Background The striped field mouse Apodemus agrarius is a wild rodent commonly found in fields in Korea. It is a known carrier of various pathogens. Amplicon-based next-generation sequencing (NGS) targeting the 16S ribosomal RNA (rRNA) gene is the most common technique used to analyze the bacterial microbiome. Although many bacterial microbiome analyses have been attempted using feces of wild animals, only a few studies have used NGS to screen for parasites. This study aimed to rapidly detect bacterial, fungal and parasitic pathogens in the guts of A. agrarius using NGS-based metabarcoding analysis. Methods We conducted 18S/16S rDNA-targeted high-throughput sequencing on cecal samples collected from A. agrarius (n = 48) trapped in May and October 2017. Taxa of protozoa, fungi, helminths and bacteria in the cecal content were then identified. Results Among the protozoa identified, the most prevalent was Tritrichomonas sp., found in all of the cecal samples, followed by Monocercomonas sp. (95.8% prevalence; in 46/48 samples) and Giardia sp. (75% prevalence; in 36/48 samples). For helminths, Heligmosomoides sp. was the most common, found in 85.4% (41/48) of samples, followed by Hymenolepis sp. (10.4%; 5/48) and Syphacia sp. (25%; 12/48). The 16S rRNA gene analysis showed that the microbial composition of the cecal samples changed by season (P = 0.005), with the linear discriminant analysis effect size showing that in the spring Escherichia coli and Lactobacillus murinus were more abundant and Helicobacter rodentium was less abundant. Helicobacter japonicus was more abundant and Prevotella_uc was less abundant in males. The microbial composition changed based on the Heligmosomoides sp. infection status (P = 0.019); specifically, Lactobacillus gasseri and Lactobacillus intestinalis were more abundant in the Heligmosomoides sp.-positive group than in the Heligmosomoides sp.-negative group. Conclusions This study demonstrated that bacterial abundance changed based on the season and specific parasitic infection status of the trapped mice. These results highlight the advantages of NGS technology in monitoring zoonotic disease reservoirs. Graphical Abstract
Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has been spreading since 2019, causing a worldwide pandemic. Amid the COVID-19 pandemic, tuberculosis, AIDS, and malaria have adversely affected the quality of life of patients and killed millions of people. In addition, COVID-19 continues to impede the delivery of health services, including those for the control of neglected tropical diseases (NTDs). Furthermore, NTDs have been reported as possible co-pathogens among patients infected with COVID-19. However, studies regarding parasitic co-infection among these patients have been limited. This review aimed to explore and describe the cases and reports of parasitic infections in the backdrop of COVID-19 to provide comprehensive knowledge regarding this aspect. We reviewed seven cases of patients who had parasitic co-infection and tested positive for COVID-19, and summarized the literature on the importance of controlling parasitic diseases. In addition, we identified recommendations for the control of parasitic diseases under possible difficulties, such as declining funding for parasitic diseases in 2020. This review highlights the growing burden of NTDs under COVID-19 that may be caused by the deficiency of healthcare infrastructure and human resources as the main reasons. Clinicians should remain vigilant for possible co-infections with parasites in COVID-19 patients, while policymakers are urged to reinforce a balanced and long-term health strategy that addresses both NTDs and COVID-19.
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