Evaluation of virulence and antimicrobial resistance in Salmonella enterica serovar Enteritidis isolates from humans and chicken- and egg-associated sources

Salmonella spp. in Domestic Ruminants, Evaluation of Antimicrobial Resistance Based on the One Health Approach-A Systematic Review and Meta-Analysis

Salmonella spp. pose a global threat as a leading cause of foodborne illnesses, particularly prevalent in the European Union (EU), where it remains the second cause of foodborne outbreaks. The emergence of antimicrobial resistance (AMR) in Salmonella spp. has become a critical concern, complicating treatment strategies and escalating the risk of severe infections. The study focuses on large and small ruminants, identifying a prevalence of Salmonella spp. in slaughterhouses and revealing varied AMR rates across antimicrobial families throughout a meta-analysis. Also, comparison with AMR in human medicine was carried out by a systematic review. The results of the present meta-analysis displayed a prevalence of Salmonella spp. in large and small ruminants at slaughterhouses of 8.01% (8.31%, cattle; 7.04%, goats; 6.12%, sheep). According to the AMR of Salmonella spp., 20, 14, and 13 out of 62 antimicrobials studied were classified as low (<5%), high (>5% but <10%), and very high (>10%), respectively. Salmonella spp. did not display AMR against aztreonam, mezlocillin, ertapenem, meropenem, cefoxitin, ceftazidime, levofloxacin, tilmicosin, linezolid, fosfomycin, furazolidone, quinupristin, trimethoprim and spectinomycin. In contrast, a prevalence of 100% of AMR has been described against ofloxacin, lincomycin, and cloxacillin. In the context of the main antibiotics used in the treatment of human salmonellosis, azithromycin was shown to have the highest resistance among Salmonella spp. isolates from humans. Regarding cephalosporins, which are also used for the treatment of salmonellosis in humans, the prevalence of Salmonella spp. resistance to this class of antibiotics was similar in both human and animal samples. Concerning quinolones, despite a heightened resistance profile in Salmonella spp. isolates from ruminant samples, there appears to be no discernible compromise to the efficacy of salmonellosis treatment in humans since lower prevalences of AMR in Salmonella spp. isolated from human specimens were observed. Although the resistance of Salmonella spp. indicates some degree of concern, most antibiotics are not used in veterinary medicine. Thus, the contribution of cattle, sheep and goats to the rise of antibiotic resistance of Salmonella spp. and its potential impact on public health appears to be relatively insignificant, due to their low prevalence in carcasses and organs. Nevertheless, the observed low prevalence of Salmonella spp. in ruminants at slaughterhouse and the correspondingly low AMR rates of Salmonella spp. to key antibiotics employed in human medicine do not indicate that ruminant livestock poses a substantial public health risk concerning the transmission of AMR. Thus, the results observed in both the meta-analysis and systematic review suggests that AMR is not solely attributed to veterinary antibiotic use but is also influenced by factors such as animal health management (i.e., biosecurity measures, prophylactic schemes) and human medicine.

High diversity of Salmonella spp. from children with diarrhea, food, and environmental sources in Kilimanjaro - Tanzania: one health approach

Salmonella is one of the most frequent causes of diarrhea globally. This study used a One Health approach to identify Salmonella species in children admitted with diarrhea and tested samples from the cases' household environment to investigate their genetic similarity using whole genome sequencing. Surveillance of hospitalized diarrhea cases among children under 5 years was conducted in rural and urban Moshi Districts in the Kilimanjaro Region of Tanzania from July 2020 through November 2022. Household visits were conducted for every child case whose parent/caregiver provided consent. Stool samples, water, domestic animal feces, meat, and milk were collected and tested for Salmonella. Isolates were sequenced on the Illumina NextSeq platform. Multilocus Sequence Typing and phylogenetic analyses were performed to map the genetic relatedness of the isolates. Salmonella was isolated from 72 (6.0%) of 1,191 samples. The prevalence of Salmonella in children with diarrhea, domestic animal feces, food, and water was 2.6% (n = 8/306), 4.6% (n = 8/174), 4.2% (n = 16/382), and 17.3% (n = 39/225), respectively. Four (1.3%) of the 306 enrolled children had a Salmonella positive sample taken from their household. The common sequence types (STs) were ST1208, ST309, ST166, and ST473. Salmonella Newport was shared by a case and a raw milk sample taken from the same household. The study revealed a high diversity of Salmonella spp., however, we detected a Salmonella clone of ST1208 isolated at least from all types of samples. These findings contribute to understanding the epidemiology of Salmonella in the region and provide insight into potential control of foodborne diseases through a One Health approach.

Biofilm formation, antimicrobial resistance genes, and genetic diversity of Salmonella enterica subspecies enterica serotype Enteritidis isolated from food and animal sources in Iran

OBJECTIVES

Salmonella enterica serovar Entritidis is an important pathogen in foodborne diseases and causes gastroenteritis. Several studies have investigated the genetic diversity of the strains of this bacterium. However, our knowledge of the discriminatory power of the molecular methods is limited.

