Prevalence and Antimicrobial Resistance of Salmonella from Antibiotic-Free Broilers During Organic and Conventional Processing

Prevalence and antibiotic resistance of Salmonella in organic and non-organic chickens on the Eastern Shore of Maryland, USA

Introduction

Salmonella infections have been intensely increasing and becoming a universal public health crisis. This study investigated the prevalence of Salmonella in organic and non-organic chickens and the antimicrobial resistance profiles and virulence genes (invA, pagC, and spvC) in recovered Salmonella isolates.

Methods

Whole chicken carcasses [organic (n = 240) and non-organic (n = 240)] were obtained monthly for 1 year (n = 480) from a retail store on the Eastern Shore of Maryland. Salmonella isolation and identification were conducted by following the whole carcass enrichment method recommended by USDA-FSIS. Confirmed Salmonella isolates (organic n = 76; non-organic n = 137) were serotyped and tested for antibiotic susceptibility and virulence genes using standard methods.

Results

Forty-nine percent (237/480) of the carcasses were positive for Salmonella. Organic and non-organic positivity rates were 37.1 and 61.8%, respectively. A significantly higher Salmonella contamination was observed in non-organic chickens (p < 0.05). The most common serovars were Salmonella Kentucky (47%), S. Infantis (35%), S. Enteritidis (6%), S. Typhimurium (5%), and S. Blockley (4%). Isolates were frequently resistant to at least one antibiotic (91.24%) or multidrug resistant (45.54%). Resistance was observed to tetracycline (82.8%), minocycline (42.3%), nitrofurantoin (40.3%), cefazolin (38.3%), ampicillin (32.1%), and ceftriaxone (26%). All isolates were susceptible to fluoroquinolone, carbapenem, and glycylcycline. The majority of isolates (99.1%) possessed at least one of three virulence genes of concern and 4.2% tested positive for all three. Ninety-five, 89, and 6.6% of isolates contained invA, pagC, and spvC genes, respectively. The spvC gene was not detected in serovars recovered from organic chickens though 92% and 82% of isolates were positive for invA and pagC. The frequency of Salmonella recovered from non-organic chickens possessing invA, pagC, and spvC genes were 97.1, 89.8, and 10.2%, respectively. Detection of invA and pagC genes showed no significant difference (p > 0.05) between organic and non-organic chickens but a significantly higher spvC gene (p < 0.05) was detected in non-organic chickens due to the majority of S. Enteritidis (92.3%) exclusively recovered from non-organic chicken carried spvC gene.

Discussion

This study reveals a high prevalence of Salmonella in both organic and non-organic chickens, which exhibit resistance to vital antibiotics and carry virulence genes, thereby creating a potential risk of salmonellosis.

Global trends in antimicrobial resistance on organic and conventional farms

The important hypothesis that organic livestock management reduces the prevalence of antimicrobial resistance is either fiercely supported or bitterly contested. Yet, empirical evidence supporting this view remains fragmentary, in part because relationships between antimicrobial use and drug resistance vary dramatically across contexts, hosts, pathogens, and country-specific regulations. Here, we synthesize global policies and definitions of 'organic' and ask if organic farming results in notable reductions in the prevalence of antimicrobial resistance when directly examined alongside conventional analogs. We synthesized the results of 72 studies, spanning 22 countries and five pathogens. Our results highlight substantial variations in country-specific policies on drug use and definitions of 'organic' that hinder broad-scale and generalizable patterns. Overall, conventional farms had slightly higher levels of antimicrobial resistance (28%) relative to organic counterparts (18%), although we found significant context-dependent variation in this pattern. Notably, environmental samples from organic and conventional farms often exhibited high levels of resistance to medically important drugs, underscoring the need for more stringent and consistent policies to control antimicrobial contaminants in the soil (particularly on organic farms, where the application of conventional manure could faciliate the spread antimicrobial resistance). Taken together, these results emphasize the challenges inherent in understanding links between drug use and drug resistance, the critical need for global standards governing organic policies, and greater investment in viable alternatives for managing disease in livestock.

