Uncommon Salmonella Infantis Variants with Incomplete Antigenic Formula in the Poultry Food Chain, Italy.

Uncommon Salmonella Infantis variants displaying only flagellar antigens phenotypically showed identical incomplete antigenic formula but differed by molecular serotyping. Although most formed rough colonies, all shared antimicrobial resistances and the presence of usg gene with wild-type Salmonella Infantis. Moreover, they were undistinguishable wild-type Salmonella Infantis by whole-genome sequencing.

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.

Oral vaccination of young broilers with a live Salmonella Typhimurium vaccine reduces caecal and internal organ colonization following a Salmonella Infantis challenge in a seeder-bird model.

Poultry products are an important source of foodborne Salmonella infections in humans. Amongst these, the prevalence of S. Infantis is rising. In this study, the protection efficacy of an authorized live-attenuated S. Typhimurium vaccine against S. Infantis, was examined using a seeder-bird model in broilers. Vaccinated birds displayed a significantly lower colonization of S. Infantis bacteria in the caeca compared to the non-vaccinated counterparts (P = 0.017), with no significant differences observed in the spleen among the groups, three days post-infection. Thirty-two days post-infection, the disparity in average S. Infantis concentration between all-vaccinated and non-vaccinated birds was significant in both caeca (P = 0.0003) and spleen (P = 0.0002). Interestingly, a third group, consisting of seeder birds that were not vaccinated but housed with vaccinated penmates, exhibited significantly lower S. Infantis levels in both caeca (P = 0.0014) and spleen (P < 0.0001) compared to the non-vaccinated group. These findings underscore the potential of a live-attenuated S. Typhimurium vaccine administered to 2-day-old chicks in conferring protection against S. Infantis in broilers up to slaughter age.

Emergence of Salmonella Infantis carrying the pESI-like plasmid from eggs in egg grading and packing plants in Korea.

The plasmid of emerging S. Infantis (pESI) or pESI-like plasmid in Salmonella enterica Infantis are consistently reported in poultry and humans worldwide. However, there has been limited research on these plasmids of S. Infantis isolated from eggs. Therefore, this study aimed to analyze the prevalence and characteristics of S. Infantis carrying the pESI-like plasmid from eggs in egg grading and packing plants. In this study, the pESI-like plasmid was only detected in 18 (78.3%) of 23 S. Infantis isolates, and it was absent in the other 9 Salmonella serovars. In particular, S. Infantis isolates carrying the pESI-like plasmid showed the significantly higher resistance to ß-lactams, phenicols, cephams, aminoglycosides, quinolones, sulfonamides, and tetracyclines than Salmonella isolates without the pESI-like plasmid (p < 0.05). Moreover, all S. Infantis isolates carrying the pESI-like plasmid were identified as extended-spectrum ß-lactamase (ESBL) producer, harboring the blaCTX-M-65 and blaTEM-1 genes, and carried non-ß-lactamase resistance genes (ant(3'')-Ia, aph(4)-Ia, aac(3)-IVa, aph(3')-Ic, sul1, tetA, dfrA14, and floR) against five antimicrobial classes. However, all isolates without the pESI-like plasmid only carried the blaTEM-1 gene among the ß-lactamase genes, and either had no non-ß-lactamase resistance genes or harbored non-ß-lactamase resistance genes against one or two antimicrobial classes. Furthermore, all S. Infantis isolates carrying the pESI-like plasmid carried class 1 and 2 integrons and the aadA1 gene cassette, but none of the other isolates without the pESI-like plasmid harbored integrons. In particular, D87Y substitution in the gyrA gene and IncP replicon type were observed in all the S. Infantis isolates carrying the pESI-like plasmid but not in the S. Infantis isolates without the pESI-like plasmid. The distribution of pulsotypes between pESI-positive and pESI-negative S. Infantis isolates was clearly distinguished, but all S. Infantis isolates were classified as sequence type 32, regardless of whether they carried the pESI-like plasmid. This study is the first to report the characteristics of S. Infantis carrying the pESI-like plasmid isolated from eggs and can provide valuable information for formulating strategies to control the spread of Salmonella in the egg industry worldwide.

Polymerase chain reaction for the in vitro detection of the pESI plasmid associated with the globally circulating Salmonella Infantis outbreak strain.

