1
|
Appelt S, Rohleder AM, Jacob D, von Buttlar H, Georgi E, Mueller K, Wernery U, Kinne J, Joseph M, Jose SV, Scholz HC. Genetic diversity and spatial distribution of Burkholderia mallei by core genome-based multilocus sequence typing analysis. PLoS One 2022; 17:e0270499. [PMID: 35793321 PMCID: PMC9258848 DOI: 10.1371/journal.pone.0270499] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/10/2022] [Indexed: 11/18/2022] Open
Abstract
Burkholderia mallei is the etiological agent of glanders, a highly contagious and often fatal disease in equids. Due to the high genetic clonality of B. mallei, high-resolution typing assays are necessary to differentiate between individual strains. Here we report on the development and validation of a robust and reproducible core genome-based Multi Locus Sequence Typing Assay (cgMLST) for B. mallei, which is based on 3328 gene targets and enables high-resolution typing at the strain level. The assay was validated using a set of 120 B. mallei genomes from public databases and 23 newly sequenced outbreak strains from in-house strain collections. In this cgMLST analysis, strains from different geographic regions were clearly distinguished by at least 70 allele differences, allowing spatial clustering while closely related and epidemiologically related strains were separated by only zero to three alleles. Neither the different sequencing technologies nor the assembly strategies had an influence on the cgMLST results. The developed cgMLST is highly robust, reproducible and can be used for outbreak investigations, source tracking and molecular characterization of new B. mallei isolates.
Collapse
Affiliation(s)
- Sandra Appelt
- Centre for Biological Threats and Special Pathogens (ZBS 2), Robert Koch Institute, Berlin, Germany
| | - Anna-Maria Rohleder
- Centre for Biological Threats and Special Pathogens (ZBS 2), Robert Koch Institute, Berlin, Germany
| | - Daniela Jacob
- Centre for Biological Threats and Special Pathogens (ZBS 2), Robert Koch Institute, Berlin, Germany
| | - Heiner von Buttlar
- Bundeswehr Institute of Microbiology, Department Bacteriology and Toxinology, Munich, Germany
| | - Enrico Georgi
- Bundeswehr Institute of Microbiology, Department Bacteriology and Toxinology, Munich, Germany
| | - Katharina Mueller
- Bundeswehr Institute of Microbiology, Department Bacteriology and Toxinology, Munich, Germany
| | - Ulrich Wernery
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates
| | - Joerg Kinne
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates
| | - Marina Joseph
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates
| | | | - Holger C. Scholz
- Centre for Biological Threats and Special Pathogens (ZBS 2), Robert Koch Institute, Berlin, Germany
- Bundeswehr Institute of Microbiology, Department Bacteriology and Toxinology, Munich, Germany
- * E-mail:
| |
Collapse
|
2
|
Zheng H, Qin J, Chen H, Hu H, Zhang X, Yang C, Wu Y, Li Y, Li S, Kuang H, Zhou H, Shen D, Song K, Song Y, Zhao T, Yang R, Tan Y, Cui Y. Genetic diversity and transmission patterns of Burkholderia pseudomallei on Hainan island, China, revealed by a population genomics analysis. Microb Genom 2021; 7. [PMID: 34762026 PMCID: PMC8743561 DOI: 10.1099/mgen.0.000659] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Burkholderia pseudomallei is a Gram-negative soil-dwelling bacillus that causes melioidosis, a frequently fatal infectious disease, in tropical and subtropical regions. Previous studies have identified the overall genetic and evolutionary characteristics of B. pseudomallei on a global scale, including its origin and transmission routes. However, beyond its known hyperendemicity foci in northern Australia and Southeast Asia, the distribution and genetic characteristics of B. pseudomallei in most tropical regions remain poorly understood, including in southern China. Here, we sequenced the genomes of 122 B. pseudomallei strains collected from Hainan, an island in southern China, in 2002–2018, to investigate the population structure, relationships with global strains, local epidemiology, and virulence and antimicrobial-resistance factors. A phylogenetic analysis and hierarchical clustering divided the Hainan strains into nine phylogenic groups (PGs), 80 % of which were concentrated within five major groups (group 1: corresponding to minor sequence types [STs], 12.3 %; group 3: ST46 and ST50, 31.1 %; group 9: ST58, 13.1 %; group 11: ST55, 8.2 %; group 15: mainly ST658, 15.6%). A phylogenetic analysis that included global strains suggested that B. pseudomallei in Hainan originated from Southeast Asian countries, transmitted in multiple historical importation events. We also identified several mutual transmission events between Hainan and Southeast Asian countries in recent years, including three importation events from Thailand and Singapore to Hainan and three exportation events from Hainan to Singapore, Malaysia, and Taiwan island. A statistical analysis of the temporal distribution showed that the Hainan strains of groups 3, 9, and 15 have dominated the disease epidemic locally in the last 5 years. The spatial distribution of the Hainan strains demonstrated that some PGs are distributed in different cities on Hainan island, and by combining phylogenic and geographic distribution information, we detected 21 between-city transmission events, indicating its frequent local transmission. The detection of virulence factor genes showed that 56 % of the Hainan strains in group 1 encode a B. pseudomallei-specific adherence factor, boaB, confirming the specific pathogenic characteristics of the Hainan strains in group 1. An analysis of the antimicrobial-resistance potential of B. pseudomallei showed that various kinds of alterations were identified in clinically relevant antibiotic resistance factors, such as AmrR, PenA and PBP3, etc. Our results clarify the population structure, local epidemiology, and pathogenic characteristics of B. pseudomallei in Hainan, providing further insight into its regional and global transmission networks and improving our knowledge of its global phylogeography.
