Evolution of Salmonella enterica virulence via point mutations in the fimbrial adhesin

It takes two to attach - endo-1,3-β-d-glucanase as a potential receptor of mannose-independent, FimH-dependent Salmonella Typhimurium binding to spinach leaves

Currently, fresh, unprocessed food has become a relevant element of the chain of transmission of enteropathogenic infections. To survive on a plant surface and further spread the infections, pathogens like Salmonella have to attach stably to the leaf surface. Adhesion, driven by various virulence factors, including the most abundant fim operon encoding type 1 fimbriae, is usually an initial step of infection, preventing physical removal of the pathogen. Adhesion properties of Salmonella's type 1 fimbriae and its FimH adhesin were investigated intensively in the past. However, there is a lack of knowledge regarding its role in interaction with plant cells. Understanding the mechanisms and structures involved in such interaction may facilitate efforts to decrease the risk of contamination and increase fresh food safety. Here, we applied Salmonella genome site-directed mutagenesis, adhesion assays, protein-protein interactions, and biophysics methods based on surface plasmon resonance to unravel the role of FimH adhesin in interaction with spinach leaves. We show that FimH is at least partially responsible for Salmonella binding to spinach leaves, and this interaction occurs in a mannose-independent manner. Importantly, we identified a potential FimH receptor as endo-1,3-β-d-Glucanase and found that this interaction is strong and specific, with a dissociation constant in the nanomolar range. This research advances our comprehension of Salmonella's interactions with plant surfaces, offering insights that can aid in minimizing contamination risks and improving the safety of fresh, unprocessed foods.

A Review of the Mechanisms of Bacterial Colonization of the Mammal Gut

A healthy animal intestine hosts a diverse population of bacteria in a symbiotic relationship. These bacteria utilize nutrients in the host's intestinal environment for growth and reproduction. In return, they assist the host in digesting and metabolizing nutrients, fortifying the intestinal barrier, defending against potential pathogens, and maintaining gut health. Bacterial colonization is a crucial aspect of this interaction between bacteria and the intestine and involves the attachment of bacteria to intestinal mucus or epithelial cells through nonspecific or specific interactions. This process primarily relies on adhesins. The binding of bacterial adhesins to host receptors is a prerequisite for the long-term colonization of bacteria and serves as the foundation for the pathogenicity of pathogenic bacteria. Intervening in the adhesion and colonization of bacteria in animal intestines may offer an effective approach to treating gastrointestinal diseases and preventing pathogenic infections. Therefore, this paper reviews the situation and mechanisms of bacterial colonization, the colonization characteristics of various bacteria, and the factors influencing bacterial colonization. The aim of this study was to serve as a reference for further research on bacteria-gut interactions and improving animal gut health.

Subversion of a family of antimicrobial proteins by Salmonella enterica

Salmonella enterica is a food-borne pathogen able to cause a wide spectrum of diseases ranging from mild gastroenteritis to systemic infections. During almost all stages of the infection process Salmonella is likely to be exposed to a wide variety of host-derived antimicrobial peptides (AMPs). AMPs are important components of the innate immune response which integrate within the bacterial membrane, thus forming pores which lead ultimately to bacterial killing. In contrast to other AMPs Bactericidal/Permeability-increasing Protein (BPI) displayed only weak bacteriostatic or bactericidal effects towards Salmonella enterica sv. Typhimurium (STM) cultures. Surprisingly, we found that sub-antimicrobial concentrations of BPI fold-containing (BPIF) superfamily members mediated adhesion of STM depending on pre-formed type 1 fimbriae. BPIF proteins directly bind to type 1 fimbriae through mannose-containing oligosaccharide modifications. Fimbriae decorated with BPIF proteins exhibit extended binding specificity, allowing for bacterial adhesion on a greater variety of abiotic and biotic surfaces likely promoting host colonization. Further, fimbriae significantly contributed to the resistance against BPI, probably through sequestration of the AMP before membrane interaction. In conclusion, functional subversion of innate immune proteins of the BPIF family through binding to fimbriae promotes Salmonella virulence by survival of host defense and promotion of host colonization.

A new Salmonella enterica serovar that was isolated from a wild sparrow presents a distinct genetic, metabolic and virulence profile

Salmonella enterica is a ubiquitous and clinically-important bacterial pathogen, able to infect and cause different diseases in a wide range of hosts. Here, we report the isolation and characterization of a new S. enterica serovar (13,23:i:-; S. Tirat-Zvi), belonging to the Havana supper-lineage that was isolated from a wild house sparrow (Passer domesticus) in Israel. Whole genome sequencing and complete assembly of its genome indicated a plasmid-free, 4.7 Mb genome that carries the Salmonella pathogenicity islands 1-6, 9, 19 and an integrative and conjugative element (ICE), encoding arsenic resistance genes. Phenotypically, S. Tirat-Zvi isolate TZ282 was motile, readily formed biofilm, more versatile in carbon source utilization than S. Typhimurium and highly tolerant to arsenic, but impaired in host cell invasion. In-vivo infection studies indicated that while S. Tirat-Zvi was able to infect and cause an acute inflammatory enterocolitis in young chicks, it was compromised in mice colonization and did not cause an inflammatory colitis in mice compared to S. Typhimurium. We suggest that these phenotypes reflect the distinctive ecological niche of this new serovar and its evolutionary adaptation to passerine birds, as a permissive host. Moreover, these results further illuminate the genetic, phenotypic and ecological diversity of S. enterica pathovars.

Salmonella adhesion is decreased by hypoxia due to adhesion and motility structure crosstalk

Initial stages of Salmonella Typhimurium infection involve a series of coordinated events aimed at reaching, attaching to, and invading host cells. Virulence factors such as flagella, fimbriae, and secretion systems play crucial roles in these events and are regulated in response to the host environment. The first point of contact between the pathogen and host is the intestinal epithelial layer, which normally serves as a barrier against invading pathogens, but can also be an entry site for pathogens. The integrity of this barrier can be modulated by the hypoxic environment of the intestines, created by the presence of trillions of microbes. Variable oxygen concentrations can strongly affect many functions of the gut, including secretion of cytokines and growth factors from the host site and affect the ability of Salmonella to persist, invade, and replicate. In this study, we investigated the first stages of Salmonella Typhimurium infection under hypoxic conditions in vitro and found that low oxygen levels significantly decreased bacterial adhesion. Using adhesion and motility assays, biofilm formation tests, as well as gene expression and cytokine secretion analysis, we identified a hypoxia-specific cross-talk between the expression of type 1 fimbriae and flagella, suggesting that altered flagellin expression levels affect the motility of bacteria and further impact their adhesion level, biofilm formation ability, and innate immune response. Overall, understanding how Salmonella interacts with its variable host environment provides insights into the virulence mechanisms of the bacterium and information regarding strategies for preventing or treating infections. Further research is required to fully understand the complex interplay between Salmonella and its host environment.

Cinnamaldehyde Resist Salmonella Typhimurium Adhesion by Inhibiting Type I Fimbriae

Salmonella Typhimurium (S. Typhimurium), a common foodborne pathogen, severely harms the public and food security. Type I fimbriae (T1F) of S. Typhimurium, plays a crucial role in the pathogenic processes; it mediates the adhesion of bacteria to the mannose receptor on the host cell, assists the bacteria to invade the host cell, and triggers an inflammatory response. Cinnamaldehyde is the main ingredient in cinnamon essential oil. In this study, cinnamaldehyde was demonstrated to inhibit the expression of T1F by hemagglutination inhibition test, transmission electron microscopy, and biofilms. The mechanism of cinnamaldehyde action was studied by proteomics technology, PCR and Western blotting. The results showed that cinnamaldehyde can inhibit T1F in S. typhimurium without the growth of bacteria, by regulating the level of expression and transcription of fimA, fimZ, fimY, fimH and fimW. Proteomics results showed that cinnamaldehyde downregulated the subunits and regulators of T1F. In addition, the invasion assays proved that cinnamaldehyde can indeed reduce the ability of S. typhimurium to adhere to cells. The results of animal experiments showed that the colonization in the intestinal tract and the expression levels of inflammatory cytokine were significantly decreased, and the intestinal mucosal immune factors MUC1 and MUC2 were increased under cinnamaldehyde treatment. Therefore, cinnamaldehyde may be a potential drug to target T1F to treat Salmonella infections.

