Andrew Brent

Diagnosis of Childhood Tuberculosis and Host RNA Expression in Africa

BACKGROUND Improved diagnostic tests for tuberculosis in children are needed. We hypothesized that transcriptional signatures of host blood could be used to distinguish tuberculosis from other diseases in African children who either were or were not infected with the human immunodeficiency virus (HIV). METHODS The study population comprised prospective cohorts of children who were undergoing evaluation for suspected tuberculosis in South Africa (655 children), Malawi (701 children), and Kenya (1599 children). Patients were assigned to groups according to whether the diagnosis was culture-confirmed tuberculosis, culture-negative tuberculosis, diseases other than tuberculosis, or latent tuberculosis infection. Diagnostic signatures distinguishing tuberculosis from other diseases and from latent tuberculosis infection were identified from genomewide analysis of RNA expression in host blood. RESULTS We identified a 51-transcript signature distinguishing tuberculosis from other diseases in the South African and Malawian children (the discovery cohort). In the Kenyan children (the validation cohort), a risk score based on the signature for tuberculosis and for diseases other than tuberculosis showed a sensitivity of 82.9% (95% confidence interval [CI], 68.6 to 94.3) and a specificity of 83.6% (95% CI, 74.6 to 92.7) for the diagnosis of culture-confirmed tuberculosis. Among patients with cultures negative for Mycobacterium tuberculosis who were treated for tuberculosis (those with highly probable, probable, or possible cases of tuberculosis), the estimated sensitivity was 62.5 to 82.3%, 42.1 to 80.8%, and 35.3 to 79.6%, respectively, for different estimates of actual tuberculosis in the groups. In comparison, the sensitivity of the Xpert MTB/RIF assay for molecular detection of M. tuberculosis DNA in cases of culture-confirmed tuberculosis was 54.3% (95% CI, 37.1 to 68.6), and the sensitivity in highly probable, probable, or possible cases was an estimated 25.0 to 35.7%, 5.3 to 13.3%, and 0%, respectively; the specificity of the assay was 100%. CONCLUSIONS RNA expression signatures provided data that helped distinguish tuberculosis from other diseases in African children with and those without HIV infection. (Funded by the European Union Action for Diseases of Poverty Program and others).

A Preliminary Study of Pneumonia Etiology Among Hospitalized Children in Kenya

Abstract Background. Pneumonia is the leading cause of childhood death in the developing world. Higher-quality etiological data are required to reduce this mortality burden. Methods. We conducted a case-control study of pneumonia etiology among children aged 1–59 months in rural Kenya. Case patients were hospitalized with World Health Organization–defined severe pneumonia (SP) or very severe pneumonia (VSP); controls were outpatient children without pneumonia. We collected blood for culture, induced sputum for culture and multiplex polymerase chain reaction (PCR), and obtained oropharyngeal swab specimens for multiplex PCR from case patients, and serum for serology and nasopharyngeal swab specimens for multiplex PCR from case patients and controls. Results. Of 984 eligible case patients, 810 (84%) were enrolled in the study; 232 (29%) had VSP. Blood cultures were positive in 52 of 749 case patients (7%). A predominant potential pathogen was identified in sputum culture in 70 of 417 case patients (17%). A respiratory virus was detected by PCR from nasopharyngeal swab specimens in 486 of 805 case patients (60%) and 172 of 369 controls (47%). Only respiratory syncytial virus (RSV) showed a statistically significant association between virus detection in the nasopharynx and pneumonia hospitalization (odds ratio, 12.5; 95% confidence interval, 3.1–51.5). Among 257 case patients in whom all specimens (excluding serum specimens) were collected, bacteria were identified in 24 (9%), viruses in 137 (53%), mixed viral and bacterial infection in 39 (15%), and no pathogen in 57 (22%); bacterial causes outnumbered viral causes when the results of the case-control analysis were considered. Conclusions. A potential etiology was detected in >75% of children admitted with SP or VSP. Except for RSV, the case-control analysis did not detect an association between viral detection in the nasopharynx and hospitalization for pneumonia.

