Global Estimates of the Prevalence and Incidence of Four Curable Sexually Transmitted Infections in 2012 Based on Systematic Review and Global Reporting

Background

Quantifying sexually transmitted infection (STI) prevalence and incidence is important for planning interventions and advocating for resources. The World Health Organization (WHO) periodically estimates global and regional prevalence and incidence of four curable STIs: chlamydia, gonorrhoea, trichomoniasis and syphilis.

Methods and Findings

WHO’s 2012 estimates were based upon literature reviews of prevalence data from 2005 through 2012 among general populations for genitourinary infection with chlamydia, gonorrhoea, and trichomoniasis, and nationally reported data on syphilis seroprevalence among antenatal care attendees. Data were standardized for laboratory test type, geography, age, and high risk subpopulations, and combined using a Bayesian meta-analytic approach. Regional incidence estimates were generated from prevalence estimates by adjusting for average duration of infection. In 2012, among women aged 15–49 years, the estimated global prevalence of chlamydia was 4.2% (95% uncertainty interval (UI): 3.7–4.7%), gonorrhoea 0.8% (0.6–1.0%), trichomoniasis 5.0% (4.0–6.4%), and syphilis 0.5% (0.4–0.6%); among men, estimated chlamydia prevalence was 2.7% (2.0–3.6%), gonorrhoea 0.6% (0.4–0.9%), trichomoniasis 0.6% (0.4–0.8%), and syphilis 0.48% (0.3–0.7%). These figures correspond to an estimated 131 million new cases of chlamydia (100–166 million), 78 million of gonorrhoea (53–110 million), 143 million of trichomoniasis (98–202 million), and 6 million of syphilis (4–8 million). Prevalence and incidence estimates varied by region and sex.

Conclusions

Estimates of the global prevalence and incidence of chlamydia, gonorrhoea, trichomoniasis, and syphilis in adult women and men remain high, with nearly one million new infections with curable STI each day. The estimates highlight the urgent need for the public health community to ensure that well-recognized effective interventions for STI prevention, screening, diagnosis, and treatment are made more widely available. Improved estimation methods are needed to allow use of more varied data and generation of estimates at the national level.     

Molecular phylogeny and phylogeography of ricefishes (Teleostei: Adrianichthyidae: Oryzias) in Sri Lanka

Ricefishes of the genus Oryzias occur commonly in the fresh and brackish waters in coastal lowlands ranging from India across Southeast Asia and on to Japan. Among the three species of Oryzias recorded from peninsular India, two widespread species, O. carnaticus and O. dancena, have previously been reported from Sri Lanka based on museum specimens derived from a few scattered localities. However, members of the genus are widespread in the coastal lowlands of Sri Lanka, a continental island separated from India by the shallow Palk Strait. Although recent molecular phylogenies of Adrianichthyidae represent near‐complete taxon representation, they lack samples from Sri Lanka. Here, based on sampling at 13 locations representative of the entire geographic and climatic regions of the island''s coastal lowlands, we investigate for the first time the molecular phylogenetic relationships and phylogeography of Sri Lankan Oryzias based on one nuclear and two mitochondrial markers. Sri Lankan Oryzias comprise two distinct non‐sister lineages within the javanicus species group. One of these is represented by samples exclusively from the northern parts of the island; it is recognized as O. dancena. This lineage is recovered as the sister group to the remaining species in the javanicus group. The second lineage represents a species that is widespread across the island''s coastal lowlands. It is recovered as the sister group of O. javanicus and is identified as O. cf. carnaticus. Ancestral‐range estimates suggest two independent colonizations of Indian subcontinent and Sri Lanka by widespread ancestral species of Oryzias during two discrete temporal windows: late Miocene and Plio‐Pleistocene. No phylogeographic structure is apparent in Sri Lankan Oryzias, suggesting that there are no strong barriers to gene flow and dispersal along the coastal floodplains, as is the case also for other generalist freshwater fishes in the island.     

Urgent need for consistent standards in functional enrichment analysis

Gene set enrichment tests (a.k.a. functional enrichment analysis) are among the most frequently used methods in computational biology. Despite this popularity, there are concerns that these methods are being applied incorrectly and the results of some peer-reviewed publications are unreliable. These problems include the use of inappropriate background gene lists, lack of false discovery rate correction and lack of methodological detail. To ascertain the frequency of these issues in the literature, we performed a screen of 186 open-access research articles describing functional enrichment results. We find that 95% of analyses using over-representation tests did not implement an appropriate background gene list or did not describe this in the methods. Failure to perform p-value correction for multiple tests was identified in 43% of analyses. Many studies lacked detail in the methods section about the tools and gene sets used. An extension of this survey showed that these problems are not associated with journal or article level bibliometrics. Using seven independent RNA-seq datasets, we show misuse of enrichment tools alters results substantially. In conclusion, most published functional enrichment studies suffered from one or more major flaws, highlighting the need for stronger standards for enrichment analysis.     

Gastrointestinal parasites of endemic and endangered free-ranging purple-faced leaf monkey (Semnopithecus vetulus) in Sri Lanka: effect of host group size and habitat type

Primates - Similar infectious agents may be shared among human and nonhuman primates due to their close proximity. Gastrointestinal parasitism is one of the main diseases which can be transmitted...     

A novel cyanolytic bacterium,Pseudomonas fluorescens BG-E as a potential biological control agent for freshwater bloom-forming cyanobacteria Pseudanabaena spp.

The majority of bacterial antagonists identified to date are active against Microcystis. Therefore, this study aimed to isolate and characterize novel cyanolytic bacterial strains antagonistic against bloom-forming filamentous cyanobacteria. The bacterial strain BG-E isolated from the Bandagiriya Wewa in Sri Lanka was identified as Pseudomonas fluorescens (MZ007859) based on the 16S rRNA gene sequencing. BG-E showed 82% and 73% cyanolytic activity (CA) against Pseudanabaena sp. LW2 (MW288948) and Pseudanabaena lonchoides LW1 (MW288940), respectively, after 10 days of inoculation. The light microscopic images affirmed the complete disintegration in the filamentous structures of the tested Pseudanabaena species. The bacterial cell density of 15% v/v showed the CA with 95% and 89% cell lysis, respectively, in P. lonchoides and Pseudanabaena sp. LW2. Moreover, the results showed that >50% CA could be achieved by 0.100 and 1.00 (OD₇₃₀) cell densities for these same species. The highest CA of the cell-free supernatant of BG-E against P. lonchoides and bacterial culture against Pseudanabaena sp. LW2 illustrated the species-specific mode of action of BG-E. Although BG-E efficiently lysed the tested cyanobacterial species, the results of the MC-biodegradation assay confirmed its inability to degrade MC-LR cyanotoxin. Further, the BG-E strain lacks the mlrABCD gene cluster which is known to be responsible for the enzymatic degradation of MCs. The overall findings highlighted the applicability of P. fluorescens BG-E as a biological controlling agent to terminate blooms of freshwater filamentous cyanobacteria genus Pseudanabaena. The incorporation of cyanotoxin-degrading heterotrophic bacteria is recommended as a means of controlling toxic Pseudanabaena blooms.