Global spread of Salmonella Enteritidis via centralized sourcing and international trade of poultry breeding stocks

Development and application of a risk assessment tool for preventing the introduction and transmission of Salmonella in poultry farms: Based on the Delphi-analytic hierarchy process

A semiquantitative risk assessment method based on the Delphi-analytic hierarchy process (AHP) can serve as a proactive tool for the prevention and control of Salmonella infections in poultry farms. This method can facilitate early warning to minimize the risk of transmission of Salmonella to chicken meat and eggs. In this study, an expert panel comprising 22 members was established. After two rounds of evaluation, a risk assessment system consisting of 10 primary indicators and 73 secondary indicators was finalized. The expert participation rate (100 %), authority coefficient (1.0), and Kendall's W value (0.222 for the first round and 0.316 for the second round) met the required standards. Moreover, the system exhibited high reliability and validity. Based on the AHP, the top three weighted primary indicators were "seedstock management" (0.2769), "feeding and management" (0.1429), and "cleaning, disinfection and harmless disposal" (0.1429). The combined weight of the secondary indicators ranged from 0.00009 to 0.03027. In total, 6423 samples, including dead embryos and environmental samples, were collected from a poultry farm. By isolating Salmonella, assessing antimicrobial resistance, and performing whole-genome sequencing, the key risk points for contamination were identified. The implementation of targeted control measures based on the risk assessment model resulted in significant improvements. In particular, the overall antibody positivity rate decreased from 65.9 % to 8 %, the isolation rate of Salmonella from dead embryos decreased from 47.5 % to 3.75 %, and the isolation rate of Salmonella from the production environment of the hatchery workshop decreased from 10.1 % to 0.9 %. Moreover, notable improvements were observed in production metrics. Overall, our established risk assessment model is suitable for environments with low Salmonella isolation rates and can effectively facilitate the prevention and control of Salmonella in poultry farms.

Genetic landscape and evolution of Acinetobacter pittii, an underestimated emerging nosocomial pathogen

As a member of Acinetobacter calcoaceticus-baumannii complex, Acinetobacter pittii has been an emerging concern in nosocomial infection due to its increasing prevalence and multidrug resistance (MDR). However, its population structure remains broadly unknown, hampering efficient tracing of its transmission and evolution. In this study, we developed a distributed core genome multilocus sequence typing (dcgMLST) for A. pittii based on 750 genomes and employed it to map the genetic landscape and evolution of A. pittii. The results demonstrated that two hierarchical clustering (HC) levels effectively correspond to genetic diversity from species (HC1100) to natural populations (HC450), as well as that a predominant lineage, HC1100_4, accounts for 33.9% of A. pittii strains. Subsequent analysis revealed that specific gene gain and loss events within HC1100_4 are linked to adaptations to environmental stress. Moreover, we identified a cluster of multidrug-resistant plasmids PT_712 responsible for the dissemination of blaNDM-1 genes within the genus of Acinetobacter. This study provides a framework for characterizing genetic diversity, evolutionary dynamics, molecular population distribution, and tracing of A. pittii, which has the potential to improve infection control strategies and public health policy.

Molecular epidemiology of Salmonella Enteritidis in humans and animals in Spain

Salmonella Enteritidis, the most prevalent serovar-causing human gastroenteritis, has been traditionally linked to poultry sources. Although antimicrobial resistance (AMR) is not common in this serovar, increasing levels of resistance to fluoroquinolones and ampicillin have been reported in the last few years. Here, 298 isolates retrieved from different sources (human, livestock, wildlife, food, and environment) and years (2002-2021) in Spain were analyzed to evaluate their diversity, the distribution of AMR-conferring genes (ARGs), and mutations and reconstruct the epidemiology of infection due to this serovar. Isolates were clustered in two major clades (I and II), with strains in clade I (including 61.5% of all human isolates) displaying a pan-susceptible phenotype and not carrying AMR determinants. In contrast, clade II included 80.7% of isolates from animal/food/environmental sources, with the majority (69.8%) harboring mutations in the quinolone resistance determinant regions (QRDR). ARGs, although rare, were mostly found in clade II strains that also carried plasmid replicons, among which IncX1 was the most common. Although higher levels of phenotypic resistance were found in animal isolates, extended-spectrum beta-lactamase, plasmid-mediated AmpC, and carbapenemase-encoding genes were only found among human isolates. In summary, the majority of human and animal isolates from Spanish sources in our collection were classified in different phylogenetic branches, suggesting that additional sources are contributing to the occurrence of foodborne infections in Spain. Furthermore, the different distributions of virulence factors and ARGs in isolates from different sources and their association with specific plasmids suggest the presence of different dynamics contributing to the selection of resistant strains.

Genomic epidemiology of Salmonella Enteritidis human infections in the Netherlands, 2019 to 2023

Salmonella enterica serotype Enteritidis (SE) is a common foodborne pathogen that can cause human salmonellosis. Identifying closely related cases is essential to control the pathogen through, e.g. outbreak investigation, but it is often challenging due to the low genetic diversity of SE, particularly with traditional typing methods. This study aimed to investigate the population structure of SE genomes collected during routine surveillance in the Netherlands using whole-genome sequencing (WGS), their clustering, temporal distribution and the association between epidemiological and phenotypic antimicrobial resistance (AMR) factors and the persistence of SE clusters. We also investigated the distribution of genotypic AMR markers among these isolates. The study collection comprised 1,669 unique SE isolates from human infections collected from Dutch surveillance between 2019 and 2023, and their relatedness was derived using core-genome multi-locus sequence typing and Hamming distances. Based on the results, the 216 clusters comprised 1,085 sequences, in addition to 584 sequences depicted as singletons. These clusters predominantly fell within three major lineages, of which two were the previously described Global and Atlantic lineages. Of these clusters, approximately a third persisted for more than 1 year during the 5-year study period. However, no statistically significant associations were found between epidemiological factors, such as age, gender and travel history, or phenotypic AMR and the persistence of SE clusters. The most common AMR genetic markers observed were related to antimicrobial classes of (fluor)quinolones, β-lactamases and aminoglycosides. This study provides a better understanding of the genomic epidemiology of SE in the Netherlands based on WGS. Further analysis that includes samples from the food-chain supply, along with higher resolution methods during a post-Coronavirus Disease of 2019 (COVID-19) period, may provide more insights into the possible causes of the persistence of SE clusters.

A Narrative Review on the Impact of Probiotic Supplementation on Muscle Development, Metabolic Regulation, and Fiber Traits Related to Meat Quality in Broiler Chickens

Public concern over drug resistance has led to governmental regulations banning the use of antibiotics as growth promoters, stimulating interest in developing complementary strategies to maintain animal production, mitigate infections, and enhance muscle characteristics and quality parameters, especially in meat-producing animals. Probiotics are recognized as a potential strategy for improving growth, primarily by promoting intestinal homeostasis. These microorganisms are suggested to modulate gut microbiota, preserving their ecosystem and influencing secondary metabolite production, which can directly or indirectly regulate skeletal muscle metabolism by influencing the expression of key muscle-related genes and the activity of various signaling factors. Several studies have documented the potential benefits of various strains of Bacillus, Enterococcus, and members of the Lactobacillaceae family on muscle characteristics. These studies have shown that probiotics not only modulated myogenic factors but also influenced proteins and enzymes involved in signaling pathways related to carbon metabolism, inflammatory response, mitochondrial dynamics, and antioxidant activity. These effects have been associated with improvements in meat quality parameters and enhanced growth performance. This manuscript seeks to present a brief overview of the impact of probiotic supplementation on muscle health and the quality of meat in broiler chickens.

ZnO-Cu/Mn nanozyme for rescuing the intestinal homeostasis in Salmonella-induced colitis

Salmonella is one of the most common foodborne pathogens, which can cause severe enteritis and intestinal microbiota imbalance. However, there are limited strategies currently available for preventing or treating Salmonella-induced colitis. Herein, we developed the Cu/Mn-co-doped ZnO tandem nanozyme (ZnO-CM) with pH-responsive multienzyme-mimicking activities via doping engineering for the treatment of Salmonella-induced colitis. Benefiting from the co-doping of Cu and Mn, ZnO-CM nanospheres exhibit remarkable peroxidase-like activity in acidic condition and superoxide dismutase- and catalase-like activities in neutral environment. Animal experiments show that ZnO-CM can efficiently inhibit bacterial growth, alleviate inflammation, and restore the intestinal barrier, resulting in good antibacterial and anti-inflammatory effects on Salmonella-induced colitis. Mechanistically, ZnO-CM functions through inhibiting the continuous accumulation of ROS, increasing the levels of tight junction proteins occludin and claudin-1, and decreasing the expression of pro-inflammatory cytokines IL-1β and IL-6 in intestine. This work not only presents an effective paradigm for Salmonella-induced colitis therapy, but also provides new sights into the prevention and treatment of other bacterial enteritis.

Bayesian phylogeographic analysis infers cross-border transmission dynamics of drug-resistant Salmonella Enteritidis

Salmonella Enteritidis (S. Enteritidis) stands as a leading cause of human salmonellosis worldwide with a tendency to spread through contaminated foodstuffs and animals. In Hong Kong, a significant proportion of food products are imported, and many cases are often caused by the consumption of contaminated food, hence making the geographical surveillance of drug-resistant S. Enteritidis important for strong public health and food safety measures. We analyzed the whole genomes of 207 S. Enteritidis from Hong Kong, Australia, Canada, mainland China, the United States of America, South Africa, Taiwan, and the United Kingdom to examine associated antimicrobial resistance and the transmission dynamics between continents. Phylogenetic cluster inferences and Bayesian phylogeographical analysis were performed. Overall, sequence type ST11 strains were dominant (92.8%, 192/207). Five phylogenomic clusters A to E were identified, where most isolates from mainland China and Hong Kong were in Cluster E. Among the 22 plasmid types identified, IncX1 was dominant in the Asian isolates. Most of the virulence genes were distributed in Salmonella pathogenicity islands -1 and -2, with two universal virulence operons responsible for the effector delivery system and bacterial cell adhesion. The phylogeographic inference analysis showed a statistically significant link between mainland China and Hong Kong with the highest relative migration rate (relativeGeoRates mean ± standard error = 2.93 ± .07, Bayes Factor [BF] = 1285.5], with some traceable to Canada (0.61 ± 0.03, BF = 6.9) and Australia (1.02 ± 0.04, BF = 4.2). Our analysis suggests hypothetical transmission of S. Enteritidis and its associated antimicrobial resistance across borders.