METHODS

In total, 34 strains of S. enteritidis were isolated from food related to animals. Antibiotic resistance of the strains, antibiotic resistance genes, and biofilm formation capacity of the strains were evaluated. For the genetic analysis of the strains, PFGE was performed using AvrII restriction enzyme.

RESULTS

Among the tested antibiotics, cefuroxime, nalidixic acid, and ciprofloxacin showed the highest resistance rates (79.4%, 47%, and 44.2%, respectively). Only three antibiotic-resistance genes were identified in these strains (blaTEM: 67.6%, tetA: 9%, and sul2: 3%). In total, 91% of the strains were biofilm producers. Clustering of strains using AvrII for 26 samples with the same XbaI PFGE profile showed that these strains were in one clone and had high homogeneity.

CONCLUSIONS

In conclusion, it is better to use a combination of several typing methods for typing strains that are genetically very close so that the results are reliable.

Multiplex polymerase spiral reaction for simultaneous detection of Salmonella typhimurium and Staphylococcus aureus

Salmonella typhimurium (S. typhimurium) and Staphylococcus aureus (S. aureus) are common food-borne pahogens that cause food poisoning in humans. In this study, we developed a method for the simultaneous determination of S. typhimurium and S. aureus based on multiplex polymerase spiral reaction (m-PSR) and melting curve analysis. Two pairs of primers were designed specifically to target the conserved invA gene of S. typhimurium and nuc gene of S. aureus, and the nucleic acid amplification reaction was achieved under isothermal conditions in the same reaction tube for 40 min at 61 °C, melting curve analysis of the amplification product was carried out. The distinct mean melting temperature allowed simultaneous differentiation of the two target bacteria in the m-PSR assay. The limit of detection of S. typhimurium and S. aureus that could be detected simultaneously was 4.1 × 10^-4 ng genomic DNA and 2 × 10¹ CFU/mL pure bacterial culture. Based on this method, analysis of artificially contaminated samples showed excellent sensitivity and specificity consistent with those of pure bacterial cultures. This method is rapid, simultaneous and promises to be a useful tool for the detection of food-borne pathogens in the food industry.

Microbial Genetics and Clonal Dissemination of Salmonella enterica Serotype Javiana Isolated from Human Populations in Arkansas, USA

Salmonella is estimated to cause over a million infections and ~400 deaths annually in the U.S. Salmonella enterica serotype Javiana strains (n = 409) that predominantly originated from the State of Arkansas over a six-year period (2003 to 2008) were studied. This period coincided with a rapid rise in the incidence of S. Javiana infections in the U.S. Children under the age of 10 displayed the highest prevalence of S. Javiana infections, regardless of sex or year of detection. Antimicrobial susceptibility to 15 different antimicrobials was assessed and 92% (n = 375) were resistant to at least one of the antimicrobials. Approximately 89% of the isolates were resistant to sulfisoxazole alone and 3% (n = 11) were resistant to different antimicrobials, including gentamicin, ciprofloxacin or ceftiofur. The pulsed-field gel electrophoresis (PFGE) analyses assessed the genotypic diversity and distribution of S. Javiana strains using XbaI restriction. Nine major clusters were identified and isolates from each group were digested with the restriction enzyme AvrII. Isolates with identical profiles of XbaI and AvrII were found to be disseminated in human populations. These distinct “types” of S. Javiana were persistent in human populations for multiple years. A subset of isolates (n = 19) with unique resistance phenotypes underwent plasmid and incompatibility (Inc) type analyses and the isolates resistant to more than one antimicrobial harbored multiple plasmids (<3 to 165 kb). Furthermore, these strains possessed 14 virulence genes, including pagC, cdtB, and iroN. The whole genome sequences (WGS) of 18 isolates that mostly originated from Arkansas from 2003 to 2011 were compared with isolates collected from different areas in the U.S. in 1999, indicating the perseverance of S. Javiana in disseminating antimicrobial resistance and virulence genes.

Expression of Genes Located on the Incompatibility Group FIB Plasmids at Transcription and Protein Levels in Iron-Modified Growth Conditions

Salmonella enterica strains often harbor plasmids representing several incompatibility groups (Inc) including IncFIB, which have been previously associated with carrying antimicrobial resistance and virulence associated genes. To better understand the distribution of virulence genes on IncFIB plasmids, we analyzed 37 complete whole genome and plasmid sequences of different S. enterica isolates from multiple serovars. Many of the sequences analyzed carried multiple virulence-associated genes, including those associated with iron acquisition systems; thus we aimed to determine how iron-rich (IR) and various iron-depleted (ID) conditions affected the transcription of iron acquisition and virulence genes including sitA, iutA, iucA, and enolase at different time intervals. sitA, iutA, and enolase from S. enterica that were grown in Luria-Bertani broth (LB) ID (LBID) conditions were substantially upregulated when compared to LBIR conditions. For both S. enterica strains that were grown at various LBID conditions, addition of 200 μM bipyridyl in the growth medium yielded the highest transcription for all four genes, followed by the 100 μM concentration. An antibody using a peptide targeting aerobactin receptor gene iutA encoded by IncFIB was generated and used to examine the protein expression in the wild-type, recipient, and transconjugant strain in LB, LBID, and LBIR growth conditions using Western blot analyses. A 70 KDa protein band was detected in the wild-type and transconjugant that carried the IncFIB plasmid, while this band was not detected in the recipient strain that lacked this plasmid.

