Factors associated with medical consumable availability in level 1 facilities in Malawi: a secondary analysis of a facility census.

BACKGROUND: Medical consumable stock-outs negatively affect health outcomes not only by impeding or delaying the effective delivery of services but also by discouraging patients from seeking care. Consequently, supply chain strengthening is being adopted as a key component of national health strategies. However, evidence on the factors associated with increased consumable availability is limited. METHODS: In this study, we used the 2018-19 Harmonised Health Facility Assessment data from Malawi to identify the factors associated with the availability of consumables in level 1 facilities, ie, rural hospitals or health centres with a small number of beds and a sparsely equipped operating room for minor procedures. We estimate a multilevel logistic regression model with a binary outcome variable representing consumable availability (of 130 consumables across 940 facilities) and explanatory variables chosen based on current evidence. Further subgroup analyses are carried out to assess the presence of effect modification by level of care, facility ownership, and a categorisation of consumables by public health or disease programme, Malawi's Essential Medicine List classification, whether the consumable is a drug or not, and level of average national availability. FINDINGS: Our results suggest that the following characteristics had a positive association with consumable availability-level 1b facilities or community hospitals had 64% (odds ratio [OR] 1·64, 95% CI 1·37-1·97) higher odds of consumable availability than level 1a facilities or health centres, Christian Health Association of Malawi and private-for-profit ownership had 63% (1·63, 1·40-1·89) and 49% (1·49, 1·24-1·80) higher odds respectively than government-owned facilities, the availability of a computer had 46% (1·46, 1·32-1·62) higher odds than in its absence, pharmacists managing drug orders had 85% (1·85, 1·40-2·44) higher odds than a drug store clerk, proximity to the corresponding regional administrative office (facilities greater than 75 km away had 21% lower odds [0·79, 0·63-0·98] than facilities within 10 km of the district health office), and having three drug order fulfilments in the 3 months before the survey had 14% (1·14, 1·02-1·27) higher odds than one fulfilment in 3 months. Further, consumables categorised as vital in Malawi's Essential Medicine List performed considerably better with 235% (OR 3·35, 95% CI 1·60-7·05) higher odds than other essential or non-essential consumables and drugs performed worse with 79% (0·21, 0·08-0·51) lower odds than other medical consumables in terms of availability across facilities. INTERPRETATION: Our results provide evidence on the areas of intervention with potential to improve consumable availability. Further exploration of the health and resource consequences of the strategies discussed will be useful in guiding investments into supply chain strengthening. FUNDING: UK Research and Innovation as part of the Global Challenges Research Fund (Thanzi La Onse; reference MR/P028004/1), the Wellcome Trust (Thanzi La Mawa; reference 223120/Z/21/Z), the UK Medical Research Council, the UK Department for International Development, and the EU (reference MR/R015600/1).

Ensemble Detection of DNA Engineering Signatures.

Synthetic biology is creating genetically engineered organisms at an increasing rate for many potentially valuable applications, but this potential comes with the risk of misuse or accidental release. To begin to address this issue, we have developed a system called GUARDIAN that can automatically detect signatures of engineering in DNA sequencing data, and we have conducted a blinded test of this system using a curated Test and Evaluation (T&E) data set. GUARDIAN uses an ensemble approach based on the guiding principle that no single approach is likely to be able to detect engineering with perfect accuracy. Critically, ensembling enables GUARDIAN to detect sequence inserts in 13 target organisms with a high degree of specificity that requires no subject matter expert (SME) review.

The changes in health service utilisation in Malawi during the COVID-19 pandemic.