Characterization of Host-Specific Genes from Pine- and Grass-Associated Species of the Fusarium fujikuroi Species Complex

The Fusarium fujikuroi species complex (FFSC) includes socioeconomically important pathogens that cause disease for numerous crops and synthesize a variety of secondary metabolites that can contaminate feedstocks and food. Here, we used comparative genomics to elucidate processes underlying the ability of pine-associated and grass-associated FFSC species to colonize tissues of their respective plant hosts. We characterized the identity, possible functions, evolutionary origins, and chromosomal positions of the host-range-associated genes encoded by the two groups of fungi. The 72 and 47 genes identified as unique to the respective genome groups were potentially involved in diverse processes, ranging from transcription, regulation, and substrate transport through to virulence/pathogenicity. Most genes arose early during the evolution of Fusarium/FFSC and were only subsequently retained in some lineages, while some had origins outside Fusarium. Although differences in the densities of these genes were especially noticeable on the conditionally dispensable chromosome of F. temperatum (representing the grass-associates) and F. circinatum (representing the pine-associates), the host-range-associated genes tended to be located towards the subtelomeric regions of chromosomes. Taken together, these results demonstrate that multiple mechanisms drive the emergence of genes in the grass- and pine-associated FFSC taxa examined. It also highlighted the diversity of the molecular processes potentially underlying niche-specificity in these and other Fusarium species.

Distinct Potentially Adaptive Accumulation of Truncation Mutations in Salmonella enterica serovar Typhi and Salmonella enterica serovar Paratyphi A

Gene inactivation through the accumulation of truncation (or premature stop codon) mutations is a common mode of evolution in bacteria. It is frequently believed to result from reductive evolutionary processes allowing purging of superfluous traits. However, several works have demonstrated that, similar to the occurrences of inactivating nonsynonymous (i.e., amino acid replacement) mutations under positive selection pressures, truncation mutations can also be adaptive where specific traits deleterious in particular environmental conditions need to be inactivated for survival. Here, we performed a comparative analysis of genome-wide accumulation of truncation mutations in Salmonella enterica serovar Typhi and Salmonella enterica serovar Paratyphi A. Considering the known convergent evolutionary trajectories in these two serovars, we expected a strong overlap of truncated genes in S. Typhi and S. Paratyphi A, emerging through either reductive or adaptive dynamics. However, we detected a distinct set of core truncated genes encoding different overrepresented functional clusters in each serovar. In 54% and 28% truncated genes in S. Typhi and S. Paratyphi A, respectively, inactivating mutations were acquired by only different subsets of isolates, instead of all isolates analyzed for that serovar. Importantly, 62% truncated genes (P < 0.001) in S. Typhi and S. Paratyphi A were also targeted by convergent amino acid mutations in different serovars, suggesting those genes to be under selection pressures. Our findings indicate significant presence of potentially adaptive truncation mutations in conjunction with the ones emerging due to reductive evolution. Further experimental and large-scale bioinformatic studies are necessary to better explore the impact of such adaptive footprints of truncation mutations in the evolution of bacterial virulence. IMPORTANCE Detecting the adaptive mutations leading to gene inactivation or loss of function is crucial for understanding their contribution in the evolution of bacterial virulence and antibiotic resistance. Such inactivating mutations, apart from being of nonsynonymous (i.e., amino acid replacement) nature, can also be truncation mutations, abruptly trimming the length of encoded proteins. Importantly, the notion of reductive evolutionary dynamics is primarily accepted toward the accumulation of truncation mutations. However, our case study on S. Typhi and S. Paratyphi A, two human-restricted systemically invasive pathogens exerting similar clinical manifestations, indicated that a significant proportion of truncation mutations emerge from positive selection pressures. The candidate genes from our study will enable directed functional assays for deciphering the adaptive role of truncation mutations in S. Typhi and S. Paratyphi A pathogenesis. Also, our genome-level analytical approach will pave the way to understand the contribution of truncation mutations in the adaptive evolution of other bacterial pathogens.

Genome placement of alpha-haemolysin cluster is associated with alpha-haemolysin sequence variation, adhesin and iron acquisition factor profile of Escherichia coli

Since the discovery of haemolysis, many studies focused on a deeper understanding of this phenotype in Escherichia coli and its association with other virulence genes, diseases and pathogenic attributes/functions in the host. Our virulence-associated factor profiling and genome-wide association analysis of genomes of haemolytic and nonhaemolytic E. coli unveiled high prevalence of adhesins, iron acquisition genes and toxins in haemolytic bacteria. In the case of fimbriae with high prevalence, we analysed sequence variation of FimH, EcpD and CsgA, and showed that different adhesin variants were present in the analysed groups, indicating altered adhesive capabilities of haemolytic and nonhaemolytic E. coli. Analysis of over 1000 haemolytic E. coli genomes revealed that they are pathotypically, genetically and antigenically diverse, but their adhesin and iron acquisition repertoire is associated with genome placement of hlyCABD cluster. Haemolytic E. coli with chromosome-encoded alpha-haemolysin had high frequency of P, S, Auf fimbriae and multiple iron acquisition systems such as aerobactin, yersiniabactin, salmochelin, Fec, Sit, Bfd and hemin uptake systems. Haemolytic E. coli with plasmid-encoded alpha-haemolysin had similar adhesin profile to nonpathogenic E. coli, with high prevalence of Stg, Yra, Ygi, Ycb, Ybg, Ycf, Sfm, F9 fimbriae, Paa, Lda, intimin and type 3 secretion system encoding genes. Analysis of HlyCABD sequence variation revealed presence of variants associated with genome placement and pathotype.

Zoonotic potential and prevalence of Salmonella serovars isolated from pets

Salmonellosis is a global health problem, affecting approximately 1.3 billion people annually. Most of these cases are related to food contamination. However, although the majority of Salmonella serovars are pathogenic to humans, animals can be asymptomatic carriers of these bacteria. Nowadays, a wide range of animals is present in human households as pets, including reptiles, amphibians, dogs, cats, ornamental birds, and rodents. Pets contaminate the environment of their owners by shedding the bacteria intermittently in their feaces. In consequence, theyare thought to cause salmonellosis through pet-to-human transmission. Each Salmonella serovar has a different zoonotic potential, which is strongly regulated by stress factors such as transportation, crowding, food deprivation, or temperature. In this review, we summarize the latest reports concerning Salmonella-prevalence and distribution in pets as well as the risk factors and means of prevention of human salmonellosis caused by contact with their pets. Our literature analysis (based on PubMed and Google Scholar databases) is limited to the distribution of Salmonella serovars found in commonly owned pet species. We collected the recent results of studies concerning testing for Salmonella spp. in biological samples, indicating their prevalence in pets, with regard to clinical cases of human salmonellosis.

Two homologous Salmonella serogroup C1-specific genes are required for flagellar motility and cell invasion

Background

Salmonella is a major bacterial pathogen associated with a large number of outbreaks of foodborne diseases. Many highly virulent serovars that cause human illness belong to Salmonella serogroup C1, and Salmonella ser. Choleraesuis is a prominent cause of invasive infections in Asia. Comparative genomic analysis in our previous study showed that two homologous genes, SC0368 and SC0595 in Salmonella ser. Choleraesuis were unique to serogroup C1. In this study, two single-deletion mutants (Δ0368 and Δ0595) and one double-deletion mutant (Δ0368Δ0595) were constructed based on the genome. All these mutants and the wild-type strain were subjected to RNA-Seq analysis to reveal functional relationships of the two serogroup C1-specific genes.

Results

Data from RNA-Seq indicated that deletion of SC0368 resulted in defects in motility through repression of σ²⁸ in flagellar regulation Class 3. Consistent with RNA-Seq data, results from transmission electron microcopy (TEM) showed that flagella were not present in △0368 and △0368△0595 mutants resulting in both swimming and swarming defects. Interestingly, the growth rates of two non-motile mutants △0368 and △0368△0595 were significantly greater than the wild-type, which may be associated with up-regulation of genes encoding cytochromes, enhancing bacterial proliferation. Moreover, the △0595 mutant was significantly more invasive in Caco-2 cells as shown by bacterial enumeration assays, and the expression of lipopolysaccharide (LPS) core synthesis-related genes (rfaB, rfaI, rfaQ, rfaY, rfaK, rfaZ) was down-regulated only in the △0368△0595 mutant. In addition, this study also speculated that these two genes might be contributing to serotype conversion for Salmonella C1 serogroup based on their apparent roles in biosynthesis of LPS and the flagella.

