PCR-based identification of Burkholderia pseudomallei

Development of a Novel Internally Controlled HrpB1 Gene-Based Real-Time qPCR Assay for Detection of Burkholderia pseudomallei

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.

Burkholderia pseudomallei in soil and natural water bodies in rural Sri Lanka: A hidden threat to public health

Burkholderia pseudomallei is the causative agent of the potentially fatal infection, melioidosis. This study provides the first evidence for the presence of B. pseudomallei in soil and water in Sri Lanka. Targeted sampling of soil and natural water sources was done between November 2019 and October 2020 over eight field visits encompassing the neighborhood of 28 culture and/or antibody-positive melioidosis patients in northwestern, western and southern Sri Lanka. A total of eight environmental isolates of B. pseudomallei (BPs-env1 to BPs-env8) were cultured from 116 soil and 117 natural water samples collected from 72 locations. The presence of B. pseudomallei in soil and natural water in these areas poses a risk of melioidosis for populations cultivating crops in such soils and using untreated water from these sources for drinking, bathing, and other domestic purposes. Identifying sites positive for B. pseudomallei may help to mitigate risk by raising public awareness of contaminated environmental sources and allowing soil and water remediation.

Biogeography and genetic diversity of clinical isolates of Burkholderia pseudomallei in Sri Lanka

Background

Melioidosis is a potentially fatal infectious disease caused by Burkholderia pseudomallei and the disease is endemic in Southeast Asia and Northern Australia. It has been confirmed as endemic in Sri Lanka. Genomic epidemiology of B. pseudomallei in Sri Lanka is largely unexplored. This study aims to determine the biogeography and genetic diversity of clinical isolates of B. pseudomallei and the phylogenetic and evolutionary relationship of Sri Lankan sequence types (STs) to those found in other endemic regions of Southeast Asia and Oceania.

Methods

The distribution of variably present genetic markers [Burkholderia intracellular motility A (bimA) gene variants bimA_BP/bimA_BM, filamentous hemagglutinin 3 (fhaB3), Yersinia-like fimbrial (YLF) and B. thailandensis-like flagellum and chemotaxis (BTFC) gene clusters and lipopolysaccharide O-antigen type A (LPS type A)] was examined among 310 strains. Multilocus sequence typing (MLST) was done for 84 clinical isolates. The phylogenetic and evolutionary relationship of Sri Lankan STs within Sri Lanka and in relation to those found in other endemic regions of Southeast Asia and Oceania were studied using e BURST, PHYLOViZ and minimum evolutionary analysis.

Results

The Sri Lankan B. pseudomallei population contained a large proportion of the rare BTFC clade (14.5%) and bimA_BM allele variant (18.5%) with differential geographic distribution. Genotypes fhaB3 and LPSA were found in 80% and 86% respectively. This study reported 43 STs (including 22 novel). e-BURST analysis which include all Sri Lankan STs (71) resulted in four groups, with a large clonal group (group 1) having 46 STs, and 17 singletons. ST1137 was the commonest ST. Several STs were shared with India, Bangladesh and Cambodia.

Conclusion

This study demonstrates the usefulness of high-resolution molecular typing to locate isolates within the broad geographical boundaries of B. pseudomallei at a global level and reveals that Sri Lankan isolates are intermediate between Southeast Asia and Oceania.

Burkholderia pseudomallei is an important cause of community acquired pneumonia, septicemia and abscesses in Sri Lanka. The risk of infection is increased after flooding following heavy rainfall. Risk groups include rice farmers and rural populations engaged in subsistence cultivation in home gardens. Nationwide surveillance has been carried out since 2006 and the state public health system offers free diagnostics and free antibiotic therapy. The incidence of melioidosis in Sri Lanka has increased in tandem with increased awareness among clinicians. This study reports the genetic diversity among Sri Lankan B. pseudomallei clinical isolates and shows that some variably present genes are regionally distributed. The population is intermediate between Southeast Asia and Oceania. This may reflect its past geological history.

Presence of 2-hydroxymyristate on endotoxins is associated with death in neonates with Enterobacter cloacae complex septic shock

Enterobacter cloacae complex species are involved in infections among critically ill patients. After a recent E.cloacae outbreak of fulminant neonatal septic shock, we conducted a study to determine whether septic shock severity and its lethal consequence are related to structural features of the endotoxin (lipopolysaccharide [LPS]) of the strains isolated from hospitalized infants and more specifically its lipid A region. It appeared that the LPSs are very heterogeneous, carrying fifteen different molecular species of lipid A. The virulence was correlated with a structural feature identified by matrix-assisted laser desorption ionization–time of flight mass spectrometry and gas chromatography coupled with mass spectrometry: the presence of 2-hydroxymyristic acid as a secondary substituent in lipid A. This is the first published evidence linking LPS structural moiety to neonatal sepsis outcome and opens the possibility of using this fatty acid marker as a detection tool for high-risk patients, which could help reduce their mortality.

