The XRE Family Transcriptional Regulator SrtR in Streptococcus suis Is Involved in Oxidant Tolerance and Virulence

Biofilm Formation, Modulation, and Transcriptomic Regulation Under Stress Conditions in Halomicronema sp

In nature, bacteria often form heterogeneous communities enclosed in a complex matrix known as biofilms. This extracellular matrix, produced by the microorganisms themselves, serves as the first barrier between the cells and the environment. It is composed mainly of water, extracellular polymeric substances (EPS), lipids, proteins, and DNA. Cyanobacteria form biofilms and have unique characteristics such as oxygenic photosynthesis, nitrogen fixation, excellent adaptability to various abiotic stress conditions, and the ability to secrete a variety of metabolites and hormones. This work focused on the characterization of the cyanobacterium Halomicronema sp. strain isolated from a brackish environment. This study included microscopic imaging, determination of phenolic content and antioxidant capacity, identification of chemicals interfering with biofilm formation, and transcriptomic analysis by RNA sequencing and real-time PCR. Gene expression analysis was centered on genes related to the production of EPS and biofilm-related transcription factors. This study led to the identification of wza1 and wzt as EPS biomarkers and luxR-05665, along with genes belonging to the TetR/AcrR and LysR families, as potential biomarkers useful for studying and monitoring biofilm formation under different environmental conditions. Moreover, this work revealed that Halomicronema sp. can grow even in the presence of strong abiotic stresses, such as high salt, and has good antioxidant properties.

Deciphering the Genetic Architecture of Staphylococcus warneri Prophage vB_G30_01: A Comprehensive Molecular Analysis

The current knowledge of Staphylococcus warneri phages is limited, with few genomes sequenced and characterized. In this study, a prophage, vB_G30_01, isolated from Staphylococcus warneri G30 was characterized and evaluated for its lysogenic host range. The phage was studied using transmission electron microscopy and a host range. The phage genome was sequenced and characterized in depth, including phylogenetic and taxonomic analyses. The linear dsDNA genome of vB_G30_01 contains 67 predicted open reading frames (ORFs), classifying it within Bronfenbrennervirinae. With a total of 10 ORFs involved in DNA replication-related and transcriptional regulator functions, vB_G30_01 may play a role in the genetics and transcription of a host. Additionally, vB_G30_01 possesses a complete set of genes related to host lysogeny and lysis, implying that vB_G30_01 may influence the survival and adaptation of its host. Furthermore, a comparative genomic analysis reveals that vB_G30_01 shares high genomic similarity with other Staphylococcus phages and is relatively closely related to those of Exiguobacterium and Bacillus, which, in combination with the cross-infection assay, suggests possible cross-species infection capabilities. This study enhances the understanding of Staphylococcus warneri prophages, providing insights into phage-host interactions and potential horizontal gene transfer.

Characterization Studies on the sugC Gene of Streptococcus suis Serotype 2 in Adhesion, Invasion, and Virulence in Mice

The sugC gene of Streptococcus suis (S. suis) is a coding gene for the ATP-binding transporter-associated protein with strong pathogenicity. In order to reveal the effect of the sugC gene on the virulence of S. suis serotype 2, a wild-type strain of TJS75, isolated from fattening pigs' brain tissue samples, was used as a parent strain, and a knockout sugC gene (ΔsugC) and complementary strain (CΔsugC) were successfully constructed via homologous recombination technology. The biological characteristics of TJS75, ΔsugC and CΔsugC were compared and analyzed through growth curves, biochemical characteristics, hemolysis characteristics, cell infection tests and pathogenicity tests on BALB/c mice. The results of the growth characteristic experiments in vitro showed that the plateau stage growth period of ΔsugC was delayed compared to the TJS75 strain, but there was no difference in the total number of bacteria. The biochemical characteristics and hemolysis ability of ΔsugC in sheep blood had no difference compared with TJS75, but its adhesion and invasion abilities in PK-15 cells were decreased. Knockout of the sugC gene had no impact on the expression levels of adhesion-related genes in TJS75 in real-time PCR analysis. In addition, the LD50 of ΔsugC in BALB/c mice was 1.47 × 108 CFU, seven times higher than that of TJS75 (LD50 = 2.15 × 107 CFU). These results illustrate that the deletion of sugC reduced the virulence of TJS75 to BALB/c mice, but its role in the adhesion and invasion of PK-15 cells in this strain needs to be further explored. In summary, this study provides evidence that the sugC gene is a virulence-related gene in the S. suis serotype 2 strain and plays a crucial role in the adhesion and invasion of S. suis. This study lays a foundation for the further exploration of the potential virulence factors and pathogenesis of S. suis.

Evaluation of Differentially Expressed Candidate Genes in Benzo[a]pyrene Degradation by Burkholderia vietnamiensis G4

Bacteria-mediated bioremediation is widely employed for its environmental benefits. The genus Burkholderia can degrade persistent organic compounds, however, little is known about its mechanisms. To increase this knowledge, Burkholderia vietnamiensis G4 bacteria were exposed to benzo[a]pyrene, a recalcitrant compound, and the expression of twelve genes of interest was analyzed at 1, 12 and 24 h. In addition, benzo[a]pyrene degradation, evaluation of cell viability and fluorescence emission of assimilated benzo[a]pyrene was performed over 28 days. The up-regulated genes were xre, paaE, livG and pckA at the three times, ACAD, atoB, bmoA and proV at 1 h and AstB at 12 h. These genes are important for bacterial survival in stress situations, breakdown and metabolization of organic compounds, and nutrient transport and uptake. Furthermore, a 52% reduction of the pollutant was observed, there was no significant variation in the viability rate of the cells, and fluorescence indicated an accumulation of benzo[a]pyrene after 24 h. Our study demonstrates the bacteria adaptability and ability to modulate the expression of genes at different times and as needed. This increases our understanding of biodegradation processes and opens new possibilities for using this bacterial strain as a tool for the bioremediation of contaminated areas.

Phenotypic and Genotypic Characterization of a Highly Virulent Erysipelothrix rhusiopathiae Strain

Erysipelothrix rhusiopathiae is responsible for erysipelas infection in pigs. Outbreaks of E. rhusiopathiae have increased in several countries, including China, over the past two decades. An E. rhusiopathiae strain (ML101) was isolated and characterized from dead pig tissue sample collected from a farm experiencing an outbreak of E. rhusiopathiae, which was responsible for the deaths of 146 sows and 308 fattening pigs within a week. Spleen swelling, gastric and bladder mucosa bleeding, and submandibular lymph node swelling and bleeding were observed through necropsy. ML101 was identified as serotype 1a via molecular analysis and immunological assays. Studies in mice demonstrated that the minimal lethal dose per animal was less than 10 colony-forming units (CFU). Notably, the minimal lethal dose in piglets was also less than 10 CFU, which is lower than that of any E. rhusiopathiae strain reported to date. The challenged piglets showed typical acute erysipelas symptoms, such as pyrexia, hemorrhage, depression, complete inappetence, reddening, and purpling skin on the buttock. Evidence of efficient horizontal transmission was observed, as healthy pigs were infected and died when cohoused with challenged piglets. Whole-genome sequencing revealed that ML101 contained a 77 kb genomic island (GI), carrying a Tn916 transposon and a multidrug resistance gene cluster (aadE-apt-spw-lsa(E)-lnu(B)-aadE-sat4-aphA3). A retrospective analysis of E. rhusiopathiae isolates via PCR indicated that the GI has been widely distributed since 2010, when outbreaks were more frequently reported in China. This study demonstrated that the highly virulent E. rhusiopathiae is responsible for the erysipelas outbreak and indicates that relevant genes located within the transmissible genetic elements may play roles in virulence. Therefore, epidemiological monitoring needs to be emphasized to better prevent and control erysipelas in the swine industry, and live attenuated vaccines should be used with caution.

