudomallei (B. pseudomallei), as a highly pathogenic organism, causes melioidosis, which is a disease of public health importance in many tropical developing countries. Here, we present and validate a novel detection technique, termed multiple cross displacement amplification combined with nanoparticles-based lateral flow biosensor (MCDA-NB), for identifying B. pseudomallei and diagnosing melioidosis. Results B. pseudomallei-MCDA targets the TTS1 (Type III secretion system gene cluster 1) to specifically design ten MCDA primers. The nanoparticles-based biosensor (NB) can be combined with B. pseudomallei-MCDA for visually, objective, simply and rapidly reporting reaction results. The optimal amplification conditions of B. pseudomallei-MCDA were 66 °C for 30 min. Assay’s sensitivity was 100 fg of genomic DNA in the pure cultures, and the analytical specificity was 100% by the examination of 257 strains, including 228 B. pseudomallei and 29 non-B. pseudomallei. As a result, the whole detection procedure was completed within 50 min, including 15 min for genomic DNA preparation, 30 min for l MCDA reaction, and 2 min for the interpretation of the results visually by biosensor. Conclusions B. pseudomallei-MCDA assay is a rapid, sensitive and specific method for the detection of B. pseudomallei, and can be used as a potential tool for melioidosis diagnose in basic, field and clinical laboratories. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02485-2.
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Affiliation(s)
- Xiaoxia Wang
- Central & Clinical Laboratory of Sanya People's Hospital, Hainan, 572000, Sanya, P. R. China
| | - Licheng Wang
- Central & Clinical Laboratory of Sanya People's Hospital, Hainan, 572000, Sanya, P. R. China
| | - Huaxiong Zhu
- Central & Clinical Laboratory of Sanya People's Hospital, Hainan, 572000, Sanya, P. R. China
| | - Chongzhen Wang
- Central & Clinical Laboratory of Sanya People's Hospital, Hainan, 572000, Sanya, P. R. China
| | - Xiong Zhu
- Central & Clinical Laboratory of Sanya People's Hospital, Hainan, 572000, Sanya, P. R. China.
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Genomic epidemiology links Burkholderia pseudomallei from individual human cases to B. pseudomallei from targeted environmental sampling in Northern Australia. J Clin Microbiol 2022; 60:e0164821. [PMID: 35080450 DOI: 10.1128/jcm.01648-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Each case of melioidosis results from a single event when a human is infected by the environmental bacterium Burkholderia pseudomallei. Darwin in tropical northern Australia has the highest incidences of melioidosis globally and the Darwin Prospective Melioidosis Study (DPMS) commenced in 1989, documenting all culture confirmed melioidosis cases. From 2000-2019 we sampled DPMS patient's environments for B. pseudomallei when a specific location was considered to have been where infection occurred. With the aim to use genomic epidemiology to understand B. pseudomallei transmission and infecting scenarios. Environmental sampling was performed at 98 DPMS patient sites, where we collected 975 environmental samples (742 soil; 233 water). Genotyping matched the clinical and epidemiologically linked environmental B. pseudomallei for 19 patients (19%), with the environmental isolates cultured from soil (n=11) or water (n=8) sources. B. pseudomallei isolates from patients and their local environments that matched on genotyping were whole genome sequenced (WGS). Of the 19 patients with a clinical-environmental genotype match, 17 pairs clustered on a Darwin core genome single-nucleotide polymorphism (SNP) phylogeny, later confirmed by single ST phylogenies and pairwise comparative genomics. When related back to patient clinical scenarios, the matched clinical and environmental B. pseudomallei pairs informed likely modes of infection: percutaneous inoculation, inhalation, and ingestion. Targeted environmental sampling for B. pseudomallei can inform infecting scenarios for melioidosis and dangerous occupational and recreational activities and identify hot spots of B. pseudomallei presence. However, WGS and careful genomics are required to avoid overcalling the relatedness between clinical and environmental isolates of B. pseudomallei.
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Hall CM, Baker AL, Sahl JW, Mayo M, Scholz HC, Kaestli M, Schupp J, Martz M, Settles EW, Busch JD, Sidak-Loftis L, Thomas A, Kreutzer L, Georgi E, Schweizer HP, Warner JM, Keim P, Currie BJ, Wagner DM. Expanding the Burkholderia pseudomallei Complex with the Addition of Two Novel Species: Burkholderia mayonis sp. nov. and Burkholderia savannae sp. nov. Appl Environ Microbiol 2022; 88:e0158321. [PMID: 34644162 PMCID: PMC8752149 DOI: 10.1128/aem.01583-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/04/2021] [Indexed: 11/20/2022] Open
Abstract
Distinct Burkholderia strains were isolated from soil samples collected in tropical northern Australia (Northern Territory and the Torres Strait Islands, Queensland). Phylogenetic analysis of 16S rRNA and whole genome sequences revealed these strains were distinct from previously described Burkholderia species and assigned them to two novel clades within the B. pseudomallei complex (Bpc). Because average nucleotide identity and digital DNA-DNA hybridization calculations are consistent with these clades representing distinct species, we propose the names Burkholderia mayonis sp. nov. and Burkholderia savannae sp. nov. Strains assigned to B. mayonis sp. nov. include type strain BDU6T (=TSD-80; LMG 29941; ASM152374v2) and BDU8. Strains assigned to B. savannae sp. nov. include type strain MSMB266T (=TSD-82; LMG 29940; ASM152444v2), MSMB852, BDU18, and BDU19. Comparative genomics revealed unique coding regions for both putative species, including clusters of orthologous genes associated with phage. Type strains of both B. mayonis sp. nov. and B. savannae sp. nov. yielded biochemical profiles distinct from each other and from other species in the Bpc, and profiles also varied among strains within B. mayonis sp. nov. and B. savannae sp. nov. Matrix-assisted laser desorption ionization time-of-flight (MLST) analysis revealed a B. savannae sp. nov. cluster separate from other species, whereas B. mayonis sp. nov. strains did not form a distinct cluster. Neither B. mayonis sp. nov. nor B. savannae sp. nov. caused mortality in mice when delivered via the subcutaneous route. The addition of B. mayonis sp. nov. and B. savannae sp. nov. results in a total of eight species currently within the Bpc. IMPORTANCEBurkholderia species can be important sources of novel natural products, and new species are of interest to diverse scientific disciplines. Although many Burkholderia species are saprophytic, Burkholderia pseudomallei is the causative agent of the disease melioidosis. Understanding the genomics and virulence of the closest relatives to B. pseudomallei, i.e., the other species within the B. pseudomallei complex (Bpc), is important for identifying robust diagnostic targets specific to B. pseudomallei and for understanding the evolution of virulence in B. pseudomallei. Two proposed novel species, B. mayonis sp. nov. and B. savannae sp. nov., were isolated from soil samples collected from multiple locations in northern Australia. The two proposed species belong to the Bpc but are phylogenetically distinct from all other members of this complex. The addition of B. mayonis sp. nov. and B. savannae sp. nov. results in a total of eight species within this significant complex of bacteria that are available for future studies.