IMPORTANCE

Antimicrobial resistance and disease severity in nontyphoidal Salmonella have constituted a serious public health challenge worldwide. Drug-resistant Salmonella Enteritidis is a leading pathogen that causes human infections primarily through the consumption of contaminated food products. Previous research focuses on the whole-genome analysis of antimicrobial resistance and virulence factors in S. Enteritidis; however, details on how this bacterium localized, expanded, and diversified from location to location remain unknown. Our study for the first time addresses this gap by investigating the phylogeographic transmission to estimate the frequency and location of cross-border spread. By evidence-based inferred transmission, we aim to uncover novel insights into the dynamic spread of S. Enteritidis, revealing the route of emergence and migration. This research is crucial for enhancing our understanding of the control strategies to safeguard human health.

Discriminant canonical analysis as a tool to determine traces of endangered native hen breed introgression through egg hatchability phenomics

OBJECTIVE

The main objective of this study was to develop a pipeline to detect phenogenomic introgression across different multivariety breeds and to validate such classification focusing on external egg and hatchability-related traits using a discriminant canonical analysis approach.

METHODS

For this, 1,368 eggs belonging a flock of 94 endangered Spanish autochthonous breed breeding hens (Andalusian Tufted, Blue Andalusian, Spanish White-Faced, and Utrerana) and a control outgroup comprising 32 eggs belonging to 4 Araucana hens were considered. Multicollinearity analysis of hatchability-related traits revealed embryonic mortality, embryonic mortality in the second stage of incubation, viable hatching chick, major diameter, and minor diameter should be discarded from the analysis (variance inflation factor ≤5) given they did not significantly contribute to variability explanation potential of the discriminant model.

RESULTS

A stepwise discriminant canonical analysis was developed and egg weight, shape index, hatchability, and fertility variables reported the highest discriminant power (Wilks' Lambda values of 0.7861, 0.7871, 0.8076, and 0.9457, respectively). The first two functions explained 85.25% intergroup variability. Interbreed and varieties proximity was evaluated using Mahalanobis distances representation and data mining cross-validation allowed to detect genetic introgression between different genotypes.

CONCLUSION

Easily collectable traits as egg weight and shape index must be considered for the development of breeding programs as a measure to ensure breed protection. The model may be translatable to other endangered breeds to optimize avian breeds conservation plans worldwide.

An MDR Salmonella Enteritidis sublineage associated with gastroenteritis outbreaks and invasive disease in China

OBJECTIVES

Salmonella enterica serovar Enteritidis (S. Enteritidis) is a commonly reported pathogen which adapts to multiple hosts and causes critical disease burden at a global level. Here, we investigated a recently derived epidemic sublineage with multidrug resistance (MDR), which have caused extended time-period and cross-regional gastroenteritis outbreaks and even invasive nontyphoidal Salmonella disease (iNTS) in China.

METHODS

Whole-genome sequencing and antimicrobial resistance (AMR) testing were applied to 729 Chinese S. Enteritidis isolates in relation to gastroenteritis outbreaks, gastrointestinal-sporadic and iNTS infections, spanning 28 years (1994-2021) in China. Phylogenomic analysis was performed to explore the population structure and evolutionary history of the Chinese isolates within a global context. Molecular investigations of AMR genes, virulence factors, mobile genetic elements and pan-genomes were also performed.

RESULTS

The Chinese S. Enteritidis collections exhibited a high level of multidrug resistance (MDR), including high resistance to nalidixic acid (97.67%). Notably, the multidrug resistance rate of iNTS strains has significantly increased over the past decade. Phylogenomic analysis showed that the majority of the Chinese isolates (98.63%) were distributed in the global pandemic lineage L1, while the other lineages were highly continent-specific. Particularly, the Chinese isolates were predominantly distributed in sublineages L1.2 (37.45%) and L1.3 (59.26%), forming two main Chinese clades (MCC1&2). The most recent common ancestor of MCC1&2 dated back to 1944 and 2004, respectively. The lineage L1, especially MCC1&2, harbored the most amount of AMR determinants and virulence genes, which was mainly due to the presence of a hybrid virulence-resistance plasmid and coexistence of different types of AMR plasmids in S. Enteritidis.

CONCLUSIONS

S. Enteritidis has evolved unique clonal clusters, MCC1&2, with critical MDR in China, which phylogenetically constitute an extension of the globally epidemic lineage and were characterized by distinct genetic traits. These clades have induced extensive outbreaks of gastroenteritis and serious cases of iNTS in China, underscoring the pressing nature and severity of this public health crisis. Implementing the One-Health strategy, longstanding routine surveillance and further genomic epidemiological studies are urgently required to capture epidemics, monitor changes in bacterial populations and determine the consequent risk to global public health.

Variation in plasmid conjugation among nontyphoidal Salmonella enterica serovars

Conjugation is a complex phenomenon involving multiple plasmid, bacterial, and environmental factors. Here we describe an IncI1 plasmid encoding multidrug antibiotic resistance to aminoglycosides, sulfonamides, and third-generation cephalosporins. This plasmid is widespread geographically among animal, human, and environmental sectors. We present data on the transmissibility of this plasmid from Salmonella enterica ser. Kentucky into 40 strains of S. enterica (10 strains each from serovars Enteritidis, Heidelberg, Infantis, and Typhimurium). Thirty seven out of 40 strains were able to take up the plasmid. Rates of conjugation were variable between strains ranging from 10-8 to 10-4. Overall, serovars Enteritidis and Typhimurium demonstrated the highest rates of conjugation, followed by Heidelberg, and then Infantis. No relationships were observed between the recipient cell surface and rate of conjugation. Recipient cell numbers correlated positively with conjugation rate and strains with high conjugation rates had marginally but significantly higher growth parameters compared to strains that took up the plasmid at lower frequencies. Environmental conditions known to impact cell growth, such as temperature, nutrient availability, and the presence of antibiotics, had a modulating effect on conjugation. Collectively, these results will further understanding of plasmid transmission dynamics in Salmonella, which is a critical first step towards the development of mitigation strategies.

Infection biology of Salmonella enterica

Salmonella enterica is the leading cause of bacterial foodborne illness in the USA, with an estimated 95% of salmonellosis cases due to the consumption of contaminated food products. Salmonella can cause several different disease syndromes, with the most common being gastroenteritis, followed by bacteremia and typhoid fever. Among the over 2,600 currently identified serotypes/serovars, some are mostly host-restricted and host-adapted, while the majority of serotypes can infect a broader range of host species and are associated with causing both livestock and human disease. Salmonella serotypes and strains within serovars can vary considerably in the severity of disease that may result from infection, with some serovars that are more highly associated with invasive disease in humans, while others predominantly cause mild gastroenteritis. These observed clinical differences may be caused by the genetic make-up and diversity of the serovars. Salmonella virulence systems are very complex containing several virulence-associated genes with different functions that contribute to its pathogenicity. The different clinical syndromes are associated with unique groups of virulence genes, and strains often differ in the array of virulence traits they display. On the chromosome, virulence genes are often clustered in regions known as Salmonella pathogenicity islands (SPIs), which are scattered throughout different Salmonella genomes and encode factors essential for adhesion, invasion, survival, and replication within the host. Plasmids can also carry various genes that contribute to Salmonella pathogenicity. For example, strains from several serovars associated with significant human disease, including Choleraesuis, Dublin, Enteritidis, Newport, and Typhimurium, can carry virulence plasmids with genes contributing to attachment, immune system evasion, and other roles. The goal of this comprehensive review is to provide key information on the Salmonella virulence, including the contributions of genes encoded in SPIs and plasmids during Salmonella pathogenesis.

Niche-specific evolution and gene exchange of Salmonella in retail pork and chicken

Salmonella exhibits extensive genetic diversity, facilitated by horizontal gene transfer occurring within and between species, playing a pivotal role in this diversification. Nevertheless, most studies focus on clinical and farm animal isolates, and research on the pangenome dynamics of Salmonella isolates from retail stage of the animal food supply chain is limited. Here, we investigated the genomes of 950 Salmonella isolates recovered from retail chicken and pork meats in seven provinces and one municipality of China in 2018. We observed a strong correlation between Salmonella sublineage diversity and the accessory genome with meat type, revealing reduced diversity associated with increased resistance. Importantly, genes associated with antibiotic, biocide, and heavy metal resistance were unevenly distributed in Salmonella from retail chicken and pork. Pork Salmonella isolates showed a higher prevalence of copper and silver resistance genes, while chicken Salmonella isolates displayed a significant predominance of genetic determinants associated with cephalosporin and ciprofloxacin resistance. Moreover, co-occurrence patterns of resistance determinants and their interaction with mobile genetic elements also correlated with meat type. In summary, our findings shed light on how Salmonella achieves their ecological niche success driven by evolution and gene changes in the retail stage of the animal food supply chain.

High carriage and possible hidden spread of multidrug-resistant Salmonella among asymptomatic workers in Yulin, China

Food workers have frequent contact with unprocessed foods, but their carriage of Salmonella and potential influence on public health have not been comprehensively assessed. We investigated Salmonella carriage among food workers compared with non-food workers based on occupational health screening of 260,315 asymptomatic workers over an 8-year surveillance period in Yulin, China. We confirmed that healthy carriers serve as natural reservoirs for Salmonella, with higher carriage rates in food workers than non-food workers. The isolates from food workers also exhibited greater serovar diversity and likely higher levels of antimicrobial resistance than those from non-food workers. Factors such as meteorological, social, and hygiene factors potentially influenced the carriage rate. Genomic analysis revealed a consistent increase in antimicrobial resistance genes among Salmonella isolates over the study period, with the majority of these antimicrobial resistance genes located on plasmids. Additionally, we identified numerous closely related bacterial clusters, which might reflect clusters of hidden local foodborne infections. This study underscores the elevated risk posed by food workers in the persistence and dissemination of Salmonella as vectors/fomites. Enhanced monitoring and targeted interventions in this group may reduce the dissemination of pathogens and antimicrobial resistance genes.