INTRODUCTION: The COVID-19 pandemic and the restriction policies implemented by the Government of Malawi may have disrupted routine health service utilisation. We aimed to find evidence for such disruptions and quantify any changes by service type and level of health care. METHODS: We extracted nationwide routine health service usage data for 2015-2021 from the electronic health information management systems in Malawi. Two datasets were prepared: unadjusted and adjusted; for the latter, unreported monthly data entries for a facility were filled in through systematic rules based on reported mean values of that facility or facility type and considering both reporting rates and comparability with published data. Using statistical descriptive methods, we first described the patterns of service utilisation in pre-pandemic years (2015-2019). We then tested for evidence of departures from this routine pattern, i.e., service volume delivered being below recent average by more than two standard deviations was viewed as a substantial reduction, and calculated the cumulative net differences of service volume during the pandemic period (2020-2021), in aggregate and within each specific facility. RESULTS: Evidence of disruptions were found: from April 2020 to December 2021, services delivered of several types were reduced across primary and secondary levels of care-including inpatient care (-20.03% less total interactions in that period compared to the recent average), immunisation (-17.61%), malnutrition treatment (-34.5%), accidents and emergency services (-16.03%), HIV (human immunodeficiency viruses) tests (-27.34%), antiretroviral therapy (ART) initiations for adults (-33.52%), and ART treatment for paediatrics (-41.32%). Reductions of service volume were greatest in the first wave of the pandemic during April-August 2020, and whereas some service types rebounded quickly (e.g., outpatient visits from -17.7% to +3.23%), many others persisted at lower level through 2021 (e.g., under-five malnutrition treatment from -15.24% to -42.23%). The total reduced service volume between April 2020 and December 2021 was 8 066 956 (-10.23%), equating to 444 units per 1000 persons. CONCLUSION: We have found substantial evidence for reductions in health service delivered in Malawi during the COVID-19 pandemic which may have potential health consequences, the effect of which should inform how decisions are taken in the future to maximise the resilience of healthcare system during similar events.

Isolation and sequencing of the spoilage yeast Kregervanrija delftensis.

New sequencing workflows can enable the genomics of microbes isolated from craft beverages. Here, we use hybrid, short, and long-read sequencing to assemble the genome of a yeast isolated from cider, Kregervanrija delftensis NCC-J. The Kregervanrija genus has few genomes available; thus, this contributes to yeast genomics.

Draft genome of the Ogataea polymorpha type strain CBS 4732.

The methylotrophic yeast Ogataea polymorpha is of significant biotechnological interest, particularly in high-temperature fermentations and for recombinant protein production. Here, we present a high-quality genome assembly for the O. polymorpha type strain CBS 4732.

Genetic basis for probiotic yeast phenotypes revealed by nanopore sequencing.

Probiotic yeasts are emerging as preventative and therapeutic solutions for disease. Often ingested via cultured foods and beverages, they can survive the harsh conditions of the gastrointestinal tract and adhere to it, where they provide nutrients and inhibit pathogens like Candida albicans. Yet, little is known of the genomic determinants of these beneficial traits. To this end, we have sequenced 2 food-derived probiotic yeast isolates that mitigate fungal infections. We find that the first strain, KTP, is a strain of Saccharomyces cerevisiae within a small clade that lacks any apparent ancestry from common European/wine S. cerevisiae strains. Significantly, we show that S. cerevisiae KTP genes involved in general stress, pH tolerance, and adherence are markedly different from S. cerevisiae S288C but are similar to the commercial probiotic yeast species S. boulardii. This suggests that even though S. cerevisiae KTP and S. boulardii are from different clades, they may achieve probiotic effect through similar genetic mechanisms. We find that the second strain, ApC, is a strain of Issatchenkia occidentalis, one of the few of this family of yeasts to be sequenced. Because of the dissimilarity of its genome structure and gene organization, we infer that I. occidentalis ApC likely achieves a probiotic effect through a different mechanism than the Saccharomyces strains. Therefore, this work establishes a strong genetic link among probiotic Saccharomycetes, advances the genomics of Issatchenkia yeasts, and indicates that probiotic activity is not monophyletic and complimentary mixtures of probiotics could enhance health benefits beyond a single species.

Estimating the health burden of road traffic injuries in Malawi using an individual-based model.

BACKGROUND: Road traffic injuries are a significant cause of death and disability globally. However, in some countries the exact health burden caused by road traffic injuries is unknown. In Malawi, there is no central reporting mechanism for road traffic injuries and so the exact extent of the health burden caused by road traffic injuries is hard to determine. A limited number of models predict the incidence of mortality due to road traffic injury in Malawi. These estimates vary greatly, owing to differences in assumptions, and so the health burden caused on the population by road traffic injuries remains unclear. METHODS: We use an individual-based model and combine an epidemiological model of road traffic injuries with a health seeking behaviour and health system model. We provide a detailed representation of road traffic injuries in Malawi, from the onset of the injury through to the final health outcome. We also investigate the effects of an assumption made by other models that multiple injuries do not contribute to health burden caused by road accidents. RESULTS: Our model estimates an overall average incidence of mortality between 23.5 and 29.8 per 100,000 person years due to road traffic injuries and an average of 180,000 to 225,000 disability-adjusted life years (DALYs) per year between 2010 and 2020 in an estimated average population size of 1,364,000 over the 10-year period. Our estimated incidence of mortality falls within the range of other estimates currently available for Malawi, whereas our estimated number of DALYs is greater than the only other estimate available for Malawi, the GBD estimate predicting and average of 126,200 DALYs per year over the same time period. Our estimates, which account for multiple injuries, predict a 22-58% increase in overall health burden compared to the model ran as a single injury model. CONCLUSIONS: Road traffic injuries are difficult to model with conventional modelling methods, owing to the numerous types of injuries that occur. Using an individual-based model framework, we can provide a detailed representation of road traffic injuries. Our results indicate a higher health burden caused by road traffic injuries than previously estimated.