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Affiliation(s)
- Carina M. Hall
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Anthony L. Baker
- Discipline of Biomedicine and Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Queensland, Australia
| | - Jason W. Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Mark Mayo
- Menzies School of Health Research, Darwin, Northern Territory, Australia
| | | | - Mirjam Kaestli
- Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - James Schupp
- Translational Genomics Research Institute, Flagstaff, Arizona, USA
| | - Madison Martz
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Erik W. Settles
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Joseph D. Busch
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Lindsay Sidak-Loftis
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Astrid Thomas
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - Lisa Kreutzer
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - Enrico Georgi
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - Herbert P. Schweizer
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Jeffrey M. Warner
- Discipline of Biomedicine and Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Queensland, Australia
| | - Paul Keim
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Bart J. Currie
- Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - David M. Wagner
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
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Saxena A, Pal V, Tripathi NK, Goel AK. A recombinase polymerase amplification lateral flow assay for rapid detection of Burkholderia pseudomallei, the causative agent of melioidosis. Braz J Microbiol 2022; 53:185-193. [PMID: 35006582 PMCID: PMC8882546 DOI: 10.1007/s42770-021-00669-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 12/24/2021] [Indexed: 01/12/2023] Open
Abstract
Burkholderia pseudomallei causes a fatal and infectious disease, melioidosis or Whitmore's disease in humans and animals. Melioidosis is present in different parts of the world and is endemic in Southeast Asia and Northern Australia. Accurate diagnosis of melioidosis is difficult due to its common flu-like symptoms, potentially long incubation period and erroneous identification as culture contaminant. Early diagnosis of the disease is essentially required for administration of suitable antibiotics and disease containment. The present study reports a rapid, specific and sensitive recombinase polymerase amplification lateral flow assay for detection of B. pseudomallei. Specific primers and probe were designed and the assay was performed at 41 °C for 20 min in a portable incubator. End products were detected using ready-to-use lateral flow strips. RPA lateral flow assay could detect ≥ 250 fg genomic DNA of B. pseudomallei and ≥ 50 copies of recombinant plasmid harbouring the target DNA sequence. The assay was found to be highly specific and did not cross-react with other bacterial strains. In artificially spiked human blood and urine samples, the detection limit of the assay was 4.8 × 104 and 4.95 × 104 CFU/mL of B. pseudomallei, respectively. The detection limit of assay after 6 h of enrichment of artificially spiked urine samples was found to be 4.95 × 103 CFU/mL of B. pseudomallei. Detection limit in artificially spiked tap water and soil samples was determined to be 7.5 × 102 CFU/mL and 3.3 × 104 CFU per 5 g of B. pseudomallei, respectively.
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Affiliation(s)
- Apoorva Saxena
- grid.418940.00000 0004 1803 2027Bioprocess Technology Division, Defence Research and Development Establishment, Jhansi Road, Gwalior, 474002 India
| | - Vijai Pal
- grid.418940.00000 0004 1803 2027Bioprocess Technology Division, Defence Research and Development Establishment, Jhansi Road, Gwalior, 474002 India
| | - Nagesh Kumar Tripathi
- grid.418940.00000 0004 1803 2027Bioprocess Technology Division, Defence Research and Development Establishment, Jhansi Road, Gwalior, 474002 India
| | - Ajay Kumar Goel
- grid.418940.00000 0004 1803 2027Bioprocess Technology Division, Defence Research and Development Establishment, Jhansi Road, Gwalior, 474002 India
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Chong YM, Chan YF, Jamaluddin MFH, Hasan MS, Pang YK, Ponnampalavanar S, Syed Omar SF, Voon KGL, Sam IC. Detection of respiratory viruses in adults with suspected COVID-19 in Kuala Lumpur, Malaysia. J Clin Virol 2021; 145:105000. [PMID: 34739838 PMCID: PMC8526124 DOI: 10.1016/j.jcv.2021.105000] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/05/2021] [Accepted: 10/16/2021] [Indexed: 12/24/2022]
Abstract
Background Reports of co-circulation of respiratory viruses during the COVID-19 pandemic and co-infections with SARS-CoV-2 vary. However, limited information is available from developing countries. Objectives We aimed to investigate the incidence of respiratory viruses in adult patients with suspected COVID-19 in Kuala Lumpur, Malaysia. Study Design We collected 198 respiratory samples from adult patients hospitalized with suspected COVID-19 in a single teaching hospital in Kuala Lumpur in February-May 2020 and tested combined oro-nasopharyngeal swabs with the NxTAG Respiratory Pathogen Panel (Luminex) and Allplex RV Essential (Seegene) assays. Forty-five negative samples further underwent viral metagenomics analysis. Results Of the 198 samples, 74 (37.4%) had respiratory pathogens, including 56 (28.3%) with SARS-CoV-2 and 18 (9.1%) positive for other respiratory pathogens. There were five (2.5%) SARS-CoV-2 co-infections, all with rhinovirus/enterovirus. Three samples (6.7%; 3/45) had viruses identified by metagenomics, including one case of enterovirus D68 and one of Saffold virus genotype 6 in a patient requiring ICU care. Most of the COVID-19 patients (91.1%; 51/56) had mild symptoms but 5.4% (3/56) died. Conclusion During the early COVID-19 period, common respiratory viruses other than SARS-CoV-2 only accounted for 9.1% of hospitalization cases with ARI and co-infections with SARS-CoV-2 were rare. Continued surveillance is important to understand the impact of COVID-19 and its associated public health control measures on circulation of other respiratory viruses. Metagenomics can identify unexpected or rare pathogens, such as Saffold virus, which is rarely described in adults.
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Affiliation(s)
- Yoong Min Chong
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Yoke Fun Chan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | | | - M Shahnaz Hasan
- Department of Anaesthesiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Yong Kek Pang
- Department of Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | | | | | - Kenny Gah Leong Voon
- Division of Pathology, International Medical University, 57000 Kuala Lumpur, Malaysia
| | - I-Ching Sam
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Medical Microbiology, University of Malaya Medical Centre, 59100 Kuala Lumpur, Malaysia.
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FRICKMANN HAGEN, POPPERT SVEN. No hints for abundance of Bacillus anthracis and Burkholderia pseudomallei in 100 environmental samples from Cameroon. Eur J Microbiol Immunol (Bp) 2021; 11:57-61. [PMID: 34478403 PMCID: PMC8614492 DOI: 10.1556/1886.2021.00014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 08/14/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Little is known on the abundance of the pathogens Bacillus anthracis and Burkholderia pseudomallei in environmental samples in Cameroon. Therefore, 100 respective samples were assessed in a proof-of-principle assessment. METHODS DNA residuals from nucleic acid extractions of 100 environmental samples, which were collected between 2011 and 2013 in the Mapé Basin of Cameroon, were screened for B. anthracis and B. pseudomallei by real-time PCR. The samples comprised soil samples with water contact (n = 88), soil samples without water contact (n = 6), plant material with water contact (n = 3), water (n = 2), and soil from a hospital dressing room (n = 1). RESULTS B. anthracis and B. pseudomallei were detected in none of the samples assessed. CONCLUSION The results indicate that at least a quantitatively overwhelming, ubiquitous occurrence of B. anthracis and B. pseudomallei in the environment in Cameroon is highly unlikely. However, the number and choice of the assessed samples limit the interpretability of the results.
