Salmonella in Foods: A Reemerging Problem

An allosteric inhibitor of the PhoQ histidine kinase with therapeutic potential against Salmonella infection

BACKGROUND

The upsurge of antimicrobial resistance demands innovative strategies to fight bacterial infections. With traditional antibiotics becoming less effective, anti-virulence agents or pathoblockers, arise as an alternative approach that seeks to disarm pathogens without affecting their viability, thereby reducing selective pressure for the emergence of resistance mechanisms.

OBJECTIVES

To elucidate the mechanism of action of compound N'-(thiophen-2-ylmethylene)benzohydrazide (A16B1), a potent synthetic hydrazone inhibitor against the Salmonella PhoP/PhoQ system, essential for virulence.

MATERIALS AND METHODS

The measurement of the activity of PhoP/PhoQ-dependent and -independent reporter genes was used to evaluate the specificity of A16B1 to the PhoP regulon. Autokinase activity assays with either the native or truncated versions of PhoQ were used to dissect the A16B1 mechanism of action. The effect of A16B1 on Salmonella intramacrophage replication was assessed using the gentamicin protection assay. The checkerboard assay approach was used to analyse potentiation effects of colistin with the hydrazone. The Galleria mellonella infection model was chosen to evaluate A16B1 as an in vivo therapy against Salmonella.

RESULTS

A16B1 repressed the Salmonella PhoP/PhoQ system activity, specifically targeting PhoQ within the second transmembrane region. A16B1 demonstrates synergy with the antimicrobial peptide colistin, reduces the intramacrophage proliferation of Salmonella without being cytotoxic and enhances the survival of G. mellonella larvae systemically infected with Salmonella.

CONCLUSIONS

A16B1 selectively inhibits the activity of the Salmonella PhoP/PhoQ system through a novel inhibitory mechanism, representing a promising synthetic hydrazone compound with the potential to function as a Salmonella pathoblocker. This offers innovative prospects for combating Salmonella infections while mitigating the risk of antimicrobial resistance emergence.

Enhancing colistin efficacy against Salmonella infections with a quinazoline-based dual therapeutic strategy

Colistin remains one of the last-resort therapies for combating infections caused by multidrug-resistant (MDR) Enterobacterales, despite its adverse nephro- and neuro-toxic effects. This study elucidates the mechanism of action of a non-antibiotic 4-anilinoquinazoline-based compound that synergistically enhances the effectiveness of colistin against Salmonella enterica. The quinazoline sensitizes Salmonella by deactivating intrinsic, mutational, and transferable resistance mechanisms that enable Salmonella to counteract the antibiotic impact colistin, together with an induced disruption to the electrochemical balance of the bacterial membrane. The attenuation of colistin resistance via the combined treatment approach also proves efficacious against E. coli, Klebsiella, and Acinetobacter strains. The dual therapy reduces the mortality of Galleria mellonella larvae undergoing a systemic Salmonella infection when compared to individual drug treatments. Overall, our findings unveil the potential of the quinazoline-colistin combined therapy as an innovative strategy against MDR bacteria.

Drug Resistance, Characterization and Phylogenetic Discrepancy of Salmonella enterica Isolates from Distinct Sources

Salmonella enterica is one of the foodborne pathogens that can infect humans, spreading from one person to another by contaminated food and water. To identify the pathogenic S. enterica from the contaminated food product, culture-based and molecular identifications, drug resistance profiling, virulence and genetic traits of the strains have been used. Herein, different animal products was subjected to screen for S. enterica prevalence, pathogenic characterization and compared with clinical Salmonella isolates (human). A total of 173 isolates from animal products and 51 isolates from clinical samples were collected. S. Typhi, S. Agona and S. Ohio were predominant serovars in blood, stool and different animal products. Both, clinical [37% (n = 19/51)] and animal product-associated isolates [21% (n = 37/173)] expressed their highest resistance to nalidixic acid. Thirty-one percentage of (n = 16/51) clinical isolates and 12% (n = 21/173) animal food-associated isolates were resistant to multiple classes of antibiotics. Class 1 integrons encoded by S. Typhi, S. Infantis and S. Emek were screened for sequence analysis, the result revealed that the cassettes encoded-aminoglycoside acetyltransferase and dihydrofolate reductase enzymes. Salmonella pathogenicity island-1 encoded-hilA gene was detected most frequently in all the isolates. PFGE profile revealed the genetic traits of the isolates which were closely linked with antibiotic-resistant properties and virulent characteristics. Only S. Enteritidis, collected from different samples had clonal similarities. In summary, drug-resistant pathogenic Salmonella prevalence was observed in the animal product that could be an important alarm to consumers with the risk of enteric fever and it causes the potential risk to public health.

