Genomic Features of High-Priority Salmonella enterica Serovars Circulating in the Food Production Chain, Brazil, 2000-2016

Antimicrobial resistance in bacteria from pig production chain: a systematic review and meta-analyses focused on the Brazilian context

Pork industry plays an important role in antibiotics consumption, which can lead to antimicrobial resistance (AMR) spread. Hence, monitoring and controlling AMR in swine production chains is essential to reduce the risks to public health. A systematic review protocol was developed to assess AMR in the pig production chain in Brazil, the fourth largest producer and exporter of pork in the world. More than 3000 strains obtained from swine chain had their antibiotic resistance characteristics assessed. Results showed a major attention to the research of swine AMR in Salmonella and Escherichia coli. Resistance against quinolones has been most investigated and high levels of resistance against tetracyclines were observed. Moreover, resistance profiles and determinants against colistin were frequently found. Meta-analyses were performed to estimate the frequency of microorganisms from the World Health Organization (WHO) global priority pathogens list of antibiotic-resistant bacteria. The results showed prevalences ≤ 0.11 of each priority group in Brazilian pork. As far as is known, this is the first research to provide a comprehensive synthesis of available data on AMR in this production chain. It may support the tackling of knowledge gaps and inspire the enhancement of policies to monitoring, controlling, and managing foodborne AMR.

Genomic Differences in Antimicrobial Resistance and Virulence Among Key Salmonella Strains of Serogroups B and D1 in Brazilian Poultry

Salmonella is a significant threat to Brazilian poultry, causing economic losses and public health risks. This study analyzed 15 Salmonella isolates along with 45 retrieved complete genomes, including serovars Gallinarum, Pullorum, Enteritidis, Typhimurium, and Heidelberg. Biochemical characterization, antimicrobial susceptibility testing, whole-genome sequencing, and comparative genomics were performed. The studied strains exhibited high levels of antimicrobial resistance, particularly to tilmicosin, penicillin/novobiocin, nalidixic acid, and streptomycin. Genomic analysis revealed diverse virulence factors and antibiotic resistance genes (ARGs), with zoonotic strains showing higher virulence compared to avian-adapted strains. Multiple plasmid types carrying ARGs were identified, highlighting the potential for horizontal gene transfer. Pangenomic and phylogenomic analyses differentiated Salmonella strains from serogroup D1 from those from serogroup B. These findings emphasize the need for comprehensive surveillance and control measures to mitigate the impact of Salmonella on both animal and human health in Brazil.

Highly resistant Salmonella Heidelberg circulating in broiler farms in southern Brazil

Salmonella Heidelberg, a serotype commonly found in Southern Brazil, is characterized by its high resistance and persistence in the poultry production. This study aimed to characterize the antimicrobial resistance of S. Heidelberg strains. In total, 100 strains isolated from poultry between 2020 and 2022 were evaluated. Phenotypic analyses were performed to determine the susceptibility of 16 antimicrobial agents and detect extended-spectrum beta-lactamase (ESBL)-producing strains. Molecular analyses were performed to detect 11 antimicrobial resistance genes (using polymerase chain reaction [PCR]) and integron class 1 genes (using real-time PCR). A total of 98% of isolates was classified as multidrug-resistant. All isolates were resistant to penicillin and lincomycin. High resistance rates (> 85%) were observed for tetracycline, doxycycline, cephalexin, amoxicillin, and ceftiofur. A significant increase (p < 0.05) in antimicrobial resistance is observed for amoxicillin, cephalexin, and ceftiofur between 2020 and 2022. No significant differences (p > 0.05) were observed in antimicrobial resistance with respect to the region of isolation, season, or company. In total, 25% of isolates were ESBL producers. Integron class 1 gene was detected in only one strain, whereas sul2 was detected in 99%, tet(A) in 66%, blaTEM in 37%, strB in 17%, cmlA in 15%, and tet(B) in 11% of the strains. Other genes were not detected or were detected in < 2% of the strains. The results showed a high overall resistance, which increased over the evaluated period. The high proportions of ESBL-producing and antimicrobial resistant strains represent a risk for highly-resistant S. Heidelberg dissemination across broiler flocks.

Genomic survey of multidrug resistant Salmonella enterica serovar Minnesota clones in chicken products

Salmonella enterica serovar Minnesota (S. Minnesota) is an emerging serovar that persists within poultry supply chains, potentially causing outbreaks in humans. Understanding its population genomics is crucial for designing preventive measures. We performed a genomic surveillance study of S. Minnesota by analyzing 259 isolates from poultry in Saudi Arabia. Whole-genome sequencing data for these isolates were analyzed to characterize emerging clones and the genetic factors underlying antimicrobial resistance and virulence. We compared the isolates to all available global genomes of S. Minnesota. Our results revealed the emergence of four clones, three of which were mixed with global strains. These clones exhibited higher levels of antimicrobial resistance and virulence due to the acquisition of multiple plasmids, particularly IncC plasmids, carrying resistance and virulence genes. IncC plasmids underwent genomic rearrangements, presenting diverse configurations of resistance genes. Our findings demonstrate the emergence and persistence of pathogenic and multidrug-resistant S. Minnesota clones.

Salmonella enterica serovar Schwarzengrund: Distribution, Virulence, and Antimicrobial Resistance

The global incidence of Salmonella enterica serovar Schwarzengrund has risen in recent years. This serotype has been isolated from poultry, retail meat, and other food products, leading to multiple outbreaks. Alongside the increase in infections, there are growing concerns about the increasing levels of antimicrobial resistance (AMR) among S. Schwarzengrund strains. This study aims to better understand the genetic factors possibly contributing to the rising prevalence of S. Schwarzengrund by analyzing the sequences of 2058 isolates from both human patients (N = 313) and food- and animal-associated sources, including chicken (N = 1145), turkey (N = 300), pork (N = 132), and other sources (N = 168). Data were obtained from GenBank and analyzed for AMR genes using AMRFinder. Additionally, putative virulence genes and plasmid transfer genes were assessed using the Virulence and AMR Plasmid Transfer Factor Database. AMR genes were found in 1269 (61.7%) of the isolates, with a total of 2478 AMR genes among the isolates, the most common being aph(3″)-Ib (N = 969, 47.1%), tet(A) (N = 190, 9.2%), and sul2 (N = 150, 7.3%), which are responsible for resistance to aminoglycoside, tetracycline, and sulfonamide, respectively. Additionally, 1060 (51.5%) isolates carried multiple plasmid transfer genes associated with IncFIB-FIC(FII) plasmids. Other plasmid types found in at least 1% of the strains included IncI1 (N = 101, 4.9%), IncHI2 (N = 62, 3.0%), or IncHI1 (N = 24, 1.2%). The virulence gene profiles of human isolates showed diversity but largely overlapped with those from different food sources. Notably, the aerobactin iron acquisition genes, associated with Salmonella's virulence and colonization, were highly prevalent among chicken isolates (N = 1019, 89.0%) but less frequent in isolates from other sources (N = 65, 7.2%). IncFIB-FIC(FII) plasmids, commonly harboring the aerobactin operon, were highly prevalent among chicken-related isolates and present in about 10% of human isolates. The diverse plasmid, AMR, and virulence gene profiles in human-associated isolates suggest that multiple factors may contribute to the increased virulence in S. Schwarzengrund.

Genomic characterization of a clonal emergent Salmonella Minnesota lineage in Brazil reveals the presence of a novel megaplasmid of resistance and virulence

Salmonella Minnesota has emerged in Brazil as the predominant serovar in poultry and poultry products, along with Salmonella Heidelberg. To understand the emergence of Salmonella Minnesota over the last few years in Brazil, we performed a comparative analysis between 69 selected S. Minnesota genomes from Pathogen Detection database and 65 clonal emergent genomes isolated from Brazil. We demonstrate the presence of multidrug resistance genes against tetracycline [tet(A)], sulfonamide (sul2), and AmpC beta-lactamase (blaCMY-2) in emergent genomes, along with the carriage of a megaplasmid of resistance and virulence (~210 kb), designated pESM (plasmid for emergent Salmonella Minnesota). pESM is an IncC/A2 plasmid predicted to increase S. Minnesota environmental tolerance to mercury (mer operon) and provide resistance to tetracycline and ampicillin due to the presence of tet(A) and blaCMY-2, respectively. Moreover, pESM carries the yersiniabactin siderophore (high-pathogenicity island of Yersinia) related to the iron uptake. The temporal inference demonstrated that the most recent common ancestor dated from ~1978 and that the clonal emergent genomes carrying the pESM belong to a completely different lineage of S. Minnesota. Our results indicate that the presence of pESM likely contributes to the emergence of S. Minnesota and is precisely related to the successful spread of this particular clonal lineage in Brazil.IMPORTANCESalmonella Minnesota has emerged in Brazil as one of the leading serovars related to human and animal infection, presenting high virulence and antibiotic resistance to drugs classified as the highest priority for clinical treatment in humans. This study performed whole-genome sequencing, temporal analysis, and phylogenetics to understand the genetic insights related to the emergence of Salmonella Minnesota in Brazil. Long-read sequencing has led to the identification and characterization of a unique megaplasmid carrying virulence, antibiotic resistance, and heavy-metal tolerance genes, which may play a central role in S. Minnesota's successful emergence in Brazil and possibly worldwide. The potentially high transmissibility of this plasmid between clones and serovars represents a risk to public health since its acquisition may increase Salmonella's fitness, virulence, resistance, and persistence. Understanding the genetic aspects related to the emergence of serovars can help devise measures to mitigate the spread of hazardous multidrug-resistant strains.

Exploring resource competition by protective lactic acid bacteria cultures to control Salmonella in food: an Achilles' heel to target?

Salmonella is a pathogenic bacterium, being the second most commonly reported foodborne pathogen in Europe, due to the ability of its different serovars to contaminate a wide variety of foods, with differences among countries. Common chemical or physical control methods are not always effective, eco-sustainable and adapted to the diversity of Salmonella serovars. Thus, great attention is given to developing complementary or alternative control methods that can be tailor made for specific situations. One of these methods is biopreservation using lactic acid bacteria, with most studies on their antagonistic activity focused on the production of antimicrobials. Less attention has been given to competition by exploitation of nutrients. This review is thus set to investigate and highlight limiting resources that may be involved in the competitive exclusion of Salmonella in food matrices. To do this the needs for nutrients and microelements and the known homeostatic pathways of Salmonella and lactic acid bacteria are examined. Finally, milk, intended for the manufacture of fermented dairy foods, is pointed out as an example of food to investigate the bioavailable macronutrients, metals and vitamins that could be involved in competition between the different species and serovars, and could be exploited for targeted biopreservation.