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Affiliation(s)
- HAGEN FRICKMANN
- Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, Hamburg, Germany
- Institute for Medical Microbiology, Virology and Hygiene, University Hospital Rostock, Rostock, Germany
| | - SVEN POPPERT
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Faculty of Medicine, University Basel, Basel, Switzerland
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Win MM, Win KKN, Wah TT, Aye SN, Htwe TT, Zin KN, Aung MT, Aung WW, Ashley EA, Smithuis F, Rigas V, Currie BJ, Mayo M, Webb JR, Ling CL, Htun ZT, Dance DA. Enhanced melioidosis surveillance in patients attending four tertiary hospitals in Yangon, Myanmar. Epidemiol Infect 2021; 149:1-23. [PMID: 34158136 PMCID: PMC8276317 DOI: 10.1017/s095026882100128x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/21/2021] [Accepted: 06/01/2021] [Indexed: 11/05/2022] Open
Abstract
To investigate the current epidemiology of melioidosis in Yangon, Myanmar, between June 2017 and May 2019 we conducted enhanced surveillance for melioidosis in four tertiary hospitals in Yangon, where the disease was first discovered in 1911. Oxidase-positive Gram-negative rods were obtained from the microbiology laboratories and further analysed at the Department of Medical Research. Analysis included culture on Ashdown agar, the three disc sensitivity test (gentamicin, colistin and co-amoxiclav), latex agglutination, API 20 NE, antibiotic susceptibility testing, and a subset underwent molecular confirmation with a Burkholderia pseudomallei specific assay. Twenty one of 364 isolates (5.7%) were confirmed as B. pseudomallei and were mostly susceptible to the antibiotics used in standard therapy for melioidosis. Ten patients were from Yangon Region, nine were from Ayeyarwaddy region, and one each was from Kayin and Rakhine States. A history of soil contact was given by seven patients, five had diabetes mellitus and one had renal insufficiency. The patients presented with septicaemia (12 cases), pneumonia (three cases), urinary tract infection (two cases) and wound infection (four cases). Eighteen patients survived to hospital discharge. This study highlights the likelihood that melioidosis may be far more common, but underdiagnosed, in more rural parts of Myanmar as in other countries in SE Asia.
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Affiliation(s)
- Mo Mo Win
- Department of Medical Research, Yangon, Myanmar
| | | | | | | | | | | | | | | | - Elizabeth A. Ashley
- Myanmar-Oxford Clinical Research Unit, Yangon, Myanmar
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Frank Smithuis
- Myanmar-Oxford Clinical Research Unit, Yangon, Myanmar
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Vanessa Rigas
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Bart J. Currie
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Mark Mayo
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Jessica R. Webb
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Clare L. Ling
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Shoklo Malaria Research Unit, Mahidol Oxford Tropical Medicine Research Unit, Maesot, Thailand
| | | | - David A.B. Dance
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Vientiane, Lao PDR
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
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Cossaboom CM, Marinova-Petkova A, Strysko J, Rodriguez G, Maness T, Ocampo J, Gee JE, Elrod MG, Gulvik CA, Liu L, Bower WA, Hoffmaster AR, Blaney DD, Salzer JS, Yoder JS, Mattioli MC, Sidwa TJ, Ringsdorf L, Morrow G, Ledezma E, Kieffer A. Melioidosis in a Resident of Texas with No Recent Travel History, United States. Emerg Infect Dis 2021; 26:1295-1299. [PMID: 32442394 PMCID: PMC7258475 DOI: 10.3201/eid2606.190975] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
To our knowledge, environmental isolation of Burkholderia pseudomallei, the causative agent of melioidosis, from the continental United States has not been reported. We report a case of melioidosis in a Texas resident. Genomic analysis indicated that the isolate groups with B. pseudomallei isolates from patients in the same region, suggesting possible endemicity to this region.
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Wong Tzeling JM, Engku Nur Syafirah EAR, Irekeola AA, Yusof W, Aminuddin Baki NN, Zueter A, Harun A, Chan YY. One-step, multiplex, dual-function oligonucleotide of loop-mediated isothermal amplification assay for the detection of pathogenic Burkholderia pseudomallei. Anal Chim Acta 2021; 1171:338682. [PMID: 34112436 DOI: 10.1016/j.aca.2021.338682] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 11/18/2022]
Abstract
This study highlights the development of a multiplex real-time loop-mediated isothermal amplification assay. The developed assay employed a dual-function oligonucleotide (DFO) which simultaneously monitors the emitted amplification signals and accelerates the amplification process. The DFO was a modification of loop primer (LP); the 5'-end and 3'-end of the LP was tagged with fluorophore and quencher, respectively. The DFO was quenched in its unbound state and fluoresces only when it anneals to the specific target during the amplification process. With the same working mechanism as LP, DFO allowed the detection of target genes in less than 1 h in a real time monitoring system. We demonstrated this detection platform with Burkholderia pseudomallei, the causative agent of melioidosis. An internal amplification control (IAC) was incorporated in the assay to rule out false negative result and to demonstrate that the assay was successfully developed in a multiplex system. The assay was 100% specific when it was evaluated against 96 B. pseudomallei clinical isolates and 48 other bacteria species. The detection limit (sensitivity) of the developed assay was 1 fg/μl of B. pseudomallei genomic DNA and 18.2 CFU/ml at the bacterial cell level. In spiked blood samples, the assay's detection limit was 14 CFU/ml. The assay's diagnostic evaluation showed 100% diagnostic sensitivity, diagnostic specificity, positive predictive value, and negative predictive value. An integrated multiplex LAMP and real-time monitoring system was successfully developed, simplifying the workflow for the rapid and specific nucleic acid diagnostic test.
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Affiliation(s)
- Jilien Michelle Wong Tzeling
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.
| | - E A R Engku Nur Syafirah
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.
| | - Ahmad Adebayo Irekeola
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia; Microbiology Unit, Department of Biological Sciences, College of Natural and Applied Sciences, Summit University Offa, PMB 4412, Offa Kwara State, Nigeria.
| | - Wardah Yusof
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.
| | - Nurul Najian Aminuddin Baki
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.
| | - AbdelRahman Zueter
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia; Department of Medical Laboratory Sciences, Faculty of Applied Health Sciences, The Hashemite University, 13133, Zarqa, Jordan.
| | - Azian Harun
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia; Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia.
| | - Yean Yean Chan
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia; Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia.
