Genomic islands from five strains of Burkholderia pseudomallei

BACKGROUND

Burkholderia pseudomallei is the etiologic agent of melioidosis, a significant cause of morbidity and mortality where this infection is endemic. Genomic differences among strains of B. pseudomallei are predicted to be one of the major causes of the diverse clinical manifestations observed among patients with melioidosis. The purpose of this study was to examine the role of genomic islands (GIs) as sources of genomic diversity in this species.

RESULTS

We found that genomic islands (GIs) vary greatly among B. pseudomallei strains. We identified 71 distinct GIs from the genome sequences of five reference strains of B. pseudomallei: K96243, 1710b, 1106a, MSHR668, and MSHR305. The genomic positions of these GIs are not random, as many of them are associated with tRNA gene loci. In particular, the 3' end sequences of tRNA genes are predicted to be involved in the integration of GIs. We propose the term "tRNA-mediated site-specific recombination" (tRNA-SSR) for this mechanism. In addition, we provide a GI nomenclature that is based upon integration hotspots identified here or previously described.

CONCLUSION

Our data suggest that acquisition of GIs is one of the major sources of genomic diversity within B. pseudomallei and the molecular mechanisms that facilitate horizontally-acquired GIs are common across multiple strains of B. pseudomallei. The differential presence of the 71 GIs across multiple strains demonstrates the importance of these mobile elements for shaping the genetic composition of individual strains and populations within this bacterial species.

Continuous CSF drainage in AD: results of a double-blind, randomized, placebo-controlled study

BACKGROUND

Alzheimer disease (AD) has been associated with abnormal cerebral clearance of macromolecules, such as amyloid and microtubule-associated-protein tau (MAP-tau). We hypothesized that improving clearance of macromolecules from the CNS might slow the progression of dementia.

OBJECTIVE

This prospective, randomized, double-blinded, placebo-controlled trial evaluated the safety and effectiveness of a surgically implanted shunt in subjects with probable AD.

METHODS

A total of 215 subjects with probable AD by National Institute of Neurological Disorders and Stroke-Alzheimer's Disease and Related Disorders Association criteria received either a low-flow ventriculoperitoneal shunt or a sham (occluded) shunt for 9 months. Longitudinal CSF sampling was performed in both active and control subjects. Primary outcome measures were the Mattis Dementia Rating Scale and the Global Deterioration Scale. CSF Abeta((1-42)) and MAP-tau also were assayed.

RESULTS

After a planned interim analysis, the study was halted for futility. Using the intent-to-treat population, no between-group differences were observed in the primary outcome measures. The surgical procedure and device were associated with 12 CNS infections, some temporally associated with CSF sampling. All were treated successfully.

CONCLUSIONS

We found no benefit to low-flow CSF shunting in subjects with mild to severe Alzheimer disease. CSF infections, while treatable, occurred more frequently than expected, in some cases likely related to CSF sampling.

Australian and Thai isolates of Burkholderia pseudomallei are distinct by multilocus sequence typing: revision of a case of mistaken identity

A recent study using multilocus sequence typing (MLST) of Burkholderia pseudomallei isolates found a sequence type (ST60) to be common to both Thailand and Australia, contradicting earlier studies showing complete distinction between isolates from these regions. The ST60 isolates reportedly from Australia had been obtained for MLST from United Kingdom and U.S. collections. We have located and characterized the original Australian isolates; they were collected in 1983, and they are neither ST60 nor B. pseudomallei isolates. The B. pseudomallei MLST database has been corrected, and there is no ST common to isolates verified as obtained from Australia or from Thailand.