Phages on filaments: A genetic screen elucidates the complex interactions between Salmonella enterica flagellin and bacteriophage Chi

The bacterial flagellum is a rotary motor organelle and important virulence factor that propels motile pathogenic bacteria, such as Salmonella enterica, through their surroundings. Bacteriophages, or phages, are viruses that solely infect bacteria. As such, phages have myriad applications in the healthcare field, including phage therapy against antibiotic-resistant bacterial pathogens. Bacteriophage χ (Chi) is a flagellum-dependent (flagellotropic) bacteriophage, which begins its infection cycle by attaching its long tail fiber to the S. enterica flagellar filament as its primary receptor. The interactions between phage and flagellum are poorly understood, as are the reasons that χ only kills certain Salmonella serotypes while others entirely evade phage infection. In this study, we used molecular cloning, targeted mutagenesis, heterologous flagellin expression, and phage-host interaction assays to determine which domains within the flagellar filament protein flagellin mediate this complex interaction. We identified the antigenic N- and C-terminal D2 domains as essential for phage χ binding, with the hypervariable central D3 domain playing a less crucial role. Here, we report that the primary structure of the Salmonella flagellin D2 domains is the major determinant of χ adhesion. The phage susceptibility of a strain is directly tied to these domains. We additionally uncovered important information about flagellar function. The central and most variable domain, D3, is not required for motility in S. Typhimurium 14028s, as it can be deleted or its sequence composition can be significantly altered with minimal impacts on motility. Further knowledge about the complex interactions between flagellotropic phage χ and its primary bacterial receptor may allow genetic engineering of its host range for use as targeted antimicrobial therapy against motile pathogens of the χ-host genera Salmonella, Escherichia, or Serratia.

An overview of the use of bacteriophages in the poultry industry: Successes, challenges, and possibilities for overcoming breakdowns

The primary contaminants in poultry are Salmonella enterica, Campylobacter jejuni, Escherichia coli, and Staphylococcus aureus. Their pathogenicity together with the widespread of these bacteria, contributes to many economic losses and poses a threat to public health. With the increasing prevalence of bacterial pathogens being resistant to most conventional antibiotics, scientists have rekindled interest in using bacteriophages as antimicrobial agents. Bacteriophage treatments have also been investigated as an alternative to antibiotics in the poultry industry. Bacteriophages' high specificity may allow them only to target a specific bacterial pathogen in the infected animal. However, a tailor-made sophisticated cocktail of different bacteriophages could broaden their antibacterial activity in typical situations with multiple clinical strains infections. Bacteriophages may not only be used in terms of reducing bacterial contamination in animals but also, under industrial conditions, they can be used as safe disinfectants to reduce contamination on food-contact surfaces or poultry carcasses. Nevertheless, bacteriophage therapies have not been developed sufficiently for widespread use. Problems with resistance, safety, specificity, and long-term stability must be addressed in particular. This review highlights the benefits, challenges, and current limitations of bacteriophage applications in the poultry industry.

Concerning Increase in Antimicrobial Resistance Patterns of Pathogenic Strains of Salmonella Isolated in Poultry Meat Products

Salmonella is considered to be one of the major foodborne pathogens associated with the consumption of contaminated poultry meat products. To the best of our knowledge this is the first extended research performed on a number of Salmonella strains isolated during 2011-2021 from poultry meat products in Romania. The aim of this study was to characterize the prevalence of pathogenic Salmonella serovars, antimicrobial susceptibility, and antimicrobial resistance genes in 112 Salmonella isolates recovered from raw poultry meat products. The results showed that Salmonella enterica serovars Enteritidis and Typhimurium were the common serotypes (56%; 25%). Overall, the majority of the isolates were resistant to at least three tested antimicrobials. High resistance was observed for tetracycline (84%), nalidixic acid (78%), and ampicillin (78%) in pathogenic Salmonella isolated during the period 2016-2021. All the pathogenic Salmonella isolated during 2016-2021 tested positive to at least one resistance gene encoding for tetracycline resistance, with the tetA gene being the most prevalent (62%). In addition, 64% (24/37) of the Salmonella isolates carried at least one of the genes (blaCMY-2, blaSHV1, blaTEM1) that code for β-Lactams resistance. The findings in this study showed a high prevalence of multi-drug resistant (MDR) Salmonella serovars in poultry meat products and a concerning increase of resistance patterns. The continuous occurrence of more resistant strains implies that effective measures should be strictly applied in this particular food chain in order to prevent their spread and guarantee microbial safety.

