WHO malaria nucleic acid amplification test external quality assessment scheme: results of distribution programmes one to three.

BACKGROUND: The World Health Organization (WHO) recommends parasite-based diagnosis of malaria. In recent years, there has been surge in the use of various kinds of nucleic-acid amplification based tests (NAATs) for detection and identification of Plasmodium spp. to support clinical care in high-resource settings and clinical and epidemiological research worldwide. However, these tests are not without challenges, including lack (or limited use) of standards and lack of reproducibility, due in part to variation in protocols amongst laboratories. Therefore, there is a need for rigorous quality control, including a robust external quality assessment (EQA) scheme targeted towards malaria NAATs. To this effect, the WHO Global Malaria Programme worked with the UK National External Quality Assessment Scheme (UK NEQAS) Parasitology and with technical experts to launch a global NAAT EQA scheme in January 2017. METHODS: Panels of NAAT EQA specimens containing five major species of human-infecting Plasmodium at various parasite concentrations and negative samples were created in lyophilized blood (LB) and dried blood spot (DBS) formats. Two distributions per year were sent, containing five LB and five DBS specimens. Samples were tested and validated by six expert referee laboratories prior to distribution. Between 37 and 45 laboratories participated in each distribution and submitted results using the online submission portal of UK NEQAS. Participants were scored based on their laboratory's stated capacity to identify Plasmodium species, and individual laboratory reports were sent which included performance comparison with anonymized peers. RESULTS: Analysis of the first three distributions revealed that the factors that most significantly affected performance were sample format (DBS vs LB), species and parasite density, while laboratory location and the reported methodology used (type of nucleic acid extraction, amplification, or DNA vs RNA target) did not significantly affect performance. Referee laboratories performed better than non-referee laboratories. CONCLUSIONS: Globally, malaria NAAT assays now inform a range of clinical, epidemiological and research investigations. EQA schemes offer a way for laboratories to assess and improve their performance, which is critical to safeguarding the reliability of data and diagnoses especially in situations where various NAAT methodologies and protocols are in use.

Fire activity across Cretaceous/Paleogene transition: Evidence from pyrogenic biomarkers preserved in the Mahadeo-Cherrapunji section, Meghalaya, India.

Previous studies on high concentrations of polycyclic aromatic hydrocarbon (PAHs) present in the shallow-marine Um-Sohryngkew River (USR) Cretaceous/Paleogene Boundary (KPB) section suggested regional fire incidences and biotic stress on life. However, such observations at the USR site have not been confirmed so far anywhere else in the region, we, therefore, do not know whether the signal was local or regional. Thus, to find out charred organic markers associated with the shelf facies KPB outcrop (at a distance of over 5 km) of the Mahadeo-Cherrapunji road (MCR) section, PAHs were analyzed using gas chromatography-mass spectroscopy. Data show a notable rise in the PAHs and exhibit maximum abundance in the shaly KPB transition layer (in biozone P0) and the immediately underlying layer. The PAH excursions match well with the major incidences of the Deccan volcanic episodes and convergence of the Indian plate with the Eurasian and Burmese plates. These events were responsible for seawater disturbances and eustatic and depositional changes, including the retreat of the Tethys. The incidence of high amount of pyogenic PAHs unrelated to the total organic carbon content is suggestive of wind-blown or aquatic system transportation. A down-thrown shallow-marine facies of the Therriaghat block was responsible for an early accumulation of PAHs. However, the spike of perylene in the immediately underlying KPB transition layer is plausibly linked to the Chicxulub impact crater core. Anomalous concentrations of combustion-derived PAHs together with the high fragmentation and dissolution of the planktonic foraminifer shells show marine biodiversity and biotic distress. Significantly, the pyrogenic PAH excursions are restricted to either the KPB layer itself or strictly below or above it, indicating regional fire incidences and attendant KPB transition (66.016 ± 0.050 Ma).

Assessors assemble: the need for harmonised external quality assessment schemes for emerging diagnostic methodologies in the field of parasitology.