Genomic diversity of Salmonella Typhimurium and its monophasic variant in pig and pork production in France

Salmonella Typhimurium and its monophasic variant (Salmonella 4,[5],12:i:-) are among the most prevalent serovars worldwide. Even though these serovars have been the focus of many studies, their spread has not yet been investigated in French pig herds and slaughterhouses at a regional scale. Here, we characterized the genomic diversity of 188 Salmonella strains belonging to sequence type (ST) 19 and 34. These strains were isolated from pigs in metropolitan France between 2014 and 2019. Samples were collected from 10 regions, three of which together represent 75% of French pig production in 2020. To contextualize the French Salmonella genomes at a worldwide level, 193 ST 34 genomes from three continents and 14 countries were also included. This study revealed little diversity in ST 34 strains circulating in France, suggesting that one or two clones are spreading within pig herds and slaughterhouses. In silico virulence and antimicrobial resistance genes were investigated to understand the prevalence of these strains among farmed pigs and in the slaughterhouse environment. A comparison with ST 34 isolates from other countries highlighted the genomic specificity of the ST 34 monophasic variants in France, with some exceptions concerning isolates from bordering countries. This work provides new insights into the dynamics of S. Typhimurium and its monophasic variant sampled in French pig herds and slaughterhouses.

IMPORTANCE

Salmonellosis is a leading cause of bacterial infection in humans and animals around the world. This study provides a snapshot of the genomic diversity of one of the most prevalent Salmonella serovars (Salmonella Typhimurium and Salmonella 4,[5],12:i:-) circulating on French pig farms between 2013 and 2021. We investigated the link between geographical and genomic diversity. The analyses revealed little diversity of the strains, suggesting that one or two clones are spreading within French pig herds. We also in silico screened genetic elements that could explain the prevalence of these strains among farmed pigs and in the slaughterhouse environment. Finally, the comparison with isolates from other countries highlighted the genomic specificity of these two French sequence type 34 clones. This work provides new insights into the dynamics of S. Typhimurium and S. 4,[5],12:i:- sampled from pig herds and slaughterhouses in France, thus laying the foundations for future analyses.

Recombinant Lactococcus lactis secreting FliC protein nanobodies for resistance against Salmonella enteritidis invasion in the intestinal tract

Salmonella Enteritidis is a major foodborne pathogen throughout the world and the increase in antibiotic resistance of Salmonella poses a significant threat to public safety. Natural nanobodies exhibit high affinity, thermal stability, ease of production, and notably higher diversity, making them widely applicable for the treatment of viral and bacterial infections. Recombinant expression using Lactococcus lactis leverages both acid resistance and mucosal colonization properties of these bacteria, allowing the effective expression of exogenous proteins for therapeutic effects. In this study, nine specific nanobodies against the flagellar protein FliC were identified and expressed. In vitro experiments demonstrated that FliC-Nb-76 effectively inhibited the motility of S. Enteritidis and inhibited its adhesion to and invasion of HIEC-6, RAW264.7, and chicken intestinal epithelial cells. Additionally, a recombinant L. lactis strain secreting the nanobody, L. lactis-Nb76, was obtained. Animal experiments confirmed that it could significantly reduce the mortality rates of chickens infected with S. Enteritidis, together with alleviating the inflammatory response caused by the pathogen. These results provide a novel strategy for the treatment of antibiotic-resistant S. Enteritidis infection in the intestinal tract.

Local Inflammatory and Systemic Antibody Responses Initiated by a First Intradermal Administration of Autogenous Salmonella-Killed Vaccines and Their Components in Pullets

Vaccination strategies are used to manage Salmonella in chickens. Salmonella-killed vaccines are considered safer since they are inactivated. However, little is known regarding the cellular immune activities at the site of vaccine administration of Salmonella-killed vaccines. The growing feather (GF) cutaneous test has been shown to be an effective bioassay to monitor local tissue/cellular responses. We assessed local and systemic antibody responses initiated by intradermal injection of Salmonella-killed vaccines into GF-pulps of 14-15-week-old pullets. Treatments consisted of two autogenous Salmonella-killed vaccines (SV1 and SV2), S. Enteritidis (SE) lipopolysaccharide (SE-LPS), and the water-oil-water (WOW) emulsion vehicle. GF-pulps were collected before (0 h) and at 6, 24, 48, and 72 h post-GF-pulp injection for leukocyte population analysis, while heparinized blood samples were collected before (0 d) and at 3, 5, 7, 10, 14, 21, and 28 d after GF-pulp injections to assess plasma levels (a.u.) of SE-specific IgM, avian IgY (IgG), and IgA antibodies using an ELISA. Injection of GF-pulps with SV1, SV2, or SE-LPS, all in a WOW vehicle, initiated inflammatory responses characterized by the recruitment of heterophils, monocytes/macrophages, and a few lymphocytes. The WOW vehicle emulsion alone recruited more lymphocytes than vaccines or SE-LPS. The SV1 and SV2 vaccines stimulated Salmonella-specific IgM and IgA early, while IgG levels were greatly elevated later during the primary response. Overall, SV1 and SV2 stimulated a heterophil and macrophage-dominated local inflammatory- and SE-specific humoral response with an isotype switch from IgM to IgG, characteristic of a T-dependent primary antibody response. This study provides comprehensive information on innate and adaptive immune responses to autogenous Salmonella-killed vaccines and their components that will find application in the management of Salmonella in poultry.

Epidemiological and molecular investigations of Salmonella isolated from duck farms in southwest and around area of Shandong, China

Salmonella is a zoonotic pathogen posing a serious risk to the farming industry and public health due to food animals serving as reservoirs for future contamination and spread of Salmonella. The present study is designed to monitor the contamination status of Salmonella in duck farms and the main control points during breeding. 160 strains of duck-derived Salmonella were isolated from the 736 samples (cloacal swabs, feces, water, feed, soil, air and dead duck embryos) collected in southwest Shandong Province and the province's surrounding area. The percentage of Salmonella-positive samples collected was 21.74 % (160/736), and the greatest prevalence from duck embryo samples (40.00 %, 36/90). These Salmonella were classified into 23 serotypes depending on their O and H antigens, in which S. Typhimurium (30.15 %), S. Kottbus (13.97 %) and S. Enteritidis (10.29 %) were the prevailing serotypes. Subsequently, the molecular subtyping was done. Clustered regularly interspaced short palindromic repeats (CRISPR) analysis showed that 41 strains of S. Typhimurium and 14 strains of S. Enteritidis were classified into 13 and 3 genotypes, respectively. 19 S. Kottbus isolates from different sources featured ST1546, ST198, ST321, and ST1690 by multilocus sequence typing (MLST) analysis, among which ST1546 belongs to S. Kottbus was a new ST. The minimum spanning tree analysis based on the two CRISPR loci and seven MLST loci from all S. Typhimurium, S. Enteritidis and S. Kottbus isolates revealed that duck embryos, feed and water were key control points to the spread of Salmonella along the breeding chain. Meanwhile, the emergence of S. Kottbus in duck flocks was considered a potential public health hazard.

Characterization of the prevalence of Salmonella in different retail chicken supply modes using genome-wide and machine-learning analyses

Salmonella is a foodborne pathogen that causes salmonellosis, of which retail chicken meat is a major source. However, the prevalence of Salmonella in different retail chicken supply modes and the threat posed to consumers remains unclear. The prevalence, serotype distribution, antibiotic resistance, and genomic characteristics of Salmonella in three supply modes of retail chicken (live poultry, frozen, and chilled) were investigated using whole-genome sequencing (WGS) and machine learning (ML). In this study, 480 retail chicken samples from live poultry, frozen, and chilled supply modes in Guangzhou from 2020 to 2021, as well as 253 Salmonella isolates (total isolation rate = 53.1 %), were collected. The prevalence of isolates in the live poultry mode (67.5 %, 81/120) was statistically higher than in the frozen (50.0 %, 120/240) and chilled (43.3 %, 52/120) (P < 0.05) modes. Serotype identification showed significant differences in the serotype distribution of Salmonella in different supply modes. S. Enteritis (46.7 %) and S. Indiana (14.2 %) were predominant in the frozen mode. S. Agona (23.5 %) and S. Saintpaul (13.6 %) were predominant in live poultry, while S. Enteritis (40.4 %) and S. Kentucky (17.3 %) were predominant in chilled mode. Antibiotic testing showed that frozen mode isolates were more resistant; the multidrug-resistant (MDR) rate of isolates in the frozen mode reached 91.8 %, significantly higher than in the chilled (86.5 %) and live (74.1 %) (P < 0.05) modes. WGS was performed on 155 top serotypes (S. Enteritidis, S. Kentucky, S. Indiana, and S. Agona). The antibiotic resistance gene analysis showed that the abundance and carrying rate of antibiotic resistance genes of Salmonella in the frozen mode (54 types, 16.1 %) were significantly higher than in other modes (live poultry: 36 types, 9.4 %, P < 0.05; chilled: 31 types, 11.6 %). The blaNDM-1 and blaNDM-9 genes encoding carbapenem resistance were found in frozen mode isolates on a complex transposon consisting of TnAS3-IS26. Virulence factors and plasmid replicons were abundant in the studied frozen mode isolates. In addition, single nucleotide polymorphism (SNP) phylogenetic tree results showed that in the frozen supply mode, the S. Enteritidis clonal clade continued to contaminate retail chicken meat and was homologous to S. Enteritidis strains found in farm chicken embryos, slaughterhouse chicken carcasses, and patients from hospitals in China (SNP 0 = 10). Notably, the pan-genome-based ML model showed that characteristic genes in frozen and live poultry isolates differed. The narZ gene was a key characteristic gene in frozen isolates, encoding nitrate reductase, relating to anaerobic bacterial growth. The ydgJ gene is a key characteristic gene in the live mode and encodes an oxidoreductase related to oxidative function in bacteria. The high prevalence of live poultry mode Salmonella and the transmission of frozen mode MDR Salmonella in this study pose serious risks to food safety and public health, emphasizing the importance of improving disinfection and cold storage measures to reduce Salmonella contamination and transmission. In conclusion, the continued surveillance of Salmonella across different supply models and the development of an epidemiological surveillance system based on WGS is necessary.