Can Nanobubble Ozone Liposomes Be A New Agent In The Fight Against Foodborne Infections?

Backrounds: In our study, a nanoparticle liposome molecule with patent application number TR2021004032 was used, and the Minimum Inhibitor Concentration (MIC) was found to be 1562 ppm. According to the ASTM F 1980 standard, it has been determined that the nanoparticle liposome solution kept at 37 days and 55 oC in return for one-year stability preserves its effectiveness. Our study aimed to show that the newly developed solution maintains its effectiveness for a long time.

METHODS

In this study, a nanobubble ozone liposome solution containing 2% ZnCl2 was used. The aging tests were conducted according to the ASTM F 1980 [1] standards. The minimum inhibitory concentration (MIC) level of the nanobubble ozone liposome solution with 2% ZnCl2 was determined as 1.562 ppm for strains of Staphylococcus aureus (ATCC 25923) and Escherichia coli (ATCC 25922) by the CLSI M07 A9 [2] standard test method. To assess the time-dependent antibacterial effect of the nanobubble liposome solution with 2% ZnCl2, the solution's efficiency at a concentration of 2000 ppm and for different time intervals was tested on strains of Salmonella enterica subsp. enterica (ATCC® 14028™) and Listeria monocytogenes (ATCC® 7644™).

RESULTS

The results showed that the antibacterial activity of the strains of S. enterica subsp. enterica started at the end of the 10th minute and the solution was effective after 30 minutes. For strains of L. monocytogenes, it was observed that the activity started at the end of the 2nd minute and the product was effective after the 10th minute. According to the ASTM F 1980 standards, it was found that the nanobubble ozone liposome solution retained its effectiveness in one-year stability tests.

CONCLUSION

As a result, the nanoparticle liposome solution, a new product, does not lose its stability and effectiveness for a long time, contrary to what is known. Although the half-life of gaseous ozone is as short as 20 minutes, the stability in the nanoparticle liposome solution has been determined as at least one year. Since nanoparticle liposome solution is a natural and slow-release product, nanobubble ozone liposome solution with 2% ZnCl2 may be used as a newly developed agent against contaminations in food processing facilities caused by biofilm-forming microorganisms through the use in disinfections of surfaces that are in direct contact with food products.

Review: Production factors affecting the quality of chicken table eggs and egg products in Europe

The hen's egg (Gallus gallus) is an animal product of great agronomic interest, with a world production of 70.9 million tonnes in 2018. China accounted for 35% of world production, followed by North America (12% of world production), the European Union (7.0 million tonnes, 10% of world production) and India (5.0 million tonnes, 7% of world production). In France, 16-17 billion eggs are produced annually (14.5 billion for table eggs) and more than 1 200 billion worldwide. In 2019, egg production increased by 3.3% compared to 2018, mainly due to the increase in Asian production, which has risen by 42% since 2000. Chicken eggs are widely used either as a low-cost, high nutritional quality food cooked by the consumer (more than 100 billion eggs consumed in Europe), or incorporated as an ingredient in many food products. The various production methods have changed considerably over the last 15 years with the consideration of animal welfare and changes in European regulations. In Europe, fewer and fewer eggs are produced in confinement and there has been a strong growth in the number of systems giving access to an outdoor run. In this review, we describe the different ways in which eggs are produced and processed into egg products to meet the growing demand for ready-to-use food products. We analyse the effect of this evolution of hen-rearing systems on the set of characteristics of eggs and egg products that determine their quality. We describe the risks and benefits associated with these new production methods and their influence or lack of influence on commercial, nutritional, microbial and chemical contamination risk characteristics, as well as the evolution of the image for the consumer. The latter covers the ethical, cultural and environmental dimensions associated with the way the egg is produced.