•

Fifteen different molecular species of lipid A is found in E. cloacae complex

•

2-Hydroxymyristate moiety on Lipid A is a virulence marker of the E. cloacae complex

•

Presence of 2-hydroxymyristate is associated with mortality in neonatal sepsis

Transcriptomics Analysis Uncovers Transient Ceftazidime Tolerance in Burkholderia Biofilms

Burkholderia pseudomallei is an etiological agent of melioidosis, a severe community-acquired infectious disease. B. pseudomallei strain K96243 is sensitive to the drug ceftazidime (CAZ), but has been shown to exhibit transient CAZ tolerance when in a biofilm form. To investigate an observed shift in gene expression profile during CAZ tolerance condition and to better understand the mechanistic aspects of this transient tolerance, RNA-sequencing was performed on B. pseudomallei K96243 from the following three states: planktonic, biofilm, and planktonic shedding. Results indicated that the expression of 651 genes (10.97%) were significantly changed in both biofilm (resistant) and planktonic shedding (sensitive) cells in comparison to the planktonic state. The top four highly expressed genes identified in both states are associated with nitrosative stress response (BPSL2368), Fe-S homeostasis (BPSL2369), and nitrate respiration (BPSS1154 and BPSS1158). Additionally, five orthologous genes, BPSL2370-BPSL2374, implicated in Fe-S cluster biogenesis, and another gene, BPSL2863, involved in DNA-binding of the stress protein ferritin, were shown to increase expression by RT-qPCR. The shift in gene expression was especially prominent at the late stages of biofilm growth (72 and 96 h), specifically in the biofilm-challenged CAZ survivor cells. This suggested that in response to stress in a biofilm, differential expression of these genes may support development of the CAZ tolerance in Burkholderia. The application of iron chelator deferoxamine (DFO) to the biofilm caused a significant reduction in biofilm formation and associated CAZ tolerance. Therefore, the shift in Fe-S metabolism when B. pseudomallei is in a biofilm may help stabilize the levels of reactive oxygen species (ROS), thereby limiting tolerance to CAZ.

Nonclonal Burkholderia pseudomallei Population in Melioidosis Case Cluster, Sri Lanka

A melioidosis case cluster of 10 blood culture–positive patients occurred in eastern Sri Lanka after an extreme weather event. Four infections were caused by Burkholderia pseudomallei isolates of sequence type 594. Whole-genome analysis showed that the isolates were genetically diverse and the case cluster was nonclonal.

Adapting Microarray Gene Expression Signatures for Early Melioidosis Diagnosis

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.

Human Melioidosis

The causative agent of melioidosis, Burkholderia pseudomallei, a tier 1 select agent, is endemic in Southeast Asia and northern Australia, with increased incidence associated with high levels of rainfall. Increasing reports of this condition have occurred worldwide, with estimates of up to 165,000 cases and 89,000 deaths per year. The ecological niche of the organism has yet to be clearly defined, although the organism is associated with soil and water. The culture of appropriate clinical material remains the mainstay of laboratory diagnosis. Identification is best done by phenotypic methods, although mass spectrometric methods have been described. Serology has a limited diagnostic role. Direct molecular and antigen detection methods have limited availability and sensitivity. Clinical presentations of melioidosis range from acute bacteremic pneumonia to disseminated visceral abscesses and localized infections. Transmission is by direct inoculation, inhalation, or ingestion. Risk factors for melioidosis include male sex, diabetes mellitus, alcohol abuse, and immunosuppression. The organism is well adapted to intracellular survival, with numerous virulence mechanisms. Immunity likely requires innate and adaptive responses. The principles of management of this condition are drainage and debridement of infected material and appropriate antimicrobial therapy. Global mortality rates vary between 9% and 70%. Research into vaccine development is ongoing.

Whole-Genome Sequences of Eight Clinical Isolates of Burkholderia pseudomallei from Melioidosis Patients in Eastern Sri Lanka

Here, we report whole-genome sequences (WGS) of eight clinical isolates of Burkholderia pseudomallei obtained from melioidosis patients with sepsis in eastern Sri Lanka.

Clinical features and outcome of patients with cutaneous melioidosis during a nosocomial outbreak in a temperate region of Australia

Six cases of cutaneous melioidosis from southwestern Australia, a non-endemic region occurred as a result of Burkholderia pseudomallei contamination of normal saline that was used for irrigating superficial wounds. Treatment with parenteral meropenem, given by continuous infusion for 2 weeks, followed by oral antibiotics was successful in all cases.

Lipid A Remodeling Is a Pathoadaptive Mechanism That Impacts Lipopolysaccharide Recognition and Intracellular Survival of Burkholderia pseudomallei

Burkholderia pseudomallei causes the severe disease melioidosis. The bacterium subverts the host immune system and replicates inside cells, and host mortality results primarily from sepsis-related complications.