A globally circulating strain of Salmonella enterica serotype Infantis containing the pESI plasmid has increased in prevalence in poultry meat samples and cases of human infections. In this study, a polymerase chain reaction (PCR) protocol was designed to detect the pESI plasmid and confirm the Infantis serotype of Salmonella isolates. Primers were tested bioinformatically to predict specificity, sensitivity, and precision. A total of 54 isolates of Salmonella serotypes Infantis, Senftenberg, and Alachua were tested, with and without the pESI plasmid carriage. Isolates of 31 additional serotypes were also screened to confirm specificity to Infantis. Specificity, sensitivity, and precision of each primer were >0.95. All isolates tested produced the expected band sizes. This PCR protocol provides a rapid and clear result for the detection of the pESI plasmid and serotype Infantis and will allow for the in vitro detection for epidemiological studies where whole-genome sequencing is not available.

Activity of plant essential oils against clinically and environmentally isolated Salmonella enterica serotypes: in vitro assays and molecular docking.

This research aimed to evaluate the antimicrobial activity of essential oils (EOs) against clinically and environmentally isolated Salmonella serotypes. Oregano, thyme, and grapefruit EO compounds were identified, and the antimicrobial activity was evaluated against the S. Saintpaul, Oranienburg, and Infantis serotypes. In addition, molecular docking was performed to explore the possible mechanisms between compounds of EOs with microbial enzymes. Thymol was the main compound identified in oregano (44.0%) and thyme (31%) EOs, while d-limonene was present in a greater proportion in grapefruit EO. Oregano EO had the highest antimicrobial activity, followed by thyme and grapefruit EOs. Oregano and thyme EOs illustrated a greater inhibitory capacity to all serotypes, particularly with the environmental S. Saintpaul. Oregano EO presented values of minimum inhibitory concentration (MIC) and minimum bactericidal concentration of 0.1 µL/mL for all serotypes, while thyme and grapefruit EOs presented MIC values of 0.1 µL/mL for the clinical serotypes S. Infantis and S. Oranienburg, respectively. Molecular docking analysis showed the optimal binding free energies for thymol and carvacrol with glucokinase, ATP-dependent-6-fructokinase, outer membrane porin C, and topoisomerase IV. Our results indicate that these EOs can inhibit clinically and environmentally isolated Salmonella serotypes and can be used as alternatives for developing natural food preservatives.

Investigation of class 1 integrons and virulence genes in the emergent Salmonella serovar Infantis in Turkey.

The emerging situation of Salmonella enterica subsp. enterica serovar Infantis (S. Infantis) in Turkey was investigated in terms of virulence genes and mobile genetic elements such as Salmonella genomic island 1 (SGI1) and class 1 (C1) integron to see whether increased multidrug resistance (MDR) and ability to cause human cases is a consequence of their possession. Screening of SGI1 (and its variants) and C1 integrons was done with conventional PCR, while screening of gene cassettes and virulence genes was conducted with real-time PCR for 70 S. Infantis isolates from poultry products. SGI1 or its variants were not detected in any of the isolates. Sixty-eight of 70 isolates were detected to carry one C1 integron of size 1.0 kb. These integrons were detected to carry ant(3″)-Ia gene cassette explaining the streptomycin/spectinomycin resistance. Sequence analysis of gene cassettes belongs to four representing isolates which showed that, although their difference in isolation date and place, genetically, they are 99.9% similar. Virulence gene screening was introduced as genotypic virulence profiles. The most dominant profile for S. Infantis isolates, among twelve genes, was gatC-tcfA, which are known to be related to colonization at specific hosts. This study revealed the high percentage of C1 integron possession in S. Infantis isolates from poultry products in Turkey. It also showed the potential of S. Infantis strains to be resistant to more antimicrobial drugs. Moreover, a dominant profile of virulence genes that are uncommon for non-typhoidal Salmonella (NTS) serovars was detected, which might explain the enhanced growth at specified hosts.

Infection dynamics of Salmonella Infantis vary considerably between chicken lines.