Global travel and migration trends have meant a huge increase in the numbers of people exposed to tropical parasitic diseases. Thus, there is an increasing need for robust, reproducible and reliable diagnostic techniques in the field. Advanced molecular and lateral flow techniques have pushed the boundaries of clinical parasite diagnostics with their enhanced sensitivities and specificities. These emerging technologies are, however, not without their challenges, and recently there has been multiple evidence of a lack of consensus among protocols and results obtained by quality assessment of these novel technologies. This commentary discusses findings from some recent quality assessment studies in the field of blood and faecal parasitology. The article also makes recommendations for a unified and harmonised approach towards delivering high-quality clinical parasitology diagnoses, especially through the use of proficiency testing.

Is host-schistosome coevolution going anywhere?

BACKGROUND: That pathogens and hosts coevolve is a powerful concept with broad theoretical and applied implications spanning from genetic theory to the medical and veterinary sciences, particularly in the context of infectious disease epidemiology. A substantial body of theory has been developed to explore the likelihood and consequences of coevolution, but few empirical studies have been conducted to test these theories, particularly for indirectly-transmitted pathogen-host systems. We initiated replicate longitudinal host-schistosome co-selection trials under different host genotype combinations: Schistosoma mansoni parasite lines were co-selected with populations of either previously resistant-selected Biomphalaria glabrata host genotypes, or unselected susceptible B. glabrata genotypes, or a mixed population of the two. All parasite lines were also passaged through their obligatory mammalian definitive host at each generation. RESULTS: We demonstrated variation in, and a reciprocal impact on, the fitness of both host and pathogen phenotype and genotype, an outcome dependent on the combinations of genotypes involved, and evidence of change over time. Most apparent was the observation that parasites appeared to rapidly adapt to those intermediate hosts previously selected for resistance. CONCLUSION: Our results illustrate the potential for host-schistosome coevolution and, in particular, suggest that host resistance may be a temporary phenomenon in nature due, in part, to rapid counter-adaptations by parasites.

A genome-wide screen to identify genes controlling the rate of entry into mitosis in fission yeast.

We have carried out a haploinsufficiency (HI) screen in fission yeast using heterozygous deletion diploid mutants of a genome-wide set of cell cycle genes to identify genes encoding products whose level determines the rate of progression through the cell cycle. Cell size at division was used as a measure of advancement or delay of the G2-M transition of rod-shaped fission yeast cells. We found that 13 mutants were significantly longer or shorter (greater than 10%) than control cells at cell division. These included mutants of the cdc2, cdc25, wee1 and pom1 genes, which have previously been shown to play a role in the timing of entry into mitosis, and which validate this approach. Seven of these genes are involved in regulation of the G2-M transition, 5 for nuclear transport and one for nucleotide metabolism. In addition we identified 4 more genes that were 8-10% longer or shorter than the control that also had roles in regulation of the G2-M transition or in nuclear transport. The genes identified here are all conserved in human cells, suggesting that this dataset will be useful as a basis for further studies to identify rate-limiting steps for progression through the cell cycle in other eukaryotes.

Population genetic structure of Schistosoma mansoni and Schistosoma haematobium from across six sub-Saharan African countries: implications for epidemiology, evolution and control.

We conducted the first meta-analysis of ten Schistosoma haematobium (one published and nine unpublished) and eight Schistosoma mansoni (two published and six unpublished) microsatellite datasets collected from individual schistosome-infected school-children across six sub-Saharan Africa countries. High levels of genetic diversity were documented in both S. haematobium and S. mansoni. In S. haematobium populations, allelic richness did not differ significantly between the ten schools, despite widely varying prevalences and intensities of infection, but higher levels of heterozygote deficiency were seen in East than in West Africa. In contrast, S. mansoni populations were more diverse in East than West African schools, but heterozygosity levels did not vary significantly with geography. Genetic structure in both S. haematobium and S. mansoni populations was documented, at both a regional and continental scale. Such structuring might be expected to slow the spread to new areas of anti-schistosomal drug resistance should it develop. There was, however, limited evidence of genetic structure at the individual host level, which might be predicted to promote the development or establishment of drug resistance, particularly if it were a recessive trait. Our results are discussed in terms of their potential implications for the epidemiology and evolution of schistosomes as well as their subsequent control across sub-Saharan Africa.

