How Salmonella became a pathogen

Effects of bcsE, luxS and rfaG genes on the physiology and pathogenicity of Salmonella Typhimurium

In this study, rfaG, luxS, and bcsE gene mutants of S. Typhimurium ATCC 14028 wild-type strain were generated, and their effects on bacterial physiology and pathogenicity were investigated. Biofilm production capacity and mobility of mutant strains were found to be significantly reduced. Immune response stimulation of 6-8 week-old BALB/c mice infected with wild-type and mutants was evaluated on days 0 and 21 for IL-6, IFN-γ, and IgG, and then systemic infection in mice was determined by the amount of Salmonella recovered from the cecum, spleen, and liver organs. The specific IgG antibody level and the expression level of the cytokines IFN-γ and IL-6 were found to be significantly reduced in mice inoculated with mutant strains compared to the control group. The highest level of colonization in the organs was found in the cecum, and the lowest level of colonization was detected in the liver. In the wild-type-infected group, splenomegaly and staining of the liver were detected. In the groups of mice infected with bcsE and luxS mutants, these symptoms were at a low level. In the groups infected with the rfaG mutant, no significant lesions were detected in the organs.

A novel approach for detecting Salmonella enterica strains frequently attributed to human illness-development and validation of the highly pathogenic Salmonella (HPS) multiplex PCR assay

Introduction

Non-typhoidal Salmonella enterica (NTS) are leading bacterial agents of foodborne illnesses and a global concern for human health. While there are over 2,600 different serovars of NTS, epidemiological data suggests that certain serovars are better at causing disease than others, resulting in the majority of reported human illnesses in the United States. To improve food safety, there is a need to rapidly detect these more pathogenic serovars to facilitate their removal from the food supply.

Methods

Addressing this need, we conducted a comparative analysis of 23 closed Salmonella genomic sequences of five serotypes. The analysis pinpointed eight genes (sseK2, sseK3, gtgA/gogA, avrA, lpfB, SspH2, spvD, and invA) that in combination, identify 7 of the 10 leading Salmonella serovars attributed to human illnesses in the US each year (i.e., Serovars of Concern or SoC). A multiplex PCR assay was developed to detect the presence of these genes, with strains amplifying five or more targets designated Highly Pathogenic Salmonella, or HPS. The utility of the resulting HPS assay for identifying SoC was examined in silico, using BLAST to determine the distribution of gene targets among closed Salmonella genome sequences in GenBank (n = 2,192 representing 148 serotypes) and by assaying 1,303 Salmonella (69 serotypes), isolated from FSIS regulatory samples.

Results and discussion

Comparison of serotypes identified by the assay as HPS, with those identified as SoC, produced an Area Under the Curve (AUC) of 92.2% with a specificity of 96% and a positive predictive value of 97.4%, indicating the HPS assay has strong ability to identify SoC. The data presented lay the groundwork for development of rapid commercial assays for the detection of SoC.

An Epidemiological Study on Salmonella in Tibetan Yaks from the Qinghai-Tibet Plateau Area in China

Salmonella is an important foodborne pathogen that can cause a range of illnesses in humans; it has also been a key focus for monitoring in the field of public health, including gastroenteritis, sepsis, and arthritis, and can also cause a decline in egg production in poultry and diarrhea and abortion in livestock, leading to death in severe cases, resulting in huge economic losses. This study aimed to investigate the isolation rate, antimicrobial resistance, serotypes, and genetic diversity of Salmonella isolated from yak feces in various regions on the Qinghai-Tibet Plateau. A total of 1222 samples of yak dung were collected from major cities in the Qinghai-Tibet Plateau area, and the sensitivity of the isolated bacteria to 10 major classes of antibiotics was determined using the K-B paper disk diffusion method for drug susceptibility. Meanwhile, the serotypes of the isolated bacteria were analyzed using the plate agglutination test for serum antigens, and their carriage of drug resistance and virulence genes was determined using PCR and gel electrophoresis experiments. The isolated bacteria were also classified using MLST (Multi-Locus Sequence Typing). The overall isolation rate for Salmonella was 18.25% (223/1222), and the results of the antibiotic susceptibility tests showed that 98.65% (220/223) of the isolated bacteria were resistant to multiple antibiotics. In the 223 isolates of Salmonella, eight classes of 20 different resistance genes, 30 serotypes, and 15 different types of virulence genes were detected. The MLST analysis identified 45 distinct sequence types (STs), including five clonal complexes, of which ST34, ST11, and ST19 were the most common. These findings contribute valuable information about strain resources, genetic profiles, and typing data for Salmonella in the Qinghai-Tibet Plateau area, facilitating improved bacterial surveillance, identification, and control in yak populations. They also provide certain data supplements for animal Salmonella infections globally, filling research gaps.

Type IV pili of Enterobacteriaceae species

Type IV pili (T4Ps) are surface filaments widely distributed among bacteria and archaea. T4Ps are involved in many cellular functions and contribute to virulence in some species of bacteria. Due to the diversity of T4Ps, different properties have been observed for homologous proteins that make up T4Ps in various organisms. In this review, we highlight the essential components of T4Ps, their functions, and similarities to related systems. We emphasize the unique T4Ps of enteric pathogens within the Enterobacteriaceae family, which includes pathogenic strains of Escherichia coli and Salmonella. These include the bundle-forming pilus (BFP) of enteropathogenic E. coli (EPEC), longus (Lng) and colonization factor III (CFA/III) of enterotoxigenic E. coli (ETEC), T4P of Salmonella enterica serovar Typhi, Colonization Factor Citrobacter (CFC) of Citrobacter rodentium, T4P of Yersinia pseudotuberculosis, a ubiquitous T4P that was characterized in enterohemorrhagic E. coli (EHEC), and the R64 plasmid thin pilus. Finally, we highlight areas for further study.

The acidic C-terminal tail of DNA Gyrase of Salmonella enterica serovar Typhi controls DNA relaxation in an acidic environment

The intracellular bacteria, Salmonella Typhi adapts to acidic conditions in the host cell by resetting the chromosomal DNA topology majorly controlled by DNA Gyrase, a Type II topoisomerase. DNA Gyrase forms a heterodimer A2B2 complex, which manages the DNA supercoiling and relaxation in the cell. DNA relaxation forms a part of the regulatory mechanism to activate the transcription of genes required to survive under hostile conditions. Acid-induced stress attenuates the supercoiling activity of the DNA Gyrase, resulting in DNA relaxation. Salmonella DNA becomes relaxed as the bacteria adapt to the acidified intracellular environment. Despite comprehensive studies on DNA Gyrase, the mechanism to control supercoiling activity needs to be better understood. A loss in supercoiling activity in E. coli was observed upon deletion of the non-conserved acidic C-tail of Gyrase A subunit. Salmonella Gyrase also contains an acidic tail at the C-terminus of Gyrase A, where its deletion resulted in reduced supercoiling activity compared to wild-type Gyrase. Interestingly, we also found that wild-type Gyrase compromises supercoiling activity at acidic pH 2-3, thereby causing DNA relaxation. The absence of a C-tail displayed DNA supercoiling to some extent between pH 2-9. Hence, the C-tail of Gyrase A might be one of the controlling factors that cause DNA relaxation in Salmonella at acidic pH conditions. We propose that the presence of the C-tail of GyraseA causes acid-mediated inhibition of the negative supercoiling activity of Gyrase, resulting in relaxed DNA that attracts DNA-binding proteins for controlling the transcriptional response.

Virulence and antimicrobial resistance profiles of Salmonella enterica isolated from foods, humans, and the environment in Mexico

Salmonella enterica genotypic and phenotypic characteristics play an important role in its pathogenesis, which could be influenced by its origin. This study evaluated the association among the antimicrobial resistance, virulence, and origin of circulating S. enterica strains in Mexico, isolated from foods, humans, and the environment. The antimicrobial susceptibility to fourteen antibiotics by the Kirby-Bauer method (n = 117), and the presence of thirteen virulence genes by multiplex PCR (n = 153) and by sequence alignments (n = 2963) were evaluated. In addition, a set of S. enterica isolates from Mexico (n = 344) previously characterized according to their genotypic and phenotypic print was included to increase the coverage of the association analysis. Strains with the presence of sopE and strains with the absence of sspH1 were significantly associated with multidrug-resistant (MDR) phenotypes (p < 0.05). The origin of the strains had significant associations with the antimicrobial profiles and some virulence genes (hilA, orgA, sifA, ssaQ, sseL, sspH1, pefA, and spvC) (p < 0.05). Animal-origin food isolates showed the highest frequency of MDR (57.2 %), followed by human isolates (30.0 %). Also, sspH1, pefA, and spvC were found in major frequency in human (32.4 %, 31.0 %, 31.7 %) and animal-origin foods (41.6 %, 10.6 %, 10.6 %) isolates. The findings highlighted that antimicrobial profiles and specific virulence genes of S. enterica strains are related to their origin. Similar genotypic and phenotypic characteristics between human and animal-origin foods isolates were found, suggesting that animal-origin foods isolates are the most responsible for human cases. The revealed associations can be used to improve risk estimation assessments in national food safety surveillance programs.

