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An Overview of Parasite Diversity
Published in Eric S. Loker, Bruce V. Hofkin, Parasitology, 2023
Eric S. Loker, Bruce V. Hofkin
It has been argued that eukaryotes are largely refractory to HGT because they often maintain separate somatic and germinal cells, with the latter more difficult for foreign DNA to invade. Yet a growing body of evidence, in many cases coming from the study of parasite genomes, suggests there are numerous examples of HGT involving eukaryotes. Bacteria and viruses are likely sources of genes for eukaryotic parasites because they are ubiquitous, metabolically very diverse, and often ingested by eukaryotes. Mobile genetic elements like transposons (what has been called the mobilome) are also another source of genetic information for eukaryotic species. The genomes of Trypanosoma, Trichomonas, Entamoeba and microsporidians show evidence of repeated and considerable HGT from prokaryotes and viruses, especially those sharing environments with them.
An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness
Published in Gut Microbes, 2021
Andrea Marfil-Sánchez, Lu Zhang, Pol Alonso-Pernas, Mohammad Mirhakkak, Melinda Mueller, Bastian Seelbinder, Yueqiong Ni, Rakesh Santhanam, Anne Busch, Christine Beemelmanns, Maria Ermolaeva, Michael Bauer, Gianni Panagiotou
To determine whether antibiotic treatment exerts selective pressure on the resistome as a whole, we analyzed the change in Pfams related to the resistome and mobilome, as well as the abundance differences of ARGs between the three groups. In the abundance comparison between the Healthy and the ICU+ groups, there were 71 statistically significant Pfams (Wilcoxon rank-sum test, P < .05) related to the resistome and/or mobilome, with 48 of them being more abundant in the ICU+ and 23 in the Healthy group (Supplementary Figure 8(a)). Interestingly, the differences between ICU– and Healthy groups were also large with 30 and 16 Pfams being more abundant in the ICU– and the Healthy group, respectively (Supplementary Figure 8(a)). In the comparison between ICU+ and ICU– there were 19 significant Pfams with 14 being more abundant in the ICU+ and 5 in the ICU– group (Supplementary Figure 8(a)).
Expansion and persistence of antibiotic-specific resistance genes following antibiotic treatment
Published in Gut Microbes, 2021
Kang Kang, Lejla Imamovic, Maria-Anna Misiakou, Maria Bornakke Sørensen, Yoshitaro Heshiki, Yueqiong Ni, Tingting Zheng, Jun Li, Mostafa M. H. Ellabaan, Marta Colomer-Lluch, Anne A. Rode, Peter Bytzer, Gianni Panagiotou, Morten O.A. Sommer
Reports of post-treatment expansion of some ARG families3,24 raised the question of how the recovery of taxonomic composition and functional profiles supported the expansion of ARGs, which must involve the persistence of ARG carrier species. As previous studies have proved the capacity of HGT event identification from paired-end signals,31,32 we addressed this question using paired phage library sequencing and plasmid identification, which identified significant enrichment of AsRGs within the mobilome (the collection of mobile elements in a microbiome). This would suggest an increased potential for HGT, which was supported by analysis of HGT-supporting paired sequencing reads partially mapping to the phage-like contigs. These data support the hypothesis that HGT events of AsRGs may occur during antibiotic treatment. Subsequent studies with larger cohorts could benefit from deploying longer read sequencing technology to pinpoint such HGT events.
Antimicrobial resistance in enteric bacteria: current state and next-generation solutions
Published in Gut Microbes, 2020
M. J. Wallace, S. R. S. Fishbein, G. Dantas
Three concerning phenomena regarding MGEs are their mobility between environments and humans, their mobility across surprisingly unrelated bacterial taxa, and the potential for permanent integration of MGEs into the genome.2 These movements are captured in a growing appreciation for the “mobilome”, the group of all genetic elements that move within a chromosome, between chromosomes, and often, through plasmids. AMR acquisition via sampling of this mobilome often occurs in environmental niches that are external to the human host (Figure 1a). Campylobacter is found in multiple animal hosts and environmental niches, and thus has the opportunity to sample multiple ARG reservoirs. Remarkably, C. jejuni and C. coli can be isolated from livestock with phenotypic resistance profiles identical to those found in the clinic, especially in the case of fluoroquinolones.16,95 These ARGs appear to cluster on genomic islands or on circulating plasmids, indicating the frequent exchange of genetic material across environments or bacteria.95,96 In a subsample of E. coli isolates from both humans and poultry, a novel incompatibility group of plasmids has been discovered carrying a blaCMY mobile element.97 In addition, multiple classes of integrons carrying AMR have been found in both commensal E. coli and S. enterica from ruminants.98,99 Future efforts should better characterize the spatiotemporal dynamics of these and other environmental MGEs as it relates to both human disease and sources of AMR in our agricultural and waste practices.