Barriers to COVID-19 Health Products in Low-and Middle-Income Countries During the COVID-19 Pandemic: A Rapid Systematic Review and Evidence Synthesis

Evaluation of a massive open online course for just-in-time training of healthcare workers

Introduction

COVID-19 created a global need for healthcare worker (HCW) training. Initially, mass trainings focused on public health workers and physicians working in intensive care units. However, in resource-constrained settings, nurses and general practitioners provide most patient care, typically lacking the training and equipment to manage critically ill patients. We developed a massive open online course (MOOC) for HCWs in resource-constrained settings aimed at training bedside providers caring for COVID-19 patients. We describe the development, implementation and analysis of this MOOC.

Methods

From May through June 2020, the course was developed by a multi-disciplinary team and launched on two online platforms in July. The 4-hour course comprises 6 video-based modules. Student knowledge was assessed using pre- and post-module quizzes and final exam, while demographics and user experience were evaluated by pre- and post-course surveys and learning platform data.

Results

From July 17th to September 24th, 30,859 students enrolled, 18,818 started, and 7,101 completed the course. Most participants worked in healthcare (78%) and resided in lower middle- (38%) or upper middle- (20%) income countries. Learners from upper middle-income and lower middle-income countries had higher completion rates. Knowledge gains were observed from pre-module to post-module quizzes and a final exam. Afterward, participants reported increased self-efficacy regarding course objectives, a 0.63 mean increase on a 4-point scale (95% CI [0.60,0.66]). Most participants (93%) would recommend the course to others.

Conclusion

This article demonstrates the potential of MOOCs to rapidly provide access to emerging medical knowledge during a public health crisis, particularly for HCWs in high- and middle-income countries.

Social Vulnerability and Compliance With World Health Organization Advice on Protective Behaviors Against COVID-19 in African and Asia Pacific Countries: Factor Analysis to Develop a Social Vulnerability Index

BACKGROUND

COVID-19 protective behaviors are key interventions advised by the World Health Organization (WHO) to prevent COVID-19 transmission. However, achieving compliance with this advice is often challenging, particularly among socially vulnerable groups.

OBJECTIVE

We developed a social vulnerability index (SVI) to predict individuals' propensity to adhere to the WHO advice on protective behaviors against COVID-19 and identify changes in social vulnerability as Omicron evolved in African countries between January 2022 and August 2022 and Asia Pacific countries between August 2021 and June 2022.

METHODS

In African countries, baseline data were collected from 14 countries (n=15,375) during the first Omicron wave, and follow-up data were collected from 7 countries (n=7179) after the wave. In Asia Pacific countries, baseline data were collected from 14 countries (n=12,866) before the first Omicron wave, and follow-up data were collected from 9 countries (n=8737) after the wave. Countries' socioeconomic and health profiles were retrieved from relevant databases. To construct the SVI for each of the 4 data sets, variables associated with COVID-19 protective behaviors were included in a factor analysis using polychoric correlation with varimax rotation. Influential factors were adjusted for cardinality, summed, and min-max normalized from 0 to 1 (most to least vulnerable). Scores for compliance with the WHO advice were calculated using individuals' self-reported protective behaviors against COVID-19. Multiple linear regression analyses were used to assess the associations between the SVI and scores for compliance to WHO advice to validate the index.

RESULTS

In Africa, factors contributing to social vulnerability included literacy and media use, trust in health care workers and government, and country income and infrastructure. In Asia Pacific, social vulnerability was determined by literacy, country income and infrastructure, and population density. The index was associated with compliance with the WHO advice in both time points in African countries but only during the follow-up period in Asia Pacific countries. At baseline, the index values in African countries ranged from 0.00 to 0.31 in 13 countries, with 1 country having an index value of 1.00. The index values in Asia Pacific countries ranged from 0.00 to 0.23 in 12 countries, with 2 countries having index values of 0.79 and 1.00. During the follow-up phase, the index values decreased in 6 of 7 African countries and the 2 most vulnerable Asia Pacific countries. The index values of the least vulnerable countries remained unchanged in both regions.