Sensitive and specific molecular detection of Burkholderia pseudomallei, the causative agent of melioidosis, in the soil of tropical northern Australia

Burkholderia pseudomallei, the cause of the severe disease melioidosis in humans and animals, is a gram-negative saprophyte living in soil and water of areas of endemicity such as tropical northern Australia and Southeast Asia. Infection occurs mainly by contact with wet contaminated soil. The environmental distribution of B. pseudomallei in northern Australia is still unclear. We developed and evaluated a direct soil B. pseudomallei DNA detection method based on the recently published real-time PCR targeting the B. pseudomallei type III secretion system. The method was evaluated by inoculating different soil types with B. pseudomallei dilution series and by comparing B. pseudomallei detection rate with culture-based detection rate for 104 randomly collected soil samples from the Darwin rural area in northern Australia. We found that direct soil B. pseudomallei DNA detection not only was substantially faster than culture but also proved to be more sensitive with no evident false-positive results. This assay provides a new tool to detect B. pseudomallei in soil samples in a fast and highly sensitive and specific manner and is applicable for large-scale B. pseudomallei environmental screening studies or in outbreak situations. Furthermore, analysis of the 104 collected soil samples revealed a significant association between B. pseudomallei-positive sites and the presence of animals at these locations and also with moist, reddish brown-to-reddish gray soils.

The epidemiology of melioidosis in the Balimo region of Papua New Guinea

The distribution of Burkholderia pseudomallei was determined in soil collected from a rural district in Papua New Guinea (PNG) where melioidosis had recently been described, predominately affecting children. In 274 samples, 2.6% tested culture-positive for B. pseudomallei. Pulsed-field gel electrophoresis using SpeI digests and rapid polymorphic DNA PCR with five primers demonstrated a single clone amongst clinical isolates and isolates cultured from the environment that was commonly used by children from whom the clinical isolates were derived. We concluded that individuals in this region most probably acquired the organism through close contact with the environment at these sites. Burkholderia thailandensis, a closely related Burkholderia sp. was isolated from 5.5% of samples tested, an observation similar to that of melioidosis-endemic areas in Thailand. This is the first report of an environmental reservoir for melioidosis in PNG and confirms the Balimo district in PNG as melioidosis endemic.

Using BOX-PCR to exclude a clonal outbreak of melioidosis

BACKGROUND

Although melioidosis in endemic regions is usually caused by a diverse range of Burkholderia pseudomallei strains, clonal outbreaks from contaminated potable water have been described. Furthermore B. pseudomallei is classified as a CDC Group B bioterrorism agent. Ribotyping, pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) have been used to identify genetically related B. pseudomallei isolates, but they are time consuming and technically challenging for many laboratories.

METHODS

We have adapted repetitive sequence typing using a BOX A1R primer for typing B. pseudomallei and compared BOX-PCR fingerprinting results on a wide range of well-characterized B. pseudomallei isolates with MLST and PFGE performed on the same isolates.

RESULTS

BOX-PCR typing compared favourably with MLST and PFGE performed on the same isolates, both discriminating between the majority of multilocus sequence types and showing relatedness between epidemiologically linked isolates from various outbreak clusters.

CONCLUSION

Our results suggest that BOX-PCR can be used to exclude a clonal outbreak of melioidosis within 10 hours of receiving the bacterial strains.

Phase II trial of imatinib (I) and docetaxel (D) in recurrent non-small cell lung cancer (NSCLC)

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Background: Second line monotherapy for NSCLC produces a response rate of 9% and a median survival of 7–8 months, regardless of the agent used. Emerging data suggest that combining an approved agent with an anti-angiogenesis inhibitor may improve efficacy in the salvage setting. Platelet Derived Growth Factor Receptor alpha (PDGFR-alpha) is involved in angiogenesis and its expression has been reported in 100% of adenocarcinoma (11/11) and 89% of squamous cell (16/18) lung cancer specimens in a small group sample. Preclinical models have shown that I inhibits PDGFR and may subsequently inhibit angiogenesis. In addition, I + D have additive anticancer activity. We initiated a phase II trial of I +D to evaluate the efficacy and safety of this combination regimen in recurrent NSCLC. Methods: Patients (pts)with pathologically confirmed NSCLC, measurable disease, no more than 1 previous platinum-based chemotherapy regimen, PS 0–1, clinically stable brain metastases and adequate organ function were eligible. Tumor samples, when available, were tested for PDGFR expression by immunohistochemistry. All pts received D 30mg/m2 intravenously weekly x 3 every 4 weeks and oral I 600mg daily for 4 cycles. Non- progressors after 4 cycles continued with I alone for a total of 12 months or until progression. Tumor response was assessed every 2 cycles. The primary endpoint was response rate. A Simon two-stage design was used with 16 patients in the first stage and accrual of a total of 32 patients planned. Results: Currently 15/16 patients for stage I of the protocol have been enrolled. A total of 24 cycles of combined I+D were given. Patient characteristics and toxicity data are described in the table below. Efficacy data is premature. Conclusion : I +D combination has been well tolerated in this relapsed population. A detailed toxicity, efficacy and PDGFR analysis will be presented.

