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BioRxiv : the Preprint Server For... Apr 2024Although horizontal gene transfer is pervasive in the intestinal microbiota, we understand only superficially the roles of most exchanged genes and how the mobile...
Although horizontal gene transfer is pervasive in the intestinal microbiota, we understand only superficially the roles of most exchanged genes and how the mobile repertoire affects community dynamics. Similarly, little is known about the mechanisms underlying the ability of a community to recover after a perturbation. Here, we identified and functionally characterized a large conjugative plasmid that is one of the most frequently transferred elements among Bacteroidales species and is ubiquitous in diverse human populations. This plasmid encodes both an extracellular polysaccharide and fimbriae, which promote the formation of multispecies biofilms in the mammalian gut. We use a hybridization-based approach to visualize biofilms in clarified whole colon tissue with unprecedented 3D spatial resolution. These biofilms increase bacterial survival to common stressors encountered in the gut, increasing strain resiliency, and providing a rationale for the plasmid's recent spread and high worldwide prevalence.
PubMed: 38746121
DOI: 10.1101/2024.04.29.590671 -
PLoS Computational Biology May 2024In this work, we quantitatively compare computer simulations and existing cell tracking data of P. aeruginosa surface motility in order to analyse the underlying...
In this work, we quantitatively compare computer simulations and existing cell tracking data of P. aeruginosa surface motility in order to analyse the underlying motility mechanism. We present a three dimensional twitching motility model, that simulates the extension, retraction and surface association of individual Type IV Pili (TFP), and is informed by recent experimental observations of TFP. Sensitivity analysis is implemented to minimise the number of model parameters, and quantitative estimates for the remaining parameters are inferred from tracking data by approximate Bayesian computation. We argue that the motility mechanism is highly sensitive to experimental conditions. We predict a TFP retraction speed for the tracking data we study that is in a good agreement with experimental results obtained under very similar conditions. Furthermore, we examine whether estimates for biologically important parameters, whose direct experimental determination is challenging, can be inferred directly from tracking data. One example is the width of the distribution of TFP on the bacteria body. We predict that the TFP are broadly distributed over the bacteria pole in both walking and crawling motility types. Moreover, we identified specific configurations of TFP that lead to transitions between walking and crawling states.
Topics: Pseudomonas aeruginosa; Models, Biological; Computer Simulation; Fimbriae, Bacterial; Computational Biology; Bayes Theorem; Movement
PubMed: 38743804
DOI: 10.1371/journal.pcbi.1012063 -
BMC Genomics May 2024Pseudomonas syringae pv. actinidiae (Psa) is an important bacterial plant pathogen that causes severe damage to the kiwifruit industry worldwide. Three Psa strains were... (Comparative Study)
Comparative Study
BACKGROUND
Pseudomonas syringae pv. actinidiae (Psa) is an important bacterial plant pathogen that causes severe damage to the kiwifruit industry worldwide. Three Psa strains were recently obtained from different kiwifruit orchards in Anhui Province, China. The present study mainly focused on the variations in virulence and genome characteristics of these strains based on the pathogenicity assays and comparative genomic analyses.
RESULTS
Three strains were identified as biovar 3 (Psa3), along with strain QSY6 showing higher virulence than JZY2 and YXH1 in pathogenicity assays. The whole genome assembly revealed that each of the three strains had a circular chromosome and a complete plasmid. The chromosome sizes ranged from 6.5 to 6.6 Mb with a GC content of approximately 58.39 to 58.46%, and a predicted number of protein-coding sequences ranging from 5,884 to 6,019. The three strains clustered tightly with 8 Psa3 reference strains in terms of average nucleotide identity (ANI), whole-genome-based phylogenetic analysis, and pangenome analysis, while they were evolutionarily distinct from other biovars (Psa1 and Psa5). Variations were observed in the repertoire of effectors of the type III secretion system among all 15 strains. Moreover, synteny analysis of the three sequenced strains revealed eight genomic regions containing 308 genes exclusively present in the highly virulent strain QSY6. Further investigation of these genes showed that 16 virulence-related genes highlight several key factors, such as effector delivery systems (type III secretion systems) and adherence (type IV pilus), which might be crucial for the virulence of QSY6.