CONCLUSIONS

In both regions, significant inequalities in social vulnerability to compliance with WHO advice were observed at baseline, and the gaps became larger after the first Omicron wave. Understanding the dimensions that influence social vulnerability to protective behaviors against COVID-19 may underpin targeted interventions to enhance compliance with WHO recommendations and mitigate the impact of future pandemics among vulnerable groups.

Critical Care in the Austere Environment

Practice of critical care in austere settings involves navigating rapidly evolving environments, where physical resources, provider availability, and healthcare capacity are constrained. Austere Critical Care focuses on maintaining the highest standard of care possible for patients while also identifying resource limitations, responding to patient surges, and adhering to proper triage practices at the austere site. This includes transferring the patient when able and necessary. This article describes the current practice of critical care medicine in the austere environment, using recent natural disasters, pandemics, and conflicts as case studies.

Health Planning in Times of COVID-19 in Burkina Faso: The Role of Its National Strategic Pandemic Management Committee

CONTEXT

Presenting the COVID-19 crisis as a pandemic misleadingly implies a certain homogeneity between the regions of the Globe in terms of their burden and reactions. However, from the outset of the crisis, countries presented different epidemiological realities and sometimes adopted divergent, even opposing measures. Curiously, the heterogeneity of responses persisted as scientific evidence accumulated about COVID-19 and the strategies for dealing with it.

CASE STUDY

This commentary aims to recount the specific experience of Burkina Faso, and how it reoriented its initial biomedical response into a multisectoral strategy. Burkina Faso set up a committee specifically to examine the effects not only of the pandemic, but also of the control measures. This committee was mandated to decompartmentalize the lens through which the COVID-19 was dealt with. It entered into dialogue with a level of stakeholders often overlooked during national health crisis: communities. As a member of this "National Committee for Crisis Management of the Pandemic", one of the co-authors contributed to its orientations and has witnessed first-hand some of the challenges it faced.

RECOMMENDATIONS

This experience suggests that the project of extricating the field of public health from medicine is advancing in Burkina Faso. In order to manage future crises more effectively and across different sectors, there is an urgent need to establish state structures and to strengthen public health systems. States need coordination units that have the legitimacy, authority and resources required to mobilize a variety of actors at the community, national and international levels.

The development and implementation of a low-cost mechanical ventilator in a low-middle-income country during the COVID-19 pandemic: The Unisabana-HERONS

Background

The COVID-19 pandemic in Latin America generated the need to develop low-cost, fast-manufacturing mechanical ventilators. The Universidad de La Sabana and the Fundacion Neumologica Colombiana designed and manufactured the Unisabana-HERONS (USH) ventilator. Here, we present the preclinical and clinical study results to evaluate its effectiveness and safety characteristics in an animal model (Yorkshire Sow) and five patients with acute respiratory failure receiving mechanical ventilatory support for 24 h.

Methods

The effectiveness and safety outcomes included maintaining arterial blood gases and pulse oximetry saturation (SpO2), respiratory pressures and volumes (during continuous monitoring) in the range of ARDS and lung-protective strategy goals, and the occurrence of barotrauma. A significance level of 0.05 was used for statistical tests. This clinical trial was registered on Clinicaltrials.gov (NCT04497623) and approved by the ethics committee.

Results

Among patients treated with the Unisabana-HERONS, the most frequent causes of acute respiratory failure were pneumonia in 3/5 (60 %) and ARDS in 2/5 (40 %). During the treatment, the ventilatory parameters related to lung protection protocols were kept within the safety range, and vital signs and blood gas were stable. The percentage of time that the respiratory pressures or volumes were out of safety range were plateau pressure >30 cm H2O: 0.00 %; driving pressure >15 cm H2O: 0.06 %; mechanical power >15 J/min: 0.00 %; and Tidal volume >8 mL/kg: 0.00 %. There were no adverse events related to the ventilator. The usability questionnaire retrieved a median score for all items between 9 and 10 (best score: 10), indicating great ease of use.