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Swe MMM, Win MM, Cohen J, Phyo AP, Lin HN, Soe K, Amorncha P, Wah TT, Win KKN, Ling C, Parker DM, Dance DAB, Ashley EA, Smithuis F. Geographical distribution of Burkholderia pseudomallei in soil in Myanmar. PLoS Negl Trop Dis 2021; 15:e0009372. [PMID: 34029325 PMCID: PMC8143414 DOI: 10.1371/journal.pntd.0009372] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 04/07/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Burkholderia pseudomallei is a Gram-negative bacterium found in soil and water in many tropical countries. It causes melioidosis, a potentially fatal infection first described in 1911 in Myanmar. Melioidosis is a common cause of sepsis and death in South and South-east Asia, but it is rarely diagnosed in Myanmar. We conducted a nationwide soil study to identify areas where B. pseudomallei is present. METHODOLOGY/PRINCIPAL FINDINGS We collected soil samples from 387 locations in all 15 states and regions of Myanmar between September 2017 and June 2019. At each site, three samples were taken at each of three different depths (30, 60 and 90 cm) and were cultured for B. pseudomallei separately, along with a pooled sample from each site (i.e. 10 cultures per site). We used a negative binomial regression model to assess associations between isolation of B. pseudomallei and environmental factors (season, soil depth, soil type, land use and climate zones). B. pseudomallei was isolated in 7 of 15 states and regions. Of the 387 sites, 31 (8%) had one or more positive samples and of the 3,870 samples cultured, 103 (2.7%) tested positive for B. pseudomallei. B. pseudomallei was isolated more frequently during the monsoon season [RR-2.28 (95% CI: 0.70-7.38)] and less in the hot dry season [RR-0.70 (95% CI: 0.19-2.56)] compared to the cool dry season, and in the tropical monsoon climate zone [RR-2.26; 95% CI (0.21-6.21)] compared to the tropical dry winter climate zone. However, these associations were not statistically significant. B. pseudomallei was detected at all three depths and from various soil types (clay, silt and sand). Isolation was higher in agricultural land (2.2%), pasture land (8.5%) and disused land (5.8%) than in residential land (0.4%), but these differences were also not significant. CONCLUSION/SIGNIFICANCE This study confirms a widespread distribution of B. pseudomallei in Myanmar. Clinical studies should follow to obtain a better picture of the burden of melioidosis in Myanmar.
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Affiliation(s)
- Myo Maung Maung Swe
- Myanmar Oxford Clinical Research Unit, Yangon, Myanmar
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Mo Mo Win
- Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
| | - Joshua Cohen
- Myanmar Oxford Clinical Research Unit, Yangon, Myanmar
| | | | | | - Kyaw Soe
- Myanmar Oxford Clinical Research Unit, Yangon, Myanmar
| | - Premjit Amorncha
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University Bangkok, Thailand
| | - Thin Thin Wah
- Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
| | - Kyi Kyi Nyein Win
- Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
| | - Clare Ling
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Shoklo Malaria Research Unit (SMRU), Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Daniel M. Parker
- Department of Population Health and Disease Prevention Program in Public Health, University of California, Irvine, CA, United States of America
| | - David A. B. Dance
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Vientiane, Lao People’s Democratic Republic
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Elizabeth A. Ashley
- Myanmar Oxford Clinical Research Unit, Yangon, Myanmar
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Vientiane, Lao People’s Democratic Republic
| | - Frank Smithuis
- Myanmar Oxford Clinical Research Unit, Yangon, Myanmar
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
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Gassiep I, Burnard D, Bauer MJ, Norton RE, Harris PN. Diagnosis of melioidosis: the role of molecular techniques. Future Microbiol 2021; 16:271-288. [PMID: 33595347 DOI: 10.2217/fmb-2020-0202] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Melioidosis is an emerging infectious disease with an estimated global burden of 4.64 million disability-adjusted life years per year. A major determinant related to poor disease outcomes is delay to diagnosis due to the fact that identification of the causative agent Burkholderia pseudomallei may be challenging. Over the last 25 years, advances in molecular diagnostic techniques have resulted in the potential for rapid and accurate organism detection and identification direct from clinical samples. While these methods are not yet routine in clinical practice, laboratory diagnosis of infectious diseases is transitioning to culture-independent techniques. This review article aims to evaluate molecular methods for melioidosis diagnosis direct from clinical samples and discuss current and future utility and limitations.
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Affiliation(s)
- Ian Gassiep
- University of Queensland Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Herston, Queensland, 4029, Australia.,Department of Infectious Diseases, Mater Hospital Brisbane, South Brisbane, Queensland, 4101, Australia
| | - Delaney Burnard
- University of Queensland Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Herston, Queensland, 4029, Australia
| | - Michelle J Bauer
- University of Queensland Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Herston, Queensland, 4029, Australia
| | - Robert E Norton
- Pathology Queensland, Townsville University Hospital, Townsville, Queensland, 4814, Australia
| | - Patrick N Harris
- University of Queensland Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Herston, Queensland, 4029, Australia.,Pathology Queensland, Royal Brisbane & Women's Hospital, Herston, Queensland, 4029, Australia
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Using Land Runoff to Survey the Distribution and Genetic Diversity of Burkholderia pseudomallei in Vientiane, Laos. Appl Environ Microbiol 2021; 87:AEM.02112-20. [PMID: 33257313 PMCID: PMC7851688 DOI: 10.1128/aem.02112-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Melioidosis is a disease of significant public health importance that is being increasingly recognized globally. The majority of cases arise through direct percutaneous exposure to its etiological agent, Burkholderia pseudomallei In the Lao People's Democratic Republic (Laos), the presence and environmental distribution of B. pseudomallei are not well characterized, though recent epidemiological surveys of the bacterium have indicated that B. pseudomallei is widespread throughout the environment in the center and south of the country and that rivers can act as carriers and potential sentinels for the bacterium. The spatial and genetic distribution of B. pseudomallei within Vientiane Capital, from where the majority of cases diagnosed to date have originated, remains an important knowledge gap. We sampled surface runoff from drain catchment areas throughout urban Vientiane to determine the presence and local population structure of the bacterium. B. pseudomallei was detected in drainage areas throughout the capital, indicating it is widespread in the environment and that exposure rates in urban Vientiane are likely more frequent than previously thought. Whole-genome comparative analysis demonstrated that Lao B. pseudomallei isolates are highly genetically diverse, suggesting the bacterium is well-established and not a recent introduction. Despite the wide genome diversity, one environmental survey isolate was highly genetically related to a Lao melioidosis patient isolate collected 13 years prior to the study. Knowledge gained from this study will augment understanding of B. pseudomallei phylogeography in Asia and enhance public health awareness and future implementation of infection control measures within Laos.IMPORTANCE The environmental bacterium B. pseudomallei is the etiological agent of melioidosis, a tropical disease with one model estimating a global annual incidence of 165,000 cases and 89,000 deaths. In the Lao People's Democratic Republic (Laos), the environmental distribution and population structure of B. pseudomallei remain relatively undefined, particularly in Vientiane Capital from where most diagnosed cases have originated. We used surface runoff as a proxy for B. pseudomallei dispersal in the environment and performed whole-genome sequencing (WGS) to examine the local population structure. Our data confirmed that B. pseudomallei is widespread throughout Vientiane and that surface runoff might be useful for future environmental monitoring of the bacterium. B. pseudomallei isolates were also highly genetically diverse, suggesting the bacterium is well-established and endemic in Laos. These findings can be used to improve awareness of B. pseudomallei in the Lao environment and demonstrates the epidemiological and phylogeographical insights that can be gained from WGS.