Insight into the Mechanism of Lysogeny Control of phiCDKH01 Bacteriophage Infecting Clinical Isolate of Clostridioides difficile

Clostridioides difficile is a causative agent of antibiotic-associated diarrhea as well as pseudomembranous colitis. So far, all known bacteriophages infecting these bacteria are temperate, which means that instead of prompt lysis of host cells, they can integrate into the host genome or replicate episomally. While C. difficile phages are capable of spontaneous induction and entering the lytic pathway, very little is known about the regulation of their maintenance in the state of lysogeny. In this study, we investigated the properties of a putative major repressor of the recently characterized C. difficile phiCDKH01 bacteriophage. A candidate protein belongs to the XRE family and controls the transcription of genes encoding putative phage antirepressors, known to be involved in the regulation of lytic development. Hence, the putative major phage repressor is likely to be responsible for maintenance of the lysogeny.

Molecular mechanisms of microbiome modulation by the eukaryotic secondary metabolite azelaic acid

Photosynthetic eukaryotes, such as microalgae and plants, foster fundamentally important relationships with their microbiome based on the reciprocal exchange of chemical currencies. Among these, the dicarboxylate metabolite azelaic acid (Aze) appears to play an important, but heterogeneous, role in modulating these microbiomes, as it is used as a carbon source for some heterotrophs but is toxic to others. However, the ability of Aze to promote or inhibit growth, as well as its uptake and assimilation mechanisms into bacterial cells are mostly unknown. Here, we use transcriptomics, transcriptional factor coexpression networks, uptake experiments, and metabolomics to unravel the uptake, catabolism, and toxicity of Aze on two microalgal-associated bacteria, Phycobacter and Alteromonas, whose growth is promoted or inhibited by Aze, respectively. We identify the first putative Aze transporter in bacteria, a 'C4-TRAP transporter', and show that Aze is assimilated through fatty acid degradation, with further catabolism occurring through the glyoxylate and butanoate metabolism pathways when used as a carbon source. Phycobacter took up Aze at an initial uptake rate of 3.8×10-9 nmol/cell/hr and utilized it as a carbon source in concentrations ranging from 10 μM to 1 mM, suggesting a broad range of acclimation to Aze availability. For growth-impeded bacteria, we infer that Aze inhibits the ribosome and/or protein synthesis and that a suite of efflux pumps is utilized to shuttle Aze outside the cytoplasm. We demonstrate that seawater amended with Aze becomes enriched in bacterial families that can catabolize Aze, which appears to be a different mechanism from that in soil, where modulation by the host plant is required. This study enhances our understanding of carbon cycling in the oceans and how microscale chemical interactions can structure marine microbial populations. In addition, our findings unravel the role of a key chemical currency in the modulation of eukaryote-microbiome interactions across diverse ecosystems.

A novel aquaporin Aagp contributes to Streptococcus suis H2O2 efflux and virulence

Streptococcus suis is a bacterium that can cause infections in pigs and humans. Although oxidative stress is common occurrence during bacterial growth and infection, the regulation networks of S. suis under oxidative stress remain poorly understood. To address this, we utilized RNA-Seq to reveal the transcriptional landscape of S. suis in response to H2O2 stress. We identified novel genes responsible for S. suis resistance to oxidative stress, including those involved in DNA repair or protection, and essential for the biosynthesis of amino acids and nucleic acids. In addition, we found that a novel aquaporin, Aagp, belonging to atypical aquaglyceroporins and widely distributed in diverse S. suis serotypes, plays a crucial role during H2O2 stress. By performing oxidative stress assays and measuring the intracellular H2O2 concentrations of the wild-type strain and Aagp mutants during H2O2 stress, we found that Aagp facilitated H2O2 efflux. Additionally, we found that Aagp might be involved in glycerol transport, as shown by the growth inhibition and H2O2 production in the presence of glycerol. Mice infection experiments indicated that Aagp contributed to S. suis virulence. This study contributes to understanding the mechanism of S. suis oxidative stress response, S. suis pathogenesis, and the function of aquaporins in prokaryotes.

XRE transcription factors conserved in Caulobacter and φCbK modulate adhesin development and phage production

The xenobiotic response element (XRE) family of transcription factors (TFs), which are commonly encoded by bacteria and bacteriophage, regulate diverse features of bacterial cell physiology and impact phage infection dynamics. Through a pangenome analysis of Caulobacter species isolated from soil and aquatic ecosystems, we uncovered an apparent radiation of a paralogous XRE TF gene cluster, several of which have established functions in the regulation of holdfast adhesin development and biofilm formation in C. crescentus. We further discovered related XRE TFs throughout the class Alphaproteobacteria and its phages, including the φCbK Caulophage, suggesting that members of this cluster impact host-phage interactions. Here we show that a closely related group of XRE transcription factors encoded by both C. crescentus and φCbK can physically interact and function to control the transcription of a common gene set, influencing processes including holdfast development and the production of φCbK virions. The φCbK-encoded XRE paralog, tgrL, is highly expressed at the earliest stages of infection and can directly inhibit transcription of host genes including hfiA, a potent holdfast inhibitor, and gafYZ, an activator of prophage-like gene transfer agents (GTAs). XRE proteins encoded from the C. crescentus chromosome also directly repress gafYZ transcription, revealing a functionally redundant set of host regulators that may protect against spurious production of GTA particles and inadvertent cell lysis. Deleting the C. crescentus XRE transcription factors reduced φCbK burst size, while overexpressing these host genes or φCbK tgrL rescued this burst defect. We conclude that this XRE TF gene cluster, shared by C. crescentus and φCbK, plays an important role in adhesion regulation under phage-free conditions, and influences host-phage dynamics during infection.

Genomic Plasticity of Acid-Tolerant Phenotypic Evolution in Acetobacter pasteurianus

Acetic acid bacteria have a remarkable capacity to cope with elevated concentrations of cytotoxic acetic acid in their fermentation environment. In particular, the high-level acetate tolerance of Acetobacter pasteurianus that occurs in vinegar industrial settings must be constantly selected for. However, the improved acetic acid tolerance is rapidly lost without a selection pressure. To understand genetic and molecular biology of this acquired acetic acid tolerance in A. pasteurianus, we evolved three strains A. pasteurianus CICIM B7003, CICIM B7003-02, and ATCC 33,445 over 960 generations (4 months) in two initial acetic acids of 20 g·L-1 and 30 g·L-1, respectively. An acetic acid-adapted strain M20 with significantly improved specific growth rate of 0.159 h-1 and acid productivity of 1.61 g·L-1·h-1 was obtained. Comparative genome analysis of six evolved strains revealed that the genetic variations of adaptation were mainly focused on lactate metabolism, membrane proteins, transcriptional regulators, transposases, replication, and repair system. Among of these, lactate dehydrogenase, acetolactate synthase, glycosyltransferase, ABC transporter ATP-binding protein, two-component regulatory systems, the type II toxin-antitoxin system (RelE/RelB/StbE), exodeoxyribonuclease III, type I restriction endonuclease, tRNA-uridine 2-sulfurtransferase, and transposase might collaboratively contribute to the improved acetic acid tolerance in A. pasteurianus strains. The balance between repair factors and transposition variations might be the basis for genomic plasticity of A. pasteurianus strains, allowing the survival of populations and their offspring in acetic acid stress fluctuations. These observations provide important insights into the nature of acquired acetic acid tolerance phenotype and lay a foundation for future genetic manipulation of these strains.