[Table: see text]

No significant financial relationships to disclose.

Use of a variable amplicon typing scheme reveals considerable variation in the accessory genomes of isolates of Burkholderia pseudomallei

Melioidosis, a disease caused by the bacterium Burkholderia pseudomallei, is endemic in southeast Asia and northern Australia. We used suppression subtractive hybridization (SSH) to identify sequences that varied between two B. pseudomallei isolates from Australia and determined the distribution of 45 SSH-derived sequences among a panel of B. pseudomallei and B. thailandensis isolates. Sequences exhibiting variable prevalence were included in a variable amplicon typing (VAT) scheme designed to score the presence or absence of 14 PCR amplicons. VAT analysis was carried out with 48 isolates from Thailand, which were typed by multilocus sequence typing (MLST), and 44 isolates from Australia of known MLST type. The VAT scheme could be used to divide the 48 isolates from Thailand into 23 VAT types and the 44 isolates from Australia into 36 VAT types. Some of the sequences included in the VAT scheme were more commonly PCR positive among isolates from Australia than among isolates from Thailand, and vice versa. No isolate from Australia was PCR positive for genomic island 11 or a putative transposase sequence, whereas four SSH-derived sequences were far more prevalent among the Australian isolates. Analysis based on the VAT scheme indicated that the isolates clustered into groups, some of which were mainly or exclusively from one geographical origin. One cluster included Australian isolates that were mostly associated with severe disease, including rare neurological melioidosis, suggesting that the content of the accessory genome may play an important role in determining the clinical manifestation of the disease.

Clinical evaluation of a type III secretion system real-time PCR assay for diagnosing melioidosis

A Burkholderia pseudomallei type III secretion system real-time PCR assay was evaluated on clinical specimens in a region where melioidosis is endemic. The PCR was positive in 30/33 (91%) patients with culture-confirmed melioidosis. All six patients with melioidosis septic shock were blood PCR positive, suggesting potential for rapid diagnosis and commencement of appropriate therapy.

Perioperative Complications of Lung Transplantation in Patients With Emphysema and Fibrosis: Experience From 1992–2002

Our objective was to describe the incidence of perioperative complications of lung transplantation among patients with emphysema and fibrosis and the morbidity and mortality risk factors.

MATERIALS AND METHODS

We performed a retrospective study of 111 lung transplant patients engrafted from 1992 to 2002 for emphysema (n = 65) or lung fibrosis (n = 46). This descriptive study included the most frequent complications during the perioperative period in the intensive care unit.

RESULTS

The most frequent intraoperative complications were reperfusion syndrome, hemodynamic instability, and cardiac arrhythmias. Among patients with emphysema, the follow-up of postoperative complications proved statistically significant on univariate analysis for an association of patient mortality with prolonged intubation (P = .005), rejection (P = .0001), hemorrhage (P = .0001), sepsis (P = .0001), renal failure (P = .001), and implantation response (P = .014). Mortality among these patients was 16.9%. Mechanical ventilation for over 48 hours and postoperative hemorrhage were the variables with the greatest predictive value for mortality in the postoperative period. Among patients with fibrosis, the complication-related mortality were reperfusion syndrome (P = .039), implantation response (P = .039), renal failure (P = .013), rejection (P = .016), and sepsis (P < .001). The mortality rate was 23.9% with sepsis (P = .000) being the most frequent cause of death in the immediate postoperative period.

