Biology subjects

Viveen, M. C.

Publications and source records attributed to Viveen, M. C..

6 recordsLinked to original sources

bioRxiv2026

RSM01, an extended half-life RSV monoclonal antibody with a high barrier to resistance

Respiratory syncytial virus (RSV) causes substantial infant morbidity and mortality, particularly in low- and middle-income countries (LMICs). RSM01 is a long-acting RSV monoclonal antibody (mAb) in development for LMICs. To date, RSM01 resistant mutants have not been able to be generated in vitro. We systematically assessed the in vitro resistance barrier of RSM01 relative to licensed RSV mAbs and the susceptibility of a panel of global contemporary strains to RSM01. The emergence of mAb-resistant mutant (MARM) was assessed for RSM01, nirsevimab, and palivizumab. Triple plaque-purified RSV-A2 and RSV-B1 were serially passaged under mAb pressure to generate MARMs, which were phenotyped and genotyped. Moderate resistance was defined as > 3-fold and high resistance > 30-fold increase in IC50 compared with parental strains. The susceptibility of contemporary clinical strains from South Africa, Argentina, and the Netherlands to RSM01 was tested in a neutralisation assay. RSV-A and B lab strains developed high resistance to palivizumab and nirsevimab, while RSM01 pressure induced moderate resistance. No MARMs demonstrated a fitness advantage; one RSM01 MARM incurred fitness costs. RSM01 potently neutralized global contemporary RSV-A and B strains. In conclusion, in vitro RSM01 resistance was infrequent and moderate, suggesting a high resistance barrier in vitro. Laboratory-selected MARMs may not directly predict clinical escape, but the confirmation of the high barrier to resistance of RSM01 is encouraging and provides an alternative in the event that resistance is observed with widespread use of current licensed anti-RSV mAbs. One Sentence SummaryIn vitro RSV resistance to RSM01 is infrequent and moderate, suggesting a high barrier to resistance.

microbiology↗

bioRxiv2025

Limited value of Nanopore adaptive sampling in a long-read metagenomic profiling workflow of clinical sputum samples

Oxford Nanopore adaptive sampling (NAS) is a method by which the long-read sequencing flowcell accepts or rejects DNA molecules that are actively being sequenced based on their initial [~]500bp sequences, selectively increasing target data output. NAS promises up to 5-10x enrichment of target sequencing yield without additional sample preparation, but this optimal performance is dependent on ideal sample parameters which may be difficult to achieve under many real-world use-cases. We evaluated the use of NAS with the current R10.4.1 flowcell chemistry for profiling clinical sputum metagenomes, achieving at best 3.1x enrichment of bacterial sequence output due to the shorter read lengths ([~]2.5kb) from the PCR amplification necessary to compensate for low DNA extraction yields. More critically, we encountered rapid pore loss during our runs that reduced total sequencing yield by an estimated 80%. We were unable to mitigate the pore loss despite extensive attempts to reduce contaminant carry-over, and we could not determine its cause but ruled out NAS and pore underloading as contributing factors. We conclude that the utility of NAS is often limited by the characteristics of the metagenomic sample studied, and that the factors contributing to pore loss need to be resolved before ONT sequencing can be reliably applied to long-read metagenomics.

microbiology↗

bioRxiv2024

Activity-Based Protein Profiling Identifies Klebsiella pneumoniae Serine Hydrolases with Potential Roles in Host-Pathogen Interactions

Klebsiella pneumoniae is a normal resident of the human gastro-intestinal tract and an opportunistic, critical priority pathogen that can cause a variety of severe systemic infections. Due to emerging multi-drug resistance of this pathogen, the discovery and validation of novel targets for the development of new treatment options is an urgent priority. Here, we explored the family of serine hydrolases, a highly druggable and functionally diverse enzyme family which is uncharacterized in K. pneumoniae. Using functionalized covalent fluorophosphonate inhibitors as activity-based probes we identified 10 serine hydrolases by mass spectrometry-based activity-based protein profiling, 7 of which were previously uncharacterized. Functional validation using transposon mutants deficient in either of the putative lysophospholipase PldB, esterase YjfP and patatin-like phospholipase YchK revealed severe growth defects in human colonic organoid co-culture models and reduced virulence during Galleria mellonella infection. Mutants deficient in the PldB and YjfP, but not YchK show increased susceptibility to killing by complement and the antimicrobial peptide antibiotic polymyxin B, suggesting a role in maintaining cell envelope integrity. Biochemical characterization and structural analysis of recombinant YjfP suggest this protein is a deacetylase. This study gives important insights into the molecular mechanisms underlying virulence and cell physiology of K. pneumoniae at the host-pathogen interface and it positions PldB, YjfP and YchK as potential antimicrobial or anti-virulence target candidates, inhibition of which might synergize with existing antibiotics and human immune defenses.