Epidemiological and clinicopathological findings in 15 fatal outbreaks of salmonellosis in dairy calves and virulence genes in the causative Salmonella enterica Typhimurium and Dublin strains

Salmonella enterica is a major food-borne pathogen that affects cattle-rearing systems worldwide. Little information is available on the epidemiology and pathology of salmonellosis and the virulence genes (VGs) carried by Salmonella in spontaneous outbreaks in cattle. We describe epidemiological findings in 15 fatal outbreaks of salmonellosis in Uruguayan dairy farms and the age, clinical signs, and pathology in 20 affected calves. We also describe the serotypes and frequencies of 17 VGs in the causative Salmonella strains and explore their associations with epidemiological, clinical, and pathological findings. Salmonella Typhimurium and Dublin were identified in 11/15 and 4/15 outbreaks, respectively. The most frequent reason for consultation was digestive disease (8 outbreaks caused by S. Typhimurium), followed by sudden death (4 outbreaks, 3 caused by S. Dublin). Morbidity, mortality, and lethality ranged 4.8-100%, 3.8-78.9%, and 10-100%, without significant differences between serotypes. Diarrhea, the most common clinical sign (14 cases), was associated with the Typhimurium serotype (OR = 26.95), especially in ≤ 30-day-old calves with fibrinous enteritis as the main autopsy finding. The Dublin serotype affected ≥ 50-day-old calves and was associated with fibrinosuppurative splenitis (p = 0.01) and tubulointerstitial nephritis (OR = 48.95). The chances of the Dublin serotype increased significantly with age. There was low variability of VG across serotypes. The pefA gene was associated with the Typhimurium serotype (OR = 21.95), macroscopic enteritis (p = 0.03), and microscopic fibrinosuppurative splenitis (p = 0.04). Understanding the epidemiology, pathology, and virulence of S. enterica at the farm level is key to delineating prevention and control strategies to mitigate its impact on animal and human health.

The Two-Component System CpxRA Represses Salmonella Pathogenicity Island 2 by Directly Acting on the ssrAB Regulatory Operon

The acquisition of Salmonella pathogenicity island 2 (SPI-2) conferred on Salmonella the ability to survive and replicate within host cells. The ssrAB bicistronic operon, located in SPI-2, encodes the SsrAB two-component system (TCS), which is the central positive regulator that induces the expression of SPI-2 genes as well as other genes located outside this island. On the other hand, CpxRA is a two-component system that regulates expression of virulence genes in many bacteria in response to different stimuli that perturb the cell envelope. We previously reported that the CpxRA system represses the expression of SPI-1 and SPI-2 genes under SPI-1-inducing conditions by decreasing the stability of the SPI-1 regulator HilD. Here, we show that under SPI-2-inducing conditions, which mimic the intracellular environment, CpxRA represses the expression of SPI-2 genes by the direct action of phosphorylated CpxR (CpxR-P) on the ssrAB regulatory operon. CpxR-P recognized two sites located proximal and distal from the promoter located upstream of ssrA. Consistently, we found that CpxRA reduces the replication of Salmonella enterica serovar Typhimurium inside murine macrophages. Therefore, our results reveal CpxRA as an additional regulator involved in the intracellular lifestyle of Salmonella, which in turn adds a new layer to the intricate regulatory network controlling the expression of Salmonella virulence genes. IMPORTANCE SPI-2 encodes a type III secretion system (T3SS) that is a hallmark for the species Salmonella enterica, which is essential for the survival and replication within macrophages. Expression of SPI-2 genes is positively controlled by the two-component system SsrAB. Here, we determined a regulatory mechanism involved in controlling the overgrowth of Salmonella inside macrophages. In this mechanism, CpxRA, a two-component system that is activated by extracytoplasmic stress, directly represses expression of the ssrAB regulatory operon; as a consequence, expression of SsrAB target genes is decreased. Our findings reveal a novel mechanism involved in the intracellular lifestyle of Salmonella, which is expected to sense perturbations in the bacterial envelope that Salmonella faces inside host cells, as the synthesis of the T3SS-2 itself.

Two Additional Connections between the Transcriptional Programs Controlling Invasion and Intracellular Replication of Salmonella: HilD-SprB Positively Regulates phoP and slyA

Salmonella virulence relies on the ability of this bacterium to invade the intestinal epithelium and to replicate inside macrophages, which are functions mainly encoded in Salmonella pathogenicity islands 1 and 2 (SPI-1 and SPI-2), respectively. Complex regulatory programs control the expression of SPI-1 and SPI-2 and functionally related genes, involving the integration of ancestral regulators and regulators that Salmonella has acquired during its evolution. Interestingly, some previous studies have revealed cross talk between the regulatory programs for SPI-1 and SPI-2. Here, we report two additional connections between the regulatory programs controlling the expression of genes for invasion and intracellular replication. Our results show that the acquired regulators HilD and SprB, both encoded in SPI-1, induce, in a cascade fashion, the expression of PhoP and SlyA, two ancestral regulators that activate the expression of SPI-2 and other genes required for intracellular replication. We provide evidence supporting that the regulation of phoP and slyA by HilD-SprB was adapted during the divergence of Salmonella from its closer species, Escherichia coli, with the acquisition of SPI-1 and thus the gain of HilD and SprB, as well as through cis-regulatory evolution of phoP and slyA. Therefore, our study further expands the knowledge about the intricate regulatory network controlling the expression of virulence genes in Salmonella. IMPORTANCE Bacteria have developed diverse regulatory mechanisms to control genetic expression, in the case of pathogenic bacteria, to induce the expression of virulence genes in particular niches during host infection. In Salmonella, an intricate regulatory network has been determined, which controls the spatiotemporal expression of the SPI-1 and SPI-2 gene clusters that mediate the invasion to and the replication inside host cells, respectively. In this study, we report two additional pathways of cross talk between the transcriptional programs for SPI-1 and SPI-2. Additionally, our results support that these additional regulatory pathways were adapted during the divergence of Salmonella from its closer species, Escherichia coli. This study further expands the knowledge about the mechanisms determining the Salmonella virulence.

The core bacterial microbiome of banana (Musa spp.)

BACKGROUND

Bananas (Musa spp.) are a globally significant crop and are severely afflicted by diseases for which there are no effective chemical controls. Banana microbiomes may provide novel solutions to these constraints but are difficult to manage due to their high diversity and variability between locations. Hence 'common core' taxa, which are a subset of the microbiome that frequent all, or most, individuals of a host species, represent logical targets for the development of microbiome management approaches. Here, we first performed a pot experiment to characterise the effects of two factors that are likely to differ between farms (viz. edaphic conditions and host genotype) on bacterial diversity in bulk soil and seven plant compartments. From this experiment, we created shortlisted core 'candidates' that were then refined using a survey of 52 field-grown Musa spp. We confirmed the importance of the core through network analysis and by comparing the sequences of our core taxa with those reported in 22 previous studies.

RESULTS

Diversity was found to differ between plant compartments and soils, but not genotypes. Therefore, we identified populations that were frequent across most plants irrespective of the soil in which they were grown. This led to the selection of 36 'common core' bacteria, that represented 65-95% of the dominant taxa in field-grown plants and were identified as highly interconnected 'hubs' using network analysis - a characteristic shown to be indicative of microbes that influence host fitness in studies of other plants. Lastly, we demonstrated that the core taxa are closely related to banana-associated bacteria observed on five other continents.

