Reliability of automated biochemical identification of Burkholderia pseudomallei is regionally dependent

Diagnostic accuracy of automation and non-automation techniques for identifying Burkholderia pseudomallei: A systematic review and meta-analysis

BACKGROUND

Burkholderia pseudomallei, a Gram-negative pathogen, causes melioidosis. Although various clinical laboratory identification methods exist, culture-based techniques lack comprehensive evaluation. Thus, this systematic review and meta-analysis aimed to assess the diagnostic accuracy of culture-based automation and non-automation methods.

METHODS

Data were collected via PubMed/MEDLINE, EMBASE, and Scopus using specific search strategies. Selected studies underwent bias assessment using QUADAS-2. Sensitivity and specificity were computed, generating pooled estimates. Heterogeneity was assessed using I2 statistics.

RESULTS

The review encompassed 20 studies with 2988 B. pseudomallei samples and 753 non-B. pseudomallei samples. Automation-based methods, particularly with updating databases, exhibited high pooled sensitivity (82.79%; 95% CI 64.44-95.85%) and specificity (99.94%; 95% CI 98.93-100.00%). Subgroup analysis highlighted superior sensitivity for updating-database automation (96.42%, 95% CI 90.01-99.87%) compared to non-updating (3.31%, 95% CI 0.00-10.28%), while specificity remained high at 99.94% (95% CI 98.93-100%). Non-automation methods displayed varying sensitivity and specificity. In-house latex agglutination demonstrated the highest sensitivity (100%; 95% CI 98.49-100%), followed by commercial latex agglutination (99.24%; 95% CI 96.64-100%). However, API 20E had the lowest sensitivity (19.42%; 95% CI 12.94-28.10%). Overall, non-automation tools showed sensitivity of 88.34% (95% CI 77.30-96.25%) and specificity of 90.76% (95% CI 78.45-98.57%).

CONCLUSION

The study underscores automation's crucial role in accurately identifying B. pseudomallei, supporting evidence-based melioidosis management decisions. Automation technologies, especially those with updating databases, provide reliable and efficient identification.

Improving the clinical recognition, prognosis, and treatment of melioidosis through epidemiology and clinical findings: The Sabah perspective

INTRODUCTION

Melioidosis is a deadly endemic disease in northern Australia and Southeast Asia, including Sabah, Malaysia, which is caused by the bacterium Burkholderia pseudomallei. It contributes to high fatality rates, mainly due to misdiagnosis leading to the wrong treatment being administered to the patients. Local epidemiology and data on clinical features could assist clinicians during diagnosis and treatment. However, these details are still scarce, particularly in Sabah.

METHODS

A retrospective study of 246 culture-confirmed melioidosis cases in Queen Elizabeth Hospital, Sabah, Malaysia was performed between 2016 and 2018. The epidemiological data and clinical and laboratory findings were extracted and analysed.

RESULTS

The annual incidence of culture-confirmed melioidosis cases was estimated to be 4.97 per 100,000 people. The mean age of the patients was 50±15 years. Males and members of the Kadazan-Dusun ethnic group accounted for the majority of the melioidosis cases. The odds ratio analysis indicated that bacteraemic melioidosis in this region was significantly associated with fever (76%), and patients having at least one underlying illness (43%), including diabetes mellitus (32%). Sixty-eight patients (28%) succumbed to melioidosis. Contrary to what is known regarding factors that promote bacteraemic melioidosis, neither patients with fever nor patients with at least one comorbid disease, including diabetes mellitus, were significantly associated with death from melioidosis. There was no statistically significant difference between patients without comorbidities (24, 27%) and those with at least one comorbid disease (26, 25%), including diabetes mellitus (18, 23%). The odds ratios indicate that melioidosis mortality in this region is related to patients showing respiratory organ-associated symptoms (29%), bacteraemia (30%), and septic shock (47%). Burkholderia pseudomallei isolates in this study were highly susceptible to ceftazidime (100%), imipenem (100%), and trimethoprim-sulfamethoxazole (98%).

