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PubMed2025

Identification of OxyR as an activator of type 1 fimbriae (fim) in Salmonella enterica serovar Typhi.

Salmonella enterica serovar Typhi (S. Typhi) encodes 14 fimbrial gene clusters, including the mannose-binding type 1 fimbriae known as Fim. Type 1 fimbriae have been implicated in biofilm formation and adhesion to host cells in Salmonella. However, their regulation in S. Typhi remains largely unknown. To identify genes affecting the regulation of fim in S. Typhi, we employed both a targeted and a genome-wide transposon-based screening approach. Overall, we identified 18 potential regulators of fim expression: 10 activators and 8 repressors. Two genes involved in the electron transport chain, yqiC and ndh, which encode the type II NADH dehydrogenase NDH-2, were identified. Both YqiC and NDH-2 contribute to the production of reactive oxygen species, prompting an investigation into the roles of oxidative stress response regulators OxyR and SoxR. We found that only OxyR regulates fim expression, which was specific to S. Typhi. OxyR acts by directly binding to the fimA promoter region. This study paves the way for future development of anti-adhesion strategies through the identification of 14 novel regulators for the most prominent fimbriae of S. Typhi.IMPORTANCEAdhesion mediated by fimbriae is one of the critical steps in the infection process. Therefore, it is essential to better understand the regulation of type 1 fimbriae (fim) in the human-specific pathogen Salmonella enterica serovar Typhi, the etiologic agent of typhoid fever. In this study, we identified 18 distinct mutants with altered regulation of fim. Furthermore, we confirmed that the DNA-binding protein OxyR directly regulates fim expression. Importantly, we also demonstrated regulatory differences in fim expression between S. Typhi and S. Typhimurium, as six of the genes identified altering fim expression in S. Typhi either did not affect fim expression in S. Typhimurium or had the contrary effect. This highlights fundamental differences between these serovars and emphasizes the need to investigate and compare aspects of gene regulation in S. Typhi.

Salmonella typhi↗

PubMed2026

Parallel evolutionary trajectories rewire enteropathogenic Escherichia coli adhesion to restore host attachment.

Enteropathogenic Escherichia coli (EPEC) causes disease in children, presenting as chronic diarrhea that can impair physical and cognitive development. The attachment of typical EPEC (tEPEC) to the gut epithelium via bundle-forming pili (BFP) is a key factor in its virulence. Yet, infections by atypical EPEC (aEPEC), which lack BFP, have become increasingly common. To investigate how aEPEC recover host-attachment in the absence of BFP, we performed experimental evolution using a non-adherent E. coli, constructed to mimic the ancestor of aEPEC, and selected adherent progeny. Highly adherent variants evolved through phase-variable activation of type I fimbriae (T1F), followed by two alternative trajectories: bacterial filamentation, which increases T1F avidity, or point mutations in the T1F adhesin FimH that enhance ligand affinity. Extending our analysis to the genomes of 327 aEPEC strains isolated from infected patients revealed that similar FimH mutations are common. We further demonstrated experimentally that these naturally occurring variants often increase epithelial-attachment. Our findings implicate T1F in aEPEC pathogenesis and suggest it may be clinically relevant for anti-adhesion therapy. More broadly, these results indicate that impaired host-attachment can be rapidly compensated by upregulating and optimizing an alternative adhesin, and that combining experimental evolution with comparative genomics can reveal evolutionary trajectories occurring in nature.

Bacterial Adhesion↗

PubMed2025

Mutant p53 disrupts antioxidant defense in fallopian tube epithelium via GSTAs suppression: A pathway to serous tubal carcinogenesis.

High grade serous ovarian cancer (HGSOC) is the most common and aggressive type of epithelial ovarian cancer. The fimbria of the fallopian tube is the likely site of origin based on the presence of distinct precancerous lesions with TP53 signatures known clinically as serous tubal intraepithelial carcinoma (STICs) detected in this region in individuals at genetically high risk or with HGSOC. Previously we identified that matched fallopian tube epithelia (FTE) from fimbria and ampulla of normal fallopian tubes from premenopausal women exhibit differential expression of genes associated with antioxidant and inflammatory pathways. One gene, glutathione S-transferase 2 (GSTA2), showed both higher expression in the fimbria and in the follicular phase (pre-ovulation) compared to the ampulla, suggesting that GSTA2 expression may regulate reactive oxygen homeostasis in these cells in response to ovulation-related stress. Here, to understand how preneoplastic genomic alterations influence regulation of oxidative stress, FTE cells were isolated from healthy tissue and introduced with p53 mutations, from which expression and function of GSTA2 and other antioxidant enzymes were investigated. Mutant p53 downregulated the expression of GSTA2 and subsequently increased DNA damage. The combination of p53 mutation and dysregulated oxidative response likely promotes the genomic instability that initially drives the transformation to high grade serous ovarian carcinoma.