microbiology↗

bioRxiv2021

Human monoclonal antibodies against Staphylococcus aureus surface antigens recognize in vitro biofilm and in vivo implant infections

Implant-associated Staphylococcus aureus infections are difficult to treat because of biofilm formation. Bacteria in a biofilm are often insensitive to antibiotics and host immunity. Monoclonal antibodies (mAbs) could provide an alternative approach to improve the diagnosis and/or treatment of biofilm-related infections. Here we show that mAbs targeting common surface components of S. aureus can recognize clinically relevant biofilm types. We identify two groups of antibodies: one group that uniquely binds S. aureus in biofilm state and one that recognizes S. aureus in both biofilm and planktonic state. In a mouse model, we show that mAb 4497 (recognizing wall teichoic acid (WTA)) specifically localizes to biofilm-infected implants. In conclusion, we demonstrate the capacity of several human mAbs to detect S. aureus biofilms in vitro and in vivo. This is an important first step to develop mAbs for imaging or treating S. aureus biofilms.

microbiology↗

bioRxiv2018

Bariatric surgery changes gut microbiota composition independent of operation type

BackgroundBariatric surgery in patients with morbid obesity, either through gastric sleeve gastrectomy or Roux-Y gastric bypass surgery, leads to sustainable weight loss, improvement of metabolic disorders and changes in the intestinal microbiota. Yet, the relationship between changes in gut microbiota, weight loss and the surgical procedure remains incompletely understood.\n\nSubjects/MethodsWe determined temporal changes in microbiota composition in 45 obese patients undergoing a crash diet followed by gastric sleeve gastrectomy (n= 22) or Roux-Y gastric bypass (n= 23). Intestinal microbiota composition was determined before intervention (baseline, S1), 2 weeks after a crash diet (S2), and 1 week (S3), 3 months (S4) and 6 months (S5) after surgery.\n\nResultsRelative to S1, the microbial diversity index declined at S2 and S3 (p< 0.05), and gradually returned to baseline levels at S5. The crash diet was associated with an increased abundance of Rikenellaceae and decreased abundances of Ruminococcaceae and Streptococcaceae (p< 0.05). After surgery, at S3, the relative abundance of Bifidobacteriaceae had decreased (compared to the moment directly after the crash diet), whereas those of Streptococcaceae and Enterobacteriaceae had increased (p< 0.05). Increased weight loss during the next 6 months was not associated without major changes in microbiota composition. Significant differences between both surgical procedures were not observed at any of the time points.\n\nConclusionsIn conclusion, undergoing a crash diet and bariatric surgery were associated with an immediate but temporary decline in the microbial diversity, with immediate and permanent changes in microbiota composition, with no differences between patients undergoing gastric sleeve gastrectomy or Roux-Y gastric bypass surgery.

microbiology↗

bioRxiv2018

Long-term expanding human airway organoids for disease modelling.

Organoids are self-organizing 3D structures grown from stem cells that recapitulate essential aspects of organ structure and function. Here we describe a method to establish long-term-expanding human airway organoids from broncho-alveolar biopsies or lavage material. The pseudostratified airway organoid epithelium consists of basal cells, functional multi-ciliated cells, mucus-producing goblet cells, and CC10-secreting club cells. Airway organoids derived from cystic fibrosis (CF) patients allow assessment of CFTR function in an organoid swelling assay. Organoid culture conditions also allow gene editing as well as the derivation of various types of lung cancer organoids. Respiratory syncytial virus (RSV) infection recapitulated central disease features and dramatically increases organoid cell motility, found to be driven by the non-structural viral NS2 protein. We conclude that human airway organoids represent versatile models for the in vitro study of hereditary, malignant, and infectious pulmonary disease.

cell biology↗