Detection and Characterization of Salmonella enterica Serotypes by Simple PCR Technologies

Polymerase chain reaction (PCR) is a molecular-based technology that has revolutionized diagnostics and characterization of pathogens, and thus affecting how we understand disease landscape. This technology has been found amenable to application on various strategies for management and control of infectious diseases. The main advantage with PCR technologies, when applied optimally, is the high sensitivity and short-turn-around time for results, thus rendering the strategy attractive to researchers in infectious diseases and public health. In this chapter, we describe PCR approaches that are innovative and easy to deploy in a laboratory with medium range infrastructure investment.

Impact of the Resistance Responses to Stress Conditions Encountered in Food and Food Processing Environments on the Virulence and Growth Fitness of Non-Typhoidal Salmonellae

The success of Salmonella as a foodborne pathogen can probably be attributed to two major features: its remarkable genetic diversity and its extraordinary ability to adapt. Salmonella cells can survive in harsh environments, successfully compete for nutrients, and cause disease once inside the host. Furthermore, they are capable of rapidly reprogramming their metabolism, evolving in a short time from a stress-resistance mode to a growth or virulent mode, or even to express stress resistance and virulence factors at the same time if needed, thanks to a complex and fine-tuned regulatory network. It is nevertheless generally acknowledged that the development of stress resistance usually has a fitness cost for bacterial cells and that induction of stress resistance responses to certain agents can trigger changes in Salmonella virulence. In this review, we summarize and discuss current knowledge concerning the effects that the development of resistance responses to stress conditions encountered in food and food processing environments (including acid, osmotic and oxidative stress, starvation, modified atmospheres, detergents and disinfectants, chilling, heat, and non-thermal technologies) exerts on different aspects of the physiology of non-typhoidal Salmonellae, with special emphasis on virulence and growth fitness.

The European Union One Health 2019 Zoonoses Report

This report of the EFSA and the European Centre for Disease Prevention and Control presents the results of zoonoses monitoring activities carried out in 2019 in 36 European countries (28 Member States (MS) and eight non-MS). The first and second most reported zoonoses in humans were campylobacteriosis and salmonellosis, respectively. The EU trend for confirmed human cases of these two diseases was stable (flat) during 2015-2019. The proportion of human salmonellosis cases due to Salmonella Enteritidis acquired in the EU was similar to that in 2017-2018. Of the 26 MS reporting on Salmonella control programmes in poultry, 18 met the reduction targets, whereas eight failed to meet at least one. The EU prevalence of Salmonella target serovar-positive flocks has been stable since 2015 for breeding hens, laying hens, broilers and fattening turkeys, with fluctuations for breeding turkey flocks. Salmonella results from competent authorities for pig carcases and for poultry tested through national control programmes were more frequently positive than those from food business operators. Shiga toxin-producing Escherichia coli (STEC) infection was the third most reported zoonosis in humans and increased from 2015 to 2019. Yersiniosis was the fourth most reported zoonosis in humans in 2019 with a stable trend in 2015-2019. The EU trend of confirmed listeriosis cases remained stable in 2015-2019 after a long period of increase. Listeria rarely exceeded the EU food safety limit tested in ready-to-eat food. In total, 5,175 food-borne outbreaks were reported. Salmonella remained the most detected agent but the number of outbreaks due to S. Enteritidis decreased. Norovirus in fish and fishery products was the agent/food pair causing the highest number of strong-evidence outbreaks. The report provides further updates on bovine tuberculosis, Brucella, Trichinella, Echinococcus, Toxoplasma, rabies, West Nile virus, Coxiella burnetii (Q fever) and tularaemia.