Female↗

PubMed2025

Type IV Pili-Associated Secretion of a Biofilm Matrix Protein From Clostridium perfringens That Forms Intermolecular Isopeptide Bonds.

Clostridium perfringens is a gram-positive, anaerobic, spore-forming bacterial pathogen of humans and animals. C. perfringens also produces type IV pili (T4P) and has two complete sets of T4P-associated genes, one of which has been shown to produce surface pili needed for cell adherence. One hypothesis about the second set of T4P genes is that they comprise a type II secretion system (TTSS) like those found in gram-negative bacteria, but for gram-positive bacteria, the TTSS would aid transit across the thick peptidoglycan (PG) layer. The secretome of mutants lacking type IV pilins was examined, and a single protein, BsaC (CPE0517), was identified as being dependent on pilin PilA3 for secretion. The bsaC gene is in an operon with genes encoding a SipW signal peptidase and two putative biofilm matrix proteins, BsaA and BsaB, both of which have remote homology to Bacillus subtilis biofilm protein TasA. Since BsaA forms long oligomers that are secreted, we analyzed BsaA monomer interactions with de novo modeling. These models projected that the monomers formed isopeptide bonds as part of a donor strand exchange process. Mutations in residues predicted to form the isopeptide bonds led to the loss of oligomerization, supporting an exchange and lock mechanism, and isopeptide bonds were detected by mass spectrometry methods. Phylogenetic analysis showed the BsaA family of proteins is widespread among bacteria and archaea, but only a subset is predicted to form isopeptide bonds.

Fimbriae, Bacterial↗

PubMed2026

A posttranslational modification of fimbriae drives pathogenicity in Klebsiella pneumoniae.

Antimicrobial resistance is a severe public health burden. Especially concerning are multidrug resistant (MDR) infections, which restrict treatment options and significantly increase mortality risk. A major cause of MDR infections worldwide is carbapenem-resistant Klebsiella pneumoniae (CRKp). The predominant CRKp sequence type worldwide is ST258. However, the factors underlying ST258's epidemic success are not well defined. Genomic analyses of clinical isolates of CRKp have found that the two-component regulatory system CrrAB is a genomic feature of ST258, suggesting that it may contribute to its global dominance. Despite this, the molecular details underpinning CrrAB's contribution to ST258 Kp biology and pathogenicity are poorly understood. We used RNA-sequencing to identify the regulon of CrrA and found that CrrAB induces the expression of a gene, encoding Crr-regulated fimbriae modifying protein (CfmP), that is essential for pathogenesis driven by this two-component system. We performed mass spectrometry analyses of fimbriae purified from Kp expressing or lacking cfmP and found that CfmP induces a novel oxidation to a histidine residue in the major pilin subunit of fimbriae, FimA. We demonstrate that this oxidation significantly increases host cell adhesion and high bacterial loads within the host. CrrAB also drives high antibiotic resistance in CRKp. Thus, our results place CrrAB at the intersection of pathogenicity and antibiotic resistance supporting its function as an important regulatory system driving the global dominance of ST258.

Klebsiella pneumoniae↗

PubMed2026

Mutations in filamentous bacteriophages spark eco-evolutionary feedbacks in Pseudomonas aeruginosa.