CONCLUSIONS

Information obtained from this study can be used by clinicians to recognise individuals with the highest risk of acquiring melioidosis, estimate an accurate prognosis, and provide effective treatment for melioidosis patients to reduce death from melioidosis.

Development of a qPCR detection approach for pathogenic Burkholderia cenocepacia associated with fresh vegetables

Natural environment serves as a reservoir for Burkholderia cepacia complex organisms, including the highly transmissible opportunistic human pathogen B. cenocepacia. Currently, there is a lack of an effective and quantitative method for B. cenocepacia detection in fresh food and other environmental niches. A quantitative real-time PCR (qPCR) detection method for B. cenocepacia bacteria was established in this study and validated using artificially inoculated fresh vegetable samples. Genome-wide comparative methods were applied to identify target regions for the design of species-specific primers. Assay specificity was measured with 12 strains of closely related Burkholderia bacteria and demonstrated the primer pair BCF6/R6 were 100% specific for detection of B. cenocepacia. The described qPCR assay evaluated B. cenocepacia with a 2 pg μl-1 limit of detection and appropriate linearity (R2 = 0.999). In 50 samples of experimentally infected produce (lettuce, onion, and celery), the assay could detect B. cenocepacia as low as 2.6 × 102 cells in each sample equal to 1 g. The established qPCR method quantitatively detects B. cenocepacia with high sensitivity and specificity, making it a promising technique for B. cenocepacia detection and epidemiological research on B. cepacia complex organisms from fresh vegetables.

Foremost report of the whole genome of Spirabiliibacterium mucosae from India and comparative genomics of the novel genus Spirabiliibacterium

Several Pasteurella like organisms isolated from various avian species were recently reclassified into new genus based on whole genome sequence analysis. One such Pasteurella like organism, Bisgaard taxon 14 was classified as Spirabiliibacterium mucosae. In the present study, a Gram-negative organism was isolated from ailing pigeons with respiratory infection from a farm in Tamil Nadu, India and the organism was misidentified as Burkholderia mallei by Vitek 2 compact system based on biochemical characterization. Since, B. mallei is highly pathogenic and zoonotic, to further confirm, 16S rDNA sequencing and analysis was carried out which revealed that the strain belonged to Bisgaard taxon 14 (Spirabiliibacterium mucosae). To further confirm the findings, whole genome sequencing of the isolate was performed. Whole genome phylogeny and average nucleotide identity (ANI) analysis showed that the genome was closely matching with Spirabiliibacterium mucosae type strain 20,609 /3. Hence, the strain from pigeon was named as Spirabiliibacterium mucosae TN_CUL_2021 and the genome was submitted in NCBI SRA database. The genome of S. mucosase TN_CUL_2021 is only the second genome available worldwide in the NCBI database. Comparative genome analysis of 26 Pasteurellaceae family strains revealed 1101 genes specific for Spirabiliibacterium mucosae. Similarly, luxS virulence gene was found only in S. mucosae and Bisgaardia hudsonensis strains. Since there are only 2 genomes available in the NCBI genome database, further studies on isolation of S. mucosae needs to be carried out to identify its epidemiology and pathogenesis so as to develop better diagnostic assays and vaccines.

Workflow for Identification of <i>Burkholderia pseudomallei</i> Clinical Isolates in Myanmar