CONCLUSIONS

Our study provides a robust list of common core bacterial taxa for Musa spp. Further research may now focus on how changes in the frequencies and activities of these most persistent taxa influence host fitness. Notably, for several of our core taxa, highly similar populations have already been isolated in previous studies and may be amenable to such experimentation. This contribution should help to accelerate the development of effective Musa spp. microbiome management practices.

The ancestral stringent response potentiator, DksA has been adapted throughout Salmonella evolution to orchestrate the expression of metabolic, motility, and virulence pathways

DksA is a conserved RNA polymerase-binding protein known to play a key role in the stringent response of proteobacteria species, including many gastrointestinal pathogens. Here, we used RNA-sequencing of Escherichia coli, Salmonella bongori and Salmonella enterica serovar Typhimurium, together with phenotypic comparison to study changes in the DksA regulon, during Salmonella evolution. Comparative RNA-sequencing showed that under non-starved conditions, DksA controls the expression of 25%, 15%, and 20% of the E. coli, S. bongori, and S. enterica genes, respectively, indicating that DksA is a pleiotropic regulator, expanding its role beyond the canonical stringent response. We demonstrate that DksA is required for the growth of these three enteric bacteria species in minimal medium and controls the expression of the TCA cycle, glycolysis, pyrimidine biosynthesis, and quorum sensing. Interestingly, at multiple steps during Salmonella evolution, the type I fimbriae and various virulence genes encoded within SPIs 1, 2, 4, 5, and 11 have been transcriptionally integrated under the ancestral DksA regulon. Consequently, we show that DksA is necessary for host cells invasion by S. Typhimurium and S. bongori and for intracellular survival of S. Typhimurium in bone marrow-derived macrophages (BMDM). Moreover, we demonstrate regulatory inversion of the conserved motility-chemotaxis regulon by DksA, which acts as a negative regulator in E. coli, but activates this pathway in S. bongori and S. enterica. Overall, this study demonstrates the regulatory assimilation of multiple horizontally acquired virulence genes under the DksA regulon and provides new insights into the evolution of virulence genes regulation in Salmonella spp.

Virulence Comparison of Salmonella enterica Subsp. enterica Isolates from Chicken and Whole Genome Analysis of the High Virulent Strain S. Enteritidis 211

Background: Salmonellaenterica is one of the common pathogens in both humans and animals that causes salmonellosis and threatens public health all over the world. Methods and Results: Here we determined the virulence phenotypes of nine Salmonellaenterica subsp. enterica (S. enterica) isolates in vitro and in vivo, including pathogenicity to chicken, cell infection, biofilm formation and virulence gene expressions. S. Enteritidis 211 (SE211) was highly pathogenic with notable virulence features among the nine isolates. The combination of multiple virulence genes contributed to the conferring of the high virulence in SE211. Importantly, many mobile genetic elements (MGEs) were found in the genome sequence of SE211, including a virulence plasmid, genomic islands, and prophage regions. The MGEs and CRISPR-Cas system might function synergistically for gene transfer and immune defense. In addition, the neighbor joining tree and the minimum spanning tree were constructed in this study. Conclusions: This study provided both the virulence phenotypes and genomic features, which might contribute to the understanding of bacterial virulence mechanisms in Salmonella enterica subsp. enterica. The first completed genomic sequence for the high virulent S. Enteritidis isolate SE211 and the comparative genomics and phylogenetic analyses provided a preliminary understanding of S. enterica genetics and laid the foundation for further study.

Revisiting the steps of Salmonella gut infection with a focus on antagonistic interbacterial interactions

A commensal microbial community is established in the mammalian gut during its development, and these organisms protect the host against pathogenic invaders. The hallmark of noninvasive Salmonella gut infection is the induction of inflammation via effector proteins secreted by the type III secretion system, which modulate host responses to create a new niche in which the pathogen can overcome the colonization resistance imposed by the microbiota. Several studies have shown that endogenous microbes are important to control Salmonella infection by competing for resources. However, there is limited information about antimicrobial mechanisms used by commensals and pathogens during these in vivo disputes for niche control. This review aims to revisit the steps that Salmonella needs to overcome during gut colonization-before and after the induction of inflammation-to achieve an effective infection. We focus on a series of reported and hypothetical antagonistic interbacterial interactions in which both contact-independent and contact-dependent mechanisms might define the outcome of the infection.

Secretory System Components as Potential Prophylactic Targets for Bacterial Pathogens

Bacterial secretory systems are essential for virulence in human pathogens. The systems have become a target of alternative antibacterial strategies based on small molecules and antibodies. Strategies to use components of the systems to design prophylactics have been less publicized despite vaccines being the preferred solution to dealing with bacterial infections. In the current review, strategies to design vaccines against selected pathogens are presented and connected to the biology of the system. The examples are given for Y. pestis, S. enterica, B. anthracis, S. flexneri, and other human pathogens, and discussed in terms of effectiveness and long-term protection.

A Single Nucleotide Polymorphism in lptG Increases Tolerance to Bile Salts, Acid, and Staining of Calcofluor-Binding Polysaccharides in Salmonella enterica Serovar Typhimurium E40

The outer membrane of Salmonella enterica plays an important role in combating stress encountered in the environment and hosts. The transport and insertion of lipopolysaccharides (LPS) into the outer membrane involves lipopolysaccharide transport proteins (LptA-F) and mutations in the genes encoding for these proteins are often lethal or result in the transport of atypical LPS that can alter stress tolerance in bacteria. During studies of heterogeneity in bile salts tolerance, S. enterica serovar Typhimurium E40 was segregated into bile salts tolerant and sensitive cells by screening for growth in TSB with 10% bile salts. An isolate (E40V) with a bile salts MIC >20% was selected for further characterization. Whole-genome sequencing of E40 and E40V using Illumina and PacBio SMRT technologies revealed a non-synonymous single nucleotide polymorphism (SNP) in lptG. Leucine at residue 26 in E40 was substituted with proline in E40V. In addition to growth in the presence of 10% bile salts, E40V was susceptible to novobiocin while E40 was not. Transcriptional analysis of E40 and E40V, in the absence of bile salts, revealed significantly greater (p < 0.05) levels of transcript in three genes in E40V; yjbE (encoding for an extracellular polymeric substance production protein), yciE (encoding for a putative stress response protein), and an uncharacterized gene annotated as an acid shock protein precursor (ASPP). No transcripts of genes were present at a greater level in E40 compared to E40V. Corresponding with the greater level of these transcripts, E40V had greater survival at pH 3.35 and staining of Calcofluor-binding polysaccharide (CBPS). To confirm the SNP in lptG was associated with these phenotypes, strain E40E was engineered from E40 to encode for the variant form of LptG (L26P). E40E exhibited the same differences in gene transcripts and phenotypes as E40V, including susceptibility to novobiocin, confirming the SNP was responsible for these differences.

Comparative genomics reveals an SNP potentially leading to phenotypic diversity of Salmonella enterica serovar Enteritidis

An SNP is a spontaneous genetic change having a potential to modify the functions of the original genes and to lead to phenotypic diversity of bacteria in nature. In this study, a phylogenetic analysis of Salmonella enterica serovar Enteritidis, a major food-borne pathogen, showed that eight strains of S. Enteritidis isolated in South Korea, including FORC_075 and FORC_078, have almost identical genome sequences. Interestingly, however, the abilities of FORC_075 to form biofilms and red, dry and rough (RDAR) colonies were significantly impaired, resulting in phenotypic differences among the eight strains. Comparative genomic analyses revealed that one of the non-synonymous SNPs unique to FORC_075 has occurred in envZ, which encodes a sensor kinase of the EnvZ/OmpR two-component system. The SNP in envZ leads to an amino acid change from Pro248 (CCG) in other strains including FORC_078 to Leu248 (CTG) in FORC_075. Allelic exchange of envZ between FORC_075 and FORC_078 identified that the SNP in envZ is responsible for the impaired biofilm- and RDAR colony-forming abilities of S. Enteritidis. Biochemical analyses demonstrated that the SNP in envZ significantly increases the phosphorylated status of OmpR in S. Enteritidis and alters the expression of the OmpR regulon. Phenotypic analyses further identified that the SNP in envZ decreases motility of S. Enteritidis but increases its adhesion and invasion to both human epithelial cells and murine macrophage cells. In addition to an enhancement of infectivity to the host cells, survival under acid stress was also elevated by the SNP in envZ. Together, these results suggest that the natural occurrence of the SNP in envZ could contribute to phenotypic diversity of S. Enteritidis, possibly improving its fitness and pathogenesis.

