Added Value of Next Generation over Sanger Sequencing in Kenyan Youth with Extensive HIV-1 Drug Resistance.

HIV-1 drug resistance testing in children and adolescents in low-resource settings is both important and challenging. New (more sensitive) drug resistance testing technologies may improve clinical care, but evaluation of their added value is limited. We assessed the potential added value of using next-generation sequencing (NGS) over Sanger sequencing for detecting nucleoside reverse transcriptase inhibitor (NRTI) and nonnucleoside reverse transcriptase inhibitor (NNRTI) drug resistance mutations (DRMs). Participants included 132 treatment-experienced Kenyan children and adolescents with diverse HIV-1 subtypes and with already high levels of drug resistance detected by Sanger sequencing. We examined overall and DRM-specific resistance and its predicted impact on antiretroviral therapy and evaluated the discrepancy between Sanger sequencing and six NGS thresholds (1%, 2%, 5%, 10%, 15%, and 20%). Depending on the NGS threshold, agreement between the two technologies was 62% to 88% for any DRM, 83% to 92% for NRTI DRMs, and 73% to 94% for NNRTI DRMs, with more DRMs detected at low NGS thresholds. NGS identified 96% to 100% of DRMs detected by Sanger sequencing, while Sanger identified 83% to 99% of DRMs detected by NGS. Higher discrepancy between technologies was associated with higher DRM prevalence. Even in this resistance-saturated cohort, 12% of participants had higher, potentially clinically relevant predicted resistance detected only by NGS. These findings, in a young, vulnerable Kenyan population with diverse HIV-1 subtypes and already high resistance levels, suggest potential benefits of more sensitive NGS over existing technology. Good agreement between technologies at high NGS thresholds supports their interchangeable use; however, the significance of DRMs identified at lower thresholds to patient care should be explored further. IMPORTANCE HIV-1 drug resistance in children and adolescents remains a significant problem in countries facing the highest burden of the HIV epidemic. Surveillance of HIV-1 drug resistance in children and adolescents is an important public health strategy, particularly in resource-limited settings, and yet, it is limited due mostly to cost and infrastructure constraints. Whether newer and more sensitive next-generation sequencing (NGS) adds substantial value beyond traditional Sanger sequencing in detecting HIV-1 drug resistance in real life settings remains an open and debatable question. In this paper, we attempt to address this issue by performing a comprehensive comparison of drug resistance identified by Sanger sequencing and six NGS thresholds. We conducted this study in a well-characterized, vulnerable cohort of children and adolescents living with diverse HIV-1 subtypes in Kenya and, importantly, failing antiretroviral therapy (ART) with already extensive drug resistance. Our findings suggest a potential added value of NGS over Sanger even in this unique cohort.

Sleep problems among Chinese clinical nurses working in general hospitals.

BACKGROUND: Epidemiological data evaluating sleep problems in clinical nurses in mainland China are scarce and an association between sleep problems and occupational stress has not been investigated. AIMS: To assess the prevalence of sleep problems and associated factors and determine their association with occupational stress among clinical nurses in general hospitals. METHODS: Nurses were selected through random cluster sampling. They answered a self-administered questionnaire, which included sociodemographic and occupational variables, the Pittsburgh Sleep Quality Index (PSQI) scoring system and the Job Content Questionnaire for evaluating occupational stress. Logistic regression analysis was used to evaluate factors associated with sleep problems. RESULTS: There were 5012 participants. Mean PSQI score of 4951 subjects included in the final analysis was 7.32 ± 3.24, with 2713 subjects having PSQI ≥8, accounting for 55% of participants. Female subjects in the intensive care unit and emergency departments were at higher risk of sleep problems. The following factors also presented a risk for sleep problems: multiple years of service, high monthly night shift frequency, primary and intermediate professional status, temporary employment status and high occupational stressors (including high psychological job demands, low job control and low workplace's social support). CONCLUSIONS: The overall prevalence rate of sleep problems among clinical nurses in general hospitals in mainland China was high. Many factors could affect the sleep quality of nurses, although occupational stress facilitates development of sleep problems. Various risk factors associated with sleep problems among nurses should be studied extensively and measures for relieving occupational stress should be undertaken.

Depersonalisation/derealisation symptoms and updating orientation in patients with vestibular disease.

BACKGROUND: Patients with vestibular disease have an increased rate of reporting symptoms of depersonalisation/derealisation (DD) and similar symptoms can be provoked in healthy subjects during caloric vestibular stimulation. OBJECTIVE: To assess the relationship between DD symptoms in patients with peripheral vestibular disease and their ability to update orientation in the environment. METHODS: Sixty healthy subjects and 50 patients with peripheral vestibular disease completed a DD questionnaire (Cox and Swinson, 2002) and a General Health Questionnaire (GHQ)-12 (Goldberg and Williams, 1988). This was followed by a test of updating spatial orientation in which subjects were exposed to 10 manually driven whole body rotations of 45 degrees, 90 degrees or 135 degrees in a square room, which contained distinctive features on the walls, in such a way that the features and corners subtended 45 degrees with respect to the subject. After each rotation subjects reported which wall or corner they were facing. Estimation error was calculated by subtracting the reported rotation from the actual rotation. RESULTS: DD scores were significantly higher in vestibular patients than in healthy subjects (p<0.05, t test). In patients, the lowest symptom scores and the lowest estimation errors were found in those with a unilateral canal paresis without balance symptoms whereas the highest scores and largest estimation errors were found in those with bilateral vestibular loss (p<0.05, ANOVA). Across all patients, DD scores were related to estimation errors (adjusted r2 = 0.25, p<0.05, ANCOVA). CONCLUSIONS: Patients with peripheral vestibular disease have a deficit in the ability to update orientation on the environment and a high prevalence of DD symptoms, which may imply a high order effect of the vestibular impairment. Derealisation symptoms in vestibular disease may be a consequence of a sensory mismatch between disordered vestibular input and other sensory signals of orientation.

