Non-tuberculous Mycobacteria in The Gambia: Prevalent Species, Carriage and Disease

Pulmonary tuberculosis-like disease caused by non-tuberculous mycobacteria (NTM) has gained attention, in part, because of its increased recognition especially in the elderly and immunocompetent population. This is an emerging problem of public health significance. With the increasing incidence of case reports and series from diverse countries and regions of the world, the distribution of NTM species isolated from clinical samples appear to vary significantly by region. However, very little is known about the contribution(s) of NTM to tuberculosis-like disease, and significant knowledge gaps exist regarding their geographical distribution, clinical and molecular epidemiology in low and middle income countries (LMIC) where there is a high burden of disease caused by Mycobacterium tuberculosis complex (MTBC). This dissertation provides a state of the art review of the current epidemiology of NTM carriage and disease in sub-Saharan Africa and presents results from a study of the epidemiology of NTM in The Gambia on pulmonary carriage and disease. I systematically searched electronic databases (PubMed, Embase, Popline, Ovid and Africa Wide Information) for English language articles on pulmonary NTM in sub-Saharan Africa published from Jan 1,1940 to Oct 1, 2016. The American Thoracic Society and Infectious Disease Society of America (ATS/IDSA) diagnostic criteria was applied to differentiate between colonisation of NTM and clinically relevant pulmonary NTM disease. Mycobacterium avium complex (MAC) species were the most frequently isolated NTM (15.0% - 57.8%) in colonisation while M. kansasii, was the most common (184 [69.2%] of 266) cause of confirmed pulmonary NTM disease. A significant proportion (2,623 [29.2%] of 8,980) of NTM isolates in the studies reviewed were not identified to species level. This and the absence of detailed clinical and radiological data hampered the assessment of the clinical relevance of all NTM isolates. A nationwide Tuberculosis prevalence survey provided a platform for me to investigate the population prevalence and molecular epidemiology of NTM in pulmonary samples in the general population of the Gambia. Here, I confirmed suspected NTM cultures from decontaminated sputa stored from the parent survey by 16S rRNA gene sequencing analysis and applied the ATS/IDSA diagnostic criteria to determine clinical relevance of identified NTM. The prevalence of NTM in pulmonary samples was 39.8% [95% Confidence Interval, CI: 35.8% – 44.0%). M. avium complex was by far the most commonly isolated NTM (71.0%), followed by M. fortuitum (9.5%) and M. nonchromogenicum (2.9%). All age groups were three times as likely to have NTM in their sputa as the 15-24 age group (p= 0.017), while urban compared to rural residents were 40 times less likely to be NTM positive (p =0.012). Collectively, these findings highlight the contribution of NTM to colonisation and the risk for over diagnosis of smear positive TB, given the prevalence in presumptive TB cases in The Gambia. I have highlighted the knowledge gap resulting from incomplete identification of NTM species in the sub-continent and the risk of misdiagnosis of pulmonary NTM as PTB when smear microscopy is the sole diagnostic modality. Additional research and surveillance is therefore required to investigate the full contribution of NTM to pulmonary disease, particularly in high risk groups and it is important to review the existing tuberculosis identification methods for presumptive tuberculosis suspects in The Gambia, and sub-continent

Analog to Digital Workflow Improvement: A Quantitative Study

This study tracked a radiology department’s conversion from utilization of a Kodak Amber analog system to a Kodak DirectView DR 5100 digital system. Through the use of ProModel(®) Optimization Suite, a workflow simulation software package, significant quantitative information was derived from workflow process data measured before and after the change to a digital system. Once the digital room was fully operational and the radiology staff comfortable with the new system, average patient examination time was reduced from 9.24 to 5.28 min, indicating that a higher patient throughput could be achieved. Compared to the analog system, chest examination time for modality specific activities was reduced by 43%. The percentage of repeat examinations experienced with the digital system also decreased to 8% vs. the level of 9.5% experienced with the analog system. The study indicated that it is possible to quantitatively study clinical workflow and productivity by using commercially available software

A Taxonomy of Noise in Voice Self-reports while Running

Smart earables offer great opportunities for conducting ubiquitous computing research. This paper shares its reflection on collecting self-reports from runners using the microphone on the smart eSense earbud device. Despite the advantages of the eSense in allowing researchers to collect continuous voice self-reports anytime anywhere, it also captured noise signals from various sources and created challenges in data processing and analysis. The paper presents an initial taxonomy of noise in runners’ voice self-reports data via eSense. This is based on a qualitative analysis of voice recordings based on eSense’s microphone with 11 runners across 14 in-the-wild running sessions. The paper discusses the details and characteristics of the observed noise, the challenges in achieving good-quality self-reports, and opportunities for extracting useful contextual information. The paper further suggests a noise-categorization API for the eSense or other similar platforms, not only for the purpose of noise-cancellation but also incorporating the mining of contextual information

A single and rapid calcium wave at egg activation in Drosophila.