Burkholderia pseudomallei causes the severe disease melioidosis. The bacterium subverts the host immune system and replicates inside cells, and host mortality results primarily from sepsis-related complications. Lipopolysaccharide (LPS) is a major virulence factor and mediator of sepsis that many pathogens capable of intracellular growth modify to reduce their immunological “footprint.” The binding strength of B. pseudomallei LPS for human LPS binding protein (hLBP) was measured using surface plasmon resonance. The structures of lipid A isolated from B. pseudomallei under different temperatures were analyzed by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS), and the gene expression of two lipid A remodeling genes, lpxO and pagL, was investigated. The LPS was characterized for its ability to trigger tumor necrosis factor alpha (TNF-α) release and to activate caspase-11-triggered pyroptosis by introduction of LPS into the cytosol. Lipid A from long-term chronic-infection isolates was isolated and characterized by MALDI-TOF MS and also by the ability to trigger caspase-11-mediated cell death. Lipid A from B. pseudomallei 1026b lpxO and pagL mutants were characterized by positive- and negative-mode MALDI-TOF MS to ultimately identify their role in lipid A structural modifications. Replication of lpxO and pagL mutants and their complements within macrophages showed that lipid A remodeling can effect growth in host cells and activation of caspase-11-mediated cytotoxicity.

Burkholderia pseudomallei-absent soil bacterial community results in secondary metabolites that kill this pathogen

Burkholderia pseudomallei is a Gram-negative bacterium found in soil and the causative agent of a severe disease in humans and animals known as melioidosis. It is intrinsically resistant to many antibiotics and has been reported resistant to the drugs of choice; ceftazidime. Microbial communities in soil in the presence and absence of B. pseudomallei were investigated using metagenomics approach. The variation in bacterial species diversity was significantly higher in soil samples without B. pseudomallei. Abundances of phyla Actinobacteria and Firmicutes were found significantly higher in B. pseudomallei-negative soils. Bacillus amyloliquefaciens KKU1 in phylum Firmicutes was discovered from negative soil and its secondary metabolites could inhibit clinical, environmental and drug resistant isolates of B. pseudomallei, together with some pathogenic Gram-negative but not Gram-positive bacteria. The antimicrobial activity from KKU 1 against B. pseudomallei was abolished when treated with proteinase K, stable in a wide range of pH and remained active after heating at 100 °C for 15 min. Precipitated proteins from KKU1 were demonstrated to cause lysis and corrugated surfaces of B. pseudomallei. The minimum inhibitory concentrations and minimum bactericidal concentrations of the precipitated proteins from KKU1 against B. pseudomallei were 0.97 μg/ml and 3.9 μg/ml. Interestingly, Native SDS-PAGE showed small active compounds of less than 6 kDa, along with other information collectively suggesting the properties of antimicrobial peptides. For the first time, culture-independent information in melioidosis endemic area could lead to a suspected source of metabolites that may help defense against B. pseudomallei and other pathogenic Gram-negative bacteria.

Melioidosis in Sri Lanka

Until recently, Sri Lanka was not considered a country with endemic melioidosis. However, an increasing number of cases is being reported. National surveillance for melioidosis was instituted after 2008. A total of 250 culture-positive cases was recorded between 2006 and May 2017. Males predominated (71.6%). The age range was wide (2⁻92 years) reflecting a ubiquity of exposure. The majority (201/250, 80%) lived in rural areas. All provinces were affected. Case load increased during the two monsoonal periods (67%). There was representation of every population group including farmers (n = 44), housewives (n = 24), school children (n = 10), professionals (n = 5), businesspersons (n = 6), white-collar workers (n = 10) and blue-collar workers (n = 8). Diabetes was the predominant risk factor (n = 163, 65.2%). Clinical presentations included community-acquired sepsis and pneumonia, superficial and deep abscesses, and septic arthritis. Mortality was 20.4% (51/250). A majority (n = 212) of isolates belonged to the YLF (Yersinia-like fimbrial) clade but 38 were BTFC (B. thailandensis-like flagellum and chemotaxis). A total of 108 isolates was genotyped and 46 sequence types (STs) were identified, 40 being novel. It is clear that melioidosis is endemic in Sri Lanka with a wide geographic and demographic distribution. There is an urgent need to extend surveillance of melioidosis to under-resourced parts of the country and to populations at high risk.

Cutaneous Melioidosis Cluster Caused by Contaminated Wound Irrigation Fluid

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.

Clinical, Bacteriologic, and Geographic Stratification of Melioidosis Emerges from the Sri Lankan National Surveillance Program

Melioidosis, a potentially fatal tropical infection, is said to be underdiagnosed in low-income countries. An increase in melioidosis cases in Sri Lanka allowed us to analyze the relationship among clinical outcome, bacteriology, epidemiology, and geography in the first 108 laboratory-confirmed cases of melioidosis from a nationwide surveillance program. The additional 76 cases of laboratory-confirmed melioidosis confirmed further associations between Burkholderia pseudomallei multilocus sequence typing (MLST) and infection phenotype; ST1137/unifocal bacteremic infection (χ² = 3.86, P < 0.05), ST1136/multifocal infection without bacteremia (χ² = 15.8, P < 0.001), and ST1132/unifocal nonbacteremic infection (χ² = 6.34, P = 0.02). ST1137 infections were predominantly seen in the Western Province, whereas ST1132, 1135, and 1136 infections predominated in the Northwestern Province. Early participating centers in the surveillance program had a lower melioidosis-associated mortality than later participants (χ² = 3.99, P < 0.05). The based upon related sequence types (eBURST) algorithm, a MLST clustering method that infers founding genotypes and patterns of descent for related isolates and clonal complexes in an unrooted tree, showed uneven distribution of sequence types (STs). There was spatial clustering of the commonest STs (ST1132, 1136, and 1137) in the Western, Northwestern, and Central provinces. The recent increase in melioidosis in Sri Lanka uncovered by laboratory-enhanced surveillance is likely to be the result of a combination of improved laboratory detection, increased clinician awareness, recruitment of clinical centers, and small outbreaks. Further development of the surveillance program into a national genotyping-supported melioidosis registry will improve melioidosis diagnosis, treatment, and prevention where underdiagnosis and mortality rates remain high.