Antimicrobial resistance patterns, virulence gene profiles, and genetic diversity of Salmonella enterica serotype Enteritidis isolated from patients with gastroenteritis in various Iranian cities

Objectives

This study aimed to evaluate antibiotic resistance profiles and presence of virulence genes among Salmonella enterica serovar Enteritidis (S. Enteritidis) isolated from patients with gastroenteritis in various regions of Iran. Moreover, genetic relatedness among the strains was assessed by pulsed-field gel electrophoresis (PFGE).

Materials and Methods

From April through September 2017, 59 Salmonella strains were isolated from 2116 stool samples. Of these strains, 27 S. Enteritidis were recovered. These strains were subjected to disk diffusion tests, polymerase chain reaction (PCR) for detection of virulence genes (invA, hilA, pefA, rck, stn, ssrA, ssaR, sefA, spvC, sipA, sipC, sopB, sopE, and sopE2), and PFGE.

Results

High prevalence of resistance towards cefuroxime (n = 20, 74.1%) and ciprofloxacin (n = 13, 48.2%) were demonstrated. All tested strains possessed invA, hilA, sefA, sipA, sopB, and sopE. The least prevalent virulence gene was rck (n = 6; 22.2%). Based on combinations of virulence genes, 12 virulotypes were observed. The most common virulotype was VP2 (n = 12; 44.4%), harboring all of the virulence genes except for rck. PFGE typing showed only two distinct fingerprints among tested strains. Each fingerprint had completely different virulotypes. Notably, VP4 (harboring all genes except for rck and spvC) was only presented in pulsotype A, while VP2 was confined to pulsotype B.

Conclusion

S. Enteritidis strains were derived from a limited number of clones, suggesting that it is highly homogenous. Future works should consider combinations of other genotyping methods together with larger sample sizes from more diverse sources.

Antimicrobial Resistance Profiling of Biofilm Forming Non Typhoidal Salmonella enterica Isolates from Poultry and Its Associated Food Products from Pakistan

Salmonellosis caused by non-typhoidal Salmonella enterica from poultry products is a major public health concern worldwide. This study aimed at estimating the pathogenicity and antimicrobial resistance in S. enterica isolates obtained from poultry birds and their food products from different areas of Pakistan. In total, 95/370 (25.67%) samples from poultry droppings, organs, eggs, and meat were positive for Salmonella. The isolates were further identified through multiplex PCR (mPCR) as Salmonella Typhimurium 14 (14.7%), Salmonella Enteritidis 12 (12.6%), and other Salmonella spp. 69 (72.6%). The phenotypic virulence properties of 95 Salmonella isolates exhibited swimming and/or swarming motility 95 (100%), DNA degrading activity 93 (97.8%), hemolytic activity 92 (96.8%), lipase activity 87 (91.6%), and protease activity 86 (90.5%). The sopE virulence gene known for conferring zoonotic potential was detected in S. Typhimurium (92.8%), S. Enteritidis (100%), and other Salmonella spp. (69.5%). The isolates were further tested against 23 antibiotics (from 10 different antimicrobial groups) and were found resistant against fifteen to twenty-one antibiotics. All isolates showed multiple drug resistance and were found to exhibit a high multiple antibiotic-resistant (MAR) index of 0.62 to 0.91. The strong biofilm formation at 37 °C reflected their potential adherence to intestinal surfaces. There was a significant correlation between antimicrobial resistance and the biofilm formation potential of isolates. The resistance determinant genes found among the isolated strains were blaTEM-1 (59.3%), blaOxA-1 (18%), blaPSE-1 (9.5%), blaCMY-2 (43%), and ampC (8.3%). The detection of zoonotic potential MDR Salmonella in poultry and its associated food products carrying cephalosporin and quinolone resistance genes presents a major threat to the poultry industry and public health.

Prevalence, virulence factor and antimicrobial resistance analysis of Salmonella Enteritidis from poultry and egg samples in Iran

Background

Salmonella enterica serovar Enteritidis (S. Enteritidis) is one of the most common serovars, associated with human salmonellosis. The food-borne outbreak of this bacterium is mainly related to the consumption of contaminated poultry meat and poultry products, including eggs. Therefore, rapid and accurate detection, besides investigation of virulence characteristics and antimicrobial resistance profiles of S. Enteritidis in poultry and poultry egg samples is essential. A total of 3125 samples (2250 poultry and 875 poultry egg samples), sent to the administrative centers of veterinary microbiology laboratories in six provinces of Iran, were examined for Salmonella contamination, according to the ISO 6579 guideline. Next, duplex PCR was conducted on 250 presumptive Salmonella isolates to detect invA gene for identification of the genus Salmonella and sdf gene for identification of S. Enteritidis. Subsequently, the S. Enteritidis isolates were examined for detection of important virulence genes (pagC, cdtB, msgA, spaN, tolC, lpfC, and spvC) and determination of antibiotic resistance patterns against nalidixic acid, trimethoprim-sulfamethoxazole, cephalothin, ceftazidime, colistin sulfate, and kanamycin by the disk diffusion method.