High prevalence and genomic features of multidrug-resistant Salmonella enterica isolated from chilled broiler chicken on retail sale in the United Arab Emirates

Non-typhoidal Salmonella represents a significant global concern for food safety and One Health. Despite the United Arab Emirates (UAE) being a leading consumer of chicken meat globally, there is a lack of comprehensive understanding regarding the prevalence and genomic characteristics of Salmonella within the country. This study aims to address this gap by conducting a thorough analysis of Salmonella prevalence, antimicrobial resistance, and genomic profiles of isolates obtained from whole broiler carcasses retailed under chilled conditions in the UAE. Our findings reveal that Salmonella was detected in 41.2 % (130/315) of the sampled chilled broiler carcasses, with notable variability observed among samples sourced from six different companies. Phenotypic antimicrobial resistance (AMR) testing, among 105 isolates, highlighted high resistance rates to tetracycline (97.1 %), nalidixic acid (93.3 %), ampicillin (92.4 %), azithromycin (75.2 %), ciprofloxacin (63.8 %), and ceftriaxone (54.3 %). Furthermore, a concerning 99 % (104/105) of the isolates exhibited multidrug resistance. Whole-genome sequencing (WGS) of 60 isolates identified five serovars, with S. infantis/Sequence Type (ST) 32 (55 %) and S. Minnesota/ST-458 (28.3 %) being the most prevalent. WGS analysis unveiled 34 genes associated with antimicrobial resistance, including mcr-1.1 (only in two isolates), conferring resistance to colistin. The two major serovars, Infantis and Minnesota, exhibited significant variation (P-values <0.001) in the distribution of major AMR genes (aadA1, blaCMY-2, blaSHV-12, qnrB19, qnrS1, sul1, and sul2). Notably, the gene qacEdelta, conferring resistance to quaternary ammonium compounds commonly found in disinfectants, was universally present in all S. Infantis isolates (n = 33), compared to only one S. Minnesota isolate. Additionally, all S. Infantis isolates harbored the IncFIB (pN55391) plasmid replicon type. Major serovars exhibited distinct distributions of antimicrobial resistance genes, underscoring the importance of serovar-specific surveillance. These findings emphasize the critical need for continuous surveillance and intervention measures to address Salmonella contamination risks in poultry products, providing valuable insights for public health and regulatory strategies not only in the UAE but also globally.

Antimicrobial resistance and genome characteristics of Salmonella enteritidis from Huzhou, China

Salmonella enteritidis is a main pathogen responsible for sporadic outbreaks of gastroenteritis, and therefore is an important public health problem. This study investigated the drug resistance and genomic characteristics of S. enteritidis isolated from clinical and food sources in Huzhou, Zhejiang Province, China, from February 1, 2021, to December 30, 2023. In total, 43 S. enteritidis strains isolated during the study period were subjected to virulence gene, drug resistance gene, genetic correlation, antibiotic resistance, and multilocus sequence typing analyses. All 43 isolates were identified as ST11, and contained 108 virulence-related genes. Drug sensitivity analysis of the 43 isolates showed resistance rates of 100% to nalidixic acid and 90.70% to ampicillin and ampicillin/sulbactam. Multidrug resistance is a serious issue, with 81.40% of strains resistant to three or more antibacterial drugs. Genome sequencing indicated that S. enteritidis possessed 23 drug resistance genes, of which 14 were common to all 43 isolates. Phylogenetic analysis based on core genome single-nucleotide polymorphisms divided the 43 S. enteritidis strains into three clusters, with the 10 samples from an outbreak forming an independent branch located in cluster 3.

CRISPR and CRISPR-MVLST reveal conserved spacer distribution and high similarity among Salmonella enterica serovar Infantis genomes from Brazil and other countries

Salmonella enterica serovar Infantis (S. Infantis) is a globally distributed non-typhoid serovar infecting humans and food-producing animals. Considering the zoonotic potential and public health importance of this serovar, strategies to characterizing, monitor and control this pathogen are of great importance. This study aimed to determine the genetic relatedness of 80 Brazilian S. Infantis genomes in comparison to 40 non-Brazilian genomes from 14 countries using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-Multi-Locus Virulence Sequence Typing (CRISPR-MVLST). CRISPR spacers were searched using CRISPR-Cas++ and fimH and sseL alleles using BLAST and MEGA X. Results were analyzed using BioNumerics 7.6 in order to obtain similarity dendrograms. A total of 23 CRISPR1 and 11 CRISPR2 alleles formed by 37 and 26 types of spacers, respectively, were detected. MVLST revealed the presence of five fimH and three sseL alleles. CRISPR's similarity dendrogram showed 32 strain subtypes, with an overall similarity ≥ 78.6. The CRISPR-MVLST similarity dendrogram showed 37 subtypes, with an overall similarity ≥ 79.2. In conclusion, S. Infantis strains isolated from diverse sources in Brazil and other countries presented a high genetic similarity according to CRISPR and CRISPR-MVLST, regardless of their source, year, and/or place of isolation. These results suggest that both methods might be useful for molecular typing S. Infantis strains using WGS data.

Comparative genomics reveals high genetic similarity among strains of Salmonella enterica serovar Infantis isolated from multiple sources in Brazil

Background

Salmonella enterica serovar Infantis (Salmonella Infantis) is a zoonotic, ubiquitous and foodborne pathogen of worldwide distribution. Despite Brazil's relevance as a major meat exporter, few studies were conducted to characterize strains of this serovar by genomic analyses in this country. Therefore, this study aimed to assess the diversity of 80 Salmonella Infantis strains isolated from veterinary, food and human sources in Brazil between 2013 and 2018 by comparative genomic analyses. Additional genomes of non-Brazilian countries (n = 18) were included for comparison purposes in some analyses.

Methods

Analyses of whole-genome multi-locus sequence typing (wgMLST), using PGAdb-builder, and of fragmented genomes, using Gegenees, were conducted to compare the 80 Brazilian strains to the 18 non-Brazilian genomes. Pangenome analyses and calculations were performed for all Salmonella Infantis genomes analyzed. The presence of prophages was determined using PHASTER for the 80 Brazilian strains. The genome plasticity using BLAST Ring Image Generator (BRIG) and gene synteny using Mauve were evaluated for 20 selected Salmonella Infantis genomes from Brazil and ten from non-Brazilian countries. Unique orthologous protein clusters were searched in ten selected Salmonella Infantis genomes from Brazil and ten from non-Brazilian countries.

Results

wgMLST and Gegenees showed a high genomic similarity among some Brazilian Salmonella Infantis genomes, and also the correlation of some clusters with non-Brazilian genomes. Gegenees also showed an overall similarity >91% among all Salmonella Infantis genomes. Pangenome calculations revealed an open pangenome for all Salmonella Infantis subsets analyzed and a high gene content in the core genomes. Fifteen types of prophages were detected among 97.5% of the Brazilian strains. BRIG and Mauve demonstrated a high structural similarity among the Brazilian and non-Brazilian isolates. Unique orthologous protein clusters related to biological processes, molecular functions, and cellular components were detected among Brazilian and non-Brazilian genomes.

Conclusion

The results presented using different genomic approaches emphasized the significant genomic similarity among Brazilian Salmonella Infantis genomes analyzed, suggesting wide distribution of closely related genotypes among diverse sources in Brazil. The data generated contributed to novel information regarding the genomic diversity of Brazilian and non-Brazilian Salmonella Infantis in comparison. The different genetically related subtypes of Salmonella Infantis from Brazil can either occur exclusively within the country, or also in other countries, suggesting that some exportation of the Brazilian genotypes may have already occurred.

A Retrospective Analysis of Salmonella Isolates across 11 Animal Species (1982-1999) Led to the First Identification of Chromosomally Encoded blaSCO-1 in the USA

Antimicrobial resistance (AMR) in non-typhoidal Salmonella is a pressing public health concern in the United States, necessitating continuous surveillance. We conducted a retrospective analysis of 251 Salmonella isolates from 11 animal species recovered between 1982 and 1999, utilizing serotyping, antimicrobial susceptibility testing, and whole-genome sequencing (WGS). Phenotypic resistance was observed in 101 isolates, with S. Typhimurium, S. Dublin, S. Agona, and S. Muenster prevailing among 36 identified serovars. Notably, resistance to 12 of 17 antibiotics was detected, with ampicillin being most prevalent (79/251). We identified 38 resistance genes, primarily mediating aminoglycoside (n = 13) and β-lactamase (n = 6) resistance. Plasmid analysis unveiled nine distinct plasmids associated with AMR genes in these isolates. Chromosomally encoded blaSCO-1 was present in three S. Typhimurium and two S. Muenster isolates from equine samples, conferring resistance to amoxicillin/clavulanic acid. Phylogenetic analysis revealed three distinct clusters for these five isolates, indicating evolutionary divergence. This study represents the first report of blaSCO-1 in the USA, and our recovered isolates harboring this gene as early as 1989 precede those of all other reports. The enigmatic nature of blaSCO-1 prompts further research into its function. Our findings highlight the urgency of addressing antimicrobial resistance in Salmonella for effective public health interventions.