A systematic review and meta-analysis of the sources of Salmonella in poultry production (pre-harvest) and their relative contributions to the microbial risk of poultry meat

Salmonella is a major foodborne pathogen associated with poultry and poultry products and a leading cause for human salmonellosis. Salmonella is known to transmit in poultry flocks both vertically and horizontally. However, there is a lack of knowledge on relative contribution of the factors on Salmonella prevalence in poultry live production system including hatchery, feed, water, environment-interior, and -exterior. Therefore, a systematic review and meta-analysis was conducted to quantify the potential sources of Salmonella during preharvest and their relative contributions to the microbial risk of poultry meat. A total of 16,800 studies identified from Google Scholar and 37 relevant studies were included in the meta-analysis for relative contributions to Salmonella positivity on broilers after applying exclusion criteria. A generalized linear mixed model approach combined with logit transformation was used in the current study to stabilize the variance. The analysis revealed that the hatchery is the most significant contributor of Salmonella with a prevalence of 48.5%. Litter, feces, and poultry house internal environment were the other 3 major contributing factors with a prevalence of 25.4, 16.3, and 7.9%, respectively. Moreover, poultry house external environment (4.7%), feed (4.8%), chicks (4.7%), and drinker water also contributed to the Salmonella positivity. Results from this meta-analysis informed the urgent need for controls in live production to further reduce Salmonella in fresh, processed poultry. The control strategies can include eliminating the sources of Salmonella and incorporating interventions in live production to reduce Salmonella concentrations in broilers.

Microbiome of Ceca from Broiler Chicken Vaccinated or Not against Coccidiosis and Fed Berry Pomaces

American cranberry (Vaccinium macrocarpon) and lowbush/wild blueberry (V. angustifolium) pomace are polyphenol-rich products having potentially beneficial effects in broiler chickens. This study investigated the cecal microbiome of broiler-vaccinated or non-vaccinated birds against coccidiosis. Birds in each of the two groups (vaccinated or non-vaccinated) were fed a basal non-supplemented diet (NC), a basal diet supplemented with bacitracin (BAC), American cranberry (CP), and lowbush blueberry (BP) pomace alone or in combination (CP + BP). At 21 days of age, cecal DNA samples were extracted and analyzed using both whole-metagenome shotgun sequencing and targeted-resistome sequencing approaches. Ceca from vaccinated birds showed a lower abundance of Lactobacillus and a higher abundance of Escherichia coli than non-vaccinated birds (p < 0.05). The highest and lowest abundance of L. crispatus and E. coli, respectively, were observed in birds fed CP, BP, and CP + BP compared to those from NC or BAC treatments (p < 0.05). Coccidiosis vaccination affected the abundance of virulence genes (VGs) related to adherence, flagella, iron utilization, and secretion system. Toxin-related genes were observed in vaccinated birds (p < 0.05) in general, with less prevalence in birds fed CP, BP, and CP + BP than NC and BAC (p < 0.05). More than 75 antimicrobial resistance genes (ARGs) detected by the shotgun metagenomics sequencing were impacted by vaccination. Ceca from birds fed CP, BP, and CP + BP showed the lowest (p < 0.05) abundances of ARGs related to multi-drug efflux pumps, modifying/hydrolyzing enzyme and target-mediated mutation, when compared to ceca from birds fed BAC. Targeted metagenomics showed that resistome from BP treatment was distant to other groups for antimicrobials, such as aminoglycosides (p < 0.05). Significant differences in the richness were observed between the vaccinated and non-vaccinated groups for aminoglycosides, β-lactams, lincosamides, and trimethoprim resistance genes (p < 0.05). Overall, this study demonstrated that dietary berry pomaces and coccidiosis vaccination significantly impacted cecal microbiota, virulome, resistome, and metabolic pathways in broiler chickens.