Results

Overall, 8.7 and 2.3% of poultry samples and 6.3 and 1.3% of eggs were contaminated with Salmonella species and S. Enteritidis, respectively. The invA and msgA genes (100%) and cdtB gene (6.3%) had the highest and the lowest prevalence rates in S. Enteritidis isolates. The spvC gene, which is mainly located on the Salmonella virulence plasmid, was detected in 50.8% of S. Enteritidis isolates. The S. Enteritidis isolates showed the highest and the lowest resistance to nalidixic acid (87.3%) and ceftazidime (11.1%), respectively. Unfortunately, 27.0% of S. Enteritidis isolates were multidrug-resistant (MDR).

Conclusion

The rate of contamination with Salmonella in the poultry and egg samples, besides the presence of antimicrobial resistant and MDR Salmonella isolates harboring the virulence genes in these samples, could significantly affect food safety and subsequently, human health. Therefore, continuous monitoring of animal-source foods, enhancement of poultry farm control measures, and limiting the use of antibiotics for prophylactic purposes in food producing animals, are essential for reducing the zoonotic risk of this foodborne pathogen for consumers and also choosing effective antibiotics for the treatment of salmonellosis.

The Antibacterial Efficacy and Mechanism of Plasma-Activated Water Against Salmonella Enteritidis (ATCC 13076) on Shell Eggs

Eggs are one of the most commonly consumed food items. Currently, chlorine washing is the most common method used to sanitize shell eggs. However, chlorine could react with organic matters to form a potential carcinogen, trihalomethanes, which can have a negative impact on human health. Plasma-activated water (PAW) has been demonstrated to inactivate microorganisms effectively without compromising the sensory qualities of shell eggs. For this study, various amounts (250, 500, 750, or 1000 mL) of PAW were generated by using one or two plasma jet(s) at 60 watts for 20 min with an air flow rate at 6 or 10 standard liters per minute (slm). After being inoculated with 7.0 log CFU Salmonella Enteritidis, one shell egg was placed into PAW for 30, 60, or 90 s with 1 or 2 acting plasma jet(s). When 2 plasma jets were used in a large amount of water (1000 mL), populations of S. Enteritidis were reduced from 7.92 log CFU/egg to 2.84 CFU/egg after 60 s of treatment. In addition, concentrations of ozone, hydrogen peroxide, nitrate, and nitrite in the PAW were correlated with the levels of antibacterial efficacy. The highest concentrations of ozone (1.22 ppm) and nitrate (55.5 ppm) were obtained with a larger water amount and lower air flow rate. High oxidation reduction potential (ORP) and low pH values were obtained with longer activation time, more plasma jet, and a lower air flow rate. Electron paramagnetic resonance (EPR) analyses demonstrated that reactive oxygen species (ROS) were generated in the PAW. The observation under the scanning electron microscope (SEM) revealed that bacterial cells were swollen, or even erupted after treatment with PAW. These results indicate that the bacterial cells lost control of cell permeability after the PAW treatment. This study shows that PAW is effective against S. Enteritidis on shell eggs in a large amount of water. Ozone, nitrate, and ROS could be the main causes for the inactivation of bacterial cells.

Antimicrobial resistance genes in bacteria from animal-based foods

Antimicrobial resistance is a worldwide public health threat. Farm animals are important sources of bacteria containing antimicrobial resistance genes (ARGs). Although the use of antimicrobials in aquaculture and livestock has been reduced in several countries, these compounds are still routinely applied in animal production, and contribute to ARGs emergence and spread among bacteria. ARGs are transmitted to humans mainly through the consumption of products of animal origin (PAO). Bacteria can present intrinsic resistance, and once antimicrobials are administered, this resistance may be selected and multiply. The exchange of genetic material is another mechanism used by bacteria to acquire resistance. Some of the main ARGs found in bacteria present in PAO are the bla, mcr-1, cfr and tet genes, which are directly associated to antibiotic resistance in the human clinic.

Virulence and Antibiotic Resistance Patterns of Extended-Spectrum Beta-Lactamase-Producing Salmonella enterica serovar Heidelberg Isolated from Broiler Chickens and Poultry Workers: A Potential Hazard

