Rapid detection of Mycobacterium ulcerans with isothermal recombinase polymerase amplification assay.

Background Access to an accurate diagnostic test for Buruli ulcer (BU) is a research priority according to the World Health Organization. Nucleic acid amplification of insertion sequence IS2404 by polymerase chain reaction (PCR) is the most sensitive and specific method to detect Mycobacterium ulcerans (M. ulcerans), the causative agent of BU. However, PCR is not always available in endemic communities in Africa due to its cost and technological sophistication. Isothermal DNA amplification systems such as the recombinase polymerase amplification (RPA) have emerged as a molecular diagnostic tool with similar accuracy to PCR but having the advantage of amplifying a template DNA at a constant lower temperature in a shorter time. The aim of this study was to develop RPA for the detection of M. ulcerans and evaluate its use in Buruli ulcer disease. Methodology and principal findings A specific fragment of IS2404 of M. ulcerans was amplified within 15 minutes at a constant 42°C using RPA method. The detection limit was 45 copies of IS2404 molecular DNA standard per reaction. The assay was highly specific as all 7 strains of M. ulcerans tested were detected, and no cross reactivity was observed to other mycobacteria or clinically relevant bacteria species. The clinical performance of the M. ulcerans (Mu-RPA) assay was evaluated using DNA extracted from fine needle aspirates or swabs taken from 67 patients in whom BU was suspected and 12 patients with clinically confirmed non-BU lesions. All results were compared to a highly sensitive real-time PCR. The clinical specificity of the Mu-RPA assay was 100% (95% CI, 84–100), whiles the sensitivity was 88% (95% CI, 77–95). Conclusion The Mu-RPA assay represents an alternative to PCR, especially in areas with limited infrastructure. Author summary Current diagnostic methods to detect M. ulcerans suffer from delayed time-to-results in most endemic countries by the prolonged period of time for the shipment and storage of samples to a distant, centralized laboratory. The M. ulcerans recombinase polymerase amplification assay (Mu-RPA) is a new, rapid diagnostic test developed for the detection of M. ulcerans infection, known commonly as Buruli ulcer, a chronic, debilitating, necrotizing disease of the skin and soft tissues. This assay is suitable for use on a portable detection device, with the potential to be used for quick diagnosis at the point of need, providing timely results to health workers at Buruli ulcer treatment clinics

Engineering with logic: Rigorous test-oracle specification and validation for TCP/IP and the Sockets API

Conventional computer engineering relies on test-and-debug development processes, with the behavior of common interfaces described (at best) with prose specification documents. But prose specifications cannot be used in test-and-debug development in any automated way, and prose is a poor medium for expressing complex (and loose) specifications. The TCP/IP protocols and Sockets API are a good example of this: they play a vital role in modern communication and computation, and interoperability between implementations is essential. But what exactly they are is surprisingly obscure: their original development focused on “rough consensus and running code,” augmented by prose RFC specifications that do not precisely define what it means for an implementation to be correct. Ultimately, the actual standard is the de facto one of the common implementations, including, for example, the 15 000 to 20 000 lines of the BSD implementation—optimized and multithreaded C code, time dependent, with asynchronous event handlers, intertwined with the operating system, and security critical. This article reports on work done in the Netsem project to develop lightweight mathematically rigorous techniques that can be applied to such systems: to specify their behavior precisely (but loosely enough to permit the required implementation variation) and to test whether these specifications and the implementations correspond with specifications that are executable as test oracles . We developed post hoc specifications of TCP, UDP, and the Sockets API, both of the service that they provide to applications (in terms of TCP bidirectional stream connections) and of the internal operation of the protocol (in terms of TCP segments and UDP datagrams), together with a testable abstraction function relating the two. These specifications are rigorous, detailed, readable, with broad coverage, and rather accurate. Working within a general-purpose proof assistant (HOL4), we developed language idioms (within higher-order logic) in which to write the specifications: operational semantics with nondeterminism, time, system calls, monadic relational programming, and so forth. We followed an experimental semantics approach, validating the specifications against several thousand traces captured from three implementations (FreeBSD, Linux, and WinXP). Many differences between these were identified, as were a number of bugs. Validation was done using a special-purpose symbolic model checker programmed above HOL4. Having demonstrated that our logic-based engineering techniques suffice for handling real-world protocols, we argue that similar techniques could be applied to future critical software infrastructure at design time, leading to cleaner designs and (via specification-based testing) more robust and predictable implementations. In cases where specification looseness can be controlled, this should be possible with lightweight techniques, without the need for a general-purpose proof assistant, at relatively little cost.EPSRC Programme Grant EP/K008528/1 REMS: Rigorous Engineering for Mainstream Systems EPSRC Leadership Fellowship EP/H005633 (Sewell) Royal Society University Research Fellowship (Sewell) St Catharine's College Heller Research Fellowship (Wansbrough), EPSRC grant GR/N24872 Wide-area programming: Language, Semantics and Infrastructure Design EPSRC grant EP/C510712 NETSEM: Rigorous Semantics for Real Systems EC FET-GC project IST-2001-33234 PEPITO Peer-to-Peer Computing: Implementation and Theory CMI UROP internship support (Smith) EC Thematic Network IST-2001-38957 APPSEM 2 NICTA was funded by the Australian Government's Backing Australia's Ability initiative, in part through the Australian Research Council

Genetic Diversity of PCR-Positive, Culture-Negative and Culture-Positive Mycobacterium ulcerans Isolated from Buruli Ulcer Patients in Ghana.