Collapse
Affiliation(s)
- Hongyuan Zheng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Jingliang Qin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China.,School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui Province, 230032, PR China
| | - Hai Chen
- Department of Clinical Laboratory, Sanya People's Hospital, Sanya, Hainan Province, 572000, PR China
| | - Hongyan Hu
- Department of Laboratory Medicine, Hainan Hospital of Chinese PLA General Hospital, Sanya, Hainan Province, 572000, PR China
| | - Xianglilan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Chao Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Yarong Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Yuanli Li
- Department of Clinical Laboratory, Sanya People's Hospital, Sanya, Hainan Province, 572000, PR China
| | - Sha Li
- Department of Clinical Laboratory, Sanya People's Hospital, Sanya, Hainan Province, 572000, PR China
| | - Huihui Kuang
- Department of Laboratory Medicine, Hainan Hospital of Chinese PLA General Hospital, Sanya, Hainan Province, 572000, PR China
| | - Hanwang Zhou
- Department of Laboratory Medicine, Hainan Hospital of Chinese PLA General Hospital, Sanya, Hainan Province, 572000, PR China
| | - Dingxia Shen
- Department of Laboratory Medicine, Hainan Hospital of Chinese PLA General Hospital, Sanya, Hainan Province, 572000, PR China
| | - Kai Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Tongyan Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Yafang Tan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China.,School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui Province, 230032, PR China
| |
Collapse
|
3
|
Zhu X, Chen H, Li S, Wang LC, Wu DR, Wang XM, Chen RS, Li ZJ, Liu ZG. Molecular Characteristics of Burkholderia pseudomallei Collected From Humans in Hainan, China. Front Microbiol 2020; 11:778. [PMID: 32457710 PMCID: PMC7223694 DOI: 10.3389/fmicb.2020.00778] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 04/01/2020] [Indexed: 12/21/2022] Open
Abstract
Melioidosis is a common infectious disease in Southeast Asia and Northern Australia. In Hainan, several cases have been reported, but no systematic study has yet been done on the molecular epidemiology profiles of the organism. An investigation of the molecular epidemiology links and population structure of Burkholderia pseudomallei would help to better understand the clonally of the isolates and differences among them. In this study, multilocus variable-number tandem repeat analysis (MLVA), and multilocus sequence typing (MLST) were applied to examine the epidemiological relatedness and population structure of 166 B. pseudomallei isolates obtained during 2002–2014 in Hainan, China. Both the MLVA_4 and MLST approaches had high discriminatory power for this population, with diversity indices of 0.9899 and 0.9457, respectively. However, the MLVA_4 assay showed a higher discriminatory power than the MLST approach, and a variable-number tandem repeat (VNTR3 933) found by the MLVA approach was the most useful in discriminating strains from this province. A total of 166 strains yielded 99 MLVA_4 genotypes, of which 34 genotypes were shared by 101 isolates, for a clustering rate of 60.8% (101/166), which suggested that some cases may have a common source. Additionally, 65 isolates showed distinct genotypes, indicating that more than 39.2% (65/166) of melioidosis cases in Hainan had epidemiologically unrelated or sporadic characteristics. The 166 isolates were resolved into 48 STs, of which five STs (ST55, -70, -46, -50, and -58) were here found to be predominant. Phylogenetic analysis of 116 isolates conducted using the eBURST v3 segregated the 48 STs into eight groups with ST50 as predicted founder, and 21 STs were found to be singletons, which suggest that the strains in the Hainan region represent a high diversity of ST clones, indicating that many B. pseudomallei clone groups are endemic to this region. Moreover, ST50 had 5 SLV, 7 DLV, 6 TLV, and 29 satellite STs and formed a radial expansion pattern, suggesting that the melioidosis epidemic in this study was mainly caused by the clonal expansion of ST 50. Phylogenetic analysis on global scale suggests that China’s isolates are closely related to isolates from Southeast Asia, particularly from Thailand and Malaysia.