Geographical and temporal distribution of multidrug-resistant Salmonella Infantis in Europe and the Americas

Recently emerged S. Infantis strains carrying resistance to several commonly used antimicrobials have been reported from different parts of the globe, causing human cases of salmonellosis and with occurrence reported predominantly in broiler chickens. Here, we performed phylogenetic and genetic clustering analyses to describe the population structure of 417 S. Infantis originating from multiple European countries and the Americas collected between 1985 and 2019. Of these, 171 were collected from 56 distinct premises located in England and Wales (E/W) between 2009 and 2019, including isolates linked to incursions of multidrug-resistant (MDR) strains from Europe associated with imported poultry meat. The analysis facilitated the comparison of isolates from different E/W sources with isolates originating from other countries. There was a high degree of congruency between the outputs of different types of population structure analyses revealing that the E/W and central European (Germany, Hungary, and Poland) isolates formed several disparate groups, which were distinct from the cluster relating to the United States (USA) and Ecuador/Peru, but that isolates from Brazil were closely related to the E/W and the central European isolates. Nearly half of the analysed strains/genomes (194/417) harboured the IncFIB(pN55391) replicon typical of the "parasitic" pESI-like megaplasmid found in diverse strains of S. Infantis. The isolates that contained the IncFIB(pN55391) replicon clustered together, despite originating from different parts of the globe. This outcome was corroborated by the time-measured phylogeny, which indicated that the initial acquisition of IncFIB(pN55391) likely occurred in Europe in the late 1980s, with a single introduction of IncFIB(pN55391)-carrying S. Infantis to the Americas several years later. Most of the antimicrobial resistance (AMR) genes were identified in isolates that harboured one or more different plasmids, but based on the short-read assemblies, only a minority of the resistance genes found in these isolates were identified as being associated with the detected plasmids, whereas the hybrid assemblies comprising the short and long reads demonstrated that the majority of the identified AMR genes were associated with IncFIB(pN55391) and other detected plasmid replicon types. This finding underlies the importance of applying appropriate methodologies to investigate associations of AMR genes with bacterial plasmids.

Salmonella Heidelberg and Salmonella Minnesota in Brazilian broilers: Genomic characterization of third-generation cephalosporin and fluoroquinolone-resistant strains

Salmonella serovars Heidelberg and Minnesota encoding antimicrobial resistance to third-generation cephalosporins and fluoroquinolones are often detected in poultry/poultry meat. We analysed the genomes of 10 Salmonella Heidelberg (SH) and 4 Salmonella Minnesota (SM) from faecal isolates of Brazilian poultry. These featured virulent and multidrug-resistant characteristics, with AmpC beta-lactamase (bla_CMY-2 ) predominance (9/14), for all SM (4/4) and some SH (3/10) located on IncC plasmid replicons. IncC carrying bla_CTX-M-2 was only detected among SH (3/10). Mutation in the gyrA/parC genes was present in all SH, whereas SM harboured parC mutation plus qnrB19 on ColRNAI plasmids (3/4). In silico resistance overall corroborated with phenotypic results. Core genome phylogenies showed close clustering and high similarities between the Brazilian and poultry meat/food isolates from Europe, and to human isolates from European countries with documented import of Brazilian poultry meat. Conjugation assays with SM successfully transferred bla_CMY-2 , and qnrB19 to an Escherichia coli recipient. The findings reinforce the ongoing antimicrobial resistance acquisition of SH and Minnesota and the risks for disseminating resistant strains and/or mobile elements which may increasingly affect importing countries and the need for controlling AMR in major poultry-exporting countries like Brazil.

Genomic analyses of drug-resistant Salmonella enterica serovar Heidelberg strains isolated from meat and related sources between 2013 and 2017 in the south region of Brazil

Salmonella enterica serovar Heidelberg (S. Heidelberg) is a zoonotic, ubiquitous, and worldwide-distributed pathogen, responsible for gastroenteritis in humans caused by the consumption of contaminated food. In this study, 11 S. Heidelberg strains isolated from chicken and bovine meat, drag swab, and animal feed between 2013 and 2017 in states of the southern region of Brazil were characterized by whole-genome sequencing (WGS) analyses. Antimicrobial resistance against 18 antimicrobials was determined by disk-diffusion and ciprofloxacin's minimum inhibitory concentration by Etest®. The search for resistance and virulence genes, plasmids, Salmonella Pathogenicity Islands (SPIs) plus multi-locus sequence typing (MLST), and single-nucleotide polymorphisms (SNPs) analyses was conducted using WGS data. All strains harbored resistance genes fosA7, aac(6')-Iaa, sul2, tet(A), bla_CMY-2, mdsA, and mdsB_, and point mutations in gyrA and parC. All strains showed a phenotypic multidrug-resistant profile, with resistant or intermediate resistant profiles against 14 antimicrobials tested. Plasmids ColpVC, IncC, IncX1, and IncI1-I(Alpha) were detected. Virulence genes related to adherence, macrophage induction, magnesium uptake, regulation, and type III secretion systems plus 10 SPIs were detected. All strains were assigned to ST15 and belonged to two SNP clusters showing high similarity to isolates from the United Kingdom, Chile, Germany, the Netherlands, China, South Africa, and South Korea. In conclusion, the presence of multidrug-resistant S. Heidelberg strains in Brazil showing a global genomic relationship may alert for the necessity of stronger surveillance measures by food safety and public health authorities to limit its spread to humans and animals through foods.

Plasmid Composition, Antimicrobial Resistance and Virulence Genes Profiles of Ciprofloxacin- and Third-Generation Cephalosporin-Resistant Foodborne Salmonella enterica Isolates from Russia

Salmonella enterica is an important foodborne pathogen worldwide. Ciprofloxacin and extended-spectrum cephalosporins are the common first-line antimicrobial drugs for the treatment of salmonellosis, antimicrobial resistance genes for which are mostly transferred via plasmids. The goal of this work was to perform genomic analysis of plasmids from foodborne S. enterica isolates obtained in Russia based on whole-genome sequencing. In the current study, 11 multidrug-resistant samples isolated in 2021 from 8 regions of Russia were selected based on their resistance to ciprofloxacin and third-generation cephalosporins (CIP-3rd). Whole-genome short-read sequencing (WGS) was performed for all isolates; the samples belonged to five different sequence types (ST32, ST469, ST11, ST142, and ST548) which had different profiles of antimicrobial resistance (AMR) and virulence genes. We have performed additional long-read sequencing of four representative S. enterica isolates, which showed that they carried pESI-like megaplasmids of 202-280 kb length harboring extended-spectrum β-lactamase genes, fluoroquinolone, tetracycline, and aminoglycosides resistance genes, as well as several virulence determinants. We believe that the WGS data obtained will greatly facilitate further studies of foodborne S. enterica isolates epidemiology in terms of their self-transmissible plasmid composition that mediated antimicrobial resistance and virulence determinants conferring selective advantages of this important bacterial pathogen.

Multiobjective response and chemometric approaches to enhance the phytochemicals and biological activities of beetroot leaves: an unexploited organic waste

Research on medicinal plants is developing each day due to inborn phytochemicals, which can encourage the progress of novel drugs. Most plant-based phytochemicals have valuable effects on well-being. Among them, beetroot leaves (BL) are known for their therapeutic properties. Here, three solvents, namely, acetonitrile, ethanol, and water, and their combinations were developed for BL extraction and simultaneous assessment of phytochemical compounds and antioxidant and antifoodborne pathogen bacteria activities. By using the augmented simplex-centroid mixture design, 40.40% acetonitrile diluted in water at 38.74% and ethanol at 20.86% favored the recovery of 49.28 mg GAE/mL (total phenolic content (TPC)) and 0.314 mg QE/mL (total flavonoid content (TFC)), respectively. Acetonitrile diluted in water at 50% guarantees the best antioxidant activity, whereas the optimal predicted mixture for the highest antibacterial activity matches 24.58, 50.17, and 25.25% of acetonitrile, ethanol, and water, respectively. These extraction conditions ensured inhibition of Staphylococcus aureus, Salmonella enterica, and Escherichia coli, respectively, at 0.402, 0.497, and 0.207 mg/mL. Under optimized conditions, at three concentrations of BL, minimal inhibitory concentration (MIC), 2 × MIC, and 4 × MIC, a linear model was employed to investigate the inhibition behavior against the three tested bacteria. The early logarithmic growth phase of these bacteria illustrated the bactericidal effect of optimized extracted BL with a logarithmic growth phase inferior to 6 h. Therefore, BL extract at 4 × MIC, which corresponds to 1.608, 1.988, and 0.828 mg/mL, was more efficient against S. aureus, S. enterica, and E. coli.

Genome characteristics of clinical Salmonella enterica population from a state public health laboratory, New Hampshire, USA, 2017–2020

Background

The implementation of whole genome sequencing (WGS) by PulseNet, the molecular subtyping network for foodborne diseases, has transformed surveillance, outbreak detection, and public health laboratory practices in the United States. In 2017, the New Hampshire Public Health Laboratories, a member of PulseNet, commenced the use of WGS in tracking foodborne pathogens across the state. We present some of the initial results of New Hampshire’s initiative to transition to WGS in tracking Salmonella enterica, a bacterial pathogen that is responsible for non-typhoidal foodborne infections and enteric fever. We characterize the population structure and evolutionary history of 394 genomes of isolates recovered from human clinical cases in New Hampshire from 2017 to 2020.

Results

The New Hampshire S. enterica population is phylogenetically diverse, consisting of 78 sequence types (ST) and 67 serotypes. Six lineages dominate the population: ST 11 serotype Enteritidis, ST 19 Typhimurium, ST 32 Infantis, ST 118 Newport, ST 22 Braenderup, and ST 26 Thompson. Each lineage is derived from long ancestral branches in the phylogeny, suggesting their extended presence in the region and recent clonal expansion. We detected 61 genes associated with resistance to 14 antimicrobial classes. Of these, unique genes of five antimicrobial classes (aminocoumarins, aminoglycosides, fluoroquinolones, nitroimidazoles, and peptides) were detected in all genomes. Rather than a single clone carrying multiple resistance genes expanding in the state, we found multiple lineages carrying different combinations of independently acquired resistance determinants. We estimate the time to the most recent common ancestor of the predominant lineage ST 11 serotype Enteritidis (126 genomes) to be 1965 (95% highest posterior density intervals: 1927–1982). Its population size expanded until 1978, followed by a population decline until 1990. This lineage has been expanding since then. Comparison with genomes from other states reveal lack of geographical clustering indicative of long-distance dissemination.

Conclusions

WGS studies of standing pathogen diversity provide critical insights into the population and evolutionary dynamics of lineages and antimicrobial resistance, which can be translated to effective public health action and decision-making. We highlight the need to strengthen efforts to implement WGS-based surveillance and genomic data analyses in state public health laboratories.