Microbial populations strongly shape their environment, which can re-route adaptation toward organism-generated fitness optima. However, the conditions that promote these eco-evolutionary feedbacks are unclear. Here, we used experimental evolution to test whether high population density, by strengthening niche construction, drives eco-evolutionary feedbacks in the bacterial pathogen Pseudomonas aeruginosa (Pa) MPAO1. We tested for adaptation to organism-modified environments by measuring the relative performance of ancestral and endpoint populations in filtrate generated by each evolutionary line sampled across generations. Contrary to expectations, we found that endpoint populations had higher performance than the ancestral strain in filtrate across nearly all evolutionary lines regardless of population density. This was caused by the emergence of hyperactive filamentous bacterio(phage) mutants during experimental passaging that inhibited the ancestral strain but not endpoint populations in modified media. Hyperactive phages emerged from one of two avirulent prophages in MPAO1's genome (Pf4 or Pf6). Hyperactive phages drove the evolution of phage resistance in bacterial populations via mutations in the type IV pilus (TIVP), the phage's binding receptor. In a follow-up experiment, we showed that these TIVP mutations pleiotropically reduced motility and conferred resistance to a TIVP-targeting virulent phage, both of which are important traits for Pa infection and treatment. Overall, this work suggests that filamentous phage evolution can drive eco-evolutionary feedbacks in bacterial populations, causing phenotypic and genetic changes that would not be anticipated from adaptation to the extrinsic environment alone.

Pseudomonas aeruginosa↗

PubMed2026

The agroenvironmental-clinical link of Proteus mirabilis: Genomic epidemiology, clonal relationships, and shared resistance and virulence profiles.

Proteus mirabilis is an opportunistic pathogen frequently associated with urinary tract infections (UTIs), with its pathogenicity driven by coordinated virulence traits such as adhesion, biofilm formation, and toxin production. The systemic emergence of antimicrobial resistance (AMR) within this species raises critical concerns regarding its persistence across clinical and environmental niches. This study investigated the virulence profiles, AMR determinants, and molecular epidemiology of P. mirabilis isolates recovered from retail vegetables and human community-acquired UTIs (CA-UTIs) in southern Brazil. A total of 310 isolates were analyzed (110 from vegetables and 200 from UTIs). Multidrug resistance was observed in 36.6-42.0% of vegetable isolates and 16.0% of UTI isolates, while extended-spectrum β-lactamase (ESBL) production reached 32.0% in the vegetable group. Notably, the carbapenemase gene blaKPC-2 was identified in vegetable isolates, representing a critical food safety concern. High-consequence resistance genes, including blaCTX-M variants, fosA3, and qnrD, were widely distributed. Furthermore, all isolates harbored multi-element virulence profiles-particularly genes encoding fimbriae, proteases, and iron acquisition systems-and exhibited strong or very strong biofilm-forming phenotypes. Clonal analysis revealed tight genetic relatedness between vegetable and clinical isolates, including indistinguishable profiles. Whole-genome sequencing identified shared sequence types (STs), most notably the high-risk clone ST773, alongside internationally reported lineages such as ST135 and ST336. Moreover, conserved mobile genetic environments flanking blaKPC-2 were structurally characterized. These findings demonstrate that food-associated P. mirabilis serves as an active agroenvironmental reservoir for virulent and multidrug-resistant lineages, posing an unmonitored risk for zoonotic dissemination and human infection within the One Health framework.

bla KPC−2↗

PubMed2025

Laboratory Evolution Reveals Transcriptional Mechanisms Underlying Thermal Adaptation of Escherichia coli.

Adaptive laboratory evolution is able to generate microbial strains, which exhibit extreme phenotypes, revealing fundamental biological adaptation mechanisms. Here, we use adaptive laboratory evolution to evolve Escherichia coli strains that grow at temperatures as high as 45.3 °C, a temperature lethal to wild-type cells. The strains adopted a hypermutator phenotype and employed multiple systems-level adaptations that made global analysis of the DNA mutations difficult. Given the challenge at the genomic level, we were motivated to uncover high-temperature tolerance adaptation mechanisms at the transcriptomic level. We employed independently modulated gene set (iModulon) analysis to reveal five transcriptional mechanisms underlying growth at high temperatures. These mechanisms were connected to acquired mutations, changes in transcriptome composition, sensory inputs, phenotypes, and protein structures. They are as follows: (i) downregulation of general stress responses while upregulating the specific heat stress responses, (ii) upregulation of flagellar basal bodies without upregulating motility and upregulation fimbriae, (iii) shift toward anaerobic metabolism, (iv) shift in regulation of iron uptake away from siderophore production, and (v) upregulation of yjfIJKL, a novel heat tolerance operon whose structures we predicted with AlphaFold. iModulons associated with these five mechanisms explain nearly half of all variance in the gene expression in the adapted strains. These thermotolerance strategies reveal that optimal coordination of known stress responses and metabolism can be achieved with a small number of regulatory mutations and may suggest a new role for large protein export systems. Adaptive laboratory evolution with transcriptomic characterization is a productive approach for elucidating and interpreting adaptation to otherwise lethal stresses.

