Characterisation of antibiotic resistance in host-adapted Salmonella enterica

Phenotypic and genetic characterization of antimicrobial resistance in Salmonella enterica serovar Choleraesuis isolates from humans and animals in Spain from 2006 to 2021

OBJECTIVES

While an increase in the levels of MDR in Salmonella enterica sevorar Choleraesuis has been reported in Europe, little is known about the situation in Spain. Therefore, we first aimed to assess the phenotypic resistance profile and to determine the presence of genetic determinants of resistance of S. Choleraesuis isolates collected in animal and human. Our second objective was to identify and characterize clusters of highly related isolates.

METHODS

We analysed 50 human and 45 animal isolates retrieved from 2006 to 2021 using the disc diffusion method and performed WGS followed by analyses of genetic determinants and phylogenetic analysis.

RESULTS

All isolates were of ST145 and corresponded to the variant Kunzendorf. Swine isolates harboured a significantly higher number of antimicrobial resistance genes than human isolates, and often carried plasmid replicons of the IncHI2/IncHI2A type (42% of all animal isolates). In addition, we identified several MDR S. Choleraesuis strains circulating in humans and swine between 2006 and 2021. The phylogenetic analyses identified four clades associated with specific patterns of resistance genes and plasmid replicons. The clades also included isolates that differed in terms of year and region of isolation as well as host of origin.

CONCLUSIONS

This One Health approach highlights that reducing human MDR S. Choleraesuis infections may require the adoption of strategies that not only seek to prevent cases in humans but also to characterize and reduce the infection burden in swine.

Salmonellosis: An Overview of Epidemiology, Pathogenesis, and Innovative Approaches to Mitigate the Antimicrobial Resistant Infections

Salmonella is a major foodborne pathogen and a leading cause of gastroenteritis in humans and animals. Salmonella is highly pathogenic and encompasses more than 2600 characterized serovars. The transmission of Salmonella to humans occurs through the farm-to-fork continuum and is commonly linked to the consumption of animal-derived food products. Among these sources, poultry and poultry products are primary contributors, followed by beef, pork, fish, and non-animal-derived food such as fruits and vegetables. While antibiotics constitute the primary treatment for salmonellosis, the emergence of antibiotic resistance and the rise of multidrug-resistant (MDR) Salmonella strains have highlighted the urgency of developing antibiotic alternatives. Effective infection management necessitates a comprehensive understanding of the pathogen's epidemiology and transmission dynamics. Therefore, this comprehensive review focuses on the epidemiology, sources of infection, risk factors, transmission dynamics, and the host range of Salmonella serotypes. This review also investigates the disease characteristics observed in both humans and animals, antibiotic resistance, pathogenesis, and potential strategies for treatment and control of salmonellosis, emphasizing the most recent antibiotic-alternative approaches for infection control.

Selection and characterization of bacteriophages specific to Salmonella Choleraesuis in swine

Background and Aim

Salmonella Choleraesuis is the most common serotype that causes salmonellosis in swine. Recently, the use of bacteriophages as a potential biocontrol strategy has increased. Therefore, this study aimed to isolate and characterize bacteriophages specific to S. Choleraesuis associated with swine infection and to evaluate the efficacy of individual phages and a phage cocktail against S. Choleraesuis strains in simulated intestinal fluid (SIF).

Materials and Methods

Three strains of S. Choleraesuis isolated from pig intestines served as host strains for phage isolation. The other 10 Salmonella serovars were also used for the phage host range test. The antibiotic susceptibility of the bacterial strains was investigated. Water samples from natural sources and drain liquid from slaughterhouses were collected for phage isolation. The isolated phages were characterized by determining the efficiency of plating against all Salmonella strains and the stability at a temperature range (4°C-65°C) and at low pH (2.5-4.0) in simulated gastric fluids (SGFs). Furthermore, morphology and genomic restriction analyses were performed for phage classification phages. Finally, S. Choleraesuis reduction in the SIF by the selected individual phages and a phage cocktail was investigated.

Results

The antibiotic susceptibility results revealed that most Salmonella strains were sensitive to all tested drugs. Salmonella Choleraesuis KPS615 was multidrug-resistant, showing resistance to three antibiotics. Nine phages were isolated. Most of them could infect four Salmonella strains. Phages vB_SCh-RP5i3B and vB_SCh-RP61i4 showed high efficiency in infecting S. Choleraesuis and Salmonella Rissen. The phages were stable for 1 h at 4°C-45°C. However, their viability decreased when the temperature increased to 65°C. In addition, most phages remained viable at a low pH (pH 2.5-4.0) for 2 h in SGF. The efficiency of phage treatment against S. Choleraesuis in SIF showed that individual phages and a phage cocktail with three phages effectively reduced S. Choleraesuis in SIF. However, the phage cocktails were more effective than the individual phages.