Four single-basepair mutations in the ptx promoter of Bordetella bronchiseptica are sufficient to activate the expression of pertussis toxin

Secretion of pertussis toxin (PT) is the preeminent virulence trait of the human pathogen Bordetella pertussis, causing whooping cough. Bordetella bronchiseptica, although it harbors an intact 12-kb ptx-ptl operon, does not express PT due to an inactive ptx promoter (Pptx), which contains 18 SNPs (single nucleotide polymorphisms) relative to B. pertussis Pptx. A systematic analysis of these SNPs was undertaken to define the degree of mutational divergence necessary to activate B. bronchiseptica Pptx. A single change (C^-13T), which created a better - 10 element, was capable of activating B. bronchiseptica Pptx sufficiently to allow secretion of low but measureable levels of active PT. Three additional changes in the BvgA-binding region, only in the context of C^-13T mutant, raised the expression of PT to B. pertussis levels. These results illuminate a logical evolutionary pathway for acquisition of this key virulence trait in the evolution of B. pertussis from a B. bronchiseptica-like common ancestor.

Characterization and protective efficacy of a sptP mutant of Salmonella Paratyphi A

Background

Salmonella Paratyphi A causes paratyphoid A, a severe systemic disease of people and remains a major public health problem in many parts of the world. In the interest of researching the roles of sptP on Salmonella Paratyphi A and developing a live‐attenuated vaccine candidate, an sptP mutant of Salmonella Paratyphi A SPA017 (SPA017ΔsptP) was constructed, and then its characterization, immunogenicity, and protective ability were evaluated.

Results

The deletion of sptP had no effect on growth and biochemical properties. Adhesion and invasion assays showed that the lack of sptP did not affect the adhesion of Salmonella Paratyphi A, but the invasive ability of the mutant strain was significantly decreased, the half‐lethal dose (LD₅₀) of the mutant strain was 1.43 × 10⁴ times of the parent strain in intraperitoneally injected mice. Single intraperitoneal vaccination with SPA017ΔsptP (1 × 10⁵ CFU) in mice did not affect the body weight or elicit clinical symptoms relative to the control group, SPA017ΔsptP bacteria were isolated from livers and spleens of vaccinated mice at 14 days postvaccination. Notably, specific humoral and cellular immune responses were significantly induced. The protective assessment showed that the mutant strain could provide high‐level protection against subsequent challenge with the wild‐type SPA017 strain.

Conclusions

These results demonstrated that SptP plays an essential role in the pathogenicity of Salmonella Paratyphi A, and Salmonella Paratyphi A lacking sptP is immunogenic and protective in mice.

Genetic boundaries delineate the potential human pathogen Salmonella bongori into discrete lineages: divergence and speciation

BACKGROUND

Salmonella bongori infect mainly cold-blooded hosts, but infections by S. bongori in warm-blooded hosts have been reported. We hypothesized that S. bongori might have diverged into distinct phylogenetic lineages, with some being able to infect warm-blooded hosts.

RESULTS

To inspect the divergence status of S. bongori, we first completely sequenced the parakeet isolate RKS3044 and compared it with other sequenced S. bongori strains. We found that RKS3044 contained a novel T6SS encoded in a pathogenicity island-like structure, in addition to a T6SS encoded in SPI-22, which is common to all S. bongori strains so far reported. This novel T6SS resembled the SPI-19 T6SS of the warm-blooded host infecting Salmonella Subgroup I lineages. Genomic sequence comparisons revealed different genomic sequence amelioration events among the S. bongori strains, including a unique CTAG tetranucleotide degeneration pattern in RKS3044, suggesting non-overlapping gene pools between RKS3044 and other S. bongori lineages/strains leading to their independent accumulation of genomic variations. We further proved the existence of a clear-cut genetic boundary between RKS3044 and the other S. bongori lineages/strains analyzed in this study.

CONCLUSIONS

The warm-blooded host-infecting S. bongori strain RKS3044 has diverged with distinct genomic features from other S. bongori strains, including a novel T6SS encoded in a previously not reported pathogenicity island-like structure and a unique genomic sequence degeneration pattern. These findings alert cautions about the emergence of new pathogens originating from non-pathogenic ancestors by acquiring specific pathogenic traits.

HilD induces expression of a novel Salmonella Typhimurium invasion factor, YobH, through a regulatory cascade involving SprB

HilD is an AraC-like transcriptional regulator encoded in the Salmonella pathogenicity island 1 (SPI-1), which actives transcription of many genes within and outside SPI-1 that are mainly required for invasion of Salmonella into host cells. HilD controls expression of target genes directly or by acting through distinct regulators; three different regulatory cascades headed by HilD have been described to date. Here, by analyzing the effect of HilD on the yobH gene in Salmonella enterica serovar Typhimurium (S. Typhimurium), we further define an additional regulatory cascade mediated by HilD, which was revealed by previous genome-wide analyses. In this regulatory cascade, HilD acts through SprB, a LuxR-like regulator encoded in SPI-1, to induce expression of virulence genes. Our data show that HilD induces expression of sprB by directly counteracting H-NS-mediated repression on the promoter region upstream of this gene. Then, SprB directly activates expression of several genes including yobH, slrP and ugtL. Interestingly, we found that YobH, a protein of only 79 amino acids, is required for invasion of S. Typhimurium into HeLa cells and mouse macrophages. Thus, our results reveal a novel S. Typhimurium invasion factor and provide more evidence supporting the HilD-SprB regulatory cascade.

Proteotyping as alternate typing method to differentiate Campylobacter coli clades

Besides Campylobacter jejuni, Campylobacter coli is the most common bacterial cause of gastroenteritis worldwide. C. coli is subdivided into three clades, which are associated with sample source. Clade 1 isolates are associated with acute diarrhea in humans whereas clade 2 and 3 isolates are more commonly obtained from environmental waters. The phylogenetic classification of an isolate is commonly done using laborious multilocus sequence typing (MLST). The aim of this study was to establish a proteotyping scheme using MALDI-TOF MS to offer an alternative to sequence-based methods. A total of 97 clade-representative C. coli isolates were analyzed by MALDI-TOF-based intact cell mass spectrometry (ICMS) and evaluated to establish a C. coli proteotyping scheme. MLST was used as reference method. Different isoforms of the detectable biomarkers, resulting in biomarker mass shifts, were associated with their amino acid sequences and included into the C. coli proteotyping scheme. In total, we identified 16 biomarkers to differentiate C. coli into the three clades and three additional sub-clades of clade 1. In this study, proteotyping has been successfully adapted to C. coli. The established C. coli clades and sub-clades can be discriminated using this method. Especially the clinically relevant clade 1 isolates can be differentiated clearly.

Phenotypic and genomic analyses of bacteriophages targeting environmental and clinical CS3-expressing enterotoxigenic Escherichia coli (ETEC) strains

Diarrhea due to infection of enterotoxigenic Escherichia coli (ETEC) is of great concern in several low and middle-income countries. ETEC infection is considered to be the most common cause of diarrhea in Bangladesh and is mainly spread through contaminated water and food. ETEC pathogenesis is mediated by the expression of enterotoxins and colonization factors (CFs) that target the intestinal mucosa. ETEC can survive for extended time periods in water, where they are likely to be attacked by bacteriophages. Antibiotic resistance is common amongst enteric pathogens and therefore is the use of bacteriophages (phage) as a therapeutic tool an interesting approach. This study was designed to identify novel phages that specifically target ETEC virulence factors. In total, 48 phages and 195 ETEC isolates were collected from water sources and stool samples. Amongst the identified ETEC specific phages, an enterobacteria phage T7, designated as IMM-002, showed a significant specificity towards colonization factor CS3-expressing ETEC isolates. Antibody-blocking and phage-neutralization assays revealed that CS3 is used as a host receptor for the IMM-002 phage. The bacterial CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR-associated) defence mechanism can invoke immunity against phages. Genomic analyses coupled with plaque assay experiments indicate that the ETEC CRISPR-Cas system is involved in the resistance against the CS3-specific phage (IMM-002) and the previously identified CS7-specific phage (IMM-001). As environmental water serves as a reservoir for ETEC, it is important to search for new antimicrobial agents such as phages in environmental water as well as the human gut. A better understanding of how the interplay between ETEC-specific phages and ETEC isolates affects the ETEC diversity, both in environmental ecosystems and within the host, is important for the development of new treatments for ETEC infections.