Effect of NaCl stress on exoproteome profiles of Bacillus amyloliquefaciens EB2003A and Lactobacillus helveticus EL2006H

Salt stress can affect survival, multiplication and ability of plant growth promoting microorganisms to enhance plant growth. Changes in a microbe's proteome profile is one of the mechanisms employed by PGPM to enhance tolerance of salt stress. This study was focused on understanding changes in the exoproteome profile of Bacillus amyloliquefaciens EB2003A and Lactobacillus helveticus EL2006H when exposed to salt stress. The strains were cultured in 100 mL M13 (B. amyloliquefaciens) and 100 mL De man, Rogosa and Sharpe (MRS) (L. helveticus) media, supplemented with 200 and 0 mM NaCl (control), at pH 7.0. The strains were then incubated for 48 h (late exponential growth phase), at 120 rpm and 30 (B. amyloliquefaciens) and 37 (L. helveticus) °C. The microbial cultures were then centrifuged and filtered sterilized, to obtain cell free supernatants whose proteome profiles were studied using LC-MS/MS analysis and quantified using scaffold. Results of the study revealed that treatment with 200 mM NaCl negatively affected the quantity of identified proteins in comparison to the control, for both strains. There was upregulation and downregulation of some proteins, even up to 100%, which resulted in identification of proteins significantly unique between the control or 200 mM NaCl (p ≤ 0.05), for both microbial species. Proteins unique to 200 mM NaCl were mostly those involved in cell wall metabolism, substrate transport, oxidative stress tolerance, gene expression and DNA replication and repair. Some of the identified unique proteins have also been reported to enhance plant growth. In conclusion, based on the results of the work described here, PGPM alter their exoproteome profile when exposed to salt stress, potentially upregulating proteins that enhance their tolerance to this stress.

Novel virulence factor Cba induces antibody-dependent enhancement (ADE) of Streptococcus suis Serotype 9 infection in a mouse model

Streptococcus suis (SS) is a zoonotic pathogen that affects the health of humans and the development of the pig industry. The SS Cba protein is a collagen adhesin, and a few of its homologs are related to the enhancement of bacterial adhesion. We compared the phenotypes of SS9-P10, SS9-P10 cba knockout strains and its complementary strains in vitro and in vivo and found that knocking out the cba gene did not affect the growth characteristics of the strain, but it significantly reduced the ability of SS to form biofilms, adhesion to host cells, phagocytic resistance to macrophages and attenuated virulence in a mouse infection model. These results indicated that Cba was a virulence related factor of SS9. In addition, Mice immunized with the Cba protein had higher mortality and more serious organ lesions after challenge, and the same was observed in passive immunization experiments. This phenomenon is similar to the antibody-dependent enhancement of infection by bacteria such as Acinetobacter baumannii and Streptococcus pneumoniae. To our knowledge, this is the first demonstration of antibody-dependent enhancement of SS, and these observations highlight the complexity of antibody-based therapy for SS infection.

A Novel XRE-Type Regulator Mediates Phage Lytic Development and Multiple Host Metabolic Processes in Pseudomonas aeruginosa

Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen, the leading cause of acute and chronic infections in immunocompromised patients, frequently with high morbidity and mortality rates. The xenobiotic response element (XRE) family proteins are the second most common transcriptional regulators (TRs) in P. aeruginosa. However, only a few XRE-like TRs have been reported to regulate multiple bacterial cellular processes, encompassing virulence, metabolism, antibiotic synthesis or resistance, stress responses, and phage infection, etc. Our understanding of what roles these XRE-like small regulatory proteins play in P. aeruginosa remains limited. Here, we aimed to decipher the role of a putative XRE-type transcriptional regulator (designated LfsT) from a prophage region on the chromosome of a clinical P. aeruginosa isolate, P8W. Southern blot and reverse transcription quantitative PCR (RT-qPCR) assays demonstrated that LfsT controlled host sensitivity to the phage PP9W2 and was essential for efficient phage replication. In addition, electrophoretic mobility shift assays (EMSAs) and transcriptional lacZ fusion analyses indicated that LfsT repressed the lysogenic development and promoted the lytic cycle of phage PP9W2 by binding to the promoter regions of the gp71 gene (encoding a CI-like repressor) and several vital phage genes. Combined with RNA-seq and a series of phenotypic validation tests, our results showed that LfsT bound to the flexible palindromic sites within the promoters upstream of several genes in the bacterial genome, regulating fatty acid (FA) metabolism, spermidine (SPD) transport, as well as the type III secretion system (T3SS). Overall, this study reveals novel regulatory roles of LfsT in P. aeruginosa, improving our understanding of the molecular mechanisms behind bacterium-phage interactions. IMPORTANCE This work elucidates the novel roles of a putative XRE family TR, LfsT, in the intricate regulatory systems of P. aeruginosa. We found that LfsT bound directly to the core promoter regions upstream of the start codons of numerous genes involved in various processes, including phage infection, FA metabolism, SPD transport, and the T3SS, regulating as the repressor or activator. The identified partial palindromic motif NAACN(5,8)GTTN recognized by LfsT suggests extensive effects of LfsT on gene expression by maintaining preferential binding to nucleotide sites under evolutionary pressure. In summary, these findings indicate that LfsT enhances metabolic activity in P. aeruginosa, while it reduces host resistance to the phage. This study helps us better understand the coevolution of bacteria and phages (e.g., survival comes at a cost) and provides clues for designing novel antimicrobials against P. aeruginosa infections.