Clinical and environmental isolates of Burkholderia pseudomallei from Brazil: Genotyping and detection of virulence gene

OBJECTIVE

To evaluate the genetic diversity of clinical and environmental isolates of Burkholderia pseudomallei (B. pseudomallei) recovered in Ceará, Brazil, and screen these isolates for the presence of type three secretion system virulence gene.

METHODS

Nineteen B. pseudomallei isolates (9 from clinical cases and 10 from soils) were analyzed. Random amplified polymorphic DNA was performed with primers OPQ-2, OPQ-4 and OPQ-16 to evaluate the genetic diversity, and type three secretion system gene was detected through polymerase chain reaction.

RESULTS

Random amplified polymorphic DNA showed a genetic relatedness of approximately 50% among the tested B. pseudomallei isolates, which were grouped into two clades, of which the biggest ones comprised 18/19 isolates for primer OPQ-2, and 17/19 isolates for primer OPQ-16. Primer OPQ-4 grouped the isolates into three clades comprising 1/19, 3/19 and 15/19 isolates. Additionally, type three secretion system gene was detected in all tested isolates.

CONCLUSIONS

This is an effort to type B. pseudomallei strains from Ceará, which is important for better understanding this pathogen, contributing for the epidemiological surveillance of melioidosis in this endemic region.

Host gene expression analysis in Sri Lankan melioidosis patients

BACKGROUND

Melioidosis is a life threatening infectious disease caused by the gram-negative bacillus Burkholderia pseudomallei predominantly found in southeast Asia and northern Australia. Studying the host transcription profiles in response to infection is crucial for understanding disease pathogenesis and correlates of disease severity, which may help improve therapeutic intervention and survival. The aim of this study was to analyze gene expression levels of human host factors in melioidosis patients and establish useful correlation with disease biomarkers, compared to healthy individuals and patients with sepsis caused by other pathogens.

METHODS

The study population consisted of 30 melioidosis cases, 10 healthy controls and 10 sepsis cases caused by other pathogens. Total RNA was extracted from peripheral blood mononuclear cells (PBMC's) of study subjects. Gene expression profiles of 25 gene targets including 19 immune response genes and 6 epigenetic factors were analyzed by real time quantitative polymerase chain reaction (RT-qPCR).

PRINCIPAL FINDINGS

Inflammatory response genes; TLR4, late onset inflammatory mediator HMGB1, genes associated with antigen presentation; MICB, PSMB2, PSMB8, PSME2, epigenetic regulators; DNMT3B, HDAC1, HDAC2 were significantly down regulated, whereas the anti-inflammatory gene; IL4 was up regulated in melioidosis patients compared to sepsis cases caused by other pathogens. Septicaemic melioidosis cases showed significant down regulation of IL8 compared to sepsis cases caused by other pathogens. HMGB1, MICB, PSMB8, PSMB2, PSME2, HDAC1, HDAC2 and DNMT3B showed consistent down regulation of gene expression in melioidosis patients compared to other sepsis infection, irrespective of comorbidities such as diabetes, duration of clinical symptoms and antibiotic treatment.

SIGNIFICANCE

Specific immune response genes and epigenetic regulators are differentially expressed among melioidosis patients and patients with sepsis caused by other pathogens. Therefore, these genes may serve as biomarkers for disease diagnosis to distinguish melioidosis from cases of sepsis due to other infections and therapeutic intervention for melioidosis.

Gene Expression Profile of Human Cytokines in Response to Burkholderia pseudomallei Infection