Conclusion

A combination of biological and transcriptomic (RNA-Seq) analyses has shown that the SC0368 and SC0595 genes are involved in biosynthesis of flagella and complete LPS, as well as in bacterial growth and virulence. Such information will aid to revealing the role of these specific genes in bacterial physiology and evolution within the serogroup C1.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07759-z.

Recent Advances in Our Understanding of the Diversity and Roles of Chaperone-Usher Fimbriae in Facilitating Salmonella Host and Tissue Tropism

Salmonella enterica is one of the most diverse and successful pathogens, representing a species with >2,600 serovars with a variety of adaptations that enable colonization and infection of a wide range of hosts. Fimbriae, thin hair-like projections that cover the surface of Salmonella, are thought to be the primary organelles that mediate Salmonella's interaction with, and adherence to, the host intestinal epithelium, representing an important step in the infection process. The recent expansion in genome sequencing efforts has enabled the discovery of novel fimbriae, thereby providing new perspectives on fimbrial diversity and distribution among a broad number of serovars. In this review, we provide an updated overview of the evolutionary events that shaped the Salmonella chaperone-usher fimbriome in light of recent phylogenetic studies describing the population structure of Salmonella enterica. Furthermore, we discuss the complexities of the chaperone-usher fimbriae-mediated host-pathogen interactions and the apparent redundant roles of chaperone-usher fimbriae in host and tissue tropism.

Whole-Genome Comparative and Pathogenicity Analysis of Salmonella enterica subsp. enterica Serovar Rissen

Salmonella are a type of bacteria known to cause food-borne illness. Their host range varies widely, and their susceptibility to the host determines its pathogenicity. Salmonella enterica serovar Rissen (S. Rissen) is a widely distributed serotype; however, its virulence and pathogenicity are poorly understood. In this study, the pathogenicity and antibiotic resistance of a representative S. Rissen isolate were investigated. The cell model results showed that S. Rissen preferred to replicate in human macrophage cells U937 compared to murine macrophage cells RAW264.7, suggesting that it has a level of host adaptability. Genome sequencing and comparison analysis revealed that the distribution and nonsynonymous single nucleotide polymorphisms of virulence factors in S. Rissen were similar to those in S. Typhi rather than to those in S. Typhimurium. Taken together, our results suggest that although S. Rissen is a common serotype distributed in swine herds, pork and chicken products, it has strong ability to infect humans.

Pre-Growth Culture Conditions Affect Type 1 Fimbriae-Dependent Adhesion of Salmonella

Among various fimbrial structures used by Salmonella enterica to colonize host tissues, type 1 fimbriae (T1F) are among the most extensively studied. Although some experiments have shown the importance of T1F in the initial stages of Salmonella infection, their exact role in the infection process is not fully known. We suggested that different outcomes of T1F investigations were due to the use of different pre-infection growth conditions for the induction of the T1F. We utilized qPCR, flow cytometry, and a wide range of adhesion assays to investigate Salmonella Choleraesuis and Salmonella Typhimurium adhesion in the context of T1F expression. We demonstrated that T1F expression was highly dependent on the pre-infection growth conditions. These growth conditions yielded T1F+ and T1F- populations of Salmonella and, therefore, could be a factor influencing Salmonella-host cell interactions. We supported this conclusion by showing that increased levels of T1F expression directly correlated with higher levels of Salmonella adherence to the intestinal epithelial IPEC-J2 cell line.

Construction of a Lectin-Glycan Interaction Network from Enterohemorrhagic Escherichia coli Strains by Multi-omics Analysis

Enterohemorrhagic Escherichia coli (EHEC) causes hemorrhagic colitis and hemolytic uremic syndrome. EHEC infection begins with bacterial adherence to the host intestine via lectin-like adhesins that bind to the intestinal wall. However, EHEC-related lectin–glycan interactions (LGIs) remain unknown. Here, we conducted a genome-wide investigation of putative adhesins to construct an LGI network. We performed microarray-based transcriptomic and proteomic analyses with E. coli EDL933. Using PSORTb-based analysis, potential outer-membrane-embedded adhesins were predicted from the annotated genes of 318 strains. Predicted proteins were classified using TMHMM v2.0, SignalP v5.0, and LipoP v1.0. Functional and protein–protein interaction analyses were performed using InterProScan and String databases, respectively. Structural information of lectin candidate proteins was predicted using Iterative Threading ASSEmbly Refinement (I-TASSER) and Spatial Epitope Prediction of Protein Antigens (SEPPA) tools based on 3D structure and B-cell epitopes. Pathway analysis returned 42,227 Gene Ontology terms; we then selected 2585 lectin candidate proteins by multi-omics analysis and performed homology modeling and B-cell epitope analysis. We predicted a total of 24,400 outer-membrane-embedded proteins from the genome of 318 strains and integrated multi-omics information into the genomic information of the proteins. Our integrated multi-omics data will provide a useful resource for the construction of LGI networks of E. coli.

The speciation and hybridization history of the genus Salmonella

Bacteria and archaea make up most of natural diversity, but the mechanisms that underlie the origin and maintenance of prokaryotic species are poorly understood. We investigated the speciation history of the genus Salmonella, an ecologically diverse bacterial lineage, within which S. enterica subsp. enterica is responsible for important human food-borne infections. We performed a survey of diversity across a large reference collection using multilocus sequence typing, followed by genome sequencing of distinct lineages. We identified 11 distinct phylogroups, 3 of which were previously undescribed. Strains assigned to S. enterica subsp. salamae are polyphyletic, with two distinct lineages that we designate Salamae A and B. Strains of the subspecies houtenae are subdivided into two groups, Houtenae A and B, and are both related to Selander’s group VII. A phylogroup we designate VIII was previously unknown. A simple binary fission model of speciation cannot explain observed patterns of sequence diversity. In the recent past, there have been large-scale hybridization events involving an unsampled ancestral lineage and three distantly related lineages of the genus that have given rise to Houtenae A, Houtenae B and VII. We found no evidence for ongoing hybridization in the other eight lineages, but detected subtler signals of ancient recombination events. We are unable to fully resolve the speciation history of the genus, which might have involved additional speciation-by-hybridization or multi-way speciation events. Our results imply that traditional models of speciation by binary fission and divergence are not sufficient to account for Salmonella evolution.

Everything You Always Wanted to Know About Salmonella Type 1 Fimbriae, but Were Afraid to Ask

Initial attachment to host intestinal mucosa after oral infection is one of the most important stages during bacterial pathogenesis. Adhesive structures, widely present on the bacterial surface, are mainly responsible for the first contact with host cells and of host-pathogen interactions. Among dozens of different bacterial adhesins, type 1 fimbriae (T1F) are one of the most common adhesive organelles in the members of the Enterobacteriaceae family, including Salmonella spp., and are important virulence factors. Those long, thin structures, composed mainly of FimA proteins, are responsible for recognizing and binding high-mannose oligosaccharides, which are carried by various glycoproteins and expressed at the host cell surface, via FimH adhesin, which is presented at the top of T1F. In this review, we discuss investigations into the functions of T1F, from the earliest work published in 1958 to operon organization, organelle structure, T1F biogenesis, and the various functions of T1F in Salmonella-host interactions. We give special attention to regulation of T1F expression and their role in binding of Salmonella to cells, cell lines, organ explants, and other surfaces with emphasis on biofilm formation and discuss T1F role as virulence factors based on work using animal models. We also discuss the importance of allelic variation in fimH to Salmonella pathogenesis, as well as role of FimH in Salmonella host specificity.

