Plasmid-associated antimicrobial resistance and virulence genes in Escherichia coli in a high arctic reindeer subspecies

Metagenomics uncovers microbiome and resistome in soil and reindeer faeces from Ny-Ålesund (Svalbard, High Arctic)

Research on the microbiome and resistome in polar environments, such as the Arctic, is crucial for understanding the emergence and spread of antibiotic resistance genes (ARGs) in the environment. In this study, soil and reindeer faeces samples collected from Ny-Ålesund (Svalbard, High Arctic) were examined to analyze the microbiome, ARGs, and biocide/metal resistance genes (BMRGs). The dominant phyla in both soil and faeces were Pseudomonadota, Actinomycetota, and Bacteroidota. A total of 2618 predicted Open Reading Frames (ORFs) containing antibiotic resistance genes (ARGs) were detected. These ARGs belong to 162 different genes across 17 antibiotic classes, with rifamycin and multidrug resistance genes being the most prevalent. We focused on investigating antibiotic resistance mechanisms in the Ny-Ålesund environment by analyzing the resistance genes and their biological pathways. Procrustes analysis demonstrated a significant correlation between bacterial communities and ARG/BMRG profiles in soil and faeces samples. Correlation analysis revealed that Pseudomonadota contributed most to multidrug and triclosan resistance, while Actinomycetota were predominant contributors to rifamycin and aminoglycoside resistance. The geochemical factors, SiO42- and NH4+, were found to significantly influence the microbial composition and ARG distribution in the soil samples. Analysis of ARGs, BMRGs, virulence factors (VFs), and pathogens identified potential health risks associated with certain bacteria, such as Cryobacterium and Pseudomonas, due to the presence of different genetic elements. This study provided valuable insights into the molecular mechanisms and geochemical factors contributing to antibiotic resistance and enhanced our understanding of the evolution of antibiotic resistance genes in the environment.

Non-Canonical Aspects of Antibiotics and Antibiotic Resistance

The understanding of antibiotic resistance, one of the major health threats of our time, is mostly based on dated and incomplete notions, especially in clinical contexts. The "canonical" mechanisms of action and pharmacodynamics of antibiotics, as well as the methods used to assess their activity upon bacteria, have not changed in decades; the same applies to the definition, acquisition, selective pressures, and drivers of resistance. As a consequence, the strategies to improve antibiotic usage and overcome resistance have ultimately failed. This review gathers most of the "non-canonical" notions on antibiotics and resistance: from the alternative mechanisms of action of antibiotics and the limitations of susceptibility testing to the wide variety of selective pressures, lateral gene transfer mechanisms, ubiquity, and societal factors maintaining resistance. Only by having a "big picture" view of the problem can adequate strategies to harness resistance be devised. These strategies must be global, addressing the many aspects that drive the increasing prevalence of resistant bacteria aside from the clinical use of antibiotics.

Prevalence of Antibiotic Resistance and Virulence Genes in Escherichia coli Carried by Migratory Birds on the Inner Mongolia Plateau of Northern China from 2018 to 2023

(1) Background: Antibiotic resistance in bacteria is an urgent global threat to public health. Migratory birds can acquire antibiotic-resistant and pathogenic bacteria from the environment or through contact with each other and spread them over long distances. The objectives of this study were to explore the relationship between migratory birds and the transmission of drug-resistant pathogenic Escherichia coli. (2) Methods: Faeces and swab samples from migratory birds were collected for isolating E. coli on the Inner Mongolia Plateau of northern China from 2018 to 2023. The resistant phenotypes and spectra of isolates were determined using a BD Phoenix 100 System. Conjugation assays were performed on extended-spectrum β-lactamase (ESBL)-producing strains, and the genomes of multidrug-resistant (MDR) and ESBL-producing isolates were sequenced and analysed. (3) Results: Overall, 179 isolates were antibiotic-resistant, with 49.7% MDR and 14.0% ESBL. Plasmids were successfully transferred from 32% of ESBL-producing strains. Genome sequencing analysis of 91 MDR E. coli strains identified 57 acquired resistance genes of 13 classes, and extraintestinal pathogenic E. coli and avian pathogenic E. coli accounted for 26.4% and 9.9%, respectively. There were 52 serotypes and 54 sequence types (STs), including ST48 (4.4%), ST69 (4.4%), ST131 (2.2%) and ST10 (2.2%). The international high-risk clonal strains ST131 and ST10 primarily carried blaCTX-M-27 and blaTEM-176. (4) Conclusions: There is a high prevalence of multidrug-resistant virulent E. coli in migratory birds on the Inner Mongolian Plateau. This indicates a risk of intercontinental transmission from migratory birds to livestock and humans.