Conclusion

These results suggest that the newly isolated phages could be promising biocontrol agents against S. Choleraesuis infection in pigs and could be orally administered. However, further in vivo studies should be conducted.

Genotypic and Phenotypic Characterization of Incompatibility Group FIB Positive Salmonella enterica Serovar Typhimurium Isolates from Food Animal Sources

Salmonella enterica is one of the most common bacterial foodborne pathogens in the United States, causing illnesses that range from self-limiting gastroenteritis to more severe, life threatening invasive disease. Many Salmonella strains contain plasmids that carry virulence, antimicrobial resistance, and/or transfer genes which allow them to adapt to diverse environments, and these can include incompatibility group (Inc) FIB plasmids. This study was undertaken to evaluate the genomic and phenotypic characteristics of IncFIB-positive Salmonella enterica serovar Typhimurium isolates from food animal sources, to identify their plasmid content, assess antimicrobial resistance and virulence properties, and compare their genotypic isolates with more recently isolated S. Typhimurium isolates from food animal sources. Methods: We identified 71 S. Typhimurium isolates that carried IncFIB plasmids. These isolates were subjected to whole genome sequencing and evaluated for bacteriocin production, antimicrobial susceptibility, the ability to transfer resistance plasmids, and a subset was evaluated for their ability to invade and persist in intestinal human epithelial cells. Results: Approximately 30% of isolates (n = 21) displayed bacteriocin inhibition of Escherichia coli strain J53. Bioinformatic analyses using PlasmidFinder software confirmed that all isolates contained IncFIB plasmids along with multiple other plasmid replicon types. Comparative analyses showed that all strains carried multiple antimicrobial resistance genes and virulence factors including iron acquisition genes, such as iucABCD (75%), iutA (94%), sitABCD (76%) and sitAB (100%). In 17 cases (71%), IncFIB plasmids, along with other plasmid replicon types, were able to conjugally transfer antimicrobial resistance and virulence genes to the susceptible recipient strain. For ten strains, persistence cell counts (27%) were noted to be significantly higher than invasion bacterial cell counts. When the genome sequences of the study isolates collected from 1998–2003 were compared to those published from subsequent years (2005–2018), overlapping genotypes were found, indicating the perseverance of IncFIB positive strains in food animal populations. This study confirms that IncFIB plasmids can play a potential role in disseminating antimicrobial resistance and virulence genes amongst bacteria from several food animal species.

Microbial synthesis of zinc oxide nanoparticles and their potential application as an antimicrobial agent and a feed supplement in animal industry: a review

In recent years, zinc oxide nanoparticles (ZnO NPs) have gained tremendous attention attributed to their unique properties. Notably, evidence has shown that zinc is an important nutrient in living organisms. As such, both prokaryotes and eukaryotes including bacteria, fungi and yeast are exploited for the synthesis of ZnO NPs by using microbial cells or enzyme, protein and other biomolecules compounds in either an intracellular or extracellular route. ZnO NPs exhibit antimicrobial properties, however, the properties of nanoparticles (NPs) are depended upon on their size and shape, which make them specific for various applications. Nevertheless, the desired size and shape of NPs can be obtained through the optimization process of microbes mediated synthesis by manipulating their reaction conditions. It should be noted that ZnO NPs are synthesized by various chemical and physical methods. Nonetheless, these methods are expensive and not environmentally friendly. On that account, the microbes mediated synthesis of ZnO NPs have rapidly evolved recently where the microbes are cleaner, eco-friendly, non-toxic and biocompatible as the alternatives to chemical and physical practices. Moreover, zinc in the form of NPs is more effective than their bulk counterparts and thus, they have been explored for many potential applications including in animals industry. Notably, with the advent of multi-drug resistant strains, ZnO NPs have emerged as the potential antimicrobial agents. This is mainly due to their superior properties in combating a broad spectrum of pathogens. Moreover, zinc is known as an essential trace element for most of the biological function in the animal's body. As such, the applications of ZnO NPs have been reported to significantly enhance the health and production of the farm animals. Thus, this paper reviews the biological synthesis of ZnO NPs by the microbes, the mechanisms of the biological synthesis, parameters for the optimization process and their potential application as an antimicrobial agent and feed supplement in the animal industry as well as their toxicological hazards on animals.