A review of Salmonella enterica with particular focus on the pathogenicity and virulence factors, host specificity and antimicrobial resistance including multidrug resistance

Salmonella genus represents the most common foodborne pathogens frequently isolated from food-producing animals that is responsible for zoonotic infections in humans and animal species including birds. Thus, Salmonella infections represent a major concern to public health, animals, and food industry worldwide. Salmonella enterica represents the most pathogenic specie and includes > 2600 serovars characterized thus far. Salmonella can be transmitted to humans along the farm-to-fork continuum, commonly through contaminated foods of animal origin, namely poultry and poultry-related products (eggs), pork, fish etc. Some Salmonella serovars are restricted to one specific host commonly referred to as "host-restricted" whereas others have broad host spectrum known as "host-adapted" serovars. For Salmonella to colonize its hosts through invading, attaching, and bypassing the host's intestinal defense mechanisms such as the gastric acid, many virulence markers and determinants have been demonstrated to play crucial role in its pathogenesis; and these factors included flagella, capsule, plasmids, adhesion systems, and type 3 secretion systems encoded on the Salmonella pathogenicity island (SPI)-1 and SPI-2, and other SPIs. The epidemiologically important non-typhoidal Salmonella (NTS) serovars linked with a high burden of foodborne Salmonella outbreaks in humans worldwide included Typhimurium, Enteritidis, Heidelberg, and Newport. The increased number of NTS cases reported through surveillance in recent years from the United States, Europe and low- and middle-income countries of the world suggested that the control programs targeted at reducing the contamination of food animals along the food chain have largely not been successful. Furthermore, the emergence of several clones of Salmonella resistant to multiple antimicrobials worldwide underscores a significant food safety hazard. In this review, we discussed on the historical background, nomenclature and taxonomy, morphological features, physical and biochemical characteristics of NTS with a particular focus on the pathogenicity and virulence factors, host specificity, transmission, and antimicrobial resistance including multidrug resistance and its surveillance.

Identification of FimH derivatives as adjuvant vaccinated with PAc that enhance protection against Streptcoccus mutans colonization

FimH is the adhesin of type I fimbriae expressed on Escherichia coli that can mediate specific adherence to host cells. High binding mutations in FimH are related to the adaptive evolution of bacteria. However, additional roles that these allelic variations may play remain elusive. To investigate novel biological functions of the mutations in FimH, we introduced four different variants of FimH by incorporating single amino acid substitutions at specific sites, namely A25P, G73R, A106, and T158P, respectively. In this study, adjuvant potential of FimH variants was evaluated by investigating their ability to trigger innate immune response to DC2.4 and adaptive immunity to improve immunological characteristics. The data revealed that purified A106 and T158P up-regulated the expression of co-stimulatory molecules critically involved in DC2.4 activation by interaction with TLR4, whereas A25P and G73R did not induce the phenotypic maturation of DC2.4. Besides, the culture of DC2.4 with A106 and T158P enhanced the release of cytokines and protein phagocytosis. When formulated with PAc, T158P elicited more robust PAc-specific IgG and IgA antibody responses compared to PBS, PAc and PAc+K12 groups and inhibited bacteria colonization. Collectively, the results confirmed that the T158P mutation located around the inter-domain interface of the protein induced a specific enhancement effect on adjuvant characteristics.

Mutational convergence acts as a major player in adaptive parallel evolution of Shigella spp

Shigella spp., emerging from multiple origins of Escherichia coli, poses a significant health threat as a causative agent of bacillary dysentery. While multiple serotypes of four different species have evolved via independent lineages, Shigella spp. are designated as a single pathotype, primarily because of their common mode of pathogenesis. Convergent horizontal transfer events have so far been attributed to the commonalities in the evolution of virulence across diverse lineages. However, the role of mutational convergence in such parallel evolution is not yet well understood. Here we have carried out a genome-wide analysis of Shigella strains from all four species to detect the core genes (i.e. the ones present in all analyzed strains) acquiring convergent mutations of evolutionarily recent origin. Simulation studies show non-neutral accumulation of these convergent mutations across species, suggesting their adaptive role in the evolution of Shigella virulence. S. dysenteriae strain 197, representing highly virulent type 1 (Sd1) clone, carries excessively high number of core genes with recent convergent mutations compared to other analyzed strains. We propose that this high frequency of adaptive convergence in S. dysenteriae strain 197 could be linked to recent re-emergence of the Sd1 clone and its increased resistance to antimicrobials.

Recombination-independent rapid convergent evolution of the gastric pathogen Helicobacter pylori

BACKGROUND

Helicobacter pylori is a human stomach pathogen, naturally-competent for DNA uptake, and prone to homologous recombination. Extensive homoplasy (i.e., phylogenetically-unlinked identical variations) observed in H. pylori genes is considered a hallmark of such recombination. However, H. pylori also exhibits a high mutation rate. The relative adaptive role of homologous recombination and mutation in species diversity is a highly-debated issue in biology. Recombination results in homoplasy. While convergent mutation can also account for homoplasy, its contribution is thought to be minor. We demonstrate here that, contrary to dogma, convergent mutation is a key contributor to Helicobacter pylori homoplasy, potentially driven by adaptive evolution of proteins.

RESULTS

Our present genome-wide analysis shows that homoplastic nonsynonymous (amino acid replacement) changes are not typically accompanied by homoplastic synonymous (silent) variations. Moreover, the majority of the codon positions with homoplastic nonsynonymous changes also contain different (i.e. non-homoplastic) nonsynonymous changes arising from mutation only. This indicates that, to a considerable extent, nonsynonymous homoplasy is due to convergent mutations. High mutation rate or limited availability of evolvable sites cannot explain this excessive convergence, as suggested by our simulation studies. Rather, the genes with convergent mutations are overrepresented in distinct functional categories, suggesting possible selective responses to conditions such as distinct micro-niches in single hosts, and to differences in host genotype, physiology, habitat and diet.

CONCLUSIONS

We propose that mutational convergence is a key player in H. pylori's adaptation and extraordinary persistence in human hosts. High frequency of mutational convergence could be due to saturation of evolvable sites capable of responding to selection pressures, while the number of mutable residues is far from saturation. We anticipate a similar scenario of mutational vs. recombinational genome dynamics or plasticity for other naturally competent microbes where strong positive selection could favor frequent convergent mutations in adaptive protein evolution.

Salmonella infection - prevention and treatment by antibiotics and probiotic yeasts: a review

Global Salmonella infection, especially in developing countries, is a health and economic burden. The use of antibiotic drugs in treating the infection is proving less effective due to the alarming rise of antibiotic-resistant strains of Salmonella, the effects of antibiotics on normal gut microflora and antibiotic-associated diarrhoea, all of which bring a growing need for alternative treatments, including the use of probiotic micro-organisms. However, there are issues with probiotics, including their potential to be opportunistic pathogens and antibiotic-resistant carriers, and their antibiotic susceptibility if used as complementary therapy. Clinical trials, animal trials and in vitro investigations into the prophylactic and therapeutic efficacies of probiotics have demonstrated antagonistic properties against Salmonella and other enteropathogenic bacteria. Nonetheless, there is a need for further studies into the potential mechanisms, efficacy and mode of delivery of yeast probiotics in Salmonella infections. This review discusses Salmonella infections and treatment using antibiotics and probiotics.

Adhesion of Salmonella to Pancreatic Secretory Granule Membrane Major Glycoprotein GP2 of Human and Porcine Origin Depends on FimH Sequence Variation

Bacterial host tropism is a primary determinant of the range of host organisms they can infect. Salmonella serotypes are differentiated into host-restricted and host-adapted specialists, and host-unrestricted generalists. In order to elucidate the underlying molecular mechanisms of host specificity in Salmonella infection, we investigated the role of the intestinal host cell receptor zymogen granule membrane glycoprotein 2 (GP2), which is recognized by FimH adhesin of type 1 fimbriae found in Enterobacteriaceae. We compared four human and two porcine GP2 isoforms. Isoforms were expressed in Sf9 cells as well as in one human (HEp-2) and one porcine (IPEC-J2) cell line. FimH genes of 128 Salmonella isolates were sequenced and the 10 identified FimH variants were compared regarding adhesion (static adhesion assay) and infection (cell line assay) using an isogenic model. We expressed and characterized two functional porcine GP2 isoforms differing in their amino acid sequence to human isoforms by approximately 25%. By comparing all isoforms in the static adhesion assay, FimH variants were assigned to high, low or no-binding phenotypes. This FimH variant-dependent binding was neither specific for one GP2 isoform nor for GP2 in general. However, cell line infection assays revealed fundamental differences: using HEp-2 cells, infection was also FimH variant-specific but mainly independent of human GP2. In contrast, this FimH variant dependency was not obvious using IPEC-J2 cells. Here, we propose an alternative GP2 adhesion/infection mechanism whereby porcine GP2 is not a receptor that determined host-specificity of Salmonella. Salmonella specialists as well as generalists demonstrated similar binding to GP2. Future studies should focus on spatial distribution of GP2 isoforms in the human and porcine intestine, especially comparing health and disease.

