Within-host evolution of Burkholderia pseudomallei over a twelve-year chronic carriage infection

UNLABELLED: Burkholderia pseudomallei causes the potentially fatal disease melioidosis. It is generally accepted that B. pseudomallei is a noncommensal bacterium and that any culture-positive clinical specimen denotes disease requiring treatment. Over a 23-year study of melioidosis cases in Darwin, Australia, just one patient from 707 survivors has developed persistent asymptomatic B. pseudomallei carriage. To better understand the mechanisms behind this unique scenario, we performed whole-genome analysis of two strains isolated 139 months apart. During this period, B. pseudomallei underwent several adaptive changes. Of 23 point mutations, 78% were nonsynonymous and 43% were predicted to be deleterious to gene function, demonstrating a strong propensity for positive selection. Notably, a nonsense mutation inactivated the universal stress response sigma factor RpoS, with pleiotropic implications. The genome underwent substantial reduction, with four deletions in chromosome 2 resulting in the loss of 221 genes. The deleted loci included genes involved in secondary metabolism, environmental survival, and pathogenesis. Of 14 indels, 11 occurred in coding regions and 9 resulted in frameshift mutations that dramatically affected predicted gene products. Disproportionately, four indels affected lipopolysaccharide biosynthesis and modification. Finally, we identified a frameshift mutation in both P314 isolates within wcbR, an important component of the capsular polysaccharide I locus, suggesting virulence attenuation early in infection. Our study illustrates a unique clinical case that contrasts a high-consequence infectious agent with a long-term commensal infection and provides further insights into bacterial evolution within the human host.

IMPORTANCE: Some bacterial pathogens establish long-term infections that are difficult or impossible to eradicate with current treatments. Rapid advances in genome sequencing technologies provide a powerful tool for understanding bacterial persistence within the human host. Burkholderia pseudomallei is considered a highly pathogenic bacterium because infection is commonly fatal. Here, we document within-host evolution of B. pseudomallei in a unique case of human infection with ongoing chronic carriage. Genomic comparison of isolates obtained 139 months (11.5 years) apart showed a strong signal of adaptation within the human host, including inactivation of virulence and immunogenic factors, and deletion of pathways involved in environmental survival. Two global regulatory genes were mutated in the 139-month isolate, indicating extensive regulatory changes favoring bacterial persistence. Our study provides insights into B. pseudomallei pathogenesis and, more broadly, identifies parallel evolutionary mechanisms that underlie chronic persistence of all bacterial pathogens.

Comparison of three molecular techniques for typing Pseudomonas aeruginosa isolates in sputum samples from patients with cystic fibrosis

Monitoring the emergence and transmission of Pseudomonas aeruginosa strains among cystic fibrosis (CF) patients is important for infection control in CF centers internationally. A recently developed multilocus sequence typing (MLST) scheme is used for epidemiologic analyses of P. aeruginosa outbreaks; however, little is known about its suitability for isolates from CF patients compared with that of pulsed-field gel electrophoresis (PFGE) and enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR). As part of a prevalence study of P. aeruginosa strains in Australian CF clinics, we compared the discriminatory power and concordance of ERIC-PCR, PFGE, and MLST among 93 CF sputum and 11 control P. aeruginosa isolates. PFGE and MLST analyses were also performed on 30 paired isolates collected 85 to 354 days apart from 30 patients attending two CF centers separated by 3,600 kilometers in order to detect within-host evolution. Each of the three methods displayed high levels of concordance and discrimination; however, overall lower discrimination was seen with ERIC-PCR than with MLST and PFGE. Analysis of the 50 ERIC-PCR types yielded 54 PFGE types, which were related by ≤ 6 band differences, and 59 sequence types, which were classified into 7 BURST groups and 42 singletons. MLST also proved useful for detecting novel and known strains and for inferring relatedness among unique PFGE types. However, 47% of the paired isolates produced PFGE patterns that within 1 year differed by one to five bands, whereas with MLST all paired isolates remained identical. MLST thus represents a categorical analysis tool with resolving power similar to that of PFGE for typing P. aeruginosa. Its focus on highly conserved housekeeping genes is particularly suited for long-term clinical monitoring and detecting novel strains.