Collective behavior and virulence arsenal of the fish pathogen Piscirickettsia salmonis in the biofilm realm

Piscirickettsiosis is a fish disease caused by the Gram-negative bacterium Piscirickettsia salmonis. This disease has a high socio-economic impact on the Chilean salmonid aquaculture industry. The bacterium has a cryptic character in the environment and their main reservoirs are yet unknown. Bacterial biofilms represent a ubiquitous mechanism of cell persistence in diverse natural environments and a risk factor for the pathogenesis of several infectious diseases, but their microbiological significance for waterborne veterinary diseases, including piscirickettsiosis, have seldom been evaluated. This study analyzed the in vitro biofilm behavior of P. salmonis LF-89^T (genogroup LF-89) and CA5 (genogroup EM-90) using a multi-method approach and elucidated the potential arsenal of virulence of the P. salmonis LF-89^T type strain in its biofilm state. P. salmonis exhibited a quick kinetics of biofilm formation that followed a multi-step and highly strain-dependent process. There were no major differences in enzymatic profiles or significant differences in cytotoxicity (as tested on the Chinook salmon embryo cell line) between biofilm-derived bacteria and planktonic equivalents. The potential arsenal of virulence of P. salmonis LF-89^T in biofilms, as determined by whole-transcriptome sequencing and differential gene expression analysis, consisted of genes involved in cell adhesion, polysaccharide biosynthesis, transcriptional regulation, and gene mobility, among others. Importantly, the global gene expression profiles of P. salmonis LF-89^T were not enriched with virulence-related genes upregulated in biofilm development stages at 24 and 48 h. An enrichment in virulence-related genes exclusively expressed in biofilms was also undetected. These results indicate that early and mature biofilm development stages of P. salmonis LF-89^T were transcriptionally no more virulent than their planktonic counterparts, which was supported by cytotoxic trials, which, in turn, revealed that both modes of growth induced important and very similar levels of cytotoxicity on the salmon cell line. Our results suggest that the aforementioned biofilm development stages do not represent hot spots of virulence compared with planktonic counterparts. This study provides the first transcriptomic catalogue to select specific genes that could be useful to prevent or control the (in vitro and/or in vivo) adherence and/or biofilm formation by P. salmonis and gain further insights into piscirickettsiosis pathogenesis.

The Role of ptsH in Stress Adaptation and Virulence in Cronobacter sakazakii BAA-894

Cronobacter sakazakii, an emerging foodborne pathogen that was isolated primarily from powdered infant formula, poses an important issue in food safety due to its high stress tolerance and pathogenicity. The Hpr (encoded by ptsH gene) has been shown to regulate carbon metabolism as well as stress response and virulence. However, the functional properties of ptsH in C. sakzakii have not been investigated. In this study, we clarified the role of ptsH in the C. sakzakii stress response and virulence, and explored its possible regulatory mechanism by RNA-seq. Compared with wild-type, the ΔptsH mutant showed a slower growth rate in the log phase but no difference in the stationary phase. Moreover, the resistance to heat stress (65 °C, 55 °C), simulated gastric fluid (pH = 2.5), biofilm formation and adhesion to HT-29 cells of ΔptsH mutant were significantly decreased, whereas the oxidative resistance (1, 5, 10 mM H₂O₂), osmotic resistance (10%, 15%, 20% NaCl), and superoxide dismutase activity were enhanced. Finally, RNA-seq analysis revealed the sulfur metabolism pathway is significantly upregulated in the ΔptsH mutant, but the bacterial secretion system pathway is dramatically downregulated. The qRT-PCR assay further demonstrated that the ΔptsH mutant has elevated levels of genes that are related to oxidative and osmotic stress (sodA, rpoS, cpxA/R, osmY). This study provides a great understanding of the role of ptsH in diverse stress responses and virulence in C. sakazakii, and it contributes to our understanding of the genetic determinant of stress resistance and pathogenicity of this important foodborne pathogen.

The characterization of Moraxella catarrhalis carried in the general population

Moraxella catarrhalis is a common cause of respiratory tract infection, particularly otitis media in children, whilst it is also associated with the onset of exacerbation in chronic obstructive pulmonary disease in adults. Despite the need for an efficacious vaccine against M. catarrhalis, no candidates have progressed to clinical trial. This study, therefore, aimed to characterize the diversity of M. catarrhalis isolated from the upper respiratory tract of healthy children and adults, to gain a better understanding of the epidemiology of M. catarrhalis and the distribution of genes associated with virulence factors, to aid vaccine efforts. Isolates were sequenced and the presence of target genes reported. Contrary to prevailing data, this study found that lipooligosaccharide (LOS) B serotypes are not exclusively associated with 16S type 1. In addition, a particularly low prevalence of LOS B and high prevalence of LOS C serotypes was observed. M. catarrhalis isolates showed low prevalence of antimicrobial resistance and a high gene prevalence for a number of the target genes investigated: ompB2 (also known as copB), ompCD, ompE, ompG1a, ompG1b, mid (also known as hag), mcaP, m35, tbpA, lbpA, tbpB, lbpB, msp22, msp75 and msp78, afeA, pilA, pilQ, pilT, mod, oppA, sbp2, mcmA and mclS.

Screening for Virulence-Related Genes via a Transposon Mutant Library of Streptococcus suis Serotype 2 Using a Galleria mellonella Larvae Infection Model

Streptococcus suis (S. suis) is a zoonotic bacterial pathogen causing lethal infections in pigs and humans. Identification of virulence-related genes (VRGs) is of great importance in understanding the pathobiology of a bacterial pathogen. To identify novel VRGs, a transposon (Tn) mutant library of S. suis strain SC19 was constructed in this study. The insertion sites of approximately 1700 mutants were identified by Tn-seq, which involved 417 different genes. A total of 32 attenuated strains were identified from the library by using a Galleria mellonella larvae infection model, and 30 novel VRGs were discovered, including transcription regulators, transporters, hypothetical proteins, etc. An isogenic deletion mutant of hxtR gene (ΔhxtR) and its complementary strain (CΔhxtR) were constructed, and their virulence was compared with the wild-type strain in G. mellonella larvae and mice, which showed that disruption of hxtR significantly attenuated the virulence. Moreover, the ΔhxtR strain displayed a reduced survival ability in whole blood, increased sensitivity to phagocytosis, increased chain length, and growth defect. Taken together, this study performed a high throughput screening for VRGs of S. suis using a G. mellonella larvae model and further characterized a novel critical virulence factor.

XRE family transcriptional regulator XtrSs modulates Streptococcus suis fitness under hydrogen peroxide stress

Streptococcus suis is an important emerging zoonosis that causes economic losses in the pig industry and severe threats to public health. Transcriptional regulators play essential roles in bacterial adaptation to host environments. In this study, we identified a novel XRE family transcriptional regulator in S. suis CZ130302, XtrSs, involved in the bacterial fitness to hydrogen peroxide stress. Based on electrophoretic mobility shift and β-galactosidase activity assays, we found that XtrSs auto-regulated its own transcription and repressed the expression of its downstream gene psePs, a surface protein with unknown function in S. suis, by binding to a palindromic sequence from the promoter region. Furthermore, we proved that the deletion of the psePs gene attenuated bacterial antioxidant response. Phylogenetic analysis revealed that XtrSs and PsePs naturally co-existed as a combination in most S. suis genomes. Collectively, we demonstrated the binding characteristics of XtrSs in S. suis and provided a new insight that XtrSs played a critical role in modulating psePs to the hydrogen peroxide resistance of S. suis.

An Inducible Microbacterium Prophage vB_MoxS-R1 Represents a Novel Lineage of Siphovirus

Lytic and lysogenic infections are the main strategies used by viruses to interact with microbial hosts. The genetic information of prophages provides insights into the nature of phages and their potential influences on hosts. Here, the siphovirus vB_MoxS-R1 was induced from a Microbacterium strain isolated from an estuarine Synechococcus culture. vB_MoxS-R1 has a high replication capability, with an estimated burst size of 2000 virions per cell. vB_MoxS-R1 represents a novel phage genus-based genomic analysis. Six transcriptional regulator (TR) genes were predicted in the vB_MoxS-R1 genome. Four of these TR genes are involved in stress responses, virulence and amino acid transportation in bacteria, suggesting that they may play roles in regulating the host cell metabolism in response to external environmental changes. A glycerophosphodiester phosphodiesterase gene related to phosphorus acquisition was also identified in the vB_MoxS-R1 genome. The presence of six TR genes and the phosphorus-acquisition gene suggests that prophage vB_MoxS-R1 has the potential to influence survival and adaptation of its host during lysogeny. Possession of four endonuclease genes in the prophage genome suggests that vB_MoxS-R1 is likely involved in DNA recombination or gene conversion and further influences host evolution.