The current study investigated the emergence of multidrug-resistance (MDR), extended-spectrum beta-lactamase (ESBL)-producing Salmonella enterica serovar Heidelberg in broiler chickens and workers in poultry farms. A total of 33 S. Heidelberg isolates were recovered; 24 from the broiler cloacal swabs and 9 from the farm workers. All the S. Heidelberg isolates were tested for susceptibility to 11 antimicrobial agents and for the presence of resistance and virulence genes. MDR strains were found in 95.8% (23/24) and 88.8% (8/9) of the broiler and human isolates, respectively. Among the MDR strains, 66.6% of the broiler isolates and 55.5% of the human isolates were ESBL producing. The majority of broiler isolates showed resistance to ampicillin (100%) and ceftriaxone (91.6%), followed by ceftazidime and imipenem, (87.5%) and (75%). The resistance rate of the human isolates to those antibiotics were lower than the broiler isolates; ampicillin (88.8%), ceftriaxone (66.6%), ceftazidime (77.7%), and imipenem (66.6%). The resistance determinant genes found among the isolated strains was bla_SHV-1, bla_TEM-1, bla_CMY-2, bla_OXA-1, bla_CMY-M2, bla_PSE-1, and ampC. The most detected ESBL genes for broiler and human isolates were ampC (63.7%) and bla_SHV-1 (56.6%), followed by bla_CMY-M2 (48.5%), bla_TEM-1 (39.4%), and bla_OXA-1 (27.3%); whereas bla_CMY-2 and bla_PSE-1 were not detected. The finding of chromosomal and plasmid virulence genes revealed that the invA (100%), stn, sipC, and rck (72.8%), spvC (66.7%), ssr (63.6%), sopB (54.6%), and hilA and sipA (3.0%), while pefA and ssaR were absent. An elevated rate of MDR Salmonella Heidelberg in chickens is of potential great health risk. This signifies the role of the food of animal origin as a reservoir of MDR Salmonella that can affect the human health.

The Optimization of Plasma-Activated Water Treatments to Inactivate Salmonella Enteritidis (ATCC 13076) on Shell Eggs

Egg is a regularly consumed food item. Currently, chlorinated water washing is the most common practice used to disinfect eggs, but this process has a negative environmental impact. A new physical technique, plasma-activated water (PAW), has been demonstrated to possess effective antibacterial activities without long-term chemical residue. In this study, air PAW was used to inactivate Salmonella enterica serovar Enteritidis on shell eggs. Different combinations of activation parameters, including water sources (reverse osmotic (RO) water, tap water), power (40 W, 50 W, 60 W) and activation time (10 min, 20 min, 30 min), were evaluated. The oxidation–reduction potential (ORP) and pH values of each combination were measured, and their antibacterial activity was tested in a bacterial suspension. Higher antibacterial activities, higher ORP values, and lower pH values were obtained with higher power, longer activation time, and lower water hardness. The antibacterial activities of PAW decreased rapidly by increasing the storage time both at room and refrigeration temperatures. Afterwards, RO water was pre-activated for 20 min at 60 W, and then the eggs inoculated with S. enteritidis were placed into PAW for 30 s, 60 s, 90 s, or 120 s with a plasma on-site treatment in the water. More than a 4 log reduction was obtained with 60-s and 120-s treatments. The results showed that the freshness indexes of the eggs treated with PAW were similar to those of the untreated controls and better than those of the eggs treated with commercial processes. In addition, observation under a scanning electron microscope also showed less surface damage of the cuticle on the PAW-treated eggs than on the commercially treated eggs. The results of this study indicate that PAW could be an effective antibacterial agent with less damage to the freshness of shell eggs than commercial methods.

Global transcriptomic analyses of Salmonella enterica in Iron-depleted and Iron-rich growth conditions

Background

Salmonella enterica possess several iron acquisition systems, encoded on the chromosome and plasmids. Recently, we demonstrated that incompatibility group (Inc) FIB plasmid-encoded iron acquisition systems (Sit and aerobactin) likely play an important role in persistence of Salmonella in human intestinal epithelial cells (Caco-2). In this study, we sought to determine global transcriptome analyses of S. enterica in iron-rich (IR) and iron-depleted (ID) growth conditions.

Results

The number of differentially-expressed genes were substantially higher for recipient (SE819) (n = 966) and transconjugant (TC) (n = 945) compared to the wild type (WT) (SE163A) (n = 110) strain in ID as compared to IR growth conditions. Several virulence-associated factors including T3SS, flagellin, cold-shock protein (cspE), and regulatory genes were upregulated in TC in ID compared to IR conditions. Whereas, IS1 and acrR/tetR transposases located on the IncFIB plasmid, ferritin and several regulatory genes were downregulated in TC in ID conditions. Enterobactin transporter (entS), iron ABC transporter (fepCD), colicin transporter, IncFIB-encoded enolase, cyclic di-GMP regulator (cdgR) and other regulatory genes of the WT strain were upregulated in ID compared to IR conditions. Conversely, ferritin, ferrous iron transport protein A (feoA), IncFIB-encoded IS1 and acrR/tetR transposases and ArtA toxin of WT were downregulated in ID conditions. SDS-PAGE coupled with LC-MS/MS analyses revealed that siderophore receptor proteins such as chromosomally-encoded IroN and, IncFIB-encoded IutA were upregulated in WT and TC in ID growth conditions. Both chromosome and IncFIB plasmid-encoded SitA was overexpressed in WT, but not in TC or recipient in ID conditions. Increased expression of flagellin was detected in recipient and TC, but not in WT in ID conditions.

Conclusion

Iron concentrations in growth media influenced differential gene expressions both at transcriptional and translational levels, including genes encoded on the IncFIB plasmid. Limited iron availability within the host may promote pathogenic Salmonella to differentially express subsets of genes encoded by chromosome and/or plasmids, facilitating establishment of successful infection.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5768-0) contains supplementary material, which is available to authorized users.