Risk score to stratify children with suspected serious bacterial infection: observational cohort study

Objectives To derive and validate a clinical score to risk stratify children presenting with acute infection. Study design and participants Observational cohort study of children presenting with suspected infection to an emergency department in England. Detailed data were collected prospectively on presenting clinical features, laboratory investigations and outcome. Clinical predictors of serious bacterial infection (SBI) were explored in multivariate logistic regression models using part of the dataset, each model was then validated in an independent part of the dataset, and the best model was chosen for derivation of a clinical risk score for SBI. The ability of this score to risk stratify children with SBI was then assessed in the entire dataset. Main outcome measure Final diagnosis of SBI according to criteria defined by the Royal College of Paediatrics and Child Health working group on Recognising Acute Illness in Children. Results Data from 1951 children were analysed. 74 (3.8%) had SBI. The sensitivity of individual clinical signs was poor, although some were highly specific for SBI. A score was derived with reasonable ability to discriminate SBI (area under the receiver operator characteristics curve 0.77, 95% CI 0.71 to 0.83) and risk stratify children with suspected SBI. Conclusions This study demonstrates the potential utility of a clinical score in risk stratifying children with suspected SBI. Further work should aim to validate the score and its impact on clinical decision making in different settings, and ideally incorporate it into a broader management algorithm including additional investigations to further stratify a childs risk.

Performance of the MGIT TBc Identification Test and Meta-Analysis of MPT64 Assays for Identification of the Mycobacterium tuberculosis Complex in Liquid Culture

ABSTRACT Rapid MPT64-based immunochromatographic tests (MPT64 ICTs) have been developed to detect Mycobacterium tuberculosis complex (MTBC) in culture. We demonstrated the noninferiority of one commercial MTP64 ICT, the MGIT TBc identification (TBcID) test, to GenoType line probe assays for MTBC identification in positive MGIT cultures. Meta-analysis of MPT64 ICT performance for identification of MTBC in liquid culture confirmed similar very high sensitivities and specificities for all three commercial MPT64 assays for which sufficient data were available.

Burden of disease in adults admitted to hospital in a rural region of coastal Kenya: an analysis of data from linked clinical and demographic surveillance systems

Summary Background Estimates of the burden of disease in adults in sub-Saharan Africa largely rely on models of sparse data. We aimed to measure the burden of disease in adults living in a rural area of coastal Kenya with use of linked clinical and demographic surveillance data. Methods We used data from 18 712 adults admitted to Kilifi District Hospital (Kilifi, Kenya) between Jan 1, 2007, and Dec 31, 2012, linked to 790 635 person-years of observation within the Kilifi Health and Demographic Surveillance System, to establish the rates and major causes of admission to hospital. These data were also used to model disease-specific disability-adjusted life-years lost in the population. We used geographical mapping software to calculate admission rates stratified by distance from the hospital. Findings The main causes of admission to hospital in women living within 5 km of the hospital were infectious and parasitic diseases (303 per 100 000 person-years of observation), pregnancy-related disorders (239 per 100 000 person-years of observation), and circulatory illnesses (105 per 100 000 person-years of observation). Leading causes of hospital admission in men living within 5 km of the hospital were infectious and parasitic diseases (169 per 100 000 person-years of observation), injuries (135 per 100 000 person-years of observation), and digestive system disorders (112 per 100 000 person-years of observation). HIV-related diseases were the leading cause of disability-adjusted life-years lost (2050 per 100 000 person-years of observation), followed by non-communicable diseases (741 per 100 000 person-years of observation). For every 5 km increase in distance from the hospital, all-cause admission rates decreased by 11% (95% CI 7–14) in men and 20% (17–23) in women. The magnitude of this decline was highest for endocrine disorders in women (35%; 95% CI 22–46) and neoplasms in men (30%; 9–45). Interpretation Adults in rural Kenya face a combined burden of infectious diseases, pregnancy-related disorders, cardiovascular illnesses, and injuries. Disease burden estimates based on hospital data are affected by distance from the hospital, and the amount of underestimation of disease burden differs by both disease and sex. Funding The Wellcome Trust, GAVI Alliance.