Constraints on lateral gene transfer in promoting fimbrial usher protein diversity and function

Fimbriae are long, adhesive structures widespread throughout members of the family Enterobacteriaceae. They are multimeric extrusions, which are moved out of the bacterial cell through an integral outer membrane protein called usher. The complex folding mechanics of the usher protein were recently revealed to be catalysed by the membrane-embedded translocation and assembly module (TAM). Here, we examine the diversity of usher proteins across a wide range of extraintestinal (ExPEC) and enteropathogenic (EPEC) Escherichia coli, and further focus on a so far undescribed chaperone–usher system, with this usher referred to as UshC. The fimbrial system containing UshC is distributed across a discrete set of EPEC types, including model strains like E2348/67, as well as ExPEC ST131, currently the most prominent multi-drug-resistant uropathogenic E. coli strain worldwide. Deletion of the TAM from a naive strain of E. coli results in a drastic time delay in folding of UshC, which can be observed for a protein from EPEC as well as for two introduced proteins from related organisms, Yersinia and Enterobacter. We suggest that this models why the TAM machinery is essential for efficient folding of proteins acquired via lateral gene transfer.

Evolution of Salmonella within Hosts

Within-host evolution has resulted in thousands of variants of Salmonella that exhibit remarkable diversity in host range and disease outcome, from broad host range to exquisite host restriction, causing gastroenteritis to disseminated disease such as typhoid fever. Within-host evolution is a continuing process driven by genomic variation that occurs during each infection, potentiating adaptation to a new niche resulting from changes in animal husbandry, the use of antimicrobials, and emergence of immune compromised populations. We discuss key advances in our understanding of the evolution of Salmonella within the host, inferred from (i) the process of host adaptation of Salmonella pathovars in the past, and (ii) direct observation of the generation of variation and selection of beneficial traits during single infections.

Salmonella is a bacterial pathogen with remarkable diversity in its host range and pathogenicity due to past within-host evolution in vertebrate species that modified ancestral mechanisms of pathogenesis.

Variation arising during infection includes point mutations, new genes acquired through horizontal gene transfer (HGT), deletions, and genomic rearrangements.

Beneficial mutations increase in frequency within the host and, if they retain the ability to be transmitted to subsequent hosts, may become fixed in the population.

Whole-genome sequencing of sequential isolates from clinical infections reveals within-host HGT and point mutations that impact therapy and clinical management.

HGT is the primary mechanism for evolution in prokaryotes and is synergised by complex networks of transfer involving the microbiome.

Within-host evolution of Salmonella, resulting in new pathovars, can proceed in the absence of HGT.

Functional Analysis of the Chaperone-Usher Fimbrial Gene Clusters of Salmonella enterica serovar Typhi

The human-specific pathogen Salmonella enterica serovar Typhi causes typhoid, a major public health issue in developing countries. Several aspects of its pathogenesis are still poorly understood. S. Typhi possesses 14 fimbrial gene clusters including 12 chaperone-usher fimbriae (stg, sth, bcf, fim, saf, sef, sta, stb, stc, std, ste, and tcf). These fimbriae are weakly expressed in laboratory conditions and only a few are actually characterized. In this study, expression of all S. Typhi chaperone-usher fimbriae and their potential roles in pathogenesis such as interaction with host cells, motility, or biofilm formation were assessed. All S. Typhi fimbriae were better expressed in minimal broth. Each system was overexpressed and only the fimbrial gene clusters without pseudogenes demonstrated a putative major subunits of about 17 kDa on SDS-PAGE. Six of these (Fim, Saf, Sta, Stb, Std, and Tcf) also show extracellular structure by electron microscopy. The impact of fimbrial deletion in a wild-type strain or addition of each individual fimbrial system to an S. Typhi afimbrial strain were tested for interactions with host cells, biofilm formation and motility. Several fimbriae modified bacterial interactions with human cells (THP-1 and INT-407) and biofilm formation. However, only Fim fimbriae had a deleterious effect on motility when overexpressed. Overall, chaperone-usher fimbriae seem to be an important part of the balance between the different steps (motility, adhesion, host invasion and persistence) of S. Typhi pathogenesis.

Role of different receptors and actin filaments on Salmonella Typhimurium invasion in chicken macrophages

Bacterial attachment to host cell is the first event for pathogen entry. The attachment is mediated through membrane expressed adhesins present on the organism and receptors on the cell surface of host. The objective of this study was to investigate the significance of Fc receptors (FcRs), actin filament polymerization, mannose receptors (MRs), carbohydrate moieties like N-linked glycans and sialic acid on chicken macrophages for invasion of S. Typhimurium. Opsonisation of S. Typhimurium resulted in three folds more invasion in chicken monocyte derived macrophages. Cytochalasin D, an inhibitor of actin filament polymerization prevented uptake of S. Typhimurium. Pre-incubation of macrophages with cytochalasin D, showed severe decrease (28 folds) in S. Typhimurium invasion. Next we attempted to analyse the role of carbohydrate receptors of macrophages in S. Typhimurium invasion. Treatment of macrophages with methyl α-d-mannopyranoside, PNGase F and neuraminidase, showed 2.5, 5 and 2.5 folds decrease in invasion respectively. Our data suggest that deglycosylation of N-linked glycans including sialic acid by PNGase F is more effective in inhibition of S. Typhimurium invasion than neuraminidase which removes only sialic acid. These findings suggested FcRs, actin filament polymerization, MRs, N-linked glycans and sialic acid may act as gateway for entry of S. Typhimurium.

Conditional Function of Autoaggregative Protein Cah and Common cah Mutations in Shiga Toxin-Producing Escherichia coli

Cah is a calcium-binding autotransporter protein involved in autoaggregation and biofilm formation. Although cah is widespread in Shiga toxin-producing Escherichia coli (STEC), we detected mutations in cah at a frequency of 31.3% in this pathogen. In STEC O157:H7 supershedder strain SS17, a large deletion results in a smaller coding sequence, encoding a protein lacking the C-terminal 71 amino acids compared with Cah in STEC O157:H7 strain EDL933. We examined the function of Cah in biofilm formation and host colonization to better understand the selective pressures for cah mutations. EDL933-Cah played a conditional role in biofilm formation in vitro: it enhanced E. coli DH5α biofilm formation on glass surfaces under agitated culture conditions that prevented autoaggregation but inhibited biofilm formation under hydrostatic conditions that facilitated autoaggregation. This function appeared to be strain dependent since Cah-mediated biofilm formation was diminished when an EDL933 cah gene was expressed in SS17. Deletion of cah in EDL933 enhanced bacterial attachment to spinach leaves and altered the adherence pattern of EDL933 to bovine recto-anal junction squamous epithelial (RSE) cells. In contrast, in trans expression of EDL933 cah in SS17 increased its attachment to leaf surfaces, and in DH5α, it enhanced its adherence to RSE cells. Hence, the ecological function of Cah appears to be modulated by environmental conditions and other bacterial strain-specific properties. Considering the prevalence of cah in STEC and its role in attachment and biofilm formation, cah mutations might be selected in ecological niches in which inactivation of Cah would result in an increased fitness in STEC during colonization of plants or animal hosts.IMPORTANCE Shiga toxin-producing Escherichia coli (STEC) harbors genes encoding diverse adhesins, and many of these are known to play an important role in bacterial attachment and host colonization. We demonstrated here that the autotransporter protein Cah confers on E. coli DH5α cells a strong autoaggregative phenotype that is inversely correlated with its ability to form biofilms and plays a strain-specific role in plant and animal colonization by STEC. Although cah is widespread in the STEC population, we detected a mutation rate of 31.3% in cah, which is similar to that reported for rpoS and fimH The formation of cell aggregates due to increased bacterium-to-bacterium interactions may be disadvantageous to bacterial populations under conditions that favor a planktonic state in STEC. Therefore, a loss-of-function mutation in cah is likely a selective trait in STEC when autoaggregative properties become detrimental to bacterial cells and may contribute to the adaptability of STEC to fluctuating environments.