Phylogenetic Analysis and Genome-Wide Association Study Applied to an Italian Listeria monocytogenes Outbreak

From May 2015 to March 2016, a severe outbreak due to Listeria monocytogenes ST7 strain occurred in Central Italy and caused 24 confirmed clinical cases. The epidemic strain was deeply investigated using whole-genome sequencing (WGS) analysis. In the interested area, the foodborne outbreak investigation identified a meat food-producing plant contaminated by the outbreak strain, carried by pork-ready-to-eat products. In the same region, in March 2018, the epidemic strain reemerged causing one listeriosis case in a 10-month-old child. The aim of this study was to investigate the phylogeny of the epidemic and reemergent strains over time and to compare them with a closer ST7 clone, detected during the outbreak and with different pulsed-field gel electrophoresis (PFGE) profiles, in order to identify genomic features linked to the persistence and the reemergence of the outbreak. An approach combining phylogenetic analysis and genome-wide association study (GWAS) revealed that the epidemic and reemergent clones were genetically closer to the ST7 clone with different PFGE profiles and strictly associated with the pork production chain. The repeated detection of both clones was probably correlated with (i) the presence of truly persistent clones and the repeated introduction of new ones and (ii) the contribution of prophage genes in promoting the persistence of the epidemic clones. Despite that no significant genomic differences were detected between the outbreak and the reemergent strain, the two related clones detected during the outbreak can be differentiated by transcriptional factor and phage genes associated with the phage LP-114.

Serotypes, Virulence-Associated Factors, and Antimicrobial Resistance of Streptococcus suis Isolates Recovered From Sick and Healthy Pigs Determined by Whole-Genome Sequencing

Streptococcus suis is ubiquitous in swine, and yet, only a small percentage of pigs become clinically ill. The objective of this study was to describe the distribution of serotypes, virulence-associated factor (VAF), and antimicrobial resistance (AMR) genes in S. suis isolates recovered from systemic (blood, meninges, spleen, and lymph node) and non-systemic (tonsil, nasal cavities, ileum, and rectum) sites of sick and healthy pigs using whole-genome sequencing. In total, 273 S. suis isolates recovered from 112 pigs (47 isolates from systemic and 136 from non-systemic sites of 65 sick pigs; 90 isolates from non-systemic sites of 47 healthy pigs) on 17 Ontario farms were subjected to whole-genome sequencing. Using in silico typing, 21 serotypes were identified with serotypes 9 (13.9%) and 2 (8.4%) as the most frequent serotypes, whereas 53 (19.4%) isolates remained untypable. The relative frequency of VAF genes in isolates from systemic (Kruskal–Wallis, p < 0.001) and non-systemic (Kruskal–Wallis, p < 0.001) sites in sick pigs was higher compared with isolates from non-systemic sites in healthy pigs. Although many VAF genes were abundant in all isolates, three genes, including dltA [Fisher's test (FT), p < 0.001], luxS (FT, p = 0.01), and troA (FT, p = 0.02), were more prevalent in isolates recovered from systemic sites compared with non-systemic sites of pigs. Among the isolates, 98% had at least one AMR gene, and 79% had genes associated with at least four drug classes. The most frequently detected AMR genes were tetO conferring resistance to tetracycline and ermB conferring resistance to macrolide, lincosamide, and streptogramin. The wide distribution of VAFs genes in S. suis isolates in this study suggests that other host and environmental factors may contribute to S. suis disease development.

Co-Occurrence of blaOXA-23 in the Chromosome and Plasmid: Increased Fitness in Carbapenem-Resistant Acinetobacter baumannii

This study aims to explore the co-occurrence of chromosomal and plasmid bla_OXA-23 in carbapenem-resistant A. baumannii (CRAB) and its influence on phenotypes. A total of 11 CRAB isolates containing copies of bla_OXA-23 on the chromosome and plasmid (CO), as well as 18 closely related isolates with bla_OXA-23, located on either the chromosome or plasmid (SI), were selected for the determination of antibiotic susceptibility, virulence phenotype, and characteristic genomic differences. The co-occurrence of bla_OXA-23 on the CRAB chromosome and plasmids did not enhance carbapenem resistance, but trimethoprim/sulfamethoxazole exhibited significantly reduced minimum inhibitory concentrations in CO. CO demonstrated a higher degree of fitness compared to SI. An increased biofilm formation ability and serum tolerance were also identified in CO, which may be associated with virulence genes, which include csuD, entE, pgaA, and plc. bla_OXA-23-carrying transposons were found at different insertion sites on the chromosome. The most common site was AbaR-type genomic islands (50%). Two types of plasmids were found in CO. The co-occurrence of bla_OXA-23 on the chromosome and a plasmid in CRAB had little effect on carbapenem susceptibility but was accompanied by increased fitness and virulence. Different origins and independent insertions of bla_OXA-23-carrying transposons were identified in both the chromosomal and plasmid sequences.

A sugar utilization phenotype contributes to the formation of genetic exchange communities in lactic acid bacteria

In prokaryotes, a major contributor to genomic evolution is the exchange of genes via horizontal gene transfer (HGT). Areas with a high density of HGT networks are defined as genetic exchange communities (GECs). Although some phenotypes associated with specific ecological niches are linked to GECs, little is known about the phenotypic influences on HGT in bacterial groups within a taxonomic family. Thanks to the published genome sequences and phenotype data of lactic acid bacteria (LAB), it is now possible to obtain more detailed information about the phenotypes that affect GECs. Here, we have investigated the relationship between HGT and internal and external environmental factors for 178 strains from 24 genera in the Lactobacillaceae family. We found a significant correlation between strains with high utilization of sugars and HGT bias. The result suggests that the phenotype of the utilization of a variety of sugars is key to the construction of GECs in this family. This feature is consistent with the fact that the Lactobacillaceae family contributes to the production of a wide variety of fermented foods by sharing niches such as those in vegetables, dairy products and brewing-related environments. This result provides the first evidence that phenotypes associated with ecological niches contribute to form GECs in the LAB family.