CONCLUSIONS

The most frequent intraoperative complications were reperfusion syndrome and hemodynamic instability. The most frequent postoperative complications were implantation response, sepsis, prolonged intubation, hemorrhage, and renal failure.

Clinical variation in melioidosis in pigs with clonal infection following possible environmental contamination from bore water

An outbreak of melioidosis occurred in pigs on a rural property in the tropical north of the Northern Territory of Australia. The pigs were mostly asymptomatic but lesions in the parotid glands suggested an oral route of infection. Skin lesions were also common and one piglet had disseminated infection. Pulsed-field gel electrophoresis showed an identical pattern amongst Burkholderia pseudomallei isolates from the pigs, with similarity to an isolate from the unchlorinated bore water supplying the property.

Preliminary immune response (IR) results of a phase 2 study with idiotype (Id) immunotherapy after treatment with CVP and rituximab for follicular non-Hodgkin’s lymphoma (FL)

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Background: Idiotype (Id) is a collection of unique immunogenic epitopes present on the surface of malignant B cells. Keyhole limpet hemocyanin (KLH) is a carrier protein used to increase antigen immunogenicity. MyVax Personalized Immunotherapy consists of the patient- and tumor-specific Id protein, produced using molecular techniques, conjugated to KLH and administered in a series of subcutaneous immunizations with the adjuvant GM-CSF. Idiotype vaccines were first studied in combination with various chemotherapeutic agents as part of initial treatment for FL. Given the widespread usage of rituximab in treating FL, the nature of IRs in patients immunized with MyVax Personalized Immunotherapy following rituximab treatment are of interest. CD19+ B cell counts following treatment with rituximab were analyzed for correlation with patient-specific Id-KLH induced humoral IR data. Methods: In a Phase 2 study, MyVax Personalized Immunotherapy following rituximab is being evaluated for patients who failed to achieve at least a PR and maintain the response over a 6 month rest period after 8 cycles of CVP chemotherapy. Eligible patients received 4 weekly doses of rituximab followed by a 13 or 26 week rest period. Patients who achieved and maintained a PR or better then received 8 immunizations with MyVax Personalized Immunotherapy over 14 weeks. CD19+ B cells and humoral IRs against Id and KLH were monitored during and 2, 8, 20, 32, 44 and 56 weeks post-immunizations. Results: 87 pts received rituximab. 52 pts went on to immunization. Median CD19 counts for all arms of the study were lower post-rituximab treatment (pre-treatment median = 76 cells/ul (N = 57) vs. post-treatment = 13 cells/ul (N = 51 evaluable); p < 0.0001). Positive results are defined as a titer >0.1 mcg/ml. 49/52 (94%) evaluable pts were able to mount anti-KLH humoral IRs post rituximab. The magnitude of the anti-KLH response was generally greater in pts with higher B cell counts when beginning immunizations. Anti-Id IRs were also observed. Conclusions: Humoral IRs to KLH occur in pts receiving MyVax Personalized Immunotherapy and correlate with regeneration of B cells post-rituximab but appear less robust than in rituximab-naïve pts.

[Table: see text]

Extreme weather events and environmental contamination are associated with case-clusters of melioidosis in the Northern Territory of Australia

BACKGROUND

Melioidosis, the infection due to the environmental organism Burkholderia pseudomallei, is endemic to northern Australia and South East Asia. It is associated with exposure to mud and pooled surface water, but environmental determinants of this disease are poorly understood. We defined case-clusters in northern Australia, determined their contribution to the observed rate of melioidosis, and explored clinical features and associated environmental factors.

METHODS

Using geographical information systems data, we examined clustering of melioidosis cases in time and geographical space in the Top End of the Northern Territory of Australia between 1990 and 2002 using a scan statistic. DNA macrorestriction analysis, resolved by pulsed field gel electrophoresis, was performed on isolates from patients.

RESULTS

We defined five case-clusters involving 27 patients that occurred within 7-28 days and/or a radius of 100-300 km. Clustered cases were associated with extreme weather events or environmental contamination; no difference in the clinical pattern of disease was noted from other patients not involved in clusters. Isolates from patients linked to environmental contamination were caused by isolates with similar DNA macrorestriction patterns, but isolates from patients linked to severe weather events had more diverse DNA macrorestriction patterns.

