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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., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Guzinski, Potter, Tang, Davies, Teale and Petrovska.)

Introduction: Salmonella enterica is a major cause of foodborne illness in the United States. A multi-drug resistant (MDR) emergent Salmonella Infantis (ESI) with a megaplasmid (pESI) was first identified in Israel and Italy and subsequently reported worldwide. The ESI clone carrying an extended spectrum β-lactamase bla CTX-M-65 on a pESI-like plasmid and a mutation in the gyr A gene has recently been found in the United States in poultry meat., Methods: We analyzed the phenotypic and genotypic antimicrobial resistance, genomics and phylogeny of 200 S. infantis isolates from animal diagnostic samples., Results: Of these, 33.5% were resistant to at least one antimicrobial and 19.5% were multi-drug resistant (MDR). Eleven isolates from different animal sources were phenotypically and genetically similar to the ESI clone. These isolates had a D87Y mutation in the gyr A gene conferring reduced susceptibility to ciprofloxacin and harbored a combination of 6-10 resistance genes: bla CTX-M-65, aac (3)-IVa, aad A1, aph (4)-Ia, aph (3')-Ia, flo R, sul 1, dfr A14, tet A, and fos A. These 11 isolates carried class I and class II integrons and three virulence genes: sinH, involved in adhesion and invasion, ybt Q and ybt P, associated with iron transport. These isolates were also closely related to each other (separated by 7 to 27 SNPs) and phylogenetically related to the ESI clone recently found in the U.S., Discussion: This dataset captured the emergence of the MDR ESI clone in multiple animal species and the first report of a pESI-like plasmid in isolates from horses in the U.S., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Srednik, Morningstar-Shaw, Hicks, Tong, Mackie and Schlater.)

Salmonella enterica serovar Infantis is one of the five main causes of human salmonellosis in the European Union (EU) and in recent years, has been increasingly reported to carry multiple antimicrobial resistance determinants, including extended-spectrum beta-lactamase (ESBL) genes. In our study, we used WGS-based tools to characterize S. Infantis strains circulating in the Abruzzo and Molise regions of Italy between 2017 and 2020 and compared this local dataset to the S. Infantis population present in Italy over the last two decades. Phylogenetic analyses demonstrated that the majority of strains isolated from poultry and turkeys from Abruzzo and Molise were closely related and belonged to one of the two main genetic clusters present in Italy, which were grouped predominantly as ESBL-producing strains that harbored pESI-like plasmid. We showed that 60% of the local strains carried multiple antibiotic resistance genes, including ESBL gene bla CTX-M-1 as well as aad A1, dfr A1, dfr A14, sul1 , and tet (A) genes present on the pESI-like megaplasmid. The analysis of strains from Abruzzo and Molise and the publicly available Italian S. Infantis sequences revealed a dramatic increase in the number of identified AMR genes in the strains isolated after 2011. Moreover, the number of strains resistant to five or more antibiotic classes increased from 20-80% in the last decade likely due to the acquisition of the megaplasmid. The persistence of the ESBL-producing and the multidrug-resistant (MDR) clone of S. Infantis in poultry populations in Italy and in Europe requires rapid and efficient intervention strategies to prevent further expansion of the clone., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Di Marcantonio, Romantini, Marotta, Chiaverini, Zilli, Abass, Di Giannatale, Garofolo and Janowicz.)

Introduction: Commensal and pathogenic strains of multidrug-resistant (MDR) Escherichia coli and non-typhoid strains of Salmonella represent a growing foodborne threat from foods of poultry origin. MDR strains of Salmonella Infantis and E. coli are frequently isolated from broiler chicks and the simultaneous presence of these two enteric bacterial species would potentially allow the exchange of mobile resistance determinants., Objectives: In order to understand possible genomic relations and to obtain a first insight into the potential interplay of resistance genes between enteric bacteria, we compared genomic diversity and mobile resistomes of S . Infantis and E. coli from broiler sources., Results: The core genome MLST analysis of 56 S . Infantis and 90 E. coli contemporary strains revealed a high genomic heterogeneity of broiler E. coli. It also allowed the first insight into the genomic diversity of the MDR clone B2 of S . Infantis, which is endemic in Hungary. We also identified new MDR lineages for S . Infantis (ST7081 and ST7082) and for E. coli (ST8702 and ST10088). Comparative analysis of antibiotic resistance genes and plasmid types revealed a relatively narrow interface between the mobile resistomes of E. coli and S . Infantis. The mobile resistance genes tet(A) , aadA1 , and sul1 were identified at an overall high prevalence in both species. This gene association is characteristic to the plasmid pSI54/04 of the epidemic clone B2 of S . Infantis. Simultaneous presence of these genes and of IncI plasmids of the same subtype in cohabitant caecal strains of E. coli and S . Infantis suggests an important role of these plasmid families in a possible interplay of resistance genes between S . Infantis and E. coli in broilers., Conclusion: This is the first comparative genomic analysis of contemporary broiler strains of S . Infantis and E. coli . The diversity of mobile resistomes suggests that commensal E. coli could be potential reservoirs of resistance for S . Infantis, but so far only a few plasmid types and mobile resistance genes could be considered as potentially exchangeable between these two species. Among these, IncI1 plasmids could make the greatest contribution to the microevolution and genetic interaction between E. coli and S . Infantis., Competing Interests: The authors declare that this study received funding from Pharma-Zentrale GmbH (Herdecke). The funder was not involved in the study design, collection, analysis, interpretation of data, the writing of the article, or the decision to submit it for publication., (Copyright © 2021 Szmolka, Wami and Dobrindt.)