Formation of phenotypic lineages in Salmonella enterica by a pleiotropic fimbrial switch

The std locus of Salmonella enterica, an operon acquired by horizontal transfer, encodes fimbriae that permit adhesion to epithelial cells in the large intestine. Expression of the std operon is bistable, yielding a major subpopulation of Std^OFF cells (99.7%) and a minor subpopulation of Std^ON cells (0.3%). In addition to fimbrial proteins, the std operon encodes two proteins, StdE and StdF, that have DNA binding capacity and control transcription of loci involved in flagellar synthesis, chemotaxis, virulence, conjugal transfer, biofilm formation, and other cellular functions. As a consequence of StdEF pleiotropic transcriptional control, Std^ON and Std^OFF subpopulations may differ not only in the presence or absence of Std fimbriae but also in additional phenotypic traits. Separation of Std^OFF and Std^ON lineages by cell sorting confirms the occurrence of lineage-specific features. Formation of Std^OFF and Std^ON lineages may thus be viewed as a rudimentary bacterial differentiation program.

We show that the std fimbrial operon of Salmonella enterica undergoes bistable expression, a trait far from exceptional among loci that encode components of the bacterial envelope. However, an unsuspected trait of the std operon is the presence of two genes that encode pleiotropic regulators of gene expression. Indeed, StdE and StdF are DNA-binding proteins that control transcription of hundreds of genes. As a consequence, StdEF govern multiple phenotypic traits, and the fimbriated and non-fimbriated Salmonella lineages may differ in motility, virulence, conjugal transfer, biofilm formation, and potentially in other phenotypic features. We hypothesize that pleiotropic control of gene expression by StdEF may contribute to adapt the non-fimbriated lineage to acute infection and the fimbriated lineage to chronic infection.

HilD and PhoP independently regulate the expression of grhD1, a novel gene required for Salmonella Typhimurium invasion of host cells

When Salmonella is grown in the nutrient-rich lysogeny broth (LB), the AraC-like transcriptional regulator HilD positively controls the expression of genes required for Salmonella invasion of host cells, such as the Salmonella pathogenicity island 1 (SPI-1) genes. However, in minimal media, the two-component system PhoP/Q activates the expression of genes necessary for Salmonella replication inside host cells, such as the SPI-2 genes. Recently, we found that the SL1344_1872 hypothetical gene, located in a S. Typhimurium genomic island, is co-expressed with the SPI-1 genes. In this study we demonstrate that HilD induces indirectly the expression of SL1344_1872 when S. Typhimurium is grown in LB; therefore, we named SL1344_1872 as grhD1 for gene regulated by HilD. Furthermore, we found that PhoP positively controls the expression of grhD1, independently of HilD, when S. Typhimurium is grown in LB or N-minimal medium. Moreover, we demonstrate that the grhD1 gene is required for the invasion of S. Typhimurium into epithelial cells, macrophages and fibroblasts, as well as for the intestinal inflammatory response caused by S. Typhimurium in mice. Thus, our results reveal a novel virulence factor of Salmonella, whose expression is positively and independently controlled by the HilD and PhoP transcriptional regulators.

Molecular and Conventional Analysis of Acute Diarrheal Isolates Identifies Epidemiological Trends, Antibiotic Resistance and Virulence Profiles of Common Enteropathogens in Shanghai

Objective: To investigate prevalence of acute diarrhea in Shanghai and analyze virulence associated-genes and antibiotic resistance of major enteropathogens using combination of conventional and molecular epidemiology methods. Method: The 412 stool specimens were obtained by systematic sampling from diarrhea patients throughout entire year 2016. Bacterial and viral pathogens were identified and bacterial isolates were cultured and screened for antibiotic resistance profiles. Two most prevalent bacteria, Vibrio parahaemolyticus and Salmonella were further typed by multi-locus sequence typing (MLST) and analyzed for presence of virulence-associated genes. The association between virulence genes, resistance phenotypes and genetic diversities was analyzed. Results: Among stool specimens testing positive for pathogens (23.1%), 59 bacterial and 36 viral pathogens were identified. V. parahaemolyticus (27/412, 6.6%), Salmonella (23/412, 5.6%) and norovirus GII (21/412, 5.1%) were three most-commonly found. Most bacterial isolates exhibited high levels of antibiotic resistance with high percentage of MDR. The drug resistance rates of V. parahaemolyticus and Salmonella isolates to cephalosporins were high, such as 100.0 and 34.8% to CFX, 55.6 and 43.4% to CTX, 92.6 and 95.7% to CXM, respectively. The most common resistance combination of V. parahaemolyticus and Salmonella was cephalosporins and quinolone. The dominant sequence types (STs) of V. parahaemolyticus and Salmonella were ST3 (70.4%) and ST11 (43.5%), respectively. The detection rates of virulence genes in V. parahaemolyticus were tlh (100%) and tdh (92.6%), without trh and ureR. Most of the Salmonella isolates were positive for the Salmonella pathogenicity islands (SPIs) genes (87-100%), and some for Salmonella plasmid virulence (SPV) genes (34.8% for spvA and spvB, 43.5% for spvC). In addition, just like the drug resistance, virulence genes exhibited wide-spread distribution among the different STs albeit with some detectable frequency linkage among Salmonella STs. Conclusion: Bacterial infections are still the major cause of severe diarrheas in Shanghai. The most common bacteria V. parahaemolyticus and Salmonella show molecular characteristics consistent with preselection of highly virulent types with exceedingly high level of antibiotic resistance.

Negative supercoiling of DNA by gyrase is inhibited in Salmonella enterica serovar Typhimurium during adaptation to acid stress

DNA in intracellular Salmonella enterica serovar Typhimurium relaxes during growth in the acidified (pH 4-5) macrophage vacuole and DNA relaxation correlates with the upregulation of Salmonella genes involved in adaptation to the macrophage environment. Bacterial ATP levels did not increase during adaptation to acid pH unless the bacterium was deficient in MgtC, a cytoplasmic-membrane-located inhibitor of proton-driven F₁ F₀ ATP synthase activity. Inhibiting ATP binding by DNA gyrase and topo IV with novobiocin enhanced the effect of low pH on DNA relaxation. Bacteria expressing novobiocin-resistant (Nov^R ) derivatives of gyrase or topo IV also exhibited DNA relaxation at acid pH, although further relaxation with novobiocin was not seen in the strain with Nov^R gyrase. Thus, inhibition of the negative supercoiling activity of gyrase was the primary cause of enhanced DNA relaxation in drug-treated bacteria. The Salmonella cytosol reaches pH 5-6 in response to an external pH of 4-5: the ATP-dependent DNA supercoiling activity of purified gyrase was progressively inhibited by lowering the pH in this range, as was the ATP-dependent DNA relaxation activity of topo IV. We propose that DNA relaxation in Salmonella within macrophage is due to acid-mediated impairment of the negative supercoiling activity of gyrase.

Biofilm Formation, Antimicrobial Resistance, and Sanitizer Tolerance of Salmonella enterica Strains Isolated from Beef Trim

In the beef industry, product contamination by Salmonella enterica is a serious public health concern, which may result in human infection and cause significant financial loss due to product recalls. Currently, the precise mechanism and pathogen source responsible for Salmonella contamination in commercial establishments are not well understood. We characterized 89 S. enterica strains isolated from beef trim with respect to their biofilm-forming ability, antimicrobial resistance, and biofilm cell survival/recovery growth after sanitizer exposure. A total of 28 Salmonella serovars was identified within these strains. The most common serovars identified were Anatum, Dublin, Montevideo, and Typhimurium, with these accounting for nearly half of the total strains. The vast majority (86%) of the strains was able to develop strong biofilms, and the biofilm-forming ability was highly strain dependent and related to cell surface expression of extracellular polymeric structures. These strains also demonstrated strong tolerance to quaternary ammonium chloride (QAC) and chlorine dioxide (ClO₂), but were more sensitive to chlorine treatment. Sanitizer tolerance and bacterial postsanitization recovery growth were closely associated with strains' biofilm-forming ability. Thirty percent of the examined strains were found resistant to multiple antimicrobial agents and the resistance phenotypes were serovar associated, but not related to strains' biofilm-forming ability. Pulsed-field gel electrophoresis analysis tended to group strains by serovar rather than by biofilm-forming ability. Collectively, these data indicate that the strong biofilm formers of certain S. enterica strains/serovars possess significant potential for causing meat product contamination in meat processing environment.