CONCLUSION

Case-clusters of melioidosis where isolates exhibit diverse DNA macrorestriction patterns in our region are linked to extreme weather events and outbreaks where isolates are predominantly of the same DNA macrorestriction pattern are linked with contamination of an environmental source.

Short report: application of a polymerase chain reaction to detect Burkholderia pseudomallei in clinical specimens from patients with suspected melioidosis

The diagnostic potential of a Burkholderia pseudomallei type three secretion system (TTS1) polymerase chain reaction (PCR) was examined on clinical specimens from 27 patients with sepsis in the Northern Territory of Australia, a region endemic for melioidosis. The TTS1 PCR was conducted on DNA extracted from a range of clinical specimens (blood, sputum, urine, joint, pericardial and pleural fluid, and swabs from skin lesions, throat, nose, and rectum). The PCR sensitivity in culture-positive clinical specimens from the nine confirmed patients with melioidosis was 65% and the specificity was 100%, with no PCR-positive results in specimens from 18 patients without melioidosis. The PCR based on the B. pseudomallei TTS1 has the potential to substantially improve the timeliness of diagnosis of melioidosis.

Isolates of Burkholderia pseudomallei from Northern Australia are distinct by multilocus sequence typing, but strain types do not correlate with clinical presentation

Melioidosis is the disease caused by the saprophytic organism Burkholderia pseudomallei. Previous studies have suggested some strain tropism and differential virulence. In this study, we defined strains by multilocus sequence typing (MLST) of isolates taken from the Top End of Australia's Northern Territory and compared the results with those of other strains typed worldwide. We specifically sought clinical and geographical correlates of strain types. Among 87 Australian isolates, 48 sequence types were defined. None of the sequence types in this study has been found elsewhere in the world. Strains were distributed widely throughout the region, and the different presentations of disease, including neurological and prostatic infection, were associated with many different strains. There was excellent congruence between pulsed-field gel electrophoresis and MLST, and the two typing methods had a similar level of strain discrimination. The work suggests that host and environmental factors may be more important in determining disease presentation than infecting strain type. It is possible that the distinct but diverse strain types found in this study reflect Australia's geographical isolation over many millions of years.

Preliminary report on the northern Australian melioidosis environmental surveillance project

An environmental surveillance programme was developed to determine whether water supplies could be a source of Burkholderia pseudomallei as noted during previous melioidosis outbreak investigations. Water supplies to communities in the three northern Australian jurisdictions (Western Australia, Northern Territory and Queensland) were sampled periodically during 2001 and 2002. Water and soil samples were collected from communities known to have had recent culture-positive melioidosis cases and nearby communities where no cases had been diagnosed. Clinical isolates of B. pseudomallei obtained from northern Australian patients during 2001 and 2002 were compared with the environmental B. pseudomallei isolates by ribotyping and pulsed-field gel electrophoresis. B. pseudomallei was isolated from 11 distinct locations, all in the Northern Territory, seven of which were associated with culture-positive melioidosis cases (>1 case at three locations). Water was implicated as a possible environmental source of melioidosis in six locations. A variety of free-living amoebae including Acanthamoeba and Hartmannella spp. that are potential hosts to B. pseudomallei were recovered from environmental specimens. Culturable B. pseudomallei was not found to be widely dispersed in the environments sampled.

Contamination of hand wash detergent linked to occupationally acquired melioidosis

Two mechanics working at a garage in tropical northern Australia simultaneously developed upper limb melioidosis ulcers. Both patients had Burkholderia pseudomallei of identical pulsed-field gel electrophoresis (PFGE) type (Spe I). Environmental sampling identified B. pseudomallei in a container of commercial hand wash detergent as the likely source of infection, although there were multiple isolates of different PFGE types to the clinical isolates.