Retracted: Antibiotic Resistance in Salmonella Enteritidis Isolates Recovered from Chicken, Chicken Breast, and Humans Through National Antimicrobial Resistance Monitoring System Between 1996 and 2014

The online e-pub version of the article entitled, Antibiotic Resistance in Salmonella Enteritidis Isolates Recovered from Chicken, Chicken Breast, and Humans Through National Antimicrobial Resistance Monitoring System Between 1996 and 2014" by Paudyal N, Pan H, Li X. Fang W. Yue M., Foodborne Pathog Dis [Epub ahead of print]; DOI: 10.1089/fpd.2017.2402 is being officially retracted from Foodborne Pathogens and Disease (FPD) due to a significant number of errors in reporting and miscalculations of the National Antimicrobial Resistance Monitoring System (NARMS) datasets reported in the paper. Authors evaluated NARMS data, which are in the public domain, and analyzed a subset of NARMS data to address questions about a specific serotype of Salmonella in humans and chicken meat. Authors analyzed Salmonella Enteritidis isolates from humans, chicken and retail chicken meat, with their minimum inhibitory concentrations (MICs) to a range of commonly used antibiotics in the US collected over a period of 1996-2014 by NARMS, to segregate isolates based on their MIC value for a certain antimicrobial and evaluate their relationship along the foodborne transmission pathway. NARMS has data on more than 185,000 isolates that can be downloaded in an accessible format. To help make these large data sets more accessible, the NARMS teams continue to develop new tools to enable users to explore them according to their own interests. As a public health surveillance system, the goal is continuous improvement and open, transparent data sharing. The NARMS partners believe this is the best way to foster a collaborative effort to combat antibiotic resistance. After the online-ahead-of-print version of the paper, which used a subset of NARMS data, was published, a significant concern was brought to the attention of the Editor-in-Chief of FPD indicating that the article contained several significant errors which could potentially lead to a misunderstanding of the resistance situation in the United States. Of particular import is with regard to the authors of the paper reversing the poultry and human resistance data found in Figure 2, which displays the overall antimicrobial resistance data and is a central element of the article. The authors correctly state it in the text, but the figure is incorrect. Additionally, there appeared to be an accidental omission of a reference to a published article which shows a strong association between quinolone-resistant Salmonella Enteritidis infections in humans and international travel (O'Donnell et al., 2014) This appears to be a critical oversight given that the intention of the study was to analyze the NARMS data to help understand the dynamics of Salmonella transmission. The authors of the published article were notified of this communication by the Editor of FPD and were provided an opportunity to respond, which they quickly did. The corresponding author, Dr. Min Yue, agreed that after he and his team reanalyzed the data, there were indeed errors in the published paper and supplied revised versions of Figure 2 and supplemental Figure 3, as well as providing a significantly revised version of the manuscript, based upon the criticisms levied against the published paper. After giving the revised manuscript and figures very careful consideration, and after significant probing of his own, the Editor of FPD determined that the significantly revised manuscript, coupled with the multiple errors presented in the figures, is simply far too weighty for a correction statement to be issued, and determined a full retraction of the published article was warranted. It is important to note that there is no indication whatsoever that the errors or miscalculations were intentional, and that Dr. Yue and his team quickly and honestly replied to the concerns raised about their work. However, in the interest of upholding the proper protocols of peer review, and in accurate and truthful reporting in the scientific literature, the Editor of Foodborne Pathogens and Diseases is issuing this full and formal retraction of the article.

Draft Genome Sequences of Four Salmonella enterica subsp. enterica Serovar Enteritidis Strains Implicated in Infections of Avian and Human Hosts

Salmonella enterica subsp. enterica serovar Enteritidis is a wide-host-range pathogen. Occasionally, it is involved in invasive infections, leading to a high mortality rate. Here, we present the draft genome sequences of four S. Enteritidis strains obtained from human and avian hosts that had been involved in bacteremia, gastroenteritis, and primary infections.

Antimicrobial resistance, virulence genes and genetic relatedness of Salmonella enterica serotype Enteritidis isolates recovered from human gastroenteritis in Tehran, Iran

OBJECTIVES

Salmonella enterica serotype Enteritidis is a major serotype associated with human salmonellosis. The main objective of this study was to determine the antibiotic susceptibility patterns and the presence of virulence-associated genes among S. Enteritidis strains isolated from patients with gastroenteritis in Tehran, Iran.

METHODS

Over a period of 14 months (May 2015 to July 2016), 44 S. Enteritidis isolates recovered from clinical sources were characterised for antimicrobial susceptibility and virulence genes. Possible genetic relatedness among the strains was also assessed using pulsed-field gel electrophoresis (PFGE).

RESULTS

Salmonella Enteritidis isolates showed high rates of resistance to ciprofloxacin (90.9%) and nalidixic acid (77.3%). Of the 44 S. Enteritidis isolates, 30 (68.2%) were resistant to three or more antibiotics. Twenty-two different antimicrobial resistance patterns were detected among the isolates. The most frequent resistance type was antibiotype 14 (resistance to ciprofloxacin, cefuroxime and nalidixic acid), occurring in 8 (18.2%) of the isolates. Notably, all of the isolates carried invA, sefA, sipA and sopE2 virulence genes. Furthermore, 17 virulence profiles were observed among the strains. The most common virulence profile was VP1 (n=17; 38.6%), harbouring all of the virulence genes. Two distinct PFGE patterns were observed among 44S. Enteritidis isolates. There was no association between virulence profiles or antibiotypes and PFGE clusters.