Influence of water activity on the heat resistance of Salmonella enterica in selected low-moisture foods

Low-moisture foods (LMF with water activity, a_w < 0.85) including pet foods and black pepper powder have consistently been associated with foodborne disease caused by Salmonella enterica. Increased heat resistance and prolonged survival at low-moisture conditions, however, remain major challenges to achieve effective inactivation of Salmonella in low-moisture foods. At low water activity (a_w) conditions, heat resistance of Salmonella is greatly enhanced when compared to high a_w conditions. This study aimed to quantify the effect of a_w on the heat resistance of Salmonella enterica in pet food pellets and black pepper powder. Pet food pellets were inoculated with two strains of heat resistant S. enterica and black pepper powder was inoculated with a 5-strain cocktail of Salmonella. Both inoculated food samples were equilibrated at 0.33, 0.54, and 0.75 a_w in controlled humidity chambers. Inoculated pet food pellets and black pepper powder in closed aluminum cells were heat treated at specific temperatures for selected times. The results showed that the Weibull model fitted well the inactivation data. At a specific temperature, the rate of inactivation increased with the increase in the a_w from 0.33 to 0.75, and the 3-log reduction times decreased for Salmonella in both food samples with the increase in a_w. Water adsorption isotherms of pet food pellets and black pepper powder at initial and treatment temperatures were developed to understand the change in a_w during heat treatments. The change in a_w during heat treatment was dependent on the type of food matrix, which possibly influenced the thermal inactivation of Salmonella in pet food pellets and black pepper powder. The quantitative analysis of heat reduction of Salmonella with respect to a_w aids in selection of the appropriate initial a_w to develop effective heat treatment protocols for adequate reduction of Salmonella in pet foods and black pepper powder.

Analysis of the Relationship of Microbial Contamination with Temperature and Cleaning Frequency and Method of Domestic Refrigerators in Japan

ABSTRACT

Hygiene management of domestic refrigerators is an important aspect of food poisoning prevention. The aim of the present study was to confirm the relationship between microbial contamination and hygiene management by measuring microbial levels and investigating temperature and cleaning frequency and method of domestic refrigerators in Japan. We analyzed three internal sections (the egg compartment, bottom shelf, and vegetable drawer) of 100 domestic refrigerators in Japan. Salmonella, Listeria monocytogenes, and Yersinia enterocolitica were not found in any of the refrigerators, but coliforms and Escherichia coli were detected in more than one household, and Staphylococcus aureus was the most frequently isolated pathogen. The prevalences of these microorganisms had similar tendencies in all three sections sampled and were highest in the vegetable drawer. The temperature distribution in the refrigerators was also investigated, and a temperature >6.1°C (improper temperature) was found in 46.2% of the areas surveyed. Only 17% of the respondents cleaned their refrigerators monthly or more often, and this frequency was lower than that reported in other countries. Fifty percent of the respondents used only water to clean the refrigerator, 10% used only an alcohol or disinfecting wipe, and 8% used only a dry cloth. Although no significant correlations were found between microbial contamination and temperatures in refrigerators, correlations were found between microbial contamination and refrigerator cleaning frequency and/or method. To our knowledge, this is the first detailed survey concerning relationships between microbial contamination and hygiene management in domestic refrigerators in Japan. The data obtained can be used to promote food poisoning management in Japanese households.

HIGHLIGHTS

The Role of the Salmonella spvB IncF Plasmid and Its Resident Entry Exclusion Gene traS on Plasmid Exclusion

Salmonella enterica cause significant illnesses worldwide. There has been a marked increase in resistance to fluoroquinolones and β-lactams/cephalosporins, antibiotics commonly used to treat salmonellosis. However, S. enterica serovars vary in their resistance to these and other antibiotics. The systemic virulence of some Salmonella serovars is due to a low copy number, IncF plasmid (65-100 kb) that contains the ADP-ribosylating toxin, SpvB. This virulence plasmid is present in only nine Salmonella serovars. It is possible that the spvB-virulence plasmid excludes other plasmids and may explain why antibiotic resistance is slow to develop in certain Salmonella serovars such as S. Enteritidis. The distribution of plasmid entry exclusion genes traS/traT and traY/excA are variable in Salmonella IncF and IncI plasmids, respectively and may account for differences in emergent antimicrobial resistance for some Salmonella serovars. The goal of this study is to determine the contribution of the Salmonella spvB-virulence plasmid in F-plasmid exclusion. From conjugation experiments, S. Typhimurium exhibited lower conjugation frequency with incFI and incFII plasmids when the spvB-virulence plasmid is present. Furthermore, introduction of cloned incFI traS into a "plasmidless" S. Typhimurium LT2 strain and Escherichia coli DH5α excluded incFI plasmid. However, deletion of the virulence plasmid traS did not affect plasmid exclusion significantly compared to a spvB control deletion. In addition, differences in F plasmid conjugation in natural Salmonella isolates did not correlate with IncF or SpvB-virulence plasmid genotype. There appear to be other plasmid or chromosomal genes at play in plasmid exclusion that may be responsible for the slow development of antibiotic resistance in certain serovars.