Burkholderia pseudomallei, the highly infectious and causative organism of melioidosis, was first identified in Myanmar in 1911. B. pseudomallei was identified in Myanmar because of its genetic relatedness to Burkholderia species. In this study, we identified two isolates of Burkholderia cenocepacia, two Acinetobacter baumannii complexes, and 18 clinical isolates of B. pseudomallei using Vitek 2. These isolates were first screened using a latex agglutination test, which showed positive results in 20 of the 22 isolates. All isolates were cultured on Ashdown՚s agar and further tested using molecular methods. Specific PCR for type III secretion system (TTSs) gene clusters indicated 19 B. pseudomallei isolates out of 22 isolates. Furthermore, 16S rRNA and recA gene sequencing were used as the gold standard methods and yielded the same results. RapID NF Plus detected 16 B. pseudomallei out of 22 isolates. Vitek 2 and RapID NF Plus should be considered key tools in the diagnosis of melioidosis and surveillance of B. pseudomallei in Myanmar; however, accurate identification must be confirmed by TTS1 PCR. This study evaluated the presumptive workflow for the investigation of B. pseudomallei infections using different methods and options, in line with the available equipment.

Research on the establishment and application of protein fingerprint spectrum database of Burkholderia pseudomallei in Hainan Province China

Burkholderia pseudomallei (B. pseudomallei) is the etiologic agent of melioidosis. The aim of this study was to establish a SuperSpectrum of B. pseudomallei in Hainan and evaluate its application value in the rapid identification of clinical isolates of B. pseudomallei. In total, 99 isolates of B. pseudomallei were obtained between 2010-2019 in different regions of Hainan Province, multilocus sequence typing (MLST) was performed, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was applied for spectrum acquisition. A SuperSpectrum was created based on the selection of 80 representative average spectra for 17 isolates of B. pseudomallei. Then we validated the SuperSpectra with 82 strains of B. pseudomallei, eight strains of Burkholderia thailandensis, two strains of Burkholderia cepacia, one strain of Burkholderia cenocepacia and one strain of Burkholderia multivorans, as well as one strain of Burkholderia gladioli identified by MLST typing, 16S rRNA gene sequencing and Vitek 2 Compact. The results showed that all samples in this study were confirmed at the species level. Protein fingerprints spectra showed that specific peaks occurred in B. pseudomallei from the Hainan region. The result of clustering typing indicated that B. pseudomallei and its closely related species could be well classified by MALDI-TOF MS at the protein level.

Humoral Immune Responses to Burkholderia pseudomallei Antigens in Captive and Wild Macaques in the Western Part of Java, Indonesia

Burkholderia pseudomallei, the Gram-negative bacterium which causes melioidosis, is a threat to human and a wide range of animal species. There is an increased concern of melioidosis in Indonesian primate facilities, especially following case reports of fatal melioidosis in captive macaques and orangutans. Our preliminary serosurveillance of immunoglobulin G (IgG) to B. pseudomallei lipopolysaccharide showed that a significant number of captive and wild macaques in the western part of Java, Indonesia, have been exposed to B. pseudomallei. To better characterize the humoral immune response in those animals, a panel of assays were conducted on the same blood plasma specimens that were taken from 182 cynomolgus macaques (M. fascicularis) and 88 pig-tailed macaques (M. nemestrina) reared in captive enclosures and wild habitats in the western part of Java, Indonesia. The enzyme-linked immunosorbent assays (ELISAs) in this study were conducted to detect IgG against B. pseudomallei proteins; alkyl hydroperoxide reductase subunit C (AhpC), hemolysin-coregulated protein (Hcp1), and putative outer membrane porin protein (OmpH). The performances of those immunoassays were compared to ELISA against B. pseudomallei LPS, which has been conducted previously. Seropositivity to at least one assay was 76.4% (139/182) and 13.6% (12/88) in cynomolgus macaques and pig-tailed macaques, respectively. Analysis of demographic factors showed that species and primate facility were significant factors. Cynomolgus macaques had higher probability of exposure to B. pseudomallei. Moreover, macaques in Jonggol facility also had higher probability, compared to macaques in other facilities. There were no statistical associations between seropositivity with other demographic factors such as sex, age group, and habitat type. There were strong positive correlations between the absorbance results of AhpC, HcpI, and OmpH assays, but not with LPS assay. Our analysis suggested that Hcp1 assay would complement LPS assay in melioidosis serosurveillance in macaques.