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A Persisting Nontropical Focus of Burkholderia pseudomallei with Limited Genome Evolution over Five Decades. mSystems 2020; 5:5/6/e00726-20. [PMID: 33172968 PMCID: PMC7657595 DOI: 10.1128/msystems.00726-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Burkholderia pseudomallei is predominantly a tropical pathogen uncommonly found in the environment of temperate climatic regions. It is unclear if introduction into temperate regions is sporadic and temporary or if B. pseudomallei can persist in such environments. B. pseudomallei was identified in the environment of southwest Western Australia with melioidosis cases between 1966 and 1991. We report a new cluster with 23 animal fatalities in the same region from 2017, with B. pseudomallei again being recovered from the environment. Comparison of the isolates from the first and second clusters using genomics revealed a single sequence type, high clonality, and limited recombination, even though the time of recovery of the isolates spanned 51 years. This is a major contrast to the extensive genomic diversity seen in the tropics. Our data support the suggestion that B. pseudomallei has the ability to persist in nontropical environments, potentially in a latent state, and has the ability to activate following favorable conditions (rainfall) and then infect animals and humans. Burkholderia pseudomallei is the causative agent of the high-mortality disease melioidosis. Although melioidosis is classified as a tropical disease, rare autochthonous cases have been reported from temperate climatic regions, with uncertainty as to whether B. pseudomallei is persistent in the local environment and whether specific genetic mechanisms facilitate the survival of B. pseudomallei outside the tropics. Sporadic cases of melioidosis occurred in a valley region (latitude 31.6°S) in southwest Western Australia, Australia, between 1966 and 1992. We report a new melioidosis cluster in the same region following high rainfall in January 2017. More than 20 animals died, and B. pseudomallei was isolated from four alpacas, a parrot, and three environmental samples taken from the farm where the alpacas resided. Epidemiological data and genomics revealed that two locations on the farm were the probable sources of the alpaca infections. We determined that B. pseudomallei isolates from the 2017 cluster belonged to sequence type 284 (ST-284), as did all isolates recovered from 1966 to 1992. Genomic analysis confirmed that the ST-284 isolates were clonal and contained conserved genomic islands and limited evidence of recombination. We identified protein-coding regions unique to these isolates that might influence the persistence of B. pseudomallei in this temperate region. We demonstrate the environmental persistence of B. pseudomallei in a temperate region for over 50 years, with limited genetic changes suggesting a latent state and with activation, potential aerosolization, and local dispersal following unusually high rainfall. IMPORTANCEBurkholderia pseudomallei is predominantly a tropical pathogen uncommonly found in the environment of temperate climatic regions. It is unclear if introduction into temperate regions is sporadic and temporary or if B. pseudomallei can persist in such environments. B. pseudomallei was identified in the environment of southwest Western Australia with melioidosis cases between 1966 and 1991. We report a new cluster with 23 animal fatalities in the same region from 2017, with B. pseudomallei again being recovered from the environment. Comparison of the isolates from the first and second clusters using genomics revealed a single sequence type, high clonality, and limited recombination, even though the time of recovery of the isolates spanned 51 years. This is a major contrast to the extensive genomic diversity seen in the tropics. Our data support the suggestion that B. pseudomallei has the ability to persist in nontropical environments, potentially in a latent state, and has the ability to activate following favorable conditions (rainfall) and then infect animals and humans.
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Testamenti VA, Surya M, Saepuloh U, Iskandriati D, Tandang MV, Kristina L, Wahyudi AT, Sajuthi D, Santi VD, Patispathika FH, Wahyu M, Nurcahyo A, Pamungkas J. Characterization of Burkholderia pseudomallei from spontaneous melioidosis in a Bornean orangutan. Vet World 2020; 13:2459-2468. [PMID: 33363342 PMCID: PMC7750211 DOI: 10.14202/vetworld.2020.2459-2468] [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] [Received: 03/29/2020] [Accepted: 10/13/2020] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND AND AIM Melioidosis is a potentially fatal disease affecting humans and a wide range of animal species; it is often underdiagnosed and underreported in veterinary medicine in Indonesia. This study aimed to characterize morphological and molecular features of Burkholderia pseudomallei, the causative agent of melioidosis which caused the death of a Bornean orangutan. MATERIALS AND METHODS Pulmonary abscess samples were cultured on several types of media, including Ashdown agar, Ashdown broth, and MacConkey agar. Type three secretion system orf 2 real-time polymerase chain reaction (PCR) and latex agglutination tests were performed to identify the bacteria. Morphological characteristics were compared to all previously published morphotypes. Subsequently, the bacteria were characterized by multilocus sequence typing (MLST) and Yersinia-like flagellum/Burkholderia thailandensis-like flagellum and chemotaxis PCR. The results of the genotyping were afterward compared to all genotypes from Southeast Asia. RESULTS Multiple morphotypes of B. pseudomallei were perceived during the growth on Ashdown agar. Furthermore, it was identified by MLST that the Type I and Type II morphotypes observed in this study were clones of a single ST, ST54, which is predominantly found in humans and the environment in Malaysia and Thailand, although a very limited number of reports was published in association with animals. Moreover, the E-BURST analysis showed that the ST is grouped together with isolates from Southeast Asian countries, including Malaysia, Thailand, Singapore, and Cambodia. ST54 was predicted to be the founding genotype of several STs from those regions. CONCLUSION B. pseudomallei ST54 that caused the death of a Bornean orangutan has a distant genetic relationship with other STs which were previously reported in Indonesia, implying a vast genetic diversity in Indonesia that has not been discovered yet.