Population genetics of Schistosoma japonicum within the Philippines suggest high levels of transmission between humans and dogs.

BACKGROUND: Schistosoma japonicum, which remains a major public health problem in the Philippines and mainland China, is the only schistosome species for which zoonotic transmission is considered important. While bovines are suspected as the main zoonotic reservoir in parts of China, the relative contributions of various non-human mammals to S. japonicum transmission in the Philippines remain to be determined. We examined the population genetics of S. japonicum in the Philippines in order to elucidate transmission patterns across host species and geographic areas. METHODOLOGY/PRINCIPAL FINDINGS: S. japonicum miracidia (hatched from eggs within fecal samples) from humans, dogs, pigs and rats, and cercariae shed from snail-intermediate hosts, were collected across two geographic areas of Samar Province. Individual isolates were then genotyped using seven multiplexed microsatellite loci. Wright's F(ST) values and phylogenetic trees calculated for parasite populations suggest a high frequency of parasite gene-flow across definitive host species, particularly between dogs and humans. Parasite genetic differentiation between areas was not evident at the definitive host level, possibly suggesting frequent import and export of infections between villages, although there was some evidence of geographic structuring at the snail-intermediate host level. CONCLUSIONS/SIGNIFICANCE: These results suggest very high levels of transmission across host species, and indicate that the role of dogs should be considered when planning control programs. Furthermore, a regional approach to treatment programs is recommended where human migration is extensive.

An insight into the genetic variation of Schistosoma japonicum in mainland China using DNA microsatellite markers.

This study presents the first microsatellite investigation into the level of genetic variation among Schistosoma japonicum from different geographical origins. S. japonicum isolates were obtained from seven endemic provinces across mainland China: Zhejiang (Jiashan County), Anhui (Guichi County), Jiangxi (Yongxiu County), Hubei (Wuhan County), Hunan (Yueyang area), Sichuan 1 (Maoshan County), Sichuan 2 (Tianquan County), Yunnan (Dali County), and also one province in the Philippines (Sorsogon). DNA from 20 individuals from each origin were screened against 11 recently isolated and characterized S. japonicum microsatellites, and a set of nine loci were selected based on their polymorphic information content. High levels of polymorphism were obtained between and within population samples, with Chinese and Philippine strains appearing to follow different lineages, and with distinct branching between provinces. Moreover, across mainland China, genotype clustering appeared to be related to habitat type and/or intermediate host morph. These results highlight the suitability of microsatellites for population genetic studies of S. japonicum and suggest that there may be different strains of S. japonicum circulating in mainland China.

MICROSATELLITE DNA VARIATION OF SCHISTOSOMA JAPONICUM IN CHINA MAINLAND / 中国血吸虫病防治杂志

Objective To study the genetic variation among Schistosoma japonicum from the mainland of China through the microsatellite investigation. Methods S.japonicum isolates were obtained from seven endemic provinces across the mainland of the People's Republic of China: Zhejiang (Jiashan), Anhui (Guichi), Jiangxi (Yongxiu), Hubei (Wuhan), Hunan (Yueyang), Sichuan (Maoshan,Tianquan), Yunnan (Dali), and also Sorsogon Province, the Philippines. DNAs from 20 individuals from each origin were screened against six recently isolated and characterized S.japonicum microsatellites, M5A, J5N, MF1, RRPS, 2AAA and MPA, which were selected based on their polymorphic information content. Results High levels of polymorphism were found between and within population samples, with Chinese and Philippine strains appearing to follow different lineages, and with distinct branching between the provinces. Moreover, across the mainland of China, genotype clustering appeared to be related to the habitat type and/or intermediate host morphology. Conclusion These results demonstrate the suitability of microsatellites for population genetic studies of S. japonicum and suggest that there may be different strains of S. japonicum in the mainland of China.