Melioidosis is an underreported infectious disease, caused by the Gram-negative bacterium Burkholderia pseudomallei. Understanding the disease susceptibility and pathogenesis is crucial for developing newer diagnostic and therapeutic strategies for this life-threatening infection. In this study, we aimed to analyze the gene expression levels of important cytokines in melioidosis patients and establish useful correlates with disease biomarkers compared to cases of sepsis infection caused by other pathogens and healthy individuals. A Qiagen common human cytokines array profiling the gene expression of 84 important cytokines by real-time quantitative PCR (RT-qPCR) was used. We analyzed 26 melioidosis cases, 5 healthy controls, and 10 cases of sepsis infection caused by other pathogens. Our results showed consistently upregulated expression of interleukins (IL) interleukin-4 (IL-4), interleukin-17 alpha (IL-17A), IL-23A, and IL-24, interferons (IFN) interferon alpha 1 (IFNA1) and interferon beta 1 (IFNB1), tumor necrosis factor (TNF) superfamily 4 (TNFSF4), transforming growth factor (TGF) superfamily, bone morphogenetic proteins 3 and 6 (BMP3 and BMP6), transforming growth factor beta 1 (TGFB1), and other growth factors, including macrophage colony-stimulating factor (M-CSF), C-fos-induced growth factor (FIGF), and platelet-derived growth factor alpha (PDGFA) polypeptide, in melioidosis patients compared to their expression in other sepsis cases, irrespective of comorbidities, duration of fever/clinical symptoms, and antibiotic treatment. Our findings indicate a dominant Th2- and Th17-type-cytokine response, suggesting that their dysregulation at initial stages of infection may play an important role in disease pathogenesis. IL-1A, interleukin-1 beta (IL-1B), and IL-8 were significantly downregulated in septicemic melioidosis patients compared to their expression in other sepsis cases. These differentially expressed genes may serve as biomarkers for melioidosis diagnosis and targets for therapeutic intervention and may help us understand immune response mechanisms. IMPORTANCE Melioidosis is a life-threatening infectious disease caused by a soil-associated Gram-negative bacterium, B. pseudomallei. Melioidosis is endemic in Southeast Asia and northern Australia; however, the global distribution of B. pseudomallei and the disease burden of melioidosisis are still poorly understood. Melioidosis is difficult to treat, as B. pseudomallei is intrinsically resistant to many antibiotics and requires a long course of antibiotic treatment. The mortality rates remain high in areas of endemicity, with reoccurrence being common. Therefore, it is imperative to diagnose the disease at an early stage and provide vital clinical care to reduce the mortality rate. With limitations in treatment and lack of a vaccine, it is crucial to study the immune response mechanisms to this infection to get a better understanding of disease susceptibility and pathogenesis. Therefore, this study aimed to analyze the gene expression levels of important cytokines to establish useful correlations for diagnostic and therapeutic purposes.

Sri Lankan National Melioidosis Surveillance Program Uncovers a Nationwide Distribution of Invasive Melioidosis

The epidemiologic status of melioidosis in Sri Lanka was unclear from the few previous case reports. We established laboratory support for a case definition and started a nationwide case-finding study. Suspected Burkholderia pseudomallei isolates were collated, identified by polymerase chain reaction assay, referred for Matrix Assisted Laser Desorption Ionization-Time of Flight analysis and multilocus sequence typing (MLST), and named according to the international MLST database. Between 2006 and early 2014, there were 32 patients with culture-confirmed melioidosis with an increasing annual total and a falling fatality rate. Patients were predominantly from rural communities, diabetic, and male. The major clinical presentations were sepsis, pneumonia, soft tissue and joint infections, and other focal infection. Burkholderia pseudomallei isolates came from all parts of Sri Lanka except the Sabaragamuwa Province, the south central hill country, and parts of northern Sri Lanka. Bacterial isolates belonged to 18 multilocus sequence types, one of which (ST 1137) was associated with septicemia and a single-organ focus (Fisher's exact, P = 0.004). Melioidosis is an established endemic infection throughout Sri Lanka, and is caused by multiple genotypes of B. pseudomallei, which form a distinct geographic group based upon related sequence types (BURST) cluster at the junction of the southeast Asian and Australasian clades.

Rapid diagnostics for melioidosis: a comparative study of a novel lateral flow antigen detection assay

The rapid diagnosis of septicaemic melioidosis will have an impact on reduction of mortality. Currently, this relies almost exclusively upon culture of the causative agent Burkholderia pseudomallei from clinical samples. In acute sepsis, blood is the preferred specimen for culture and therefore should be the target for a rapid diagnostic tool. A lateral flow immunoassay (LFI) for the detection of B. pseudomallei antigen has been developed. This was compared with molecular detection using the targets T3SS1 and IpxO. Forty-five clinical samples of EDTA blood, which were culture-positive, were tested using both modalities. The LFI had a sensitivity of 40 %, whilst molecular detection had a sensitivity of 20 %. The poor performance of molecular detection has been described previously and is largely related to the use of whole-blood specimens collected into blood tubes containing EDTA. Whilst suboptimal, the LFI would be an adjunct in the rapid diagnosis of melioidosis.

Laboratory diagnosis of melioidosis: past, present and future

Melioidosis is an emerging, potentially fatal disease caused by Burkholderia pseudomallei, which requires prolonged antibiotic treatment to prevent disease relapse. However, difficulties in laboratory diagnosis of melioidosis may delay treatment and affect disease outcomes. Isolation of B. pseudomallei from clinical specimens has been improved with the use of selective media. However, even with positive cultures, identification of B. pseudomallei can be difficult in clinical microbiology laboratories, especially in non-endemic areas where clinical suspicion is low. Commercial identification systems may fail to distinguish between B. pseudomallei and closely related species such as Burkholderia thailandensis. Genotypic identification of suspected isolates can be achieved by sequencing of gene targets such as groEL which offer higher discriminative power than 16S rRNA. Specific PCR-based identification of B. pseudomallei has also been developed using B. pseudomallei-specific gene targets such as Type III secretion system and Tat-domain protein. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry, a revolutionary technique for pathogen identification, has been shown to be potentially useful for rapid identification of B. pseudomallei, although existing databases require optimization by adding reference spectra for B. pseudomallei. Despite these advances in bacterial identification, diagnostic problems encountered in culture-negative cases remain largely unresolved. Although various serological tests have been developed, they are generally unstandardized "in house" assays and have low sensitivities and specificities. Although specific PCR assays have been applied to direct clinical and environmental specimens, the sensitivities for diagnosis remain to be evaluated. Metabolomics is an uprising tool for studying infectious diseases and may offer a novel approach for exploring potential diagnostic biomarkers. The metabolomics profiles of B. pseudomallei culture supernatants can be potentially distinguished from those of related bacterial species including B. thailandensis . Further studies using bacterial cultures and direct patient samples are required to evaluate the potential of metabolomics for improving diagnosis of melioidosis.