Effect of in feed administration of different butyrate formulations on Salmonella Enteritidis colonization and cecal microbiota in broilers

Butyrate has been used extensively as a feed additive to improve gut health and to decrease Salmonella colonization in poultry. Salmonella mainly colonizes the ceca so butyrate concentrations should be increased in this gut segment. Discrepancies on the effects of butyrate on Salmonella colonization, described in the scientific literature, could thus be due to butyrate release location effects. In this study, newly developed butyrate formulations were evaluated for their effect on cecal butyrate concentrations and on colonization by Salmonella Enteritidis. In a first trial, broilers were randomly allocated to 7 dietary treatment groups with formulations based on different approaches to modify the butyrate release profile: release from wax matrices based on diffusion/erosion; micropellets supposedly release butyrate around pH 7 in the colon; tributyrin is based on the hydrolysis of esters in the small intestine. Fat-protected butyrate was included as a reference, because of its known effect on reduction of Salmonella colonization. Four days after infection, the number of cfu Salmonella per g cecal content and spleen were determined. Butyrate formulations in a wax matrix significantly reduced the Salmonella colonization in cecal content. In a second trial, wax and fat-protected butyrate treatments were replicated and results from the first trial were confirmed. Compared to the control group a higher proportion of butyrate concentration was observed in ceca for those groups with reduced Salmonella colonization. This was associated with a beneficial shift in the cecal microbiota. In conclusion, formulations that increase cecal butyrate concentrations are superior in protecting against Salmonella Enteritidis colonization.

Proteomic analysis of the antimicrobial effects of sublethal concentrations of thymol on Salmonella enterica serovar Typhimurium

Salmonella enterica serovar Typhimurium is an important foodborne pathogen that causes serious and extensive food contamination as well as disease and death worldwide. Considering the increasing severity of antibiotic resistance, antibiotic alternatives are urgently needed. As a natural biocide and a component of some essential oils from herbs, thymol is capable of killing various bacteria through a potentially unique mechanism, although the targets of thymol have not been completely elucidated. In this study, the variation in the whole proteome of Salmonella after thymol stress was evaluated using the SWATH multiplex technique. The strain Salmonella Typhimurium CVCC541 was treated with a sublethal concentration (75 μg/mL) of thymol, which rapidly increased the permeability of bacterial membranes at the tested concentration. Thymol destroyed the integrity of the bacterial membrane, as observed by transmission electron microscopy. The proteomes of the treated and untreated cells were characterized after an 8-h treatment. The proteomic analysis of thymol-treated cells indicated that 144 proteins exhibited upregulation or downregulation compared with the control cells, particularly those involved in cellular structure and metabolism. The results of this study showed that thymol may play an antimicrobial role in altering the membrane permeability, virulence change, and antioxidant response of Salmonella Typhimurium. The results of the present study provide an improved understanding of the proteomic response of Salmonella Typhimurium to thymol stress, including the identification of promising targets for the future exploration of innovative approaches to control Salmonella Typhimurium.

Performance and Accuracy of Four Open-Source Tools for In Silico Serotyping of Salmonella spp. Based on Whole-Genome Short-Read Sequencing Data