Evaluation of temperature–pulse centile charts in identifying serious bacterial illness: observational cohort study

Background Distinguishing serious bacterial infection (SBI) from milder/self-limiting infections is often difficult. Interpretation of vital signs is confounded by the effect of temperature on pulse and respiratory rate. Temperature–pulse centile charts have been proposed to improve the predictive value of pulse rate in the clinical assessment of children with suspected SBI. Objectives To assess the utility of proposed temperature–pulse centile charts in the clinical assessment of children with suspected SBI. Study design and participants The predictive value for SBI of temperature–pulse centile categories, pulse centile categories and Advanced Paediatric Life Support (APLS) defined tachycardia were compared among 1360 children aged 3 months to 10 years presenting with suspected infection to a hospital emergency department (ED) in England; and among 325 children who presented to hospitals in the UK with meningococcal disease. Main outcome measure SBI. Results Among children presenting to the ED, 55 (4.0%) had SBI. Pulse centile category, but not temperature–pulse centile category, was strongly associated with risk of SBI (p=0.0005 and 0.288, respectively). APLS defined tachycardia was also strongly associated with SBI (OR 2.90 (95% CI 1.60 to 5.26), p=0.0002). Among children with meningococcal disease, higher pulse and temperature–pulse centile categories were both associated with more severe disease (p=0.004 and 0.041, respectively). Conclusions Increased pulse rate is an important predictor of SBI, supporting National Institute for Health and Clinical Excellence recommendations that pulse rate be routinely measured in the assessment of febrile children. Temperature–pulse centile charts performed more poorly than pulse alone in this study. Further studies are required to evaluate their utility in monitoring the clinical progress of sick children over time.

Souvenirs to make your skin crawl

A 54 year old man presented 3 weeks after a fortnight holiday in Belize with ‘boils’ on both ankles. His family doctor had prescribed oral flucloxacillin for presumed bacterial furunculosis, but both lesions had slowly increased in size, accompanied by a serous discharge and intermittent ‘stabbing’ pains. Examination revealed tender, furunculoid lesions with central puncta (figure, A). Subcutaneous myiasis was diagnosed. Petroleum jelly was applied to occlude the pores, causing larval spiracles to protrude (figure, B), but the larvae could not be removed intact with forceps alone. Small incisions were required to remove a second-stage instar larva of Dermatobia hominis from each lesion (figure, C). When last reviewed several weeks later he had had no further recurrence of his symptoms and both lesions had completely healed without complications. Figure 1 Subcutaneous myiasis due to Dermatobia hominis Human subcutaneous myiasis is caused by the larvae (maggots) of Cordylobia anthropophaga (‘tumbu’ fly) in sub-Saharan Africa, and Dermatobia hominis (‘tropical bot fly’) in Central and South America. Female D. hominis flies attach their eggs to mosquitoes or muscoid flies, which deposit them on warm-blooded hosts (e.g. cattle, humans); body warmth then triggers the larvae to ‘hatch’ and penetrate the hosts skin. Over 6-12 weeks the larvae develop subcutaneously through three stages, producing furunculoid lesions with central pores through which they breathe via spiracles and excrete serous/sero-purulent gut secretions. Left alone the third-stage larva will eventually leave the host and pupate in the soil to emerge as an adult fly in 1-3 months. Tumbu fly larvae, and first-stage instar larvae of D. hominis, can usually be removed by simply occluding the pore, forcing the larva to emerge for air, when it may be extruded by gentle squeezing. However, barb-like rows of backward-projecting spines make second-stage and third-stage larvae of D. hominis more difficult to remove (figure, D), and over-zealous attempts to remove larvae piecemeal could exacerbate local inflammation by release of larval antigens. Surgical removal is therefore often required. Antibiotics are rarely indicated as bacterial super-infection is uncommon, probably because of bacteriostatic activity of larval gut secretions.