Collapse
Affiliation(s)
- Xiong Zhu
- Sanya People's Hospital, Sanya, China
| | - Hai Chen
- Sanya People's Hospital, Sanya, China
| | - Sha Li
- Sanya People's Hospital, Sanya, China
| | | | | | | | - Ru-Shou Chen
- The Third People's Hospital of Hainan Province, Sanya, China
| | - Zhen-Jun Li
- State Key Laboratory for Infectious Disease Prevention and Control, China Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Zhi-Guo Liu
- Sanya People's Hospital, Sanya, China.,State Key Laboratory for Infectious Disease Prevention and Control, China Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| |
Collapse
|
4
|
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.
Collapse
|
5
|
Merritt AJ, Peck M, Gayle D, Levy A, Ler YH, Raby E, Gibbs TM, Inglis TJJ. Cutaneous Melioidosis Cluster Caused by Contaminated Wound Irrigation Fluid. Emerg Infect Dis 2018; 22. [PMID: 27438887 PMCID: PMC4982149 DOI: 10.3201/eid2208.151149] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Burkholderia pseudomallei can cause healthcare-associated infections outside its recognized tropical zone. Melioidosis usually occurs after environmental exposure to Burkholderia pseudomallei in the tropics. A cluster of 5 cutaneous melioidosis cases occurred in suburban southwest Australia after an earlier case in January 2012. We collected environmental samples at the first patient’s home in January 2012 and from a nearby health center in December 2013 after 2 new cases occurred in the same postal district. We isolated genotypically identical B. pseudomallei from the first patient and 5 other patients in the district. Environmental sampling implicated an opened bottle of saline wound irrigation fluid containing >106B. pseudomallei/mL. The bottle included instructions to discard within 24 hours of opening. No further cases of B. pseudomallei infection occurred after removing the contaminated bottle. This cutaneous melioidosis cluster demonstrates that B. pseudomallei can survive and disseminate in widely used medical fluids beyond its known geographic distribution, highlighting a need to use these products according to manufacturers’ instructions.
Collapse
|
6
|
Nejati F, Fateh A, Nojoumi SA, Rahbar M, Behrouzi A, Vaziri F, Siadat SD. MLVA typing of Haemophilus influenzae isolated from two Iranian university hospitals. IRANIAN JOURNAL OF MICROBIOLOGY 2018; 10:30-36. [PMID: 29922416 PMCID: PMC6004631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND AND OBJECTIVES Different serotypes of Haemophilus influenzae is now divided into 2 divisions: encapsulated and unencapsulated. Multiple locus variable number tandem repeat analysis (MLVA) includes such specifications as the extra power of separation, ease of data interpretation, and epidemiological data accordance, which have made it an appropriate molecular device for good typing and phylogenetic analysis of bacterial pathogens. MATERIALS AND METHODS In this research, cultured samples were studied and strains identified through biochemical tests were recognized. Moreover, DNA was extracted and studied qualitatively and quantitatively. Four pairs of specialized primers related to H. influenzae variable number tandem repeats (VNTR) and preparation of PCR were designed according to the regulated program. Also, electrophoresis of PCR products was performed. Finally, the interpretation of electrophoresis gel was done with respect to the observable bands showing the presence or absence of the required sequence in the samples related to every primer. RESULTS This study was the first MLVA typing of the unencapsulated H. influenzae in Iran. In this research, the VNTR sequences were tested in 30 strains without the unencapsulated H. influenzae. Among 30 mentioned strains, for which MLVA profile was obtained in this research, 25 different MLVA types were observed. Likewise, there was no repetition in VNTR sequences resulting from PCR in few H. influenzae. In all these cases, the number of repetitions in MLVA profile was determined as 0, except for one of the primers in 4 strains, which was 16%. However, this did not occur for the other VNTRs. CONCLUSION The highest diversity of the repeats was for VNTR5 (7 types), followed by VNTR6 with 6 types of repeats, and VNTR12-1 and VNTR12-2 with 3 different types.