Conclusion

The Unisabana-HERONS ventilator effectively provided adequate gas exchange and maintained the ventilatory parameters in the range of lung protection strategies in humans and an animal model. Furthermore, it is straightforward to use and is a low-cost medical device.

The effect of COVID-19 on the non-COVID health outcomes of crisis-affected peoples: a systematic review

BACKGROUND

The COVID-19 pandemic posed considerable risks to populations affected by humanitarian crises in low- and middle-income countries (LMICs). However, there is limited understanding of how the pandemic may have affected non-COVID health outcomes among crisis-affected populations. Our aim was to examine the evidence on the impact of the COVID-19 pandemic on non-COVID-19 health outcomes for crisis-affected populations in LMICs.

METHODS

A systematic review methodology was applied following PRISMA guidelines. Eligibility criteria were: crisis-affected populations in LMICS; COVID-19; and all health topics, except for sexual and reproductive health which was covered in a linked review. Five bibliographic databases and additional grey literature sources were searched. The search period was from 2019 to 31 July 2022. Eligible papers were extracted and analysed using a narrative synthesis approach based on the study objectives and relevant health access and systems frameworks. A quality appraisal was also conducted.

FINDINGS

4320 articles were screened, and 15 eligible studies were identified and included in this review. Ten studies collected health outcomes data. Eight related to mental health, which generally showed worse mental health outcomes because of the pandemic, and pandemic-related stressors were identified. Two studies assessed physical health outcomes in children, while none addressed physical health outcomes among adults. Nine studies reported on access to healthcare, revealing worse access levels due to the pandemic and noting key barriers to care. Seven studies reported on the impact on health systems, with key challenges including reduced and distorted health care funding, reduced staff capacity, interrupted medicines and supplies, weak information and mixed-messaging, and weak leadership. All fifteen studies on the social determinants of health, particularly highlighting the effect of increasing poverty, the role of gender, and food insecurity on health outcomes. The quality of papers was limited overall.

CONCLUSION

This review found some limited evidence indicating negative mental health effects, increased barriers to accessing care, damage to health systems and magnified impacts on the social determinants of health for crisis-affected people during the COVID-19 pandemic. However, the small number and limited quality of the studies make the overall strength of evidence quite weak.

The COVID-19 pandemic and neurology: A survey on previous and continued restrictions for clinical practice, curricular training, and health economics

BACKGROUND AND PURPOSE

The COVID-19 pandemic has significantly impacted health systems worldwide. Here, we assessed the pandemic's impact on clinical service, curricular training, and financial burden from a neurological viewpoint during the enforced lockdown periods and the assumed recovery by 2023.

METHODS

An online 18-item survey was conducted by the European Academy of Neurology (EAN) NeuroCOVID-19 Task Force among the EAN community. The survey was online between February and March 2023. Questions related to general, demographic, clinical, work, education, and economic aspects.

RESULTS

We collected 430 responses from 79 countries. Most health care professionals were aged 35-44 years, with >15 years of work experience. The key findings of their observations were as follows. (i) Clinical services were cut back in all neurological subspecialties during the most restrictive COVID-19 lockdown period. The most affected neurological subspecialties were services for patients with dementia, and neuromuscular and movement disorders. The levels of reduction and the pace of recovery were distinct for acute emergencies and in- and outpatient care. Recovery was slow for sleep medicine, autonomic nervous system disorders, neurorehabilitation, and dementia care. (ii) Student and residency rotations and grand rounds were reorganized, and congresses were converted into a virtual format. Conferences are partly maintained in a hybrid format. (iii) Affordability of neurological care and medication shortage are emerging issues.