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.

Melioidosis in Colombia, description of a clinical case and epidemiological considerations

Melioidosis is an infectious disease caused by Burkholderia pseudomallei whose clinical diagnosis can be difficult due not only to its varied clinical presentation but also to the difficulties in the microbiological diagnosis.Thus, it may be necessary to use molecular techniques for its proper identification once it is suspected. There are few antibiotics available for the treatment of this disease, which must be used over a long period of time. Although it is known to be endemic in Thailand, Malaysia, Singapore, Vietnam, and Australia, in Colombia there are few reported cases. We describe a case of melioidosis in the northern region of Colombia. Additionally, we review its clinical characteristics and treatment and we describe the local epidemiology of this disease.

Melioidosis: An Australian Perspective

Burkholderia pseudomallei is endemic in northern Australia, with cases of melioidosis most commonly occurring during the wet season in individuals with diabetes, hazardous alcohol use, and chronic kidney disease. Pneumonia is the most common presentation and the majority of patients are bacteraemic—however, infection may involve almost any organ, with the skin and soft tissues, genitourinary system, visceral organs, and bone and joints affected most commonly. Central nervous system involvement is rarer, but has a high attributable mortality. Increased awareness of the disease amongst healthcare providers, ready access to appropriate antibiotic therapy and high-quality intensive care services has resulted in a sharp decline in the case fatality rate over the last 20 years. Further improvement in clinical outcomes will require a greater understanding of the disease′s pathophysiology, its optimal management, and more effective strategies for its prevention.

Melioidosis in Mexico, Central America, and the Caribbean

Burkholderia pseudomallei is the causative agent of melioidosis, an endemic disease in tropical areas around the world. Cumulative human cases have demonstrated that melioidosis is prevalent and increasingly recognized in the American continent. Even though the first reports of melioidosis in Mexico, Central America, and the Caribbean Islands date back to the late 1940s, the potential of the disease as a public health concern in the region has not been fully appreciated. Unfortunately, recent studies predicting the global distribution of the disease and the demonstration of melioidosis endemicity in Puerto Rico have not increased recognition of the disease by health professionals in this region. Furthermore, a lack of both diagnostic capacity and awareness of the disease has resulted in a limited number of studies that have attempted to accurately determine its prevalence and geographical distribution. In this review, a summary of reported cases in the countries of this region are presented, as well as recommendations to increase the diagnosis and awareness of the disease as an important public health problem in Mexico, Central America, and the Caribbean islands.

Melioidosis in Malaysia: Incidence, Clinical Challenges, and Advances in Understanding Pathogenesis

Malaysia is an endemic hot spot for melioidosis; however, a comprehensive picture of the burden of disease, clinical presentations, and challenges faced in diagnosis and treatment of melioidosis is not available. This review provides a nonexhaustive overview of epidemiological data, clinical studies, risk factors, and mortality rates from available literature and case reports. Clinical patterns of melioidosis are generally consistent with those from South and Southeast Asia in terms of common primary presentations with diabetes as a major risk factor. Early diagnosis and appropriate management of Malaysian patients is a key limiting factor, which needs to be addressed to reduce serious complications and high mortality and recurrence rates. Promoting awareness among the local healthcare personnel is crucial to improving diagnostics and early treatment, as well as educating the Malaysian public on disease symptoms and risk factors. A further matter of urgency is the need to make this a notifiable disease and the establishment of a national melioidosis registry. We also highlight local studies on the causative agent, Burkholderia pseudomallei, with regards to bacteriology and identification of virulence factors as well as findings from host⁻pathogen interaction studies. Collectively, these studies have uncovered new correlations and insights for further understanding of the disease.