Not all that is malaria is falciparum

A 52-year-old woman presented with fever following 3 weeks in South Africa. 10 days earlier she had developed a headache, non-productive cough, fever, myalgia, and chills. She had not been taking malaria prophylaxis. She travelled regularly to Africa with her work, including Malawi, Kenya, Ghana, and Nigeria in the preceding year. Examination was unremarkable. A full blood count and serum biochemistry were normal, apart from a mildly raised C-reactive protein (25 mg/L). Following 24 h observation, her headache persisted but she remained afebrile, and two thick and thin fi lms and OptiMAL rapid malaria tests (Flow Inc, Portland, OR, USA) were negative for malaria. A viral upper respiratory tract infection was suspected, until a third malaria fi lm was reported to show Plasmodium ovale schizonts. Since P ovale infection is rare in South Africa, the patient was treated with oral artemether-lumefantrine (80 mg/480 mg at 0, 8, 24, 36, 48, and 60 h) to cover Plasmodium falciparum, pending further review of her blood fi lms. This review confi rmed scanty trophozoites (fi gure, A) and schizonts (fi gure, B) of P ovale. She made a rapid recovery and received primaquine (15 mg daily for 14 days) to eliminate parasite hypnozoites. 2 years later, she remains well and has had no further malaria episodes. The sensitivity of microscopy for malaria diagnosis increases with the number of blood fi lms examined. This case reinforces the importance of doing a minimum of three fi lms, the sensitivity of which is more than 95% in the hands of an experienced microscopist. Although rapid malaria tests are increasingly used, their sensitivity for P ovale (20–30%) and Plasmodium malariae (20–50%) is poor, so they should not be relied upon for diagnosis. Microscopy remains the method of choice, particularly if these species are suspected. Although P ovale infection is rarely life-threatening, prompt diagnosis and radical cure of the liver stage are nevertheless important to prevent recurrent bouts of illness, which become increasing diffi cult to diagnose as time away from malaria endemic areas increases. This patient was probably infected in west Africa, where P ovale is most prevalent, underlining the importance of a full travel history.

Bacteriological diagnosis of childhood TB: a prospective observational study

Childhood TB diagnosis is challenging. Studies in adults suggest Microscopic Observation Drug Susceptibility (MODS) culture or the Xpert MTB/RIF assay might be used to expand bacteriological diagnosis. However data from children are more limited. We prospectively compared MODS and Xpert MTB/RIF with standard microscopy and culture using the BD MGIT 960 system among 1442 Kenyan children with suspected TB. 97 specimens from 54 children were TB culture-positive: 91 (94%) by MGIT and 74 (76%) by MODS (p = 0.002). 72 (74%) culture-positive and 7 culture-negative specimens were Xpert MTB/RIF positive. Xpert MTB/RIF specificity was 100% (99.7–100%) among 1164 specimens from 892 children in whom TB was excluded, strongly suggesting all Xpert MTB/RIF positives are true positives. The sensitivity of MGIT, MODS and Xpert MTB/RIF was 88%, 71% and 76%, respectively, among all 104 true positive (culture and/or Xpert MTB/RIF positive) specimens. MGIT, MODS and Xpert MTB/RIF on the initial specimen identified 40/51 (78%), 33/51 (65%) and 33/51 (65%) culture-confirmed pulmonary TB cases, respectively; Xpert MTB/RIF detected 5 additional culture-negative cases. The high sensitivity and very high specificity of the Xpert MTB/RIF assay supports its inclusion in the reference standard for bacteriological diagnosis of childhood TB in research and clinical practice.

Author Correction: Bacteriological diagnosis of childhood TB: a prospective observational study.

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