Large-scale genomic analysis reveals the pESI-like megaplasmid presence in Salmonella Agona, Muenchen, Schwarzengrund, and Senftenberg

Salmonella spp. remains one of the main pathogens causing diarrhea in humans worldwide. Lately, Salmonella Infantis has become endemic in several European, American, and Asian countries, presenting a multi-drug resistance profile and increased virulence. Various studies have attributed the high endemicity of Salmonella Infantis to pESI (plasmid to Emergent Salmonella Infantis). The ease of Salmonella to acquire pESI is of concern to health authorities and the food production chain. We searched for the presence of pESI in Salmonella genomes from the NCBI to understand the distribution of pESI worldwide and predict the main serovars and sequence types associated with the plasmid. We identified the pESI backbone, virulence, and resistance genes among Salmonella spp. isolated from 45 countries on five continents. We found the pESI-like structure in four different serovars: S. Muenchen, S. Schwarzengrund, S. Agona and S. Senftenberg. The pESI markers were also identified in 24 different sequence types. Most of the analyzed genomes were isolated from poultry, especially broiler and chicken. These results confirm the high dissemination of pESI-like megaplasmid among Salmonella Infantis worldwide and its ability to infect different serovars, as well as placing poultry production as the most favorable environment for pESI dissemination. Therefore, further studies are needed to prevent the spread of pESI to humans and the food chain.

Prevalence of efflux pump and heavy metal tolerance encoding genes among Salmonella enterica serovar Infantis strains from diverse sources in Brazil

Salmonella enterica subspecies enterica serovar Infantis (S. Infantis) is a non-typhoid, zoonotic and foodborne serovar with worldwide distribution, and often associated with increasing antimicrobial resistance. Efflux pumps are antimicrobial resistance mechanisms able to promote and increase resistance levels to multiple distinct drug classes. Heavy metal tolerance genes have been demonstrated to promote resistance against these compounds and act in the co-selection of antimicrobial resistant strains. Despite the relevance of S. Infantis in clinical and non-clinical fields, few studies worldwide have investigated the occurrence of such genes in strains from diverse sources. Therefore, the present study aimed at determining the prevalence of antimicrobial efflux pump and heavy metal tolerance genes and their genomic relatedness through core-genome multi-locus sequence typing (cgMLST) of 80 S. Infantis strains isolated from food, environmental, human and animal sources from 2013 to 2018 in Brazil. Twenty efflux pump encoding genes were detected, with 17 of these (acrA, acrB, baeR, crp, emrB, emrR, hns, kdpE, kpnF, marA, marR, mdtK, msbA, rsmA, sdiA, soxR and soxS) detected in all strains studied, golS in 98.75%, mdfA in 58.75% and tet(A) in 37.5%. Tolerance genes to arsenic (arsR) were detected in 100% of the strains, gold (golS and golT) in 98.75%, silver (silABCDEFPRS) in 36.25% and mercury (merR and merT) in 1.25%. cgMLST demonstrated a closer genetic relationship among strains harboring similar profiles of heavy metal and efflux pump encoding genes, despite their origin. In conclusion, the high prevalence of some efflux pump and heavy metal tolerance encoding genes alert us about the importance of strong surveillance measures to monitor resistance and the transmission of S. Infantis among diverse sources in Brazil.

Antimicrobial resistance and genetic background of non-typhoidal Salmonella enterica strains isolated from human infections in São Paulo, Brazil (2000-2019)

Salmonella enterica causes Salmonellosis, an important infection in humans and other animals. The number of multidrug-resistant (MDR) phenotypes associated with Salmonella spp. isolates is increasing worldwide, causing public health concern. Here, we aim to characterize the antimicrobial-resistant phenotype of 789 non-typhoidal S. enterica strains isolated from human infections in the state of São Paulo, Brazil, along 20 years (2000-2019). Among the non-susceptible isolates, 31.55, 14.06, and 13.18% were resistant to aminoglycosides, tetracycline, and β-lactams, respectively. Moreover, 68 and 11 isolates were considered MDR and Extended Spectrum β-Lactamase (ESBL) producers, respectively, whereas one isolate was colistin-resistant. We selected four strains to obtain a draft of the Genome Sequence; one S. Infantis (ST32), one S. Enteritidis (ST11), one S. I 4,[5],12:i:- (ST19), and one S. Typhimurium (ST313). Among them, three presented at least one of the following antimicrobial resistance genes (AMR) linked to mobile DNA: blaTEM-1B, dfrA1, tetA, sul1, floR, aac(6')-laa, and qnrE1. This is the first description of the plasmid-mediated quinolone resistance (PMQR) gene qnrE1 in a clinical isolate of S. I 4,[5],12:i:-. The S. Typhimurium is a colistin-resistant isolate, but did not harbor mcr genes, but it presented mutations within the mgrB, pmrB, and pmrC regions that might be linked to the colistin-resistant phenotype. The virulence pattern of the four isolates resembled the virulence pattern of the highly pathogenic S. Typhimurium UK-1 reference strain in assays involving the in vivo Galleria mellonella model. In conclusion, most isolates studied here are susceptible, but a small percentage present an MDR or ESBL-producer and pathogenic phenotype. Sequence analyses revealed plasmid-encoded AMR genes, such as β-lactam and fluoroquinolone resistance genes, indicating that these characteristics can be potentially disseminated among other bacterial strains.

Salmonella Heidelberg side-step gene loss of respiratory requirements in chicken infection model

Among the important recent observations involving anaerobic respiration was that an electron acceptor produced as a result of an inflammatory response to Salmonella Typhimurium generates a growth advantage over the competing microbiota in the lumen. In this regard, anaerobically, salmonellae can oxidize thiosulphate (S₂O₃^2-) converting it into tetrathionate (S₄O₆^2-), the process by which it is encoded by ttr gene cluster (ttrSRttrBCA). Another important pathway under aerobic or anaerobic conditions is the 1,2-propanediol-utilization mediated by the pdu gene cluster that promotes Salmonella expansion during colitis. Therefore, we sought to compare in this study, whether Salmonella Heidelberg strains lacking the ttrA, ttrApduA, and ttrACBSR genes experience a disadvantage during cecal colonization in broiler chicks. In contrast to expectations, we found that the gene loss in S. Heidelberg potentially confers an increase in fitness in the chicken infection model. These data argue that S. Heidelberg may trigger an alternative pathway involving the use of an alternative electron acceptor, conferring a growth advantage for S. Heidelberg in chicks.

Emergence, Dissemination and Antimicrobial Resistance of the Main Poultry-Associated Salmonella Serovars in Brazil

Salmonella infects poultry, and it is also a human foodborne pathogen. This bacterial genus is classified into several serovars/lineages, some of them showing high antimicrobial resistance (AMR). The ease of Salmonella transmission in farms, slaughterhouses, and eggs industries has made controlling it a real challenge in the poultry-production chains. This review describes the emergence, dissemination, and AMR of the main Salmonella serovars and lineages detected in Brazilian poultry. It is reported that few serovars emerged and have been more widely disseminated in breeders, broilers, and layers in the last 70 years. Salmonella Gallinarum was the first to spread on the farms, remaining as a concerning poultry pathogen. Salmonella Typhimurium and Enteritidis were also largely detected in poultry and foods (eggs, chicken, turkey), being associated with several human foodborne outbreaks. Salmonella Heidelberg and Minnesota have been more widely spread in recent years, resulting in frequent chicken/turkey meat contamination. A few more serovars (Infantis, Newport, Hadar, Senftenberg, Schwarzengrund, and Mbandaka, among others) were also detected, but less frequently and usually in specific poultry-production regions. AMR has been identified in most isolates, highlighting multi-drug resistance in specific poultry lineages from the serovars Typhimurium, Heidelberg, and Minnesota. Epidemiological studies are necessary to trace and control this pathogen in Brazilian commercial poultry production chains.

Comparative Genomic Analysis Discloses Differential Distribution of Antibiotic Resistance Determinants between Worldwide Strains of the Emergent ST213 Genotype of Salmonella Typhimurium

Salmonella enterica constitutes a global public health concern as one of the main etiological agents of human gastroenteritis. The Typhimurium serotype is frequently isolated from human, animal, food, and environmental samples, with its sequence type 19 (ST19) being the most widely distributed around the world as well as the founder genotype. The replacement of the ST19 genotype with the ST213 genotype that has multiple antibiotic resistance (MAR) in human and food samples was first observed in Mexico. The number of available genomes of ST213 strains in public databases indicates its fast worldwide dispersion, but its public health relevance is unknown. A comparative genomic analysis conducted as part of this research identified the presence of 44 genes, 34 plasmids, and five point mutations associated with antibiotic resistance, distributed across 220 genomes of ST213 strains, indicating the MAR phenotype. In general, the grouping pattern in correspondence to the presence/absence of genes/plasmids that confer antibiotic resistance cluster the genomes according to the geographical origin where the strain was isolated. Genetic determinants of antibiotic resistance group the genomes of North America (Canada, Mexico, USA) strains, and suggest a dispersion route to reach the United Kingdom and, from there, the rest of Europe, then Asia and Oceania. The results obtained here highlight the worldwide public health relevance of the ST213 genotype, which contains a great diversity of genetic elements associated with MAR.

Clustered Regularly Interspaced Short Palindromic Repeats Genotyping of Multidrug-Resistant Salmonella Heidelberg Strains Isolated From the Poultry Production Chain Across Brazil

Salmonella enterica subsp. enterica serovar Heidelberg has been associated with a broad host range, such as poultry, dairy calves, swine, wild birds, environment, and humans. The continuous evolution of S. Heidelberg raises a public health concern since there is a global dispersal of lineages harboring a wide resistome and virulome on a global scale. Here, we characterized the resistome, phylogenetic structure and clustered regularly interspaced short palindromic repeats (CRISPR) array composition of 81 S. Heidelberg strains isolated from broiler farms (n = 16), transport and lairage (n = 5), slaughterhouse (n = 22), and retail market (n = 38) of the poultry production chain in Brazil, between 2015 and 2016 using high-resolution approaches including whole-genome sequencing (WGS) and WGS-derived CRISPR genotyping. More than 91% of the S. Heidelberg strains were multidrug-resistant. The total antimicrobial resistance (AMR) gene abundances did not vary significantly across regions and sources suggesting the widespread distribution of antibiotic-resistant strains from farm to market. The highest AMR gene abundance was observed for fosA7, aac(6')-Iaa, sul2, tet(A), gyrA, and parC for 100% of the isolates, followed by 88.8% for bla CMY-2. The β-lactam resistance was essentially driven by the presence of the plasmid-mediated AmpC (pAmpC) bla CMY-2 gene, given the isolates which did not carry this gene were susceptible to cefoxitin (FOX). Most S. Heidelberg strains were classified within international lineages, which were phylogenetically nested with Salmonella strains from European countries; while CRISPR genotyping analysis revealed that the spacer content was overall highly conserved, but distributed into 13 distinct groups. In summary, our findings underscore the potential role of S. Heidelberg as a key pathogen disseminated from farm to fork in Brazil and reinforce the importance of CRISPR-based genotyping for salmonellae. Hence, we emphasized the need for continuous mitigation programs to monitor the dissemination of this high-priority pathogen.