Exploring of spectrum beta lactamase producing multidrug-resistant Salmonella enterica serovars in goat meat markets of Bangladesh

The emergence of Salmonella enterica serovars that produce extended-spectrum beta-lactamase and exhibit multi-drug resistance (MDR) poses a substantial global threat, contributing to widespread foodborne illnesses and presenting an alarming issue for public health. This study specifically concentrated on the isolation and identification of ESBL-resistant genes (bla TEM, bla SHV, bla CTX-M1, bla CTX-M2, bla CTX-M9, MultiCase ACC, MultiCase MOX, MultiCase DHA, bla OXA) and the antibiogram profiling of Salmonella enterica serovars found in goat meat samples procured from retail outlets in Bangladesh. During the research in the Sylhet district of Bangladesh, researchers gathered a total of 210 samples of goat meat from 13 different Upazilas. Primarily, cultural and biochemical methods were used for isolation of bacteria from the selected samples. Salmonella enterica serovars Typhimurium and Enteritidis, along with three ESBL-resistant genes, were identified through polymerase chain reactions (PCRs). The disk diffusion test was used to determine antimicrobial susceptibilities. Out of 210 samples analysed, Salmonella spp. was detected in 18.10 % (38 out of 210), with S. Enteritidis and S. Typhimurium found in 9.05 % (19 out of 210) and 5.24 % (11 out of 210) of the samples, respectively. A total of 72.73 % (8/11) of S. Enteritidis and 100 % (19/19) of S. Typhimurium isolates were positive by Multidrug-resistant patterns. The positive outcomes were found of S. Typhimurium tested 63.16 % (12 out of 19) for the bla TEM gene and 21.05 % (4/19) for the bla SHV, gene. The study proposes that the retail goat meat market channel could be a prominent transmission way of ESBL-producing MDR Salmonella enterica serovars, representing a significant public health hazard.

Development of a Colorimetric and SERS Dual-Signal Platform via dCas9-Mediated Chain Assembly of Bifunctional Au@Pt Nanozymes for Ultrasensitive and Robust Salmonella Assay

Timely screening for harmful pathogens is a great challenge in emergencies where traditional culture methods suffer from long assay time and alternative methods are limited by poor accuracy and low robustness. Herein, we present a dCas9-mediated colorimetric and surface-enhanced Raman scattering (SERS) dual-signal platform (dCas9-CSD) to address this challenge. Strategically, the platform used dCas9 to accurately recognize the repetitive sequences in amplicons produced by loop-mediated isothermal amplification (LAMP), forming nucleic acid frameworks that assemble numerous bifunctional gold-platinum (Au@Pt) nanozymes into chains on the surface of streptavidin-magnetic beads (SA-MB). The collected Au@Pt converted colorless 3,3',5,5'-tetramethylbenzidine (TMB) to blue oxidized TMB (oxTMB) via its Pt shell and then enhanced the Raman signal of oxTMB by its Au core. Therefore, the presence of Salmonella could be dexterously converted into cross-validated colorimetric and SERS signals, providing more reliable conclusions. Notably, dCas9-mediated secondary recognition of amplicons reduced background signal caused by nontarget amplification, and two-round signal amplification consisting of LAMP reaction and Au@Pt catalysis greatly improved the sensitivity. With this design, Salmonella as low as 1 CFU/mL could be detected within 50 min by colorimetric and SERS modes. The robustness of dCas9-CSD was further confirmed by various real samples such as lake water, cabbage, milk, orange juice, beer, and eggs. This work provides a promising point-of-need tool for pathogen detection.

Filamentous bacteria-induced sludge bulking can alter antibiotic resistance gene profiles and increase potential risks in wastewater treatment systems

Sludge bulking caused by filamentous bacteria is a prevalent issue in wastewater treatment systems. While previous studies have primarily concentrated on controlling sludge bulking, the biological risks associated with it have been overlooked. This study demonstrates that excessive growth of filamentous bacteria during sludge bulking can significantly increase the abundance of antibiotic resistance genes (ARGs) in activated sludge. Through metagenomic analysis, we identified specific ARGs carried by filamentous bacteria, such as Sphaerotilus and Thiothrix, which are responsible for bulking. Additionally, by examining over 1,000 filamentous bacterial genomes, we discovered a diverse array of ARGs across different filamentous bacteria derived from wastewater treatment systems. Our findings indicate that 74.84% of the filamentous bacteria harbor at least one ARG, with the occurrence frequency of ARGs in these bacteria being approximately 1.5 times higher than that in the overall bacterial population in activated sludge. Furthermore, genomic and metagenomic analyses have shown that the ARGs in filamentous bacteria are closely linked to mobile genetic elements and are frequently found in potentially pathogenic bacteria, highlighting potential risks posed by these filamentous bacteria. These insights enhance our understanding of ARGs in activated sludge and underscore the importance of risk management in wastewater treatment systems.

Dietary α-linolenic acid supplementation enhances resistance to Salmonella Typhimurium challenge in chickens by altering the intestinal mucosal barrier integrity and cecal microbes

Salmonella is an important foodborne pathogen. Given the ban on the use of antibiotics during the egg-laying period in China, finding safe and effective alternatives to antibiotics to reduce Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) infections in chickens is essential for the prevention and control of this pathogen and the protection of human health. Numerous studies have shown that unsaturated fatty acids have a positive effect on intestinal inflammation and resistance to infection by intestinal pathogens. Here we investigated the protective effect of α-linolenic acid (ALA) against S. Typhimurium infection in chickens and further explored its mechanism of action. We added different proportions of ALA to the feed and observed the effect of ALA on S. Typhimurium colonization using metagenomic sequencing technology and physiological index measurements. The role of gut flora on S. Typhimurium colonization was subsequently verified by fecal microbiota transplantation (FMT). We found that ALA protects chickens from S. Typhimurium infection by reducing intestinal inflammation through remodeling the gut microbiota, up-regulating the expression of ileocecal barrier-related genes, and maintaining the integrity of the intestinal epithelium. Our data suggest that supplementation of feed with ALA may be an effective strategy to alleviate S. Typhimurium infection in chickens.

First Data on WGS-Based Typing and Antimicrobial Resistance of Human Salmonella Enteritidis Isolates in Greece

Salmonella enterica subsp. enterica serotype Enteritidis (S. Enteritidis) is one of the major causes of foodborne infections and is responsible for many national and multi-country foodborne outbreaks worldwide. In Greece, human salmonellosis is a mandatory notifiable disease, with laboratory surveillance being on a voluntary basis. This study aims to provide the first insights into the genetic characteristics and antimicrobial resistance profiles of 47 S. Enteritidis human isolates using whole-genome sequencing (WGS) technology. The S. Enteritidis population was mainly resistant to fluoroquinolones due to gyrA point mutations, whereas one isolate presented a multi-resistant plasmid-mediated phenotype. ST11 was the most frequent sequence type, and phylogenetic analysis through the cgMLST and SNP methods revealed considerable genetic diversity. Regarding virulence factors, 8 out of the 24 known SPIs and C63PI were detected. Due to the observed variability between countries, it is of utmost importance to record the circulating S. Enteritidis strains' structure and genomic epidemiology at the national level. WGS is a valuable tool that is revolutionizing our approach to Salmonella by providing a deeper understanding of these pathogens and their impact on human health.

The peptidoglycan-associated lipoprotein gene mutant elicits robust immunological defense in mice against Salmonella enteritidis

Background

Salmonella enteritidis (S. enteritidis), a zoonotic pathogen with a broad host range, presents a substantial threat to global public health safety. Vaccination stands as an effective strategy for the prevention and control of S. enteritidis infection, highlighting an immediate clinical need for the creation of safe and efficient attenuated live vaccines.

Methods

In this study, a S. enteritidis peptidoglycan-associated lipoprotein (pal) gene deletion strain (Δpal), was constructed. To assess its virulence, we conducted experiments on biofilm formation capability, motility, as well as cell and mouse infection. Subsequently, we evaluated the immune-protective effect of Δpal.

Results

It was discovered that deletion of the pal gene reduced the biofilm formation capability and motility of S. enteritidis. Cell infection experiments revealed that the Δpal strain exhibited significantly decreased abilities in invasion, adhesion, and intracellular survival, with downregulation of virulence gene expression, including mgtC, invH, spvB, sipA, sipB, ssaV, csgA, and pipB. Mouse infection experiments showed that the LD50 of Δpal increased by 104 times, and its colonization ability in mouse tissue organs was significantly reduced. The results indicated that the pal gene severely affected the virulence of S. enteritidis. Further, immunogenicity evaluation of Δpal showed a significant enhancement in the lymphocyte transformation proliferation capability of immunized mice, producing high titers of specific IgG and IgA, suggesting that Δpal possesses good immunogenicity. Challenge protection tests demonstrated that the strain could provide 100% immune protection against wild-type strains in mice.

Discussion

This study proves that the pal gene influences the virulence of S. enteritidis, and Δpal could serve as a candidate strain for attenuated live vaccines, laying the foundation for the development of attenuated live vaccines against Salmonella.

The Poultry Red Mite, Dermanyssus gallinae, travels far but not frequently, and takes up permanent residence on farms

Management of Dermanyssus gallinae, a cosmopolitan hematophagous mite responsible for damage in layer poultry farming, is hampered by a lack of knowledge of its spatio-temporal population dynamics. Previous studies have shown that the circulation of this pest between farms is of strictly anthropogenic origin, that a mitochondrial haplogroup has been expanding on European farms since the beginning of the 21st century and that its local population growth may be particularly rapid. To refine our understanding of how D. gallinae spreads within and among farms, we characterized the genetic structure of mite populations at different spatial scales and sought to identify the main factors interrupting gene flow between poultry houses and between mitochondrial haplogroups. To this end, we selected and validated the first set of nuclear microsatellite markers for D. gallinae and sequenced a region of the CO1-encoding mitochondrial gene in a subsample of microsatellite-genotyped mites. We also tested certain conditions required for effective contamination of a poultry house through field experimentation, and conducted a survey of practices during poultry transfers. Our results confirm the role of poultry transport in the dissemination of mite populations, but the frequency of effective contamination after the introduction of contaminated material into poultry houses seems lower than expected. The high persistence of mites on farms, even during periods when poultry houses are empty and cleaned, and the very large number of nodes in the logistic network (large number of companies supplying pullets or transporting animals) undoubtedly explain the very high prevalence on farms. Substantial genetic diversity was measured in farm populations, probably as a result of the mite's known haplodiploid mode of sexual reproduction, coupled with the dense logistic network. The possibility of the occasional occurrence of asexual reproduction in this sexually reproducing mite was also revealed in our analyses, which could explain the extreme aggressiveness of its demographic dynamics under certain conditions.

