Practical biosafety in the tuberculosis laboratory: containment at the source is what truly counts.

In industrialised countries, sufficient resources for establishing and maintaining fully equipped biosafety level 3 (BSL-3) laboratories according to international standards are generally available. BSL-3 laboratories are designed to provide several layers of containment to protect the laboratory worker as well as the outside environment and community from risk of exposure in case of local contamination. However, such facilities are scarce in high-burden settings, primarily due to the high financial burden and complexity of the initial construction and/or regular maintenance. Measures to prevent unintended exposure to Mycobacterium tuberculosis during laboratory manipulation of specimens and cultures is the first, and by far the most important, aspect of containment. This paper focuses on the need for risk containment at source. Assuming that in many settings the establishment of BSL-3 laboratories with all the required features is not achievable, this paper also discusses the minimum requirements necessary to mitigate risks associated with particular laboratory procedures. The term 'TB containment laboratory' is used throughout this paper to describe the minimum requirements for a laboratory suitable for high-risk procedures. The TB containment laboratory has many, but not all, of the features of a BSL-3 laboratory.

Reflex testing for Lynch syndrome: if we build it, will they come? Lessons learned from the uptake of clinical genetics services by individuals with newly diagnosed colorectal cancer (CRC).

The aim of this qualitative study was to examine the experience of individuals facing a choice about genetic counselling/testing in the context of newly diagnosed colorectal cancer (CRC). Nineteen individuals with newly diagnosed CRC, including 12 individuals who accepted genetic counselling ("acceptors") and 7 individuals who declined genetic counselling ("refusers"), were interviewed using a standardized questionnaire guide which focused on motivations and barriers experienced in the decision process. Data were analyzed using Karlsson's Empirical Phenomenological method of data analysis (Karlsson in Psychological qualitative research from a phenomenological perspective. Almgvist and Wiksell International, Stockholm, 1993). Three major themes were identified: facing challenges in health literacy; mapping an unknown territory; and adjusting to cancer. The study participants' testimonies provided novel insights into potential reasons for patient non-engagement in pilot studies of reflex testing for Lynch syndrome, and allowed us to formulate several recommendations for enhancing patient engagement. Our study findings suggest that patient engagement in clinical cancer genetics services, including reflex testing for Lynch syndrome, can only be achieved by addressing current health literacy issues, by deconstructing current misconceptions related to potential abuses of genetic information, by emphasizing the clinical utility of genetic assessment, and by adapting genetics practices to the specific context of cancer care.

Genetic services for hereditary breast/ovarian and colorectal cancers - physicians' awareness, use and satisfaction.

OBJECTIVES: In 2000, the Ministry of Health in Ontario, Canada, introduced a publicly funded program to provide genetic services for hereditary breast/ovarian and colorectal cancers. We surveyed physicians to determine their awareness, use and satisfaction with this program. METHODS: A self-administered questionnaire was mailed to a random sample of 25% of Ontario family physicians and all gynecologists, oncologists (radiation, surgical and medical), gastroenterologists and general surgeons. RESULTS: Response rate was 49% (n = 1,427). Awareness of genetic testing for breast/ovarian cancer was high (91%) but less for colorectal cancer (60%). Use of services was associated with physician age of 40 or greater, urban location, confidence in knowledge of referral criteria and core competencies in genetics, and awareness of the program and where to refer. Almost half were dissatisfied with notification about the program. CONCLUSIONS: Ontario physicians are aware of cancer genetics services, and use is associated with increased knowledge of services, and confidence in skills. They would like more timely services and education about hereditary cancers and susceptibility testing.

Critical appraisal of current recommendations and practices for tuberculosis sputum smear microscopy.