Socio-demographic factors associated with early antenatal care visits among pregnant women in Malawi: 2004-2016.

INTRODUCTION: In 2016, the WHO published recommendations increasing the number of recommended antenatal care (ANC) visits per pregnancy from four to eight. Prior to the implementation of this policy, coverage of four ANC visits has been suboptimal in many low-income settings. In this study we explore socio-demographic factors associated with early initiation of first ANC contact and attending at least four ANC visits ("ANC4+") in Malawi using the Malawi Demographic and Health Survey (MDHS) data collected between 2004 and 2016, prior to the implementation of new recommendations. METHODS: We combined data from the 2004-5, 2010 and 2015-16 MDHS using Stata version 16. Participants included all women surveyed between the ages of 15-49 who had given birth in the five years preceding the survey. We conducted weighted univariate, bivariate and multivariable logistic regression analysis of the effects of each of the predictor variables on the binary endpoint of the woman attending at least four ANC visits and having the first ANC attendance within or before the four months of pregnancy (ANC4+). To determine whether a factor was included in the model, the likelihood ratio test was used with a statistical significance of P< 0.05 as the threshold. RESULTS: We evaluated data collected in surveys in 2004/5, 2010 and 2015/6 from 26386 women who had given birth in the five years before being surveyed. The median gestational age, in months, at the time of presenting for the first ANC visit was 5 (inter quartile range: 4-6). The proportion of women initiating ANC4+ increased from 21.3% in 2004-5 to 38.8% in 2015-16. From multivariate analysis, there was increasing trend in ANC4+ from women aged 20-24 years (adjusted odds ratio (aOR) = 1.27, 95%CI:1.05-1.53, P = 0.01) to women aged 45-49 years (aOR = 1.91, 95%CI:1.18-3.09, P = 0.008) compared to those aged 15-19 years. Women from richest socio-economic position ((aOR = 1.32, 95%CI:1.12-1.58, P<0.001) were more likely to demonstrate ANC4+ than those from low socio-economic position. Additionally, women who had completed secondary (aOR = 1.24, 95%CI:1.02-1.51, P = 0.03) and tertiary (aOR = 2.64, 95%CI:1.65-4.22, P<0.001) education were more likely to report having ANC4+ than those with no formal education. Conversely increasing parity was associated with a reduction in likelihood of ANC4+ with women who had previously delivered 2-3 (aOR = 0.74, 95%CI:0.63-0.86, P<0.001), 4-5 (aOR = 0.65, 95%CI:0.53-0.80, P<0.001) or greater than 6 (aOR = 0.61, 95%CI: 0.47-0.79, <0.001) children being less likely to demonstrate ANC4+. CONCLUSION: The proportion of women reporting ANC4+ and of key ANC interventions in Malawi have increased significantly since 2004. However, we found that most women did not access the recommended number of ANC visits in Malawi, prior to the 2016 WHO policy change which may mean that women are less likely to undertake the 2016 WHO recommendation of 8 contacts per pregnancy. Additionally, our results highlighted significant variation in coverage according to key socio-demographic variables which should be considered when devising national strategies to ensure that all women access the appropriate frequency of ANC visits during their pregnancy.

Engineered yeast genomes accurately assembled from pure and mixed samples.

Yeast whole genome sequencing (WGS) lacks end-to-end workflows that identify genetic engineering. Here we present Prymetime, a tool that assembles yeast plasmids and chromosomes and annotates genetic engineering sequences. It is a hybrid workflow-it uses short and long reads as inputs to perform separate linear and circular assembly steps. This structure is necessary to accurately resolve genetic engineering sequences in plasmids and the genome. We show this by assembling diverse engineered yeasts, in some cases revealing unintended deletions and integrations. Furthermore, the resulting whole genomes are high quality, although the underlying assembly software does not consistently resolve highly repetitive genome features. Finally, we assemble plasmids and genome integrations from metagenomic sequencing, even with 1 engineered cell in 1000. This work is a blueprint for building WGS workflows and establishes WGS-based identification of yeast genetic engineering.