The Possible Influence of Non-synonymous Point Mutations within the FimA Adhesin of Non-typhoidal Salmonella (NTS) Isolates in the Process of Host Adaptation

Non-typhoidal Salmonella (NTS) remains a global pathogen that affects a wide range of animal species. We analyzed a large number of NTS isolates of different host origins, including Salmonella Heidelberg (n = 80, avian), S. Dublin (50, bovine), S. Typhimurium var 5- (n = 40, porcine), S. 4,5,12,:i:- (n = 40, porcine), S. Cerro (n = 16, bovine), and S. Montevideo (n = 14, bovine), using virulence profiling of the bcfC, mgtC, ssaC, invE, pefA, stn, sopB, and siiE virulence-associated genes, a biofilm production assay, pulsed field gel electrophoresis, and the full-length sequencing of the fimA (adhesin) and iroN (receptor) genes. We determined a key amino acid substitution, A169 (i.e., threonine changed to alanine at position 169), in the FimA protein that changed ligand affinity of FimA toward N-acetyl-D-glucosamine. This finding clearly indicates the important role of non-synonymous single nucleotide polymorphism (nsSNPs) in adhesin functionality that may impact the host tropism of NTS. This nsSNP was found in S. Heidelberg and S. Cerro isolates. Although this was not the case for the IroN receptor, the phylogeny of this receptor and different host origins of NTS isolates were positively correlated, suggesting existence of specific host immune selective pressures on this unique receptor in S. enterica. We found that pefA, a gene encoding major fimbrial subunit, was the most-segregative virulence factor. It was associated with S. Heidelberg, S. Typhimurium var 5- and S. 4,5,12,:i:- but not with the rest of NTS strains. Further, we observed a significantly higher frequency of non-biofilm producers among NTS strains that do not carry pefA (42.5%) compared to S. Heidelberg (2.5%) and S. Typhimurium var 5- (7.5%) and S. 4,5,12,:i:- (0%). This study provides new insights into the host adaptation of avian and mammalian NTS isolates that are based on the bacterial antigens FimA and IroN as well as the interrelationships between host adaptation, overall genetic relatedness, and virulence potential in these NTS isolates.

The Novel Type 1 Fimbriae FimH Receptor Calreticulin Plays a Role in Salmonella Host Specificity

It was suggested that minor differences in the structure of FimH are most likely associated with differences in its adhesion specificities and may determine the tropism of various Salmonella serovars to different species and tissues. We have recently shown that FimH adhesins from host-adapted serovars, e.g., Salmonella Choleraesuis (SCh), bind to other glycoprotein receptors compared to FimH from host-unrestricted Salmonella Enteritidis (SE). Here we identify porcine calreticulin expressed by swine intestinal cells as a host-specific receptor for SCh FimH adhesin, suggesting that such an interaction may contribute to SCh host specificity. Calreticulin was identified by 2D electrophoresis and mass spectrometry as a glycoprotein that was bound specifically by recombinant SCh FimH protein, but not by FimH from SE. The functionality of calreticulin as a specific receptor of SCh FimH adhesin was further confirmed by adhesion and invasion of mutated strains of SCh carrying different variants of FimH proteins to IPEC-J2 cells with overexpression and silenced expression of calreticulin. It was found that SCh carrying the active variant of FimH adhered and invaded IPEC-J2 cells with calreticulin overexpression at significantly higher numbers than those of SCh expressing the non-active variant or SE variant of FimH. Moreover, binding of SCh carrying the active variant of FimH to IPEC-J2 with silenced calreticulin expression was significantly weaker. Furthermore, we observed that SCh infection induces translocation of calreticulin to cell membrane. All of the aforementioned results lead to the general conclusion that Salmonella host specificity requires not only special mechanisms and proteins expressed by the pathogen but also specifically recognized receptors expressed by a specific host.

Mutation-Driven Divergence and Convergence Indicate Adaptive Evolution of the Intracellular Human-Restricted Pathogen, Bartonella bacilliformis

Among all species of Bartonella, human-restricted Bartonella bacilliformis is the most virulent but harbors one of the most reduced genomes. Carrión’s disease, the infection caused by B. bacilliformis, has been afflicting poor rural populations for centuries in the high-altitude valleys of the South American Andes, where the pathogen’s distribution is probably restricted by its sand fly vector’s range. Importantly, Carrión’s disease satisfies the criteria set by the World Health Organization for a disease amenable to elimination. However, to date, there are no genome-level studies to identify potential footprints of B. bacilliformis (patho)adaptation. Our comparative genomic approach demonstrates that the evolution of this intracellular pathogen is shaped predominantly via mutation. Analysis of strains having publicly-available genomes shows high mutational divergence of core genes leading to multiple sub-species. We infer that the sub-speciation event might have happened recently where a possible adaptive divergence was accelerated by intermediate emergence of a mutator phenotype. Also, within a sub-species the pathogen shows inter-clonal adaptive evolution evidenced by non-neutral accumulation of convergent amino acid mutations. A total of 67 non-recombinant core genes (over-representing functional categories like DNA repair, glucose metabolic process, ATP-binding and ligase) were identified as candidates evolving via adaptive mutational convergence. Such convergence, both at the level of genes and their encoded functions, indicates evolution of B. bacilliformis clones along common adaptive routes, while there was little diversity within a single clone.

How host-restriction, intracellularity and genome reduction interplay to exert or maintain virulence is poorly characterized. The fact that B. bacilliformis is the most pathogenic Bartonella and has a highly reduced genome makes it an attractive model to gain insights into (patho)adaptive evolution of intracellular pathogens. Also, B. bacilliformis is known to lack many virulence genes present in other Bartonella, indicating unique strategies of (patho)adaptation. Our study reveals a prevalent nature of mutational force in B. bacilliformis evolution with two distinct outcomes: (a) mutational divergence leading to sub-speciation, possibly recently, via accelerated accumulation and fixation of favorable mutations mediated by a mutator phenotype; and (b) mutational convergence between clones of a sub-species exhibiting shared functional trajectories of adaptive evolution. Our findings highlight positions accumulating adaptive mutations in candidate genes, offering future functional studies to elucidate B. bacilliformis virulence evolution, and of broad application to intracellular pathogens with a reduced gene repertoire.

The Non-Fimbriate Phenotype Is Predominant among Salmonella enterica Serovar Choleraesuis from Swine and Those Non-Fimbriate Strains Possess Distinct Amino Acid Variations in FimH

Although most Salmonella serovars are able to infect a range of animal hosts, some have acquired the ability to cause systemic infections of specific hosts. For example, Salmonella enterica serovar Choleraesuis is primarily associated with systemic infection in swine. Adherence to host epithelial cells is considered a prerequisite for initial infection, and fimbrial appendages on the outer membrane of the bacteria are implicated in this process. Although type 1 fimbriae encoded by the fim gene cluster are commonly found in Salmonella serovars, it is not known whether S. Choleraesuis produces this fimbrial type and if and how fimbriae are involved in pathogenesis. In the present study, we demonstrated that only four out of 120 S. Choleraesuis isolates from pigs with salmonellosis produced type 1 fimbriae as assayed by the yeast agglutination test and electron microscopy. One of the 116 non-type 1 fimbria-producing isolates was transformed with plasmids carrying different fim genes from S. Typhimurium LB5010, a type 1 fimbria-producing strain. Our results indicate that non-type 1 fimbria-producing S. Choleraesuis required only an intact fimH to regain the ability to produce fimbrial appendages. Sequence comparison revealed six amino acid variations between the FimH of the non-type 1 fimbria-producing S. Choleraesuis isolates and those of the type 1 fimbria-producing S. Choleraesuis isolates. S. Choleraesuis that produced type 1 fimbriae contained FimH with an amino acid sequence identical to that of S. Typhimurium LB5010. Site-directed mutagenesis leading to the replacement of the non-conserved residues revealed that a change from glycine to valine at position of 63 (G63V) resulted in a non-type 1 fimbria-producing S. Choleraesuis being able to express type 1 fimbriae on its outer membrane. It is possible that this particular amino acid change prevents this polypeptide from proper interaction with other Fim subunits required for assembly of an intact type 1 fimbrial shaft in S. Choleraesuis; however, it remains to be determined if and how the absence of type 1 fimbriae production is related to the systemic infection of the swine host by S. Choleraesuis.

