Biology subjects

Zingl, F. G.

Publications and source records attributed to Zingl, F. G..

8 recordsLinked to original sources

bioRxiv2026

Antibody-recruiting molecules based on mimotope fusion peptides and a dimeric antibiotic

New therapeutic approaches are needed to treat infections due to multidrug resistant (MDR) Gram-negative bacteria. The use of antibody-recruiting molecules (ARMs) is a promising approach to address the MDR problem given their potential to engage both the adaptive and innate immune systems to treat bacterial infections. Here we present two new strategies to create ARMs. First, we show that a 9-mer antimicrobial peptide (K6) can be fused to a 11-mer mimotope peptide recognized by antibodies targeting the Vibrio cholerae O1 O-antigen to produce an ARM peptide (FZ5) that can render E. coli more sensitive to complement killing in the presence of antibodies that recognize this mimotope. FZ5 can drive killing by complement in the presence of rabbit antibodies raised against O1 serogroup V. cholerae as well as antibodies present in human sera elicited by immunization with the live attenuated cholera vaccine PanChol. We also describe a strategy that combines bacterial surface binding with hapten display through the use of homodimers of the antibiotic streptomycin (Str) and anti-Str antibodies elicited by Str-protein conjugate vaccines. When combined with dimeric Str derivatives and human complement, polyclonal anti-streptomycin antisera kills E. coli by targeting the Str hapten. Dimeric forms of Str also significantly enhanced killing of a Str-resistant P. aeruginosa clinical isolate dependent on low levels of human complement and polyclonal anti-Str antibody. Together these data suggest that anti-bacterial ARM molecules based on mimotope display through simple synthetic fusion peptides, or dimeric haptens have promise as new approaches for the treatment of MDR bacterial infections.

microbiology↗

bioRxiv2026

AI-guided discovery of antimicrobial peptides for urinary tract infections leveraging a new catalogue of the human urinary microbiome

Urinary tract infections (UTIs) are common infections that pose a critical burden on healthcare and society. Despite growing recognition that the human urinary tract harbors its own microbiome, its composition, functional potential, and alterations in UTI remain limited. Here, we leveraged the publicly available whole-metagenome shotgun sequencing data from 450 urinary microbiome samples collected in four independent cohorts together with genome assembly and metagenomic binning to construct an extensive human urinary microbiome catalog consisting of [~]1.3 million non-redundant microbial genes and 705 non-redundant metagenome-assembled genomes (nrMAGs). We found that microbiomes from patients with UTI carry significantly more genes linked to antibiotic resistance and virulence vs controls. There was an enrichment of multiple Escherichia strains in patients with UTI from two independent case-control cohorts. UTIs are becoming multidrug-resistant, and we used machine learning models to identify potential antimicrobial peptides (AMPs) in 705 nrMAGs. Furthermore, we experimentally demonstrated that two of these AMPs exhibited strong inhibitory activity against uropathogenic Escherichia coli strains. Our study provides a valuable resource for studying the human urinary microbiome and suggests urinary microbiome-derived AMPs represent a source of new therapeutics for UTIs.

microbiology↗

bioRxiv2025

Vibrio cholerae serotype impacts pathogenicity

The O1 serogroup of Vibrio cholerae has caused all cholera pandemics and for over a century V. cholerae O1 outbreak strains have been characterized by their serotype. The two V. cholerae serotypes differ by the presence (Ogawa) or absence (Inaba) of methylation of the terminal sugar on the lipopolysaccharide O1-antigen. Serotype switching often occurs during epidemics and has historically been attributed to the pathogen adapting to immune pressures. Here we address the impact of serotype on V. cholerae pathogenicity using otherwise isogenic Ogawa and Inaba versions of several clinical V. cholerae O1 isolates. Our findings indicate that O1 antigen methylation in Ogawa strains promotes V. cholerae colonization, infectivity and resistance to antimicrobial peptides. We propose that methylation of the O1 antigen elevates colonization by shielding the bacterium from cationic antimicrobial peptides at the pH of the small intestine. These observations provide insights into the biological significance of the V. cholerae O1 serotypes.

microbiology↗

bioRxiv2025

Adapting CRISPR-associated transposons for rapid and high-throughput reverse genetics

CRISPR-associated transposons (CAST) use guide RNAs to direct their transposition and are being harnessed as tools for programmable genome engineering across diverse bacterial species. However, CAST systems have not been adapted for high-throughput genetic screening. Here, we present MultiCAST, a streamlined platform for rapid and scalable guide RNA-directed transposon insertion in bacteria. MultiCAST generates targeted insertions in a single step through conjugative delivery of conditionally replicative plasmids encoding the CAST enzymatic machinery and a selectable mini-transposon expressing the guide RNA. By leveraging the inserted guide sequence as a molecular barcode, MultiCAST enables pooled, high-throughput genetic screens using only amplicon sequencing. We identified factors that influence transposition efficiency and the accuracy of insertion frequency measurements derived from guide sequencing. Adjusting the ratio of donor and recipient strain during conjugation mitigates guide-transposon "crosstalk", in which a single recipient cell acquires multiple donor plasmids containing distinct guides. Furthermore, we developed a machine learning-based predictive model for selecting highly active guides based on target sequence features that strongly correlate with activity. The nucleoid-associated protein H-NS was also found to inhibit CAST activity, providing a mechanistic explanation for variable insertion frequencies among non-essential genes. To demonstrate the scalability of MultiCAST, we screened a pooled mutant population created from >5,200 guides targeting 88 genes in E. coli across twelve nutrient conditions, accurately identifying genes with condition-specific fitness effects. The simplicity, speed, and throughput of MultiCAST make genome-scale functional screens more accessible across a wide range of bacterial species. SignificanceEfficient gene disruption is essential for understanding bacterial gene function, but traditional genetic approaches are labor-intensive and generally not well-suited for high-throughput studies. We developed MultiCAST, a simple and scalable method that harnesses guide RNA-directed CRISPR-associated transposons for targeted bacterial gene disruption. MultiCAST enables single and pooled transposon mutagenesis in a single step and eliminates the need for complex sequencing library preparation protocols by using the guide sequence as a quantifiable surrogate for mutant abundance. This approach allows thousands of mutants to be generated and screened simultaneously across multiple conditions using only amplicon sequencing. By dramatically reducing the time, cost, and complexity of reverse genetics, MultiCAST opens new possibilities for genome-scale functional studies, accelerating the discovery of bacterial gene functions.

