Description of the viral community in fecal content of common carp (Cyprinus carpio) living in a naturally preserved wetland on Mexican plateau

IntroductionThe common carp (Cyprinus carpio) is a species that has been used worldwide as a source of protein for humans because of its adaptive capacity to the environment; however, it is also an invasive species. In Mexico, it was introduced to provide an easily accessible source of protein to people in rural areas until its extensive nationwide distribution. The community of viruses in these fish is not completely known. MethodsMassive sequencing, i.e., whole metagenome shotgun (WMS) sequencing, and bioinformatic analysis were used to describe the viral community of common carp (Cyprinus carpio) living in a natural preserved wetland. ResultsThrough sequencer Illumina NextSeq 500/550 we got 484,953,684 sequences from ten samples of fecal content of carp (5 samples to DNA and 5 samples to RNA). The virome comprised 30 viral families (13 DNA families and 17 RNA families), among which viruses related to vertebrates stood out, for example Orthoherpesviridae, Parvoviridae, Astroviridae, Poxviridae, Hantaviridae and Picornaviridae.DiscussionThe most abundant viral taxa corresponded to bacteriophages, most of which are of polyphyletic origin. The results of this work contribute to the knowledge of the different viral taxa found in the common carp in the wild and indicate that these viral taxa may play a role in health and productivity of fish farms

Lower IgG somatic hypermutation rates during acute dengue virus infection is compatible with a germinal center-independent B cell response

Reads, clonal groups, and lineages numbers per individual and condition. The table shows the number of raw and used sequences as well as the number of clonotypes and lineages per individual. (XLS 30 kb

Characterization of immunoglobulin loci in the gigantic genome of Ambystoma mexicanum

BackgroundThe axolotl, Ambystoma mexicanum is a unique biological model for complete tissue regeneration. Is a neotenic endangered species and is highly susceptible to environmental stress, including infectious disease. In contrast to other amphibians, the axolotl is particularly vulnerable to certain viral infections. Like other salamanders, the axolotl genome is one of the largest (32 Gb) and the impact of genome size on Ig loci architecture is unknown. To better understand the immune response in axolotl, we aimed to characterize the immunoglobulin loci of A. mexicanum and compare it with other model vertebrates.MethodsThe most recently published genome sequence of A. mexicanum (V6) was used for alignment-based annotation and manual curation using previously described axolotl Ig sequences or reference sequences from other vertebrates. Gene models were further curated using A. mexicanum spleen RNA-seq data. Human, Xenopus tropicalis, Danio rerio (zebrafish), and eight tetrapod reference genomes were used for comparison.ResultsCanonical A. mexicanum heavy chain (IGH), lambda (IGL), sigma (IGS), and the putative surrogate light chain (SLC) loci were identified. No kappa locus was found. More than half of the IGHV genes and the IGHF gene are pseudogenes and there is no clan I IGHV genes. Although the IGH locus size is proportional to genome size, we found local size restriction in the IGHM gene and the V gene intergenic distances. In addition, there were V genes with abnormally large V-intron sizes, which correlated with loss of gene functionality.ConclusionThe A. mexicanum immunoglobulin loci share the same general genome architecture as most studied tetrapods. Consistent with its large genome, Ig loci are larger; however, local size restrictions indicate evolutionary constraints likely to be imposed by high transcriptional demand of certain Ig genes, as well as the V(D)J recombination over very long genomic distance ranges. The A. mexicanum has undergone an extensive process of Ig gene loss which partially explains a reduced potential repertoire diversity that may contribute to its impaired antibody response

Presence and Persistence of <i>ESKAPEE</i> Bacteria before and after Hospital Wastewater Treatment

The metagenomic surveillance of antimicrobial resistance in wastewater has been suggested as a methodological tool to characterize the distribution, status, and trends of antibiotic-resistant bacteria. In this study, a cross-sectional collection of samples of hospital-associated raw and treated wastewater were obtained from February to March 2020. Shotgun metagenomic sequencing and bioinformatic analysis were performed to characterize bacterial abundance and antimicrobial resistance gene analysis. The main bacterial phyla found in all the samples were as follows: Proteobacteria, Bacteroides, Firmicutes, and Actinobacteria. At the species level, ESKAPEE bacteria such as E. coli relative abundance decreased between raw and treated wastewater, but S. aureus, A. baumannii, and P. aeruginosa increased, as did the persistence of K. pneumoniae in both raw and treated wastewater. A total of 172 different ARGs were detected; blaOXA, blaVEB, blaKPC, blaGES, mphE, mef, erm, msrE, AAC(6′), ant(3″), aadS, lnu, PBP-2, dfrA, vanA-G, tet, and sul were found at the highest abundance and persistence. This study demonstrates the ability of ESKAPEE bacteria to survive tertiary treatment processes of hospital wastewater, as well as the persistence of clinically important antimicrobial resistance genes that are spreading in the environment