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Affiliation(s)
| | - Maryati Surya
- Primate Research Center, IPB University, Bogor 16128, Indonesia
| | - Uus Saepuloh
- Primate Research Center, IPB University, Bogor 16128, Indonesia
| | - Diah Iskandriati
- Primatology Graduate Study Program, Graduate School of IPB University, Bogor 16128, Indonesia
- Primate Research Center, IPB University, Bogor 16128, Indonesia
| | | | - Lia Kristina
- Borneo Orangutan Survival Foundation, Bogor 16128, Indonesia
| | - Aris Tri Wahyudi
- Department of Biology, Faculty of Mathematics and Natural Sciences, IPB University, Bogor 16680, Indonesia
| | - Dondin Sajuthi
- Primatology Graduate Study Program, Graduate School of IPB University, Bogor 16128, Indonesia
- Primate Research Center, IPB University, Bogor 16128, Indonesia
- Department of Clinics, Reproduction, and Pathology, Faculty of Veterinary Medicine, IPB University, Bogor 16680, Indonesia
| | - Vivi Dwi Santi
- Borneo Orangutan Survival Foundation, Bogor 16128, Indonesia
| | | | - Muhtadin Wahyu
- Borneo Orangutan Survival Foundation, Bogor 16128, Indonesia
| | - Anton Nurcahyo
- Borneo Orangutan Survival Foundation, Bogor 16128, Indonesia
| | - Joko Pamungkas
- Primatology Graduate Study Program, Graduate School of IPB University, Bogor 16128, Indonesia
- Primate Research Center, IPB University, Bogor 16128, Indonesia
- Department of Animal Infectious Diseases and Veterinary Public Health, Faculty of Veterinary Medicine, IPB University, Bogor 16680, Indonesia
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Stone NE, Hall CM, Browne AS, Sahl JW, Hutton SM, Santana-Propper E, Celona KR, Guendel I, Harrison CJ, Gee JE, Elrod MG, Busch JD, Hoffmaster AR, Ellis EM, Wagner DM. Burkholderia pseudomallei in Soil, US Virgin Islands, 2019. Emerg Infect Dis 2020; 26:2773-2775. [PMID: 33079041 PMCID: PMC7588534 DOI: 10.3201/eid2611.191577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The distribution of Burkholderia pseudomallei in the Caribbean is poorly understood. We isolated B. pseudomallei from US Virgin Islands soil. The soil isolate was genetically similar to other isolates from the Caribbean, suggesting that B. pseudomallei might have been introduced to the islands multiple times through severe weather events.
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Testamenti VA, Noviana R, Iskandriati D, Norris MH, Jiranantasak T, Tuanyok A, Wahyudi AT, Sajuthi D, Pamungkas J. Humoral Immune Responses to Burkholderia pseudomallei Antigens in Captive and Wild Macaques in the Western Part of Java, Indonesia. Vet Sci 2020; 7:E153. [PMID: 33050516 PMCID: PMC7712568 DOI: 10.3390/vetsci7040153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 02/07/2023] Open
Abstract
Burkholderia pseudomallei, the Gram-negative bacterium which causes melioidosis, is a threat to human and a wide range of animal species. There is an increased concern of melioidosis in Indonesian primate facilities, especially following case reports of fatal melioidosis in captive macaques and orangutans. Our preliminary serosurveillance of immunoglobulin G (IgG) to B. pseudomallei lipopolysaccharide showed that a significant number of captive and wild macaques in the western part of Java, Indonesia, have been exposed to B. pseudomallei. To better characterize the humoral immune response in those animals, a panel of assays were conducted on the same blood plasma specimens that were taken from 182 cynomolgus macaques (M. fascicularis) and 88 pig-tailed macaques (M. nemestrina) reared in captive enclosures and wild habitats in the western part of Java, Indonesia. The enzyme-linked immunosorbent assays (ELISAs) in this study were conducted to detect IgG against B. pseudomallei proteins; alkyl hydroperoxide reductase subunit C (AhpC), hemolysin-coregulated protein (Hcp1), and putative outer membrane porin protein (OmpH). The performances of those immunoassays were compared to ELISA against B. pseudomallei LPS, which has been conducted previously. Seropositivity to at least one assay was 76.4% (139/182) and 13.6% (12/88) in cynomolgus macaques and pig-tailed macaques, respectively. Analysis of demographic factors showed that species and primate facility were significant factors. Cynomolgus macaques had higher probability of exposure to B. pseudomallei. Moreover, macaques in Jonggol facility also had higher probability, compared to macaques in other facilities. There were no statistical associations between seropositivity with other demographic factors such as sex, age group, and habitat type. There were strong positive correlations between the absorbance results of AhpC, HcpI, and OmpH assays, but not with LPS assay. Our analysis suggested that Hcp1 assay would complement LPS assay in melioidosis serosurveillance in macaques.
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Affiliation(s)
- Vincentius Arca Testamenti
- Primatology Study Program, Graduate School of IPB University, Bogor, Jawa Barat 16128, Indonesia; (D.I.); (D.S.)
| | | | - Diah Iskandriati
- Primatology Study Program, Graduate School of IPB University, Bogor, Jawa Barat 16128, Indonesia; (D.I.); (D.S.)
- Primate Research Center, IPB University, Bogor, Jawa Barat 16128, Indonesia;
| | - Michael H. Norris
- Spatial Epidemiology & Ecology Research Laboratory, Department of Geography, University of Florida, Gainesville, FL 32611, USA;
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA; (T.J.); (A.T.)
| | - Treenate Jiranantasak
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA; (T.J.); (A.T.)
- Department of Infectious Diseases and Immunology, University of Florida, Gainesville, FL 32610, USA
| | - Apichai Tuanyok
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA; (T.J.); (A.T.)
- Department of Infectious Diseases and Immunology, University of Florida, Gainesville, FL 32610, USA
| | - Aris Tri Wahyudi
- Department of Biology, Faculty of Mathematics and Natural Sciences, IPB University, Bogor, Jawa Barat 16680, Indonesia;
| | - Dondin Sajuthi
- Primatology Study Program, Graduate School of IPB University, Bogor, Jawa Barat 16128, Indonesia; (D.I.); (D.S.)
- Primate Research Center, IPB University, Bogor, Jawa Barat 16128, Indonesia;
- Department of Clinics, Reproduction, and Pathology, Faculty of Veterinary Medicine, IPB University, Bogor, Jawa Barat 16680, Indonesia
| | - Joko Pamungkas
- Primatology Study Program, Graduate School of IPB University, Bogor, Jawa Barat 16128, Indonesia; (D.I.); (D.S.)