Centralized industrialization of pork in Europe and America contributes to the global spread of Salmonella enterica

Salmonella enterica causes severe food-borne infections through contamination of the food supply chain. Its evolution has been associated with human activities, especially animal husbandry. Advances in intensive farming and global transportation have substantially reshaped the pig industry, but their impact on the evolution of associated zoonotic pathogens such as S. enterica remains unresolved. Here we investigated the population fluctuation, accumulation of antimicrobial resistance genes and international serovar Choleraesuis transmission of nine pig-enriched S. enterica populations comprising more than 9,000 genomes. Most changes were found to be attributable to the developments of the modern pig industry. All pig-enriched salmonellae experienced host transfers in pigs and/or population expansions over the past century, with pigs and pork having become the main sources of S. enterica transmissions to other hosts. Overall, our analysis revealed strong associations between the transmission of pig-enriched salmonellae and the global pork trade.

Prevalence, Molecular Detection, and Antimicrobial Resistance of Salmonella Isolates from Poultry Farms across Central Ethiopia: A Cross-Sectional Study in Urban and Peri-Urban Areas

A cross-sectional study was conducted to assess the prevalence, molecular detection, and antimicrobial resistance of Salmonella isolates within 162 poultry farms in selected urban and peri-urban areas of central Ethiopia. A total of 1515 samples, including cloacal swabs (n = 763), fresh fecal droppings (n = 188), litter (n = 188), feed (n = 188), and water (n = 188), were bacteriologically tested. The molecular detection of some culture-positive isolates was performed via polymerase chain reaction (PCR) by targeting spy and sdfl genes for Salmonella Typhimurium and Salmonella Enteritidis, respectively. Risk factors for the occurrence of the bacterial isolates were assessed. Antimicrobial susceptibility testing of PCR-confirmed Salmonella isolates was conducted using 12 antibiotics. In this study, it was observed that 50.6% of the farms were positive for Salmonella. The overall sample-level prevalence of Salmonella was 14.4%. Among the analyzed risk factors, the type of production, breed, and sample type demonstrated a statistically significant association (p < 0.05) with the bacteriological prevalence of Salmonella. The PCR test disclosed that 45.5% (15/33) and 23.3% (10/43) of the isolates were positive for genes of Salmonella Typhimurium and Salmonella Enteritidis, respectively. The antimicrobial susceptibility test disclosed multi-drug resistance to ten of the tested antibiotics that belong to different classes. Substantial isolation of Salmonella Typhimurium and Salmonella Enteritidis in poultry and on poultry farms, along with the existence of multi-drug resistant isolates, poses an alarming risk of zoonotic and food safety issues. Hence, routine flock testing, farm surveillance, biosecurity intervention, stringent antimicrobial use regulations, and policy support for the sector are highly needed.

Genomic characterisation of the population structure and antibiotic resistance of Salmonella enterica serovar Infantis in Chile, 2009-2022

Background

Multidrug-resistant (MDR) Salmonella Infantis has disseminated worldwide, mainly linked to the consumption of poultry products. Evidence shows dissemination of this pathogen in Chile; however, studies are primarily limited to phenotypic data or involve few isolates. As human cases of Salmonella Infantis infections have substantially increased in recent years, this study aimed to characterise the genomic epidemiology and antimicrobial-resistance profiles of isolates obtained from different sources, aiming to inform effective surveillance and control measures.

Methods

We sequenced 396 Salmonella Infantis genomes and analysed them with all publicly available genomes of this pathogen from Chile (440 genomes in total), representing isolates from environmental, food, animal, and human sources obtained from 2009 to 2022. Based on bioinformatic and phenotypic methods, we assessed the population structure, dissemination among different niches, and antimicrobial resistance (AMR) profiles of Salmonella Infantis in the country.

Findings

The genomic and phylogenetic analyses showed that Salmonella Infantis from Chile comprised several clusters of highly related isolates dominated by sequence type 32. The HC20_343 cluster grouped an important proportion of all isolates. This was the only cluster associated with pESI-like megaplasmids, and up to 12 acquired AMR genes/mutations predicted to result in an MDR phenotype. Accordingly, antimicrobial-susceptibility testing revealed a strong concordance between the AMR genetic determinants and their matching phenotypic expression, indicating that a significant proportion of HC20_343 isolates produce extended-spectrum β-lactamases and have intermediate fluoroquinolone resistance. HC20_343 Salmonella Infantis were spread among environmental, animal, food, and human niches, showing a close relationship between isolates from different years and sources, and a low intra-source genomic diversity.

Interpretation

Our findings show a widespread dissemination of MDR Salmonella Infantis from the HC20_343 cluster in Chile. The high proportion of isolates with resistance to first-line antibiotics and the evidence of active transmission between the environment, animals, food, and humans highlight the urgency of improved surveillance and control measures in the country. As HC20_343 isolates predominate in the Americas, our results suggest a high prevalence of ESBL-producing Salmonella Infantis with intermediate fluoroquinolone resistance in the continent.

Funding

Partially supported by the Food and Drug Administration (FDA) of the U.S. Department of Health and Human Services as part of an award, FDU001818, with 30% percent funded by FDA/HHS; and by Agencia de Investigación y Desarrollo de Chile (ANID) through FONDECYT de Postdoctorado Folio 3230796 and Folio 3210317, FONDECYT Regular Folio 1231082, and ANID-Millennium Science Initiative Program-ICN2021_044.

CheV enhances the virulence of Salmonella Enteritidis, and the Chev-deleted Salmonella vaccine provides immunity in mice

BACKGROUND

Salmonella enteritidis (SE) is a major zoonotic pathogen and causes infections in a variety of hosts. The development of novel vaccines for SE is necessary to eradicate this pathogen. Genetically engineered attenuated live vaccines are more immunogenic and safer. Thus, to develop a live attenuated Salmonella vaccine, we constructed a cheV gene deletion strain of SE (named ΔcheV) and investigated the role of cheV in the virulence of SE. First, the ability to resist environmental stress in vitro, biofilm formation capacity, drug resistance and motility of ΔcheV were analyzed. Secondly, the bacterial adhesion, invasion, intracellular survival assays were performed by cell model. Using a mouse infection model, an in vivo virulence assessment was conducted. To further evaluate the mechanisms implicated by the reduced virulence, qPCR analysis was utilized to examine the expression of the strain's major virulence genes. Finally, the immune protection rate of ΔcheV was evaluated using a mouse model.

RESULTS

Compared to C50336, the ΔcheV had significantly reduced survival ability under acidic, alkaline and thermal stress conditions, but there was no significant difference in survival under oxidative stress conditions. There was also no significant change in biofilm formation ability, drug resistance and motility. It was found that the adhesion ability of ΔcheV to Caco-2 cells remained unchanged, but the invasion ability and survival rate in RAW264.7 cells were significantly reduced. The challenge assay results showed that the LD50 values of C50336 and ΔcheV were 6.3 × 105 CFU and 1.25 × 107 CFU, respectively. After the deletion of the cheV gene, the expression levels of fimD, flgG, csgA, csgD, hflK, lrp, sipA, sipB, pipB, invH, mgtC, sodC, rfbH, xthA and mrr1 genes were significantly reduced. The live attenuated ΔcheV provided 100% protection in mice against SE infection.

CONCLUSION

All the results confirmed that the deletion of the cheV gene reduces the virulence of SE and provides significant immune protection in mice, indicating that ΔcheV could be potential candidates to be explored as live-attenuated vaccines.

Salmonella enterica serovars linked with poultry in India: antibiotic resistance profiles and carriage of virulence genes

Salmonella is an important poultry pathogen with zoonotic potential. Being a foodborne pathogen, Salmonella-contaminated poultry products can act as the major source of infection in humans. In India, limited studies have addressed the diversity of Salmonella strains of poultry origin. This study represented 26 strains belonging to Salmonella serovars Typhimurium, Infantis, Virchow, Kentucky, and Agona. The strains were tested for resistance to 14 different antimicrobial agents using the Kirby-Bauer disk-diffusion assay. The presence of the invA, hilA, agfA, lpfA, sopE, and spvC virulence genes was assessed by polymerase chain reaction (PCR), and the genetic diversity was assessed by Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR). The highest resistance to tetracycline (n = 17; 65.38%) followed by nalidixic acid (n = 16; 61.53%) was detected among the strains. Among the strains (n = 17) phenotypically resistant to tetracycline, 94% (n = 16) were also positive for the tetA gene. Based on the presence of virulence genes, the strains were characterized into three virulence profiles (PI, P2, and P3). Among the investigated virulence genes, invA, hilA, agfA, and lpfA were present in all strains. The sopE gene was mostly associated with serovars Virchow (n = 3; 100%) and Typhimurium (n = 8; 80%), whereas spvC gene was exclusive for two Typhimurium strains that lacked sopE gene. ERIC-PCR profiling indicated clusters correlating their serovar, geographical, and farm origins. These results demonstrate that Salmonella isolates with a wide genetic range, antibiotic resistance, and virulence characteristics can colonize poultry. The presence of such strains is crucial for both food safety and public health.

Isolation, Identification, Antimicrobial Resistance, Genotyping, and Whole-Genome Sequencing Analysis of Salmonella Enteritidis Isolated from a Food-Poisoning Incident

Salmonella enterica is a common pathogen in humans and animals that causes food poisoning and infection, threatening public health safety. We aimed to investigate the genome structure, drug resistance, virulence characteristics, and genetic relationship of a Salmonella strain isolated from patients with food poisoning. The pathogen strain 21A was collected from the feces of patients with food poisoning, and its minimum inhibitory concentration against commonly used antibiotics was determined using the strip test and Kirby-Bauer disk methods. Subsequently, WGS analysis was used to reveal the genome structural characteristics and the carrying status of resistance genes and virulence genes of strain 21A. In addition, an MLST-based minimum spanning tree and an SNP-based systematic spanning tree were constructed to investigate its genetic evolutionary characteristics. The strain 21A was identified by mass spectrometry as S. enterica, which was found to show resistance to ampicillin, piperacillin, sulbactam, levofloxacin, and ciprofloxacin. The WGS and bioinformatics analyses revealed this strain as Salmonella Enteritidis belonging to ST11, which is common in China, containing various resistance genes and significant virulence characteristics. Strain 21A was closely related to the SJTUF strains, a series strains from animal, food and clinical sources, as well as from Shanghai, China, which were located in the same evolutionary clade. According to the genetic makeup of strain 21A, the change G > A was found to be the most common variation. We have comprehensively analyzed the genomic characteristics, drug resistance phenotype, virulence phenotype, and genetic evolution relationship of S. Enteritidis strain 21A, which will contribute towards an in-depth understanding of the pathogenic mechanism of S. Enteritidis and the effective prevention and control of foodborne diseases.