Melioidosis in Brunei Darussalam

Melioidosis continues to be a major health care problem in Brunei Darussalam. The age of patients, gender distribution, risk factors, and clinical presentations are similar to those reported from other countries in the region. The incidence of melioidosis was high during the wet months and in the Temburong district, which has the highest annual rainfall. In spite of adequate facilities for diagnosis and treatment, the mortality remains high (27%). Women and those presenting with septic shock had higher mortality. There is a case for making melioidosis a notifiable disease in Brunei Darussalam. Coordinated efforts between policy-makers and various stakeholders are required to effectively combat the disease.

Influence of Biochemical Features of Burkholderia pseudomallei Strains on Identification Reliability by Vitek 2 System

Background:

Burkholderia pseudomallei is a Gram-negative saprophytic soil bacterium that causes melioidosis, a potentially fatal disease endemic in wet tropical areas. The currently available biochemical identification systems can misidentify some strains of B. pseudomallei. The aim of the present study was to identify the biochemical features of B. pseudomallei, which can affect its correct identification by Vitek 2 system.

Materials and Methods:

The biochemical patterns of 40 B. pseudomallei strains were obtained using Vitek 2 GN cards. The average contribution of biochemical tests in overall dissimilarities between correctly and incorrectly identified strains was assessed using nonmetric multidimensional scaling.

Results:

It was found (R statistic of 0.836, P = 0.001) that a combination of negative N-acetyl galactosaminidase, β-N-acetyl glucosaminidase, phosphatase, and positive D-cellobiase (dCEL), tyrosine arylamidase (TyrA), and L-proline arylamidase (ProA) tests leads to low discrimination of B. pseudomallei, whereas a set of positive dCEL and negative N-acetyl galactosaminidase, TyrA, and ProA determines the wrong identification of B. pseudomallei as Burkholderia cepacia complex.

Conclusion:

The further expansion of the Vitek 2 identification keys is needed for correct identification of atypical or regionally distributed biochemical profiles of B. pseudomallei.

Development of a multiplex PCR assay for the detection and differentiation of Burkholderia pseudomallei, Burkholderia mallei, Burkholderia thailandensis, and Burkholderia cepacia complex

Two species of Burkholderia pseudomallei complex (Bpc), B. pseudomallei and B. mallei, can cause severe life-threatening infections. Rapidly discerning individual species within the group and separating them from other opportunistic pathogens of the Burkholderia cepacia complex (Bcc) is essential to establish a correct diagnosis and for epidemiological surveillance. In this study, a multiplex PCR assay based on the detection of an individual set of chromosomal beta-lactamase genes for single-step identification and differentiation of B. pseudomallei, B. mallei, B. thailandensis, and Bcc was developed. Two pairs of primers specific to a distinct class of B metallo-beta-lactamase genes and a pair of primers specific to the oxacillin-hydrolyzing class D beta-lactamase gene were demonstrated to successfully discriminate species within Bpc and from Bcc. The assay sensitivity was 9561 genomic equivalents (GE) for B. pseudomallei, 7827 GE for B. mallei, 8749 GE for B. thailandensis and 6023 GE for B. cepacia.

Melioidosis diagnostic workshop, 2013

Melioidosis is a severe disease that can be difficult to diagnose because of its diverse clinical manifestations and a lack of adequate diagnostic capabilities for suspected cases. There is broad interest in improving detection and diagnosis of this disease not only in melioidosis-endemic regions but also outside these regions because melioidosis may be underreported and poses a potential bioterrorism challenge for public health authorities. Therefore, a workshop of academic, government, and private sector personnel from around the world was convened to discuss the current state of melioidosis diagnostics, diagnostic needs, and future directions.

Evaluation of the Remel RapID NF plus rapid biochemical method for identification of Burkholderia pseudomallei

Typical methods for the identification of Burkholderia pseudomallei colonies produce results in 18 h. The Remel RapID NF Plus kit produces results in 4 h. We used the kit for 190 stored B. pseudomallei isolates and correctly identified 189 of them. This kit produces consistent results for known B. pseudomallei isolates.