XRE-Type Regulator BioX Acts as a Negative Transcriptional Factor of Biotin Metabolism in Riemerella anatipestifer

Biotin is essential for the growth and pathogenicity of microorganisms. Damage to biotin biosynthesis results in impaired bacterial growth and decreased virulence in vivo. However, the mechanisms of biotin biosynthesis in Riemerella anatipestifer remain unclear. In this study, two R. anatipestifer genes associated with biotin biosynthesis were identified. AS87_RS05840 encoded a BirA protein lacking the N-terminal winged helix-turn-helix DNA binding domain, identifying it as a group I biotin protein ligase, and AS87_RS09325 encoded a BioX protein, which was in the helix-turn-helix xenobiotic response element family of transcription factors. Electrophoretic mobility shift assays demonstrated that BioX bound to the promoter region of bioF. In addition, the R. anatipestifer genes bioF (encoding 7-keto-8-aminopelargonic acid synthase), bioD (encoding dethiobiotin synthase), and bioA (encoding 7,8-diaminopelargonic acid synthase) were in an operon and were regulated by BioX. Quantitative reverse transcription-PCR showed that transcription of the bioFDA operon increased in the mutant Yb2ΔbioX in the presence of excessive biotin, compared with that in the wild-type strain Yb2, suggesting that BioX acted as a repressor of biotin biosynthesis. Streptavidin blot analysis showed that BirA caused biotinylation of BioX, indicating that biotinylated BioX was involved in metabolic pathways. Moreover, as determined by the median lethal dose, the virulence of Yb2ΔbioX was attenuated 500-fold compared with that of Yb2. To summarize, the genes birA and bioX were identified in R. anatipestifer, and BioX was found to act as a repressor of the bioFDA operon involved in the biotin biosynthesis pathway and identified as a bacterial virulence factor. IMPORTANCE Riemerella anatipestifer is a causative agent of diseases in ducks, geese, turkeys, and various other domestic and wild birds. Our study reveals that biotin synthesis of R. anatipestifer is regulated by the BioX through binding to the promoter region of the bioF gene to inhibit transcription of the bioFDA operon. Moreover, bioX is required for R. anatipestifer pathogenicity, suggesting that BioX is a potential target for treatment of the pathogen. R. anatipestifer BioX has thus been identified as a novel negative regulator involved in biotin metabolism and associated with bacterial virulence in this study.

Transcriptome analysis unveils survival strategies of Streptococcus parauberis against fish serum

Streptococcus parauberis is an important bacterial fish pathogen that causes streptococcosis in a variety of fish species including the olive flounder. Despite its importance in the aquaculture industry, little is known about the survival strategy of S. parauberis in the host. Therefore, the objective of this study was to produce genome-wide transcriptome data and identify key factors for the survival of S. parauberis SPOF3K in its host. To this end, S. parauberis SPOF3K was incubated in olive flounder serum and nutrient-enriched media as a control. Although S. parauberis SPOF3K proliferated in both culture conditions, the transcriptomic patterns of the two groups were very different. Interestingly, the expression levels of genes responsible for the replication of an S. parauberis plasmid in the presence of olive flounder serum were higher than those in the absence of olive flounder serum, indicating that this plasmid may play an important role in the survival and proliferation of S. parauberis in the host. Several ATP-binding cassette transporters known to transport organic substrates (e.g., biotin and osmoprotectants) that are vital for bacterial survival in the host were significantly up-regulated in S. parauberis cultured in serum. In addition, groEL, dnaK operon, and members of the clp protease family, which are known to play important roles in response to various stressors, were up-regulated in S. parauberis incubated in serum, thus limiting damage and facilitating cellular recovery. Moreover, important virulence factors including the hyaluronic acid capsule (has operon), sortase A (srtA), C5a peptidase (scp), and peptidoglycan O-acetyltransferase (oatA) were significantly upregulated in S. paraubers in serum. These results indicate that S. paraubers can resist and evade the humoral immune responses of fish. The transcriptomic data obtained in this study provide a better understanding of the mode of action of S. parauberis in fish.

Genetic analysis and pathogenicity of different sequence types of Streptococcus suis isolated from pigs in southern China

In this study, 52 Streptococcus suis isolates from pigs in southern China were divided into four known sequence types (STs) and six new STs, using multilocus sequence typing. Ten representative isolates were selected from 10 STs for the analysis of whole genome sequences. Virulence was assessed in 10 isolates, which were classified into three pathogenic groups. The prevalence of virulence-associated factors in the moderately pathogenic group was higher than that in the highly pathogenic group. The isolates from ST1 complex and serotype 2 were allocated to the moderately pathogenic group, while the isolates from the highly pathogenic group belonged to the non-ST1 complex and non-serotype 2. Three clusters were obtained based on multilocus sequence typing sequences: cluster III isolates from the nasal cavity of healthy pigs were classified into the highly pathogenic group and showed many peculiarities compared with cluster I and II isolates in virulence genotypes, genetic typing and pathogenesis, indicating a potential independent evolutionary line. Our results suggest that S. suis infections in China are becoming more complicated with constantly mutating isolates, which makes it difficult to distinguish their virulence by recognized typing methods. Thus, increased investigation and monitoring of these infections should be a priority for the swine industry in China.

Two novel XRE-like transcriptional regulators control phenotypic heterogeneity in Photorhabdus luminescens cell populations

BACKGROUND

The insect pathogenic bacterium Photorhabdus luminescens exists in two phenotypically different forms, designated as primary (1°) and secondary (2°) cells. Upon yet unknown environmental stimuli up to 50% of the 1° cells convert to 2° cells. Among others, one important difference between the phenotypic forms is that 2° cells are unable to live in symbiosis with their partner nematodes, and therefore are not able to re-associate with them. As 100% switching of 1° to 2° cells of the population would lead to a break-down of the bacteria's life cycle the switching process must be tightly controlled. However, the regulation mechanism of phenotypic switching is still puzzling.

RESULTS

Here we describe two novel XRE family transcriptional regulators, XreR1 and XreR2, that play a major role in the phenotypic switching process of P. luminescens. Deletion of xreR1 in 1° or xreR2 in 2° cells as well as insertion of extra copies of xreR1 into 2° or xreR2 into 1° cells, respectively, induced the opposite phenotype in either 1° or 2° cells. Furthermore, both regulators specifically bind to different promoter regions putatively fulfilling a positive autoregulation. We found initial evidence that XreR1 and XreR2 constitute an epigenetic switch, whereby XreR1 represses xreR2 expression and XreR2 self-reinforces its own gene by binding to XreR1.

CONCLUSION

Regulation of gene expression by the two novel XRE-type regulators XreR1 and XreR2 as well as their interplay represents a major regulatory process in phenotypic switching of P. luminescens. A fine-tuning balance between both regulators might therefore define the fate of single cells to convert from the 1° to the 2° phenotype.

Chitin Attenuates Expression of Listeria monocytogenes Virulence Genes in vitro

External signals are crucial for bacteria to sense their immediate environment and fine-tune gene expression accordingly. The foodborne pathogen Listeria monocytogenes senses a range of environmental cues in order to activate or deactivate the virulence-inducing transcriptional factor PrfA during transition between infectious and saprophytic lifecycles. Chitin is an abundant biopolymer formed from linked β-(1-4)-N-acetyl-D-glucosamine residues associated with fungi, the exoskeleton of insects and often incorporated into foods as a thickener or stabilizer. L. monocytogenes evolved to hydrolyse chitin, presumably, to facilitate nutrient acquisition from competitive environments such as soil where the polymer is abundant. Since mammals do not produce chitin, we reasoned that the polymer could serve as an environmental signal contributing to repression of L. monocytogenes PrfA-dependent expression. This study shows a significant downregulation of the core PrfA-regulon during virulence-inducing conditions in vitro in the presence of chitin. Our data suggest this phenomenon occurs through a mechanism that differs from PTS-transport of oligosaccharides generated from either degradation or chitinase-mediated hydrolysis of the polymer. Importantly, an indication that chitin can repress virulence expression of a constitutively active PrfA^∗ mutant is shown, possibly mediated via a post-translational modification inhibiting PrfA^∗ activity. To our knowledge, this is the first time that chitin is reported as a molecule with anti-virulence properties against a pathogenic bacterium. Thus, our findings identify chitin as a signal which may downregulate the virulence potential of the pathogen and may provide an alternative approach toward reducing disease risk.