CONCLUSION
Three Psa strains were identified and showed variant virulence in kiwifruit plant. Complete genome sequences and comparative genomic analyses further provided a theoretical basis for the potential pathogenic factors responsible for kiwifruit bacterial canker.
Topics: Pseudomonas syringae; Phylogeny; Genome, Bacterial; China; Actinidia; Virulence; Plant Diseases; Genomics
PubMed: 38734623
DOI: 10.1186/s12864-024-10384-1 -
MBio May 2024Extracellular cytochrome filaments are proposed to serve as conduits for long-range extracellular electron transfer. The primary functional physiological evidence has...
UNLABELLED
Extracellular cytochrome filaments are proposed to serve as conduits for long-range extracellular electron transfer. The primary functional physiological evidence has been the reported inhibition of Fe(III) oxide reduction when the gene for the filament-forming cytochrome OmcS is deleted. Here we report that the OmcS-deficient strain from that original report reduces Fe(III) oxide as well as the wild-type, as does a triple mutant in which the genes for the other known filament-forming cytochromes were also deleted. The triple cytochrome mutant displayed filaments with the same 3 nm diameter morphology and conductance as those produced by heterologously expressing the PilA pilin gene. Fe(III) oxide reduction was inhibited when the pilin gene in cytochrome-deficient mutants was modified to yield poorly conductive 3 nm diameter filaments. The results are consistent with the concept that 3 nm diameter electrically conductive pili (e-pili) are required for long-range extracellular electron transfer. In contrast, rigorous physiological functional evidence is lacking for cytochrome filaments serving as conduits for long-range electron transport.
IMPORTANCE
Unraveling microbial extracellular electron transfer mechanisms has profound implications for environmental processes and advancing biological applications. This study on challenges prevailing beliefs on cytochrome filaments as crucial components thought to facilitate long-range electron transport. The discovery of an OmcS-deficient strain's unexpected effectiveness in Fe(III) oxide reduction prompted a reevaluation of the key conduits for extracellular electron transfer. By exploring the impact of genetic modifications on ' performance, this research sheds light on the importance of 3-nm diameter electrically conductive pili in Fe(III) oxide reduction. Reassessing these mechanisms is essential for uncovering the true drivers of extracellular electron transfer in microbial systems, offering insights that could revolutionize applications across diverse fields.
Topics: Electron Transport; Geobacter; Cytochromes; Oxidation-Reduction; Ferric Compounds; Fimbriae, Bacterial; Fimbriae Proteins
PubMed: 38717196
DOI: 10.1128/mbio.00690-24 -
Brazilian Journal of Microbiology :... Jun 2024Salmonella spp. and Escherichia coli are implicated in human and animal infections and require antimicrobial treatment in many situations. Faecal samples of healthy...
Salmonella spp. and Escherichia coli are implicated in human and animal infections and require antimicrobial treatment in many situations. Faecal samples of healthy white-lipped peccaries (Pecari tajacu) (n = 30) and collared peccaries (Tayassu pecari ) (n = 60) obtained in three farms located in the Midwest Brazil. The antimicrobial profiles of commensal E. coli from P. tajacu and T. pecari from commercial herds in Brazil were isolated and analyzed and virulence genes were detected. Among 90 healthy animals, no Salmonella spp. were isolated. However, 30 samples (27%) tested positive for E. coli, with 18 isolates from P. tajacu and 12 from T. pecari, representing frequencies of 58.0% and 38.7%, respectively. Additionally, other Enterobacteriaceae family bacteria were detected but not included in this analysis. However, individual samples from 30 animals tested positive for E. coli, of which 16 were isolated from P. tajacu presenting multidrug resistance and six were isolated from T. pecari presenting a similar pattern. The E. coli virulence genes detected were papC (pilus-associated pyelonephritis) in five isolates, tsh (temperature-sensitive hemagglutinin) in one isolate, and eae (enteric attachment and effacement) in one isolate. The serum resistance gene, iss (increased serum survival), was detected in four isolates. An association between these genes and the presence of hemolysin was also observed in one isolate. Thus, T. pecari and P. tajacu are potential reservoirs of pathogenic and multidrug-resistant and E. coli. Faecal E. coli of healthy P. tajacu and T. pecari could act as a possible reservoir of antimicrobial resistance genes in environment.