ABSTRACTSalmonella (S.) Infantis is the most common serovar in broilers and broiler meat in the European Union. In the field, fast-growing broilers are reported to be more affected than slow-growing and layer birds. The present study investigated the infection dynamics and immunological response of four chicken lines in the course of a S. Infantis infection. Two commercial chicken lines, Ross 308 and Hubbard ISA-JA-757, and two experimental chicken lines, specific pathogen free (SPF) layers and broilers, were infected at 2 days of age. Investigations focused on faecal shedding, bacterial colonization, humoral and cellular immune response. Ross and SPF broilers proved mainly as high shedders followed by Hubbard. SPF layers showed the least shedding. This is in agreement with the caecal colonization; SPF layers harboured significantly less bacteria. Systemic spread of S. Infantis to liver and spleen was highest in Ross broilers compared to the other lines. Spread of infection to in-contact birds, was noticed 5 days post infection in every line. Antibody response occurred in every chicken line from 21 days of age onwards. In contrast to the other chicken lines, significant differences in T cell subsets and monocytes/macrophages were found between infected and negative Hubbard birds at 7 days of age. Uninfected SPF birds had significantly higher immune cell counts than uninfected commercial birds, a fact important for future experimental settings. The results illustrate that the infection dynamics of S. Infantis is influenced by the chicken line resulting in a higher risk of transmission to humans from fast-growing broilers.RESEARCH HIGHLIGHTS Infection dynamics of Salmonella Infantis differs between chicken lines.Layers showed less faecal shedding and caecal colonization compared to broilers.Fast-growing broilers proved more susceptible than slow-growing broilers.

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), ß-lactams (blaTEM-1 ; blaCTX-M-8 ; blaCMY-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.

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.

Molecular epidemiology and antimicrobial resistance profiles of Salmonella isolates from dairy heifer calves and adult lactating cows in a Mediterranean pasture-based system of Australia.

Dairy cows can be reservoirs of foodborne pathogens such as Salmonella that pose serious public health risks to humans. The study was designed to examine the molecular epidemiology and antimicrobial resistance profiles of Salmonella isolates from dairy heifer calves and adult lactating cows in the pasture-based system of Australia. A total of 838 animals (328 heifer calves and 510 lactating cows) from 22 farms were sampled. Overall, 54 Salmonella isolates were recovered (calves 28/328 and cows 26/510). A herd-level Salmonella prevalence of 50% (95% confidence interval: 31%-69%) was recorded. Within-herd prevalence for Salmonella ranged between 4%-29% and 4%-45% among the heifer calves and adult lactating cows, respectively. Three different serovars were identified with Salmonella Infantis being the most common serovar (n = 33, 61%) followed by Salmonella Kiambu (n = 20, 37.0%) and one isolate of Salmonella Cerro (2%). The highest antimicrobial resistance prevalence of Salmonella isolates was found against streptomycin (n = 31, 57%), followed by cefoxitin (n = 12, 22%), ceftriaxone (n = 2, 4%), and chloramphenicol (n = 1, 2%). Multiple class resistance was observed on 4 isolates against cefoxitin, chloramphenicol, and streptomycin. Multilocus sequence types ST32 (61%), ST309 (37%), and ST367 (2%) were strongly linked to the serovars Salmonella Infantis, Salmonella Kiambu, and Salmonella Cerro, respectively. Whole genome sequencing of Salmonella isolates detected only 2 resistance genes: aac(6') gene that confers resistance against aminoglycosides among 40.7% of the isolates, and a single isolate positive for the blaDHA-16 gene. Two distinct clusters among the serovars were observed suggesting 2 independent sources of spread. Despite the low prevalence of antimicrobial resistance among Salmonella from the dairy farms, our findings contribute to the regional and national understanding of antimicrobial resistance in dairy herds in Australia. There is need for continued antimicrobial resistance stewardship and surveillance programs to ensure the production of high-quality food products and the long-term protection of both animal and human health.

Evaluation of 3-week-old layer chicks intratracheally challenged with Salmonella isolates from serogroup c1 (O:6,7) and Salmonella Enteritidis.