Low rates of Pseudomonas aeruginosa misidentification in isolates from cystic fibrosis patients

Pseudomonas aeruginosa is an important cause of pulmonary infection in cystic fibrosis (CF). Its correct identification ensures effective patient management and infection control strategies. However, little is known about how often CF sputum isolates are falsely identified as P. aeruginosa. We used P. aeruginosa-specific duplex real-time PCR assays to determine if 2,267 P. aeruginosa sputum isolates from 561 CF patients were correctly identified by 17 Australian clinical microbiology laboratories. Misidentified isolates underwent further phenotypic tests, amplified rRNA gene restriction analysis, and partial 16S rRNA gene sequence analysis. Participating laboratories were surveyed on how they identified P. aeruginosa from CF sputum. Overall, 2,214 (97.7%) isolates from 531 (94.7%) CF patients were correctly identified as P. aeruginosa. Further testing with the API 20NE kit correctly identified only 34 (59%) of the misidentified isolates. Twelve (40%) patients had previously grown the misidentified species in their sputum. Achromobacter xylosoxidans (n = 21), Stenotrophomonas maltophilia (n = 15), and Inquilinus limosus (n = 4) were the species most commonly misidentified as P. aeruginosa. Overall, there were very low rates of P. aeruginosa misidentification among isolates from a broad cross section of Australian CF patients. Additional improvements are possible by undertaking a culture history review, noting colonial morphology, and performing stringent oxidase, DNase, and colistin susceptibility testing for all presumptive P. aeruginosa isolates. Isolates exhibiting atypical phenotypic features should be evaluated further by additional phenotypic or genotypic identification techniques.

Prenatal hypoxia leads to increased muscle sympathetic nerve activity, sympathetic hyperinnervation, premature blunting of NPY signalling and hypertension in adult life

Adverse conditions prenatally increase the risk of cardiovascular disease, including hypertension. Chronic hypoxia in utero (CHU) causes endothelial dysfunction, but whether sympathetic vasoconstrictor nerve functioning is altered is unknown. We, therefore, compared in male CHU and control (N) rats muscle sympathetic nerve activity, vascular sympathetic innervation density, and mechanisms of sympathetic vasoconstriction. In young (Y)-CHU and Y-N rats (≈3 months), baseline arterial blood pressure was similar. However, tonic muscle sympathetic nerve activity recorded focally from arterial vessels of spinotrapezius muscle had higher mean frequency in Y-CHU than in Y-N rats (0.56±0.075 versus 0.33±0.036 Hz), and the proportions of single units with high instantaneous frequencies (1–5 and 6–10 Hz) being greater in Y-CHU rats. Sympathetic innervation density of tibial arteries was ≈50% greater in Y-CHU than in Y-N rats. Increases in femoral vascular resistance evoked by sympathetic stimulation at low frequency (2 Hz for 2 minutes) and bursts at 20 Hz were substantially smaller in Y-CHU than in Y-N rats. In Y-N only, the neuropeptide Y Y1-receptor antagonist BIBP3226 attenuated these responses. By contrast, baseline arterial blood pressure was higher in middle-aged (M)-CHU than in M-N rats (≈9 months; 139±3 versus 126±3 mmHg, respectively). BIBP3226 had no effect on femoral vascular resistance increases evoked by 2 Hz or 20 Hz bursts in M-N or M-CHU rats. These results indicate that fetal programming induced by prenatal hypoxia causes an increase in centrally generated muscle sympathetic nerve activity in youth and hypertension by middle age. This is associated with blunting of sympathetically evoked vasoconstriction and its neuropeptide Y component that may reflect premature vascular aging and contribute to increased risk of cardiovascular disease

An analysis of the attitudes of dental patients attending general dental practice in Galway

AIM: To describe the patterns of dental attendance and attitudes towards tooth loss of general dental practice patients in Galway.

OBJECTIVES: 1. To determine the pattern of adult dental attendance in general practices in Galway; and, 2. To examine the oral health attitudes of these patients.

METHOD: Questionnaires were distributed to 311 consecutive adult patients in the waiting rooms of ten general dental practices in Galway, which were randomly selected from the telephone directory.

RESULTS: A total of 254 of the 311 questionnaires distributed were fully completed, returned and included in the results, giving a response rate of 81.7%. A total of 59% of dentate participants attended their dentist for annual or biannual examinations compared to 23% of edentate patients. Some 10.5% of medical card holders and 0.5% of non-medical card holders were edentulous.

CONCLUSIONS: The data from the survey indicated that medical card holders in Galway were more likely to be edentulous than nonmedical card holders. Edentate patients were less likely to be regular dental attenders than dentate patients.