Depersonalisation/derealisation symptoms in vestibular disease.

BACKGROUND: Depersonalisation is a subjective experience of unreality and detachment from the self often accompanied by derealisation; the experience of the external world appearing to be strange or unreal. Feelings of unreality can be evoked by disorienting vestibular stimulation. OBJECTIVE: To identify the prevalence of depersonalisation/derealisation symptoms in patients with peripheral vestibular disease and experimentally to induce these symptoms by vestibular stimulation. METHODS: 121 healthy subjects and 50 patients with peripheral vestibular disease participated in the study. For comparison with the patients a subgroup of 50 age matched healthy subjects was delineated. All completed (1) an in-house health screening questionnaire; (2) the General Health Questionnaire (GHQ-12); (3) the 28-item depersonalisation/derealisation inventory of Cox and Swinson (2002). Experimental verification of "vestibular induced" depersonalisation/derealisation was assessed in 20 patients and 20 controls during caloric irrigation of the labyrinths. RESULTS: The frequency and severity of symptoms in vestibular patients was significantly higher than in controls. In controls the most common experiences were of "déjà vu" and "difficulty in concentrating/attending". In contrast, apart from dizziness, patients most frequently reported derealisation symptoms of "feel as if walking on shifting ground", "body feels strange/not being in control of self", and "feel 'spacey' or 'spaced out'". Items permitted discrimination between healthy subjects and vestibular patients in 92% of the cases. Apart from dizziness, caloric stimulation induced depersonalisation/derealisation symptoms which healthy subjects denied ever experiencing before, while patients reported that the symptoms were similar to those encountered during their disease. CONCLUSIONS: Depersonalisation/derealisation symptoms are both different in quality and more frequent under conditions of non-physiological vestibular stimulation. In vestibular disease, frequent experiences of derealisation may occur because distorted vestibular signals mismatch with the other sensory input to create an incoherent frame of spatial reference which makes the patient feel he or she is detached or separated from the world.

Experimental investigation of an unstable ring resonator with 90-deg beam rotation for a chemical oxygen iodine laser.

We report the experimental results of an unstable ring resonator with 90-deg beam rotation for a kilowatt class chemical oxygen iodine laser (COIL). The distributions of near-field phase and far-field intensity were measured. A beam quality of 1.6 was achieved when the COIL average output power was approximately 5 kW.

[What do reviewers look for in 'original articles' submitted for publication in the Nederlands Tijdschrift voor Geneeskunde?]. / Waarop letten beoordelaars van 'oorspronkelijke stukken' die ter publicatie zijn aangeboden aan het Nederlands Tijdschrift voor Geneeskunde?

OBJECTIVE: To determine to what extent reviewers of the Nederlands Tijdschrift voor Geneeskunde (Dutch Journal of Medicine, NTvG) use specific criteria when reviewing original articles. DESIGN: Descriptive. SETTING: Editorial office of the NTvG. METHODS: From 21 October 1993 to 1 March 1994, 89 original research manuscripts were received. Of these, 60 (67%) were submitted to reviewers. Each manuscript was sent to a second reviewer, with the same expertise, as well. On the basis of two checklists with a total of 16 quality elements, the manuscripts were analysed and compared with the chief editor's judgement. The results of each individual referee were correlated with his year of graduation. The duration of the peer review procedure was established. RESULTS: The reviewers of the NTvG responded to 46% of the explicit questions from the editors (list one), while they commented upon 43% of the criteria in the second implicit list. There was no relation with the year of graduation. Approximately 12% of the flaws in the manuscripts, as assessed by the editor, were missed. About 42% of the correct elements in the manuscript were not mentioned in the evaluation. The interrater agreement between paired reviewers was 0.26 (kappa); on average 10.4 of the 16 checkpoints were mentioned or not by both. Peer review took 41 days on average. CONCLUSION: Only a small fraction of the flaws in a manuscript were missed by the reviewers. Peer review is reasonably uniform at the NTvG, but would probably benefit from standardization.

Escherichia coli associated with acute measles and diarrhoea at Kenyatta National Hospital, Kenya.