This report is the consensus-based, agreed position of the participants in a workshop for experts in sputum smear microscopy organised in August 2005 by the International Union Against Tuberculosis and Lung Disease (The Union), and as such reflects their views, but not necessarily those of their respective organisations. The group reviewed current practices in sputum smear microscopy for tuberculosis (TB) and suggests considering certain changes in standard guidelines for the sputum collection strategy and the definition of sputum smear-positive TB. The Ziehl-Neelsen staining guidelines need to incorporate a wider error margin for widespread application under field conditions. Quality assurance is of utmost importance, and needs more commitment from National Tuberculosis Programmes and other health authorities. In particular, allocation of sufficient resources for rechecking and integration of laboratory supervision must be ensured. Countries must make better investments in the purchase of high quality microscopes and laboratory supplies. To address the human resource crisis, personnel without specific laboratory schooling can, in principle, be trained to respond to immediate needs for TB diagnostic microscopy services. Periodic reporting on acid-fast smear examinations is highly desirable for regular monitoring and a more balanced provision of supplies.

Nocardia infections in cats: a retrospective multi-institutional study of 17 cases.

OBJECTIVE: To record 17 cases of nocardiosis in cats from eastern Australia and to compare this series with cases previously reported. DESIGN: Retrospective/prospective study. RESULTS: Nocardia spp infections were diagnosed in 17 cats over 14 years from the three eastern states of Australia. There were no isolates from dogs during this period, but one isolate from a koala and two from dairy cows. The majority of cats presented with spreading lesions of the subcutis and skin associated with draining sinus tract(s). Early cutaneous lesions consisted of circumscribed abscesses. Infections spread at a variable rate, generally by extension to adjacent tissues. Lesions were generally located in regions subjected to cat bite or scratch injuries, including limbs, body wall, inguinal panniculus and nasal bridge. In some other cases, lesions were situated on distal extremities. The clinical course was variable, from chronic, indolent, initially localised infections to acute fulminating disease. Of the 17 cats, 14 were domestic crossbreds and three were purebreds. There was a preponderance of male cats (12 castrated, 1 entire young adult, 1 entire kitten). Nine of 17 cats were 10 years or older. Interestingly, the majority of infections were attributable to N nova. Immediate and/or predisposing causes could be identified in all cases, and included: renal transplantation [one cat]; chronic corticosteroid administration [three cats]; catabolic state following chylothorax surgery [one cat]; fight injuries [seven cats]; FIV infections [three of seven cats tested]. Of the 17 cats, three were apparently cured. Four were thought to be cured, but infection recurred after several months. Three cats responded partially but were euthanased, while another was improving when it died of unrelated complications. Two died despite treatment and two were euthanased without an attempt at therapy. For two cats there were either insufficient records or the patient was lost to follow up. CONCLUSION: Nocardiosis is a rare, serious disease. Currently it is more common in cats than dogs. Nocardial panniculitis may be clinically indistinguishable from the syndrome caused by rapidly growing mycobacteria. Although the prognosis is guarded, patients with localised infections caused by N nova often respond to appropriate therapy. If definitive treatment is delayed because of misdiagnosis, the disease tends to become chronic, extensive and refractory. Insufficient duration of therapy leads to disease recurrence.

Heart defects and other malformations in the Inuit in Canada: a baseline study.

OBJECTIVES: Birth defects occur in all ethnic groups, remaining an important world-wide cause of perinatal and infant morbidity. This contributes greatly to an excess of health care dollars allocated to the care and repair of those affected. This is especially true when those affected live in remote geographical locations. STUDY DESIGN: A chart review of 2567 live births of children of Inuit parents residing in Arctic Quebec (Nunavik) and on Baffin Island (Nunavut) between 1989 and 1994 (five years) was carried out compared to rates of anomalies of the Alberta Congenital Anomalies Surveillance System (ACASS). RESULTS: Birth defects were higher in the Inuit sample in nearly every major ICD-9 category with the exception of neural tube defects, eye anomalies and chromosome abnormalities. (Total: 99.7/1000 Vs 51.5/1000; OR 1.93 95% CI 1.7-2.3). Congenital heart defects were significantly increased 22.9/1000 Vs 5.6/1000, with an OR of 4.18 (95% CI 3.2-5.4) in the ICD-9 category 745. In particular, ventricular septal defects (VSDs) and atrial septal defects (ASDs) (OR 4.9 CI 3.5-6.9 and 4.6 CI 2.9-7.2) were frequent. CONCLUSIONS: A high rate of heart defects was an important contributor to the nearly two times rate of total birth defects in the Inuit compared to the ACASS. Further study should be carried out to determine the contributing factors. Genetic predisposition to specific heart defects, and a diet low in folate and vitamin A are considerations. The use of alcohol may exacerbate vitamin status in pregnancy. Optimizing vitamin status in the periconceptional period may reduce the rate of birth defects.

