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Widespread dissemination of Salmonella, Escherichia coli and Campylobacter resistant to medically important antimicrobials in the poultry production continuum in Canada
The Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) monitors Escherichia coli, Salmonella and Campylobacter and their resistance to antimicrobials in broiler chickens at the farm and slaughter plant levels. In response to many years of CIPARS’ observations and farmers’ data, the Chicken Farmers of Canada implemented a strategy to reduce antimicrobial use in 2014. As resistance genes can be transmitted vertically from parents to their offspring, a study was conducted in broiler breeder flocks to assess the frequency of target bacteria, their antimicrobial resistance (AMR) and to obtain a comprehensive picture of AMR in poultry production. Spent breeder flocks slaughtered between 2018 and 2021 were sampled and data from broiler flocks at the farm and slaughter plants were assessed. Salmonella was most frequently detected in farm broiler chickens (46%), while Campylobacter was most frequently detected in broiler breeders (73%). In Campylobacter , high levels (20–24%) of ciprofloxacin resistance were found across the three production stages, and was highest in farm broiler chickens (24%). In E. coli, an indicator organism, low-level ceftriaxone resistance and occasional isolates that were non-susceptible to ciprofloxacin were noted. Using the indicator, fully susceptible E. coli , broiler breeders had the highest frequency (54%) compared to farm (36%) and slaughtered (35%) broiler chickens . In Salmonella broiler breeders had the highest resistance to most antimicrobials tested.Fully susceptible Salmonella was lowest in broiler breeders (16%) compared to farm (42%) and slaughtered (42%) broiler chickens. Salmonella serovars differed between the production stages, but S. Kentucky was the most predominant. Resistance to critically important antimicrobials in human medicine and regional variations in resistance profiles were observed. This study suggests that broiler breeders carry foodborne bacteria resistant to antimicrobials used in human medicine, demonstrating their role in the maintenance of AMR in poultry and the need to adopt a harmonized sector-wide AMU strategy.
Journal Article
Global spread of Salmonella Enteritidis via centralized sourcing and international trade of poultry breeding stocks
A pandemic of
Salmonella enterica
serotype Enteritidis emerged in the 1980s due to contaminated poultry products. How
Salmonella
Enteritidis rapidly swept through continents remains a historical puzzle as the pathogen continues to cause outbreaks and poultry supply becomes globalized. We hypothesize that international trade of infected breeding stocks causes global spread of the pathogen. By integrating over 30,000
Salmonella
Enteritidis genomes from 98 countries during 1949–2020 and international trade of live poultry from the 1980s to the late 2010s, we present multifaceted evidence that converges on a high likelihood, global scale, and extended protraction of
Salmonella
Enteritidis dissemination via centralized sourcing and international trade of breeding stocks. We discovered recent, genetically near-identical isolates from domestically raised poultry in North and South America. We obtained phylodynamic characteristics of global
Salmonella
Enteritidis populations that lend spatiotemporal support for its dispersal from centralized origins during the pandemic. We identified concordant patterns of international trade of breeding stocks and quantitatively established a driving role of the trade in the geographic dispersal of
Salmonella
Enteritidis, suggesting that the centralized origins were infected breeding stocks. Here we demonstrate the value of integrative and hypothesis-driven data mining in unravelling otherwise difficult-to-probe pathogen dissemination from hidden origins.
Salmonella enterica
serotype Enteritidis is a pathogen of poultry that can cause outbreaks in humans. Here the authors use genomic and trade data to investigate a pandemic in the 1980s, finding evidence that international trade of breeding stocks led to global spread of the pathogen.
Journal Article
Raise happy chickens : how to raise healthy chickens and other poultry in your outdoor space
A quickly accessible but authoritative guide, suitable for total beginners, that provides all the information you need to start keeping your own chickens.Telling you which breed of bird lays best and providing useful guidance on housing, equipment and the necessities of day-to-day care, it meets all the needs of anyone who dreams of a garden full of happy, clucking birds. It also goes beyond just chickens to other types of poultry, and gives advice and practical guidelines on housing, with full explanation of key areas like welfare, behavior and diet.
Book
Bacteriophage therapy to combat bacterial infections in poultry
Infections in poultry are an economic and health problem in Europe and worldwide. The most common infections are associated with salmonellosis, colibacillosis, campylobacteriosis, and others. The prevalence of
Campylobacter
-positive poultry flocks in European countries varies from 18% to 90%. In the United States, the prevalence of infected flocks is nearly 90%. A similar percentage of infection has been noted for salmonellosis (about 75–90%) and
E. coli
(90–95%). The occurence of
Clostridium perfringens
is a major problem for the poultry industry, with some estimates suggesting colonization of as many as 95% of chickens, resulting in clinical or subclinical infections. In the US, annual economic losses due to
Salmonella
infections run from $1.188 billion to over $11.588 billion, based on an estimated 1.92 million cases. Similar costs are observed in the case of other types of infections. In 2005 economic losses in the the poultry industry due to mortalities reached 1,000,000 USD.