Salmonella in eggs and egg-laying chickens: pathways to effective control

Eggs contaminated with Salmonella have been internationally significant sources of human illness for several decades. Most egg-associated illness has been attributed to Salmonella serovar Enteritidis, but a few other serovars (notably S. Heidelberg and S. Typhimurium) are also sometimes implicated. The edible interior contents of eggs typically become contaminated with S. Enteritidis because the pathogen's unique virulence attributes enable it to colonize reproductive tissues in systemically infected laying hens. Other serovars are more commonly associated with surface contamination of eggshells. Both research and field experience have demonstrated that the most effective overall Salmonella control strategy in commercial laying flocks is the application of multiple interventions throughout the egg production cycle. At the preharvest (egg production) level, intervention options of demonstrated efficacy include vaccination and gastrointestinal colonization control via treatments such as prebiotics, probiotics, and bacteriophages, Effective environmental management of housing systems used for commercial laying flocks is also essential for minimizing opportunities for the introduction, transmission, and persistence of Salmonella in laying flocks. At the postharvest (egg processing and handling) level, careful regulation of egg storage temperatures is critical for limiting Salmonella multiplication inside the interior contents.

Prevalence and antibiotics resistance status of Salmonella in raw meat consumed in various areas of Lahore, Pakistan

This study reports the prevalence and antibiotics resistance status of Salmonella detected in raw meat from Lahore, Pakistan. Overall, N = 111 meat samples, were collected from local markets. Salmonella was recovered from 57 (51.35%) samples, including 45.83% of poultry, 60% of buffalo, 64.28% of cow, and 60% of goat meat samples. The predominant Salmonella strains were Salmonella enterica serovars; Typhimurium (45.4%), Typhi (27.2%), and Enteritidis (18.1%), identified by VITEK system and 16S rRNA gene sequencing. The isolates exhibited high resistance to Erythromycin (100%), Cefepime (98.24%), Colistin (94.73%), Azithromycin (92.98%), Tetracycline (87.71%), Polymyxin B (84.21%), Ciprofloxacin (84.21%), Trimethoprim-Sulfamethoxazole (80.70%), Nalidixic Acid (80.70%), Kanamycin (78.94%), Chloramphenicol (77.19%), Streptomycin (71.92%) and Ampicillin (64.91%). While the isolates exhibited more susceptibility to Meropenem (75.43%) and Amikacin (73.68%). N = 8 strains were designated as Multidrug Resistant (MDR) and N = 3 as Extensively Drug-Resistant (XDR) Salmonella. The PCR-based detection of resistance genes revealed the presence of blaTEM-1 gene (100%), catA1 gene (64%), and gyrA gene (18%). The whole genome sequencing (WGS) of two selected strains and subsequent downstream analysis confirmed the strains as MDR and XDR Salmonella enterica serovar Typhi. The study showed that raw meat consumed in Lahore carries a significantly high number of drug-resistant Salmonella.

Genomic analysis of almost 8,000 Salmonella genomes reveals drivers and landscape of antimicrobial resistance in China

IMPORTANCE

We established the largest Salmonella genome database from China and presented the landscape and spatiotemporal dynamics of antimicrobial resistance genes. We also found that economic, climatic, and social factors can drive the rise of antimicrobial resistance. The Chinese local Salmonella genome database version 2 was released as an open-access database (https://nmdc.cn/clsgdbv2) and thus can assist surveillance studies across the globe. This database will help inform interventions for AMR, food safety, and public health.

Serovars, Virulence and Antimicrobial Resistance Genes of Non-Typhoidal Salmonella Strains from Dairy Systems in Mexico

Salmonella isolated from dairy farms has a significant effect on animal health and productivity. Different serogroups of Salmonella affect both human and bovine cattle causing illness in both reservoirs. Dairy cows and calves can be silent Salmonella shedders, increasing the possibility of dispensing Salmonella within the farm. The aim of this study was to determine the genomic characteristics of Salmonella isolates from dairy farms and to detect the presence of virulence and antimicrobial resistance genes. A total of 377 samples were collected in a cross-sectional study from calves, periparturient cow feces, and maternity beds in 55 dairy farms from the states of Aguascalientes, Baja California, Chihuahua, Coahuila, Durango, Mexico, Guanajuato, Hidalgo, Jalisco, Queretaro, San Luis Potosi, Tlaxcala, and Zacatecas. Twenty Salmonella isolates were selected as representative strains for whole genome sequencing. The serological classification of the strains was able to assign groups to only 12 isolates, but with only 5 of those being consistent with the genomic serotyping. The most prevalent serovar was Salmonella Montevideo followed by Salmonella Meleagridis. All isolates presented the chromosomal aac(6')-Iaa gene that confers resistance to aminoglycosides. The antibiotic resistance genes qnrB19, qnrA1, sul2, aph(6)-Id, aph(3)-ld, dfrA1, tetA, tetC, flor2, sul1_15, mph(A), aadA2, blaCARB, and qacE were identified. Ten pathogenicity islands were identified, and the most prevalent plasmid was Col(pHAD28). The main source of Salmonella enterica is the maternity areas, where periparturient shedders are contaminants and perpetuate the pathogen within the dairy in manure, sand, and concrete surfaces. This study demonstrated the necessity of implementing One Health control actions to diminish the prevalence of antimicrobial resistant and virulent pathogens including Salmonella.

Egg-associated Salmonella enterica serovar Enteritidis: comparative genomics unveils phylogenetic links, virulence potential, and antimicrobial resistance traits

Salmonella enterica serovar Enteritidis (SE) remains a frequent cause of foodborne illnesses associated with the consumption of contaminated hen eggs. Such a food-pathogen association has been demonstrated epidemiologically, but the molecular basis for this association has not been explored. Comparative genomic analysis was implemented to decipher the phylogenomic characteristics, antimicrobial resistance, and virulence potential of eggs-associated SE. Analyzing 1,002 genomes belonging to 841 sequence types of food-isolated SE strains suggests a high genomic similarity within the egg-related lineage, which is phylogenetically close to SE strains isolated from poultry but is different from those isolated from beef. Core genome- and single nucleotide polymorphism (SNP)-based phylogeny of 74 SE strains of egg origin showcased two distinct sublineages. Time-scaled phylogeny supported the possibility of a common ancestor of egg-related SE lineages. Additionally, genome mining revealed frequent antibiotic resistance due to the presence of aac(6')-Iaa and mdsAB encoded on the genomes of egg-associated SE strains. For virulence gene profiling, 103-113 virulence determinants were identified in the egg-associated SE, which were comparable to 112 determinants found in human-associated SE, emphasizing the capacity of egg-associated strains to infect humans and cause diseases. The findings of this study proved the genomic similarity of egg-associated SE strains, and these were closely related to poultry strains. The egg-associated strains also harbor virulence genes equivalent to those found in human-associated SE strains. The analysis provided critical insights into the genetic structure, phylogenomics, dynamics of virulence, and antibiotic resistance of Salmonella Enteritidis, circulating in eggs and emphasizing the necessity of implementing anti-Salmonella intervention strategies, starting at the production stage of the poultry supply chain.

Prevalence and genomic characterization of Salmonella isolates from commercial chicken eggs retailed in traditional markets in Ghana

Salmonella enterica are important foodborne bacterial pathogens globally associated with poultry. Exposure to Salmonella-contaminated eggs and egg-related products is a major risk for human salmonellosis. Presently, there is a huge data gap regarding the prevalence and circulating serovars of Salmonella in chicken eggs sold in Ghana. In this study, 2,304 eggs (pools of six per sample unit) collected from informal markets in Accra, Kumasi and Tamale, representing the three ecological belts across Ghana, were tested for Salmonella. Antimicrobial susceptibility testing and Whole Genome Sequencing (WGS) of the isolates were performed using standard microdilution protocols and the Illumina NextSeq platform, respectively. The total prevalence of Salmonella was 5.5% with a higher rate of contamination in eggshell (4.9%) over egg content (1.8%). The serovars identified were S. Ajiobo (n = 1), S. Chester (n = 6), S. Hader (n = 7), S. enteritidis (n = 2); and S. I 4:b:- (n = 8). WGS analysis revealed varied sequence types (STs) that were serovar specific. The S. I 4:b:- isolates had a novel ST (ST8938), suggesting a local origin. The two S. enteritidis isolates belonged to ST11 and were identified with an invasive lineage of a global epidemic clade. All isolates were susceptible to ampicillin, azithromycin, cefotaxime, ceftazidime, gentamicin, meropenem, and tigecycline. The phenotypic resistance profiles to seven antimicrobials: chloramphenicol (13%), ciprofloxacin (94%), and nalidixic acid (94%), colistin (13%), trimethoprim (50%) sulfamethoxazole (50%) and tetracycline (50%) corresponded with the presence of antimicrobial resistance (AMR) determinants including quinolones (gyrA (D87N), qnrB81), aminoglycosides (aadA1), (aph(3")-Ib aph(6)-Id), tetracyclines (tet(A)), phenicols (catA1), trimethoprim (dfrA14 and dfrA1). The S. enteritidis and S. Chester isolates were multidrug resistant (MDR). Several virulence factors were identified, notably cytolethal distending toxin (cdtB gene), rck, pef and spv that may promote host invasion and disease progression in humans. The findings from this study indicate the presence of multidrug resistant and virulent strains of Salmonella serovars in Ghanaian chicken eggs, with the potential to cause human infections. This is a critical baseline information that could be used for Salmonella risk assessment in the egg food chain to mitigate potential future outbreaks.