Infections of the subcutis and skin of dogs caused by rapidly growing mycobacteria.

Nine dogs with panniculitis due to rapidly growing mycobacteria (RGM) were examined over 17 years. Dogs were two to 15 years; five were male, four were female. All were obese or in good condition. Antecedent injury, typically a dog bite or vehicular trauma, could be identified in some patients, while one bitch had hyperadrenocorticism. Infections involved different locations, although the cervicothoracic region, dorsum or flank were most often affected. Patients were systemically well, apart from one dog with pyrexia and two with pain or lameness. Cytology demonstrated pyogranulomatous inflammation, but in only one case was it possible to see acid-fast bacilli (AFB) in smears. Histology demonstrated chronic active pyogranulomatous panniculitis and dermatitis; AFB could be detected in only four specimens. Culture of aspirates or resected tissues demonstrated RGM in all cases, comprising six Mycobacterium smegmatis group and three Mycobacterium fortuitum group isolates. Resection of infected tissues, perioperative injectable antimicrobials and long courses of oral antimicrobials chosen according to susceptibility data generally effected a cure, although some cases recurred.

Germline E-cadherin mutations in hereditary diffuse gastric cancer: assessment of 42 new families and review of genetic screening criteria.

BACKGROUND: Mutations in the E-cadherin (CDH1) gene are a well documented cause of hereditary diffuse gastric cancer (HDGC). Development of evidence based guidelines for CDH1 screening for HDGC have been complicated by its rarity, variable penetrance, and lack of founder mutations. METHODS: Forty three new gastric cancer (GC) families were ascertained from multiple sources. In 42 of these families at least one gastric cancer was pathologically confirmed to be a diffuse gastric cancer (DGC); the other family had intestinal type gastric cancers. Screening of the entire coding region of the CDH1 gene and all intron/exon boundaries was performed by bi-directional sequencing. RESULTS: Novel mutations were found in 13 of the 42 DGC families (31% overall). Twelve of these mutations occur among the 25 families with multiple cases of gastric cancer and with pathologic confirmation of diffuse gastric cancer phenotype in at least one individual under the age of 50 years. The mutations found include small insertions and deletions, splice site mutations, and three non-conservative amino acid substitutions (A298T, W409R, and R732Q). All three missense mutations conferred loss of E-cadherin function in in vitro assays. Multiple cases of breast cancers including pathologically confirmed lobular breast cancers were observed both in mutation positive and negative families. CONCLUSION: Germline truncating CDH1 mutations are found in 48% of families with multiple cases of gastric cancer and at least one documented case of DGC in an individual under 50 years of age. We recommend that these criteria be used for selecting families for CDH1 mutational analysis.

A cluster of tuberculosis associated with use of a marijuana water pipe.

SETTING: New cases of pulmonary tuberculosis (TB) were noted in a cluster of young Caucasian males, an unusual ethnic group for this disease in Queensland, Australia. It was noted that marijuana water pipe ('bong') smoking was common amongst cases and contacts. OBJECTIVE: To report this cluster of TB and to investigate whether shared use of a marijuana water pipe was associated with transmission of TB. DESIGN: All contacts were identified and screened according to standard protocols. Cases were asked to list contacts with whom they had shared a marijuana water pipe. RESULTS: Five cases of open pulmonary TB were identified clinically and on sputum culture, and all isolates of Mycobacterium tuberculosis were identical on typing. Of 149 contacts identified, 114 (77%) completed screening, and 57 (50%) had significant tuberculin skin test (TST) reactions on follow-up. Of 45 contacts who had shared a marijuana water pipe with a case, 29 (64%) had a significant TST reaction. CONCLUSION: Sharing a marijuana water pipe with a case of pulmonary TB was associated with transmission of TB (OR 2.22, 95 % CI 0.96-5.17), although the most important risk factor for acquiring TB infection in this cluster was close household contact with a case (OR 4.91, 95% CI 1.13-20.70).