Topics: Animals; Escherichia coli; Salmonella; Brazil; Virulence Factors; Anti-Bacterial Agents; Feces; Artiodactyla; Escherichia coli Infections; Salmonella Infections, Animal; Virulence; Prevalence; Drug Resistance, Bacterial; Microbial Sensitivity Tests
PubMed: 38713279
DOI: 10.1007/s42770-024-01359-1 -
Infection and Immunity Jun 2024[group A streptococcus (GAS)] is a human pathogen capable of infecting diverse tissues. To successfully infect these sites, GAS must detect available nutrients and...
[group A streptococcus (GAS)] is a human pathogen capable of infecting diverse tissues. To successfully infect these sites, GAS must detect available nutrients and adapt accordingly. The phosphoenolpyruvate transferase system (PTS) mediates carbohydrate uptake and metabolic gene regulation to adapt to the nutritional environment. Regulation by the PTS can occur through phosphorylation of transcriptional regulators at conserved PTS-regulatory domains (PRDs). GAS has several PRD-containing stand-alone regulators with regulons encoding both metabolic genes and virulence factors [PRD-containing virulence regulators (PCVRs)]. One is RofA, which regulates the expression of virulence genes in multiple GAS serotypes. It was hypothesized that RofA is phosphorylated by the PTS in response to carbohydrate levels to coordinate virulence gene expression. In this study, the RofA regulon of M1T1 strain 5448 was determined using RNA sequencing. Two operons were consistently differentially expressed across growth in the absence of RofA; the pilus operon was downregulated, and the capsule operon was upregulated. This correlated with increased capsule production and decreased adherence to keratinocytes. Purified RofA-His was phosphorylated by PTS proteins EI and HPr, and phosphorylated RofA-FLAG was detected when GAS was grown in low-glucose C medium. Phosphorylated RofA was not observed when C medium was supplemented 10-fold with glucose. Mutations of select histidine residues within the putative PRDs contributed to the phosphorylation of RofA, although phosphorylation of RofA was still observed, suggesting other phosphorylation sites exist in the protein. Together, these findings support the hypothesis that RofA is a PCVR that may couple sugar metabolism with virulence regulation.
Topics: Streptococcus pyogenes; Gene Expression Regulation, Bacterial; Bacterial Proteins; Virulence Factors; Virulence; Phosphorylation; Humans; Regulon; Operon; Streptococcal Infections; Phosphoenolpyruvate Sugar Phosphotransferase System; Keratinocytes
PubMed: 38712951
DOI: 10.1128/iai.00083-24 -
Frontiers in Cellular and Infection... 2024Detailed assessment of the population structure of group B (GBS) among adults is still lacking in Saudi Arabia. Here we characterized a representative collection of...
INTRODUCTION
Detailed assessment of the population structure of group B (GBS) among adults is still lacking in Saudi Arabia. Here we characterized a representative collection of isolates from colonized and infected adults.
METHODS
GBS isolates (n=89) were sequenced by Illumina and screened for virulence and antimicrobial resistance determinants. Genetic diversity was assessed by single nucleotide polymorphisms and core-genome MLST analyses.