microbiology↗

bioRxiv2025

Anoxia activates CRISPR-Cas immunity in the intestine

The natural context in which CRISPR-Cas systems are active in Enterobacteriaceae has remained enigmatic. Here, we find that the Citrobacter rodentium Type I-E CRISPR-Cas system is activated by the oxygen-responsive transcriptional regulator Fnr in the anoxic mouse intestine. Since Fnr-dependent regulation is predicted in ~41% of Enterobacteriaceae cas3 orthologs, we propose that anoxic regulation of CRISPR-Cas immunity is an adaptation that protects Enterobacteriaceae against threats arising from the intestinal microbiome.

microbiology↗

bioRxiv2025

A connection between Vibrio cholerae motility and inter-animal transmission

Outbreaks of cholera are caused by the highly transmissive pathogen Vibrio cholerae. Here, a transposon screen revealed that inactivation of the V. cholerae motility-linked gene motV increases infant mouse intestinal colonization. Compared to wild-type V. cholerae, a {Delta}motV mutant, which exhibits heightened motility in the form of constitutive straight swimming, localizes to the crypts earlier in infection and over a larger area of the small intestine. Aberrant localization of the mutant was associated with an increased number of V. cholerae initiating infection, and elevated pathogen burden, diarrhea, and lethality. Moreover, the deletion of motV causes V. cholerae to transmit from infected suckling mice to naive littermates more efficiently. Even in the absence of cholera toxin, the {Delta}motV mutant continues to transmit between animals, although less than in the presence of toxin, indicating that phenotypes other than cholera toxin-driven diarrhea contribute to transmission. Collectively, this work provides experimental evidence linking intra-animal bottlenecks, colonization, and disease to inter-animal transmission.

microbiology↗

bioRxiv2024

The Mla pathway promotes Vibrio cholerae re-expansion from stationary phase

Bacteria have evolved diverse strategies to ensure survival under nutrient-limited conditions, where rapid energy generation is not achievable. Here, we performed a transposon insertion site sequencing loss-of-function screen to identify Vibrio cholerae genes that promote the pathogens fitness in stationary phase. We discovered that the Mla (maintenance of lipid asymmetry) pathway, which is crucial for transferring phospholipids from the outer to the inner membrane, is critical for stationary phase fitness. Competition experiments with barcoded and fluorophore labeled wild-type and mlaE mutant V. cholerae revealed that the Mla pathway promotes re-expansion from 48h stationary phase cultures. The mutants defect in transitioning out of stationary phase into active growth (culturability) was also observed in monocultures at 48h. However, by 96h the culturability of the mutant and wild-type strains were equivalent. By monitoring the abundances of genomically barcoded libraries of wild-type and {Delta}mlaE strains, we observed that a few barcodes dominated the mutant culture at 96h, suggesting that the similarity of the population sizes at this time was caused by expansion of a subpopulation containing a mutation that suppressed the mlaE mutants defect. Whole genome sequencing revealed that mlaE suppressors inactivated flagellar biosynthesis. Additional mechanistic studies support the idea that the Mla pathway is critical for the maintenance of V. choleraes culturability as it promotes energy homeostasis, likely due to its role in regulating outer membrane vesicle shedding. Together our findings provide insights into the cellular processes that control re-expansion from stationary phase and demonstrate a previously undiscovered role for the Mla pathway. ImportanceBacteria regularly encounter conditions with nutrient scarcity, where cell growth and division are minimal. Knowledge of the pathways that enable re-growth following nutrient restriction are limited. Here, using the cholera pathogen, we uncovered a role for the Mla pathway, a system that enables phospholipid re-cycling, in promoting Vibrio cholerae re-expansion from stationary phase cultures. Cells labeled with DNA barcodes or fluorophores were useful to demonstrate that though the abundances of wild-type and Mla mutant cells were similar in stationary phase cultures, they had marked differences in their capacities to regrow on plates. Of note, Mla mutant cells lose cell envelope components including high energy phospholipids due to OMV shedding. Our findings suggest that the defects in cellular energy homeostasis which emerge in the absence of the Mla pathway underlie its importance in maintaining V. cholerae culturability.

microbiology↗

bioRxiv2022

Reemergence of cholera in Haiti

Cholera was absent from Haiti until an inadvertent introduction by United Nations security forces in October 2010. The ensuing epidemic sickened 820,000 and caused 9,792 reported deaths1. The last cholera case in Haiti was recorded in January 2019, and in February 2022, Haiti was declared to have eliminated cholera2. In late September of 2022, a new outbreak began in Port-au-Prince and rapidly expanded to 964 suspected cases by mid-October of which 115 were confirmed by culture.3 Here, we present genomic and phenotypic analysis of the Vibrio cholerae isolated from a stool sample collected on September 30th, 2022 of an index case - a 10-year-old girl who presented with watery diarrhea and severe dehydration - to address the origins of the epidemic.

microbiology↗