Antibiotic-Resistant Salmonella in the Food Supply and the Potential Role of Antibiotic Alternatives for Control

Salmonella enterica is one of the most ubiquitous enteropathogenic bacterial species on earth, and comprises more than 2500 serovars. Widely known for causing non-typhoidal foodborne infections (95%), and enteric (typhoid) fever in humans, Salmonella colonizes almost all warm- and cold-blooded animals, in addition to its extra-animal environmental strongholds. The last few decades have witnessed the emergence of highly virulent and antibiotic-resistant Salmonella, causing greater morbidity and mortality in humans. The emergence of several Salmonella serotypes resistant to multiple antibiotics in food animals underscores a significant food safety hazard. In this review, we discuss the various antibiotic-resistant Salmonella serotypes in food animals and the food supply, factors that contributed to their emergence, their antibiotic resistance mechanisms, the public health implications of their spread through the food supply, and the potential antibiotic alternatives for controlling them.

Transmissible Plasmid Containing Salmonella enterica Heidelberg Isolates Modulate Cytokine Production During Early Stage of Interaction with Intestinal Epithelial Cells

The variation in cytokine production during bacterial invasion of human intestinal epithelial cells (IECs) is a contributing factor for progression of the infection. A few Salmonella enterica Heidelberg strains isolated from poultry products harbor transmissible plasmids (TPs), including those that encode a type-IV secretion system. Earlier, we showed that these TPs are responsible for increased virulence during infection. This study examines the potential role of these TPs in cytokine production in IECs. This study showed that S. Heidelberg strains containing TPs (we refer as virulent strains) caused decreased interleukin (IL)-10 production in IECs after 1 h infection. The virulent strains induced a high level of tumor necrosis factor-α production under identical conditions. The virulent strains of S. Heidelberg also altered the production of IL-2, IL-17, and granulocyte macrophage colony-stimulating factor compared to an avirulent strain. As a part of infection, bacteria cross the epithelial barrier and encounter intestinal macrophages. Hence, we examined the cytotoxic mechanism of strains of S. Heidelberg in macrophages. Scanning electron microscopy showed cell necrosis occurs during the early stage of infection. In conclusion, virulent S. Heidelberg strains were able to modify the host cytokine profile during the early stages of infection and also caused necrosis in macrophages.

Salmonella pathogenicity and host adaptation in chicken-associated serovars

Enteric pathogens such as Salmonella enterica cause significant morbidity and mortality. S. enterica serovars are a diverse group of pathogens that have evolved to survive in a wide range of environments and across multiple hosts. S. enterica serovars such as S. Typhi, S. Dublin, and S. Gallinarum have a restricted host range, in which they are typically associated with one or a few host species, while S. Enteritidis and S. Typhimurium have broad host ranges. This review examines how S. enterica has evolved through adaptation to different host environments, especially as related to the chicken host, and continues to be an important human pathogen. Several factors impact host range, and these include the acquisition of genes via horizontal gene transfer with plasmids, transposons, and phages, which can potentially expand host range, and the loss of genes or their function, which would reduce the range of hosts that the organism can infect. S. Gallinarum, with a limited host range, has a large number of pseudogenes in its genome compared to broader-host-range serovars. S. enterica serovars such as S. Kentucky and S. Heidelberg also often have plasmids that may help them colonize poultry more efficiently. The ability to colonize different hosts also involves interactions with the host's immune system and commensal organisms that are present. Thus, the factors that impact the ability of Salmonella to colonize a particular host species, such as chickens, are complex and multifactorial, involving the host, the pathogen, and extrinsic pressures. It is the interplay of these factors which leads to the differences in host ranges that we observe today.

Longitudinal study of distributions of similar antimicrobial-resistant Salmonella serovars in pigs and their environment in two distinct swine production systems

