Fighting antimicrobial resistance : who should lead the agenda?

The TWENDE consortium (https://infection.st-andrews.ac.uk/twende-overview/) is funded by the European and Developing Countries Clinical Trials Partnership (EDCTP).Publisher PDFPeer reviewe

The role and implications of RNAscope and mRNA in the diagnosis of tuberculosis

Funding: The authors’ research on host biomarkers of TB diagnosis is supported by the Wellcome Trust Institutional Strategic Support fund of the University of St Andrews, grant code 204821/Z/16/Z.Peer reviewe

Mycobacterial load assay

Tuberculosis is a difficult disease to treat, a process made more harder as tools to monitor treatment response only provide a result long after the patient has provided a sample. The mycobacterial load assay (MBLA) provides a simple molecular test to quantify and determine the viability of M. tuberculosis in human or other samples.Postprin

Experimental Models of Cryptococcosis

Cryptococcosis is a life-threatening fungal disease that infects around one million people each year. Establishment and progression of disease involves a complex interplay between the fungus and a diverse range of host cell types. Over recent years, numerous cellular, tissue, and animal models have been exploited to probe this host-pathogen interaction. Here we review the range of experimental models that are available for cryptococcosis research and compare the relative advantages and limitations of the different systems

United Kingdom–East and Southern Africa partnership at the forefront of developing first ever test that measures patient tuberculosis burden in hours

EDCTP for funding the development and trialling of the Molecular bacterial load assay test. GCRF, SCF, PanACEA and University of St Andrews School of Medicine for funding the MBLA stakeholders conference. We acknowledge funding from European and Developing countries Clinical Trials Partnership for funding the development and trialling of the Molecular bacterial load assay test. Funding from Scottish Funding Council – Global Challenges Research Fund, Pan-African Consortium for Evaluation of anti-tuberculosis Antibiotics and University of St Andrews School of Medicine for made the MBLA stakeholders conference possible.Mycobacterium tuberculosis has caused tuberculosis (TB) in humans for at least 3 millennia, but the disease has evaded eradication efforts by all human civilisations despite promising technological advancements. The World Health Organization (WHO) has set a target of ending the TB epidemic by 2035. Going by the current rate of progress, it is estimated that it will take another 160 years to realise the WHO End TB Strategy’s target. Accelerating the eradication of TB will require effective tools for diagnosis, vaccines and medicines to treat the disease, and efficient implementation thereof. This presents a great opportunity for innovators in East Africa and the world over to chip in and develop the best technologies to end TB. With funding from the European and Developing Countries Clinical Trials Partnership (EDCTP), partnerships between the UK-based University of St Andrews and research institutions in East and Southern Africa have led to the development of the first ever test – the molecular bacterial load assay (MBLA) – that measures the number of TB bacteria in a patient and reveals if this number is declining as a patient progresses on treatment. Initial assay results are available within 4 hours. Real-time knowledge of patient mycobacterial burden and the effectiveness of prescribed medications are crucial for timely clinical decisions on patient management.Publisher PDFPeer reviewe

Tuberculosis bacteria detection and counting in fluorescence microscopy images using a multi-stage deep learning pipeline

The manual observation of sputum smears by fluorescence microscopy for the diagnosis and treatment monitoring of patients with tuberculosis (TB) is a laborious and subjective task. In this work, we introduce an automatic pipeline which employs a novel deep learning-based approach to rapidly detect Mycobacterium tuberculosis (Mtb) organisms in sputum samples and thus quantify the burden of the disease. Fluorescence microscopy images are used as input in a series of networks, which ultimately produces a final count of present bacteria more quickly and consistently than manual analysis by healthcare workers. The pipeline consists of four stages: annotation by cycle-consistent generative adversarial networks (GANs), extraction of salient image patches, classification of the extracted patches, and finally, regression to yield the final bacteria count. We empirically evaluate the individual stages of the pipeline as well as perform a unified evaluation on previously unseen data that were given ground-truth labels by an experienced microscopist. We show that with no human intervention, the pipeline can provide the bacterial count for a sample of images with an error of less than 5%.Publisher PDFPeer reviewe

OMNIgene.SPUTUM suppresses contaminants whilst maintaining Mycobacterium tuberculosis viability and obviates cold-chain transport

The study was funded by DNA Genotek Inc. Canada, the manufacturer of OMNIgene.SPUTUM (grant number SMD0-Z0B014).Tuberculosis (TB) diagnostics are centralised, requiring long-distance transportation of specimens in most resource-limited settings. We evaluated the ability of OMNIgene.SPUTUM (OM-S) to obviate cold-chain transport of TB specimens. A two-arm (same-day and after 5 days sample processing) study was conducted to assess contamination rates and Mycobacterium tuberculosis viability in OM-S-treated samples against the standard decontamination procedure (SDP) in Mozambique, using Lowenstein Jensen (LJ) and mycobacterial growth indicator tube (MGIT) culture and molecular bacterial load assay. 270 specimens were processed using OM-S and SDP in same-day and 5-day arms. Contamination was lower in OM-S-treated than SDP-treated cultures: 12% versus 15% and 2% versus 27% in the same-day and 5-day arms, respectively. M. tuberculosis recovery in OM-S-treated LJ cultures was 10% and 56% higher in the same-day and 5-day arms, respectively, than SDP-treated cultures, but lower in MGIT (52% and 28% lower in the same-day and 5-day arms, respectively). M. tuberculosis viable count was 1log estimated CFU·mL−1 lower in 5-day OM-S-treated sputa. OM-S was more effective at liquefying sputum with a shorter sample processing time: 22 min for culture. OM-S is simple to use and has demonstrated a high potency to suppress contaminants, maintenance of viability at ambient temperatures and higher M. tuberculosis recovery, particularly in the solid LJ cultures. Optimisation of OM-S to achieve higher MGIT culture positivity and shorter time to result will increase its application and utility in the clinical management of TB.Publisher PDFPeer reviewe

