Antibacterial T6SS effectors with a VRR-Nuc domain induce target cell death via DNA Double-Strand Breaks

The T6SS (Type VI secretion System) secretes antibacterial effectors into target competitors. Salmonella spp. encode five phylogenetically distinct T6SSs. Here we characterize the function of the SPI-22 T6SS of S. bongori, showing that it has antibacterial activity. We identify a group of antibacterial T6SS effectors (TseV1-4) containing an N-terminal PAAR-like domain and a C-terminal VRR-Nuc domain encoded next to cognate immunity proteins that contain the DUF3396 domain (TsiV1-4). TseV2 and TseV3 are toxic when expressed in Escherichia coli and bacterial competition assays confirm that TseV2 and TseV3 are secreted by the SPI-22 T6SS. Phylogenetic analysis reveals that TseV1-4 are evolutionarily related to enzymes involved in DNA repair. TseV2 and TseV3 maintained the ability to bind DNA, but instead cause specific DNA double-strand breaks and induce the SOS response in target cells. The crystal structure of the TseV3:TsiV3 complex reveals that the immunity protein likely blocks the effector interaction with the DNA substrate. These results expand our knowledge on the function of Salmonella pathogenicity islands, the evolution of toxins used in biological conflicts, and the endogenous mechanism regulating the activity of these toxins.

Prevalence of IncFIB Plasmids Found among Salmonella enterica Serovar Schwarzengrund Isolates from Animal Sources in Taiwan Using Whole-Genome Sequencing

Salmonella enterica serovar Schwarzengrund is one of the most frequently isolated Salmonella serotypes responsible for human and poultry infections in Taiwan, and it has raised public health concerns. To better facilitate the understanding of transmission patterns and the dynamics of epidemics, sharing molecular data on pathogen profiles is urgently needed. The objectives of the current study were to determine and establish baseline data of S. enterica serovar Schwarzengrund isolates from 23 epidemiologically unrelated sources from year 2000 to 2018 and examine their phenotypic and genotypic characteristics. Genomic DNA of the Salmonella isolates was extracted and subjected to whole-genome sequencing using an Illumina platform. Results showed that all selected isolates exhibited multidrug resistance, and six of those were resistant to ciprofloxacin phenotypically. Genotypically, these isolates carried genes resistant to aminoglycoside (100%), phenicol (91.3%), β-lactams (69.5%), folate pathway antagonist (100%), tetracycline (82.6%), and fluoroquinolone (4.3%). Moreover, these isolates harbor integrons with five different gene cassettes identified for the first time, which are associated with resistance to trimethoprim, streptomycin, tetracycline, sulfonamide, chloramphenicol, and gentamicin. Furthermore, prevalence of IncFIB plasmid was found among studied isolates, which may increase its ability to colonize the chicken cecum and cause extra-intestinal disease. Salmonella pathogenicity islands SPI-1 to SPI-5, SPI-13, and SPI-14, as well as C63PI locus, were also detected in all isolates. This study demonstrated that a considerable high antimicrobial resistance with high virulence levels of Salmonella were found from animal sources. Sharing data on these pathogen profiles can not only help increase the reproducibility and accessibility of genomic analysis but can also support surveillance and epidemiological investigations for salmonellosis in the region.

Salmonella enterica Subsp. houtenae Associated with an Abscess in Young Roe Deer (Capreolus capreolus)

Background: S. enterica subsp. houtenae has been rarely documented, and very limited genomic information is available. This report describes a rare case of primary extraintestinal salmonellosis in a young roe deer, associated with Salmonella enterica subsp. houtenae. Methods: A traditional cultural-based analysis was carried out from the contents of a neck abscess; biochemical identification and PCR assay were performed to isolate and identify the pathogen. Through whole-genome sequencing (WGS), multilocus sequence typing (MLST), core genome MLST (cgMLST), and the Salmonella pathogenicity islands (SPIs) survey, resistome and virulome genes were investigated to gain insight into the virulence and antimicrobial resistance of S. houtenae. Results: Biochemical identification and PCR confirmed the presence of Salmonella spp. in the swelling. The WGS analysis identified Salmonella enterica subspecies houtenae serovar 43:z4,z23:- and ST 958. The virulence study predicted a multidrug resistance pattern with resistance shown against aminoglycosides, tetracycline, beta-lactamase, fluoroquinolones, fosfomycin, nitroimidazole, aminocoumarin, and peptide. Fifty-three antibiotic-resistant genes were identified. No plasmids were detected. Conclusion: This study demonstrates the importance of continuous surveillance of pathogenic salmonellae. Biomolecular analyses combined with epidemiological data can provide important information about poorly described Salmonella strains and can help to improve animal welfare.