The aim of this longitudinal study was to determine and compare the prevalences and genotypic profiles of antimicrobial-resistant (AR) Salmonella isolates from pigs reared in antimicrobial-free (ABF) and conventional production systems at farm, at slaughter, and in their environment. We collected 2,889 pig fecal and 2,122 environmental (feed, water, soil, lagoon, truck, and floor swabs) samples from 10 conventional and eight ABF longitudinal cohorts at different stages of production (farrowing, nursery, finishing) and slaughter (postevisceration, postchill, and mesenteric lymph nodes [MLN]). In addition, we collected 1,363 carcass swabs and 205 lairage and truck samples at slaughter. A total of 1,090 Salmonella isolates were recovered from the samples; these were isolated with a significantly higher prevalence in conventionally reared pigs (4.0%; n = 66) and their environment (11.7%; n = 156) than in ABF pigs (0.2%; n = 2) and their environment (0.6%; n = 5) (P < 0.001). Salmonella was isolated from all stages at slaughter, including the postchill step, in the two production systems. Salmonella prevalence was significantly higher in MLN extracted from conventional carcasses than those extracted from ABF carcasses (P < 0.001). We identified a total of 24 different serotypes, with Salmonella enterica serovar Typhimurium, Salmonella enterica serovar Anatum, Salmonella enterica serovar Infantis, and Salmonella enterica serovar Derby being predominant. The highest frequencies of antimicrobial resistance (AR) were exhibited to tetracycline (71%), sulfisoxazole (42%), and streptomycin (17%). Multidrug resistance (resistance to ≥ 3 antimicrobials; MDR) was detected in 27% (n = 254) of the Salmonella isolates from the conventional system. Our study reports a low prevalence of Salmonella in both production systems in pigs on farms, while a higher prevalence was detected among the carcasses at slaughter. The dynamics of Salmonella prevalence in pigs and carcasses were reciprocated in the farm and slaughter environment, clearly indicating an exchange of this pathogen between the pigs and their surroundings. Furthermore, the phenotypic and genotypic fingerprint profile results underscore the potential role played by environmental factors in dissemination of AR Salmonella to pigs.

Population dynamics of Salmonella enterica serotypes in commercial egg and poultry production

Fresh and processed poultry have been frequently implicated in cases of human salmonellosis. Furthermore, increased consumption of meat and poultry has increased the potential for exposure to Salmonella enterica. While advances have been made in reducing the prevalence and frequency of Salmonella contamination in processed poultry, there is mounting pressure on commercial growers to prevent and/or eliminate these human pathogens in preharvest production facilities. Several factors contribute to Salmonella colonization in commercial poultry, including the serovar and the infectious dose. In the early 1900s, Salmonella enterica serovars Pullorum and Gallinarum caused widespread diseases in poultry, but vaccination and other voluntary programs helped eradicate pullorum disease and fowl typhoid from commercial flocks. However, the niche created by the eradication of these serovars was likely filled by S. Enteritidis, which proliferated in the bird populations. While this pathogen remains a significant problem in commercial egg and poultry production, its prevalence among poultry has been declining since the 1990s. Coinciding with the decrease of S. Enteritidis, S. Heidelberg and S. Kentucky have emerged as the predominant serovars in commercial broilers. In this review, we have highlighted bacterial genetic and host-related factors that may contribute to such shifts in Salmonella populations in commercial poultry and intervention strategies that could limit their colonization.

Salmonella antibiotic-mutant strains reduce fecal shedding and organ invasion in broiler chicks

We investigated the exposure to antibiotics in the production of antibiotic-mutant strains of Salmonella. Ten isolates of poultry origin were assayed for antibiotic susceptibilities. One strain of Salmonella Enteritidis, one of Salmonella Heidelberg, and one of Salmonella Typhimurium were selected to induce antimicrobial resistance. Each strain was exposed to high concentrations of streptomycin, rifampicin, and nalidixic acid, respectively. Parent and antibiotic-mutant strains were assayed for antibiotic susceptibilities using a commercial microdilution test and the disk susceptibility test. The strains were assessed for virulence genes and evaluated for fecal shedding, cecal colonization, organ invasion, and mean Salmonella counts after inoculation in 1-day-old chicks. The study revealed that exposure to high concentrations of streptomycin produced the antibiotic-mutant strain SE/LABOR/USP/08 and the exposure to rifampicin produced the antibiotic-mutant SH/LABOR/USP/08. These strains showed significantly reduced fecal shedding (P≤0.05) and organ invasion, persisting less than the parental strains and showing no clinical signs in inoculated chicks. High concentrations of nalidixic acid produced the antibiotic-mutant strain ST/LABOR/USP/08, which did not show any differences compared with the parent strain. Likewise, SE/LABOR/USP/08 did not show the expression of plasmid-encoded fimbriae (pefA) and plasmid virulence protein (spvC), suggesting that after exposure to streptomycin, the parent isolate lost the original gene expression, reducing fecal shedding and organ invasion in inoculated chicks.