Characteristics of MDR E. coli strains isolated from Pet Dogs with clinic diarrhea: A pool of antibiotic resistance genes and virulence-associated genes

The increasing number of multi-drug resistant (MDR) bacteria in companion animals poses a threat to both pet treatment and public health. To investigate the characteristics of MDR Escherichia coli (E. coli) from dogs, we detected the antimicrobial resistance (AMR) of 135 E. coli isolates from diarrheal pet dogs by disc diffusion method (K-B method), and screened antibiotic resistance genes (ARGs), virulence-associated genes (VAGs), and population structure (phylogenetic groups and MLST) by polymerase chain reaction (PCR) for 74 MDR strains, then further analyzed the association between AMRs and ARGs or VAGs. Our results showed that 135 isolates exhibited high resistance to AMP (71.11%, 96/135), TET (62.22%, 84/135), and SXT (59.26%, 80/135). Additionally, 54.81% (74/135) of the isolates were identified as MDR E. coli. In 74 MDR strains, a total of 12 ARGs in 6 categories and 14 VAGs in 4 categories were observed, of which tetA (95.95%, 71/74) and fimC (100%, 74/74) were the most prevalent. Further analysis of associations between ARGs and AMRs or VAGs in MDR strains revealed 23 significant positive associated pairs were observed between ARGs and AMRs, while only 5 associated pairs were observed between ARGs and VAGs (3 positive associated pairs and 2 negative associated pairs). Results of population structure analysis showed that B2 and D groups were the prevalent phylogroups (90.54%, 67/74), and 74 MDR strains belonged to 42 STs (6 clonal complexes and 23 singletons), of which ST10 was the dominant lineage. Our findings indicated that MDR E. coli from pet dogs carry a high diversity of ARGs and VAGs, and were mostly belong to B2/D groups and ST10. Measures should be taken to prevent the transmission of MDR E. coli between companion animals and humans, as the fecal shedding of MDR E. coli from pet dogs may pose a threat to humans.

High-throughput functional trait testing for bacterial pathogens

Functional traits are characteristics that affect the fitness and metabolic function of a microorganism. There is growing interest in using high-throughput methods to characterize bacterial pathogens based on functional virulence traits. Traditional methods that phenotype a single organism for a single virulence trait can be time consuming and labor intensive. Alternatively, machine learning of whole-genome sequences (WGS) has shown some success in predicting virulence. However, relying solely on WGS can miss functional traits, particularly for organisms lacking classical virulence factors. We propose that high-throughput assays for functional virulence trait identification should become a prominent method of characterizing bacterial pathogens on a population scale. This work is critical as we move from compiling lists of bacterial species associated with disease to pathogen-agnostic approaches capable of detecting novel microbes. We discuss six key areas of functional trait testing and how advancing high-throughput methods could provide a greater understanding of pathogens.

Occurrence and antimicrobial resistance of Salmonella species and potentially pathogenic Escherichia coli in free-living seals of Canadian Atlantic and eastern Arctic waters