An Environmental Shiga Toxin-Producing Escherichia coli O145 Clonal Population Exhibits High-Level Phenotypic Variation That Includes Virulence Traits

Shiga toxin-producing Escherichia coli (STEC) serotype O145 is one of the major non-O157 serotypes associated with severe human disease. Here we examined the genetic diversity, population structure, virulence potential, and antimicrobial resistance profiles of environmental O145 strains recovered from a major produce production region in California. Multilocus sequence typing analyses revealed that sequence type 78 (ST-78), a common ST in clinical strains, was the predominant genotype among the environmental strains. Similarly, all California environmental strains belonged to H28, a common H serotype in clinical strains. Although most environmental strains carried an intact fliC gene, only one strain retained swimming motility. Diverse stx subtypes were identified, including stx1a, stx2a, stx2c, and stx2e. Although no correlation was detected between the stx genotype and Stx1 production, high Stx2 production was detected mainly in strains carrying stx2a only and was correlated positively with the cytotoxicity of Shiga toxin. All environmental strains were capable of producing enterohemolysin, whereas only 10 strains were positive for anaerobic hemolytic activity. Multidrug resistance appeared to be common, as nearly half of the tested O145 strains displayed resistance to at least two different classes of antibiotics. The core virulence determinants of enterohemorrhagic E. coli were conserved in the environmental STEC O145 strains; however, there was large variation in the expression of virulence traits among the strains that were highly related genotypically, implying a trend of clonal divergence. Several cattle isolates exhibited key virulence traits comparable to those of the STEC O145 outbreak strains, emphasizing the emergence of hypervirulent strains in agricultural environments.

General Overview on Nontuberculous Mycobacteria, Biofilms, and Human Infection

Nontuberculous mycobacteria (NTM) are emergent pathogens whose importance in human health has been growing. After being regarded mainly as etiological agents of opportunist infections in HIV patients, they have also been recognized as etiological agents of several infections on immune-competent individuals and healthcare-associated infections. The environmental nature of NTM and their ability to assemble biofilms on different surfaces play a key role in their pathogenesis. Here, we review the clinical manifestations attributed to NTM giving particular importance to the role played by biofilm assembly.

Allelic variation contributes to bacterial host specificity

Understanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population and functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. Together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts.

One of the key aspects for controlling infectious diseases is understanding how pathogens cross host species. Here the authors conduct a genome-wide analysis of Salmonella and show a high degree of variation, enabling host-adapted colonization among Salmonella intestinal and systemic serovars.

Type 1 fimbriae are important factors limiting the dissemination and colonization of mice by Salmonella Enteritidis and contribute to the induction of intestinal inflammation during Salmonella invasion

We have recently shown that Salmonella Gallinarum type 1 fimbriae with endogenous mannose-resistant (MR) variant of the FimH protein increase systemic dissemination of S. Gallinarum and colonization of internal organs in comparison to the S. Gallinarum fimH knockout strain or the mutant expressing mannose-sensitive (MS) FimH variant from S. Enteritidis. Elaborating from these studies, we proposed that MS variants of FimH are advantageous in gastrointestinal infections, in contrast to MR FimH variants which decrease intestinal colonization and promote their systemic spreading. To support our hypothesis, we carried out in vivo studies using mice infected with wild-type S. Enteritidis and its fimH knockout strain (S. Enteritidis), which was characterized by significantly lower adhesion and invasiveness of murine ICE-1 intestinal cells. Using bioluminescence imaging, we observed that the loss of MS FimH adhesin correlates well with the highly increased colonization of mice by these bacteria. The appearance of the mutant strain was observed much earlier than wild-type Salmonella, and mice infected with 10⁴–10⁷S. Enteritidis fimH::kan CFUs had significantly (P < 0.05) shorter infection-free time than animals inoculated with wild-type S. Enteritidis. Infections caused by non-typhoid Salmonella, such as S. Enteritidis, are associated with massive inflammation of the lamina propria and lymph nodes in the intestinal tract. Therefore, we evaluated the role of MS type 1 fimbriae in the induction of cytokine expression and secretion, using murine ICE-1 intestinal cells. We showed that the expression, as well as secretion, of Il-1b, Il-6, Il-10, and Il-12b was significantly higher in cells infected with wild-type S. Enteritidis compared to cells infected with the mutant strain. Based on our results, we propose that type 1 fimbriae may play an important role in the pathogenicity of S. Enteritidis and may contribute to an intestinal inflammatory response.

Obligate insect endosymbionts exhibit increased ortholog length variation and loss of large accessory proteins concurrent with genome shrinkage

Extreme genome reduction has been observed in obligate intracellular insect mutualists and is an assumed consequence of fixed, long-term host isolation. Rapid accumulation of mutations and pseudogenization of genes no longer vital for an intracellular lifestyle, followed by deletion of many genes, are factors that lead to genome reduction. Size reductions in individual genes due to small-scale deletions have also been implicated in contributing to overall genome shrinkage. Conserved protein functional domains are expected to exhibit low tolerance for mutations and therefore remain relatively unchanged throughout protein length reduction while nondomain regions, presumably under less selective pressures, would shorten. This hypothesis was tested using orthologous protein sets from the Flavobacteriaceae (phylum: Bacteroidetes) and Enterobacteriaceae (subphylum: Gammaproteobacteria) families, each of which includes some of the smallest known genomes. Upon examination of protein, functional domain, and nondomain region lengths, we found that proteins were not uniformly shrinking with genome reduction, but instead increased length variability and variability was observed in both the functional domain and nondomain regions. Additionally, as complete gene loss also contributes to overall genome shrinkage, we found that the largest proteins in the proteomes of nonhost-restricted bacteroidetial and gammaproteobacterial species often were inferred to be involved in secondary metabolic processes, extracellular sensing, or of unknown function. These proteins were absent in the proteomes of obligate insect endosymbionts. Therefore, loss of genes encoding large proteins not required for host-restricted lifestyles in obligate endosymbiont proteomes likely contributes to extreme genome reduction to a greater degree than gene shrinkage.

Nontuberculous mycobacteria pathogenesis and biofilm assembly

Nontuberculous mycobacteria (NTM) are emergent pathogens whose importance in human health has been gaining relevance after being recognized as etiological agents of opportunist infections in HIV patients. Currently, NTM are recognized as etiological agents of several respiratory and extra-respiratory infections of immune-competent individuals. The environmental nature of NTM together with the ability to assemble biofilms on different surfaces plays a key role on their pathogenesis. In the present work the ability of three fast-growing NTM (Mycobacterium smegmatis, Mycobacterium fortuitum and Mycobacterium chelonae) to persist within a model of human alveolar macrophages was evaluated. Most often human infections with NTM occur by contact with the environment. Biofilms can work as environmental reservoirs. For this reason, it was decided to evaluate the ability of NTM to assemble biofilms on different surfaces. Scanning electron microscopy was used to elucidate the biofilm structure. The ability to assemble biofilms was connected with the ability to spread on solid media known as sliding. Biofilm assembly and intracellular persistence seems to be ruled by different mechanisms.