CONCLUSIONS

Recovery of neurological services up to spring 2023 has been incomplete following substantial disruption of neurological care, medical education, and health economics in the wake of the COVID-19 pandemic. The continued limitations for the delivery of neurological care threaten brain health and call for action on a global scale.

Effect of distributing locally produced cloth facemasks on COVID-19-like illness and all-cause mortality-a cluster-randomised controlled trial in urban Guinea-Bissau

Facemasks have been employed to mitigate the spread of SARS-CoV-2. The community effect of providing cloth facemasks on COVID-19 morbidity and mortality is unknown. In a cluster randomised trial in urban Bissau, Guinea-Bissau, clusters (geographical areas with an average of 19 houses), were randomised to an intervention or control arm using computer-generated random numbers. Between 20 July 2020 and 22 January 2021, trial participants (aged 10+ years) living in intervention clusters (n = 90) received two 2-layer cloth facemasks, while facemasks were only distributed later in control clusters (n = 91). All participants received information on COVID-19 prevention. Trial participants were followed through a telephone interview for COVID-19-like illness (3+ symptoms), care seeking, and mortality for 4 months. End-of-study home visits ensured full mortality information and distribution of facemasks to the control group. Individual level information on outcomes by trial arm was compared in logistic regression models with generalised estimating equation-based correction for cluster. Facemasks use was mandated. Facemask use in public areas was assessed by direct observation. We enrolled 39,574 trial participants among whom 95% reported exposure to groups of >20 persons and 99% reported facemasks use, with no difference between trial arms. Observed use was substantially lower (~40%) with a 3%, 95%CI: 0-6% absolute difference between control and intervention clusters. Half of those wearing a facemask wore it correctly. Few participants (532, 1.6%) reported COVID-19-like illness; proportions did not differ by trial arm: Odds Ratio (OR) = 0.81, 95%CI: 0.57-1.15. 177 (0.6%) participants reported consultations and COVID-19-like illness (OR = 0.83, 95%CI: 0.56-1.24); 89 participants (0.2%) died (OR = 1.34, 95%CI: 0.89-2.02). Hence, though trial participants were exposed to many people, facemasks were mostly not worn or not worn correctly. Providing facemasks and messages about correct use did not substantially increase their use and had limited impact on morbidity and mortality. Trial registration: clinicaltrials.gov: NCT04471766.

Factors associated with the utilization of diagnostic tools among countries with different income levels during the COVID-19 pandemic

BACKGROUND

Disparities in the utilization of essential medical products are a key factor contributing to inequality in health outcomes. We aimed to analyze the trends and influencing factors in using Coronavirus disease 2019 (COVID-19) diagnostic tools and disparities in countries with different income levels.

METHODS

We conducted a cross-sectional study using open and publicly available data sources. Data were mainly collected from the Foundation for Innovative New Diagnostics, "Our World in Data," and the Global Burden of Disease databases. Negative binomial regression model and generalized linear mixed model were employed to investigate into five sets of factors associated with the usage of diagnostics: severity of COVID-19, socioeconomic status, health status, medical service capacity, and rigidity of response. Dominance analysis was utilized to compare the relative importance of these factors. The Blinder-Oaxaca decomposition was used to decompose the difference in the usage of diagnostics between countries.

RESULTS

The total COVID-19 testing rate ranged from 5.13 to 22,386.63 per 1000 people from March 2020 to October 2022 and the monthly testing rate declined dramatically from January 2022 to October 2022 (52.37/1000 vs 5.91/1000).. The total testing rate was primarily associated with socioeconomic status (37.84%), with every 1 standard deviation (SD) increase in Gross Domestic Product per capita and the proportion of people aged ≥ 70, the total testing rate increased by 88% and 31%. And so is the medical service capacity (33.66%), with every 1 SD increase in health workforce density, the number increased by 38%. The monthly testing rate was primarily associated with socioeconomic status (34.72%) and medical service capacity (28.67%), and the severity of COVID-19 (21.09%). The average difference in the total testing rates between high-income and low-income countries was 2726.59 per 1000 people, and 2493.43 (91.45%) of the differences could be explained through the five sets of factors.