Evolution of Salmonella-Host Cell Interactions through a Dynamic Bacterial Genome

Salmonella Typhimurium has a broad arsenal of genes that are tightly regulated and coordinated to facilitate adaptation to the various host environments it colonizes. The genome of Salmonella Typhimurium has undergone multiple gene acquisition events and has accrued changes in non-coding DNA that have undergone selection by regulatory evolution. Together, at least 17 horizontally acquired pathogenicity islands (SPIs), prophage-associated genes, and changes in core genome regulation contribute to the virulence program of Salmonella. Here, we review the latest understanding of these elements and their contributions to pathogenesis, emphasizing the regulatory circuitry that controls niche-specific gene expression. In addition to an overview of the importance of SPI-1 and SPI-2 to host invasion and colonization, we describe the recently characterized contributions of other SPIs, including the antibacterial activity of SPI-6 and adhesion and invasion mediated by SPI-4. We further discuss how these fitness traits have been integrated into the regulatory circuitry of the bacterial cell through cis-regulatory evolution and by a careful balance of silencing and counter-silencing by regulatory proteins. Detailed understanding of regulatory evolution within Salmonella is uncovering novel aspects of infection biology that relate to host-pathogen interactions and evasion of host immunity.

Molecular Characterization of Salmonella from Human and Animal Origins in Uganda

Sporadic Salmonella outbreaks with varying clinical presentations have been on the rise in various parts of Uganda. The sources of outbreaks and factors underlying the different clinical manifestation are curtailed by paucity of information on Salmonella genotypes and the associated virulence genes. This study reports molecular diversity of Salmonella enterica and their genetic virulence profiles among human and animal isolates. Characterization was done using Kauffman-White classification scheme and virulence genes analysis using multiplex PCR. Overall, 52% of the isolates belonged to serogroup D, 16% to serogroup E, 15% to poly F, H-S, and 12% to serogroup B. Serogroups A, C1, and C2 each consisted of only one isolate representing 5%. Virulence genes located on SPI-1 [spaN and sipB] and on SPI-2 [spiA] in addition to pagC and msgA were equally distributed in isolates obtained from all sources. Plasmid encoded virulence gene spvB was found in <5% of isolates from both human epidemic and animal origins whereas it occurred in 80% of clinical isolates. This study reveals that serogroup D is the predominant Salmonella serogroup in circulation and it is widely shared among animals and humans and calls for joint and coordinated surveillance for one health implementation in Uganda.

Determination of regional relationships among Salmonella spp. isolated from retail pork circulating in the Chiang Mai municipality area using a WGS data approach

Salmonella is recognized as a significant zoonotic foodborne pathogen, and pork products are involved in one-fifth of infections. Whole genome sequencing data of Salmonella isolated from retail's pork circulating in the Chiang Mai Municipality area between April 2013 and September 2014, were used to focus on genetic diversity and proven in pig-human transmission based on Multilocus Sequence Typing (MLST). Additionally, WGS data were used to investigate virulence genes, to assess the hazard or pathogenic potential transferred into the food production chain. In this study, all 32 Salmonella strains were classified into 11 Sequence Types (STs). ST469 accounted for the majority (41%). The sequence types of two other strains, 6% of the total, could not be identified. All tested strains carried at least 15 virulence genes. The most frequent gene profile was "sfm-fim-sop-inv.-org-sip-spa-sif-fli-flg-hil-spr-ssa-sse-pag-bss" (47%). Salmonella circulating in the study area demonstrated competence in biofilm production, host cell adhesion, host cell invasion, and host cell survival. Based on the phenotypic and genotypic findings, as well as pathogen source, it appears possible that a common supply chain or common infection source might be presented in the retail pork system in the study area. In addition, an epidemiological comparison of the Salmonella genotypes from the current study with those from other areas such as People's Republic of China (PR China) and the Lao People's Democratic Republic (Lao PDR) was generated by Minimum spanning tree (MST). Identical strains originating from humans, animals and food were found. The findings indicate that contamination can be occured at all levels including pre-harvest, the farm-slaughterhouse-retail chain and consumers over different geographical areas. Acquiring information about infection sources and transmission routes will hopefully motivate all sectors to enforce strict sanitation controls at all production stages including the consumer level.

Influence of Salmonella enterica serovar Pullorum pathogenicity island 2 on type III secretion system effector gene expression in chicken macrophage HD11 cells

Salmonella pathogenicity island 2 (SPI2) can encode type III secretion system 2 (T3SS2) which plays an important role in systemic disease development through delivering different effector proteins into host cells. Here, the influence of Salmonella Pullorum pathogenicity island 2 on T3SS2 effector gene expression was studied using qRT-PCR in chicken macrophage HD11 cells. Our results showed that all the detected genes (including pseudogenes sifB, sspH2 and steC) can express in HD11 cells of S. Pullorum infection; deletion of SPI2 of S. Pullorum did not significantly affect the expression of genes cigR, gtgA, slrP, sopD, sseK1, steB and steC, but had a significant effect on the expression of genes pipB2, sifB, sopD2, sseJ, sseL, sspH2, steD, sifA, pipB and steA at different degrees. These results suggest that SPI2 can significantly affect the expression of some T3SS2 effector genes. Some effectors may have secretion pathways other than T3SS2 and pseudogenes may play roles in the process of S. Pullorum infection.

Evolution of bopA Gene in Burkholderia: A Case of Convergent Evolution as a Mechanism for Bacterial Autophagy Evasion

Autophagy is an important defense mechanism targeting intracellular bacteria to restrict their survival and growth. On the other hand, several intracellular pathogens have developed an antiautophagy mechanism to facilitate their own replication or intracellular survival. Up to now, no information about the origin or evolution of the antiautophagic genes in bacteria is available. BopA is an effector protein secreted by Burkholderia pseudomallei via the type three secretion system, and it has been shown to play a pivotal role in their escape from autophagy.  The evolutionary origin of bopA was examined in this work. Sequence similarity searches for BopA showed that no homolog of BopA was detected in eukaryotes. However, eukaryotic linear motifs were detected in BopA. The phylogenetic tree of the BopA proteins in our analysis is congruent with the species phylogeny derived from housekeeping genes. Moreover, there was no obvious difference in GC content values of bopA gene and their respective genomes. Integrated information on the taxonomic distribution, phylogenetic relationships, and GC content of the bopA gene of Burkholderia revealed that this gene was acquired via convergent evolution, not from eukaryotic host through horizontal gene transfer (HGT) event. This work has, for the first time, characterized the evolutionary mechanism of bacterial evasion of autophagy. The results of this study clearly demonstrated the role of convergent evolution in the evolution of how bacteria evade autophagy.

Bacterial secretion systems and regulation of inflammasome activation

Innate immunity is critical for host defenses against pathogens, but many bacteria display complex ways of interacting with innate immune signaling, as they may both activate and evade certain pathways. Gram-negative bacteria can exhibit specialized nanomachine secretion systems for delivery of effector proteins into mammalian cells. Bacterial types III, IV, and VI secretion systems (T3SS, T4SS, and T6SS) are known for their impact on caspase-1-activating inflammasomes, necessary for producing bioactive inflammatory cytokines IL-1β and IL-18, key participants of anti-bacterial responses. Here, we discuss how these secretion systems can mediate triggering and inhibition of inflammasome signaling. We propose that a fine balance between secretion system-mediated activation and inhibition can determine net activation of inflammasome activity and control inflammation, clearance, or spread of the infection.

Ecological Opportunity, Evolution, and the Emergence of Flea-Borne Plague

The plague bacillus Yersinia pestis is unique among the pathogenic Enterobacteriaceae in utilizing an arthropod-borne transmission route. Transmission by fleabite is a recent evolutionary adaptation that followed the divergence of Y. pestis from the closely related food- and waterborne enteric pathogen Yersinia pseudotuberculosis A combination of population genetics, comparative genomics, and investigations of Yersinia-flea interactions have disclosed the important steps in the evolution and emergence of Y. pestis as a flea-borne pathogen. Only a few genetic changes, representing both gene gain by lateral transfer and gene loss by loss-of-function mutation (pseudogenization), were fundamental to this process. The emergence of Y. pestis fits evolutionary theories that emphasize ecological opportunity in adaptive diversification and rapid emergence of new species.