Collapse
Affiliation(s)
- Faranak Nejati
- Department of Mycobacteriology & Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology & Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Ali Nojoumi
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Rahbar
- Department of Microbiology, Reference Health Laboratories Research Center, Ministry of Health and Medical Education, Tehran, Iran
| | - Ava Behrouzi
- Department of Mycobacteriology & Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Farzam Vaziri
- Department of Mycobacteriology & Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran,Corresponding authors: Farzam Vaziri & Seyed Davar Siadat, PhD, Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran. Tel: +982166968853, Fax: +982166496721
| | - Seyed Davar Siadat
- Department of Mycobacteriology & Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran,Corresponding authors: Farzam Vaziri & Seyed Davar Siadat, PhD, Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran. Tel: +982166968853, Fax: +982166496721
| |
Collapse
|
7
|
Zueter AR, Rahman ZA, Abumarzouq M, Harun A. Multilocus sequence types of clinical Burkholderia pseudomallei isolates from peninsular Malaysia and their associations with disease outcomes. BMC Infect Dis 2018; 18:5. [PMID: 29291714 PMCID: PMC5748966 DOI: 10.1186/s12879-017-2912-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 12/13/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Previous studies on the Burkholderia pseudomallei genetic diversity among clinical isolates from melioidosis-endemic areas have identified genetic factors contributing to differential virulence. Although it has been ruled out in Australian and Thai B. pseudomallei populations, it remains unclear whether B. pseudomallei sequence types (STs) correlate with disease in Malaysian patients with melioidosis. METHODS In this study, multi-locus sequence typing (MLST) was performed on clinical B. pseudomallei isolates collected from Kelantan state of Malaysia, patients' clinical data were reviewed and then genotype-risk correlations were investigated. RESULTS Genotyping of 83 B. pseudomallei isolates revealed 32 different STs, of which 13(40%) were novel. The frequencies of the STs among the 83 isolates ranged from 1 to 12 observations, and ST54, ST371 and ST289 were predominant. All non-novel STs reported in this study have also been identified in other Asian countries. Based on the MLST data analysis, the phylogenetic tree showed clustering of the STs with each other, as well as with the STs from Southeast Asia and China. No evidence for associations between any of B. pseudomallei STs and clinical melioidosis presentation was detected. In addition, the bacterial genotype clusters in relation with each clinical outcome were statistically insignificant, and no risk estimate was reported. This study has expanded the data for B. pseudomallei on MLST database map and provided insights into the molecular epidemiology of melioidosis in Peninsular Malaysia. CONCLUSION This study concurs with previous reports concluding that infecting strain type plays no role in determining disease presentation.
Collapse
Affiliation(s)
- Abdel Rahman Zueter
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, The Hashemite University, Zarqa, Jordan. .,Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia.
| | - Zaidah Abdul Rahman
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Mahmoud Abumarzouq
- Department of Orthopedic, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Azian Harun
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia
| |
Collapse
|
8
|
Price EP, Currie BJ, Sarovich DS. Genomic Insights Into the Melioidosis Pathogen, Burkholderia pseudomallei. CURRENT TROPICAL MEDICINE REPORTS 2017. [DOI: 10.1007/s40475-017-0111-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
9
|
Sarovich DS, Chapple SNJ, Price EP, Mayo M, Holden MTG, Peacock SJ, Currie BJ. Whole-genome sequencing to investigate a non-clonal melioidosis cluster on a remote Australian island. Microb Genom 2017; 3:e000117. [PMID: 29026657 PMCID: PMC5610713 DOI: 10.1099/mgen.0.000117] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 04/20/2017] [Indexed: 12/22/2022] Open
Abstract
Melioidosis is a tropical disease caused by the bacterium Burkholderia pseudomallei. Outbreaks are uncommon and can generally be attributed to a single point source and strain. We used whole-genome sequencing to analyse B. pseudomallei isolates collected from an historical 2-year long case cluster that occurred in a remote northern Australian indigenous island community, where infections were previously linked to a contaminated communal water supply. We analysed the genome-wide relatedness of the two most common multilocus sequence types (STs) involved in the outbreak, STs 125 and 126. This analysis showed that although these STs were closely related on a whole-genome level, they demonstrated evidence of multiple recombination events that were unlikely to have occurred over the timeframe of the outbreak. Based on epidemiological and genetic data, we also identified two additional patients not previously associated with this outbreak. Our results confirm the previous hypothesis that a single unchlorinated water source harbouring multiple B. pseudomallei strains was linked to the outbreak, and that increased melioidosis risk in this community was associated with Piper methysticum root (kava) consumption.