CONCLUSIONS

Overall, this study provides valuable information on the virulence gene content, antibiotic resistance and genetic diversity of S. Enteritidis isolated from human sources in Iran.

Molecular characterization of antimicrobial multi-drug resistance in non-typhoidal Salmonellae from chicken and clam in Mangalore, India

Salmonella enterica has been documented as one of the leading causes of salmonellosis throughout the world and is most commonly associated with the consumption of contaminated food products. Thus, this research was aimed at studying the antimicrobial susceptibility pattern and detection of quinolone resistance in Salmonella spp isolated from food of animal origin. Thirty-six Salmonella isolates comprising 8 from poultry and 28 from seafood (clams) were identified, serotyped and characterized for their antimicrobial susceptibility against 10 different antibiotics. Plasmid DNA was isolated from all the isolates by alkaline lysis, quinolone resistant non-typhoidal S.Weltevreden were examined for mutation in the DNA gyrase coding gene. Among the 36 Salmonella isolates, 20 were S. weltevreden (8 from poultry and 12 from seafood) and 16 were S.Typhimurium (from seafood). All the isolates showed multiple resistance to nalidixic acid, tetracycline, co-trimoxazole and nitrofurantoin, but, interestingly, the isolates were 100% susceptible to ampicillin, chloramphenicol and gentamicin. Resistant isolates from the study carried the genes responsible for resistance to respective antibiotics. The strain S130 isolated in the study showed single point mutation, Asp87Gly, at position 87 in quinolone resistance determining region. It revealed mutation in quinolone resistance determining region as a cause for quinolone resistance in non-typhoidal Salmonellae. The occurrence of genes accountable for plasmid mediated resistance to quinolones (viz., qnrA, qnrB and qnrS) in plasmid of non-typhoidal Salmonellae isolates provides evidence for plasmid mediated quinolone resistance.

Genetic diversity and virulence genes of Salmonella enterica subspecies enterica serotype Enteritidis isolated from meats and eggs

Salmonella enterica subspecies enterica serotype Enteritidis (S. Enteritidis) is one of the leading causes of food-borne gastroenteritis associated with the consumption of contaminated food products of animal origin. Little is known about the genetic diversity and virulence content of S. Enteritidis isolated from poultry meats and eggs in Iran. A total of 34 S. Enteritidis strains were collected from different food sources of animal origin in Tehran from May 2015 to July 2016. All of the S. Enteritidis strains were serotyped, antimicrobial susceptibility tested, and characterized for virulence genes. Pulsed-field gel electrophoresis (PFGE) was also applied for comparison of genetic relatedness. All of the strains harbored invA, hilA, ssrA, sefA, spvC, and sipA genes. A high prevalence of resistance against certain antibiotics such as cefuroxime (79.4%), nalidixic acid (47%), and ciprofloxacin (44.2%) was also observed. Regarding PFGE, S. Enteritidis strains from different sources showed considerable overlap, suggesting the lack of diversity among these isolates. Moreover, no correlation between virulence profiles or antibiotypes and PFGE clusters was observed. In conclusion, our study provided valuable information on virulence gene content, antibiotic resistance, and genetic diversity of S. Enteritidis isolated from food sources.

Effects of antimicrobial use in agricultural animals on drug-resistant foodborne salmonellosis in humans: A systematic literature review

Controversy continues concerning antimicrobial use in food animals and its relationship to drug-resistant infections in humans. We systematically reviewed published literature for evidence of a relationship between antimicrobial use in agricultural animals and drug-resistant meat or dairy-borne non-typhoidal salmonellosis in humans. Based on publications from the United States (U.S.), Canada, and Denmark from January 2010 to July 2014, 858 articles received title and abstract review, 104 met study criteria for full article review with 68 retained for which data are presented. Antibiotic exposure in both cattle and humans found an increased likelihood of Salmonella colonization, whereas in chickens, animals not exposed to antibiotics (organic) were more likely to be Salmonella positive and those that had antibiotic exposure were more likely to harbor antimicrobial resistant Salmonella organisms. In swine literature, only tylosin exposure was examined and no correlation was found among exposure, Salmonella colonization, or antimicrobial resistance. No studies that identified farm antimicrobial use also traced antimicrobial-resistant Salmonella from farm to fork.

Epidemiological, molecular characterization and antibiotic resistance of Salmonella enterica serovars isolated from chicken farms in Egypt

BACKGROUND

Salmonella is one of major causes of foodborne outbreaks globally. This study was conducted to estimate the prevalence, typing and antibiotic susceptibilities of Salmonella enterica serovars isolated from 41 broiler chicken farms located in Kafr El-Sheikh Province in Northern Egypt during 2014-2015. The clinical signs and mortalities were observed.

