61 research outputs found
Emergence and clonal spread of CTX-M-65-Producing Escherichia coli from retail meat in Portugal
Research Areas: MicrobiologyThe emergence and dissemination of resistance to third- and fourth-generation
cephalosporins among Enterobacteriaceae from different sources impose a global
public health threat. Here, we characterized by whole-genome sequencing four
Escherichia coli strains harboring the blaCTX−M−65 gene identified among 49 isolates
from beef and pork collected at retail. The genomic content was determined using
the Center for Genomic Epidemiology web tools. Additionally, the prediction and
reconstruction of plasmids were conducted, the genetic platform of the blaCTX−M−65
genes was investigated, and phylogenetic analysis was carried out using 17 other
genomes with the same sequence type and harboring the blaCTX−M−65 gene. All strains
harbored blaCTX−M−65, blaOXA−1, and blaTEM−1B, and one also carried the blaSHV−12
gene. Other resistance genes, namely, qnrS2, aac(60
)-Ib-c, dfrA14, sul2, tetA, and
mphA, were present in all the genomes; the mcr-1.1 gene was identified in the colistinresistant strains. They belong to sequence type 2179, phylogenetic group B1, and
serotype O9:H9 and carried plasmids IncI, IncFIC(FII), and IncFIB. All strains share an
identical genetic environment with IS903 and ISEcp1 flanking the blaCTX−M−65 gene. It
seems likely that the blaCTX−M−65 gene is located in the chromosome in all isolates
based on deep in silico analysis. Our findings showed that the strains are clonally
related and belong to two sub-lineages. This study reports the emergence of CTX-M-65-
producing E. coli in Portugal in food products of animal origin. The chromosomal location
of the blaCTX−M−65 gene may ensure a stable spread of resistance in the absence of
selective pressure.info:eu-repo/semantics/publishedVersio
Host-associated and Environmental Microbiomes in an Open-Sea Mediterranean Gilthead Sea Bream Fish Farm
Gilthead seabream is among the most important farmed fish species in the Mediterranean Sea. Several approaches are currently applied to assure a lower impact of diseases and higher productivity, including the exploration of the fish microbiome and its manipulation as a sustainable alternative to improve aquaculture practices. Here, using 16S rRNA gene high-throughput sequencing, we explored the microbiome of farmed seabream to assess similarities and differences among microbial assemblages associated to different tissues and compare them with those in the surrounding environment. Seabream had distinct associated microbiomes according to the tissue and compared to the marine environment. The gut hosted the most diverse microbiome; different sets of dominant ASVs characterized the environmental and fish samples. The similarity between fish and environmental microbiomes was higher in seawater than sediment (up to 7.8 times), and the highest similarity (3.9%) was observed between gill and seawater, suggesting that gills are more closely interacting with the environment. We finally analyzed the potential connections occurring among microbiomes. These connections were relatively low among the host's tissues and, in particular, between the gut and the others fish-related microbiomes; other tissues, including skin and gills, were found to be the most connected microbiomes. Our results suggest that, in mariculture, seabream microbiomes reflect only partially those in their surrounding environment and that the host is the primary driver shaping the seabream microbiome. These data provide a step forward to understand the role of the microbiome in farmed fish and farming environments, useful to enhance disease control, fish health, and environmental sustainability
Results from EQAS 2002:The External Quality Assurance System 2002 of the WHO Global Salmonella Surveillance and Laboratory Support Project (Global Salm-Surv)
Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance
Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, evolution, and transmission of individual antibiotic resistance genes (ARGs) is essential to develop sustainable strategies combatting this threat. Here, we use metagenomic sequencing to analyse ARGs in 757 sewage samples from 243 cities in 101 countries, collected from 2016 to 2019. We find regional patterns in resistomes, and these differ between subsets corresponding to drug classes and are partly driven by taxonomic variation. The genetic environments of 49 common ARGs are highly diverse, with most common ARGs carried by multiple distinct genomic contexts globally and sometimes on plasmids. Analysis of flanking sequence revealed ARG-specific patterns of dispersal limitation and global transmission. Our data furthermore suggest certain geographies are more prone to transmission events and should receive additional attention
Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance
Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, evolution, and transmission of individual antibiotic resistance genes (ARGs) is essential to develop sustainable strategies combatting this threat. Here, we use metagenomic sequencing to analyse ARGs in 757 sewage samples from 243 cities in 101 countries, collected from 2016 to 2019. We find regional patterns in resistomes, and these differ between subsets corresponding to drug classes and are partly driven by taxonomic variation. The genetic environments of 49 common ARGs are highly diverse, with most common ARGs carried by multiple distinct genomic contexts globally and sometimes on plasmids. Analysis of flanking sequence revealed ARG-specific patterns of dispersal limitation and global transmission. Our data furthermore suggest certain geographies are more prone to transmission events and should receive additional attention.info:eu-repo/semantics/publishedVersio
DANMAP 2010:DANMAP 2010 - Use of antimicrobial agents and occurrence of antimicrobial resistance in bacteria from food animals, food and humans in Denmark
DANMAP 2011:DANMAP 2011 - Use of antimicrobial agents and occurrence of antimicrobial resistance in bacteria from food animals, food and humans in Denmark
Danish Integrated Antimicrobial Resistance Monitoring and Research Program
This program has led to changes in the use of antimicrobial agents in Denmark and other countries
DANMAP 2012:DANMAP 2012 - Use of antimicrobial agents and occurrence of antimicrobial resistance in bacteria from food animals, food and humans in Denmark
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