Three-dimensional reconstructions of extracellular matrix polymers using automated electron tomography.

The extracellular matrix is an intricate network of macromolecules which provides support for cells and a framework for tissues. The detailed structure and organisation of most matrix polymers is poorly understood. These polymers have a complex ultrastructure, and it has proved a major challenge both to define their structural organisation and to relate this to their biological function. However, new approaches using automated electron tomography are beginning to reveal important insights into the molecular assembly and structural organisation of two of the most abundant polymer systems in the extracellular matrix. We have generated three-dimensional reconstructions of collagen fibrils from bovine cornea and fibrillin microfibrils from ciliary zonules. Analysis of these data has provided new insights into the organisation and function of these large macromolecular assemblies.

Direct wet surface imaging of an anaerobic biofilm by environmental scanning electron microscopy: application to landfill clay liner barriers.

To contain domestic waste and its associated pollution within a landfill, engineered mineral (clay) barriers are used and are designed to have a permeability of 1 x 10(-9) m/s (Westlake 1995). The rate of permeability of various porous media has shown to be influenced by the clogging of flow paths (media pores) due to biofilm formation (Charckalis and Marshall 1990, Cunningham et al. 1991). The term biofilm is given to describe the colonies of surface adherent microorganisms (Donlan et al. 1994). In this study, permeability experiments were built and modified to act as microcosms to investigate the influence of biofilm formation on the permeability of clay barriers. Traditional scanning electron microscopy methods disrupt or destroy the biofilm and previous anaerobic studies have involved building closed cells (such as miniature continuous culture chambers) that utilise light microscopes (Robin Jones et al. 1997). This paper examines the application of the environmental scanning electron microscope (ESEM) to the direct examination of the clay interface and biofilm formation in situ within the microcosm.

Corneal collagen fibril structure in three dimensions: Structural insights into fibril assembly, mechanical properties, and tissue organization.

The ability of the cornea to transmit light while being mechanically resilient is directly attributable to the formation of an extracellular matrix containing orthogonal sheets of collagen fibrils. The detailed structure of the fibrils and how this structure underpins the mechanical properties and organization of the cornea is understood poorly. In this study, we used automated electron tomography to study the three-dimensional organization of molecules in corneal collagen fibrils. The reconstructions show that the collagen molecules in the 36-nm diameter collagen fibrils are organized into microfibrils (approximately 4-nm diameter) that are tilted by approximately 15 degrees to the fibril long axis in a right-handed helix. An unexpected finding was that the microfibrils exhibit a constant-tilt angle independent of radial position within the fibril. This feature suggests that microfibrils in concentric layers are not always parallel to each other and cannot retain the same neighbors between layers. Analysis of the lateral structure shows that the microfibrils exhibit regions of order and disorder within the 67-nm axial repeat of collagen fibrils. Furthermore, the microfibrils are ordered at three specific regions of the axial repeat of collagen fibrils that correspond to the N- and C-telopeptides and the d-band of the gap zone. The reconstructions also show macromolecules binding to the fibril surface at sites that correspond precisely to where the microfibrils are most orderly.

A preliminary validation of a family history assessment form to select women at risk for breast or ovarian cancer for referral to a genetics center.

The medical community and general population have become aware that genetic testing is available to look for BRCA1 and BRCA2 mutations. However, criteria for who should be referred for genetic counseling and possible subsequent testing have yet to be determined, and many genetics centers have been overwhelmed by the demand for service. We set out to develop a family history assessment tool (FHAT) that could be used by physicians to select individuals for genetic counseling. Arbitrarily, we chose individuals who would have an approximate doubling of their lifetime risk for breast or ovarian cancer. The FHAT was then applied to 184 unrelated families, with an index patient who had breast or ovarian cancer and who had accepted the offer of BRCA1 BRCA2 testing. Data were compiled to compare the number of individuals who would have been referred for genetic counseling and the number of mutation-positive individuals who would have been screened out from counseling using FHAT, the tables from Claus, and the BRCAPRO system. In this population, FHAT was effective in minimizing both the number of referrals and the likelihood of missing women who were later found to be mutation-positive.