CONCLUSIONS

Redoubling the efforts, such as local manufacturing, regulatory reliance, and strengthening the community health workforce and laboratory capacity in low- and middle-income countries (LMICs) cannot be more significant for ensuring sustainable and equitable access to diagnostic tools during pandemic.

Detection of SARS-CoV-2 in saliva by a low-cost LSPR-based sensor

The SARS-CoV-2 pandemic started more than 3 years ago, but the containment of the spread is still a challenge. Screening is imperative for informed decision making by government authorities to contain the spread of the virus locally. The access to screening tests is disproportional, due to the lack of access to reagents, equipment, finances or because of supply chain disruptions. Low and middle-income countries have especially suffered with the lack of these resources. Here, we propose a low cost and easily constructed biosensor device based on localized surface plasmon resonance, or LSPR, for the screening of SARS-CoV-2. The biosensor device, dubbed "sensor" for simplicity, was constructed in two modalities: (1) viral detection in saliva and (2) antibody against COVID in saliva. Saliva collected from 18 patients were tested in triplicates. Both sensors successfully classified all COVID positive patients (among hospitalized and non-hospitalized). From the COVID negative patients 7/8 patients were correctly classified. For both sensors, sensitivity was determined as 100% (95% CI 79.5-100) and specificity as 87.5% (95% CI 80.5-100). The reagents and equipment used for the construction and deployment of this sensor are ubiquitous and low-cost. This sensor technology can then add to the potential solution for challenges related to screening tests in underserved communities.

Vitamin D and Zinc Supplementation to Improve Treatment Outcomes among COVID-19 Patients in India: Results from a Double-Blind Randomized Placebo-Controlled Trial

BACKGROUND

There remains a need to identify low-cost interventions to improve coronavirus disease 2019 (COVID-19) outcomes. Vitamin D and zinc play a role in respiratory infections and could hold value as part of therapeutic regimens.

OBJECTIVES

To determine the effect of vitamin D or zinc supplementation on recovery from COVID-19.

METHODS

We conducted a double-blind, randomly assigned 2 x 2 factorial placebo-controlled trial with 1:1:1:1 allocation ratio, enrolling nonpregnant adults with COVID-19 from hospitals in Mumbai and Pune, India (NCT04641195). Participants (N = 181) were randomly assigned to vitamin D3 (180,000 IU bolus, then 2000 IU daily), zinc (40 mg daily), vitamin D3 and zinc, or placebo, for 8 wk. Participants were followed until 8 wk. The primary outcome was time to resolution of fever, cough, and shortness of breath. Secondary outcomes were duration of individual symptoms; need for assisted ventilation; duration of hospital stay; all-cause mortality; and blood biomarkers, including nutritional, inflammatory, and immunological markers.

RESULTS

We observed no effect of vitamin D or zinc supplementation on time to resolution of all 3 symptoms [vitamin D hazard ratio (HR): 0.92; 95% confidence interval (95% CI): 0.66, 1.30; P = 0.650; zinc HR: 0.94; 95% CI: 0.67, 1.33; P = 0.745)]. Neither vitamin D nor zinc supplementation was associated with secondary outcomes, except for increased endline serum vitamin D with vitamin D supplementation [median (interquartile range) difference between endline and baseline for vitamin D: 5.3 ng/mL (-2.3 to 13.7); for no vitamin D: -1.4 ng/mL (-5.6 to 3.9); P = 0.003]. We observed nonsignificant increases in serum zinc at endline following zinc supplementation. There was no evidence of interaction between vitamin D and zinc supplementation, no effect of either on hypercalcemia, and no adverse events.

CONCLUSIONS

Results suggest that neither vitamin D nor zinc supplementation improves COVID-19 treatment outcomes in this population. However, much larger-scale evidence, particularly from populations with vitamin D or zinc deficiency and severe infection, is required to corroborate our findings. This trial was registered at ClinicalTrials.gov and the Clinical Trials Registry of India as NCT04641195 and CTRI/2021/04/032593 respectively.