Whole-genome sequencing for One Health surveillance of antimicrobial resistance in conflict zones: a case study of Salmonella spp. and Campylobacter spp. in the West Bank, Palestine

Antimicrobial resistance (AMR) is a critical global concern driven by the overuse, misuse, and/or usage of inadequate antibiotics on humans, animals' agriculture, and as a result of contaminated environments. This study is the first One Health survey in the Middle East that incorporated whole-genome sequencing (WGS) to examine the spread of AMR in Campylobacter spp. and Salmonella spp. This cross-sectional study was conducted to examine the role of AMR at the human-animal-environmental interface and was performed in Ramallah/Al-Bireh and Jerusalem governorates of the central West Bank, Palestine. In 2021 and 2022, a total of 592 samples were collected and analyzed. From a total of 65 Campylobacter jejuni and 19 Salmonella spp. isolates, DNA was extracted for WGS using Oxford Nanopore Technologies MinION platform. We found that the dominant serotypes of C. jejuni and Salmonella enterica were present in chicken manure, chicken meat sold in markets, and feces of asymptomatic farm workers, with high genetic similarities between the isolates regardless of origin. Additionally, our results showed rapid strain turnover in C. jejuni from the same sites between 2021 and 2022. Most of the positive Salmonella spp. samples were multidrug-resistant (MDR) S. enterica serovar Muenchen carrying the plasmid of emerging S. infantis (pESI) megaplasmid, conferring resistance to multiple antibiotics. Our findings highlight the spread of MDR foodborne pathogens from animals to humans through the food chain, emphasizing the importance of a One Health approach that considers the interconnections between human, animal, and environmental health. IMPORTANCE Prior to this study, there existed hardly an integrated human-animal-environmental study of Salmonellosis and Campylobacteriosis and related AMR in Middle Eastern countries. The few existing studies lack robust epidemiological study designs, adequate for a One Health approach, and did not use WGS to determine the circulating serotypes and their AMR profiles. Civil unrest and war in Middle Eastern countries drive AMR because of the breakdown of public health and food security services. This study samples simultaneously humans, animals, and the environment to comprehensively investigate foodborne pathogens in the broiler chicken production chain in Palestine using WGS. We show that identical serotypes of C. jejuni and S. enterica can be found in samples from chicken farms, chicken meat sold in markets, and asymptomatic broiler chicken production workers. The most striking feature is the rapid dynamic of change in the genetic profile of the detected species in the same sampling locations. The majority of positive Salmonella spp. samples are MDR S. enterica serovar Muenchen isolates carrying the pESI megaplasmid. The results demonstrate a close relationship between the S. enterica serovar Muenchen isolates found in our sample collection and those responsible for 40% of all clinical Salmonella spp. isolates in Israel as previously reported, with a sequence identity of over 99.9%. These findings suggest the transboundary spread of MDR S. enterica serovar Muenchen strains from animals to humans through the food chain. The study underscores the importance of combining integrated One Health studies with WGS for detecting environmental-animal-human transmission of foodborne pathogens that could not be detected otherwise. This study showcases the benefits of integrated environmental-animal-human sampling and WGS for monitoring AMR. Environmental samples, which may be more accessible in conflict-torn places where monitoring systems are limited and regulations are weak, can provide an effective AMR surveillance solution. WGS of bacterial isolates provides causal inference of the distribution and spread of bacterial serotypes and AMR in complex social-ecological systems. Consequently, our results point toward the expected benefits of operationalizing a One Health approach through closer cooperation of public and animal health and food safety authorities.

An Overview of Antimicrobial Resistance Profiles of Publicly Available Salmonella Genomes with Sufficient Quality and Metadata

Salmonella enterica (S. enterica) is a commensal organism or pathogen causing diseases in animals and humans, as well as widespread in the environment. Antimicrobial resistance (AMR) has increasingly affected both animal and human health and continues to raise public health concerns. A decade ago, it was estimated that the increased use of whole genome sequencing (WGS) combined with sharing of public data would drastically change and improve the surveillance and understanding of Salmonella epidemiology and AMR. This study aimed to evaluate the current usefulness of public WGS data for Salmonella surveillance and to investigate the associations between serovars, antibiotic resistance genes (ARGs), and metadata. Out of 191,306 Salmonella genomes deposited in European Nucleotide Archive and NCBI databases, 47,452 WGS with sufficient minimum metadata (country, year, and source) of S. enterica were retrieved from 116 countries and isolated between 1905 and 2020. For in silico analysis of the WGS data, KmerFinder, SISTR, and ResFinder were used for species, serovars, and AMR identification, respectively. The results showed that the five common isolation sources of S. enterica are human (29.10%), avian (22.50%), environment (11.89%), water (9.33%), and swine (6.62%). The most common ARG profiles for each class of antimicrobials are β-lactam (blaTEM-1B; 6.78%), fluoroquinolone [(parC[T57S], qnrB19); 0.87%], folate pathway antagonist (sul2; 8.35%), macrolide [mph(A); 0.39%], phenicol (floR; 5.94%), polymyxin B (mcr-1.1; 0.09%), and tetracycline [tet(A); 12.95%]. Our study reports the first overview of ARG profiles in publicly available Salmonella genomes from online databases. All data sets from this study can be searched at Microreact.

Practical Preventive Considerations for Reducing the Public Health Burden of Poultry-Related Salmonellosis

With poultry products as one of the leading reservoirs for the pathogen, in a typical year in the United States, it is estimated that over one million individuals contract non-typhoidal Salmonella infections. Foodborne outbreaks associated with Salmonella infections in poultry, thus, continue to remain a significant risk to public health. Moreover, the further emergence of antimicrobial resistance among various serovars of Salmonella is an additional public health concern. Feeding-based strategies (such as use of prebiotics, probiotics, and/or phytobiotics as well as essential oils), non-feeding-based strategies (such as use of bacteriophages, vaccinations, and in ovo strategies), omics tools and surveillance for identifying antibiotic-resistance genes, post-harvest application of antimicrobials, and biosecurity measures at poultry facilities are practical interventions that could reduce the public health burden of salmonellosis and antibiotic resistance associated with poultry products. With the escalating consumption of poultry products around the globe, the fate, prevalence, and transmission of Salmonella in agricultural settings and various poultry-processing facilities are major public health challenges demanding integrated control measures throughout the food chain. Implementation of practical preventive measures discussed in the current study could appreciably reduce the public health burden of foodborne salmonellosis associated with poultry products.

Nigella sativa-chitosan nanoparticles: Novel intestinal mucosal immunomodulator controls and protects against Salmonella enterica serovar Enteritidis infection in broilers

BACKGROUND

Salmonella Enteritidis (SE) propagates in chickens' gastrointestinal surfaces and is transmitted to humans, causing food poisoning. Oral supplementation with natural nanoparticles can overcome the harsh gastrointestinal conditions facing oral vaccines and requires no antibiotic administration to protect against microbial infection. This study was designed to study Nigella sativa-chitosan nanoparticles (CNP-NS) prophylactic immunomodulatory efficacy against SE infection in broiler chicks. The CNP-NS was prepared and characterized, and its in vivo immunomodulatory activities against an avian virulent-MDR SE-induced challenge in chicks were investigated.

RESULT

To verify the immune-protective activities of the CNP-NS, colony forming units (CFU) in the liver and fecal droppings; intestinal histopathological alterations and immune cell recruitment; MUC-2, TLR-4, cecal cytokines, and specific IgA gene expression levels were assessed. On the 7th and 12th days after the SE challenge, the CNP-NS supplemented chicks showed complete clearance of SE CFU in livers and fecal droppings, as well as an improvement in food conversion rate compared to non-supplemented CNP-NS that revealed the presence of the challenge SE CFU on the same days. A prominent influx of antigen presenting cells and lymphoid aggregates into the intestinal wall, spleen, and liver was detected with improvements in the intestinal villi morphometry of the CNP-NS-supplemented chicks. The changes of INF-γ, IL-1β, and IL-4 cecal cytokines, as well as TLR-4, MUC-2, and IgA mRNA expression levels, confirm CNP-NS immunomodulatory activities and provide a mechanism(s) for its protective actions against the induced SE challenge of the tested chickens.

CONCLUSION

These findings suggest promising useful insights into CNP-NS supplementation as a safe food additive for poultry meat consumers' and a protective immunomodulator of the chickens' mucosal immune systems. It could be recommended for epidemiological purposes to reduce the risk of SE food poisoning and transmission to humans.

Allosteric probe-triggered isothermal amplification to activate CRISPR/Cas12a for sensitive electrochemiluminescence detection of Salmonella

We report an electrochemiluminescence (ECL) sensor for Salmonella detection based on allosteric probe as a bio-recognition element and CRISPR/Cas12a as a signal amplification strategy. In the presence of Salmonella, the structure switching occurs on allosteric probes, resulting in their hybridization with primers to trigger isothermal amplification. Salmonella is then released to initiate the next reaction cycle accompanying by generating a large amount of dsDNA, which are subsequently recognized by CRISPR-gRNA for activating the trans-cleavage activity of Cas12a. Furthermore, the activated Cas12a can indiscriminately cut the ssDNA which is bound to the electrode, enabling the release of the ECL emitter porphyrinic Zr metal - organic framework (MOF, PCN-224) and exhibiting a decreased ECL signal accordingly. The linear range is 50 CFU·mL^-1-5 × 10⁶ CFU·mL^-1 and the detection limit is calculated to be 37 CFU·mL^-1. This method sensitively detects Salmonella in different types of real samples, indicating it is a promising strategy for Salmonella detection.

A bacteriophage cocktail delivered in feed significantly reduced Salmonella colonization in challenged broiler chickens

AbstractNontyphoidal Salmonella spp. are a leading cause of human gastrointestinal infections and are commonly transmitted via consumption of contaminated meat. To limit the spread of Salmonella and other food-borne pathogens in the food chain, bacteriophage (phage) therapy could be used during rearing or pre-harvest stages of animal production. This study was conducted to determine if a phage cocktail delivered in-feed is capable of reducing Salmonella colonization in experimentally-challenged chickens and to determine the optimal phage dose. 672 broilers were divided into six treatment groups T1 (no phage diet and unchallenged); T2 (phage diet 10⁶ PFU/day); T3 (challenged group); T4 (phage diet 10⁵ PFU/day and challenged); T5 (phage diet 10⁶ PFU/day and challenged); and T6 (phage diet 10⁷ PFU/day and challenged). The liquid phage cocktail was added to mash diet with ad libitum access available throughout the study. By day 42 (concluding day of the study) no Salmonella was detected in faecal samples collected from group T4. Salmonella was isolated from a small number of pens in groups T5 (3/16) and T6 (2/16) at ∼4 × 10² CFU/g. In comparison Salmonella was isolated from 7/16 pens in T3 at ∼3 × 10⁴ CFU/g. Phage treatment at all three doses had a positive impact on growth performance in challenged birds with increased weight gains in comparison to challenged birds with no phage diet. We showed delivering phages via feed was effective at reducing Salmonella colonization in chickens and our study highlights phages offer a promising tool to target bacterial infections in poultry.