Prevalence of virulence and antimicrobial resistance genes in Salmonella spp. isolated from commercial chickens and human clinical isolates from South Africa and Brazil

Salmonellosis is a significant public health concern around the world. The injudicious use of antimicrobial agents in poultry production for treatment, growth promotion and prophylaxis has resulted in the emergence of drug resistant strains of Salmonella. The current study was conducted to investigate the prevalence of virulence and antimicrobial resistance genes from Salmonella isolated from South African and Brazilian broiler chickens as well as human clinical isolates. Out of a total of 200 chicken samples that were collected from South Africa 102 (51%) tested positive for Salmonella using the InvA gene. Of the overall 146 Salmonella positive samples that were screened for the iroB gene most of them were confirmed to be Salmonella enterica with the following prevalence rates: 85% of human clinical samples, 68.6% of South African chicken isolates and 70.8% of Brazilian chicken samples. All Salmonella isolates obtained were subjected to antimicrobial susceptibility testing with 10 antibiotics. Salmonella isolates from South African chickens exhibited resistance to almost all antimicrobial agents used, such as tetracycline (93%), trimethoprim-sulfamthoxazole (84%), trimethoprim (78.4%), kanamycin (74%), gentamicin (48%), ampicillin (47%), amoxicillin (31%), chloramphenicol (31%), erythromycin (18%) and streptomycin (12%). All samples were further subjected to PCR in order to screen some common antimicrobial and virulence genes of interest namely spiC, pipD, misL, orfL, pse-1, tet A, tet B, ant (3")-la, sul 1 and sul. All Salmonella positive isolates exhibited resistance to at least one antimicrobial agent; however, antimicrobial resistance patterns demonstrated that multiple drug resistance was prevalent. The findings provide evidence that broiler chickens are colonised by pathogenic Salmonella harbouring antimicrobial resistance genes. Therefore, it is evident that there is a need for prudent use of antimicrobial agents in poultry production systems in order to mitigate the proliferation of multiple drug resistance across species.

A multi-drug resistant Salmonella Typhimurium ST213 human-invasive strain (33676) containing the bla CMY-2 gene on an IncF plasmid is attenuated for virulence in BALB/c mice

Background

Classical strains of Salmonella enterica serovar Typhimurium (Typhimurium) predominantly cause a self-limiting diarrheal illness in humans and a systemic disease in mice. In this study, we report the characterization of a strain isolated from a blood-culture taken from a 15-year old woman suffering from invasive severe salmonellosis, refractory to conventional therapy with extended-spectrum cephalosporin (ESC).

Results

The strain, named 33676, was characterized as multidrug-resistant Salmonella serogroup A by biochemical, antimicrobial and serological tests. Multilocus sequence typing (MLST) and XbaI macrorestrictions (PFGE) showed that strain 33676 belonged to the Typhimurium ST213 genotype, previously described for other Mexican Typhimurium strains. PCR analyses revealed the presence of IncA/C, IncFIIA and ColE1-like plasmids and the absence of the Salmonella virulence plasmid (pSTV). Conjugation assays showed that the ESC-resistance gene bla_CMY-2 was carried on the conjugative IncF plasmid, instead of the IncA/C plasmid, as found in previously studied ST213 strains. Although the IncA/C plasmid conferred most of the observed antimicrobial resistances it was not self-conjugative; it was rather able to conjugate by co-integrating with the IncF plasmid. Strain 33676 was fully attenuated for virulence in BALB/c mice infections. Both type-three secretion system (T3SS), encoded in Salmonella pathogenicity islands 1 and 2 (SPI-1 and SPI-2), were functional in the 33676 strain and, interestingly, this strain produced the H2 FljB flagellin instead of the H1 FliC flagellin commonly expressed by S. enterica strains.

Conclusions

Strain 33676 showed two main features that differentiate it from the originally described ST213 strains: 1) the bla_CMY-2 gene was not carried on the IncA/C plasmid, but on a conjugative IncF plasmid, which may open a new route of dissemination for this ESC-resistance gene, and 2) it expresses the H2 FljB flagella, in contrast with the other ST213 and most Typhimurium reference strains. To our knowledge this is the first report of an IncF bla_CMY-2-carrying plasmid in Salmonella.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0633-7) contains supplementary material, which is available to authorized users.

Complete Closed Genome Sequences of Salmonella enterica subsp. enterica Serotypes Anatum, Montevideo, Typhimurium, and Newport, Isolated from Beef, Cattle, and Humans

Salmonella enterica spp. are a diverse group of bacteria with a wide range of virulence potential. To facilitate genome comparisons across this virulence spectrum, we present eight complete closed genome sequences of four S. enterica serotypes (Anatum, Montevideo, Typhimurium, and Newport), isolated from various cattle samples and from humans.

Protein Acetylation Is Involved in Salmonella enterica Serovar Typhimurium Virulence

Salmonella causes a range of diseases in different hosts, including enterocolitis and systemic infection. Lysine acetylation regulates many eukaryotic cellular processes, but its function in bacteria is largely unexplored. The acetyltransferase Pat and NAD(+)-dependent deacetylase CobB are involved in the reversible protein acetylation in Salmonella Typhimurium. Here, we used cell and animal models to evaluate the virulence of pat and cobB deletion mutants in S. Typhimurium and found that pat is critical for bacterial intestinal colonization and systemic infection. Next, to understand the underlying mechanism, genome-wide transcriptome was analyzed. RNA sequencing data showed that the expression of Salmonella pathogenicity island 1 (SPI-1) is partially dependent on pat In addition, we found that HilD, a key transcriptional regulator of SPI-1, is a substrate of Pat. The acetylation of HilD by Pat maintained HilD stability and was essential for the transcriptional activation of HilA. Taken together, these results suggest that a protein acetylation system regulates SPI-1 expression by controlling HilD in a posttranslational manner to mediate S. Typhimurium virulence.

Control regions for chromosome replication are conserved with respect to sequence and location among Escherichia coli strains

In Escherichia coli, chromosome replication is initiated from oriC by the DnaA initiator protein associated with ATP. Three non-coding regions contribute to the activity of DnaA. The datA locus is instrumental in conversion of DnaA^ATP to DnaA^ADP (datA dependent DnaA^ATP hydrolysis) whereas DnaA rejuvenation sequences 1 and 2 (DARS1 and DARS2) reactivate DnaA^ADP to DnaA^ATP. The structural organization of oriC, datA, DARS1, and DARS2 were found conserved among 59 fully sequenced E. coli genomes, with differences primarily in the non-functional spacer regions between key protein binding sites. The relative distances from oriC to datA, DARS1, and DARS2, respectively, was also conserved despite of large variations in genome size, suggesting that the gene dosage of either region is important for bacterial growth. Yet all three regions could be deleted alone or in combination without loss of viability. Competition experiments during balanced growth in rich medium and during mouse colonization indicated roles of datA, DARS1, and DARS2 for bacterial fitness although the relative contribution of each region differed between growth conditions. We suggest that this fitness advantage has contributed to conservation of both sequence and chromosomal location for datA, DARS1, and DARS2.