Leveraging lessons from the COVID-19 pandemic to strengthen low-income and middle-income country preparedness for future global health threats

Although the global COVID-19 pandemic response was quick to develop medical countermeasures, it failed to fully prevent morbidity and mortality in high-income countries and low-income and middle-income countries (LMICs). As new variants and post-COVID-19 condition continue to emerge and affect health systems and economies, the full human and economic cost is yet to be felt. We should now learn from these shortcomings and implement more inclusive and equitable frameworks to prevent and respond to outbreaks. This Series offers specific learnings from COVID-19 vaccination campaigns and non-pharmaceutical interventions, highlighting the need for resilient, inclusive, and equitable health systems. Taking action to rebuild trust and invest in resilient local manufacturing capacity, supply chains, regulatory frameworks, and placing LMIC voices at the centre of decision making will help to ensure preparedness for future threats. It is time to move beyond mere talk of learning and implementing lessons and instead take action towards a more resilient future.

Interactive SARS-CoV-2 dashboard for real-time geospatial visualisation of sewage and clinical surveillance data from Dhaka, Bangladesh: a tool for public health situational awareness

Throughout the COVID-19 pandemic, many dashboards were created to visualise clinical case incidence. Other dashboards have displayed SARS-CoV-2 sewage data, largely from countries with formal sewage networks. However, very few dashboards from low-income and lower-middle-income countries integrated both clinical and sewage data sets. We created a dashboard to track in real-time both COVID-19 clinical cases and the level of SARS-CoV-2 virus in sewage in Dhaka, Bangladesh. The development of this dashboard was a collaborative iterative process with Bangladesh public health stakeholders to include specific features to address their needs. The final dashboard product provides spatiotemporal visualisations of COVID-19 cases and SARS-CoV-2 viral load at 51 sewage collection sites in 21 wards in Dhaka since 24 March 2020. Our dashboard was updated weekly for the Bangladesh COVID-19 national task force to provide supplemental data for public health stakeholders making public policy decisions on mitigation efforts. Here, we highlight the importance of working closely with public health stakeholders to create a COVID-19 dashboard for public health impact. In the future, the dashboard can be expanded to track trends of other infectious diseases as sewage surveillance is increased for other pathogens.

A multi-country survey on access to healthcare and treatment services among individuals with critical medical care needs during the first wave of the pandemic

BACKGROUND

Healthcare services were significantly interrupted during the early phase of the COVID-19 pandemic. The aim of the present study was to determine the associations between sociodemographic factors and healthcare access during the first wave of the COVID-19 pandemic among individuals with critical care needs.

METHODS

This was a secondary analysis of the data of 5,156 participants recruited from 152 countries during the first wave of the COVID-19 pandemic. The dependent variables were self-reported difficulty of access to health care, challenges with obtaining medication, and the use of alternative medical services. The independent variables were age at last birthday; sex at birth, level of education, employment status and the macro-social vulnerability status. The confounding variable was the country income level. Three multivariable logistic regression analyses were conducted to determine the associations between the dependent variables and the independent variables after adjusting for the confounder.

RESULTS

Difficulty accessing health care services and obtaining medications was experienced by 1922 (37.3%) and 3746 (72.7%) participants respectively. Also, 1433 (27.8%) used alternative medical care. Retirees (AOR:1.59), unemployed (AOR:1.198), people living with HIV (AOR:2.36) and at increased risk of COVID-19 (AOR:2.10), people who used drugs (AOR:1.83) and transacted sex (AOR:1.971) had significantly higher odds for reporting difficulty with access to health care. Males (AOR:1.23), respondents with secondary level of education (AOR:1.39), retirees (AOR:2.19), unemployed (AOR:1.47), people living with HIV (AOR:2.46), people who used drugs (AOR:1.79), transacted sex (AOR:2.71) and those who might be (AOR: 1.66) and were at (AOR: 2.3) increased risk of severe COVID-19 had significantly higher odds for reporting difficulty with access to medications. People who used drugs (AOR:2.093) transacted sex (AOR:1.639), who might be (AOR: 1.211) and were at (AOR: 1.511) increased risk of severe COVID-19, and who had difficulty accessing usual healthcare (AOR: 9.047) and obtaining medications (AOR:2.16) had significantly higher odds of reporting alternative medical care use. People living with HIV (AOR:0.562) had significantly lower odds of using alternative medical care.