The giant adhesin SiiE of Salmonella enterica

Salmonella enterica is a Gram-negative, food-borne pathogen, which colonizes the intestinal tract and invades enterocytes. Invasion of polarized cells depends on the SPI1-encoded type III secretion system (T3SS) and the SPI4-encoded type I secretion system (T1SS). The substrate of this T1SS is the non-fimbrial giant adhesin SiiE. With a size of 595 kDa, SiiE is the largest protein of the Salmonella proteome and consists of 53 repetitive bacterial immunoglobulin (BIg) domains, each containing several conserved residues. As known for other T1SS substrates, such as E. coli HlyA, Ca²⁺ ions bound by conserved D residues within the BIg domains stabilize the protein and facilitate secretion. The adhesin SiiE mediates the first contact to the host cell and thereby positions the SPI1-T3SS to initiate the translocation of a cocktail of effector proteins. This leads to actin remodeling, membrane ruffle formation and bacterial internalization. SiiE binds to host cell apical membranes in a lectin-like manner. GlcNAc and α2–3 linked sialic acid-containing structures are ligands of SiiE. Since SiiE shows repetitive domain architecture, we propose a zipper-like binding mediated by each individual BIg domain. In this review, we discuss the characteristics of the SPI4-T1SS and the giant adhesin SiiE.

rpoS-Regulated core genes involved in the competitive fitness of Salmonella enterica Serovar Kentucky in the intestines of chickens

Salmonella enterica serovar Kentucky has become the most frequently isolated serovar from poultry in the United States over the past decade. Despite its prevalence in poultry, it causes few human illnesses in the United States. The dominance of S. Kentucky in poultry does not appear to be due to single introduction of a clonal strain, and its reduced virulence appears to correlate with the absence of virulence genes grvA, sseI, sopE, and sodC1. S. Kentucky's prevalence in poultry is possibly attributable to its metabolic adaptation to the chicken cecum. While there were no difference in the growth rate of S. Kentucky and S. Typhimurium grown microaerophilically in cecal contents, S. Kentucky persisted longer when chickens were coinfected with S. Typhimurium. The in vivo advantage that S. Kentucky has over S. Typhimurium appears to be due to differential regulation of core Salmonella genes via the stationary-phase sigma factor rpoS. Microarray analysis of Salmonella grown in cecal contents in vitro identified several metabolic genes and motility and adherence genes that are differentially activated in S. Kentucky. The contributions of four of these operons (mgl, prp, nar, and csg) to Salmonella colonization in chickens were assessed. Deletion of mgl and csg reduced S. Kentucky persistence in competition studies in chickens infected with wild-type or mutant strains. Subtle mutations affecting differential regulation of core Salmonella genes appear to be important in Salmonella's adaptation to its animal host and especially for S. Kentucky's emergence as the dominant serovar in poultry.

Escherichia coli common pilus (ECP) targets arabinosyl residues in plant cell walls to mediate adhesion to fresh produce plants

Outbreaks of verotoxigenic Escherichia coli are often associated with fresh produce. However, the molecular basis to adherence is unknown beyond ionic lipid-flagellum interactions in plant cell membranes. We demonstrate that arabinans present in different constituents of plant cell walls are targeted for adherence by E. coli common pilus (ECP; or meningitis-associated and temperature-regulated (Mat) fimbriae) for E. coli serotypes O157:H7 and O18:K1:H7. l-Arabinose is a common constituent of plant cell wall that is rarely found in other organisms, whereas ECP is widespread in E. coli and other environmental enteric species. ECP bound to oligosaccharides of at least arabinotriose or longer in a glycan array, plant cell wall pectic polysaccharides, and plant glycoproteins. Recognition overlapped with the antibody LM13, which binds arabinanase-sensitive pectic epitopes, and showed a preferential affinity for (1→5)-α-linked l-arabinosyl residues and longer chains of arabinan as demonstrated with the use of arabinan-degrading enzymes. Functional adherence in planta was mediated by the adhesin EcpD in combination with the structural subunit, EcpA, and expression was demonstrated with an ecpR-GFP fusion and ECP antibodies. Spinach was found to be enriched for ECP/LM13 targets compared with lettuce. Specific recognition of arabinosyl residues may help explain the persistence of E. coli in the wider environment and association of verotoxigenic E. coli with some fresh produce plants by exploitation of a glycan found only in plant, not animal, cells.

Pathogenicity of Shigella in chickens

Shigellosis in chickens was first reported in 2004. This study aimed to determine the pathogenicity of Shigella in chickens and the possibility of cross-infection between humans and chickens. The pathogenicity of Shigella in chickens was examined via infection of three-day-old SPF chickens with Shigella strain ZD02 isolated from a human patient. The virulence and invasiveness were examined by infection of the chicken intestines and primary chicken intestinal epithelial cells. The results showed Shigella can cause death via intraperitoneal injection in SPF chickens, but only induce depression via crop injection. Immunohistochemistry and transmission electron microscopy revealed the Shigella can invade the intestinal epithelia. Immunohistochemistry of the primary chicken intestinal epithelial cells infected with Shigella showed the bacteria were internalized into the epithelial cells. Electron microscopy also confirmed that Shigella invaded primary chicken intestinal epithelia and was encapsulated by phagosome-like membranes. Our data demonstrate that Shigella can invade primary chicken intestinal epithelial cells in vitro and chicken intestinal mucosa in vivo, resulting in pathogenicity and even death. The findings suggest Shigella isolated from human or chicken share similar pathogenicity as well as the possibility of human-poultry cross-infection, which is of public health significance.

Natural rpoS mutations contribute to population heterogeneity in Escherichia coli O157:H7 strains linked to the 2006 US spinach-associated outbreak

We previously reported significantly different acid resistance between curli variants derived from the same Escherichia coli O157:H7 strain, although the curli fimbriae were not associated with this phenotypic divergence. Here we investigated the underlying molecular mechanism by examining the genes encoding the common transcriptional regulators of curli biogenesis and acid resistance. rpoS null mutations were detected in all curli-expressing variants of the 2006 spinach-associated outbreak strains, whereas a wild-type rpoS was present in all curli-deficient variants. Consequently curli-expressing variants were much more sensitive to various stress challenges than curli-deficient variants. This loss of general stress fitness appeared solely to be the result of rpoS mutation since the stress resistances could be restored in curli-expressing variants by a functional rpoS. Comparative transcriptomic analyses between the curli variants revealed a large number of differentially expressed genes, characterized by the enhanced expression of metabolic genes in curli-expressing variants, but a marked decrease in transcription of genes related to stress resistances. Unlike the curli-expressing variants of the 1993 US hamburger-associated outbreak strains (Applied Environmental Microbiology 78: 7706-7719), all curli-expressing variants of the 2006 spinach-associated outbreak strains carry a functional rcsB gene, suggesting an alternative mechanism governing intra-strain phenotypic divergence in E. coli O157:H7.

Host specificity of bacterial pathogens

Most pathogens are able to infect multiple hosts but some are highly adapted to a single-host species. A detailed understanding of the basis of host specificity can provide important insights into molecular pathogenesis, the evolution of pathogenic microbes, and the potential for pathogens to cross the species barrier to infect new hosts. Comparative genomics and the development of humanized mouse models have provided important new tools with which to explore the basis of generalism and specialism. This review will examine host specificity of bacterial pathogens with a focus on generalist and specialist serovars of Salmonella enterica.

The major fimbrial subunit protein of Edwardsiella tarda: vaccine potential, adjuvant effect, and involvement in host infection

Edwardsiella tarda is a Gram-negative bacterium that is reckoned one of the most severe fish pathogens. In this study, we analyzed the biological properties of the E. tarda major fimbrial subunit protein, FimA. We found that mutation of fimA resulted in defective biofilm growth, attenuated infectivity against host cells, and impaired ability to disseminate into and colonize host tissues following experimental infection. When used as a subunit vaccine, recombinant FimA (rFimA) elicited a high level of protection in turbot (Scophthalmus maximus) against lethal E. tarda challenge. Immunological analysis showed that rFimA vaccination induced production of specific serum antibodies that bound to live E. tarda via interaction with the FimA on bacterial cells, and that antibody-E. tarda interaction blocked bacterial infection. Furthermore, passive immunization of turbot with anti-rFimA serum before E. tarda infection reduced bacterial loads in fish tissues to significant extents. To examine the adjuvant potential of FimA, turbot were vaccinated with rVhhP2, a protective Vibrio harveyi antigen, in the presence or absence of rFimA. Subsequent analysis showed that the presence of rFimA significantly augmented the protectivity of rVhhP2. ELISA and quantitative real time RT-PCR showed that rFimA significantly increased rVhhP2-specific serum antibody production and enhanced the expression of immune relevant genes. Taken together, these results indicate that FimA is a virulence-associated protein that possesses vaccine as well as adjuvant potentials, and that the immunoprotectivity of FimA is most likely due to its ability to induce specific immune response that inhibits E. tarda infection.