Facilitating taxonomy and phylogenetics: An informative and cost-effective protocol integrating long amplicon PCRs and third-generation sequencing.

Phylogenetic inference has become a standard technique in integrative taxonomy and systematics, as well as in biogeography and ecology. DNA barcodes are often used for phylogenetic inference, despite being strongly limited due to their low number of informative sites. Also, because current DNA barcodes are based on a fraction of a single, fast-evolving gene, they are highly unsuitable for resolving deeper phylogenetic relationships due to saturation. In recent years, methods that analyse hundreds and thousands of loci at once have improved the resolution of the Tree of Life, but these methods require resources, experience and molecular laboratories that most taxonomists do not have. This paper introduces a PCR-based protocol that produces long amplicons of both slow- and fast-evolving unlinked mitochondrial and nuclear gene regions, which can be sequenced by the affordable and portable ONT MinION platform with low infrastructure or funding requirements. As a proof of concept, we inferred a phylogeny of a sample of 63 spider species from 20 families using our proposed protocol. The results were overall consistent with the results from approaches based on hundreds and thousands of loci, while requiring just a fraction of the cost and labour of such approaches, making our protocol accessible to taxonomists worldwide.

Prenatal syphilis screening among pregnant Medicaid enrollees by sexually transmitted infection history as well as race and ethnicity.

BACKGROUND: Congenital syphilis can cause severe morbidity, including miscarriage and stillbirth, and rates are increasing rapidly within the United States. However, congenital syphilis can be prevented with early detection and treatment of syphilis during pregnancy. Current screening recommendations propose that all women should be screened early in pregnancy, whereas women with elevated risks for congenital syphilis should be screened again later in pregnancy. The rapid increase in congenital syphilis rates suggests that there are still gaps in prenatal syphilis screening. OBJECTIVE: This study aimed to examine associations between the odds of prenatal syphilis screening and sexually transmitted infection history or other patient characteristics across 3 states with elevated rates of congenital syphilis. STUDY DESIGN: We used the Medicaid claims data from Kentucky, Louisiana, and South Carolina for women with deliveries between 2017 and 2021. Within each state, we examined the log-odds of prenatal syphilis screening as a function of the mother's health history, demographic factors, and Medicaid enrollment history. Patient history was established using a 4-year lookback period of the Medicaid claims data; in state A, sexually transmitted infection surveillance data were used to improve the sexually transmitted infection history. RESULTS: The prenatal syphilis screening rates varied by state, ranging from 62.8% to 85.1% of deliveries to women without a recent history of sexually transmitted infections and from 78.1% to 91.1% of deliveries to women with a previous sexually transmitted infection. For the main outcome of syphilis screening at any time during pregnancy, deliveries associated with previous sexually transmitted infections had 1.09 to 1.37 times higher adjusted odds ratios of undergoing screening. Deliveries to women with continuous Medicaid coverage throughout the first trimester also had higher odds of syphilis screening at any time (adjusted odds ratio, 2.45-3.15). Among deliveries to women with a previous sexually transmitted infection, only 53.6% to 63.6% underwent first-trimester screening and this rate was still just 55.0% to 69.5% when considering only deliveries to women with a previous sexually transmitted infection and full first-trimester Medicaid coverage. Fewer delivering women underwent third-trimester screening (20.3%-55.8% of women with previous sexually transmitted infection). Compared with deliveries to White women, deliveries to Black women had lower odds of first-trimester screening (adjusted odds ratio, 0.85 in all states) but higher odds of third-trimester screening (adjusted odds ratio, 1.23-2.03), potentially impacting maternal and birth outcomes. For state A, linkage to surveillance data doubled the rate of detection of a previous sexually transmitted infection because 53.0% of deliveries by women with a previous sexually transmitted infection would not have had sexually transmitted infection history detected using Medicaid claims alone. CONCLUSION: A previous sexually transmitted infection and continuous preconception Medicaid enrollment were associated with higher rates of syphilis screening, but Medicaid claims alone do not fully capture the sexually transmitted infection history of patients. The overall screening rates were lower than would be expected given that all women should undergo prenatal screening, but the rates in the third trimester were particularly low. Of note, there are gaps in early screening for non-Hispanic Black women who had lower odds of first-trimester screening when compared with non-Hispanic White women despite being at elevated risk for syphilis.

Rapid and cost-effective generation of single specimen multilocus barcoding data from whole arthropod communities by multiple levels of multiplexing.

In light of the current biodiversity crisis, molecular barcoding has developed into an irreplaceable tool. Barcoding has been considerably simplified by developments in high throughput sequencing technology, but still can be prohibitively expensive and laborious when community samples of thousands of specimens need to be processed. Here, we outline an Illumina amplicon sequencing approach to generate multilocus data from large collections of arthropods. We reduce cost and effort up to 50-fold, by combining multiplex PCRs and DNA extractions from pools of presorted and morphotyped specimens and using two levels of sample indexing. We test our protocol by generating a comprehensive, community wide dataset of barcode sequences for several thousand Hawaiian arthropods from 14 orders, which were collected across the archipelago using various trapping methods. We explore patterns of diversity across the Archipelago and compare the utility of different arthropod trapping methods for biodiversity explorations on Hawaii, highlighting undergrowth beating as highly efficient method. Moreover, we show the effects of barcode marker, taxonomy and relative biomass of the targeted specimens and sequencing coverage on taxon recovery. Our protocol enables rapid and inexpensive explorations of diversity patterns and the generation of multilocus barcode reference libraries across whole ecosystems.