With the exception to Salmonella enterica serotype Typhimurium and S. Enteritidis (serogroups B [O:4] and D [O:9], respectively), there have been very few studies conducted on the respiratory tract as route of infection in chickens with salmonellas from serogroup C1 (O:6,7). Therefore, the purpose of this present study was to determine the potential organ invasion by Salmonella enterica serotype Potsdam (SP), S. Mbandaka (SM), and S. Infantis (SI) from serogroup C1 (O:6,7) and compare their characteristics with those of S. Enteritidis (SE) on intratracheally (IT) challenged 3-week-old layer chicks. A total of 360 one-day-old White Leghorn layer chicks were acquired from a commercial hatchery and randomly assigned into four treatment groups (SP, SM, SI, and SE, respectively), consisting of three independent trials. Chicks were grown up to 21 days (3 weeks) and IT-challenged thereafter with 106 CFU of respective salmonella organisms per group (n = 30). Chicks (n = 5) were humanely sacrificed every 24 h for 6 days post-IT infection and organs such as lung, heart, liver, spleen, kidney and caecal content were cultured for salmonella. All treatment groups exhibited colonization of lungs and caecal contents at 1 d (P = 0.475) and 4 d (P = 0.696) post-IT infection, respectively. There was no isolation of SP, SM, and SI in heart, liver, spleen, and kidney. In contrast, SE was obtained from heart, liver, and spleen of IT-infected chicks. The findings of this study contribute to a better understanding of the importance of the respiratory route in salmonella infection in poultry.

Construction and in vitro characterisation of aroA defective (aroAΔ) mutant Salmonella Infantis.

Poultry vaccine programs are important for control of Salmonella infections. Although there are vaccines for Salmonella Enteritidis, Salmonella Typhimurium and Salmonella Typhi, there are no vaccines for Salmonella Infantis which has an increased rate in the world. In this study, it was aimed to generate aroA gene deleted mutant bacteria for the constitution of S. Infantis vaccine prototype and the in vitro characterisation of this bacterium. S. Infantis auxotrophic mutant which has a block at any step of chorismate pathway has been constituted for the first time in the world and it was determined that this bacterium gets susceptibility against some antibiotics and antimicrobial substances. It was also observed that the adhesion and invasion rate of mutant strain tenfold decreased in comparison with the field strain in cell culture assay. It is understood from the in vitro evaluation of this mutant strain that it can be used as a vaccine candidate in further vaccine development studies.

Simultaneous oral administration of Salmonella Infantis and S. Typhimurium in chicks.

BACKGROUND: To confirm the hypothesis that Salmonella enterica subspecies enterica serovar (S.) Infantis has higher basic reproductive rates in chicks compared with other Salmonella serovars, 1-day-old specific-pathogen-free chicks (n = 8) were challenged simultaneously with S. Infantis and S. Typhimurium per os. Challenged chicks (Group A) were then housed with non-infected chicks (Group B, n = 4) for 6 days (from 2 to 8 days of age). Group B birds were then housed with other non-infected birds (Group C, n = 4), which were then transferred to cages containing a further group of untreated chicks (Group D, n = 2). A control group consisting of four non-infected chicks was used for comparison. All chickens were humanely sacrificed at 18 days of age, and Salmonella from bowel and liver samples were enumerated. RESULTS: Both serovars were isolated from all groups except the control group. S. Typhimurium was isolated at a greater frequency than S. Infantis from the bowel samples of chicks from Groups B, C and D, while no differences in colonisation rates were observed between the two serovars in liver samples from Groups B, C and D. S. Typhimurium, but not S. Infantis, was immunohistochemically detected in the lamina propria of the cecum and rectum in five birds of Group A. Despite the competitive administration, neither of the two serovars completely excluded the other, and no differences were observed in basic reproductive rates between the two serovars. CONCLUSIONS: These findings, together with data from previous studies, suggest that the initial quantitative domination of S. Infantis in chicken flocks may explain why this serovar is predominant in broiler chickens.

Outbreak of Salmonella infantis gastroenteritis among people who had eaten at a hash house in southern Italy.

OBJECTIVES: To describe an outbreak of acute gastroenteritis in people who had eaten at a hash house in southern Italy. STUDY DESIGN: Case-control study. METHODS: A clinical case of gastroenteritis was defined as a person who had eaten at the hash house from 29 August to 4 September 2011 and who experienced defined gastrointestinal symptoms within 72 hours, or a person with a laboratory-confirmed salmonella infection without symptoms. A convenience sample was enrolled as the control group. Environmental and human samples were collected, and Salmonella infantis was identified by polymerase chain reaction. Univariate analysis was performed for each food type, and multivariate analysis was performed for each food type and demographic variable (gender, age). RESULTS: Twenty-three cases of gastroenteritis were notified between 1 and 4 September 2011, two of which were admitted to the local hospital. Multivariate analysis showed that porchetta [odds ratio (OR) 22.0, 95% confidence interval (CI) 3.2-152.6, z = 3.13, P = 0.002] and roasted meat (OR 14.4, 95% CI 1.7-122.0, z = 2.45, P = 0.014) were associated with gastrointestinal symptoms. Environmental and human isolates exhibited the same sequence type (ST 32). CONCLUSIONS: This experience highlighted that, in the control of a foodborne outbreak, integrated epidemiological and laboratory surveillance enables rapid identification of the source of infection, thus reducing the risk of an epidemic.

