Wastewater-Based Epidemiology is a tool to face and mitigate COVID-19 outbreaks by evaluating conditions in a speci c community. This study aimed to analyze the microbiome pro les using nanopore technology for full-length 16S rRNA sequencing in wastewater samples collected from a penitentiary (P), a residential care home (RCH), and a quarantine or health care facilities (HCF). The HCF microbiome was strongly associated with enteric bacteria previously reported in patients with chronic disease and psychological disorders. During the study, the wastewater samples from the RCH and the P were negative for SARS-CoV-2 based on qPCRs, except during the fourth week when was detected. Unexpectedly, the wastewater microbiome from RCH and P prior to week four was correlated with the samples collected from the HCF, suggesting a core bacterial community is expelled from the digest tract of individuals infected with SARS-CoV-2. We provide novel evidence that the wastewater microbiome associated with gastrointestinal manifestations appears to precede the SARS-CoV-2 detection in sewage. This nding suggests that the wastewaters microbiome can be applied as an indicator of community-wide SARS-CoV-2 surveillance.
Caligus rogercresseyi, commonly known as sea louse, is an ectoparasite copepod that impacts the salmon aquaculture in Chile, causing losses of hundreds of million dollars per year. This pathogen is mainly controlled by immersion baths with delousing drugs, which can lead to resistant traits selection in lice populations. Bioassays are commonly used to assess louse drug sensitivity, but the current procedures may mask relevant molecular responses. This study aimed to discover novel coding genes and non-coding RNAs that could evidence drug sensitivity at the genomic level. Sea lice samples from populations with contrasting sensitivity to delousing drugs were collected. Bioassays using azamethiphos, cypermethrin, and deltamethrin drugs were conducted to evaluate the sensitivity and to collect samples for RNA-sequencing. Transcriptome sequencing was conducted on samples exposed to each drug to evaluate the presence of coding and non-coding RNAs associated with the response of these compounds. The results revealed specific transcriptome patterns in lice exposed to azamethiphos, deltamethrin, and cypermethrin drugs. Enrichment analyses of Gene Ontology terms showed specific biological processes and molecular functions associated with each delousing drug analyzed. Furthermore, novel long non-coding RNAs (lncRNAs) were identified in C. rogercresseyi and tightly linked to differentially expressed coding genes. A significant correlation between gene transcription patterns and phenotypic effects was found in lice collected from different salmon farms with contrasting drug treatment efficacies. The significant correlation among gene transcription patterns with the historical background of drug sensitivity suggests novel molecular mechanisms of pharmacological resistance in lice populations.
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