French research strategy to tackle antimicrobial resistance

Comparative Genome Analysis of Enterococcus cecorum Reveals Intercontinental Spread of a Lineage of Clinical Poultry Isolates

Enterococcus cecorum is an emerging pathogen responsible for osteomyelitis, spondylitis, and femoral head necrosis causing animal suffering and mortality and requiring antimicrobial use in poultry. Paradoxically, E. cecorum is a common inhabitant of the intestinal microbiota of adult chickens. Despite evidence suggesting the existence of clones with pathogenic potential, the genetic and phenotypic relatedness of disease-associated isolates remains little investigated. Here, we sequenced and analyzed the genomes and characterized the phenotypes of more than 100 isolates, the majority of which were collected over the last 10 years from 16 French broiler farms. Comparative genomics, genome-wide association studies, and the measured susceptibility to serum, biofilm-forming capacity, and adhesion to chicken type II collagen were used to identify features associated with clinical isolates. We found that none of the tested phenotypes could discriminate the origin of the isolates or the phylogenetic group. Instead, we found that most clinical isolates are grouped phylogenetically, and our analyses selected six genes that discriminate 94% of isolates associated with disease from those that are not. Analysis of the resistome and the mobilome revealed that multidrug-resistant clones of E. cecorum cluster into a few clades and that integrative conjugative elements and genomic islands are the main carriers of antimicrobial resistance. This comprehensive genomic analysis shows that disease-associated clones of E. cecorum belong mainly to one phylogenetic clade. IMPORTANCE Enterococcus cecorum is an important pathogen of poultry worldwide. It causes a number of locomotor disorders and septicemia, particularly in fast-growing broilers. Animal suffering, antimicrobial use, and associated economic losses require a better understanding of disease-associated E. cecorum isolates. To address this need, we performed whole-genome sequencing and analysis of a large collection of isolates responsible for outbreaks in France. By providing the first data set on the genetic diversity and resistome of E. cecorum strains circulating in France, we pinpoint an epidemic lineage that is probably also circulating elsewhere that should be targeted preferentially by preventive strategies in order to reduce the burden of E. cecorum-related diseases.

Antibiotics and antibiotic-resistant bacteria in greywater: Challenges of the current treatment situation and predictions of future scenario

The current work reviews the quantitative microbiological risk assessment of antibiotic-resistant bacteria (ARB) in greywater and discusses the international strategies currently used for reducing antimicrobial resistance. The work highlights the countries that have a plan for the treatment and reuse of greywater and the current guidelines used in these countries. The paper also investigates the role of greywater in the distribution of antimicrobial resistance because of antibiotics and ARB. A bibliometric analysis was conducted for the studies on greywater, pathogenic bacteria, and antibiotics. The studies obtained from Scopus database were screened and compared to obtain the data for global antimicrobial resistance in 2000 and 2021. The strategies used by developed countries that led to the reduction in the recorded antimicrobial resistance are also listed. The challenges and limitations associated with the current plans adopted by several countries to minimise the spreading of the antimicrobial resistance are highlighted, while proposed solutions are provided. Two main issues associated with the distribution of antimicrobial resistance are (1) the absence of a plan in developing counties and presence of antimicrobial agents and ARB in the environment and (2) the difficulties in the current treatment technologies used for the removal of these antimicrobial agents from the water and wastewater. Based on the review and discussion, it was concluded that more advanced technologies are required to ensure total elimination of the antimicrobial agents and ARB from the environment. In addition, a new international standard should be drafted for the ARB in the environment, as they differ from the one currently used for medical applications.