Luteolin: A Phytochemical to Mitigate S. Typhimurium Flagellin-Induced Inflammation in a Chicken In Vitro Hepatic Model

The use of natural feed supplements is an alternative tool to diminish the damage caused by certain bacteria, improving animal health and productivity. The present research aimed to investigate the proinflammatory effect of flagellin released from the bacterial flagellum of Salmonella enterica serovar Typhimurium and to attenuate the induced inflammation with luteolin as a plant-derived flavonoid on a chicken primary hepatocyte-non-parenchymal cell co-culture. Cells were cultured in a medium supplemented with 250 ng/mL flagellin and 4 or 16 µg/mL luteolin for 24 h. Cellular metabolic activity, lactate dehydrogenase (LDH) activity, interleukin-6, 8, 10 (IL-6, IL-8, IL-10), interferon-α, γ (IFN-α, IFN-γ), hydrogen peroxide (H₂O₂) and malondialdehyde (MDA) concentrations were determined. Flagellin significantly increased the concentration of the proinflammatory cytokine IL-8 and the ratio of IFN-γ/IL-10, while it decreased the level of IL-10, indicating that the model served adequate to study inflammation in vitro. Luteolin treatment at 4 µg/mL did not prove to be cytotoxic, as reflected by metabolic activity and extracellular LDH activity, and significantly reduced the flagellin-triggered IL-8 release of the cultured cells. Further, it had a diminishing effect on the concentration of IFN-α, H₂O₂ and MDA and restored the level of IL-10 and the ratio of IFN-γ/IL-10 when applied in combination with flagellin. These results suggest that luteolin at lower concentrations may protect hepatic cells from an excessive inflammatory response and act as an antioxidant to attenuate oxidative damage.

Production systems and important antimicrobial resistant-pathogenic bacteria in poultry: a review

Economic losses and market constraints caused by bacterial diseases such as colibacillosis due to avian pathogenic Escherichia coli and necrotic enteritis due to Clostridium perfringens remain major problems for poultry producers, despite substantial efforts in prevention and control. Antibiotics have been used not only for the treatment and prevention of such diseases, but also for growth promotion. Consequently, these practices have been linked to the selection and spread of antimicrobial resistant bacteria which constitute a significant global threat to humans, animals, and the environment. To break down the antimicrobial resistance (AMR), poultry producers are restricting the antimicrobial use (AMU) while adopting the antibiotic-free (ABF) and organic production practices to satisfy consumers' demands. However, it is not well understood how ABF and organic poultry production practices influence AMR profiles in the poultry gut microbiome. Various Gram-negative (Salmonella enterica serovars, Campylobacter jejuni/coli, E. coli) and Gram-positive (Enterococcus spp., Staphylococcus spp. and C. perfringens) bacteria harboring multiple AMR determinants have been reported in poultry including organically- and ABF-raised chickens. In this review, we discussed major poultry production systems (conventional, ABF and organic) and their impacts on AMR in some potential pathogenic Gram-negative and Gram-positive bacteria which could allow identifying issues and opportunities to develop efficient and safe production practices in controlling pathogens.

The Prevalence of Salmonella and Campylobacter on Broiler Meat at Different Stages of Commercial Poultry Processing

In poultry processing, Salmonella and Campylobacter contaminations are major food safety concerns. Peracetic acid (PAA) is an antimicrobial commonly used in commercial poultry processing to reduce pathogen prevalence so as to meet the USDA-FSIS performance standards. The objective of this study was to determine the prevalence of Salmonella and Campylobacter on broiler meat in various steps of commercial poultry processing in plants that use PAA. Post-pick, pre-chill, post-chill, and drumstick chicken samples were collected from three processing plants and mechanically deboned meat (MDM) was collected from two of the three plants. Each plant was sampled thrice, and 10 samples were collected from each processing step during each visit. Among the 420 samples, 79 were contaminated with Salmonella and 155 were contaminated with Campylobacter. Salmonella and Campylobacter contamination on the post-pick samples averaged 32.2%. Significant reductions in Salmonella and Campylobacter were observed in pre-chill to post-chill samples, where the prevalence was reduced from 34% and 64.4% to nondetectable limits and 1.1%, respectively (p < 0.001). Salmonella and Campylobacter remained undetectable on the drumstick samples in all three processing plants. However, the prevalence of Salmonella and Campylobacter on MDM was similar to the post-pick prevalence, which suggests substantial cross-contamination from post-chill to MDM.