MsrR is a thiol-based oxidation-sensing regulator of the XRE family that modulates C. glutamicum oxidative stress resistance

Background

Corynebacterium glutamicum thrives under oxidative stress caused by the inevitably extreme environment during fermentation as it harbors antioxidative stress genes. Antioxidant genes are controlled by pathway-specific sensors that act in response to growth conditions. Although many families of oxidation-sensing regulators in C. glutamicum have been well described, members of the xenobiotic-response element (XRE) family, involved in oxidative stress, remain elusive.

Results

In this study, we report a novel redox-sensitive member of the XER family, MsrR (multiple stress resistance regulator). MsrR is encoded as part of the msrR-3-mst (3-mercaptopyruvate sulfurtransferase) operon; msrR-3-mst is divergent from multidrug efflux protein MFS. MsrR was demonstrated to bind to the intergenic region between msrR-3-mst and mfs. This binding was prevented by an MsrR oxidation-mediated increase in MsrR dimerization. MsrR was shown to use Cys62 oxidation to sense oxidative stress, resulting in its dissociation from the promoter. Elevated expression of msrR-3-mst and mfs was observed under stress. Furthermore, a ΔmsrR mutant strain displayed significantly enhanced growth, while the growth of strains lacking either 3-mst or mfs was significantly inhibited under stress.

Conclusion

This report is the first to demonstrate the critical role of MsrR-3-MST-MFS in bacterial stress resistance.

The Novel Streptococcal Transcriptional Regulator XtgS Negatively Regulates Bacterial Virulence and Directly Represses PseP Transcription

Streptococcus agalactiae (group B streptococcus [GBS]) has received continuous attention for its involvement in invasive infections and its broad host range. Transcriptional regulators have an important impact on bacterial adaptation to various environments. Research on transcriptional regulators will shed new light on GBS pathogenesis. In this study, we identified a novel XRE-family transcriptional regulator encoded on the GBS genome, designated XtgS. Our data demonstrate that XtgS inactivation significantly increases bacterial survival in host blood and animal challenge test, suggesting that it is a negative regulator of GBS pathogenicity. Further transcriptomic analysis and quantitative reverse transcription-PCR (qRT-PCR) mainly indicated that XtgS significantly repressed transcription of its upstream gene pseP Based on electrophoretic mobility shift and lacZ fusion assays, we found that an XtgS homodimer directly binds a palindromic sequence in the pseP promoter region. Meanwhile, the PseP and XtgS combination naturally coexists in diverse Streptococcus genomes and has a strong association with sequence type, serotype diversification and host adaptation of GBS. Therefore, this study reveals that XtgS functions as a transcriptional regulator that negatively affects GBS virulence and directly represses PseP expression, and it provides new insights into the relationships between transcriptional regulator and genome evolution.

Antibiotic resistance related to biofilm formation in Streptococcus suis

Streptococcus suis (S. suis) is an important zoonotic agent, which seriously impacts the pig industry and human health in various countries. Biofilm formation is likely contributing to the virulence and drug resistance in S. suis. A better knowledge of biofilm formation as well as to biofilm-dependent drug resistance mechanisms in S. suis can be of great significance for the prevention and treatment of S. suis infections. This literature review updates the latest scientific data related to biofilm formation in S. suis and its impact on drug tolerance and resistance.Key points• Biofilm formation is the important reasons for drug resistance of SS infections.• The review includes the regulatory mechanism of SS biofilm formation.• The review includes the drug resistance mechanisms of SS biofilm.

Differential Expression and PAH Degradation: What Burkholderia vietnamiensis G4 Can Tell Us?

Petroleum is the major energy matrix in the world whose refining generates chemical byproducts that may damage the environment. Among such waste, polycyclic aromatic hydrocarbons (PAH) are considered persistent pollutants. Sixteen of these are considered priority for remediation, and among them is benzo(a)pyrene. Amid remediation techniques, bioremediation stands out. The genus Burkholderia is amongst the microorganisms known for being capable of degrading persistent compounds; its strains are used as models to study such ability. High-throughput sequencing allows researchers to reach a wider knowledge about biodegradation by bacteria. Using transcripts and mRNA analysis, the genomic regions involved in this aptitude can be detected. To unravel these processes, we used the model B. vietnamiensis strain G4 in two experimental groups: one was exposed to benzo(a)pyrene and the other one (control) was not. Six transcriptomes were generated from each group aiming to compare gene expression and infer which genes are involved in degradation pathways. One hundred fifty-six genes were differentially expressed in the benzo(a)pyrene exposed group, from which 33% are involved in catalytic activity. Among these, the most significant genomic regions were phenylacetic acid degradation protein paaN, involved in the degradation of organic compounds to obtain energy; oxidoreductase FAD-binding subunit, related to the regulation of electrons within groups of dioxygenase enzymes with potential to cleave benzene rings; and dehydrogenase, described as accountable for phenol degradation. These data provide the basis for understanding the bioremediation of benzo(a)pyrene and the possible applications of this strain in polluted environments.

Transcriptome profiling reveals the molecular processes for survival of Lysinibacillus fusiformis strain 15-4 in petroleum environments

A bacterial strain designated Lysinibacillus fusiformis 15-4 was isolated from oil-free soil on the Qinghai-Tibet Plateau, which can grow well utilizing petroleum hydrocarbons as a carbon source at a lower temperature. To deeply characterize the molecular adaptations and metabolic processes of this strain when grown in a petroleum-containing environment, transcriptome analysis was performed. A total of 4664 genes and the expression of 3969 genes were observed in strain 15-4. When the strain was grown in petroleum-containing medium, 2192 genes were significantly regulated, of which 1312 (60%) were upregulated and 880 (40%) were downregulated. This strain degraded and adapted to petroleum via modulation of diverse molecular processes, including improvements in transporter activity, oxidoreductase/dehydrogenase activity, two-component system/signal transduction, transcriptional regulation, fatty acid catabolism, amino acid metabolism, and environmental stress responses. Many strain-specific genes were involved in the oxidation of hydrocarbon compounds, such as several luciferase family alkane monooxygenase genes, flavin-utilizing monooxygenase family genes, and flavoprotein-like family alkanesulfonate monooxygenase genes. Several cold shock protein genes were also induced suggesting adaptation to cold environments and the potential for petroleum degradation at low temperatures. The results obtained in this study may broaden our understanding of molecular adaptation of bacteria to hydrocarbon-containing environments and may provide valuable data for further study of L. fusiformis.