Dynamics of Salmonella enterica and antimicrobial resistance in the Brazilian poultry industry and global impacts on public health

Non-typhoidal Salmonella enterica is a common cause of diarrhoeal disease; in humans, consumption of contaminated poultry meat is believed to be a major source. Brazil is the world's largest exporter of chicken meat globally, and previous studies have indicated the introduction of Salmonella serovars through imported food products from Brazil. Here we provide an in-depth genomic characterisation and evolutionary analysis to investigate the most prevalent serovars and antimicrobial resistance (AMR) in Brazilian chickens and assess the impact to public health of products contaminated with S. enterica imported into the United Kingdom from Brazil. To do so, we examine 183 Salmonella genomes from chickens in Brazil and 357 genomes from humans, domestic poultry and imported Brazilian poultry products isolated in the United Kingdom. S. enterica serovars Heidelberg and Minnesota were the most prevalent serovars in Brazil and in meat products imported from Brazil into the UK. We extended our analysis to include 1,259 publicly available Salmonella Heidelberg and Salmonella Minnesota genomes for context. The Brazil genomes form clades distinct from global isolates, with temporal analysis suggesting emergence of these Salmonella Heidelberg and Salmonella Minnesota clades in the early 2000s, around the time of the 2003 introduction of the Enteritidis vaccine in Brazilian poultry. Analysis showed genomes within the Salmonella Heidelberg and Salmonella Minnesota clades shared resistance to sulphonamides, tetracyclines and beta-lactams conferred by sul2, tetA and blaCMY-2 genes, not widely observed in other co-circulating serovars despite similar selection pressures. The sul2 and tetA genes were concomitantly carried on IncC plasmids, whereas blaCMY-2 was either co-located with the sul2 and tetA genes on IncC plasmids or independently on IncI1 plasmids. Long-term surveillance data collected in the UK showed no increase in the incidence of Salmonella Heidelberg or Salmonella Minnesota in human cases of clinical disease in the UK following the increase of these two serovars in Brazilian poultry. In addition, almost all of the small number of UK-derived genomes which cluster with the Brazilian poultry-derived sequences could either be attributed to human cases with a recent history of foreign travel or were from imported Brazilian food products. These findings indicate that even should Salmonella from imported Brazilian poultry products reach UK consumers, they are very unlikely to be causing disease. No evidence of the Brazilian strains of Salmonella Heidelberg or Salmonella Minnesota were observed in UK domestic chickens. These findings suggest that introduction of the Salmonella Enteritidis vaccine, in addition to increasing antimicrobial use, could have resulted in replacement of salmonellae in Brazilian poultry flocks with serovars that are more drug resistant, but less associated with disease in humans in the UK. The plasmids conferring resistance to beta-lactams, sulphonamides and tetracyclines likely conferred a competitive advantage to the Salmonella Minnesota and Salmonella Heidelberg serovars in this setting of high antimicrobial use, but the apparent lack of transfer to other serovars present in the same setting suggests barriers to horizontal gene transfer that could be exploited in intervention strategies to reduce AMR. The insights obtained reinforce the importance of One Health genomic surveillance.

Rural Raccoons (Procyon lotor) Not Likely to Be a Major Driver of Antimicrobial Resistant Human Salmonella Cases in Southern Ontario, Canada: A One Health Epidemiological Assessment Using Whole-Genome Sequence Data

Non-typhoidal Salmonella infections represent a substantial burden of illness in humans, and the increasing prevalence of antimicrobial resistance among these infections is a growing concern. Using a combination of Salmonella isolate short-read whole-genome sequence data from select human cases, raccoons, livestock and environmental sources, and an epidemiological framework, our objective was to determine if there was evidence for potential transmission of Salmonella and associated antimicrobial resistance determinants between these different sources in the Grand River watershed in Ontario, Canada. Logistic regression models were used to assess the potential associations between source type and the presence of select resistance genes and plasmid incompatibility types. A total of 608 isolates were obtained from the following sources: humans (n = 58), raccoons (n = 92), livestock (n = 329), and environmental samples (n = 129). Resistance genes of public health importance, including blaCMY−2, were identified in humans, livestock, and environmental sources, but not in raccoons. Most resistance genes analyzed were significantly more likely to be identified in livestock and/or human isolates than in raccoon isolates. Based on a 3,002-loci core genome multi-locus sequence typing (cgMLST) scheme, human Salmonella isolates were often more similar to isolates from livestock and environmental sources, than with those from raccoons. Rare instances of serovars S. Heidelberg and S. Enteritidis in raccoons likely represent incidental infections and highlight possible acquisition and dissemination of predominantly poultry-associated Salmonella by raccoons within these ecosystems. Raccoon-predominant serovars were either not identified among human isolates (S. Agona, S. Thompson) or differed by more than 350 cgMLST loci (S. Newport). Collectively, our findings suggest that the rural population of raccoons on swine farms in the Grand River watershed are unlikely to be major contributors to antimicrobial resistant human Salmonella cases in this region.

Assessment of maternal immunity against Salmonella enterica serovar Heidelberg in progeny of broiler breeders vaccinated with different formulations of bacterins

Salmonella Heidelberg (SH) has been reported in broiler flocks of many countries. The ability of some SH strains from poultry origin to cause foodborne infections in humans is a concern. Usually infection of broiler flocks by SH occurs in the first days of life. Therefore, control measures should start early post-hatch. One of the strategies is to generate high titers of anti-Salmonella IgY in breeders by using bacterins to provide passive immunity to their progeny. In this study three broiler breeder flocks were submitted to three Salmonella vaccination regimes (two doses of vaccine 1, two doses of vaccine 2 and non-vaccinated). When breeders were 30 and 55 weeks-old, part of their offspring were separated and challenged with a SH strain at three days of age. Dissemination to organs, caecal colonization and faecal excretion of SH were evaluated over 20 days. Chicks from vaccinated 30 week-old breeders presented lower amounts of SH in caecal content at 1, 3 and 6 days-post infection, correlating with high titers of maternal anti-Salmonella IgY in their yolk. In contrast, there were no differences in counts of SH in caecal content of chicks when their parents were 55 weeks-old and titers of IgY were reduced. Amounts of SH in liver and spleen were low and there were no differences among birds over the experiment. Progeny from 30 week-old flock vaccinated with vaccine 1 also showed lower SH faecal shedding than the remaining birds. Apparently, the maternal IgY was associated with reductions in intestinal infection by SH.

Molecular genotyping reveals inter-regional relatedness among antimicrobial resistant Salmonella Minnesota strains isolated from poultry farm and humans, Brazil

Genetic profiles of Salmonella Minnesota isolates were analyzed using pulsed-field gel electrophoresis (PFGE). In total, 13 isolates obtained from the broiler industry collected in the states of Minas Gerais (11) and São Paulo (2), as well as five recovered from cases of foodborne infections in humans in the states of Minas Gerais (2), Santa Catarina (1), and Rio Grande do Sul (2), were submitted to PFGE. These 18 S. Minnesota isolates together with other 12 of poultry origin were also subjected to antimicrobial susceptibility testing. The PFGE analysis of 18 strains of S. Minnesota generated a dendrogram that grouped the isolates with 83-90% similarity into four main clusters. Among them, cluster "A" grouped the majority of isolates (13), including two of human origin that showed 90% similarity with a broiler isolate, both recovered in Minas Gerais. The S. Minnesota isolates showed resistance to tetracycline (80%), cefoxitin (80%), ceftazidime (46.7%), nalidixic acid (23.3%), ciprofloxacin (13.3%), and streptomycin (10%). No resistance to gentamicin, chloramphenicol, meropenem, nitrofurantoin, and sulfamethoxazole-trimethoprim was found. Moreover, 23.3% of the evaluated isolates presented multi-resistance profile, all from Minas Gerais. The results highlight the importance of further studies involving S. Minnesota, which is prevalent in the Brazilian broiler flocks and could provoke foodborne infection in humans.

Genomic characteristics and comparative genomics of Salmonella enterica subsp. enterica serovar Schwarzengrund strain S16 isolated from chicken feces

Background

Salmonella enterica subsp. enterica serovar Schwarzengrund (S. Schwarzengrund) is most frequently isolated from commensals humans or poultry. Here we report S. Schwarzengrund strain S16, the first sequenced genome in the Republic of Korea. Additionally, genome sequencing for strain S16 was performed and compared with other S. Schwarzengrund genomes obtained from public database.

Results

Strain S16 was isolated from chicken feces. The complete genome consists of one chromosome and one plasmid. The genome size is 4,822,755 bp with 4852 coding sequences. Strain S16 was determined as serovar Schwarzengrund by in silico serotyping and typed as sequence type (ST) 96. Forty-six S. Schwarzengrund genomes yielded a pangenome of 7112 genes, core-genome of 3374 genes, accessory-genome of 2906 genes, and unique-genome of 835 genes. Eighty-one genes were unique to strain S16, including hypothetical proteins and transcriptional regulators. Genotypic analysis of antibiotic resistance of strain S16 confirmed resistance to amikacin, ciprofloxacin, sulfamethoxazole, streptomycin, and tetracycline. Unlike other S. Schwarzengrund genomes, strain S16 had a mutation of gyrB. Moreover, similar to other S. Schwarzengrund genomes reported in other countries, strain S16 was harbored for 153 virulence genes including Saf operon and cdtB gene. All the antibiotic resistance genes and virulence genes were present in the core- or accessory-genomes.