A descriptive analysis of health practices, barriers to healthcare and the unmet need for cervical cancer screening in the Lower Napo River region of the Peruvian Amazon.

OBJECTIVES: To undertake an descriptive analysis of the health needs, healthcare practices and barriers to accessing healthcare faced by women in Lower Napo River Region, Peru, and to understand health literacy regarding cervical cancer and the need for more effective cervical cancer screening services. METHODS: We performed a community-based needs assessment adapting Demographic and Health survey methodology with additional questions determining female health literacy on cervical cancer and assessing the availability and need for cervical cancer screening services. We surveyed women (N = 121) across all households in six communities along the Lower Napo River, Loreto, Peru, in May 2015. Data were collected as part of the larger Amazon Community Based Participation Cervical Cancer Screen-and-Treat Programme. Survey data were compared to national results from ENDES 2014. RESULTS: Comparison between our findings and the ENDES 2014 survey highlighted considerable inequality between indigenous or mixed indigenous, rural populations in Loreto, Peru, and national population data averages over level of formal education, literacy, barriers to accessing healthcare and maternal and sexual health. Even though only 5.9% (N = 7/117) of women had no formal health insurance coverage, money was reported as the leading barrier accessing healthcare (N = 88/117, 75.2%). Health literacy regarding cervical and breast cancer was poor. A high proportion of women highlighted fear of screening processes (70.8%, N = 80/113) and lack of available services (53.6%, N = 60/112) as barriers to cervical cancer screening. CONCLUSION: Although progress has been made in improving healthcare access in Peru, such gains have not been experienced equitably and women living in remote communities face persistent marginalization regarding their health. There is a significant need for education related to and screening for cervical cancer in this region that is tailored to the reality of women's lives in remote communities in Loreto.

Characterization of Individual Human Antibodies That Bind Pertussis Toxin Stimulated by Acellular Immunization.

Despite high vaccination rates, the incidence of whooping cough has steadily been increasing in developing countries for several decades. The current acellular pertussis (aP) vaccines all include the major protective antigen pertussis toxin (PTx) and are safer, but they appear to be less protective than infection or older, whole-cell vaccines. To better understand the attributes of individual antibodies stimulated by aP, we isolated plasmablast clones recognizing PTx after booster immunization of two donors. Five unique antibody sequences recognizing native PTx were recovered and expressed as recombinant human IgG1 antibodies. The antibodies all bind different epitopes on the PTx S1 subunit, B oligomer, or S1-B subunit interface, and just one clone neutralized PTx in an in vitro assay. To better understand the epitopes bound by the nonneutralizing S1-subunit antibodies, comprehensive mutagenesis with yeast display provided a detailed map of the epitope recognized by antibodies A8 and E12. Residue R76 is required for antibody A8 binding and is present on the S1 surface but is only partially exposed in the holotoxin, providing a structural explanation for A8's inability to neutralize holotoxin. The B-subunit-specific antibody D8 inhibited PTx binding to a model receptor and neutralized PTx in vitro as well as in an in vivo leukocytosis assay. This is the first study, to our knowledge, to identify individual human antibodies stimulated by the acellular pertussis vaccine and demonstrates the feasibility of using these approaches to address outstanding issues in pertussis vaccinology, including mechanisms of accelerated waning of protective immunity despite repeated aP immunization.

Genetic engineering of host organisms for pharmaceutical synthesis.

Pharmaceutical production hosts may be derived from almost any organism, from Chinese Hamster Ovary (CHO) cell lines to isolated actinomycetes. Each host can be improved, historically only through adaptive evolution. Recently, the maturation of organism engineering has expanded the available models, methods, and tools for altering host phenotypes. New tools like CRISPR-associated endonucleases promise to enable precise cellular reprogramming and to access previously intractable hosts. In this review, we discuss the most recent advances in engineering several types of pharmaceutical production hosts. These include model organisms, potential platform hosts with advantageous metabolism or physiology, specialized producers capable of unique biosynthesis, and CHO, the most widely used recombinant protein production host. To realize improved engineered hosts, an increasing number of approaches involving DNA sequencing and synthesis, host rewriting technologies, computational methods, and organism engineering strategies must be used. Integrative workflows that enable application of the right combination of methods to the right production host could enable economical production solutions for emerging human health treatments.