Biology subjects

Chong, C. E.

Publications and source records attributed to Chong, C. E..

6 recordsLinked to original sources

bioRxiv2026

Dual ATPase-activated DNA hemimethylation and cleavage by the MANTIS defence system

Bacterial defence systems are diverse and form major barriers to horizontal gene transfer and bacteriophage (phage) infection. Though restriction-modification systems were the first such defences discovered and remain the most widespread, the basis of self/non-self discrimination in many newly identified methylation-based systems remains unclear. Here, we define the mechanism of a widely distributed BREX-related defence family, previously termed Gao_RL, which we rename MANTIS (Methyltransferase, ATPases and Nuclease Targeting Inverted-repeat Sequences). Using phage infection and plasmid transformation assays in Pseudomonas aeruginosa, biochemical reconstitution, and structural biology, we show that MANTIS establishes self-identity through adenine hemimethylation of short asymmetric DNA sequences. Unexpectedly, a AAA+ ATPase (MtsA) and a co-regulator (MtsB) are both required to recruit and activate the methyltransferase MtsC, revealing a previously unknown ATP-dependent mode of epigenetic modification. DNA recognition by the MtsABC complex then triggers restriction by a dimeric helicase-nuclease effector (MtsD), with activity dependent on target-site architecture: inverted pairs of unmodified sites support robust restriction, whereas direct repeats or single sites are restricted less efficiently. Consistent with this model, virulent phages show strand-biased depletion of MANTIS target sites, indicating evolutionary pressure to evade restriction. Together, these findings reveal how dual ATPases couple self-modification to non-self restriction and provide a framework for understanding the expanding landscape of methylation-based defence systems.

molecular biology↗

bioRxiv2026

SigA forms amyloid fibrils and supports the competition of Shigella with the microbiota

Shigella sonnei is an enteropathogen that causes bacillary dysentery. During the first step of its virulence cycle, it must outcompete the resident microbiota to establish its own niche. Here we report that SigA, the sole SPATE (Serine Protease Autotransporter of Enterobacteriaceae) family member in S. sonnei, plays an indirect but central role in this process. A genome-wide analysis showed that the SPATE family includes SigA, Pic, SepA, and Sat. We demonstrated that SigA self-assembles into amyloid fibrils (F-SigA) independently of its protease activity. F-SigA remains associated with the S. sonnei surface in vitro and in vivo. Purified F-SigA fibrils have a diameter of 17.7 {+/-} 3.2 nm, and their amyloid organization was confirmed using specific markers and biochemical methods. F-SigA is secreted into the lumen in vivo and localizes to the surface of the colonic epithelium. We found that colicin E1 (ColE1) interacts with F-SigA amyloid fibrils, and that F-SigA-ColE1 complexes display antimicrobial activity that promotes S. sonnei competition with other bacteria. Because Pic, another Shigella SPATE, also forms amyloid fibrils, we anticipate that this virulence mechanism may be relevant across a wide range of Shigella strains and enterobacteria and may serve additional roles during the Shigella virulence cycle.

microbiology↗

bioRxiv2026

Flex-It: A global standardised genotyping framework for Shigella flexneri

Shigella flexneri is the leading causative agent of shigellosis globally. The public health threat posed by S. flexneri is compounded by its emergence as a sexually transmissible infection, importance of international travel in driving dissemination, and the increasing prevalence of antimicrobial resistance (AMR). A rapid and robust computational method is needed to enhance genomic surveillance and systematically explore features of the population structure of this WHO priority pathogen, which is scalable and readily implementable across jurisdictions, particularly as vaccine development efforts are underway. Here, we present Flex-It, a genomic framework and genotyping scheme implemented in Mykrobe for S. flexneri serotypes 1-5, X & Y, compatible with previous approaches used to describe S. flexneris population structure. To develop Flex-It, we curated a retrospective dataset of 5,819 publicly available S. flexneri genomes. We characterised the global population structure for S. flexneri, exploring geographical and temporal traits, and showed the granular diversity of AMR and serotype profiles. We applied Flex-It to >13,000 genomes routinely generated by public health laboratories from Australia, the UK and the USA across a ten-year period. We found significant genotype diversity in all three locations, with the emergence of genotypes with converged resistance to all major drugs currently used for treatment. Flex-It provides an open-source, novel genotyping method that rapidly characterises S. flexneri and its ciprofloxacin resistance determinants in <1 minute from both short and long whole-genome sequencing reads. Flex-It provides the community with a standardised nomenclature to monitor the emergence and spread of S. flexneri lineages.

microbiology↗

bioRxiv2025

Defence systems drive accessory genome interactions in Pseudomonas aeruginosa.

