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.

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.

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.

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.

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.

Melioidosis presenting as lymphadenitis: a case report

BACKGROUND

Melioidosis is an infection caused by the facultative intracellular gram-negative bacterium; Burkholderia pseudomallei. It gives rise to protean clinical manifestations and has a varied prognosis. Although it was rare in Sri Lanka increasing numbers of cases are being reported with high morbidity and mortality. Here we report a case of melioidosis presenting with lymphadenitis which was diagnosed early and treated promptly with a good outcome.

CASE PRESENTATION

A 53-year-old Sinhalese woman with diabetes presented with fever and left sided painful inguinal lymphadenitis for one month. She had undergone incision and drainage of a thigh abscess three months previously and had been treated with a short course of antibiotics. There was no record that abscess material was tested microbiologically.She had neutrophil leukocytosis and elevated inflammatory markers. Initial pus culture revealed a scanty growth of "Pseudomonas sp." and Escherichia coli which were sensitive to ceftazidime and resistant to gentamicin.Due to the history of diabetes, recurrent abscess formation and the suggestive sensitivity pattern of the bacterial isolates, we actively investigated for melioidosis. The bacterial isolate was subsequently identified as B. pseudomallei by polymerase chain reaction and antibodies to melioidin antigen were found to be raised at a titre of 1:160.The patient was treated with high dose intravenous ceftazidime for four weeks followed by eradication therapy with cotrimoxazole and doxycycline. As the patient was intolerant to cotrimoxazole, the antibiotics were changed to a combination of co-amoxyclav and doxycycline and continued for 12 weeks. The patient was well after 6 months without any relapse.

CONCLUSIONS

Melioidosis is an emerging infection in South Asia. It may present with recurrent abscesses. Therefore it is very important to send pus for culture whenever an abscess is drained. However, it should be noted that the reporting laboratory may be unfamiliar with this bacterium and the isolate may be misidentified as Pseudomonas or even E. coli. Melioidosis should be suspected when an isolate with the typical antibiotic sensitivity pattern of ceftazidime sensitivity and gentamicin resistance is cultured, especially in a patient with diabetes. This will expedite diagnosis and prompt treatment leading to an excellent prognosis.