Emergence of Salmonella Infantis carrying the pESI megaplasmid in commercial farms of five major integrated broiler operations in Korea.

Considering Salmonella transmission occurs through several routes in integrated broiler operations, control of nontyphoidal Salmonella in commercial farms is essential. This study aimed to compare the distribution of persistent Salmonella serovars in environments and dead chickens between 5 major integrated broiler operations in Korea. The prevalence of Salmonella-positive farms in dust prior to placement by operations was 0 to 25%, but the prevalence in dust and feces at the time of depletion was increased to 16.7 to 41.7% and 16.7 to 66.7%, respectively. Moreover, the prevalence of farms with Salmonella in chickens that died within 1 week old and at 4 to 5 weeks old ranged from 8.3 to 58.3% and 16.7 to 41.7%, respectively. The prevalence of Salmonella enterica serovar Infantis-positive farms in dust prior to placement and in chickens that died within 1 week old was 5.2 and 3.4%, respectively, but the prevalence in dust and feces at the time of depletion and in chickens that died at 4 to 5 weeks old was significantly increased to 27.6, 41.4, and 20.7%, respectively (P < 0.05). Interestingly, the plasmid of emerging S. Infantis (pESI) was only identified in S. Infantis, and the prevalence of multidrug-resistance was significantly higher in pESI-positive S. Infantis (99.2%) than in pESI-negative S. Infantis (6.7%) (P < 0.05). The distribution of pulsotypes between pESI-positive and pESI-negative S. Infantis were varied, but a majority of S. Infantis were clustered only 2 pulsotypes. Moreover, pESI-positive S. Infantis harbored more virulence factors than pESI-negative S. Infantis. This study is the first report on characteristics of S. Infantis carrying the pESI plasmid in commercial broiler farms in Korea.

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.

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

Background: Multidrug-resistant (MDR) Salmonella Infantis has disseminated worldwide, mainly linked to the consumption of poultry products. Evidence shows dissemination of this pathogen in Chile; however, studies are primarily limited to phenotypic data or involve few isolates. As human cases of Salmonella Infantis infections have substantially increased in recent years, this study aimed to characterise the genomic epidemiology and antimicrobial-resistance profiles of isolates obtained from different sources, aiming to inform effective surveillance and control measures. Methods: We sequenced 396 Salmonella Infantis genomes and analysed them with all publicly available genomes of this pathogen from Chile (440 genomes in total), representing isolates from environmental, food, animal, and human sources obtained from 2009 to 2022. Based on bioinformatic and phenotypic methods, we assessed the population structure, dissemination among different niches, and antimicrobial resistance (AMR) profiles of Salmonella Infantis in the country. Findings: The genomic and phylogenetic analyses showed that Salmonella Infantis from Chile comprised several clusters of highly related isolates dominated by sequence type 32. The HC20_343 cluster grouped an important proportion of all isolates. This was the only cluster associated with pESI-like megaplasmids, and up to 12 acquired AMR genes/mutations predicted to result in an MDR phenotype. Accordingly, antimicrobial-susceptibility testing revealed a strong concordance between the AMR genetic determinants and their matching phenotypic expression, indicating that a significant proportion of HC20_343 isolates produce extended-spectrum ß-lactamases and have intermediate fluoroquinolone resistance. HC20_343 Salmonella Infantis were spread among environmental, animal, food, and human niches, showing a close relationship between isolates from different years and sources, and a low intra-source genomic diversity. Interpretation: Our findings show a widespread dissemination of MDR Salmonella Infantis from the HC20_343 cluster in Chile. The high proportion of isolates with resistance to first-line antibiotics and the evidence of active transmission between the environment, animals, food, and humans highlight the urgency of improved surveillance and control measures in the country. As HC20_343 isolates predominate in the Americas, our results suggest a high prevalence of ESBL-producing Salmonella Infantis with intermediate fluoroquinolone resistance in the continent. Funding: Partially supported by the Food and Drug Administration (FDA) of the U.S. Department of Health and Human Services as part of an award, FDU001818, with 30% percent funded by FDA/HHS; and by Agencia de Investigación y Desarrollo de Chile (ANID) through FONDECYT de Postdoctorado Folio 3230796 and Folio 3210317, FONDECYT Regular Folio 1231082, and ANID-Millennium Science Initiative Program-ICN2021_044.