Culture of Mycobacterium ulcerans from Buruli ulcer patients has very low sensitivity. Thus confirmation of M. ulcerans infection is primarily based on PCR directed against IS2404. In this study we compare the genotypes obtained by variable number of tandem repeat analysis of DNA from IS2404-PCR positive cultures with that obtained from IS2404 positive, culture-negative tissue. A significantly greater genetic heterogeneity was found among culture-negative samples compared with that found in cultured strains but a single genotype is over-represented in both sample sets. This study provides evidence that both the focal location of bacteria in a lesion as well as differences in the ability to culture a particular genotype may underlie the low sensitivity of culture. Though preliminary, data from this work also suggests that mycobacteria previously associated with fish disease (M. pseudoshottsii) may be pathogenic for humans

Combined Inflammatory and Metabolic Defects Reflected by Reduced Serum Protein Levels in Patients with Buruli Ulcer Disease

Buruli ulcer is a skin disease caused by Mycobacterium ulcerans that is spreading in tropical countries, with major public health and economic implications in West Africa. Multi-analyte profiling of serum proteins in patients and endemic controls revealed that Buruli ulcer disease down-regulates the circulating levels of a large array of inflammatory mediators, without impacting on the leukocyte composition of peripheral blood. Notably, several proteins contributing to acute phase reaction, lipid metabolism, coagulation and tissue remodelling were also impacted. Their down-regulation was selective and persisted after the elimination of bacteria with antibiotic therapy. It involved proteins with various functions and origins, suggesting that M. ulcerans infection causes global and chronic defects in the host’s protein metabolism. Accordingly, patients had reduced levels of total serum proteins and blood urea, in the absence of signs of malnutrition, or functional failure of liver or kidney. Interestingly, slow healers had deeper metabolic and coagulation defects at the start of antibiotic therapy. In addition to providing novel insight into Buruli ulcer pathogenesis, our study therefore identifies a unique proteomic signature for this disease

Providing insight into the incubation period of Mycobacterium ulcerans disease: two case reports.

BACKGROUND: Buruli ulcer caused by Mycobacterium ulcerans is endemic in parts of West Africa and is most prevalent among the 5-15 years age group; Buruli ulcer is uncommon among neonates. The mode of transmission and incubation period of Buruli ulcer are unknown. We report two cases of confirmed Buruli ulcer in human immunodeficiency virus-unexposed, vaginally delivered term neonates in Ghana. CASE PRESENTATION: Patient 1: Two weeks after hospital delivery, a baby born to natives of the Ashanti ethnic group of Ghana was noticed by her mother to have a papule with associated edema on the right anterior chest wall and neck that later ulcerated. There was no restriction of neck movements. The diagnosis of Buruli ulcer was confirmed on the basis of a swab sample that had a positive polymerase chain reaction result for the IS2404 repeat sequence of M. ulcerans. Patient 2: This patient, from the Ashanti ethnic group in Ghana, had the mother noticing a swelling in the baby's left gluteal region 4 days after birth. The lesion progressively increased in size to involve almost the entire left gluteal region. Around the same time, the mother noticed a second, smaller lesion on the forehead and left side of neck. The diagnosis of Buruli ulcer was confirmed by polymerase chain reaction when the child was aged 4 weeks. Both patients 1 and 2 were treated with oral rifampicin and clarithromycin at recommended doses for 8 weeks in addition to appropriate daily wound dressing, leading to complete healing. Our report details two cases of polymerase chain reaction-confirmed Buruli ulcer in children whose lesions appeared at ages 14 and 4 days, respectively. The mode of transmission of M. ulcerans infection is unknown, so the incubation period is difficult to estimate and is probably dependent on the infective dose and the age of exposure. In our study, lesions appeared 4 days after birth in patient 2. Unless the infection was acquired in utero, this would be the shortest incubation period ever recorded. CONCLUSIONS: Buruli ulcer should be included in the differential diagnosis of neonates who present with characteristic lesions. The incubation period of Buruli ulcer in neonates is probably shorter than is reported for adults

“It Is Me Who Endures but My Family That Suffers”: Social Isolation as a Consequence of the Household Cost Burden of Buruli Ulcer Free of Charge Hospital Treatment