Seal populations in Canadian waters provide sustenance to coastal communities. There is potential for pathogenic and/or antimicrobial-resistant bacteria to transfer to humans through inadvertent faecal contamination of seal products. The objective of this study was to investigate the occurrence and potential antimicrobial resistance of Salmonella spp., Escherichia coli and Listeria monocytogenes in faecal samples collected from grey seals (Halichoerus grypus) in the Gulf of St. Lawrence and from ringed seals (Pusa hispida) in Frobisher Bay and Eclipse Sound, Nunavut, Canada. Grey seals were harvested during commercial hunts or during scientific sampling; ringed seals were collected by Inuit hunters during subsistence harvests. Virulence genes defining pathogenic E. coli were identified by PCR, and antimicrobial susceptibility testing was performed on recovered isolates. In grey seals, E. coli was detected in 34/44 (77%) samples, and pathogenic E. coli (extraintestinal E. coli [ExPEC], enteropathogenic E. coli [EPEC] or ExPEC/EPEC) was detected in 13/44 (29%) samples. Non-susceptibility to beta-lactams and quinolones was observed in isolates from 18 grey seals. In ringed seals from Frobisher Bay, E. coli was detected in 4/45 (9%) samples; neither virulence genes nor antimicrobial resistance was detected in these isolates. In ringed seals from Eclipse Sound, E. coli was detected in 8/50 (16%) samples and pathogenic E. coli (ExPEC and ExPEC/EPEC) in 5/50 (10%) samples. One seal from Eclipse Sound had an E. coli isolate resistant to beta-lactams. A monophasic Salmonella Typhimurium was recovered from 8/50 (16%) seals from Eclipse Sound. All Salmonella isolates were resistant to ampicillin, streptomycin, sulfisoxazole and tetracycline. L. monocytogenes was not detected in any sample. These findings suggest that seals may act as important sentinel species and as reservoirs or vectors for antimicrobial-resistant and virulent E. coli and Salmonella species. Further characterization of these isolates would provide additional insights into the source and spread of antimicrobial resistance and virulence genes in these populations of free-living seals.

Whole Genome Sequencing of Escherichia coli and Enterococcus spp. in wildlife-livestock interface: a pilot study

OBJECTIVES

This pilot study provides a multidisciplinary investigation to monitor livestock-wildlife interface. Ecological data, microbiological investigations, and whole genome sequencing were used to characterize eight bacterial isolates obtained from sympatric domestic and wild ruminants in Maiella National Park (Italy) in terms of genetic patterns of antimicrobial resistance.

METHODS

Using selective culturing of fresh fecal samples of monitored and georeferenced populations of Apennine chamois, goats, red deer, and sheep, Escherichia coli, Enterococcus faecium, and Enterococcus faecalis isolates were isolated and subjected to minimum inhibitory concentration determination and whole genome sequencing.

RESULTS

The analyzed isolates showed phenotypic and genotypic resistance to tetracycline and critically important antibiotics such as linezolid and carbapenems. Virulence genes related to biofilm regulation and Shiga toxins were also detected. Furthermore, serotypes related to nosocomial infections, harbouring plasmids recognized as important mobile resistance gene transmitters, were identified.

CONCLUSIONS

This multidisciplinary pilot study represents a promising initial step to identify the environmental drivers and the transmission routes of antimicrobial resistance and virulence factors, providing new data on bacteria from rare and endangered species such as Apennine chamois.

The Phenomenon of Antibiotic Resistance in the Polar Regions: An Overview of the Global Problem

The increasing prevalence of antibiotic resistance is a global problem in human and animal health. This leads to a reduction in the therapeutic effectiveness of the measures used so far and to the limitation of treatment options, which may pose a threat to human health and life. The problem of phenomenon of antibiotic resistance affects more and more the polar regions. This is due to the increase in tourist traffic and the number of people staying at research stations, unmodernised sewage systems in inhabited areas, as well as the migration of animals or the movement of microplastics, which may contain resistant bacteria. Research shows that the presence of antibiotic resistance genes is more dominant in zones of human and wildlife influence than in remote areas. In a polluted environment, there is evidence of a direct correlation between human activity and the spread and survival of antibiotic-resistant bacteria. Attention should be paid to the presence of resistance to synthetic and semi-synthetic antibiotics in the polar regions, which is likely to be correlated with human presence and activity, and possible steps to be taken. We need to understand many more aspects of this, such as bacterial epigenetics and environmental stress, in order to develop effective strategies for minimizing the spread of antibiotic resistance genes. Studying the diversity and abundance of antibiotic resistance genes in regions with less anthropogenic activity could provide insight into the diversity of primary genes and explain the historical evolution of antibiotic resistance.