Provision of resin bonded bridgework for a patient with microstomia secondary to scleroderma

Scleroderma is a connective tissue disorder that can present with orofacial involvement. A 48 year-old patient presented to Cork University Dental Hospital with concerns about the appearance of her upper central incisor teeth, which had become progressively mobile in recent years. A diagnosis of localised scleroderma had been made a number of years previously by her medical practitioner and the patient reported that her scleroderma-associated microstomia had progressed significantly in recent years. Most reports of this condition advocate the use of sectional impression trays and sectional dentures to replace missing teeth. This report describes the use of resin-bonded bridgework (RBB) and discusses the possible advantages of this treatment option over those already presented in the literature.

An evidence based approach for the provision of resin-bonded bridgework

Resin bonded bridgework (RBB) is a technique often overlooked by practitioners despite a large amount of evidence supporting the technique. In Cork University Dental School an evidence-based, standardised approach for the delivery of RBB by undergraduate students has been developed over the past 10 years. The aim of this study was to evaluate the success of this standardised approach on the delivery of RBB by students. 222 bridges were reviewed which had been delivered over a 6 year time period between 2002 and 2007. A success rate of 84.1% was achieved with a mean survival time of 41 months. This study illustrates that predictable and highly successful RBB can be delivered by inexperienced clinicians using an evidence-based, standardised approach.

Toothwear and the older patient

Toothwear is commonly observed in dentate older patients and may be physiological or pathological in nature. Toothwear can be caused by abrasion, attrition, erosion or a combination of aetiologies. Where treatment is required, a number of options exist, including the use of adhesive materials and fixed and removable prosthodontics.

CLINICAL RELEVANCE: With patients retaining natural teeth into old age, physiological and pathological toothwear amongst dentate older patients is an increasingly common presentation.

Limitations of Dental Panoramic Tomography in the anterior mandible

Dental Panoramic Tomography (DPT) is a widely used and valuable examination in dentistry. One area prone to artefacts and therefore misinterpretation is the anterior region of the mandible. This case study discusses a periapical radiolucency related to lower anterior teeth that is discovered to be a radiographic artefact. Possible causes of the artefact include a pronounced depression in the mental region of the mandible or superimposition of intervertebral spaces. Additional limitations of the DPT image include superimposition of radio-opaque structures, reduced image detail compared to intra-oral views and uneven magnification. These problems often make the DPT inappropriate for imaging the anterior mandible.

CLINICAL RELEVANCE: Panoramic radiography is often unsuitable for radiographic examination of the anterior mandible.

Patient preferences for dental clinical attire: a cross-sectional survey in a dental hospital

AIMS AND OBJECTIVES: This cross sectional descriptive study was designed to survey patient opinion towards dental clinical attire, name badges and commonly used cross-infection control measures.

METHOD: Patients attending a dental hospital for a consultation appointment were asked to complete a questionnaire accompanied by photographs of models portraying a range of clinical attire. A representative sample of patients completed 188 questionnaires over a four week period.

RESULTS: The study found that the majority of patients felt clinical attire was important and that they preferred dental professionals to wear name badges. The majority of patients also preferred dentists to use both safety glasses and face masks. When asked to indicate which clinical attire was most appropriate for a consultant/specialist to wear, the overwhelming opinion was that of smart dress accompanied with a white coat. In addition, most respondents wished their dentist to wear a traditional white, dental tunic.

CONCLUDING REMARKS: It is hoped that this study will be informative for the dental team and that the results will be taken into consideration when considering appropriate clinical attire in accordance with patient opinions.

Accelerated rehabilitation of an edentulous patient with an implant retained dental prosthesis: a case report

This case report details the successful rehabilitation of an edentulous patient using a complete upper prosthesis and a lower implant retained overdenture. The provision of care was split between a specialist centre and a primary care setting. This approach reduced inconvenience to the patient. Modern surgical and prosthodontic techniques also reduced the total delivery time. After initial consultation a new set of complete dentures was prescribed with changes in design to the originals. The patient was also planned for placement of two mandibular implants to stabilise and retain the mandibular denture. The first line of treatment involved provision of a new set of dentures constructed by the patient's general dental practitioner. Dental implants were then placed in a specialist centre and the patient returned to the dental practice for attachment of the lower denture to the dental implants. The benefits and success of mandibular implant retained dentures are well documented. With delivery of the overdenture, the patient reported increased satisfaction with his prostheses which allowed him to eat a greater range of foods and enabled him to feel confident when speaking and socialising.