Activation is an essential process that accompanies fertilisation in all animals and heralds major cellular changes, most notably, resumption of the cell cycle. While activation involves wave-like oscillations in intracellular Ca(2+) concentration in mammals, ascidians and polychaete worms and a single Ca(2+) peak in fish and frogs, in insects, such as Drosophila, to date, it has not been shown what changes in intracellular Ca(2+) levels occur. Here, we utilise ratiometric imaging of Ca(2+) indicator dyes and genetically encoded Ca(2+) indicator proteins to identify and characterise a single, rapid, transient wave of Ca(2+) in the Drosophila egg at activation. Using genetic tools, physical manipulation and pharmacological treatments we demonstrate that the propagation of the Ca(2+) wave requires an intact actin cytoskeleton and an increase in intracellular Ca(2+) can be uncoupled from egg swelling, but not from progression of the cell cycle. We further show that mechanical pressure alone is not sufficient to initiate a Ca(2+) wave. We also find that processing bodies, sites of mRNA decay and translational regulation, become dispersed following the Ca(2+) transient. Based on this data we propose the following model for egg activation in Drosophila: exposure to lateral oviduct fluid initiates an increase in intracellular Ca(2+) at the egg posterior via osmotic swelling, possibly through mechano-sensitive Ca(2+) channels; a single Ca(2+) wave then propagates in an actin dependent manner; this Ca(2+) wave co-ordinates key developmental events including resumption of the cell cycle and initiation of translation of mRNAs such as bicoid.This work was supported by the University of Cambridge, ISSF to T.T.W. [grant number 097814]; and Wellcome Trust Senior Research Fellowship to I.D. [grant number 096144].This is the final version of the article. It first appeared from the Company of Biologists via http://dx.doi.org/10.1242/bio.20141129

A tuberculosis nationwide prevalence survey in Gambia, 2012.

OBJECTIVE: To estimate the population prevalence of active pulmonary tuberculosis in Gambia. METHODS: Between December 2011 and January 2013, people aged ≥ 15 years participating in a nationwide, multistage cluster survey were screened for active pulmonary tuberculosis with chest radiography and for tuberculosis symptoms. For diagnostic confirmation, sputum samples were collected from those whose screening were positive and subjected to fluorescence microscopy and liquid tuberculosis cultures. Multiple imputation and inverse probability weighting were used to estimate tuberculosis prevalence. FINDINGS: Of 100 678 people enumerated, 55 832 were eligible to participate and 43 100 (77.2%) of those participated. A majority of participants (42 942; 99.6%) were successfully screened for symptoms and by chest X-ray. Only 5948 (13.8%) were eligible for sputum examination, yielding 43 bacteriologically confirmed, 28 definite smear-positive and six probable smear-positive tuberculosis cases. Chest X-ray identified more tuberculosis cases (58/69) than did symptoms alone (43/71). The estimated prevalence of smear-positive and bacteriologically confirmed pulmonary tuberculosis were 90 (95% confidence interval, CI: 53-127) and 212 (95% CI: 152-272) per 100 000 population, respectively. Tuberculosis prevalence was higher in males (333; 95% CI: 233-433) and in the 35-54 year age group (355; 95% CI: 219-490). CONCLUSION: The burden of tuberculosis remains high in Gambia but lower than earlier estimates of 490 per 100 000 population in 2010. Less than half of all cases would have been identified based on smear microscopy results alone. Successful control efforts will require interventions targeting men, increased access to radiography and more accurate, rapid diagnostic tests

Changes in the Molecular Epidemiology of Pediatric Bacterial Meningitis in Senegal After Pneumococcal Conjugate Vaccine Introduction.