Pathogenicity Island in Salmonella

Considering a complex set of interplay with its host, Salmonella needs numerous genes for its full virulence. These genes responsible for invasion, survival, and extra intestinal spread are located on pathogenicity islands known as Salmonella pathogenicity islands (SPIs) that are thought to be acquired by horizontal gene transfer. A total of 17 SPIs (1–17) are recognized so far. The type III secretion system (T3SS) encoded by SPI-1 is considered as the most important virulence factor for Salmonella that delivers effector proteins necessary for invasion and production of enteritis. Among various SPIs, the role in virulence is well proven for SPI1 and SPI2 and further insight into the complex regulatory network of SPIs can contribute to drug investigation and prevention of infection.

Virulence Factors of Salmonella Typhi

S. Typhi is an enteric bacillus which belongs,to the genus Salmonella in the family Enterobacteriacaea and it is a multi–organs pathogen which inhibits the lymphatic tissues of the small intestine, liver, spleen, and blood stream of infected humans.S.Typhi has a mixture of features that make it an efficient pathogen. This species contains an endotoxin that is characteristic of Gram-negative organisms, as well as the virulence-enhancing Vi antigen. Many of the S. Typhi virulence factors are clustered in some areas of the chromosome known as Salmonella pathogenicity islands (SPI), such as adhesion, invasion, and toxin genes. A protein known as invasin that permits non-phagocytic cells is also produced and excreted by the bacterium., Where it is capable of intracellular living. The oxidative burst of leukocytes may also be inhibited, making innate immune reaction ineffective.

Comparative Genomic Analysis of 450 Strains of Salmonella enterica Isolated from Diseased Animals

Salmonella is a leading cause of bacterial infections in animals and humans. We sequenced a collection of 450 Salmonella strains from diseased animals to better understand the genetic makeup of their virulence and resistance features. The presence of Salmonella pathogenicity islands (SPIs) varied by serotype. S. Enteritidis carried the most SPIs (n = 15), while S. Mbandaka, S. Cerro, S. Meleagridis, and S. Havana carried the least (n = 10). S. Typhimurium, S. Choleraesuis, S. I 4,5,12:i:-, and S. Enteritidis each contained the spv operon on IncFII or IncFII-IncFIB hybrid plasmids. Two S. IIIa carried a spv operon with spvD deletion on the chromosome. Twelve plasmid types including 24 hybrid plasmids were identified. IncA/C was frequently associated with S. Newport (83%) and S. Agona (100%) from bovine, whereas IncFII (100%), IncFIB (100%), and IncQ1 (94%) were seen in S. Choleraesuis from swine. IncX (100%) was detected in all S. Kentucky from chicken. A total of 60 antimicrobial resistance genes (ARGs), four disinfectant resistances genes (DRGs) and 33 heavy metal resistance genes (HMRGs) were identified. The Salmonella strains from sick animals contained various SPIs, resistance genes and plasmid types based on the serotype and source of the isolates. Such complicated genomic structures shed light on the strain characteristics contributing to the severity of disease and treatment failures in Salmonella infections, including those causing illnesses in animals.

Genome Sequence of an Emerging Salmonella enterica Serovar Infantis and Genomic Comparison with Other S. Infantis Strains

Salmonella enterica serovar Infantis (S. Infantis) is one of the dominant serovars of the bacterial pathogen S. enterica. In recent years, the number of human infections caused by S. Infantis has been increasing in many countries, and often the emerging population harbors a unique virulence-resistant megaplasmid called plasmid of emerging S. Infantis (pESI). Here, we report the complete gap-free genome sequence of the S. Infantis Israeli emerging clone and compare its chromosome and pESI sequences with other complete S. Infantis genomes. We show a conserved presence of the Salmonella pathogenicity islands 1–6, 9, 11, 12, and CS54 and a common integration of five bacteriophages in the S. Infantis chromosome. In contrast, we found variable presence of additionally three chromosomally integrated phages and eight modular regions in pESI, which contribute to the genetic and phenotypic diversity (including antimicrobial resistance) of this ubiquitous foodborne pathogen.