Calcium transcriptionally regulates movement, recombination and other functions of Xylella fastidiosa under constant flow inside microfluidic chambers

Xylella fastidiosa is a xylem‐limited bacterial pathogen causing devastating diseases in many economically important crops. Calcium (Ca) is a major inorganic nutrient in xylem sap that influences virulence‐related traits of this pathogen, including biofilm formation and twitching motility. This study aimed to adapt a microfluidic system, which mimics the natural habitat of X. fastidiosa, for whole transcriptome analysis under flow conditions. A microfluidic chamber with two parallel channels was used, and RNA isolated from cells grown inside the system was analysed by RNA‐Seq. Ca transcriptionally regulated the machinery of type IV pili and other genes related to pathogenicity and host adaptation. Results were compared to our previous RNA‐Seq study in biofilm cells in batch cultures (Parker et al., 2016, Environ Microbiol 18, 1620). Ca‐regulated genes in both studies belonged to similar functional categories, but the number and tendencies (up‐/downregulation) of regulated genes were different. Recombination‐related genes were upregulated by Ca, and we proved experimentally that 2 mM Ca enhances natural transformation frequency. Taken together, our results suggest that the regulatory role of Ca in X. fastidiosa acts differently during growth in flow or batch conditions, and this can correlate to the different phases of growth (planktonic and biofilm) during the infection process.

A putative transcription regulator involved in the virulence attenuation of an acriflavine-resistant vaccine strain of Erysipelothrix rhusiopathiae, the causative agent of swine erysipelas

Acriflavine, an acridine dye that causes frameshift mutations, has been used to attenuate various veterinary pathogens for the development of live vaccines. Erysipelothrix rhusiopathiae Koganei 65-0.15 strain (Koganei) (serovar 1a) is the acriflavine-resistant live vaccine currently used in Japan for the control of swine erysipelas. To investigate the attenuation mechanisms of the Koganei strain, we analyzed the draft genome sequence of the Koganei strain against the reference genome sequence of the E. rhusiopathiae Fujisawa strain (serovar 1a). The sequence analysis revealed a high degree of sequence similarity between the two strains and identified a total of 98 sequence differences within 80 protein-coding sequences. Among them, insertions/deletions (indels) were identified in 9 genes, of which 7 resulted in frameshift and premature termination. To investigate whether these mutations resulted in the attenuation of the Koganei strain, we focused on the indel mutation identified in ERH_0661, an XRE family transcriptional regulator. We introduced the mutation into ERH_0661 of the Fujisawa strain and restored the mutation of the Koganei strain. Animal experiments using the recombinant strains showed that mice survived inoculation with 10³ colony forming units (CFUs) (equivalent to approximately 100 50% lethal doses [LD50] of the wild-type Fujisawa) of the recombinant Fujisawa strain, and the mice became ill after inoculation with 10⁸ CFUs of the recombinant Koganei strain. These results suggest that the transcriptional regulator ERH_0661 is involved in the virulence of E. rhusiopathiae and that the ERH_0661 mutation is partially responsible for the attenuation of the Koganei strain.

Transcriptomic analysis of smooth versus rough Brucella melitensis Rev.1 vaccine strains reveals insights into virulence attenuation

Brucella melitensis Rev.1 is the live attenuated Elberg-originated vaccine strain of the facultative intracellular Brucella species, and is widely used to control brucellosis in small ruminants. However, Rev.1 may cause abortions in small ruminants that have been vaccinated during the last trimester of gestation, it is pathogenic to humans, and it induces antibodies directed at the O-polysaccharide (O-PS) of the smooth lipopolysaccharide, thus making it difficult to distinguish between vaccinated and infected animals. Rough Brucella strains, which lack O-PS and are considered less pathogenic, have been introduced to address these drawbacks; however, as Rev.1 confers a much better immunity than the rough mutants, it is still considered the reference vaccine for the prophylaxis of brucellosis in small ruminants. Therefore, developing an improved vaccine strain, which lacks the Rev.1 drawbacks, is a highly evaluated task, which requires a better understanding of the molecular mechanisms underlying the virulence attenuation of Rev.1 smooth strains and of natural Rev.1 rough strains, which are currently only partly understood. As the acidification of the Brucella-containing vacuole during the initial stages of infection is crucial for their survival, identifying the genes that contribute to their survival in an acidic environment versus a normal environment will greatly assist our understanding of the molecular pathogenic mechanisms and the attenuated virulence of the Rev.1 strain. Here, we compared the transcriptomes of the smooth and natural rough Rev.1 strains, each grown under either normal or acidic conditions. We found 12 key genes that are significantly downregulated in the Rev.1 rough strains under normal pH, as compared with Rev.1 smooth strains, and six highly important genes that are significantly upregulated in the smooth strains under acidic conditions, as compared with Rev.1 rough strains. All 18 differentially expressed genes are associated with bacterial virulence and survival and may explain the attenuated virulence of the rough Rev.1 strains versus smooth Rev.1 strains, thus providing new insights into the virulence attenuation mechanisms of Brucella. These highly important candidate genes may facilitate the design of new and improved brucellosis vaccines.

CopA Protects Streptococcus suis against Copper Toxicity

Streptococcus suis is a zoonotic pathogen that causes great economic losses to the swine industry and severe threats to public health. A better understanding of its physiology would contribute to the control of its infections. Although copper is an essential micronutrient for life, it is toxic to cells when present in excessive amounts. Herein, we provide evidence that CopA is required for S. suis resistance to copper toxicity. Quantitative PCR analysis showed that copA expression was specifically induced by copper. Growth curve analyses and spot dilution assays showed that the ΔcopA mutant was defective in media supplemented with elevated concentrations of copper. Spot dilution assays also revealed that CopA protected S. suis against the copper-induced bactericidal effect. Using inductively coupled plasma-optical emission spectroscopy, we demonstrated that the role of CopA in copper resistance was mediated by copper efflux. Collectively, our data indicated that CopA protects S. suis against the copper-induced bactericidal effect via copper efflux.

Antigen I/II Participates in the Interactions of Streptococcus suis Serotype 9 With Phagocytes and the Development of Systemic Disease

Streptococcus suis is an important porcine bacterial pathogen and a zoonotic agent causing a variety of pathologies including sudden death, septic shock, and meningitis. Though serotype 2 is the most studied serotype due to its presence worldwide, serotype 9 is responsible for the greatest number of porcine cases in Spain, the Netherlands, and Germany. Regardless of its increasing importance, very few studies have investigated S. suis serotype 9 virulence factors and pathogenesis. Antigens I/II (AgI/II) are multimodal adhesion proteins implicated in host respiratory tract and oral cavity persistence of various pathogenic human streptococci. It was recently demonstrated that AgI/II is involved in various bacterial functions for serotype 9, participating in the initial steps of the pathogenesis of the infection. However, its contribution to the systemic infection remains unknown. As such, we evaluated herein the role of the S. suis serotype 9 AgI/II in the interactions with phagocytes and the development of systemic disease in a mouse model of infection. Results demonstrated that the presence of AgI/II is important for the development of clinical systemic disease by promoting bacterial survival in blood possibly due to its effect on S. suis phagocytosis, as shown with macrophages and dendritic cells. Furthermore, AgI/II directly participates in dendritic cell activation and pro-inflammatory mediator production following recognition by the Toll-like receptor pathway, which may contribute to the exacerbated systemic inflammation responsible for host death. Taken together, this study demonstrates that the S. suis serotype 9 AgI/II is important for virulence during systemic infection and development of disease. In fact, this is the first study to describe a role of an AgI/II family member in systemic bacterial disease.