BACKGROUND: Bacterial meningitis is a major cause of mortality among children under 5 years of age. Senegal is part of World Health Organization-coordinated sentinel site surveillance for pediatric bacterial meningitis surveillance. We conducted this analysis to describe the epidemiology and etiology of bacterial meningitis among children less than 5 years in Senegal from 2010 and to 2016. METHODS: Children who met the inclusion criteria for suspected meningitis at the Centre Hospitalier National d'Enfants Albert Royer, Senegal, from 2010 to 2016 were included. Cerebrospinal fluid specimens were collected from suspected cases examined by routine bacteriology and molecular assays. Serotyping, antimicrobial susceptibility testing, and whole-genome sequencing were performed. RESULTS: A total of 1013 children were admitted with suspected meningitis during the surveillance period. Streptococcus pneumoniae, Neisseria meningitidis, and Haemophilus accounted for 66% (76/115), 25% (29/115), and 9% (10/115) of all confirmed cases, respectively. Most of the suspected cases (63%; 639/1013) and laboratory-confirmed (57%; 66/115) cases occurred during the first year of life. Pneumococcal meningitis case fatality rate was 6-fold higher than that of meningococcal meningitis (28% vs 5%). The predominant pneumococcal lineage causing meningitis was sequence type 618 (n = 7), commonly found among serotype 1 isolates. An ST 2174 lineage that included serotypes 19A and 23F was resistant to trimethoprim-sulfamethoxazole. CONCLUSIONS: There has been a decline in pneumococcal meningitis post-pneumococcal conjugate vaccine introduction in Senegal. However, disease caused by pathogens covered by vaccines in widespread use still persists. There is need for continued effective monitoring of vaccine-preventable meningitis

Syndemics of syphilis, HCV infection, and methamphetamine use along the east coast of China

An upsurge in club drug use has been observed in recent years in some cities of China, especially methamphetamine, which is quickly replacing heroin to become the most widespread drug across the nation. This study investigated the type of drugs used, syphilis and hepatitis C virus (HCV) infection and the correlates for syphilis, HCV and unprotected commercial sex behavior among drug users in two cities along the east coast of China. A cross-sectional survey conducted in 2010 provided demographics, sexual and drug use behaviors, HIV knowledge and the utilization of intervention services among drug users. Blood samples were tested for HIV, syphilis, and HCV infection. Of 805 eligible participants, 0.2% were infected with HIV, 3.7% with HCV, and 9.6% with syphilis. Of the participants, 96.6% were methamphetamine users, 11.9% reported ever having used ≥2 types of these drugs, and 11.4% reported ever injecting drugs. In the multivariable logistic regression analysis, participants infected with syphilis were more likely to be female (adjusted odds ratio (AOR)=2.8, 95% confidence interval (CI): 1.2-6.5), have ever had commercial sex in the past 12 months (AOR=2.0, 95% CI: 1.0-3.9), be infected with HCV (AOR=12.1, 95% CI: 4.1-20.3) and less likely to have ever had sex with regular partners in the past 12 months (AOR=0.2, 95% CI: 0.1-0.6). Participants infected with HCV were more likely to have ever injected drugs (AOR=2.7, 95% CI: 1.1-6.5) and be infected with syphilis (AOR=8.0, 95% CI: 3.5-18.0). Participants who had unprotected sex with commercial sex partners in the last sexual encounter were more likely to be female (AOR=2.9, 95% CI:1.7-4.9), have middle school or lower level education (AOR=3.4, 95% CI:2.0-5.5), never have received intervention in the last year (AOR=2.1, 95%CI:1.2-3.6) and be infected with syphilis (AOR=4.2, 95% CI:2.4-7.4). Methamphetamine is the predominant drug used among the drug users, the prevalence of syphilis and HCV infection are alarmingly high, and unprotected commercial sex was common among this group. The findings highlight the need for effective, multifaceted interventions addressing sexual and drug use-related risky behaviors among this group. Further research is needed to better understand the causal pathway of the syndemics.https://doi.org/10.1186/1471-2458-14-17

Adjuvanted multi-epitope vaccines protect HLA-A*11:01 transgenic mice against Toxoplasma gondii