RESULTS
Genome sequences revealed 28 sequence types (STs) and nine distinct serotypes, including uncommon serotypes VII and VIII. Majority of these STs (n=76) belonged to the human-associated clonal complexes (CCs) CC1 (33.71%), CC19 (25.84%), CC17 (11.24%), CC10/CC12 (7.87%), and CC452 (6.74%). Major CCs exhibited intra-lineage serotype diversity, except for the hypervirulent CC17, which exclusively expressed serotype III. Virulence profiling revealed that nearly all isolates (94.38%) carried at least one of the four alpha family protein genes (i.e., , , , and ), and 92.13% expressed one of the two serine-rich repeat surface proteins Srr1 or Srr2. In addition, most isolates harbored the pilus island (PI)-2a alone (15.73%) or in combination with PI-1 (62.92%), and those carrying PI-2b alone (10.11%) belonged to CC17. Phylogenetic analysis grouped the sequenced isolates according to CCs and further subdivided them along with their serotypes. Overall, isolates across all CC1 phylogenetic clusters expressed Srr1 and carried the PI-1 and PI-2a loci, but differed in genes encoding the alpha-like proteins. CC19 clusters were dominated by the III///PI-1+PI-2a (43.48%, 10/23) and V///PI-1+PI-2a (34.78%, 8/23) lineages, whereas most CC17 isolates (90%, 9/10) had the same III///P1-2b genetic background. Interestingly, genes encoding the CC17-specific adhesins HvgA and Srr2 were detected in phylogenetically distant isolates belonging to ST1212, suggesting that other highly virulent strains might be circulating within the species. Resistance to macrolides and/or lincosamides across all major CCs (n=48) was associated with the acquisition of (62.5%, 30/48), (27.1%, 13/48), (8.3%, 4/48), and (2.1%, 1/48) genes, whereas resistance to tetracycline was mainly mediated by presence of (64.18%, 43/67) and (20.9%, 14/67) alone or in combination (13.43%, 9/67).
DISCUSSION
These findings underscore the necessity for more rigorous characterization of GBS isolates causing infections.
Topics: Humans; Saudi Arabia; Streptococcus agalactiae; Streptococcal Infections; Virulence; Multilocus Sequence Typing; Drug Resistance, Bacterial; Genome, Bacterial; Genetic Variation; Serogroup; Virulence Factors; Polymorphism, Single Nucleotide; Anti-Bacterial Agents; Adult; Phylogeny; Whole Genome Sequencing; Genomics; Genotype; Microbial Sensitivity Tests; Female
PubMed: 38711928
DOI: 10.3389/fcimb.2024.1377993 -
Science Advances May 2024Tad (tight adherence) pili, part of the type IV pili family, are crucial for mechanosensing, surface adherence, bacteriophage (phage) adsorption, and cell-cycle...
Tad (tight adherence) pili, part of the type IV pili family, are crucial for mechanosensing, surface adherence, bacteriophage (phage) adsorption, and cell-cycle regulation. Unlike other type IV pilins, Tad pilins lack the typical globular β sheet domain responsible for pilus assembly and phage binding. The mechanisms of Tad pilus assembly and its interaction with phage ΦCb5 have been elusive. Using cryo-electron microscopy, we unveiled the Tad pilus assembly mechanism, featuring a unique network of hydrogen bonds at its core. We then identified the Tad pilus binding to the ΦCb5 maturation protein (Mat) through its β region. Notably, the amino terminus of ΦCb5 Mat is exposed outside the capsid and phage/pilus interface, enabling the attachment of fluorescent and affinity tags. These engineered ΦCb5 virions can be efficiently assembled and purified in , maintaining infectivity against , which presents promising applications, including RNA delivery and phage display.
Topics: Caulobacter crescentus; Fimbriae, Bacterial; Cryoelectron Microscopy; Bacteriophages; Fimbriae Proteins; Escherichia coli; Viral Proteins
PubMed: 38701202
DOI: 10.1126/sciadv.adl4450 -
Infection and Immunity Jun 2024Adherent and invasive (AIEC) is a pathobiont that is involved in the onset and exacerbation of Crohn's disease. Although the inducible expression of virulence traits is...