Klebsiella pneumoniae carbapenamases in Escherichia coli isolated from humans and livestock in rural South-Western Uganda

Funding: This work was supported by; The "Holistic Approach to Unravel Antibacterial Resistance in East Africa” project which was a 3-year Global Context Consortia Award (MR/S004785/1) funded by the National Institute for Health Research, Medical Research Council and the Department of Health and Social Care, UK.Background The accumulation of resistance genes in Escherichia coli (E. coli) strains imposes limitations in the therapeutic options available for the treatment of infections caused by E.coli. Production of Klebsiella pneumoniae carbapenemase (KPC) by E. coli renders it resistant to broad-spectrum β-lactam antibiotics. Globally there is existing evidence of spread of carbapenem-resistant E. coli in both humans and livestock driven by acquisition of the several other carbapenemase genes. Overall, there is little information regarding the extent of KPC gene distribution in E. coli. We set out to determine the prevalence, and evaluate the phenotypic and genotypic patterns of KPC in E. coli isolated from humans and their livestock in rural south western Uganda. Methods A laboratory-based, descriptive cross-sectional study was conducted involving 96 human and 96 livestock isolates collected from agro-pastoralist communities in Mbarara district in south western Uganda. Phenotypic and molecular methods (PCR) were used for presence and identification of KPC genes in the E. coli isolates. A chi-square test of independence was used to evaluate the differences in resistant patterns between carbapenems and isolates. Results The overall prevalence of carbapenem resistance by disk diffusion susceptibility testing (DST) for both humans and livestock isolates were 41.7% (80/192). DST-based resistance was identical in both human and livestock isolates (41.7%). The prevalence of carbapenem resistance based on Modified Hodge Test (MHT) was 5% (2/40) and 10% (4/40) for humans and livestock isolates respectively. Both human and livestock isolates, 48.7% (95/192) had the KPC gene, higher than phenotypic expression; 41.7% (80/192). blaKPC gene prevalence was overall similar in human isolates (51%; 49/96) vs livestock isolates (47.9%; 46/96). Approximately, 19% (15/80) of the isolates were phenotypically resistant to carbapenems and over 70% (79/112) of the phenotypically sensitive strains harbored the blaKPC gene. Conclusion Our results suggest that both human and livestock isolates of E. coli in our setting carry the blaKPC gene with a high percentage of strains not actively expressing the blaKPC gene. The finding of fewer isolates carrying the KPC gene than those phenotypically resistant to carbapenems suggests that other mechanisms are playing a role in this phenomenon, calling for further researcher into this phenomenon.Publisher PDFPeer reviewe

Detection and quantification of viable Mycobacterium tuberculosis bacilli in saline-processed stool samples by Tuberculosis Molecular Bacterial Load Assay : a potential alternative for processing stool

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Systematic assessment of clinical and bacteriological markers for tuberculosis reveals discordance and inaccuracy of symptom-based diagnosis for treatment response monitoring

This work was supported by Commonwealth PhD studentship award to Dr Bariki Mtafya (Award number: TZS-2016-718) at University of St Andrews and European and Developing Countries Clinical Trials Partnership through TWENDE project (grant number; TWENDE-EDCTP-CSA-2014-283) and PanACEA II (grant number; 97118-PanACEA-TRIA.2015.1102) awarded to Professor Stephen Gillespie and Dr Wilber Sabiiti at the University of St Andrews, UK.Background : Clinical symptoms are the benchmark of tuberculosis (TB) diagnosis and monitoring of treatment response but is not clear how they relate to TB bacteriology, particularly the novel tuberculosis Molecular Bacterial Load Assay (TB-MBLA). Methods : Presumptive cases were bacteriologically confirmed for TB and assessed for symptom and bacteriological resolution using smear microscopy (SM), culture and TB-MBLA over 6-month treatment course. Kaplan Meier and Kappa statistics were used to test relationship between symptom- and bacteriological-positivity. Results : A cohort of 46 bacteriologically confirmed TB cases were analysed for treatment response over a six-month treatment course. Pre-treatment symptom and bacteriological positivity concurred in over 70% of the cases. This agreement was lost in over 50% of cases whose chest pain, night sweat, and loss of appetite had resolved by week 2 of treatment. Cough resolved at a 3.2% rate weekly and was 0.3% slower than the combined bacteriological (average of MGIT and TB-MBLA positivity) resolution rate, 3.5% per week. Drop in TB-MBLA positivity reflected fall in bacillary load, 5.7±1.3- at baseline to 0.30±1.0- log10 eCFU/mL at month 6, and closer to cough resolution than other bacteriological measures, accounting for the only one bacteriologically positive case out of seven still coughing at month 6. Low baseline bacillary load patients were more likely to be bacteriologically negative, HR 5.6, p=0.003 and, HR 3.2, p=0.014 by month-2 and 6 of treatment respectively. Conclusion : The probability of clinical symptoms reflecting bacteriological positivity weakens as patient progresses on anti-TB therapy, making symptom-based diagnosis a less reliable marker of treatment response.Publisher PDFPeer reviewe