[Lung transplantation for pulmonary fibrosis: perioperative morbidity and mortality]

Lung transplantation has become a valid therapeutic option for patients with pulmonary fibrosis in terminal stage, and the number of such interventions has increased exponentially in recent years. We undertook a retrospective study of 46 pulmonary fibrosis patients who received lung transplants from 1992 through 2002 with the aim of describing the most common intra- and early postoperative complications in the recovery unit. We also aimed to analyze the impact of each complication on mortality during the study period. The most frequent complications during surgery were reperfusion syndrome (47.5%), hemodynamic instability (41%), arrhythmias (23.9%), and pulmonary hypertension (15%), with exitus secondary to reperfusion syndrome. The most common postoperative complications were infection (56.5%), reimplantation response (45.7%), and kidney failure (19.6%). Overall mortality during the study period was 23.9%. The following complications were statistically significant in the univariate analysis of the relation with mortality: reperfusion syndrome (p=0.039), reimplantation response (p=0.039), kidney failure (p=0.013), rejection (p=0.016), and sepsis (p<0.001). The only complication that remained significant in the multivariate analysis was sepsis (p<0.001). In spite of the considerable progress made, intra- and postoperative complications continue to be a real threat for the transplanted lung patient. Sepsis was the strongest predictor of poor prognosis in the early recovery period.

Assessment of low-flow CSF drainage as a treatment for AD: results of a randomized pilot study

OBJECTIVE

This prospective, randomized, controlled study was designed to investigate the safety, feasibility, and preliminary efficacy of long-term CSF drainage via a low-flow ventriculoperitoneal shunt in subjects suffering from AD.

METHODS

Twenty-nine subjects selected for probable AD (National Institute of Neurological and Communicative Diseases and Stroke-Alzheimer's Disease and Related Dementias Association criteria) were screened to exclude normal pressure hydrocephalus or other etiologies of dementia and randomized to treatment (shunt) or no treatment groups. The study endpoint was the comparison of group performance on psychometric testing at quarterly intervals for 1 year. Shunted subjects had CSF withdrawn for MAP-tau and Abeta((1-42)) assays at the same time intervals.

RESULTS

There was no mortality from the surgical procedure, and no patient sustained a subdural hematoma. Five notable postoperative adverse events, which resolved without permanent neurologic deficit, were reported in the shunt group. Group mean Mattis Dementia Rating Scale total scores showed little change over the year in the shunt-treatment group, in contrast to a decline in the control group (p = 0.06). Mini-Mental State Examination mean scores supported a trend in favor of shunt treatment (p = 0.1). There was a concomitant decrease in ventricular CSF concentrations of AD biomarkers MAP-tau and Abeta((1-42)).

CONCLUSIONS

The surgical procedure and the device are reasonably safe. Adverse events were consistent with shunt procedures for hydrocephalus in this older population. The endpoint data show a trend in favor of the treated group. A larger, randomized, double-blinded, controlled, clinical trial is underway.

Yield of intestinal metaplasia in patients with suspected short-segment Barrett's esophagus (SSBE) on repeat endoscopy

Biopsies from short segments of columnar appearing mucosa in the distal esophagus often fail to reveal intestinal metaplasia (IM). The yield of IM on repeat upper endoscopy (EGD) and biopsy in these patients is not known. Our aim was to prospectively evaluate the yield of IM on repeat EGD in patients with suspected SSBE (negative for IM on first EGD). Forty-three patients with suspected SSBE underwent repeat EGD with biopsy. This included 42 men and 1 woman, mean age 53 years (range: 45-90) with a mean columnar mucosa length of 1.26 cm (range: 0.5-2.5). On repeat EGD, 10 of 43 patients (23.2%) had evidence of IM. There was no statistically significant difference between the patients with proven SSBE on repeat EGD compared to those with persistent negative IM with regards to age, ethnicity, length of columnar mucosa, GERD symptoms, and hiatal hernia size. In conclusion, more than 20% of patients with suspected SSBE have evidence of IM (ie, proven SSBE) on repeat EGD. Thus repeat EGD with biopsy may be warranted in patients with tongues of columnar mucosa in the distal esophagus but no IM on the first biopsy to confirm the diagnosis of SSBE.