- Primate Research Center, IPB University, Bogor, Jawa Barat 16128, Indonesia;
- Department of Animal Infectious Diseases and Veterinary Public Health, Faculty of Veterinary Medicine, IPB University, Bogor, Jawa Barat 16680, Indonesia
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O'Connor C, Kenna D, Walsh A, Zamarreño DV, Dance D. Imported melioidosis in the United Kingdom: Increasing incidence but continued under-reporting. CLINICAL INFECTION IN PRACTICE 2020. [DOI: 10.1016/j.clinpr.2020.100051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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Webb JR, Win MM, Zin KN, Win KKN, Wah TT, Ashley EA, Smithuis F, Swe MMM, Mayo M, Currie BJ, Dance DAB. Myanmar Burkholderia pseudomallei strains are genetically diverse and originate from Asia with phylogenetic evidence of reintroductions from neighbouring countries. Sci Rep 2020; 10:16260. [PMID: 33004984 PMCID: PMC7530998 DOI: 10.1038/s41598-020-73545-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/11/2020] [Indexed: 02/08/2023] Open
Abstract
Melioidosis was first identified in Myanmar in 1911 but for the last century it has remained largely unreported there. Burkholderia pseudomallei was first isolated from the environment of Myanmar in 2016, confirming continuing endemicity. Recent genomic studies showed that B. pseudomallei originated in Australia and spread to Asia, with phylogenetic evidence of repeated reintroduction of B. pseudomallei across countries bordered by the Mekong River and the Malay Peninsula. We present the first whole-genome sequences of B. pseudomallei isolates from Myanmar: nine clinical and seven environmental isolates. We used large-scale comparative genomics to assess the genetic diversity, phylogeography and potential origins of B. pseudomallei in Myanmar. Global phylogenetics demonstrated that Myanmar isolates group in two distantly related clades that reside in a more ancestral Asian clade with high amounts of genetic diversity. The diversity of B. pseudomallei from Myanmar and divergence within our global phylogeny suggest that the original introduction of B. pseudomallei to Myanmar was not a recent event. Our study provides new insights into global patterns of B. pseudomallei dissemination, most notably the dynamic nature of movement of B. pseudomallei within densely populated Southeast Asia. The role of anthropogenic influences in both ancient and more recent dissemination of B. pseudomallei to Myanmar and elsewhere in Southeast Asia and globally requires further study.
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Affiliation(s)
- Jessica R Webb
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia.
| | - Mo Mo Win
- Department of Medical Research, Yangon, Myanmar
| | - Khwar Nyo Zin
- Microbiology Laboratory, Yangon General Hospital, Yangon, Myanmar
| | | | | | - Elizabeth A Ashley
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
- Myanmar-Oxford Clinical Research Unit, Yangon, Myanmar
| | - Frank Smithuis
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
- Myanmar-Oxford Clinical Research Unit, Yangon, Myanmar
| | - Myo Maung Maung Swe
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Mark Mayo
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Bart J Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- Department of Infectious Diseases and Northern Territory Medical Program, Royal Darwin Hospital, Darwin, NT, Australia
| | - David A B Dance
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
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Saiprom N, Sangsri T, Tandhavanant S, Sengyee S, Phunpang R, Preechanukul A, Surin U, Tuanyok A, Lertmemongkolchai G, Chantratita W, West TE, Chantratita N. Genomic loss in environmental and isogenic morphotype isolates of Burkholderia pseudomallei is associated with intracellular survival and plaque-forming efficiency. PLoS Negl Trop Dis 2020; 14:e0008590. [PMID: 32991584 PMCID: PMC7546507 DOI: 10.1371/journal.pntd.0008590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 10/09/2020] [Accepted: 07/13/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Burkholderia pseudomallei is an environmental bacterium that causes melioidosis. A facultative intracellular pathogen, B. pseudomallei can induce multinucleated giant cells (MNGCs) leading to plaque formation in vitro. B. pseudomallei can switch colony morphotypes under stress conditions. In addition, different isolates have been reported to have varying virulence in vivo, but genomic evolution and the relationship with plaque formation is poorly understood. METHODOLOGY/PRINCIPLE FINDINGS To gain insights into genetic underpinnings of virulence of B. pseudomallei, we screened plaque formation of 52 clinical isolates and 11 environmental isolates as well as 4 isogenic morphotype isolates of B. pseudomallei strains K96243 (types II and III) and 153 (types II and III) from Thailand in A549 and HeLa cells. All isolates except one environmental strain (A4) and K96243 morphotype II were able to induce plaque formation in both cell lines. Intracellular growth assay and confocal microscopy analyses demonstrated that the two plaque-forming-defective isolates were also impaired in intracellular replication, actin polymerization and MNGC formation in infected cells. Whole genome sequencing analysis and PCR revealed that both isolates had a large genomic loss on the same region in chromosome 2, which included Bim cluster, T3SS-3 and T6SS-5 genes. CONCLUSIONS/SIGNIFICANCE Our plaque screening and genomic studies revealed evidence of impairment in plaque formation in environmental isolates of B. pseudomallei that is associated with large genomic loss of genes important for intracellular multiplication and MNGC formation. These findings suggest that the genomic and phenotypic differences of environmental isolates may be associated with clinical infection.
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Affiliation(s)
- Natnaree Saiprom
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Tanes Sangsri
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Microbiology, Princess of Naradhiwas University, Narathiwat, Thailand
| | - Sarunporn Tandhavanant
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sineenart Sengyee
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rungnapa Phunpang
- 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
| | - Anucha Preechanukul
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Uriwan Surin
- Department of Medical Laboratory, Nakhon Phanom Hospital, Nakhon Phanom, Thailand
| | - Apichai Tuanyok
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States of America
| | - Ganjana Lertmemongkolchai
- Centre for Research and Development of Medical Diagnostic Laboratories, Department of Clinical Immunology, Faculty of Associated Medical Science, Khon Kaen University, Khon Kaen, Thailand
| | - Wasun Chantratita
- Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - T. Eoin West
- Division of Pulmonary, Critical Care & Sleep Medicine, Harborview Medical Center, University of Washington, Seattle, WA, United States of America
| | - 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
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47
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Adapting Microarray Gene Expression Signatures for Early Melioidosis Diagnosis. J Clin Microbiol 2020; 58:JCM.01906-19. [PMID: 32350042 DOI: 10.1128/jcm.01906-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 04/17/2020] [Indexed: 12/24/2022] Open
Abstract
Melioidosis is caused by Burkholderia pseudomallei and is predominantly seen in tropical regions. The clinical signs and symptoms of the disease are nonspecific and often result in misdiagnosis, failure of treatment, and poor clinical outcome. Septicemia with septic shock is the most common cause of death, with mortality rates above 40%. Bacterial culture is the gold standard for diagnosis, but it has low sensitivity and takes days to produce definitive results. Early laboratory diagnosis can help guide physicians to provide treatment specific to B. pseudomallei In our study, we adapted host gene expression signatures obtained from microarray data of B. pseudomallei-infected cases to develop a real-time PCR diagnostic test using two differentially expressed genes, AIM2 (absent in melanoma 2) and FAM26F (family with sequence similarity 26, member F). We tested blood from 33 patients with B. pseudomallei infections and 29 patients with other bacterial infections to validate the test and determine cutoff values for use in a cascading diagnostic algorithm. Differentiation of septicemic melioidosis from other sepsis cases had a sensitivity of 82%, specificity of 93%, and negative and positive predictive values (NPV and PPV) of 82% and 93%, respectively. Separation of cases likely to be melioidosis from those unlikely to be melioidosis in nonbacteremic situations showed a sensitivity of 40%, specificity of 54%, and NPV and PPV of 44% and 50%, respectively. We suggest that our AIM2 and FAM26F expression combination algorithm could be beneficial for early melioidosis diagnosis, offering a result within 24 h of admission.