DNA methylation subgroups and the CpG island methylator phenotype in gastric cancer: a comprehensive profiling approach

BACKGROUND: Methylation-induced silencing of promoter CpG islands in tumor suppressor genes plays an important role in human carcinogenesis. In colorectal cancer, the CpG island methylator phenotype (CIMP) is defined as widespread and elevated levels of DNA methylation and CIMP+ tumors have distinctive clinicopathological and molecular features. In contrast, the existence of a comparable CIMP subtype in gastric cancer (GC) has not been clearly established. To further investigate this issue, in the present study we performed comprehensive DNA methylation profiling of a well-characterised series of primary GC.

METHODS: The methylation status of 1,421 autosomal CpG sites located within 768 cancer-related genes was investigated using the Illumina GoldenGate Methylation Panel I assay on DNA extracted from 60 gastric tumors and matched tumor-adjacent gastric tissue pairs. Methylation data was analysed using a recursively partitioned mixture model and investigated for associations with clinicopathological and molecular features including age, Helicobacter pylori status, tumor site, patient survival, microsatellite instability and BRAF and KRAS mutations.

RESULTS: A total of 147 genes were differentially methylated between tumor and matched tumor-adjacent gastric tissue, with HOXA5 and hedgehog signalling being the top-ranked gene and signalling pathway, respectively. Unsupervised clustering of methylation data revealed the existence of 6 subgroups under two main clusters, referred to as L (low methylation; 28% of cases) and H (high methylation; 72%). Female patients were over-represented in the H tumor group compared to L group (36% vs 6%; P = 0.024), however no other significant differences in clinicopathological or molecular features were apparent. CpG sites that were hypermethylated in group H were more frequently located in CpG islands and marked for polycomb occupancy.

CONCLUSIONS: High-throughput methylation analysis implicates genes involved in embryonic development and hedgehog signaling in gastric tumorigenesis. GC is comprised of two major methylation subtypes, with the highly methylated group showing some features consistent with a CpG island methylator phenotype.

The frequency of gastrointestinal endocrine tumours in a well-defined population--Northern Ireland 1970-1985

The reported incidence of gastrointestinal endocrine tumours is variable. In Northern Ireland circumstances allowing such an assessment are favourable with a central diagnostic laboratory and register established to collect data on tumours from a well-defined population of 1.5 million people. From 1970 to 1985, 368 cases were recorded of which 85 per cent were carcinoid tumours. The annual incidence of carcinoid tumours was 1.3 per 100,000 of the population and the majority occurred in the appendix (61 per cent). No patients presented with the carcinoid syndrome. The annual incidence for other tumours was 0.12 per 100,000 for insulinomas; islet cell tumours of unknown type 0.07; Zollinger-Ellison syndrome 0.05; and multiple endocrine neoplasia (MEN) 0.05. There were two cases of VIPoma, one glucagonoma, one neurotensinoma and one tumour producing ACTH. It is possible that some tumours are more uncommon than others because of difficulty in diagnosis.

Aspirin and folic acid for the prevention of recurrent colorectal adenomas

BACKGROUND & AIMS: Although observational studies have found regular aspirin use to be associated with a reduced risk of colorectal neoplasia, results from randomized trials using aspirin have been inconsistent. Dietary folate intake also has been found to be associated with a reduced risk of colorectal neoplasms in observational studies.

METHODS: A multicenter, randomized, double-blind trial of aspirin (300 mg/day) and folate supplements (0.5 mg/day) to prevent colorectal adenoma recurrence was performed using a 2 x 2 factorial design. All patients had an adenoma (>/=0.5 cm) removed in the 6 months before recruitment and were followed-up at 4-month intervals with a second colonoscopy after approximately 3 years. The primary outcome measure was a colorectal adenoma diagnosed after baseline.

RESULTS: A total of 945 patients were recruited into the study, of whom 853 (90.3%) underwent a second colonoscopy. In total, 99 (22.8%) of 434 patients receiving aspirin had a recurrent adenoma compared with 121 (28.9%) of 419 patients receiving placebo (relative risk, 0.79; 95% confidence interval [CI], 0.63-0.99). A total of 104 patients developed an advanced colorectal adenoma; 41 (9.4%) of these were in the aspirin group and 63 (15.0%) were in the placebo group (relative risk, 0.63; 95% CI, 0.43-0.91). Folate supplementation was found to have no effect on adenoma recurrence (relative risk, 1.07; 95% CI, 0.85-1.34).

CONCLUSIONS: Aspirin (300 mg/day) but not folate (0.5 mg/day) use was found to reduce the risk of colorectal adenoma recurrence, with evidence that aspirin could have a significant role in preventing the development of advanced lesions.