Pathological findings and diagnostic implications of a rhesus macaque (Macacca mulatta) model of aerosol exposure to Burkholderia mallei (glanders)

Burkholderia mallei is a Gram-negative bacillus that causes a pneumonic disease known as glanders in equids and humans, and a lymphatic infection known as farcy, primarily in equids. With the potential to infect humans by the respiratory route, aerosol exposure can result in severe, occasionally fatal, pneumonia. Today, glanders infections in humans are rare, likely due to less frequent contact with infected equids than in the past. Acutely ill humans often have non-specific clinical signs and in order to diagnose cases, especially in scenarios of multiple cases in an unexpected setting, rapid diagnostics for B. mallei may be critical. The pathogenesis of acute glanders in the rhesus macaque (Macaca mulatta) was studied as an initial effort to improve diagnostic methods. In the study described here, the diagnostic techniques of PCR, culture and histopathology were compared. The results indicated that PCR may provide rapid, non-invasive diagnosis of glanders in some cases. As expected, PCR results were positive in lung tissue in 11/12 acutely infected rhesus macaques, but more importantly in terms of diagnostic algorithm development, PCR results were frequently positive in non-invasive samples such as broncho-alveolar lavage or nasal swabs (7/12) and occasionally in blood (3/12). However, conventional bacterial culture failed to recover bacteria in many of these samples. The study showed that the clinical presentation of aerosol-exposed rhesus macaques is similar to descriptions of human glanders and that PCR has potential for rapid diagnosis of outbreaks, if not individual cases.

Volatile-sulfur-compound profile distinguishes Burkholderia pseudomallei from Burkholderia thailandensis

Solid-phase microextraction gas chromatography-mass spectrometry (SPME-GCMS) was used to show that dimethyl sulfide produced by Burkholderia pseudomallei is responsible for its unusual truffle-like smell and distinguishes the species from Burkholderia thailandensis. SPME-GCMS can be safely used to detect dimethyl sulfide produced by agar-grown B. pseudomallei.

Systematic review and consensus guidelines for environmental sampling of Burkholderia pseudomallei

Background

Burkholderia pseudomallei, a Tier 1 Select Agent and the cause of melioidosis, is a Gram-negative bacillus present in the environment in many tropical countries. Defining the global pattern of B. pseudomallei distribution underpins efforts to prevent infection, and is dependent upon robust environmental sampling methodology. Our objective was to review the literature on the detection of environmental B. pseudomallei, update the risk map for melioidosis, and propose international consensus guidelines for soil sampling.

Methods/Principal Findings

An international working party (Detection of Environmental Burkholderia pseudomallei Working Party (DEBWorP)) was formed during the VIth World Melioidosis Congress in 2010. PubMed (January 1912 to December 2011) was searched using the following MeSH terms: pseudomallei or melioidosis. Bibliographies were hand-searched for secondary references. The reported geographical distribution of B. pseudomallei in the environment was mapped and categorized as definite, probable, or possible. The methodology used for detecting environmental B. pseudomallei was extracted and collated. We found that global coverage was patchy, with a lack of studies in many areas where melioidosis is suspected to occur. The sampling strategies and bacterial identification methods used were highly variable, and not all were robust. We developed consensus guidelines with the goals of reducing the probability of false-negative results, and the provision of affordable and ‘low-tech’ methodology that is applicable in both developed and developing countries.

Conclusions/Significance

The proposed consensus guidelines provide the basis for the development of an accurate and comprehensive global map of environmental B. pseudomallei.

Melioidosis is a serious infectious disease caused by the Tier 1 selected agent and Gram-negative environmental saprophyte, Burkholderia pseudomallei. The organism is commonly found in soil and water in melioidosis endemic areas. Infection in humans occurs following bacterial inoculation, inhalation or ingestion. There is a striking lack of accurate information on the global risk of melioidosis, something that could be determined from the global distribution of environmental B. pseudomallei. Soil sampling to detect the presence of B. pseudomallei has been ad hoc, poorly standardized, and the available information poorly collated. Negative studies are almost never reported, and there is no published review on this topic. We responded to this problem during the VI^th World Melioidosis Congress held in Townsville, Australia in December 2010 by forming the ‘Detection of Environmental Burkholderia pseudomallei Working Party (DEBWorP)’. We have since worked together to undertake a systematic review, map the available information, and reach a consensus on low cost methods for the detection of environmental B. pseudomallei. Our goal is to promote the use of these consensus methods and encourage people worldwide to participate in an effort to produce a comprehensive global map of environmental B. pseudomallei.