During the last decade, Salmonella enterica subspecies enterica serovar Infantis ( S . Infantis) has become more prevalent across Europe with an increased capability to persist in broiler farms. In this study, we aimed to identify potential genetic causes for the increased emergence and longer persistence of S . Infantis in German poultry farms by high-throughput-sequencing. Broiler derived S . Infantis strains from two decades, the 1990s ( n = 12) and the 2010s ( n = 18), were examined phenotypically and genotypically to detect potential differences responsible for increased prevalence and persistence. S . Infantis organisms were characterized by serotyping and determining antimicrobial susceptibility using the microdilution method. Genotypic characteristics were analyzed by whole genome sequencing (WGS) to detect antimicrobial resistance and virulence genes as well as plasmids. To detect possible clonal relatedness within S . Infantis organisms, 17 accessible genomes from previous studies about emergent S . Infantis were downloaded and analyzed using complete genome sequence of SI119944 from Israel as reference. In contrast to the broiler derived antibiotic-sensitive S . Infantis strains from the 1990s, the majority of strains from the 2010s (15 out of 18) revealed a multidrug-resistance (MDR) phenotype that encodes for at least three antimicrobials families: aminoglycosides [ ant(3")-Ia ], sulfonamides ( sul1 ), and tetracyclines [ tet(A) ]. Moreover, these MDR strains carry a virulence gene pattern missing in strains from the 1990s. It includes genes encoding for fimbriae clusters, the yersiniabactin siderophore, mercury and disinfectants resistance and toxin/antitoxin complexes. In depth genomic analysis confirmed that the 15 MDR strains from the 2010s carry a pESI-like megaplasmid with resistance and virulence gene patterns detected in the emerged S . Infantis strain SI119944 from Israel and clones inside and outside Europe. Genotyping analysis revealed two sequence types (STs) among the resistant strains from the 2010s, ST2283 ( n = 13) and ST32 ( n = 2). The sensitive strains from the 1990s, belong to sequence type ST32 ( n = 10) and ST1032 ( n = 2). Therefore, this study confirms the emergence of a MDR S . Infantis pESI-like clone of ST2283 in German broiler farms with presumably high tendency of dissemination. Further studies on the epidemiology and control of S . Infantis in broilers are needed to prevent the transfer from poultry into the human food chain., (Copyright © 2020 García-Soto, Abdel-Glil, Tomaso, Linde and Methner.)

Introduction: The emergence and spread of new strains of zoonotic bacteria, such as multidrug resistant (MDR) Salmonella Infantis, represent a growing health risk for humans in and outside Europe due to foodborne infections of poultry meat origin., Objectives: In order to understand genome relations of S . Infantis strains from Hungary and from different geographic regions, we performed a comprehensive genome analysis of nine Hungarian and 67 globally selected strains of S . Infantis and 26 Salmonella strains representing 13 non-Infantis serovars., Results: Analyses of whole-, and accessory genomes, showed that almost all S . Infantis strains were separated from the non-Infantis serovars. S . Infantis strains from Hungary formed subclusters based on their time of isolation. In whole genome sequence analysis, the Swiss strains of S . Infantis were closely related to each other and clustered together with subclusters of strains from Hungary, Japan, Italy, United States, and Israel. The accessory genome analysis revealed that the Swiss strains were distinct from most of the strains investigated, including the Hungarian ones. Analysis of the cloud genes offered the most detailed insight into the genetic distance and relationship of S . Infantis strains confirming that the Swiss and Hungarian strains belonged to different lineages. As expected, core genome analysis provided the least discriminatory power for analysis of S . Infantis. Genomic sequences of nine strains from Brazil, Israel, Mexico, Nigeria, and Senegal (deposited as S . Infantis) proved to be outliers from the S . Infantis clade. They were predicted to be Salmonella Rissen, Salmonella Ouakarm, Salmonella Kentucky, Salmonella Thompson, and Salmonella enterica subsp. diarizonae ., Conclusion: Accessory genome of S . Infantis showed the highest diversity suggesting a faster evolution than that of the whole genomes contributing to the emergence of multiple genetic variants of S . Infantis worldwide. Accordingly, in spite of the comprehensive analysis of several genomic characteristics, no epidemiologic links between these S . Infantis strains from different countries could be established. It is also concluded that several strains originally designated as S . Infantis need in databanks reclassification., (Copyright © 2020 Nagy, Szmolka, Wilk, Kiss, Szabó, Pászti, Nagy and Olasz.)