RESULTS

In total 615 clinical samples were collected from broiler flocks from different organs (liver, intestinal content and gall bladder). Salmonella infection was identified in 17 (41%) broiler chicken flocks and 67 Salmonella isolates were collected. Recovered isolates were serotyped as 58 (86.6%) S. enterica serovar Typhimurium, 6 (9%) S. enterica serovar Enteritidis and 3 (4.5%) were non-typable. The significant high mortality rate was observed only in 1-week-old chicks. sopE gene was detected in 92.5% of the isolates which indicating their ability to infect humans. All S. enterica serovar Enteritidis isolates were susceptible to all tested antimicrobials. The phenotypically resistant S. enterica serovar Typhimurium isolates against ampicillin, tetracycline, sulphamethoxazole and chloramphenicol were harbouring BlaTEM, (tetA and tetC), (sul1 and sul3) and (cat1 and floR), respectively. The sensitivity rate of S. enterica serovar Typhimurium to gentamycin, trimethoprim/sulphamethoxazole and streptomycin were 100, 94.8, 89.7%, respectively. The silent streptomycin antimicrobial cassettes were detected in all Salmonella serovars. A class one integron (dfrA12, orfF and aadA2) was identified in three of S. enterica serovar Typhimurium strains.

CONCLUSIONS

To the best of our knowledge, this study considered first report discussing the prevalence, genotyping, antibiotic susceptibility and public health significance of S. enterica serovars in broilers farms of different ages in Delta Egypt. Further studies are mandatory to verify the location of some resistance genes that are within or associated with the class one integron.

Draft Genome Sequences of Four Salmonella enterica Strains Isolated from Turkey-Associated Sources

We report the draft genomes of four Salmonella enterica isolates evaluated for the contribution of plasmids to virulence. Strains SE163A, SE696A, and SE710A carry plasmids demonstrated to facilitate plasmid-associated virulence, while SE819 is less virulent and has been used as a recipient for conjugation experiments to assess plasmid-encoded virulence mechanisms.

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 plasmid virulence gene spvB enhances bacterial virulence by inhibiting autophagy in a zebrafish infection model

Salmonella enterica serovar typhimurium (S. typhimurium) is a facultative intracellular pathogen that can cause gastroenteritis and systemic infection in a wide range of hosts. Salmonella plasmid virulence gene spvB is closely related to bacterial virulence in different cells and animal models, and the encoded protein acts as an intracellular toxin required for ADP-ribosyl transferase activity. However, until now there is no report about the pathogenecity of spvB gene on zebrafish. Due to the outstanding advantages of zebrafish in analyzing bacteria-host interactions, a S. typhimurium infected zebrafish model was set up here to study the effect of spvB on autophagy and intestinal pathogenesis in vivo. We found that spvB gene could decrease the LD50 of S. typhimurium, and the strain carrying spvB promoted bacterial proliferation and aggravated the intestinal damage manifested by the narrowed intestines, fallen microvilli, blurred epithelium cell structure and infiltration of inflammatory cells. Results demonstrated the enhanced virulence induced by spvB in zebrafish. In spvB-mutant strain infected zebrafish, the levels of Lc3 turnover and Beclin1 expression increased, and the double-membraned autophagosome structures were observed, suggesting that spvB can inhibit autophagy activity. In summary, our results indicate that S. typhimurium strain containing spvB displays more virulence, triggering an increase in bacterial survival and intestine injuries by suppressing autophagy for the first time. This model provides novel insights into the role of Salmonella plasmid virulence gene in bacterial pathogenesis, and can help to further elucidate the relationship between bacteria and host immune response.

Comparative analysis of virulence and resistance profiles of Salmonella Enteritidis isolates from poultry meat and foodborne outbreaks in northern Jordan

This study was conducted to isolate Salmonella Enteritidis from poultry samples and compare their virulence and antibiotic resistance profiles to S. Enteritidis isolated from outbreaks in northern Jordan. Two hundred presumptive isolates were obtained from 302 raw poultry samples and were subjected to further analysis and confirmation. A phylogenic tree based on 16S rRNA sequencing was constructed and selected isolates representing each cluster were further studied for their virulence in normal adult Swiss white mice. The most virulent strains were isolated from poultry samples and had an LD 50 of 1.55 × 10 (5) CFU, while some of the outbreak isolates were avirulent in mice. Antibiotic resistance profiling revealed that the isolates were resistant to seven of eight antibiotics screened with each isolate resistant to multiple antibiotics (from two to six). Of the poultry isolates, 100%, 88.9%, 77.8%, 66.7%, and 50% showed resistance to nalidixic acid, ciprofloxacin, ampicillin, cephalothin, and cefoperazone, respectively. Two outbreak isolates were sensitive to all tested antibiotics, while 71.4% were resistant to cefoperazone and only 28.6% showed resistance to nalidixic acid. Salmonella outbreak isolates were genetically related to poultry isolates as inferred from the 16S rRNA sequencing, yet were phenotypically different. Although outbreak strains were similar to poultry isolates, when tested in the mouse model, some of the outbreak isolates were highly virulent while others were avirulent. This might be due to a variation in susceptibility of the mouse to different S. Enteritidis isolates.