Bacterial genomes represent dynamic ecological systems in which mutational selection and dynamic accessory genome element complements drive evolution. Emerging evidence suggests that bacterial defence systems, which protect against phages and other mobile genetic elements, interact through cooperative, competitive, and antagonistic relationships. These interactions can influence horizontal gene transfer, shape phage susceptibility, and the diversification of genome composition across environments. Recent ecological studies describe non-random co-occurrence and avoidance of defence systems, suggesting that they may emerge from ecological and evolutionary interactions, rather than by chance. This necessitates exploring whether these patterns reflect functional compatibility, shared selection pressures imposed by ecological niche, or if they merely arise from co-localisations of convenience. Understanding these patterns is key to elucidating how the accessory genome evolves and how defence systems constrain or facilitate genome plasticity. To investigate these patterns, in their genomic context, and provide a resource for future investigations, we analysed the distributions of defence systems and other accessory genome elements in a recently curated global dataset of 2,940 Pseudomonas aeruginosa genomes. Genomic defence system content varied by ecological niche, with higher numbers per genome in non-cystic fibrosis derived isolates (average n=7.9) compared to cystic fibrosis-derived isolates (average n=6.5). We identified multiple associations (n=426) and dissociations (n=50) among defence systems, and among other accessory genome elements, many of which had a plausible biological explanation. We also quantitated the relative interactions among accessory genome elements which revealed that defence systems and anti-defence systems engage in the most accessory genome interactions, compared with e.g. antimicrobial resistance genes, plasmids, phages, suggesting that systems are a major driving force in the ecological dynamics of the bacterial accessory genome. Together, these patterns provide new insights into the evolutionary forces shaping bacterial genomes, provide a valuable resource of quantitated interactions in a highly curated Pseudomonas aeruginosa dataset, and establish a framework for future mechanistic and ecological investigations of defence system interactions.

microbiology↗

bioRxiv2022

Shigella serotypes associated with carriage in humans establish persistent infection in zebrafish

Shigella represents a paraphyletic group of human-adapted Escherichia coli lineages that converged towards the same enteropathogenic pathovar. In low-income countries, Shigella is typically transmitted by ingestion of contaminated water and food, while in high-income countries sexual transmission among men who have sex with men (MSM) is the dominant route of transmission. Although more than 40 different serotypes of Shigella have been reported globally, within the MSM community the majority of reported cases are attributed to three Shigella serotypes: the Shigella sonnei unique serotype (Ss) and the Shigella flexneri serotypes 2a and 3a. Here, using a zebrafish infection model, we demonstrate that Shigella can establish persistent infection in vivo. In this case, bacteria are not cleared by the host immune system and become tolerant to therapeutic doses of antibiotics. We show that persistence is dependent on the Shigella O-Antigen, a key constituent of the bacterial cell surface and determinant of serotype classification. Representative isolates of three Shigella serotypes associated with global dissemination and MSM transmission (S. sonnei Ss, S. flexneri 2a and 3a) all persist in zebrafish, while a serotype not associated with MSM transmission (S. flexneri 5a) does not. Strikingly, Shigella serotypes which establish persistent infection fail to promote macrophage cell death in vivo. We conclude that zebrafish can be a valuable platform to illuminate host and pathogen factors underlying the establishment of persistent infection with Shigella in humans. HighlightsO_LIShigella can establish persistent infection in zebrafish C_LIO_LIEstablishment of persistent infection in vivo depends on Shigella serotype C_LIO_LIThe same serotypes establishing persistent infection in zebrafish are prevalent in a patient group in whom persistent infection is observed C_LIO_LIShigella serotypes which establish persistent infection fail to promote macrophage cell death in vivo C_LI In BriefIn high-income countries, sexual transmission among men who have sex with men (MSM) is the dominant cause of domestic Shigella transmission. Torraca et al. discover that three serotypes of Shigella associated with MSM transmission also persist in zebrafish. These results indicate that Shigella serotypes associated with MSM transmission can establish carriage in the host, and highlight the use of zebrafish infection to study Shigella persistent infection in humans.

microbiology↗

bioRxiv2022

Comparative genomics of Staphylococcus capitis reveals determinants of speciation

Staphylococcus capitis is primarily described as a human skin commensal but is now emergent as an opportunistic pathogen isolated from bloodstream and prosthetic joint infections, and neonatal intensive care unit (NICU) associated sepsis. We used comparative genomic analyses of S. capitis to provide new insights of commensal scalp isolates from varying skin states, and to expand our current knowledge of the species populations (scalp isolates, n = 59, contextual isolates, n = 127). A highly recombinogenic population structure was revealed, with genomes including the presence of a range of previously described staphylococcal virulence factors, cell wall-associated proteins, and two-component systems. Genomic differences between the two described S. capitis subspecies were explored and reveal determinants associated exclusively with each. The subspecies ureolyticus was distinguished from subspecies capitis by differences in antimicrobial resistance genes and gene clusters linked to survival on the skin. This study will aid further research into classification of S. capitis and virulence linked phylogroups that is important to monitor the spread and evolution of S. capitis.

microbiology↗