A label-free fiber ring laser biosensor for ultrahigh sensitivity detection of Salmonella Typhimurium

The rapid detection of low concentrations of Salmonella Typhimurium (S. Typhimurium) is an essential preventive measure for food safety and prevention of foodborne illness. The study presented in this paper addresses this critical issue by proposing a single mode-tapered seven core-single mode (STSS) fiber ring laser (FRL) biosensor for S. Typhimurium detection. The experimental results show that the specific detection time of S. Typhimurium is less than 20 min and the wavelength shift can achieve -0.906 nm for an S. Typhimurium solution (10 cells/mL). Furthermore, at a lower concentration of 1 cell/mL applied to the biosensor, a result of -0.183 nm is observed in 9% of samples (1/11), which indicates that the proposed FRL biosensor has the ability to detect 1 cell/mL of S. Typhimurium. In addition, the detection results in chicken and pickled pork samples present an average deviation of -27% and -23%, respectively, from the measured results in phosphate buffered saline. Taken together, these results show the proposed FRL biosensor may have potential applications in the fields of food safety monitoring, medical diagnostics, etc.

Rapid geographical source attribution of Salmonella enterica serovar Enteritidis genomes using hierarchical machine learning

Salmonella enterica serovar Enteritidis is one of the most frequent causes of Salmonellosis globally and is commonly transmitted from animals to humans by the consumption of contaminated foodstuffs. In the UK and many other countries in the Global North, a significant proportion of cases are caused by the consumption of imported food products or contracted during foreign travel, therefore, making the rapid identification of the geographical source of new infections a requirement for robust public health outbreak investigations. Herein, we detail the development and application of a hierarchical machine learning model to rapidly identify and trace the geographical source of S. Enteritidis infections from whole genome sequencing data. 2313 S. Enteritidis genomes, collected by the UKHSA between 2014-2019, were used to train a 'local classifier per node' hierarchical classifier to attribute isolates to four continents, 11 sub-regions, and 38 countries (53 classes). The highest classification accuracy was achieved at the continental level followed by the sub-regional and country levels (macro F1: 0.954, 0.718, 0.661, respectively). A number of countries commonly visited by UK travelers were predicted with high accuracy (hF1: >0.9). Longitudinal analysis and validation with publicly accessible international samples indicated that predictions were robust to prospective external datasets. The hierarchical machine learning framework provided granular geographical source prediction directly from sequencing reads in <4 min per sample, facilitating rapid outbreak resolution and real-time genomic epidemiology. The results suggest additional application to a broader range of pathogens and other geographically structured problems, such as antimicrobial resistance prediction, is warranted.

Facial Preparation of Cyclometalated Iridium (III) Nanowires as Highly Efficient Electrochemiluminescence Luminophores for Biosensing

In this study, highly efficient ECL luminophores composed of iridium complex-based nanowires (Ir-NCDs) were synthesized via covalently linking bis(2-phenylpyridine)-(4-carboxypropyl-2,2'-bipyridyl) iridium(III) hexafluorophosphate with nitrogen-doped carbon quantum dots (NCDs). The ECL intensity of the nanowires showed a five-fold increase in ECL intensity compared with the iridium complex monomer under the same experimental conditions. A label-free ECL biosensing platform based on Ir-NCDs was established for Salmonella enteritidis (SE) detection. The ECL signal was quenched linearly in the range of 10²-10⁸ CFU/mL for SE with a detection limit of 10² CFU/mL. Moreover, the relative standard deviations (RSD) of the stability within and between batches were 0.98% and 3.9%, respectively. In addition, the proposed sensor showed high sensitivity, selectivity and stability towards SE in sheep feces samples with satisfactory results. In summary, the excellent ECL efficiency of Ir-NCDs demonstrates the prospects for Ir(III) complexes in bioanalytical applications.

Ecology and epidemiology of Salmonella spp. isolated from the environment and the roles played by wild animals in their maintenance

Salmonella is a ubiquitous organism of public health importance that causes diarrhea and other systemic disease syndromes. The ecology and epidemiology of the organism in addition to the roles played by wild animals are important in understanding its disease. Relevant published peer-reviewed literature was obtained after imputing the study's keywords into the Google search engine. The publications were thereafter saved for the study. The study revealed the ecology of Salmonella is directly related to its epidemiology. These were found to be either positively or negatively influenced by the living and non-living parts of the environment. Free-ranging and captive wild animals can serve as asymptomatic carriers of Salmonella, therefore, help to maintain the cycle of the disease since wildlife serves as reservoir hosts to over 70% of emerging zoonotic diseases. Cockroaches transmit Salmonella through their feces, and body parts and when ingested by birds and animals. The statistically significant over 83% of Salmonella isolation in lizards suggests the reptile could be a source of Salmonella distribution. Snakes, foxes, badgers, rodents, and raccoons have been reported to have Salmonella as a natural component of their gut with the ability to shed the organism often. The high occurrence (>45%) of diverse Salmonella serovars coupled with the fact that some of these animals were handled, kept as pets and consumed by man portends these animals as potential sources of transmission of the organism and the disease. The etiology and epidemiology of Salmonella are overtly affected by several environmental factors which also determine their survival and maintenance. The roles played by wild animals in the relationship, transmission, growth or interaction within and between Salmonella spp., the occurrence, prevalence, and distribution of the organism help maintain the organism in the environment. An understanding of the roles played by the different parts of the environment and wild animals in the ecology and epidemiology of Salmonella can help make informed decisions on the prevention and control of the diseases it causes. This review aimed to investigate the relationship between ecology, epidemiology, and environment, including the roles played by wild animals in the maintenance of the organism and its disease.

Genomic Epidemiology and Multilevel Genome Typing of Australian Salmonella enterica Serovar Enteritidis

Salmonella enterica serovar Enteritidis is one of the leading causes of salmonellosis in Australia. In this study, a total of 568 S. Enteritidis isolates from two Australian states across two consecutive years were analyzed and compared to international strains, using the S. Enteritidis multilevel genome typing (MGT) database, which contained 40,390 publicly available genomes from 99 countries. The Australian S. Enteritidis isolates were divided into three phylogenetic clades (A, B, and C). Clades A and C represented 16.4% and 3.5% of the total isolates, respectively, and were of local origin. Clade B accounted for 80.1% of the isolates which belonged to seven previously defined lineages but was dominated by the global epidemic lineage. At the MGT5 level, three out of five top sequence types (STs) in Australia were also top STs in Asia, suggesting that a fair proportion of Australian S. Enteritidis cases may be epidemiologically linked with Asian strains. In 2018, a large egg-associated local outbreak was caused by a recently defined clade B lineage prevalent in Europe and was closely related, but not directly linked, to three European isolates. Additionally, over half (54.8%) of predicted multidrug resistance (MDR) isolates belonged to 10 MDR-associated MGT-STs, which were also frequent in Asian S. Enteritidis . Overall, this study investigated the genomic epidemiology of S. Enteritidis in Australia, including the first large local outbreak, using MGT. The open MGT platform enables a standardized and sharable nomenclature that can be effectively applied to public health for unified surveillance of S. Enteritidis nationally and globally. IMPORTANCE Salmonella enterica serovar Enteritidis is a leading cause of foodborne infections. We previously developed a genomic typing database (MGTdb) for S. Enteritidis to facilitate global surveillance of this pathogen. In this study, we examined the genomic features of Australian S. Enteritidis using the MGTdb and found that Australian S. Enteritidis is mainly epidemiologically linked with Asian strains (especially strains carrying antimicrobial resistance genes), followed by European strains. The first large-scale egg-associated local outbreak in Australia was caused by a recently defined lineage prevalent in Europe, and three European isolates in the MGTdb were closely related but not directly linked to this outbreak. In summary, the S. Enteritidis MGTdb open platform is shown to be a potentially powerful tool for national and global public health surveillance of this pathogen.

Seminal Bacterioflora of Two Rooster Lines: Characterization, Antibiotic Resistance Patterns and Possible Impact on Semen Quality

This study aimed to characterize the bacterial profiles and their association with selected semen quality traits among two chicken breeds. Thirty Lohmann Brown and thirty ROSS 308 roosters were selected for semen quality estimation, including sperm motility, membrane and acrosome integrity, mitochondrial activity, and DNA fragmentation. The oxidative profile of the semen, including the production of reactive oxygen species (ROS), antioxidant capacity, protein, and lipid oxidation, were assessed as well. Moreover, the levels of pro-inflammatory cytokines, including tumor necrosis factor alpha (TNF-α), interleukins 1 and 6 (IL-1, IL-6) and C-reactive protein, as well as the concentrations of selected antibacterial proteins (cathelicidin, β-defensin and lysozyme) in the seminal plasma were evaluated with the enzyme-linked immunosorbent assay. The prevailing bacterial genera identified by the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry were Citrobacter spp., Enterococcus spp., Escherichia spp. and Staphylococcus spp. While the bacterial load was significantly higher in the ROSS 308 line (p < 0.05), a higher number of potentially uropathogenic bacteria was found in the Lohmann Brown roosters. Antimicrobial susceptibility tests revealed a substantial resistance of randomly selected bacterial strains, particularly to ampicillin, tetracycline, chloramphenicol, and tobramycin. Furthermore, Lohmann Brown ejaculates containing an increased proportion of Escherichia coli presented with significantly (p < 0.05) elevated levels of TNF-α and IL-6, as well as ROS overproduction and lipid peroxidation. Inversely, significantly (p < 0.05) higher levels of β-defensin and lysozyme were found in the semen collected from the ROSS 308 roosters, which was characterized by a higher quality in comparison to the Lohmann Brown roosters. In conclusion, we emphasize the criticality of bacteriospermia in the poultry industry and highlight the need to include a more complex microbiological screening of semen samples designated for artificial insemination.