Genometa - A Fast and Accurate Classifier for Short Metagenomic Shotgun Reads

Metagenomic studies use high-throughput sequence data to investigate microbial communities in situ. However, considerable challenges remain in the analysis of these data, particularly with regard to speed and reliable analysis of microbial species as opposed to higher level taxa such as phyla. We here present Genometa, a computationally undemanding graphical user interface program that enables identification of bacterial species and gene content from datasets generated by inexpensive high-throughput short read sequencing technologies. Our approach was first verified on two simulated metagenomic short read datasets, detecting 100% and 94% of the bacterial species included with few false positives or false negatives. Subsequent comparative benchmarking analysis against three popular metagenomic algorithms on an Illumina human gut dataset revealed Genometa to attribute the most reads to bacteria at species level (i.e. including all strains of that species) and demonstrate similar or better accuracy than the other programs. Lastly, speed was demonstrated to be many times that of BLAST due to the use of modern short read aligners. Our method is highly accurate if bacteria in the sample are represented by genomes in the reference sequence but cannot find species absent from the reference. This method is one of the most user-friendly and resource efficient approaches and is thus feasible for rapidly analysing millions of short reads on a personal computer.

Mothers’ perception of recovery and satisfaction with patent medicine dealers’ treatment of childhood febrile conditions in rural communities

Background Infant mortality in rural areas of Nigeria can be minimized if childhood febrile conditions are treated by trained health personnel, deployed to primary healthcare centres (PHCs) rather than the observed preference of mothers for patent medicine dealers (PMDs). However, health service utilization/patronage is driven by consumer satisfaction and perception of services/product value. The objective of this study was to determine ‘mothers’ perception of recovery’ and ‘mothers’ satisfaction’ after PMD treatment of childhood febrile conditions, as likely drivers of mothers’ health-seeking behaviour, which must be targeted to reverse the trend. Methods Ugwuogo-Nike, in Enugu, Nigeria, has many PMDs/PHCs, and was selected based on high prevalence of childhood febrile conditions. In total, 385 consenting mothers (aged 15–45 years) were consecutively recruited at PMD shops, after purchasing drugs for childhood febrile conditions, in a cross-sectional observational study using a pre-tested instrument; 33 of them (aged 21–47 years) participated in focus group discussions (FGDs). Qualitative data were thematically analysed while a quantitative study was analysed with Z score and Chi square statistics, at p < 0.05. Results Most participants in FGDs perceived that their child had delayed recovery, but were satisfied with PMDs’ treatment of childhood febrile conditions, for reasons that included politeness, caring attitude, drug availability, easy accessibility, flexibility in pricing, shorter waiting time, their God-fearing nature, and disposition as good listeners. Mothers’ satisfaction with PMDs’ treatment is significantly (p < 0.05) associated with mothers’ perception of recovery of their child (χ2 = 192.94, df = 4; p < 0.0001; Cramer’s V = 0.7079). However, predicting mothers’ satisfaction with PMDs’ treatment from a knowledge of mothers’ perception of recovery shows a high accord (lambda[A from B] = 0.8727), unlike when predicting mothers’ perception of recovery based on knowledge of mothers’ satisfaction with PMDs’ treatment (lambda[A from B] = 0.4727). Conclusions Mothers’ satisfaction could be the key ‘driver’ of mothers’ health-seeking behaviour and is less likely to be influenced by mothers’ perception of recovery of their child. Therefore, mothers’ negative perception of their child’s recovery may not induce proportionate decline in mothers’ health-seeking behaviour (patronage of PMDs), which might be influenced mainly by mothers’ satisfaction with the positive attributes of PMDs’ personality/practice and sets an important agenda for PHC reforms.