The CpxRA two-component system of adherent and invasive contributes to epithelial cell invasion and early-stage intestinal fitness in a dysbiotic mouse model mediated by type 1 fimbriae expression.
Adherent and invasive (AIEC) is a pathobiont that is involved in the onset and exacerbation of Crohn's disease. Although the inducible expression of virulence traits is a critical step for AIEC colonization in the host, the mechanism underlying AIEC colonization remains largely unclear. We here showed that the two-component signal transduction system CpxRA contributes to AIEC gut competitive colonization by activating type 1 fimbriae expression. CpxRA from AIEC strain LF82 functioned as a transcriptional regulator, as evidenced by our finding that an isogenic mutant exhibits reduced expression of , a known regulon gene. Transcription levels of in LF82 increased in response to envelope stress, such as exposure to antimicrobials compromising the bacterial membrane, whereas the mutant did not exhibit this response. Furthermore, we found that the mutant exhibits less invasiveness into host cells than LF82, primarily due to reduced expression of the type 1 fimbriae. Finally, we found that the mutant is impaired in gut competitive colonization in a mouse model. The colonization defects were reversed by the introduction of a plasmid encoding the gene or expressing the type 1 fimbriae. Our findings indicate that modulating CpxRA activity could be a promising approach to regulating AIEC-involved Crohn's disease.
Topics: Animals; Mice; Fimbriae, Bacterial; Escherichia coli; Gene Expression Regulation, Bacterial; Epithelial Cells; Escherichia coli Infections; Bacterial Adhesion; Disease Models, Animal; Escherichia coli Proteins; Humans; Bacterial Proteins; Virulence; Protein Kinases; Intestines; Female
PubMed: 38700334
DOI: 10.1128/iai.00132-24 -
NPJ Biofilms and Microbiomes May 2024Post-weaning diarrhoea (PWD) in piglets presents a widespread problem in industrial pig production and is often caused by enterotoxigenic E. coli (ETEC) strains. Current...
Post-weaning diarrhoea (PWD) in piglets presents a widespread problem in industrial pig production and is often caused by enterotoxigenic E. coli (ETEC) strains. Current solutions, such as antibiotics and medicinal zinc oxide, are unsustainable and are increasingly being prohibited, resulting in a dire need for novel solutions. Thus, in this study, we propose and evaluate a protein-based feed additive, comprising two bivalent heavy chain variable domain (VH) constructs (VH-(GGGGS)-VH, BL1.2 and BL2.2) as an alternative solution to manage PWD. We demonstrate in vitro that these constructs bind to ETEC toxins and fimbriae, whilst they do no affect bacterial growth rate. Furthermore, in a pig study, we show that oral administration of these constructs after ETEC challenge reduced ETEC proliferation when compared to challenged control piglets (1-2 log units difference in gene copies and bacterial count/g faeces across day 2-7) and resulted in week 1 enrichment of three bacterial families (Prevotellaceae (estimate: 1.12 ± 0.25, q = 0.0054), Lactobacillaceae (estimate: 2.86 ± 0.52, q = 0.0012), and Ruminococcaceae (estimate: 0.66 ± 0.18, q = 0.049)) within the gut microbiota that appeared later in challenged control piglets, thus pointing to an earlier transition towards a more mature gut microbiota. These data suggest that such VH constructs may find utility in industrial pig production as a feed additive for tackling ETEC and reducing the risk of PWD in piglet populations.
Topics: Animals; Enterotoxigenic Escherichia coli; Swine; Diarrhea; Gastrointestinal Microbiome; Escherichia coli Infections; Swine Diseases; Weaning; Animal Feed; Feces
PubMed: 38697985
DOI: 10.1038/s41522-024-00514-8