Collapse
Affiliation(s)
- Derek S Sarovich
- 1Global and Tropical Health Division, Menzies School of Health Research, Darwin, Australia.,2Centre for Animal Health Innovation, University of the Sunshine Coast, Sippy Downs, Australia
| | - Stephanie N J Chapple
- 1Global and Tropical Health Division, Menzies School of Health Research, Darwin, Australia.,3Melbourne Medical School, University of Melbourne, Melbourne, Australia
| | - Erin P Price
- 1Global and Tropical Health Division, Menzies School of Health Research, Darwin, Australia.,2Centre for Animal Health Innovation, University of the Sunshine Coast, Sippy Downs, Australia
| | - Mark Mayo
- 1Global and Tropical Health Division, Menzies School of Health Research, Darwin, Australia
| | - Matthew T G Holden
- 4School of Medicine, Medical and Biological Sciences, University of St Andrews, St Andrews, UK.,5Wellcome Trust Sanger Institute, Cambridge, UK
| | - Sharon J Peacock
- 5Wellcome Trust Sanger Institute, Cambridge, UK.,6Department of Medicine, University of Cambridge, Cambridge, UK
| | - Bart J Currie
- 1Global and Tropical Health Division, Menzies School of Health Research, Darwin, Australia.,7Department of Infectious Diseases and Northern Territory Medical Program, Royal Darwin Hospital, Darwin, Australia
| |
Collapse
|
10
|
Lin Y, Wu Q, Liu X, Dong S, Wu L, Pei H, Xu K, Xia Q. Molecular tracking investigation of melioidosis cases reveals regional endemicity in Hainan, China. Biomed Rep 2016; 5:766-770. [PMID: 28105344 DOI: 10.3892/br.2016.795] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/13/2016] [Indexed: 11/05/2022] Open
Abstract
Sporadic cases of melioidosis have been reported in Hainan, China for decades; however, to the best of our knowledge, there are no accurate source-identification investigations confirming that melioidosis is endemic. Four indigenous melioidosis cases were identified, which prompted the performance of contact microbiologic and molecular techniques to evaluate endemicity. Environmental samples were collected from various locations surrounding each patient's residence. The samples were screened for Burkholderia pseudomallei (B. pseudomallei) using Ashdown culture medium, and confirmed by polymerase chain reaction and 16S ribosomal DNA sequencing. Clinical and environmental isolates of B. pseudomallei were evaluated by multilocus sequence typing (MLST) and 4-locus multilocus variable number tandem repeat analysis (MLVA-4) for evidence of homology between them. Analysis by MLST indicated that one environmental sample and one clinical colony were sequence type-46, as well as type (8, 3, 11, 9) by MLVA-4. The evidence indicates a likely geographical and epidemiological association. Taken together, B. pseudomallei from the environmental samples in addition to the high molecular homology between the clinical and environmental isolates indicates, at least, regional endemicity of melioidosis in Hainan, China.
Collapse
Affiliation(s)
- Yingzi Lin
- Key Laboratory of Translational Medicine for Tropical Diseases, Ministry of Education, and Faculty of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou, Hainan 571199, P.R. China
| | - Qiang Wu
- Key Laboratory of Translational Medicine for Tropical Diseases, Ministry of Education, and Faculty of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou, Hainan 571199, P.R. China
| | - Xiang Liu
- Key Laboratory of Translational Medicine for Tropical Diseases, Ministry of Education, and Faculty of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou, Hainan 571199, P.R. China
| | - Sufang Dong
- Key Laboratory of Translational Medicine for Tropical Diseases, Ministry of Education, and Faculty of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou, Hainan 571199, P.R. China
| | - Lixian Wu
- Key Laboratory of Translational Medicine for Tropical Diseases, Ministry of Education, and Faculty of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou, Hainan 571199, P.R. China
| | - Hua Pei
- Key Laboratory of Translational Medicine for Tropical Diseases, Ministry of Education, and Faculty of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou, Hainan 571199, P.R. China
| | - Ke Xu
- Key Laboratory of Translational Medicine for Tropical Diseases, Ministry of Education, and Faculty of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou, Hainan 571199, P.R. China
| | - Qianfeng Xia
- Key Laboratory of Translational Medicine for Tropical Diseases, Ministry of Education, and Faculty of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou, Hainan 571199, P.R. China
| |
Collapse
|
11
|
Currie BJ, Price EP, Mayo M, Kaestli M, Theobald V, Harrington I, Harrington G, Sarovich DS. Use of Whole-Genome Sequencing to Link Burkholderia pseudomallei from Air Sampling to Mediastinal Melioidosis, Australia. Emerg Infect Dis 2016; 21:2052-4. [PMID: 26488732 PMCID: PMC4622230 DOI: 10.3201/eid2111.141802] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The frequency with which melioidosis results from inhalation rather than percutaneous inoculation or ingestion is unknown. We recovered Burkholderia pseudomallei from air samples at the residence of a patient with presumptive inhalational melioidosis and used whole-genome sequencing to link the environmental bacteria to B. pseudomallei recovered from the patient.