Application of polymerase chain reaction to detect burkholderia pseudomallei and Brucella species in buffy coat from patients with febrile illness among rural and peri-urban population

Context:

Melioidosis and Brucellosis are important endemic infections among people in India, especially in rural settings. Conventional detection techniques have several limitations. Only a few studies exist on the prevalence of Melioidosis and Brucellosis in rural area especially in India.

Aim:

We sought to evaluate detection of Burkholderia pseudomallei and Brucella spp. among patients presenting febrile illness.

Material and Methods:

Previously described polymerase chain reaction (PCR) assays for both pathogens were evaluated with Deoxyribonucleic acid extracts of buffy coat samples collected from 301 patients recruited prospectively. Data was not amenable to statistical analysis.

Results:

The PCR showed specific amplification and no non-specific amplification with heterologous Gram-negative bacilli. The lower limit of detection of the assay for B. pseudomallei was determined to be 1 colony-forming unit /mL and for Brucella it was 1.95 × 10³ plasmids per microliter. Blood culture in automated blood culture system was negative for all the samples. This prospective study carried out in southern India for the first time. PCR for Brucella was positive in 1% of the patient samples whereas 0.3% was positive for B. pseudomallei.

Conclusion:

The finding of Brucella and Burkholderia infections in our populations leads us to suggest that tests for Brucella and B. pseudomallei should also form part of a diagnostic platform for patients with Pyrexia of unknown origin in tropical developing countries.

Use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis for rapid confirmation of Burkholderia pseudomallei in septicemic melioidosis

Burkholderia pseudomallei was quickly identified from blood cultures collected from septicemic patients by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis using an in-house reference library. This procedure reduced the time to definitive identification by more than 24 hours. This analysis is a useful addition to laboratory methods for early recognition of septicemic melioidosis in non-endemic settings.

Clinical-epidemiological features of 13 cases of melioidosis in Brazil

The aim of this work was to catalog the clinical and ecoepidemiological characteristics of melioidosis in Brazil. The clinical-epidemiological features of melioidosis in Ceará are similar to those in other regions where the disease is endemic. These findings support the inclusion of this Brazilian state as part of the zone of endemicity for melioidosis.

Comparison of TaqMan PCR assays for detection of the melioidosis agent Burkholderia pseudomallei in clinical specimens

Melioidosis is an emerging infectious disease caused by the soil bacterium Burkholderia pseudomallei. In diagnostic and forensic settings, molecular detection assays need not only high sensitivity with low limits of detection but also high specificity. In a direct comparison of published and newly developed TaqMan PCR assays, we found the TTS1-orf2 assay to be superior in detecting B. pseudomallei directly from clinical specimens. The YLF/BTFC multiplex assay (targeting the Yersinia-like fimbrial/Burkholderia thailandensis-like flagellum and chemotaxis region) also showed high diagnostic sensitivity and provides additional information on possible geographic origin.

The aftermath of the Western Australian melioidosis outbreak

Melioidosis became a notifiable disease in Western Australia (WA) 2 years after the West Kimberley melioidosis outbreak. Two cases of melioidosis caused by the outbreak genotype of Burkholderia pseudomallei (National Collection of Type Cultures [NCTC] 13177) occurred in 1998 and 1999 in persons who visited the outbreak location at the time. No other infections caused by the outbreak strain have been recorded in WA since that time, despite an average of four culture-positive cases per year. Sporadic cases of melioidosis often follow tropical storms and cyclones during summer, and they have been detected outside the endemic area when cyclones travel far inland. In 2007, environmental isolates resembling NCTC 13177 were found 500 km east of the outbreak location after unusually severe weather. Recent whole-genome analysis places NCTC 13177 genetically close to other Australian isolates. Additional biogeographic and ecological studies are needed to establish the relative importance of environmental cofactors in disease pathogenesis.

[Mission oriented diagnostic real-time PCR]

In out of area military missions soldiers are potentially exposed to bacteria that are endemic in tropical areas and can be used as biological agents. It can be difficult to culture these bacteria due to sample contamination, low number of bacteria or pretreatment with antibiotics. Commercial biochemical identification systems are not optimized for these agents which can result in misidentification. Immunological assays are often not commercially available or not specific. Real-time PCR assays are very specific and sensitive and can shorten the time required to establish a diagnosis markedly. Therefore, real-time PCRs for the identification of Bacillus anthracis, Brucella spp., Burkholderia mallei und Burkholderia pseudomallei, Francisella tularensis und Yersinia pestis have been developed. PCR results can be false negative due to inadequate clinical samples, low number of bacteria in samples, DNA degradation, inhibitory substances and inappropriate DNA preparation. Hence, it is crucial to cultivate the organisms as a prerequisite for adequate antibiotic therapy and typing of the agent. In a bioterrorist scenario samples have to be treated according to rules applied in forensic medicine and documentation has to be flawless.