Despite free of charge biomedical treatment, the cost burden of Buruli ulcer disease (Bu) hospitalisation in Central Cameroon accounts for 25% of households' yearly earnings, surpassing the threshold of 10%, which is generally considered catastrophic for the household economy, and calling into question the sustainability of current Bu programmes. The high non-medical costs and productivity loss for Bu patients and their households make household involvement in the healing process unsustainable. 63% of households cease providing social and financial support for patients as a coping strategy, resulting in the patient's isolation at the hospital. Social isolation itself was cited by in-patients as the principal cause for abandonment of biomedical treatment. These findings demonstrate that further research and investment in Bu are urgently needed to evaluate new intervention strategies that are socially acceptable and appropriate in the local context

High prevalence of multidrug-resistant tuberculosis among patients with rifampicin resistance using GeneXpert Mycobacterium tuberculosis/rifampicin in Ghana

AbstractObjective/BackgroundDrug-resistant strains of tuberculosis (TB) represent a major threat to global TB control. In low- and middle-income countries, resource constraints make it difficult to identify and monitor cases of resistance using drug susceptibility testing and culture. Molecular assays such as the GeneXpert Mycobacterium tuberculosis/rifampicin may prove to be a cost-effective solution to this problem in these settings. The objective of this study is to evaluate the use of GeneXpert in the diagnosis of pulmonary TB since it was introduced into two tertiary hospitals in Ghana in 2013.MethodsA 2-year retrospective audit of clinical cases involving patients who presented with clinically suspected TB or documented TB not improving on standard therapy and had samples sent for GeneXpert testing.ResultsGeneXpert identified 169 cases of TB, including 17 cases of rifampicin-resistant TB. Of the seven cases with final culture and drug susceptibility testing results, six demonstrated further drug resistance and five of these were multidrug-resistant TB.ConclusionThese findings call for a scale-up of TB control in Ghana and provide evidence that the expansion of GeneXpert may be an optimal means to improve case finding and guide treatment of drug-resistant TB in this setting

Understanding perceptions on 'Buruli' in northwestern Uganda: A biosocial investigation.

BACKGROUND: An understudied disease, little research thus far has explored responses to Buruli ulcer and quests for therapy from biosocial perspective, despite reports that people seek biomedical treatment too late. METHODS AND FINDINGS: Taking an inductive approach and drawing on long-term ethnographic fieldwork in 2013-14, this article presents perspectives on this affliction of people living and working along the River Nile in northwest Uganda. Little is known biomedically about its presence, yet 'Buruli', as it is known locally, was and is a significant affliction in this region. Establishing a biosocial history of 'Buruli', largely obscured from biomedical perspectives, offers explanations for contemporary understandings, perceptions and practices. CONCLUSIONS/SIGNIFICANCE: We must move beyond over-simplifying and problematising 'late presentation for treatment' in public health, rather, develop biosocial approaches to understanding quests for therapy that take into account historical and contemporary contexts of health, healing and illness. Seeking to understand the context in which healthcare decisions are made, a biosocial approach enables greater depth and breadth of insight into the complexities of global and local public health priorities such as Buruli ulcer

Clinical and microbiological predictors of healing in Buruli ulcer disease.

INTRODUCTION: Wound measurements are relevant in monitoring the rate of healing (RoH) and may predict time to healing. Predicting the time to healing can help improve the management of Buruli ulcer. We examine three methods for the determination of RoH and their use as predictors of time to healing. METHODS: Lesion measurements of Buruli ulcer patients treated from 2007 to 2022 were obtained with acetate sheet tracings (2D) or Aranz software (3D) fortnightly. RoH was determined using the absolute area, percentage area reduction and linear methods at 4 weeks post onset of antibiotic treatment. Predicted time to healing was compared to the actual healing time. Baseline characteristics were assessed for associations with healing. RESULTS: All three methods for calculating the RoH significantly distinguished between fast and slow healers (p < 0.0001). The predicted healing time using the linear method was comparable to the actual healing time for fast healers (p = 0.34). The RoH was influenced by the form of lesion, with plaques [OR 2.19 5 %CI (1.2-3.6), p = 0.009], and oedemas [OR 8.5; 95 %CI (1.9--36.9), p = 0.004] being associated with delayed healing. The proportion of patients with paradoxical reactions 16 % vs 3 %, p < 0.0001), higher baseline bacterial load (75/104;72 % vs 21/47;45 %, p = 0.001) and delayed clearance of viable organisms (71/104;68 % vs 9/47;19 %, p < 0.0001) was higher in the slow healers than the fast healers. CONCLUSION: Predicted healing rates were comparatively lower for slow healers than fast healers. Baseline characteristics associated with healing can be explored for an improved disease management plan to reduce patient and caregiver anxiety