Collapse
|
12
|
Abstract
Melioidosis is an infectious disease caused by Burkholderia pseudomallei, a bacterium endemic in Southeast Asia and northern Australia. In New Caledonia, sporadic cases were first described in 2005; since then, more cases have been identified. To improve our understanding of melioidosis epidemiology in New Caledonia, we compared the local cases and B. pseudomallei isolates with those from endemic areas. Nineteen melioidosis cases have been diagnosed in New Caledonia since 1999, mostly severe and with frequent bacteraemia, leading to three (16%) fatalities. All but one occurred in the North Province. Besides sporadic cases caused by non-clonal strains, we also identified a hotspot of transmission related to a clonal group of B. pseudomallei that is phylogenetically related to Australian strains.
Collapse
|
13
|
Chen H, Xia L, Zhu X, Li W, Du X, Wu D, Hai R, Shen X, Liang Y, Cai H, Zheng X. Burkholderia pseudomallei sequence type 562 in China and Australia. Emerg Infect Dis 2015; 21:166-8. [PMID: 25531912 PMCID: PMC4285272 DOI: 10.3201/eid2101.140156] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
|
14
|
Tracing melioidosis back to the source: using whole-genome sequencing to investigate an outbreak originating from a contaminated domestic water supply. J Clin Microbiol 2015; 53:1144-8. [PMID: 25631791 DOI: 10.1128/jcm.03453-14] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Melioidosis, a disease of public health importance in Southeast Asia and northern Australia, is caused by the Gram-negative soil bacillus Burkholderia pseudomallei. Melioidosis is typically acquired through environmental exposure, and case clusters are rare, even in regions where the disease is endemic. B. pseudomallei is classed as a tier 1 select agent by the Centers for Disease Control and Prevention; from a biodefense perspective, source attribution is vital in an outbreak scenario to rule out a deliberate release. Two cases of melioidosis within a 3-month period at a residence in rural northern Australia prompted an investigation to determine the source of exposure. B. pseudomallei isolates from the property's groundwater supply matched the multilocus sequence type of the clinical isolates. Whole-genome sequencing confirmed the water supply as the probable source of infection in both cases, with the clinical isolates differing from the likely infecting environmental strain by just one single nucleotide polymorphism (SNP) each. For the first time, we report a phylogenetic analysis of genomewide insertion/deletion (indel) data, an approach conventionally viewed as problematic due to high mutation rates and homoplasy. Our whole-genome indel analysis was concordant with the SNP phylogeny, and these two combined data sets provided greater resolution and a better fit with our epidemiological chronology of events. Collectively, this investigation represents a highly accurate account of source attribution in a melioidosis outbreak and gives further insight into a frequently overlooked reservoir of B. pseudomallei. Our methods and findings have important implications for outbreak source tracing of this bacterium and other highly recombinogenic pathogens.
Collapse
|
15
|
Zehnder AM, Hawkins MG, Koski MA, Lifland B, Byrne BA, Swanson AA, Rood MP, Gee JE, Elrod MG, Beesley CA, Blaney DD, Ventura J, Hoffmaster AR, Beeler ES. Burkholderia pseudomallei isolates in 2 pet iguanas, California, USA. Emerg Infect Dis 2014; 20:304-6. [PMID: 24447394 PMCID: PMC3901496 DOI: 10.3201/eid2002.131314] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Burkholderia pseudomallei, the causative agent of melioidosis, was isolated from abscesses of 2 pet green iguanas in California, USA. The international trade in iguanas may contribute to importation of this pathogen into countries where it is not endemic and put persons exposed to these animals at risk for infection.
Collapse
|
16
|
Distribution of Burkholderia pseudomallei in northern Australia, a land of diversity. Appl Environ Microbiol 2014; 80:3463-8. [PMID: 24657869 DOI: 10.1128/aem.00128-14] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Burkholderia pseudomallei is a Gram-negative soil bacillus that is the etiological agent of melioidosis and a biothreat agent. Little is known about the biogeography of this bacterium in Australia, despite its hyperendemicity in the northern region of this continent. The population structure of 953 Australian B. pseudomallei strains representing 779 and 174 isolates of clinical and environmental origins, respectively, was analyzed using multilocus sequence typing (MLST). Bayesian population structure and network SplitsTree analyses were performed on concatenated MLST loci, and sequence type (ST) diversity and evenness were examined using Simpson's and Pielou's indices and a multivariate dissimilarity matrix. Bayesian analysis found two B. pseudomallei populations in Australia that were geographically distinct; isolates from the Northern Territory were grouped mainly into the first population, whereas the majority of isolates from Queensland were grouped in a second population. Differences in ST evenness were observed between sampling areas, confirming that B. pseudomallei is widespread and established across northern Australia, with a large number of fragmented habitats. ST analysis showed that B. pseudomallei populations diversified as the sampling area increased. This observation was in contrast to smaller sampling areas where a few STs predominated, suggesting that B. pseudomallei populations are ecologically established and not frequently dispersed. Interestingly, there was no identifiable ST bias between clinical and environmental isolates, suggesting the potential for all culturable B. pseudomallei isolates to cause disease. Our findings have important implications for understanding the ecology of B. pseudomallei in Australia and for potential source attribution of this bacterium in the event of unexpected cases of melioidosis.