From farm to fork: Spread of a multidrug resistant Salmonella Infantis clone encoding blaCTX-M-1 on pESI-like plasmids in Central Italy.

Salmonella enterica subsp. enterica serovar Infantis (S. Infantis) is one of the "top five Salmonella serovars" of clinical significance in the European Union (EU). Antimicrobial resistant and extended spectrum ß-lactamase (ESBL) AmpC-producing S. Infantis have been described in food production systems and human clinical samples in Italy. Recently, an increase of MDR S. Infantis carrying blaCTX-M genes involved in 3rd generation cephalosporin resistance was noticed in the EU, including Italy, mainly due to the spread of S. Infantis harboring a pESI-like plasmid. The aim of this study was to investigate the occurrence of the S. Infantis pESI-like plasmid among antibiotic resistant S. Infantis strains isolated at different points of the food chain, and to provide a phylogenetic analysis to gain further insight on their transmission pathways from 'farm to fork'. MDR S. Infantis strains (n. 35) isolated from 2016 to 2021 at different stages of the food chain (animals, food, food-related environments, and humans) were investigated with in depth molecular characterization using real-time PCR, S1 nuclease pulsed-field gel electrophoresis (S1-PFGE) and whole genome sequencing (WGS). Our study reported the occurrence of S. Infantis strains harboring pESI-like plasmids, carrying blaCTX-M-1 genes, in Central Italy, at different sampling points along the food chain. Results confirmed the presence of a plasmid with a molecular size around 224-310 kb, thus consistent with the pESI-like, in 97 % of the 35 samples investigated. Two variants of S. Infantis pESI-like IncFIB(K)_1_Kpn3 were detected, one associated with the European clone carrying blaCTX-M-1 (21 isolates) and the other associated with U.S. isolates carrying blaCTX-M-65 (2 isolates, pESI-like U.S. variant). The majority was resistant to 3rd generation cephalosporins but none of the strains tested positive for the carbapenemase encoding genes. A total of 118 virulence genes were identified in isolates harboring the pESI-like plasmid. cgMLST and SNP-based analysis revealed the presence of one main cluster, composed by strains isolated from the environment, animals, food and humans. The results of this investigation underline the importance of phylogenetic studies to monitor and understand pathogen and AMR spread in a One Health approach.

The transcriptional regulation of the horizontally acquired iron uptake system, yersiniabactin and its contribution to oxidative stress tolerance and pathogenicity of globally emerging salmonella strains.

The bacterial species Salmonella enterica (S. enterica) is a highly diverse pathogen containing more than 2600 distinct serovars, which can infect a wide range of animal and human hosts. Recent global emergence of multidrug resistant strains, from serovars Infantis and Muenchen is associated with acquisition of the epidemic megaplasmid, pESI that augments antimicrobial resistance and pathogenicity. One of the main pESI's virulence factors is the potent iron uptake system, yersiniabactin encoded by fyuA, irp2-irp1-ybtUTE, ybtA, and ybtPQXS gene cluster. Here we show that yersiniabactin, has an underappreciated distribution among different S. enterica serovars and subspecies, integrated in their chromosome or carried by different conjugative plasmids, including pESI. While the genetic organization and the coding sequence of the yersiniabactin genes are generally conserved, a 201-bp insertion sequence upstream to ybtA, was identified in pESI. Despite this insertion, pESI-encoded yersiniabactin is regulated by YbtA and the ancestral Ferric Uptake Regulator (Fur), which binds directly to the ybtA and irp2 promoters. Furthermore, we show that yersiniabactin genes are specifically induced during the mid-late logarithmic growth phase and in response to iron-starvation or hydrogen peroxide. Concurring, yersiniabactin was found to play a previously unknown role in oxidative stress tolerance and to enhance intestinal colonization of S. Infantis in mice. These results indicate that yersiniabactin contributes to Salmonella fitness and pathogenicity in vivo and is likely to play a role in the rapid dissemination of pESI among globally emerging Salmonella lineages.