Development and evaluation of polymerase chain reaction assay to detect Burkholderia genus and to differentiate the species in clinical specimens

Molecular-based techniques are becoming desirable as tools for identification of infectious diseases. Amongst the Burkholderia spp., there is a need to differentiate Burkholderia pseudomallei from Burkholderia cepacia, as misidentification could lead to false treatment of patients. In this study, conventional PCR assay targeting three genes was developed. Primers were designed for the amplification of Burkholderia genus-specific groEL gene, B. pseudomallei-specific mprA gene and B. cepacia-specific zmpA gene. The specificity and sensitivity of the assay was tested with 15 negative control strains and 71 Burkholderia spp. isolates including positive controls B. pseudomallei K96243 and ATCC B. cepacia strain. All B. pseudomallei strains were positive for groEL (139 bp) and mprA (162 bp), indicating a sensitivity of 100%. All B. cepacia strains produced amplicons for detection of groEL and zmpA (147 bp). Specificity using negative strains was 100%. In this study, a PCR assay specific for the detection of Burkholderia spp. and differentiation of the genus B. pseudomallei and B. cepacia was developed. The conventional assay has to be performed separately for each species due to the similar size of the PCR products amplified. This format may therefore be recommended for use as a diagnostic tool in laboratories where real-time PCR machines are not available. However, the real-time PCR was able to detect and differentiate the genus and species in single duplex assay.

A diagnosis of Burkholderia pseudomallei directly in a bronchoalveolar lavage by polymerase chain reaction

Melioidosis is an infectious disease caused by the Gram-negative bacterium Burkholderia pseudomallei. Interest in the molecular identification of B. pseudomallei has increased after its classification as a category B agent by the US Centers for Disease Control and Prevention. The present article reports a diagnosis of B. pseudomallei directly in a bronchoalveolar lavage by polymerase chain reaction amplification. The results obtained show that direct detection of the 16-23s spacer sequence in bronchoalveolar lavage is a quick and specific test to diagnose melioidosis.

Inactivation of virulent Burkholderia pseudomallei by sunlight

The goal of this study was to determine the sensitivity of virulent Burkholderia pseudomallei to natural sunlight. We describe solar dosimetry calibrated to integrate radiation between 295 and 305 nm and an exposure system that minimizes thermal effects on bacterial cells. Burkholderia pseudomallei cells were either exposed to sunlight in UV transparent dishes or maintained in the dark covered by opaque foil. The cells maintained in the dark remained at constant levels for the duration of all experiments. The exposed cells nearby were killed with a kinetic studied through 5 Log10 inactivation. We found that cells in stationary phase of growth were nearly two-fold more resistant to sunlight than cells in lag or exponential growth. A virulent strain of B. pseudomallei that produced mucoid colonies showed sensitivity to sunlight similar to both a virulent strain that produced nonmucoid colonies and a strain of B. thailandensis. The inactivation of B. pseudomallei by sunlight in different types of water of environmental relevance or inside amoebae was investigated. The sensitivity of virulent B. pseudomallei was calculated and its comparison with previous studies employing monochromatic germicidal light (254 nm) is discussed. This may be the first report in the open literature of the inactivation of a virulent biological threat agent by natural sunlight. These data should assist in estimating the risk for contracting melioidosis and in predicting the time period during which B. pseudomallei remains infectious after an accidental or intentional release in the environment.

Comparison of routine bench and molecular diagnostic methods in identification of Burkholderia pseudomallei

This study compared the identification of Burkholderia pseudomallei with that of related organisms. Bench tests and latex agglutination were compared with molecular identification. Using bench tests and latex agglutination alone, 100% (30/30) of B. pseudomallei isolates were correctly identified. Amoxicillin-clavulanate susceptibility testing was also a good and simple discriminatory test.

Deployable laboratory response to emergence of melioidosis in central Sri Lanka

A portable molecular diagnostic laboratory was used to provide molecular confirmation of suspected melioidosis cases seen at Peradeniya Hospital, central Sri Lanka. Soil supernatants from rice field and rubber plantation samples also produced PCR-positive results. These procedures could be used for melioidosis field work in other remote locations.

Principia ætiologica: taking causality beyond Koch's postulates

There is no single accepted method to establish a causal relationship between an infective agent and its corresponding infectious disease. Different biomedical disciplines use a patchwork of distinct but overlapping approaches. To a greater or lesser extent these are based on criteria known as the Koch–Henle postulates, or ‘Koch's postulates' for short. Deficiencies in Koch's postulates were recognized by their principal author shortly after their formulation. Now, over a century later, a more rigorous method to test causality has still to be finalized. One contender is a method that uses molecular methods to establish a causal relationship (‘molecular Koch's postulates'). Recognizing the wider range of contemporary approaches used to build an argument for a causal relationship, the use of a more inclusive approach to establish proof of causality is proposed. This method uses an argument built from a series of assertions. Assertion 1: congruence or reproducible correlation of a taxonomically defined life form with the clinico-pathological and epidemiological features of infection. Assertion 2: consistency of the demonstrable biological response in the subject to an encounter with the prospective infective agent. Assertion 3: progressive or cumulative dissonance as an explanation for pathophysiological processes at every known level of biological organization in the subject. Assertion 4: curtailment of that pathophysiological process on the deliberate introduction of a specified biomedical intervention. Evidence to implicate the candidate biological entity as an initiator of or primer for cumulative dissonance places it in a subcategory of micro-organisms to be known as ‘priobes’. A priobe is the sufficient and necessary antecedent cause of a pathophysiological process evident as an infectious disease.