Collapse
|
17
|
Chiou CS. Multilocus variable-number tandem repeat analysis as a molecular tool for subtyping and phylogenetic analysis of bacterial pathogens. Expert Rev Mol Diagn 2014; 10:5-7. [DOI: 10.1586/erm.09.76] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
18
|
Jakupciak JP, Wells JM, Karalus RJ, Pawlowski DR, Lin JS, Feldman AB. Population-Sequencing as a Biomarker of Burkholderia mallei and Burkholderia pseudomallei Evolution through Microbial Forensic Analysis. J Nucleic Acids 2013; 2013:801505. [PMID: 24455204 PMCID: PMC3877622 DOI: 10.1155/2013/801505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 10/01/2013] [Accepted: 10/02/2013] [Indexed: 11/18/2022] Open
Abstract
Large-scale genomics projects are identifying biomarkers to detect human disease. B. pseudomallei and B. mallei are two closely related select agents that cause melioidosis and glanders. Accurate characterization of metagenomic samples is dependent on accurate measurements of genetic variation between isolates with resolution down to strain level. Often single biomarker sensitivity is augmented by use of multiple or panels of biomarkers. In parallel with single biomarker validation, advances in DNA sequencing enable analysis of entire genomes in a single run: population-sequencing. Potentially, direct sequencing could be used to analyze an entire genome to serve as the biomarker for genome identification. However, genome variation and population diversity complicate use of direct sequencing, as well as differences caused by sample preparation protocols including sequencing artifacts and mistakes. As part of a Department of Homeland Security program in bacterial forensics, we examined how to implement whole genome sequencing (WGS) analysis as a judicially defensible forensic method for attributing microbial sample relatedness; and also to determine the strengths and limitations of whole genome sequence analysis in a forensics context. Herein, we demonstrate use of sequencing to provide genetic characterization of populations: direct sequencing of populations.
Collapse
Affiliation(s)
| | | | | | | | - Jeffrey S. Lin
- The Johns Hopkins University, Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD 20723, USA
| | - Andrew B. Feldman
- The Johns Hopkins University, Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD 20723, USA
| |
Collapse
|
19
|
Hill AA, Mayo M, Kaestli M, Price EP, Richardson LJ, Godoy D, Spratt BG, Currie BJ. Melioidosis as a consequence of sporting activity. Am J Trop Med Hyg 2013; 89:365-6. [PMID: 23732257 DOI: 10.4269/ajtmh.12-0744] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
In the tropical city of Darwin, Northern Territory, Australia, dry season soil sampling cultured Burkholderia pseudomallei from 7 (70%) of 10 sports fields. However, during the 23 years of the Darwin Prospective Melioidosis Study, only 5 (0.6%) of 785 melioidosis cases have been attributed to infection from sports fields. In one soccer player with cutaneous melioidosis, B. pseudomallei cultured from the player was identical by multilocus sequence typing and multilocus variable-number tandem repeat analysis with an isolate recovered from soil at the location on the sports field where he was injured. Melioidosis is uncommon in otherwise healthy sports persons in melioidosis-endemic regions but still needs consideration in persons with abrasion injuries that involve contact with soil.
Collapse
Affiliation(s)
- Audrey A Hill
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia.
| | | | | | | | | | | | | | | |
Collapse
|
20
|
Hampton V, Kaestli M, Mayo M, Choy JL, Harrington G, Richardson L, Benedict S, Noske R, Garnett ST, Godoy D, Spratt BG, Currie BJ. Melioidosis in Birds and Burkholderia pseudomallei Dispersal, Australia. Emerg Infect Dis 2012; 17:1310-2. [PMID: 21762599 PMCID: PMC3381411 DOI: 10.3201/eid1707.100707] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|
21
|
Mukhopadhyay C, Kaestli M, Vandana KE, Sushma K, Mayo M, Richardson L, Tuanyok A, Keim P, Godoy D, Spratt BG, Currie BJ. Molecular characterization of clinical Burkholderia pseudomallei isolates from India. Am J Trop Med Hyg 2011; 85:121-3. [PMID: 21734136 DOI: 10.4269/ajtmh.2011.11-0166] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Multilocus sequence typing of seven isolates of Burkholderia pseudomallei from India showed considerable diversity, with six different sequence types. Possible dissemination of melioidosis by historical trading routes is supported by links to strains from Southeast Asia, China, and Africa and the presence of the Burkholderia mallei allele of the bimA gene.
