Pritt, Bobbi S

Abstract Background Tick populations have expanded in many parts of the globe, bringing with them an enhanced appreciation and discovery of novel tickborne pathogens, as well an increased in reported human cases of tickborne disease. Targeted and unbiased (shotgun) clinical metagenomic sequencing tests are increasingly used for detection of known and emerging infectious agents and have recently been employed for detection of tickborne pathogens. Content This review describes the types of metagenomic sequencing assays used for detection of emerging tickborne pathogens and reviews the recent literature on this topic. Important diagnostic and interpretative challenges are also covered. Summary Metagenomic analysis has emerged as a powerful tool for detection, discovery, characterization, and classification of tickborne pathogens. Shotgun metagenomics is especially promising because it allows for detection of all tickborne bacteria, viruses, and parasites in a single specimen. Despite the potential advantages, there are several important challenges, including high cost, complexity of testing and interpretation, and slow turnaround time. No doubt, these challenges will diminish with increased use and advances in the field.

Cyclospora cayetanensis is an intestinal coccidian parasite transmitted to humans through the consumption of oocysts in fecally contaminated food and water. Infection is found worldwide and is highly endemic in tropical and subtropical regions with poor sanitation. Disease in developed countries is usually observed in travelers and in seasonal outbreaks associated with imported produce from endemic areas. Recently, summertime outbreaks in the United States have also been linked to locally grown produce. Cyclosporiasis causes a diarrheal illness which may be severe in infants, the elderly, and immunocompromised individuals. The increased adoption of highly sensitive molecular diagnostic tests, including commercially available multiplex panels for gastrointestinal pathogens, has facilitated the detection of infection and likely contributed to the increased reports of cases in developed countries. This manuscript reviews important aspects of the biology, epidemiology, and clinical manifestations of C. cayetanensis and provides an in-depth discussion of current laboratory diagnostic methods.

We report an unusual case of appendicitis in a 9-year-old girl in whom the wall of the appendix contained necrotizing granulomas, as well as eggs of Enterobius vermicularis. Although luminal E vermicularis adult parasites are commonly identified in the appendix and luminal eggs are occasionally seen, intramural worms and eggs are rare. We are unaware of earlier reports of ectopic intramural eggs in the appendix. It is important to and make a correct diagnosis, as both, the patient, as well as the family should be treated for enterobiasis.

Abstract The raging COVID-19 pandemic in India and reports of “vaccine breakthrough infections” globally have raised alarm mandating the characterization of the immuno-evasive features of SARS-CoV-2. Here, we systematically analyzed over 1.3 million SARS-CoV-2 genomes from 178 countries and performed whole-genome viral sequencing from 53 COVID-19 patients, including 20 vaccine breakthrough infections. We identified 116 Spike protein mutations that increased in prevalence during at least one surge in SARS-CoV-2 test positivity in any country over a three-month window. Deletions in the Spike protein N-terminal domain (NTD) are highly enriched for these ‘surge-associated mutations’ (Odds Ratio = 18.2, 95% CI: 7.53-48.7; p=1.465x10-18). In the recent COVID-19 surge in India, an NTD deletion (ΔF157/R158) increased over 10-fold in prevalence from February 2021 (1.1%) to April 2021 (15%). During the recent surge in Chile, an NTD deletion (Δ246-253) increased rapidly over 30-fold in prevalence from January 2021 (0.86%) to April 2021 (33%). Strikingly, these simultaneously emerging deletions associated with surges in different parts of the world both occur at an antigenic supersite that is targeted by neutralizing antibodies. Finally, we generated clinically annotated SARS-CoV-2 whole genome sequences and identified deletions within this NTD antigenic supersite in a patient with vaccine breakthrough infection (Δ156-164) and other deletions from unvaccinated severe COVID-19 patients that could represent emerging deletion-prone regions. Overall, the expanding repertoire of Spike protein deletions throughout the pandemic and their association with case surges and vaccine breakthrough infections point to antigenic minimalism as an emerging evolutionary strategy for SARS-CoV-2 to evade immune responses. This study highlights the urgent need to sequence SARS-CoV-2 genomes at a larger scale globally and to mandate a public health policy for transparent reporting of relevant clinical annotations (e.g. vaccination status) in order to aid the development of comprehensive therapeutic strategies.

Rapid and accurate diagnostic testing is essential to bring the ongoing COVID-19 pandemic to an end. As the demand for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing continues to increase amid supply shortages, many laboratories have investigated the use of sources other than nasopharyngeal (NP) swabs.

Background Schistosomiasis is a parasitic disease that affects the health of hundreds of millions of people worldwide. Affordable diagnostic methods are necessary for developing countries to monitor schistosomiasis rates and treat infected individuals, particularly in, Madagascar, a country with the world’s fifth highest rate of schistosomiasis. Methods We established the prevalence rate of schistosomiasis among the local population served by a clinic in rural northwestern Madagascar. Additionally, we compared different low-cost methods for schistosomiasis detection, including empirical diagnostic methods in use before this study. 500 patients were recruited in this study, of whom 380 received three tests—urine microscopy, point-of-care circulating cathodic antigen (POC-CCA) testing, and urinalysis to screen for Schistosoma haematobium and Schistosoma mansoni. Results By combining these modalities, we recorded a schistosomiasis prevalence rate of 64.47%, which was significantly higher than the 4.84% of patients who were diagnosed and treated through previous empirical methods. Conclusions Our results indicate that screening tests are a necessary component of schistosomiasis control programs. The clinic continued to use urinalysis strip testing and urine microscopy to detect schistosomiasis after this study and decided to discontinue the use of POC-CCA S. mansoni urine testing because of cost. Increased awareness of schistosomiasis resulting from this screening program led to the installation of multiple infrastructure projects in local communities to improve access to potable water, demonstrating community benefits of schistosomiasis screening that extend beyond the identification of infected individuals.

Reported cases of tick-borne diseases have steadily increased for more than a decade. In the United States, a majority of tick-borne infections are caused by bacteria.