Adaptability Challenges for Organic Broiler Chickens: A Commentary

Simple Summary

Organic poultry shows an increasing productive trend, rising from 3% in 2017 to 8% in 2019. Regulation EU 848/2018 puts great emphasis on the ability of broilers to adapt to outdoor systems as being essential for organic production. Organic poultry operators meet with regulatory constraints, consumer concerns, and challenges in terms of nutrition, welfare, health, and sustainability. The present commentary considers recent studies on and innovations in these topics that can affect organic production in addition to recent studies on animal adaptability to this production system. It reflects on the concept of broiler adaptability to organic systems not only as a classic genotype–environment interaction but as a necessary prerequisite for facing these relevant challenges.

Abstract

As organic and conventional poultry production increased in the last decade, so did consumers’ concerns, sustainability requirements, and animal welfare as well as health issues. According to Reg. EU 848/2008 on organic production, poultry must be adapted to organic outdoor systems and cope with all the regulatory constraints in terms of nutrition, health, and welfare. Adaptability must take into account the above challenges, constraints, and concerns. Chicken adaptability should not only mean being able to use pasture and outdoor areas, but also mean being able to overcome, or be resilient to, the challenges of organic farming without compromising welfare, performance, and product quality. This commentary identifies solutions to the new challenges that organic poultry chains must face in future productive scenarios, detects consumer viewpoints to provide a perspective on organic poultry production, and summarizes as well as defines chicken adaptability to organic production, assessing the main factors of chicken adaptability.

Pharmacokinetics and Pharmacodynamics of Colistin Combined With Isopropoxy Benzene Guanidine Against mcr-1-Positive Salmonella in an Intestinal Infection Model

Plasmid-borne colistin resistance mediated by mcr-1 is a growing problem, which poses a serious challenge to the clinical application of colistin for Gram-negative bacterial infections. Drug combination is one of the effective strategies to treat colistin-resistant bacteria. Here, we found a guanidine compound, namely, isopropoxy benzene guanidine (IBG), which boosted the efficacy of colistin against mcr-1-positive Salmonella. This study aimed to develop a pharmacokinetics/pharmacodynamics (PK/PD) model by combining colistin with IBG against mcr-1-positive Salmonella in an intestinal infection model. Antibiotic susceptibility testing, checkerboard assays and time-kill curves were used to investigate the antibacterial activity of the synergistic activity of the combination. PK studies of colistin in the intestine were determined through oral gavage of single dose of 2, 4, 8, and 16 mg/kg of body weight in broilers with intestinal infection. On the contrary, PD studies were conducted over 24 h based on a single dose ranging from 2 to 16 mg/kg. The inhibitory effect Imax model was used for PK/PD modeling. The combination of colistin and IBG showed significant synergistic activity. The AUC0−24h/MIC index was used to evaluate the relationship between PK and PD, and the correlation was &gt;0.9085. The AUC0−24h /MIC targets in combination required to achieve the bacteriostatic action, 3-log10 kill, and 4-log10 kill of bacterial counts were 47.55, 865.87, and 1894.39, respectively. These results can facilitate the evaluation of the use of IBG as a potential colistin adjuvant in the treatment of intestinal diseases in broilers caused by colistin-resistant Salmonella.

Isolation and molecular characterization of multidrug-resistant Salmonella enterica serovars

BACKGROUND

Salmonellosis is a foodborne zoonosis leaving gastrointestinal illness and drug-resistant genes to the consumers. To prevent Salmonella contamination associated health issues in the chicken meat sold in Riyadh city in Saudi Arabia. The evaluation of the Salmonella isolates from the meat sample needs to be screened for the composition of Salmonella serotypes and antimicrobial resistance pattern at the molecular level.

METHODS AND RESULTS

Using specific growth media for Salmonella spp., swabs taken from the whole-body surfaces of 200 chilled broiler chickens from different vendors in the city of Riyadh, were screened for Salmonella contamination. Biochemical and molecular characterization of the isolates showed the presence of the serovars, Salmonella enterica, Salmonella Enteritidis, S. Typhimurium, S. Kentucky, and S. Tennessee. The isolated serovars exhibited multidrug resistance [MDR] resistance to antibiotics. Molecular characterization of the different serovars shows the presence of sixteen drug-resistant genes. The drug resistance mechanism at the molecular level varied with serotypes according to the nature of the antibiotics they encountered. A comparative study of the nature of the drug-resistant gene and the common antibiotics used in poultry farming in that province matches much, indicating adaptive variation in S. enterica serotypes to survive in the host's gut biome. The resistance genes from the chicken meat have every chance to get into the human system. The native microbes in consumers may acquire drug-resistant genes from S. entericus serovars. Such conditions may lead to treatment complications in the hosts.