The establishment of Enterobacteriaceae and Salmonella London in a new dairy farm environment

Salmonella spp. are important zoonotic pathogens in humans and animals. A longitudinal study was conducted at the Iowa State University's campus (at the Dairy/Animal Science Education and Discovery Facility) to observe change in Enterobacteriaceae (specifically Salmonella) before and after the placement of dairy livestock. To our knowledge, this is the first study that evaluated environmental changes of Gram-negative organisms in a new dairy farm environment. Environmental samples were taken using drag swabs and immediately processed in the laboratory using phenotypic methods (replica plating, the BBL Crystal Identification System for enteric/nonfermenter organisms™, and plating on specialized media/broths). Genotypic methods were also used (BAX PCR™ and pulsed-field gel electrophoresis). Organisms identified as Salmonella were sent to the National Veterinary Services Laboratory (Ames, IA) for confirmatory serotyping. Resistance to antibiotics (ampicillin, nalidixic acid, and tetracycline) was determined by replica plating of Enterobacteriaceae and Salmonella isolates using the guidelines of the National Antimicrobial Resistance Monitoring System and Clinical and Laboratory Standards Institute. The microflora of Enterobacteriaceae changed as cattle were introduced and as time progressed. Additionally, multidrug-resistant isolates began to appear immediately after cattle were introduced (multidrug-resistant isolates were rare prior to introduction of livestock). Variables such as temperature and humidity did not affect the proliferation of bacterial organisms. Seventeen Salmonella isolates were identified as Salmonella London and three isolates as Salmonella Montevideo. Based on pulsed-field gel electrophoresis-generated dendrograms, it is likely that 17 Salmonella London isolates and 3 Salmonella Montevideo isolates are clonal.

Comparison of Salmonella serovar isolation and antimicrobial resistance patterns from porcine samples between 2003 and 2008

Food-borne Salmonella infections can produce symptoms from mild gastroenteritis to severe systemic disease and death, representing an important public health issue in U.S. livestock and livestock products, which have been implicated as frequent sources of Salmonella contamination. Concerns have been raised about the spread of antibiotic resistance in Salmonella strains, particularly those that originate from food animal sources, as a result of prophylactic and therapeutic antimicrobial use in these species. Longitudinal comparisons of Salmonella serovars isolated from porcine tissues submitted to the Iowa State University Veterinary Diagnostic Laboratory in 2003 and 2008 were conducted to evaluate changes in serovar dynamics and antimicrobial resistance. Incidence of recovered group C Salmonella enterica serovar Choleraesuis var. Kunzendorf decreased between 2003 and 2008, while recovery of group B strains Salmonella Typhimurium var. 5-(formerly, Copenhagen), Salmonella Agona, Salmonella Derby, Salmonella Heidelberg, and Salmonella Typhimurium increased. Significant changes in resistance interpretation were seen in Salmonella Derby with regard to spectinomycin and sulfadimethoxine; in Salmonella Heidelberg with regard to florfenicol, spectinomycin, and sulfadimethoxine; and in Salmonella Choleraesuis var. Kunzendorf, Salmonella Typhimurium, Salmonella Typhimurium var. 5-, and Salmonella Agona with regard to spectinomycin. Only 2 of 293 isolates in 2003 and 5 of 395 isolates in 2008 were resistant to enrofloxacin. Utilizing antibiotics approved for use in food animals to evaluate antimicrobial resistance provides more specific information on the selection pressure exerted on Salmonella populations through the use of these drugs.

Evaluation of pulsed-field gel electrophoresis profiles for identification of Salmonella serotypes

Pulsed-field gel electrophoresis (PFGE) is a standard typing method for isolates from Salmonella outbreaks and epidemiological investigations. Eight hundred sixty-six Salmonella enterica isolates from eight serotypes, including Heidelberg (n = 323), Javiana (n = 200), Typhimurium (n = 163), Newport (n = 93), Enteritidis (n = 45), Dublin (n = 25), Pullorum (n = 9), and Choleraesuis (n = 8), were subjected to PFGE, and their profiles were analyzed by random forest classification and compared to conventional hierarchical cluster analysis to determine potential predictive relationships between PFGE banding patterns and particular serotypes. Cluster analysis displayed only the underlying similarities and relationships of the isolates from the eight serotypes. However, for serotype prediction of a nonserotyped Salmonella isolate from its PFGE pattern, random forest classification provided better accuracy than conventional cluster analysis. Discriminatory DNA band class markers were identified for distinguishing Salmonella serotype Heidelberg, Javiana, Typhimurium, and Newport isolates.