Collapse
Affiliation(s)
- Chiranjay Mukhopadhyay
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal University, Karnataka, India.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Hassan MRA, Pani SP, Peng NP, Voralu K, Vijayalakshmi N, Mehanderkar R, Aziz NA, Michael E. Incidence, risk factors and clinical epidemiology of melioidosis: a complex socio-ecological emerging infectious disease in the Alor Setar region of Kedah, Malaysia. BMC Infect Dis 2010; 10:302. [PMID: 20964837 PMCID: PMC2975659 DOI: 10.1186/1471-2334-10-302] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Accepted: 10/21/2010] [Indexed: 12/31/2022] Open
Abstract
Background Melioidosis, a severe and fatal infectious disease caused by Burkholderia pseudomallei, is believed to an emerging global threat. However, data on the natural history, risk factors, and geographic epidemiology of the disease are still limited. Methods We undertook a retrospective analysis of 145 confirmed cases extracted from a hospital-based Melioidosis Registry set up from 2005 in Hospital Sultanah Bahiyah, Alor Setar, Kedah state, Malaysia, in order to provide a first description of the contemporary incidence, risk factors, and clinical epidemiology of the disease in this putatively high risk region of the country. Results The incidence of melioidosis in Alor Setar is remarkably high at 16.35 per 100,000 population per year. The mean age of patients was 50.40 years, with infection varying nonlinearly with age. Males (75.2%; P < 0.0001) predominated and the majority of cases were Malays (88.9%). The overall, crude mortality rate among the study patients was 33.8%. The proportions of cases and deaths were significantly greater among patients involved in farming, forestry and fishing and the unemployed (χ2 = 30.57, P < 0.0001). A majority of cases (62.75%) were culture positive, with mortality in these patients being 45.05%. A large proportion (83.0%) of culture positives was also bacteremic. Pneumonia accounted for 42.06% of primary diagnoses followed in importance by soft tissue abscess. In patients with pneumonia and who were culture positive, the mortality rate was as high as 65.00%. Diabetes mellitus constituted the major underlying risk factor for developing and dying from melioidosis, occurring in 57% of all diagnosed cases. The age distribution of diabetes paralleled that of melioidosis cases. There were linear associations between cases and deaths with monthly rainfall. Conclusions Melioidosis represents a complex socio-ecological public health problem in Kedah, being strongly related with age, occupation, rainfall and predisposing chronic diseases, such as diabetes mellitus. Among cases, bacteremic patients were associated with significantly high mortality despite provision of the recommended antibacterial therapy. The burden of this disease is likely to grow in this region unless better informed interventions targeted at high-risk groups and associated diseases are urgently implemented.
Collapse
|
23
|
Association of the melioidosis agent Burkholderia pseudomallei with water parameters in rural water supplies in Northern Australia. Appl Environ Microbiol 2010; 76:5305-7. [PMID: 20543039 DOI: 10.1128/aem.00287-10] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We analyzed water parameters and the occurrence of the melioidosis agent Burkholderia pseudomallei in 47 water bores in Northern Australia. B. pseudomallei was associated with soft, acidic bore water of low salinity but high iron levels. This finding aids in identifying water supplies at risk of contamination with this pathogenic bacterium.
Collapse
|
24
|
Michelle Wong Su Yen, Lisanti O, Thibault F, Toh Su San, Loh Gek Kee, Hilaire V, Jiali L, Neubauer H, Vergnaud G, Ramisse V. Validation of ten new polymorphic tandem repeat loci and application to the MLVA typing of Burkholderia pseudomallei isolates collected in Singapore from 1988 to 2004. J Microbiol Methods 2009; 77:297-301. [PMID: 19327380 DOI: 10.1016/j.mimet.2009.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2009] [Revised: 03/14/2009] [Accepted: 03/16/2009] [Indexed: 10/21/2022]
Abstract
Multiple locus variable number of tandem repeat (VNTR) analysis (MLVA) has been shown to be very promising for the typing of Burkholderia pseudomallei and mallei. The currently available set of loci requires high resolution allele size measurement due to short repeat units. The present work was aimed at expanding the available set of VNTR loci, and generating data from a collection of 102 B. pseudomallei strains isolated in Singapore between 1988 and 2004 including few additional strains of various origins as references. Ten new VNTRs with a longer array size have been identified compatible with standard agarose gel separation, and a reference database of 72 genotypes was created which can be queried on the Internet.
Collapse
Affiliation(s)
- Michelle Wong Su Yen
- Microbiology Group, Defence Medical and Environmental Research Institute, DSO National Laboratories, 117610 Singapore, Singapore
| | | | | | | | | | | | | | | | | | | |
Collapse
|