Infections caused by these pathogens, often through poultry products, are also a serious public health issue.
The progressive increase in the number of multi-drug resistant bacteria and the complete ban on the use of antibiotics in livestock feed in the EU, as well as the partial ban in the US, have led to the growth of research on the use of bacteriophages to combat bacterial infections in humans and animals.
The high success rate and safety of phage therapy in comparison with antibiotics are partly due to their specificity for selected bacteria and the ability to infect only one species, serotype or strain. This mechanism does not cause the destruction of commensal bacterial flora. Phages are currently being used with success in humans and animals in targeted therapies for slow-healing infections. They have also found application in the US in eliminating pathogens from the surface of foods of animal and plant origin. At a time of growing antibiotic resistance in bacteria and the resulting restrictions on the use of antibiotics, bacteriophages can provide an alternative means of eliminating pathogens.
Journal Article
Metagenomic insights into microbial diversity and potential pathogenic transmission in poultry farm environments of Bangladesh
The microbiome plays a critical role in poultry health and productivity, influencing growth, immunity, and the overall farm ecosystem. This study investigated microbial diversity, antibiotic resistance pathways, and functional potential across various components of poultry ecosystems—cloacal swabs, droppings, feed, hand swabs, soil, and water—in different districts of Bangladesh. Using 16S rRNA gene amplicon sequencing, we identified 2,745 Operational Taxonomic Units (OTUs) and analyzed microbial richness, community structure, and functional pathways. Alpha diversity metrics revealed that droppings exhibited the highest microbial richness (726 OTUs in Noakhali), while feed samples showed the lowest diversity (211 OTUs). Beta diversity analysis indicated significant differences in microbial composition across sample sources, with PERMANOVA confirming that sample origin accounted for 51.45% of the variability (
p
< 0.001). Proteobacteria dominated the microbial communities (48.36%), followed by Firmicutes (19.83%) and Cyanobacteria (12.02%). Key genera of concern, such as
Enterobacter
(26.62% in hand swabs),
Acinetobacter
(30.87% in cloacal swabs), and
Shigella
(22.89% in cloacal swabs), were identified, highlighting potential contamination and zoonotic risks. Conversely, beneficial genera like
Lactobacillus
(36.89% in feed) and
Enterococcus
(10.78% in droppings) were prevalent, suggesting roles in gut health and nutrient cycling. Functional pathway analysis (KEGG) revealed that carbohydrate and amino acid metabolism were highly active in droppings and feed, reflecting nutrient utilization. Antimicrobial resistance (AMR) pathways, such as 23S rRNA-methyltransferase and multidrug efflux pumps, were widespread, with pathogenic genera (
Enterobacter
,
Acinetobacter
,
Shigella
,
Pseudomonas
) showing strong positive correlations with AMR pathways. These findings underscore the influence of environmental factors on microbial diversity and functional potential in poultry farming. The study highlights the need for improved management practices and biosecurity measures to mitigate risks associated with microbial pathogens and antimicrobial resistance, ultimately supporting healthier and more sustainable poultry production in Bangladesh.
Journal Article
Evaluation of lyophilized bacteriophage cocktail efficiency against multidrug-resistant Salmonella in broiler chickens
Currently, phage biocontrol is increasingly used as a green and natural technology for treating
Salmonella
and other infections, but phages exhibit instability and activity loss during storage. Therefore, in this study, the effects of lyophilization on the activity and stability of phage cocktails for the control of multidrug-resistant
Salmonella
in broiler chickens were determined. Eight serotypes of
Salmonella
were isolated and identified from broiler chicken farms, and bacteriophages against multidrug-resistant
Salmonella
enterica subsp. enterica serovar Kentucky,
Salmonella
enterica subsp. enterica serovar Typhimrium and
Salmonella
enterica subsp. enterica serovar Enteritidis were isolated. The bacteriophage cocktail was prepared and lyophilized, and it was subjected to in vitro and in vivo examinations. A reconstituted lyophilized bacteriophage cocktail was used for the oral treatment of chicks before and after challenge with multidrug-resistant
S.
Kentucky. The colonization of cecum by
S.
Kentucky was detected by using real-time PCR, and the serum levels of IgM, IgA and IL-4 and pathological changes in the different groups were detected. Three Caudovirales phages families were identified including
Autographiviridae
,
Straboviridae
and
Drexlerviridae
against multidrug-resistant
S.
Kentucky,
S.
Typhimrium
and S.
Enteritidis. The groups treated with the bacteriophage cocktail showed no clinical signs, no postmortem lesions, and a mortality rate of 0%, which improved the growth performance parameters. Additionally, the estimated serum levels of IgM, IgA and IL-4 were significantly greater in the bacteriophage cocktail-treated groups. Lyophilization effectively preserves the long-term storage stability of phages. Therefore, lyophilized bacteriophage cocktail therapy is a valuable approach for controlling multidrug-resistant
Salmonella
infections in broiler chickens.
Journal Article