Escherichia coli↗

PubMed2019

Large-scale genome analysis of bovine commensal Escherichia coli reveals that bovine-adapted E. coli lineages are serving as evolutionary sources of the emergence of human intestinal pathogenic strains.

How pathogens evolve their virulence to humans in nature is a scientific issue of great medical and biological importance. Shiga toxin (Stx)-producing Escherichia coli (STEC) and enteropathogenic E. coli (EPEC) are the major foodborne pathogens that can cause hemolytic uremic syndrome and infantile diarrhea, respectively. The locus of enterocyte effacement (LEE)-encoded type 3 secretion system (T3SS) is the major virulence determinant of EPEC and is also possessed by major STEC lineages. Cattle are thought to be the primary reservoir of STEC and EPEC. However, genome sequences of bovine commensal E. coli are limited, and the emerging process of STEC and EPEC is largely unknown. Here, we performed a large-scale genomic comparison of bovine commensal E. coli with human commensal and clinical strains, including EPEC and STEC, at a global level. The analyses identified two distinct lineages, in which bovine and human commensal strains are enriched, respectively, and revealed that STEC and EPEC strains have emerged in multiple sublineages of the bovine-associated lineage. In addition to the bovine-associated lineage-specific genes, including fimbriae, capsule, and nutrition utilization genes, specific virulence gene communities have been accumulated in stx- and LEE-positive strains, respectively, with notable overlaps of community members. Functional associations of these genes probably confer benefits to these E. coli strains in inhabiting and/or adapting to the bovine intestinal environment and drive their evolution to highly virulent human pathogens under the bovine-adapted genetic background. Our data highlight the importance of large-scale genome sequencing of animal strains in the studies of zoonotic pathogens.

Animals↗

PubMed2026

Intra-strain genomic microevolution and phage resistance in Pseudomonas aeruginosa PAO1 laboratory isolates.

Pseudomonas aeruginosa is a major opportunistic pathogen, and its laboratory reference strain, PAO1, is widely used in microbiological and genetic studies. However, PAO1 often exhibits phenotypic variability that can affect experimental reproducibility. Our PAO1 stock, obtained from a public biobank, is resistant to PP7, a pilus-dependent single-stranded RNA phage known to infect PAO1. This suggests the presence of genetic variants in the stock. To check this possibility, we isolated six phenotypically distinct variants (GU1-GU6) and performed genomic and phenotypic analyses. Notable differences were observed among the isolates in terms of motility, pyocyanin production, and susceptibility to PP7. Whole-genome sequencing revealed that four of the six variants harbored mutations in pilus-associated genes. Among these, GU3 carried a mutation in pilT, which encodes a motor protein essential for type IV pilus retraction, and the loss of retraction led to the PP7 resistance. GU2, GU4, and GU6 shared a nonsense mutation in pilJ, a gene involved in chemotaxis and pilus extension, resulting in reduced twitching motility and lower PP7 infection efficiency. Additionally, we found that a mutation in lasR, a master regulator of quorum sensing, promoted the replication of prophage Pf6, which was integrated into the PAO1 genome. Pf6 replication interferes with PP7 infection, providing an alternative mechanism of resistance. These findings offer new insights into the complexity of phage-host interactions and emphasize the importance of routine verification and careful handling of P. aeruginosa sublines used in bacteriological and phage research.IMPORTANCEPhenotypic and genotypic variability in Pseudomonas aeruginosa PAO1 has been widely reported, raising concerns regarding the reproducibility of laboratory studies that rely on this reference strain. In this study, we isolated six PAO1 variants from a single laboratory stock and demonstrated that they differed markedly in motility, pyocyanin production, and susceptibility to the ssRNA phage PP7. Whole-genome sequencing has revealed that even a single mutation in a pilus-associated gene can profoundly affect bacterial motility and phage susceptibility. Furthermore, we showed that a mutation in lasR, a key regulator of the quorum-sensing system, triggered replication of the Pf6 prophage, which in turn hindered PP7 infection. These findings underscore the dynamic nature of laboratory strains and highlight the need for caution when interpreting results from phage-host interaction studies using reference strains. Our results provide a new understanding of how subtle genetic changes in model strains influence experimental outcomes in microbiology.

Pseudomonas aeruginosa↗