The two-component system CpxR/A represses the expression of Salmonella virulence genes by affecting the stability of the transcriptional regulator HilD

Salmonella enterica can cause intestinal or systemic infections in humans and animals mainly by the presence of pathogenicity islands SPI-1 and SPI-2, containing 39 and 44 genes, respectively. The AraC-like regulator HilD positively controls the expression of the SPI-1 genes, as well as many other Salmonella virulence genes including those located in SPI-2. A previous report indicates that the two-component system CpxR/A regulates the SPI-1 genes: the absence of the sensor kinase CpxA, but not the absence of its cognate response regulator CpxR, reduces their expression. The presence and absence of cell envelope stress activates kinase and phosphatase activities of CpxA, respectively, which in turn controls the level of phosphorylated CpxR (CpxR-P). In this work, we further define the mechanism for the CpxR/A-mediated regulation of SPI-1 genes. The negative effect exerted by the absence of CpxA on the expression of SPI-1 genes was counteracted by the absence of CpxR or by the absence of the two enzymes, AckA and Pta, which render acetyl-phosphate that phosphorylates CpxR. Furthermore, overexpression of the lipoprotein NlpE, which activates CpxA kinase activity on CpxR, or overexpression of CpxR, repressed the expression of SPI-1 genes. Thus, our results provide several lines of evidence strongly supporting that the absence of CpxA leads to the phosphorylation of CpxR via the AckA/Pta enzymes, which represses both the SPI-1 and SPI-2 genes. Additionally, we show that in the absence of the Lon protease, which degrades HilD, the CpxR-P-mediated repression of the SPI-1 genes is mostly lost; moreover, we demonstrate that CpxR-P negatively affects the stability of HilD and thus decreases the expression of HilD-target genes, such as hilD itself and hilA, located in SPI-1. Our data further expand the insight on the different regulatory pathways for gene expression involving CpxR/A and on the complex regulatory network governing virulence in Salmonella.

Characteristics of invasion-reduced hilA gene mutant of Salmonella Enteritidis in vitro and in vivo

Salmonella enterica serovar Enteritidis (Salmonella Enteritidis) is a facultative intracellular pathogen that causes huge losses in poultry industry and also food poisoning in humans due to its being a food-borne pathogen. Functions of Invasion-related genes need to be explored, as invasion is a key step for Salmonella infection. In this study, a transposon mutant library of Salmonella Enteritidis isolate SM6 was constructed and screened for the invasion-related genes via incubation with Caco-2 cells. Three stably attenuated mutants were identified for significantly reduced invasion with insertions all in hilA (hyperinvasive locus A) gene. We constructed and evaluated the hilA deletion mutant in vivo and in vitro. SM6△hilA showed significantly reduced ability to invade Caco-2 cells and decreased pathogenicity in chicks. However, the bacterial load and pathological damage in the cecum were significantly higher than those in the SM6 in vivo. Present results provide new evidences for pathogenicity research on Salmonella Enteritidis.

Integrated circuits: how transcriptional silencing and counter-silencing facilitate bacterial evolution

Horizontal gene transfer is a major contributor to bacterial evolution and diversity. For a bacterial cell to utilize newly-acquired traits such as virulence and antibiotic resistance, new genes must be integrated into the existing regulatory circuitry to allow appropriate expression. Xenogeneic silencing of horizontally-acquired genes by H-NS or other nucleoid-associated proteins avoids adventitious expression and can be relieved by other DNA-binding counter-silencing proteins in an environmentally-responsive and physiologically-responsive manner. Biochemical and genetic analyses have recently demonstrated that counter-silencing can occur at a variety of promoter architectures, in contrast to classical transcriptional activation. Disruption of H-NS nucleoprotein filaments by DNA bending is a suggested mechanism by which silencing can be relieved. This review discusses recent advances in our understanding of the mechanisms and importance of xenogeneic silencing and counter-silencing in the successful integration of horizontally-acquired genes into regulatory networks.

Mobile effector proteins on phage genomes

Bacteriophage genomes found in a range of bacterial pathogens encode a diverse array of virulence factors ranging from superantigens or pore forming lysins to numerous exotoxins. Recent studies have uncovered an entirely new class of bacterial virulence factors, called effector proteins or effector toxins, which are encoded within phage genomes that reside among several pathovars of Escherichia coli and Salmonella enterica. These effector proteins have multiple domains resulting in proteins that can be multifunctional. The effector proteins encoded within phage genomes are translocated directly from the bacterial cytosol into their eukaryotic target cells by specialized bacterial type three secretion systems (T3SSs). In this review, we will give an overview of the different types of effector proteins encoded within phage genomes and examine their roles in bacterial pathogenesis.

Punicalagin inhibits Salmonella virulence factors and has anti-quorum-sensing potential

Punicalagin, an essential component of pomegranate rind, has been demonstrated to possess antimicrobial activity against several food-borne pathogens, but its activity on the virulence of pathogens and its anti-quorum-sensing (anti-QS) potential have been rarely reported. This study investigated the efficacy of subinhibitory concentrations of punicalagin on Salmonella virulence factors and QS systems. A broth microdilution method was used to determine the MICs of punicalagin for 10 Salmonella strains. Motility assay and quantitative reverse transcription (RT)-PCR were performed to evaluate the effects of punicalagin on the virulence attributes and QS-related genes of Salmonella. The MICs of punicalagin for several Salmonella strains ranged from 250 to 1,000 μg/ml. Motility assays showed that punicalagin, at 1/16× MIC and 1/32× MIC, significantly decreased bacterial swimming and swarming motility, which corresponded to downregulation of the motility-related genes (fliA, fliY, fljB, flhC, and fimD) in RT-PCR assays. RT-PCR also revealed that punicalagin downregulated the expression of most of the selected genes involved in Salmonella virulence. Moreover, a QS inhibition assay indicated that punicalagin dose dependently inhibited the production of violacein by Chromobacterium violaceum and repressed the expression of QS-related genes (sdiA and srgE) in Salmonella. In addition, punicalagin significantly reduced Salmonella invasion of colonic cells (P<0.01) with no impact on adhesion. These findings suggest that punicalagin has the potential to be developed as an alternative or supplemental agent for prevention of Salmonella infection.

Comparative genomic analysis between typhoidal and non-typhoidal Salmonella serovars reveals typhoid-specific protein families

BACKGROUND

The genus Salmonella contains more than 2600 serovars. While most cause a self-limiting gastroenteritis, four serovars, S. Typhi, S. Paratyphi A, B and C, elicit typhoid, a potentially fatal systemic infection. Because of the prevalence in certain regions, such as South Asia, and the disease severity of typhoidal Salmonella infections, comprehensive studies are needed to elucidate the pathogenesis of diseases caused by these typhoidal serovars.

RESULTS

We performed comparative genomic analyses on eight human typhoidal strains and 27 non-human typhoidal Salmonella strains to elucidate their evolutionary relationships and identify the genes specific to the four typhoidal serovars. Our results indicate that Salmonella may have an open pan-genome. A core-genome based phylogeny demonstrated that divergence between S. Paratyphi A and S. Typhi took place not long ago and S. Paratyphi B shared a recent common ancestor with S. Paratyphi C. Of great interest, the divergence between S. Paratyphi B and S. Paratyphi C was shown to be more recent than that between S. Paratyphi A and S. Typhi. Alignment and comparisons of the genomes identified unique complements of protein families to each of the typhoidal serovars. Most of these protein families are phage related and some are candidate virulence factors. Importantly, we found 88 protein families specific to two to three of the four typhoidal serovars. All but two of the 88 genes are present in S. Typhi, with a few in the three paratyphoidal serovars but none in the non-human typhoidal serovars. Most of these genes are predicted to encode hypothetical proteins and some are known to code for virulence factors such as Vi polysaccharide related proteins.

CONCLUSIONS

By comprehensive genomic comparisons, we identified protein families specific to the human typhoidal serovars, which will greatly facilitate investigations on typhoid pathogenesis.

Salmonella Typhi shdA: pseudogene or allelic variant?

ShdA from Salmonella Typhimurium (ShdASTm) is a large outer membrane protein that specifically recognizes and binds to fibronectin. ShdASTm is involved in the colonization of the cecum and the Peyer's patches of terminal ileum in mice. On the other hand, shdA gene from Salmonella Typhi (shdASTy) has been considered a pseudogene (i.e. a nonfunctional sequence of genomic DNA) due to the presence of deletions and mutations that gave rise to premature stop codons. In this work we show that, despite the deletions and mutations, shdASTy is fully functional. S. Typhi ΔshdA mutants presented an impaired adherence and invasion of HEp-2 pre-treated with TGF-β1, an inducer of fibronectin production. Moreover, shdA from S. Typhi and S. Typhimurium seem to be equivalent since shdASTm restored the adherence and invasion of S. Typhi ΔshdA mutant to wild type levels. In addition, anti-FLAG mAbs interfered with the adherence and invasion of the S. Typhi shdA-3xFLAG strain. Finally, shdASTy encodes a detectable protein when heterologously expressed in Escherichia coli DH5α. The data presented here show that shdASTy is not a pseudogene, but a different functional allele compared with shdASTm.