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48
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Chua KH, Tan EW, Chai HC, Puthucheary SD, Lee PC, Puah SM. Rapid identification of melioidosis agent by an insulated isothermal PCR on a field-deployable device. PeerJ 2020; 8:e9238. [PMID: 32518734 PMCID: PMC7261116 DOI: 10.7717/peerj.9238] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/05/2020] [Indexed: 12/17/2022] Open
Abstract
Background Burkholderia pseudomallei causes melioidosis, a serious illness that can be fatal if untreated or misdiagnosed. Culture from clinical specimens remains the gold standard but has low diagnostic sensitivity. Method In this study, we developed a rapid, sensitive and specific insulated isothermal Polymerase Chain Reaction (iiPCR) targeting bimA gene (Burkholderia Intracellular Motility A; BPSS1492) for the identification of B. pseudomallei. A pair of novel primers: BimA(F) and BimA(R) together with a probe were designed and 121 clinical B. pseudomallei strains obtained from numerous clinical sources and 10 ATCC non-targeted strains were tested with iiPCR and qPCR in parallel. Results All 121 B. pseudomallei isolates were positive for qPCR while 118 isolates were positive for iiPCR, demonstrating satisfactory agreement (97.71%; 95% CI [93.45–99.53%]; k = 0.87). Sensitivity of the bimA iiPCR/POCKIT assay was 97.52% with the lower detection limit of 14 ng/µL of B. pseudomallei DNA. The developed iiPCR assay did not cross-react with 10 types of non-targeted strains, indicating good specificity. Conclusion This bimA iiPCR/POCKIT assay will undoubtedly complement other methodologies used in the clinical laboratory for the rapid identification of this pathogen.
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Affiliation(s)
- Kek Heng Chua
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - E Wei Tan
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Hwa Chia Chai
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - S D Puthucheary
- Faculty of Medicine, University of Malaya, University of Malaya, Kuala Lumpur, Malaysia
| | - Ping Chin Lee
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah, Malaysia
| | - Suat Moi Puah
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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49
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Choi JY, Hii KC, Bailey ES, Chuang JY, Tang WY, Yuen Wong EK, Ti T, Pau KS, Berita A, Saihidi I, Ting J, Chua TT, Toh TH, AuCoin DP, DeShazer D, Gray GC. Burkholderia pseudomallei Detection among Hospitalized Patients, Sarawak. Am J Trop Med Hyg 2020; 102:388-391. [PMID: 31769397 DOI: 10.4269/ajtmh.19-0625] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Burkholderia pseudomallei infections are prevalent in Southeast Asia and northern Australia and often misdiagnosed. Diagnostics are often neither sensitive nor rapid, contributing up to 50% mortality rate. In this 2018 pilot study, we enrolled 100 patients aged 6 months-79 years from Kapit Hospital in Sarawak, Malaysia, with symptoms of B. pseudomallei infection. We used three different methods for the detection of B. pseudomallei: a real-time polymerase chain reaction (PCR) assay, a rapid lateral flow immunoassay, and the standard-of-care bacterial culture-the gold standard. Among the 100 participants, 24 (24%) were positive for B. pseudomallei by one or more of the detection methods. Comparing the two individual diagnostic methods against the gold standard-bacterial culture-of any positive test, there was low sensitivity for each test (25-44%) but high specificity (93-98%). It seems clear that more sensitive diagnostics or a sensitive screening diagnostic followed by specific confirmatory diagnostic is needed for this disease.
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Affiliation(s)
- Jessica Y Choi
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina.,Duke Global Health Institute, Duke University, Durham, North Carolina
| | - King Ching Hii
- Kapit Hospital, Ministry of Health Malaysia, Kapit, Sarawak, Malaysia
| | - Emily S Bailey
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina.,Duke Global Health Institute, Duke University, Durham, North Carolina
| | - Jia Yun Chuang
- Kapit Hospital, Ministry of Health Malaysia, Kapit, Sarawak, Malaysia
| | - Wei Yieng Tang
- Kapit Hospital, Ministry of Health Malaysia, Kapit, Sarawak, Malaysia
| | | | - Tiana Ti
- Kapit Hospital, Ministry of Health Malaysia, Kapit, Sarawak, Malaysia
| | - Kat Siong Pau
- Kapit Hospital, Ministry of Health Malaysia, Kapit, Sarawak, Malaysia
| | - Antoinette Berita
- Kapit Hospital, Ministry of Health Malaysia, Kapit, Sarawak, Malaysia
| | - Izreena Saihidi
- Kapit Hospital, Ministry of Health Malaysia, Kapit, Sarawak, Malaysia
| | - Jakie Ting
- Faculty of Medicine, SEGi University, Kota Damansara, Malaysia.,Clinical Research Center, Sibu Hospital, Ministry of Health Malaysia, Sibu, Sarawak, Malaysia
| | - Tiing-Tiing Chua
- Clinical Research Center, Sibu Hospital, Ministry of Health Malaysia, Sibu, Sarawak, Malaysia
| | - Teck-Hock Toh
- Faculty of Medicine, SEGi University, Kota Damansara, Malaysia.,Clinical Research Center, Sibu Hospital, Ministry of Health Malaysia, Sibu, Sarawak, Malaysia
| | | | - David DeShazer
- US Army Medical Research Institute of Infectious Diseases, Ft. Detrick, Maryland
| | - Gregory C Gray
- Emerging Infectious Diseases Program, Duke-NUS Medical School, Singapore.,Duke Global Health Institute, Duke University, Durham, North Carolina.,Global Health Research Center, Duke-Kunshan University, Kunshan, China.,Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina
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50
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Whole-genome sequencing of Burkholderia pseudomallei from an urban melioidosis hot spot reveals a fine-scale population structure and localised spatial clustering in the environment. Sci Rep 2020; 10:5443. [PMID: 32214186 PMCID: PMC7096523 DOI: 10.1038/s41598-020-62300-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 12/17/2019] [Indexed: 11/12/2022] Open
Abstract
Melioidosis is a severe disease caused by the environmental bacterium Burkholderia pseudomallei that affects both humans and animals throughout northern Australia, Southeast Asia and increasingly globally. While there is a considerable degree of genetic diversity amongst isolates, B. pseudomallei has a robust global biogeographic structure and genetic populations are spatially clustered in the environment. We examined the distribution and local spread of B. pseudomallei in Darwin, Northern Territory, Australia, which has the highest recorded urban incidence of melioidosis globally. We sampled soil and land runoff throughout the city centre and performed whole-genome sequencing (WGS) on B. pseudomallei isolates. By combining phylogenetic analyses, Bayesian clustering and spatial hot spot analysis our results demonstrate that some sequence types (STs) are widespread in the urban Darwin environment, while others are highly spatially clustered over a small geographic scale. This clustering matches the spatial distribution of clinical cases for one ST. Results also demonstrate a greater overall isolate diversity recovered from drains compared to park soils, further supporting the role drains may play in dispersal of B. pseudomallei STs in the environment. Collectively, knowledge gained from this study will allow for better understanding of B. pseudomallei phylogeography and melioidosis source attribution, particularly on a local level.
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