We compared the performance of four open-source in silico Salmonella typing tools (SeqSero, SeqSero2, Salmonella In Silico Typing Resource [SISTR], and Metric Oriented Sequence Typer [MOST]) to assess their potential for replacing laboratory serological testing with serovar predictions from whole-genome sequencing data. We conducted a retrospective analysis of 1,624 Salmonella isolates of 72 serovars submitted to the German National Salmonella Reference Laboratory between 1999 and 2019. All isolates are derived from animal and foodstuff origins. We conducted Illumina short-read sequencing and compared the in silico serovar prediction results with the results of routine laboratory serotyping. We found the best-performing in silico serovar prediction tool to be SISTR, with 94% correctly typed isolates, followed by SeqSero2 (87%), SeqSero (81%), and MOST (79%). Furthermore, we found that mapping-based tools like SeqSero and SeqSero2 (allele mode) were more reliable for the prediction of monophasic variants, while sequence type and cluster-based methods like MOST and SISTR (core-genome multilocus sequence type [cgMLST]), showed greater resilience when confronted with GC-biased sequencing data. We showed that the choice of library preparation kit could substantially affect O antigen detection, due to the low GC content of the wzx and wzy genes. Although the accuracy of computational serovar predictions is still not quite on par with traditional serotyping by Salmonella reference laboratories, the command-line tools investigated in this study perform a rapid, efficient, inexpensive, and reproducible analysis, which can be integrated into in-house characterization pipelines. Based on our results, we find SISTR most suitable for automated, routine serotyping for public health surveillance of Salmonella IMPORTANCE Salmonella spp. are important foodborne pathogens. To reduce the number of infected patients, it is essential to understand which subtypes of the bacteria cause disease outbreaks. Traditionally, characterization of Salmonella requires serological testing, a laboratory method by which Salmonella isolates can be classified into over 2,600 distinct subtypes, called serovars. Due to recent advances in whole-genome sequencing, many tools have been developed to replace traditional testing methods with computational analysis of genome sequences. It is crucial to validate that these tools, many already in use for routine surveillance, deliver accurate and reliable serovar information. In this study, we set out to compare which of the currently available open-source command-line tools is most suitable to replace serological testing. A thorough evaluation of the differing computational approaches is highly important to ensure the backward compatibility of serotyping data and to maintain comparability between laboratories.

Pattern of increased antimicrobial resistance of Salmonella isolates in the Eastern Province of KSA

OBJECTIVES

The antimicrobial resistance of Salmonella species is increasing worldwide. This study was conducted to determine the pattern of antimicrobial susceptibility of Salmonella species in a tertiary hospital from 2011 to 2018.

METHODS

In this retrospective study, the medical records of all patients with Salmonella infections were reviewed. The clinical, demographic, and microbiological data of the selected patients were analysed.

RESULTS

A total of 752 patients were included. The resistance of Salmonella species to antimicrobial drugs increased from 24.6% in 2011 to 37.8% in 2018 (p = 0.002). By 2018 all Salmonella isolates were completely resistant to cefalotin, cefuroxime, and cefoxitin, while we found some susceptibility to other cephalosporins and ciprofloxacin. The most commonly isolated Salmonella serogroups were groups D (36.5%), C (23.5%), and B (11.7%).

CONCLUSIONS

The incidence of resistance of Salmonella to antibiotics is on the rise. The results of this study highlight the need for an active monitoring system of antibiotic usage in humans and domestic animals.

Salmonella control in poultry flocks and its public health impact

An increase in confirmed human salmonellosis cases in the EU after 2014 triggered investigation of contributory factors and control options in poultry production. Reconsideration of the five current target serovars for breeding hens showed that there is justification for retaining Salmonella Enteritidis, Salmonella Typhimurium (including monophasic variants) and Salmonella Infantis, while Salmonella Virchow and Salmonella Hadar could be replaced by Salmonella Kentucky and either Salmonella Heidelberg, Salmonella Thompson or a variable serovar in national prevalence targets. However, a target that incorporates all serovars is expected to be more effective as the most relevant serovars in breeding flocks vary between Member State (MS) and over time. Achievement of a 1% target for the current target serovars in laying hen flocks is estimated to be reduced by 254,400 CrI95[98,540; 602,700] compared to the situation in 2016. This translates to a reduction of 53.4% CrI95[39.1; 65.7] considering the layer-associated human salmonellosis true cases and 6.2% considering the overall human salmonellosis true cases in the 23 MSs included in attribution modelling. A review of risk factors for Salmonella in laying hens revealed that overall evidence points to a lower occurrence in non-cage compared to cage systems. A conclusion on the effect of outdoor access or impact of the shift from conventional to enriched cages could not be reached. A similar review for broiler chickens concluded that the evidence that outdoor access affects the occurrence of Salmonella is inconclusive. There is conclusive evidence that an increased stocking density, larger farms and stress result in increased occurrence, persistence and spread of Salmonella in laying hen flocks. Based on scientific evidence, an impact of Salmonella control programmes, apart from general hygiene procedures, on the prevalence of Campylobacter in broiler flocks at the holding and on broiler meat at the end of the slaughter process is not expected.