Colistin-resistance mediated by mobilisable and plasmid-borne mcr genes has emerged worldwide, threatening the efficacy of colistin, a last resort antibiotic increasingly used for treating human invasive infections by multidrug-resistant or extensively drug-resistant Enterobacteriaceae . In this study, we report the first evidence of mcr -1-mediated colistin resistance in four multidrug resistant (MDR) out of 324 Salmonella infantis from the Italian antimicrobial resistance (AMR) monitoring (2001-2017) in broilers and broiler meat. Two were also Extended Spectrum Beta-Lactamases (ESBL)-producing isolates. Characterization by whole genome sequencing (WGS), located mcr -1.1 on an incX4 plasmid. Phylogenetic analysis of these isolates with selected Italian S . Infantis previously isolated from animals, meat and human clinical cases with unknown epidemiological relationship, demonstrated that ESBL-producing, mcr -1-positive isolates belonged to the emerging pESI-like-positive-ESBL-producing clone described in Italy in 2015.

Salmonella enterica serovar Infantis ( S . Infantis) is a common source of foodborne gastroenteritis worldwide. Here, Lactobacillus rhamnosus GG (LGG) was administrated to weaned piglets for 1 week before S . Infantis challenge. S . Infantis caused decreased ileal mucosal microbiota diversity, a dramatic Lactobacillus amylovorus bloom, and decreased abundance of Arsenicicoccus, Janibacter, Kocuria, Nocardioides, Devosia, Paracoccus, Psychrobacter , and Weissella . The beneficial effect of LGG correlated with the moderate expansion of L. amylovorus, L. agilis , and several members of the phyla Proteobacteria, Firmicutes , and Bacteroidetes . S . Infantis translocation to the liver was decreased in the LGG-pretreated piglets. An in vitro model of LGG and S . Infantis co-incubation (involving the porcine intestinal epithelial cell line IPEC-J2) was established, and nalidixic acid was used to kill the extracellular S . Infantis. LGG suppressed the initial S . Infantis invasion in the IPEC-J2 cells and deceased the rate of cell death. LGG inhibited S . Infantis-induced autophagy and promoted epidermal growth factor receptor (EGFR) and Akt phosphorylation in both the ileum and IPEC-J2 cells. Our findings suggest that LGG inhibited S . Infantis-induced autophagy by promoting EGFR-mediated activation of the negative mediator Akt, which, in turn, suppressed intestinal epithelial cell death and thus restricted systemic S . Infantis infection. LGG can restore the gut microbiota balance and preserve the autophagy-related intestinal epithelial barrier, thereby controlling infections.

Objectives: The aim of this study was to characterize a collection of 520 Salmonella enterica serovar Infantis strains isolated from food (poultry meat), human infections and environmental sources from the years 2010, 2013 and 2015 in Switzerland. Methods: We performed antimicrobial susceptibility testing and pulsed-field gel electrophoresis (PFGE) analysis on all 520 S . Infantis isolates, and whole genome sequencing (WGS) on 32 selected isolates. Results: The majority (74.8%) of the isolates was multidrug resistant (MDR). PFGE analysis revealed that 270 (51.9%) isolates shared an identity of 90%. All isolates subjected to WGS belonged to sequence type (ST) 32 or a double-locus variant thereof (one isolate). Seven (21.9%) of the sequenced isolates were phylogenetically related to the broiler-associated clone B that emerged in Hungary and subsequently spread within and outside of Europe. In addition, three isolates harboring bla CTX-M-65 on a predicted large (∼320 kb) plasmid grouped in a distinct cluster. Conclusion: This study documents the presence of the Hungarian clone B and related clones in food and human isolates between 2010 and 2015, and the emergence of a bla CTX-M-65 harboring MDR S . serovar Infantis lineage.