Conclusions

Complete genome of strain S16 was sequenced. Comparative genomic analysis revealed several genes responsible for antibiotic resistance and specific genomic features of strain S16 and identified virulence factors that might contribute to the human and animal pathogenicity of other S. Schwarzengrund genomes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13099-021-00476-8.

Genomic characterization and antimicrobial resistance profiles of Salmonella enterica serovar Infantis isolated from food, humans and veterinary-related sources in Brazil

AIMS

To characterize the genetic relatedness, phenotypic and genotypic antimicrobial resistance and plasmid content of 80 Salmonella Infantis strains isolated from food, humans and veterinary sources from 2013 to 2018 in Brazil.

METHODS AND RESULTS

Pulsed-field gel electrophoresis and single-nucleotide polymorphism analysis showed major clusters containing 50% and 38.8% of the strains studied respectively. Multilocus sequence typing assigned all strains to ST32. Disk-diffusion revealed that 90% of the strains presented resistant or intermediate resistant profiles and 38.8% displayed multidrug resistance. Resistance genes for aminoglycosides (aac(6')-Iaa; aadA12; aph(3″-Ib; aph(6)-Id), β-lactams (bla_TEM-1 ; bla_CTX-M-8 ; bla_CMY-2 ), trimethoprim (dfrA8), tetracycline (tet(A)), amphenicols (floR), sulfonamide (sul2), efflux pumps (mdsA; mdsB), chromosomal point mutations in gyrB, parC, acrB and pmrA were detected. Strains harboured IncI, IncF, IncX, IncQ, IncN and IncR plasmids.

CONCLUSIONS

The presence of a prevalent S. Infantis subtype in Brazil and the high antimicrobial resistance rates reinforced the potential hazard of this serovar for the public health and food safety fields.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first study characterizing a large set of S. Infantis from Brazil by whole-genome sequencing, which provided a better local and global comprehension about the distribution and characteristics of this serovar of importance in the food, human and veterinary fields.

Multidrug-Resistant and Extended-Spectrum β-Lactamase-Producing Salmonella enterica Serotype Heidelberg Is Widespread in a Poultry Processing Facility in Southern Brazil

ABSTRACT

This study was conducted to characterize the distribution of Salmonella isolates in a poultry processing facility and to identify their antibiotic resistance profiles. Salmonella enterica was detected in 146 samples (66.7%), and 125 isolates were identified as Salmonella Heidelberg (n = 123), Salmonella Abony (n = 1), and Salmonella O:4,5 (n = 1). Salmonella Heidelberg isolates were subjected to XbaI macrorestriction analysis and pulsed-field gel electrophoresis. The 66 pulsotypes obtained were grouped into four major clusters, indicating cross-contamination and persistence of this serotype in the processing facility. Selected S. enterica isolates were characterized by their antibiotic resistance, and most (n = 122, 97.6%) were multidrug resistant. Resistance to third-generation cephalosporins ceftazidime (84 isolates, 67.2%) and cefotaxime and ceftriaxone (91 isolates, 72.8%) was particularly prevalent. Production of extended-spectrum β-lactamases (ESBL) was identified in 24 isolates (19.2%), and ESBL-producing isolates were resistant to at least eight antibiotics. This study revealed the high prevalence of Salmonella Heidelberg in the poultry chain, providing insight into the ecology of this pathogen in this facility. The high prevalence of multidrug-resistant S. enterica is a concern due to the potential consequences for public health.

HIGHLIGHTS

Using whole-genome sequence data to examine the epidemiology of Salmonella, Escherichia coli and associated antimicrobial resistance in raccoons (Procyon lotor), swine manure pits, and soil samples on swine farms in southern Ontario, Canada

To better understand the contribution of wildlife to the dissemination of Salmonella and antimicrobial resistance in Salmonella and Escherichia coli, we examined whole-genome sequence data from Salmonella and E. coli isolates collected from raccoons (Procyon lotor) and environmental sources on farms in southern Ontario. All Salmonella and phenotypically resistant E. coli collected from raccoons, soil, and manure pits on five swine farms as part of a previous study were included. We assessed for evidence of potential transmission of these organisms between different sources and farms utilizing a combination of population structure assessments (using core-genome multi-locus sequence typing), direct comparisons of multi-drug resistant isolates, and epidemiological modeling of antimicrobial resistance (AMR) genes and plasmid incompatibility (Inc) types. Univariable logistic regression models were fit to assess the impact of source type, farm location, and sampling year on the occurrence of select resistance genes and Inc types. A total of 159 Salmonella and 96 resistant E. coli isolates were included. A diversity of Salmonella serovars and sequence types were identified, and, in some cases, we found similar or identical Salmonella isolates and resistance genes between raccoons, soil, and swine manure pits. Certain Inc types and resistance genes associated with source type were consistently more likely to be identified in isolates from raccoons than swine manure pits, suggesting that manure pits are not likely a primary source of those particular resistance determinants for raccoons. Overall, our data suggest that transmission of Salmonella and AMR determinants between raccoons and swine manure pits is uncommon, but soil-raccoon transmission appears to be occurring frequently. More comprehensive sampling of farms, and assessment of farms with other livestock species, as well as additional environmental sources (e.g., rivers) may help to further elucidate the movement of resistance genes between these various sources.

Molecular characterization of Salmonella spp. and Listeria monocytogenes strains from biofilms in cattle and poultry slaughterhouses located in the federal District and State of Goiás, Brazil

Listeria monocytogenes and Salmonella spp. are considered important foodborne pathogens that are commonly associated with foods of animal origin. The aim of this study was to perform molecular characterization of L. monocytogenes and Salmonella spp. isolated from biofilms of cattle and poultry slaughterhouses located in the Federal District and State of Goiás, Brazil. Fourteen L. monocytogenes isolates and one Salmonella sp. were detected in poultry slaughterhouses. No isolates were detected in cattle slaughterhouses. All L. monocytogenes isolates belonged to lineage II, and 11 different pulsotypes were detected. Pulsed-field gel electrophoresis analysis revealed the dissemination of two strains within one plant, in addition to the regional dissemination of one of them. The Salmonella isolate was identified via whole genome sequencing as Salmonella enterica serovar Minnesota ST548. In the sequence analysis, no premature stop codons were detected in the inlA gene of Listeria. All isolates demonstrated the ability to adhere to Caco-2 cells, while 50% were capable of invading them. Antimicrobial resistance was detected in 57.1% of the L. monocytogenes isolates, and resistance to sulfonamide was the most common feature. The tetC, ermB, and tetM genes were detected, and four isolates were classified as multidrug-resistant. Salmonella sp. was resistant to nine antimicrobials and was classified as multidrug-resistant. Resistance genes qnrB19, blaCMY-2, aac(6')-Iaa, sul2, and tetA, and a mutation in the parC gene were detected. The majority (78.5%) of the L. monocytogenes isolates were capable of forming biofilms after incubation at 37°C for 24 h, and 64.3% were capable of forming biofilms after incubation at 12°C for 168 h. There was no statistical difference in the biofilm-forming capacity under the different evaluated conditions. Salmonella sp. was capable of forming biofilms at both tested temperatures. Biofilm characterization was confirmed by collecting the samples consistently, at the same sampling points, and by assessing biofilm formation in vitro. These results highlight the potential risk of cross-contamination in poultry slaughterhouses and the importance of surveillance and pathogen control maintenance programs within the meat production industry.

Whole Genome Sequencing Analysis of Salmonella enterica Serovar Typhi: History and Current Approaches

In recent years, the advance in whole-genome sequencing technology has changed the study of infectious diseases. The emergence of genome sequencing has improved the understanding of infectious diseases, which has revamped many fields, such as molecular microbiology, epidemiology, infection control, and vaccine production. In this review we discuss the findings of Salmonella enterica serovar Typhi genomes, publicly accessible from the initial complete genome to the recent update of Salmonella enterica serovar Typhi genomes, which has greatly improved Salmonella enterica serovar Typhi and other pathogen genomic research. Significant information on genetic changes, evolution, antimicrobial resistance, virulence, pathogenesis, and investigation from the genome sequencing of S. Typhi is also addressed. This review will gather information on the variation of the Salmonella enterica serovar Typhi genomes and hopefully facilitate our understanding of their genome evolution, dynamics of adaptation, and pathogenesis for the development of the typhoid point-of-care diagnostics, medications, and vaccines.

Isolation and molecular characterization of multidrug-resistant Salmonella enterica serovars

BACKGROUND

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

METHODS AND RESULTS

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

CONCLUSIONS

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

Recent Evolution and Genomic Profile of Salmonella enterica Serovar Heidelberg Isolates from Poultry Flocks in Brazil

Salmonella enterica serovar Heidelberg is isolated from poultry-producing regions around the world. In Brazil, S. Heidelberg has been frequently detected in poultry flocks, slaughterhouses, and chicken meat. The goal of the present study was to assess the population structure, recent temporal evolution, and some important genetic characteristics of S. Heidelberg isolated from Brazilian poultry farms. Phylogenetic analysis of 68 S. Heidelberg genomes sequenced here and additional whole-genome data from NCBI demonstrated that all isolates from the Brazilian poultry production chain clustered into a monophyletic group, here called S. Heidelberg Brazilian poultry lineage (SH-BPL). Bayesian analysis defined the time of the most recent common ancestor (tMRCA) as 2004, and the overall population size (N_e) was constant until 2008, when an ∼10-fold N_e increase was observed until circa 2013. SH-BPL presented at least two plasmids with replicons ColpVC (n = 68; 100%), IncX1 (n = 66; 97%), IncA/C2 (n = 65; 95.5%), ColRNAI (n = 43; 63.2%), IncI1 (n = 32; 47%), ColMG828, Col156, IncHI2A, IncHI2, IncQ1, IncX4, IncY, and TrfA (each with n < 4; <4% each). Antibiotic resistance genes were found, with high frequencies of fosA7 (n = 68; 100%), mdf(A) (n = 68; 100%), tet(34) (n = 68; 100%), sul2 (n = 64; 94.1%), and blaCMY-2 (n = 56; 82.3%), along with an overall multidrug resistance (MDR) profile. Ten Salmonella pathogenicity islands (SPI1 to SPI5, SPI9, and SPI11 to SPI14) and 139 virulence genes were also detected. The SH-BPL profile was like those of other previous S. Heidelberg isolates from poultry around the world in the 1990s. In conclusion, the present study demonstrates the recent introduction (2004) and high level of dissemination of an MDR S. Heidelberg lineage in Brazilian poultry operations. IMPORTANCE S. Heidelberg is the most frequent serovar in several broiler farms from the main Brazilian poultry-producing regions. Therefore, avian-source foods (mainly chicken carcasses) commercialized in the country and exported to other continents are contaminated with this foodborne pathogen, generating several national and international economic losses. In addition, isolates of this serovar are usually resistant to antibiotics and can cause human invasive and septicemic infection, representing a public health concern. This study demonstrates the use of whole-genome sequencing (WGS) to obtain epidemiological information for one S. Heidelberg lineage highly spread among Brazilian poultry farms. This information will help to define biosecurity measures to control this important Salmonella serovar in Brazilian and worldwide poultry operations.