We created and tested multi-epitope DNA or protein vaccines with TLR4 ligand emulsion adjuvant (gluco glucopyranosyl lipid adjuvant in a stable emulsion [GLA-SE]) for their ability to protect against Toxoplasma gondii in HLA transgenic mice. Our constructs each included 5 of our best down-selected CD8(+) T cell-eliciting epitopes, a universal CD4(+) helper T lymphocyte epitope (PADRE), and a secretory signal, all arranged for optimal MHC-I presentation. Their capacity to elicit immune and protective responses was studied using immunization of HLA-A*11:01 transgenic mice. These multi-epitope vaccines increased memory CD8(+) T cells that produced IFN-γ and protected mice against parasite burden when challenged with T. gondii. Endocytosis of emulsion-trapped protein and cross presentation of the antigens must account for the immunogenicity of our adjuvanted protein. Thus, our work creates an adjuvanted platform assembly of peptides resulting in cross presentation of CD8(+) T cell-eliciting epitopes in a vaccine that prevents toxoplasmosis

Secondary structure of rhBMP-2 in a protective biopolymeric carrier material

Efficient delivery of growth factors is one of the great challenges of tissue engineering. Polyelectrolyte multilayer films (PEM) made of biopolymers have recently emerged as an interesting carrier for delivering recombinant human bone morphogenetic protein 2 (rhBMP-2 noted here BMP-2) to cells in a matrix-bound manner. We recently showed that PEM made of poly(l-lysine) and hyaluronan (PLL/HA) can retain high and tunable quantities of BMP-2 and can deliver it to cells to induce their differentiation in osteoblasts. Here, we investigate quantitatively by Fourier transform infrared spectroscopy (FTIR) the secondary structure of BMP-2 in solution as well as trapped in a biopolymeric thin film. We reveal that the major structural elements of BMP-2 in solution are intramolecular β-sheets and unordered structures as well as α-helices. Furthermore, we studied the secondary structure of rhBMP-2 trapped in hydrated films and in dry films since drying is an important step for future applications of these bioactive films onto orthopedic biomaterials. We demonstrate that the structural elements were preserved when BMP-2 was trapped in the biopolymeric film in hydrated conditions and, to a lesser extent, in dry state. Importantly, its bioactivity was maintained after drying of the film. Our results appear highly promising for future applications of these films as coatings of biomedical materials, to deliver bioactive proteins while preserving their bioactivity upon storage in dry state.This work was supported by the French Ministry of Research through an ANR-EmergenceBIO grant (ANR-09-EBIO-012-01), by the European Commission (FP7 program) via a European Research Council starting grant (BIOMIM, GA 259370), and by GRAVIT (081012_FIBIOS). C.P. is grafetul to IUF for financial support

The Ser82 RAGE variant affects lung function and serum RAGE in smokers and sRAGE production in vitro

Introduction: Genome-Wide Association Studies have identified associations between lung function measures and Chronic Obstructive Pulmonary Disease (COPD) and chromosome region 6p21 containing the gene for the Advanced Glycation End Product Receptor (AGER, encoding RAGE). We aimed to (i) characterise RAGE expression in the lung, (ii) identify AGER transcripts, (iii) ascertain if SNP rs2070600 (Gly82Ser C/T) is associated with lung function and serum sRAGE levels and (iv) identify whether the Gly82Ser variant is functionally important in altering sRAGE levels in an airway epithelial cell model. Methods: Immunohistochemistry was used to identify RAGE protein expression in 26 human tissues and qPCR was used to quantify AGER mRNA in lung cells. Gene expression array data was used to identify AGER expression during lung development in 38 fetal lung samples. RNA-Seq was used to identify AGER transcripts in lung cells. sRAGE levels were assessed in cells and patient serum by ELISA. BEAS2B-R1 cells were transfected to overexpress RAGE protein with either the Gly82 or Ser82 variant and sRAGE levels identified. Results: Immunohistochemical assessment of 6 adult lung samples identified high RAGE expression in the alveoli of healthy adults and individuals with COPD. AGER/RAGE expression increased across developmental stages in human fetal lung at both the mRNA (38 samples) and protein levels (20 samples). Extensive AGER splicing was identified. The rs2070600T (Ser82) allele is associated with higher FEV1, FEV1/FVC and lower serum sRAGE levels in UK smokers. Using an airway epithelium model overexpressing the Gly82 or Ser82 variants we found that HMGB1 activation of the RAGE-Ser82 receptor results in lower sRAGE production. Conclusions: This study provides new information regarding the expression profile and potential role of RAGE in the human lung and shows a functional role of the Gly82Ser variant. These findings advance our understanding of the potential mechanisms underlying COPD particularly for carriers of this AGER polymorphism