CONCLUSION

We identified populations who had challenges with access to healthcare and obtaining medications used alternative medical care except for people living with HIV. Priority attention should be given to alternative medical care use during future health pandemics.

Towards a transactional medicine approach to combating global emerging pathogens: the case of COVID-19

When the COVID-19 pandemic struck and China reported the first case to the World Health Organization in December 2019, there was no evidence-based treatment to combat it. With the catastrophic situation that followed, materialised by a considerable number of deaths, researchers, doctors, traditional healers, and governments of all nations committed themselves to find therapeutic solutions, including preventive and curative. There are effective treatments offered both by modern medicine and traditional medicine for COVID-19 today. However, other therapeutic proposals have not been approved due to the lack of effectiveness and scientific rigour during their development process. Proponents of modern medicine prefer biomedical therapies while in some countries, traditional treatments are used regularly because of their availability, affordability and satisfaction they bring to the population. In this paper, we propose a transactional medicine approach where the interaction between traditional and modern medicine produces a change. With this approach, the promoters of traditional medicine and those of modern medicine will be able to acquire knowledge through the experience produced by their encounters. Transactional medicine aims to be a model for decolonising medicine and recognising the value of both traditional and modern medicine in the fight against COVID-19 and other global emerging pathogens.

Host DNA depletion can increase the sensitivity of Mycobacterium spp. detection through shotgun metagenomics in sputum

Identification and phenotypic drug-susceptibility testing for mycobacteria are time-consuming and challenging but essential for managing mycobacterial infections. Next-generation sequencing (NGS) technologies can increase diagnostic speed and quality, but standardization is still lacking for many aspects (e.g., unbiased extraction, host depletion, bioinformatic analysis). Targeted PCR approaches directly on sample material are limited by the number of targets that can be included. Unbiased shotgun metagenomics on direct material is hampered by the massive amount of host DNA, which should be removed to improve the microbial detection sensitivity. For this reason, we developed a method for NGS-based diagnosis of mycobacteria directly from patient material. As a model, we used the non-tuberculous mycobacterium (NTM) Mycobacterium abscessus. We first compared the efficiency of three different DNA extraction kits for isolating DNA (quality and concentration). The two most efficient kits were then used in a follow-up study using artificial sputum. Finally, one extraction kit was selected and further evaluated for DNA isolation from a patients’ sputum mixture spiked with M. abscessus at three concentrations (final concentrations 108, 107, 106  CFU/ml). The spiked sputum samples were processed with and without saponin treatment (ST) in combination with DNAse treatment prior to bacterial DNA extraction to evaluate the recovery of bacteria and depletion of host DNA by PCR and Illumina sequencing.

While Ct values of the qPCR targeting mycobacterial ITS DNA remained rather stable, Ct values in the qPCR targeting the human β-actin gene increased by five Ct values in ST samples. In subsequent Illumina sequencing, a decrease of 89% of reads mapped to the human genome was observed in ST samples. The percentage of reads mapped to M. abscessus (108 CFU/ml) increased by 89%, and the sequencing depth increased two times when undergoing ST.

In conclusion, the sensitivity of M. abscessus detection in artificial sputum was increased using a saponin pre-treatment step. The saponin followed by the DNase I treatment approach could be efficiently applied to detect and characterize mycobacterial infections, including tuberculosis, directly from sputum.