Dissection of Highly Prevalent qnrS1-Carrying IncX Plasmid Types in Commensal Escherichia coli from German Food and Livestock

Plasmids are mobile genetic elements, contributing to the spread of resistance determinants by horizontal gene transfer. Plasmid-mediated quinolone resistances (PMQRs) are important determinants able to decrease the antimicrobial susceptibility of bacteria against fluoroquinolones and quinolones. The PMQR gene qnrS1, especially, is broadly present in the livestock and food sector. Thus, it is of interest to understand the characteristics of plasmids able to carry and disseminate this determinant and therewith contribute to the resistance development against this class of high-priority, critically important antimicrobials. Therefore, we investigated all commensal Escherichia (E.) coli isolates, with reduced susceptibility to quinolones, recovered during the annual zoonosis monitoring 2017 in the pork and beef production chain in Germany (n = 2799). Through short-read whole-genome sequencing and bioinformatics analysis, the composition of the plasmids and factors involved in their occurrence were determined. We analysed the presence and structures of predominant plasmids carrying the PMQR qnrS1. This gene was most frequently located on IncX plasmids. Although the E. coli harbouring these IncX plasmids were highly diverse in their sequence types as well as their phenotypic resistance profiles, the IncX plasmids-carrying the qnrS1 gene were rather conserved. Thus, we only detected three distinct IncX plasmids carrying qnrS1 in the investigated isolates. The IncX plasmids were assigned either to IncX1 or to IncX3. All qnrS1-carrying IncX plasmids further harboured a β-lactamase gene (bla). In addition, all investigated IncX plasmids were transmissible. Overall, we found highly heterogenic E. coli harbouring conserved IncX plasmids as vehicles for the most prevalent qnr gene qnrS1. These IncX plasmids may play an important role in the dissemination of those two resistance determinants and their presence, transfer and co-selection properties require a deeper understanding for a thorough risk assessment.

Exploring Phenolic Compounds as Quorum Sensing Inhibitors in Foodborne Bacteria

The emergence of multidrug-resistant bacteria stimulates the search for new substitutes to traditional antimicrobial agents, especially molecules with antivirulence properties, such as those that interfere with quorum sensing (QS). This study aimed to evaluate the potential of phenolic compounds for QS inhibition in a QS biosensor strain (Chromobacterium violaceum) and three foodborne bacterial species (Aeromonas hydrophila, Salmonella enterica serovar Montevideo, and Serratia marcescens). Initially, an in silico molecular docking study was performed to select the compounds with the greatest potential for QS inhibition, using structural variants of the CviR QS regulator of C. violaceum as target. Curcumin, capsaicin, resveratrol, gallic acid, and phloridizin presented good affinity to at least four CviR structural variants. These phenolic compounds were tested for antimicrobial activity, inhibition of biofilm formation, and anti-QS activity. The antimicrobial activity when combined with kanamycin was also assessed. Curcumin, capsaicin, and resveratrol inhibited up to 50% of violacein production by C. violaceum. Biofilm formation was inhibited by resveratrol up to 80% in A. hydrophila, by capsaicin and curcumin up to 40% in S. Montevideo and by resveratrol and capsaicin up to 60% in S. marcescens. Curcumin completely inhibited swarming motility in S. marcescens. Additionally, curcumin and resveratrol increased the sensitivity of the tested bacteria to kanamycin. These results indicate that curcumin and resveratrol at concentrations as low as 6μM are potential quorum sensing inhibitors besides having antimicrobial properties at higher concentrations, encouraging applications in the food and pharmaceutical industries.

Phylogenetic relationship and genomic characterization of Salmonella Typhimurium strains isolated from swine in Brazil

Salmonella Typhimurium has been transmitted between humans and animals. Although, Brazil has been one of the largest pork meat exporters worldwide, there are few studies that characterized epidemiologically S. Typhimurium strains from swine. The aims of this work were to study the phylogenetic relationship of S. Typhimurium genomes isolated from swine in Brazil among themselves and with other genomes isolated from several sources and countries using wgMLST and cgMLST and to perform the search of Salmonella pathogenicity islands (SPIs). In addition, for S. Typhimurium strains from swine to compare the virulence and antimicrobial resistance genes by VFDB and ResFinder, genetic content by BLAST Atlas and orthologous proteins clusters by OrthoVenn. The constructed phylogenetic trees by wgMLST and cgMLST grouped the majority (92.3% and 80.7%, respectively) of the strains isolated from swine in Brazil into the same group. All the isolates contained important SPIs (SPI-1, SPI-2, SPI-3, SPI-5 and SPI-9). A total of 100 and 31 virulence and resistance genes were detected in the S. Typhimurium strains isolated from swine, respectively. The BLAST Atlas and orthologous proteins analysis found regions of phages and differences in metabolic, regulatory and cellular processes among S. Typhimurium LT2 and S. Typhimurium isolates from swine. In conclusion, molecular typing based in the wgMLST and cgMLST suggested that the S. Typhimurium isolates from swine studied were genetically related. The pathogenic potential of the strains studied was corroborated by the presence of important SPIs and virulence genes. The high number of antimicrobial resistance genes detected is worrying and reinforced their potential risk in swine in Brazil. The comparison by BLAST Atlas suggested differences in mobile genetic elements among S. Typhimurium LT2 and S. Typhimurium isolates from swine in Brazil. The orthologous proteins analysis revealed unique genes related to important cellular processes in the strains from swine.

Molecular Characterization and Survive Abilities of Salmonella Heidelberg Strains of Poultry Origin in Brazil

The aim of the study was to evaluate the genotypic and phenotypic characteristics of 20 strains of S. Heidelberg (SH) isolated from broilers produced in southern Brazil. The similarity and presence of genetic determinants linked to virulence, antimicrobial resistance, biofilm formation, and in silico-predicted metabolic interactions revealed this serovar as a threat to public health. The presence of the ompC, invA, sodC, avrA, lpfA, and agfA genes was detected in 100% of the strains and the luxS gene in 70% of them. None of the strains carries the bla_SHV, mcr-1, qnrA, qnrB, and qnrS genes. All strains showed a multidrug-resistant profile to at least three non-β-lactam drugs, which include colistin, sulfamethoxazole, and tetracycline. Resistance to penicillin, ceftriaxone (90%), meropenem (25%), and cefoxitin (25%) were associated with the presence of bla_CTX–M and bla_CMY–2 genes. Biofilm formation reached a mature stage at 25 and 37°C, especially with chicken juice (CJ) addition. The sodium hypochlorite 1% was the least efficient in controlling the sessile cells. Genomic analysis of two strains identified more than 100 virulence genes and the presence of resistance to 24 classes of antibiotics correlated to phenotypic tests. Protein-protein interaction (PPI) prediction shows two metabolic pathways correlation with biofilm formation. Virulence, resistance, and biofilm determinants must be constant monitoring in SH, due to the possibility of occurring infections extremely difficult to cure and due risk of the maintenance of the bacterium in production environments.

EFSA Panel on Biological Hazards (BIOHAZ), Koutsoumanis K, Allende A, Álvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Ru G, Simmons M, Skandamis P, Suffredini E, Argüello H, Berendonk T, Cavaco LM, Gaze W, Schmitt H, Topp E, Guerra B, Liébana E, Stella P, Peixe L. Role played by the environment in the emergence and spread of antimicrobial resistance (AMR) through the food chain

The role of food-producing environments in the emergence and spread of antimicrobial resistance (AMR) in EU plant-based food production, terrestrial animals (poultry, cattle and pigs) and aquaculture was assessed. Among the various sources and transmission routes identified, fertilisers of faecal origin, irrigation and surface water for plant-based food and water for aquaculture were considered of major importance. For terrestrial animal production, potential sources consist of feed, humans, water, air/dust, soil, wildlife, rodents, arthropods and equipment. Among those, evidence was found for introduction with feed and humans, for the other sources, the importance could not be assessed. Several ARB of highest priority for public health, such as carbapenem or extended-spectrum cephalosporin and/or fluoroquinolone-resistant Enterobacterales (including Salmonella enterica), fluoroquinolone-resistant Campylobacter spp., methicillin-resistant Staphylococcus aureus and glycopeptide-resistant Enterococcus faecium and E. faecalis were identified. Among highest priority ARGs bla CTX -M, bla VIM, bla NDM, bla OXA -48-like, bla OXA -23, mcr, armA, vanA, cfr and optrA were reported. These highest priority bacteria and genes were identified in different sources, at primary and post-harvest level, particularly faeces/manure, soil and water. For all sectors, reducing the occurrence of faecal microbial contamination of fertilisers, water, feed and the production environment and minimising persistence/recycling of ARB within animal production facilities is a priority. Proper implementation of good hygiene practices, biosecurity and food safety management systems is very important. Potential AMR-specific interventions are in the early stages of development. Many data gaps relating to sources and relevance of transmission routes, diversity of ARB and ARGs, effectiveness of mitigation measures were identified. Representative epidemiological and attribution studies on AMR and its effective control in food production environments at EU level, linked to One Health and environmental initiatives, are urgently required.