Three hundred and three children under 5 years old with acute measles and diarrhoea (cases) and 300 other age-matched children with diarrhoea (controls) were examined for enteroadherent E. coli (EAEC) and other agents including rotavirus and Cryptosporidium. EAEC was determined by tissue culture of HEP-2 cells. Other agents were determined by conventional methods. EAEC was identified from both cases and control accounting for 10.3% (31/303) and 15.2% (46/300) respectively. Other bacterial agents were: 10.3% (31/303) from cases and 12.8% (39/300) from controls. A higher detection rate of enteroparasites was found among cases 15% (45/300) than controls 8.9% (27/300) whereas rotavirus was the reverse, 3% (9/303) in cases and 30.3% (92/300) in controls. To our knowledge characterization of EAEC has not been done before and therefore might be attributing factor to some of our unexplained diarrhoeal cases.

Evaluation of culture media and antimicrobial susceptibility of Helicobacter pylori.

Isolation of Helicobacter pylori on artificial culture is hampered by the lack of reliable and cheap media. In this study, three different types of culture media were evaluated for isolation of H. pylori from clinical specimens. These media included: Modified Thayer-Martin (MTM), Skirrow's campylobacter agar and chocolate agar. Modified Thayer-Martin agar was superior in isolation to others with an isolation rate of 47% (31/66). The size of colonies on this media were larger and clearly defined. Growth was detectable after 4 days of incubation, with a maximum growth after 7 days. Thirty one strains of H. pylori isolated from cases were tested against ten antibiotics (ampicillin, tetracycline, gentamicin, erythromycin, chloramphenicol, nalidixic acid, colistin, kanamycin, sulpharazole and metronidazole) in Mueller-Hinton agar, to determine the minimum inhibitory concentration (MIC). H. pylori was very susceptible to most drugs but resistant to nalidixic acid.

Helicobacter pylori in peptic ulcer disease in Kenya.

Sixty six patients with dyspeptic symptoms underwent upper gastrointestinal endoscopy and biopsies for Helicobacter pylori culture. The number of H. pylori isolated increased with age reaching a peak at 51 to 60 years of age. Antral gastritis closely followed by duodenitis accounted for the highest number of H. pylori isolated, (87.5% and 85.7% respectively). In patients with duodenal ulceration only, 57% had H. pylori isolated from their antral biopsies, a result that was just slightly higher than that where no endoscopic diagnosis was made (50%).

Enhancement of Campylobacter jejuni virulence by serial passage in chicks.

Four isolates of Campylobacter jejuni were studied to determine changes in virulence following six serial passages in chicks. Chicks that received invasive isolates exhibited diarrhea and depressed weight gain. Immature mice were used to assess virulence of the passaged isolates of C. jejuni. Nine-day-old mice infected with passaged isolates showed lethargy, dehydration, depression, decreased weight gain, and occult blood in feces. Mouse pups inoculated with the third and sixth chick passage levels of an invasive isolate showed significant depression in mean daily weight gain and elevated mortality compared with controls and subjects inoculated with unpassaged isolates. This study demonstrated enhancement of virulence in a C. jejuni isolate following chick passage. In contrast, three other passaged isolates failed to show any consistent increase in virulence.

The characterization of Vibrio cholerae isolated in Kenya in 1983.

A total of 245 strains of Vibrio cholerae 01 and two strains of V. cholerae non-01 were isolated and collected from diarrhoeal patients in Homa Bay District Hospital and the other medical facilities in Nyanza Province, Kenya in 1983. The majority of V. cholerae 01 tested were Ogawa type (with the exception of nine Inaba type), biotype E1 Tor (except one untypable strain) and Celebes original type (except one cured type). Haemolytic activity to sheep red blood cells was detected in 75.5% of isolates. Out of 245 strains of V. cholerae 01, 184 were resistant to tetracycline, streptomycin and ampicillin. All were sensitive to chloramphenicol and nalidixic acid. Only one strain of V. cholerae 01 was sensitive to all five antimicrobial agents tested. An environmental cholera survey was done after the cholera outbreak subsided. Twenty strains of V. cholerae non-01 were isolated from water samples in Nyanza Province but none of V. cholerae 01 was isolated.

Enterotoxigenic Escherichia coli infection in childhood diarrhoea in Mombasa, Kenya.

PIP: This study was carried out at the Coast General Hospital in Mombasa, Kenya, during the dry month of March, 1984. Stool specimens were collected from 81 infants and children aged 0-36 months and with diarrhea of less than 7 days' duration. 35 age-matched children, who visited the hospitals with complaints other than gastrointestinal, served as controls. None of the children had received previous antibiotic therapy. Stools were checked for enterotoxigenic Escherichia coli (ETEC). E. coli isolates were assayed for labile toxin (LT) and stable toxin (ST) production by the Biken test and the suckling mouse assay, respectively. 19 ETEC were isolated from children with diarrhea, constituting an isolation rate of 23.5%. No ETEC were isolated from the controls. ST producers predominated (94.7%). Results indicate that the rates of ETEC isolation increase with age. In the majority of cases (16/19) ETEC caused diarrhea which was watery, with the number of motions ranging from 3 to 10 times. Fever was present in 9 patients. Mucus and blood were observed in very few cases. Vomiting was frequent (10/19) but abdominal pain was less common (5/10).^ieng