CONCLUSIONS

The results indicated that Salmonella infections constituted a potential risk to consumers through chicken flocks and noted that the genotypic resistance pattern to antibiotics draws attention in terms of both human and animal health. Also, promote other options for poultry farming, avoiding antibiotics supplementation.

Characteristics of Salmonella From Chinese Native Chicken Breeds Fed on Conventional or Antibiotic-Free Diets

Salmonella is a common food-borne Gram-negative pathogen with multiple serotypes. Pullorum disease, caused by Salmonella Pullorum, seriously threatens the poultry industry. Many previous studies were focused on the epidemiological characteristics of Salmonella infections in conventional antibiotic use poultry. However, little is known about Salmonella infections in chicken flocks fed on antibiotic-free diets. Herein, we investigated and compared Salmonella infections in three Chinese native breeders fed on antibiotic-free diets, including the Luhua, Langya, and Qingjiaoma chickens, and one conventional breeder, the Bairi chicken, via analyzing 360 dead embryos in 2019. The results showed that the main Salmonella serotypes detected in a total of 155 isolates were S. Pullorum (82.6%) and S. Enteritidis (17.4%). Coinfection with two serotypes of Salmonella was specifically found in Bairi chicken. The sequence type (ST) in S. Pullorum was ST92 (n = 96) and ST2151 (n = 32), whereas only ST11 (n = 27) was found in S. Enteritidis. The Salmonella isolates from three breeder flocks fed on antibiotic-free diets exhibited phenotypic heterogeneity with a great variety of drug resistance spectrum. Most of the isolates among three chicken breeds Luhua (64.9%, 50/77), Langya (60%, 12/20) and Qingjiaoma (58.3%, 7/12) fed on antibiotic-free diets were resistant to only one antibiotic (erythromycin), whereas the rate of resistance to one antibiotic in conventional Bairi chicken isolates was only 4.3% (2/46). The multidrug-resistance rate in Salmonella isolates from layer flocks fed on antibiotic-free diets (20.2%, 22/109) was significantly (P < 0.0001) lower than that from chickens fed on conventional diets (93.5%, 43/46). However, high rate of resistance to erythromycin (97.4%~100%) and streptomycin (26%~41.7%) were also found among three breeder flocks fed on antibiotic-free diets, indicating resistance to these antibiotics likely spread before antibiotic-free feeding in poultry farms. The findings of this study supplement the epidemiological data of salmonellosis and provide an example of the characteristics of Salmonella in the chicken flocks without direct antibiotic selective pressure.

Antimicrobial Resistance of Escherichia coli from Retail Poultry Meats in Korea

ABSTRACT

Antimicrobial-resistant bacteria in poultry meat pose a threat to public health. This article is the first to report the prevalence of antimicrobial-resistant Escherichia coli in retail poultry meat labeled with various claims of antibiotic use in Korea. A total of 719 E. coli strains were isolated from 1,107 raw poultry (chicken and duck) meat samples purchased from nationwide retail stores between 2017 and 2019. All strains were tested for antimicrobial susceptibility with a broth microdilution method. The prevalence of antimicrobial-resistant E. coli in chicken was significantly higher than that in duck for almost all antibiotics tested, and 87.9% of E. coli strains in chicken samples were multidrug resistant. The most prevalent types of antimicrobial resistance in these E. coli strains from poultry meat were to nalidixic acid (75.7%), ampicillin (69.1%), and tetracycline (64.0%), consistent with national sales data for veterinary antibiotics in the Korean poultry production industry. Organic or antibiotic-free and conventional chicken products were equally likely to be contaminated with antimicrobial-resistant E. coli. Contamination may occur during slaughtering and subsequent processing, and antibiotic use is permitted in certain cases under organic or antibiotic-free poultry standards. Therefore, close surveillance is required throughout the chicken production chain to prevent the spread of antimicrobial-resistant E. coli strains.

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