Antimicrobial Use in Brazilian Swine Herds: Assessment of Use and Reduction Examples

Brazil, as a major pig producer, is currently experiencing the widespread use of antimicrobials as a serious issue to be addressed. For measures to be taken in this direction, the extent of the problem must be known. The goal of this study was to evaluate the use of antimicrobials in 25 Brazilian swine herds. Antimicrobial use from birth to slaughter was correlated with biosecurity and productivity. After the first assessment (2016; M0), 13 herds implemented good practices to reduce antimicrobial use. Four years after the implementation of these measures (2020; M1), data about antimicrobial usage from these herds were collected. The results of the first assessment (M0) demonstrated a troublesome scenario: the mean value of antimicrobials used was 358.4 mg/kg of pig produced; the median of the pig’s lifetime exposure to antimicrobials was 73.7%, and the median number of drugs used was seven. A positive correlation between the antimicrobials consumed and the pig’s antimicrobial exposure time was detected. Nevertheless, these data did not correlate with biosecurity score or productivity. A significant difference was detected in M1, where a median 30% reduction in antimicrobials consumed was detected. There was also a 44.3% reduction of the pig’s lifetime exposure to antimicrobials. The median number of drugs used was reduced from seven to five. Antimicrobial use did not always reflect the sanitary condition or the real therapeutic needs, easily leading to overuse.

Whole-Genome Sequencing Reveals the Presence of the blaCTX-M-65 Gene in Extended-Spectrum β-Lactamase-Producing and Multi-Drug-Resistant Clones of Salmonella Serovar Infantis Isolated from Broiler Chicken Environments in the Galapagos Islands

Salmonella Infantis, a common contaminant of poultry products, is known to harbor mobile genetic elements that confer multi-drug resistance (MDR) and have been detected in many continents. Here, we report four MDR S. Infantis strains recovered from poultry house environments in Santa Cruz Island of the Galapagos showing extended-spectrum β-lactamase (ESBL) resistance and reduced fluoroquinolone susceptibility. Whole-genome sequencing (WGS) revealed the presence of the ESBL-conferring bla_CTX-M-65 gene in an IncFIB-like plasmid in three S. Infantis isolates. Multi-locus sequence typing (MLST) and single nucleotide variant/polymorphism (SNP) SNVPhyl analysis showed that the S. Infantis isolates belong to sequence type ST32, likely share a common ancestor, and are closely related (1–3 SNP difference) to bla_CTX-M-65-containing clinical and veterinary S. Infantis isolates from the United States and Latin America. Furthermore, phylogenetic analysis of SNPs following core-genome alignment (i.e., ParSNP) inferred close relatedness between the S. Infantis isolates from Galapagos and the United States. Prophage typing confirmed the close relationship among the Galapagos S. Infantis and was useful in distinguishing them from the United States isolates. This is the first report of MDR bla_CTX-M-65-containing S. Infantis in the Galapagos Islands and highlights the need for increased monitoring and surveillance programs to determine prevalence, sources, and reservoirs of MDR pathogens.

Influence of different periods of pre-slaughter fasting on microbiological quality of bullfrog carcasses (Lithobates catesbeianus)

ABSTRACT The aim of this study was to evaluate the influence of different periods of pre-slaughter fasting (F1: 2 to 24 hours and F2: 48 to 72 hours) on the counts of hygiene indicator microorganisms and the presence of Salmonella spp. in carcasses of bullfrogs. Two different stages of the slaughter process were analyzed: after bleeding (A) and after the final carcasses cleaning (B). Samples from each fasting period were analyzed to count hygiene indicator microorganisms (n=30) and Salmonella spp. (n=140). For aerobic mesophilic microorganisms, the variation in fasting periods caused a reduction of 0.69 log10 CFU / g (P<0.05) in F2 when compared to F1 at point B of the slaughter. Coliforms at 35º C and Escherichia coli showed no differences (P >0.05) between the fasting analyzed periods. Considering the presence of E. coli, it was observed that F2 resulted in a reduction of 30% (P<0.05) positivity on point B. For Salmonella spp., the results showed that F2 contributed to an 11.5% reduction in the presence of this bacteria at point B. (P<0.05). Therefore, it is concluded that 48 to 72 hours of pre-slaughter fasting resulted in a positive impact on the microbiological quality of bullfrog carcasses.

Genomic investigation of antimicrobial resistance determinants and virulence factors in Salmonella enterica serovars isolated from contaminated food and human stool samples in Brazil

This study investigated the antimicrobial resistance determinants, virulence factors and identified serovars in 37 Salmonella enterica strains isolated from human stool and contaminated foods linked to outbreaks that occurred in Brazil over 7 years using whole genome sequencing (WGS). Phylogenetic analysis of selected serovars (S. Typhimurium, S. Infantis, S. London, and S. Johannesburg) was performed. Ten distinct serovars were identified and, 51% of the tested strains (n = 19) showed disagreement with the previous conventional serotyping. The antimicrobial resistance (AMR) determinants or plasmids varied among the strains. Resistome analysis revealed the presence of resistance genes to aminoglycosides [aac (6')-laa, aph (3″)-lb, aph (6)-ld, aadA1 and aadA2], sulfonamides (sul1), trimethoprin (dfrA8), fosfomycin (fosA7) and tetracyclines (tetA, tetB, tetC), as well as point mutations in parC (T57S) and gyrA (S83F). Plasmidome showed the presence of IncHI2, IncHI2A, IncFIB (S), IncFII (S), IncI1 and p0111 plasmids. Eight Salmonella pathogenicity islands and up to 102 stress and/or virulence genes were identified in the evaluated genomes. Virulence genes of K88 fimbrial adhesin were first reported in S. enterica (S. Pomona, S. Bredeney and S. Mbandaka strains). pilW gene was first identified in S. Pomona. Phylogenetic analysis showed that some serovars circulated in Brazil for decades, primarily within the poultry production chain. Findings highlighted the virulence and AMR determinants in strains that may lead to recurring food outbreaks.

Genomic Analysis of Antimicrobial Resistance and Resistance Plasmids in Salmonella Serovars from Poultry in Nigeria

Antimicrobial resistance is a global public health concern, and resistance genes in Salmonella, especially those located on mobile genetic elements, are part of the problem. This study used phenotypic and genomic methods to identify antimicrobial resistance and resistance genes, as well as the plasmids that bear them, in Salmonella isolates obtained from poultry in Nigeria. Seventy-four isolates were tested for susceptibility to eleven commonly used antimicrobials. Plasmid reconstruction and identification of resistance and virulence genes were performed with a draft genome using in silico approaches in parallel with plasmid extraction. Phenotypic resistance to ciprofloxacin (50.0%), gentamicin (48.6%), nalidixic acid (79.7%), sulphonamides (71.6%) and tetracycline (59.5%) was the most observed. Antibiotic resistance genes (ARGs) detected in genomes corresponded well with these observations. Commonly observed ARGs included sul1, sul2, sul3, tet (A), tet (M), qnrS1, qnrB19 and a variety of aminoglycoside-modifying genes, in addition to point mutations in the gyrA and parC genes. Multiple ARGs were predicted to be located on IncN and IncQ1 plasmids of S. Schwarzengrund and S. Muenster, and most qnrB19 genes were carried by Col (pHAD28) plasmids. Seventy-two percent (19/24) of S. Kentucky strains carried multidrug ARGs located in two distinct variants of Salmonella genomic island I. The majority of strains carried full SPI-1 and SPI-2 islands, suggesting full virulence potential.

Genomic Characteristics of Colistin-Resistant Salmonella enterica subsp. enterica Serovar Infantis from Poultry Farms in the Republic of Serbia

The antimicrobial susceptibility testing was conducted on 174 single isolates from poultry farms in Serbia and it was determined that seven Salmonella spp. were multidrug resistant. Sixteen serotypes were detected, but only serotype Infantis confirmed reduced susceptibility to colistin. Seven colistin resistant Salmonella Infantis were studied in detail using the WGS approach. Three sequence types were identified corresponding to different epizootiology region. The isolate from the Province of Vojvodina 3842 and isolates from Jagodina (92 and 821) are represented by the sequence type ST413 and ST11, respectively. Four isolates from Kraljevo are ST32, a common S. Infantis sequence type in humans, poultry and food. The fosfomycin resistance gene fosA7 in isolate 3842 and the vgaA gene in isolate 8418/2948 encoding resistance to pleuromutilins were reported for the first time in serovar Infantis. The changes in relative expression of the phoP/Q, mgrB and pmrA/B genes were detected. Single nucleotide polymorphisms of the pmrB gene, including transitions Val164Gly or Val164Met, and Arg92Pro are described. Analyses of quinolone resistance determining region revealed substitutions Ser83Tyr in GyrA protein and Thr57Ser and Ser80Arg in ParC protein. Based on WGS data, there are two major clusters among analyzed Salmonella Infantis isolates from central Serbia.

Genomic Characterization of Salmonella Minnesota Clonal Lineages Associated with Poultry Production in Brazil

Salmonella serotype Minnesota has been increasingly detected in Brazilian poultry farms and food products (chicken meat, eggs) in recent years. In addition, S. Minnesota isolates from poultry are generally resistant to several antibiotics and persistent in farm environments. The present study aimed to assess phylogenomic diversity of S. Minnesota isolates from the poultry production chain in Brazil. In total, 107 worldwide S. Minnesota whole genomes (including 12 from Brazil) were analyzed using a comparative approach. Phylogenetic analysis demonstrated two clades more related to poultry production in Brazil: S. Minnesota poultry lineages I and II (SM-PLI and SM-PLII). Phylodynamic analysis demonstrated that SM-PLI had a common ancestor in 1915, while SM-PLII originated circa 1971. SM-PLII encompassed a higher number of isolates and presented a recent increase in effective population size (mainly from 2009 to 2012). Plasmids IncA/C2 and ColRNA, antimicrobial resistance genes (aph(3')-Ia, blaCMY-2, qnrB19, sul2, and tet(A)) and mainly a virulence genetic cluster (including the yersiniabactin operon) were detected in isolates from SM-PLI and/or SM-PLII. This study demonstrates the dissemination of two distinct S. Minnesota lineages with high resistance to antibiotics and important virulence genetic clusters in Brazilian poultry farms.