Healthcare-Associated Infections: The Role of Microbial and Environmental Factors in Infection Control—A Narrative Review

Infectious Diseases and Therapy, Год журнала: 2025, Номер unknown

Опубликована: Апрель 10, 2025

Язык: Английский

---

Genomics for antimicrobial resistance—progress and future directions

Antimicrobial Agents and Chemotherapy, Год журнала: 2025, Номер unknown

Опубликована: Апрель 14, 2025

ABSTRACT Antimicrobial resistance (AMR) is a critical global public health threat, with bacterial pathogens of primary concern. Pathogen genomics has revolutionized the study and provided deep insights into mechanisms dissemination AMR, precision whole-genome sequencing informing better control strategies. However, generating actionable data from genomic surveillance diagnostic efforts requires integration at clinical interface that goes beyond academic to identify mechanisms, undertake post hoc analyses outbreaks, share after research publications. In addition timely data, consideration also needs be given epidemiological sampling frames, analysis, reporting meet International Organization for Standardization (ISO) standards generation reports are interpretable “end-users.” Importantly, ensuring all countries have equitable access technology critical, through sharing following FAIR principles (findable, accessible, interoperable, re-usable). this review, we describe (i) advances in approaches AMR understand emergence, evolution, transmission key requirements enable work (ii) discuss emerging future applications interface, including barriers implementation. Harnessing genomics-enhanced embedding robust reproducible workflows within practice promises maximize impact pathogen globally coming decade.

Язык: Английский

---

A Dynamic and Effective Peptide-Based Strategy for Promptly Addressing Emerging SARS-CoV-2 Variants of Concern

Pharmaceuticals, Год журнала: 2024, Номер 17(7), С. 891 - 891

Опубликована: Июль 4, 2024

Genomic surveillance based on sequencing the entire genetic code of SARS-CoV-2 involves monitoring and studying changes variations in disease-causing organisms such as viruses bacteria. By tracing virus, it is possible to prevent epidemic spread community, ensuring a ‘precision public health’ strategy. A peptide-based design was applied provide an efficacious strategy that able counteract any emerging viral variant concern dynamically promptly affect outcomes pandemic at early stage while waiting for production anti-variant-specific vaccine, which require longer times. The inhibition interaction between receptor-binding domain (RBD) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) one cellular receptors (DPP4) its routinely bind infect human cells intriguing therapeutic approach virus from entering cells. Among other modalities developed this purpose, peptides surely offer unique advantages, including ease synthesis, serum stability, low immunogenicity toxicity, small distribution chain costs. Here, we obtained potent new inhibitor rearrangement previously identified peptide has been rationally designed cell dipeptidyl peptidase 4 sequence, ubiquitous membrane protein known RBD-SPIKE virus. This novel (named DPP4-derived), conceived endogenous “drug”, capable targeting latest tested variants with high affinity, reducing VSV* DG-Fluc pseudovirus Omicron’s infection capacity by up 14%, revealed vitro testing Calu-3 Surface plasmon resonance (SPR) confirmed binding affinity DPP4-derived Omicron RBD.

Язык: Английский

---

Thinking beyond pathogen surveillance: building resilient biotech ecosystems to combat the next pandemic

Frontiers in Science, Год журнала: 2024, Номер 2

Опубликована: Сен. 10, 2024

Язык: Английский

---

Fast-forwarding collaborative surveillance

Frontiers in Science, Год журнала: 2024, Номер 2

Опубликована: Апрель 25, 2024

Язык: Английский

---

Genomic surveillance and pathogen intelligence

Frontiers in Science, Год журнала: 2024, Номер 2

Опубликована: Апрель 25, 2024

Keywords: pathogen intelligence, whole genome sequencing, genomic epidemiology, drug resistance, microbial, One Health, SARS-CoV-2, pandemic preparedness

Язык: Английский

---

Tracing the transmission of carbapenem-resistant Enterobacteriales at the patient:ward environmental nexus

medRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июль 5, 2024

Structured summary Introduction Colonisation and infection with Carbapenem-resistant Enterobacterales (CRE) in healthcare settings poses significant risks, especially for vulnerable patients. Genomic analysis can be used to trace transmission routes, supporting antimicrobial stewardship informing control strategies. Here we genomic track the movement of CREs within clinical environmental samples. Methods 25 isolates were cultured from patient samples or swabs, that tested positive OXA-48-like variants using NG-Test® CARBA-5 test whole genome sequenced (WGS) Oxford Nanopore Technologies (ONT). 158 swabs 52 wastewater collected ward environment. 60 (matching isolate genera; Klebsiella, Enterobacter, Citrobacter Escherichia ) isolated Metagenomic sequencing was undertaken on 36 swab Results 21/25 (84%) had >1 bla OXA gene 19/25 (76%) harboured NDM gene. most commonly 27/52 (51.9%), then stick 5/43 (11.6%) sponge 5/115 (4.3%). 11/60 (18%) at 1.9% (1/60) NDM-1 . genes found 2/36 (5.5%) metagenomic Discussion Potential putative patient-patient patient-ward shown. ONT expedite decisions whilst awaiting reference laboratory results, providing economic care benefits. sampling needs optimization improve sensitivity.

Язык: Английский

---

CavitOmiX Drug Discovery: Engineering Antivirals with Enhanced Spectrum and Reduced Side Effects for Arboviral Diseases

Viruses, Год журнала: 2024, Номер 16(8), С. 1186 - 1186

Опубликована: Июль 24, 2024

Advancing climate change increases the risk of future infectious disease outbreaks, particularly zoonotic diseases, by affecting abundance and spread viral vectors. Concerningly, there are currently no approved drugs for some relevant such as arboviral diseases chikungunya, dengue or zika. The development novel inhibitors takes 10-15 years to reach market faces critical challenges in preclinical clinical trials, with approximately 30% trials failing due side effects. As an early response emerging CavitOmiX allows a rapid computational screening databases containing 3D point-clouds representing binding sites identify candidates off-label use. This process, known drug repurposing, reduces time cost regulatory approval. Here, we present potential use, targeting ADP-ribose site Alphavirus chikungunya non-structural protein 3. Additionally, demonstrate silico design approach, considering effects at earliest stages development. We use genetic algorithm iteratively refine (i) reduced off-target activity (ii) improved different variants across related species, provide broad-spectrum safe antivirals future.

Язык: Английский

---

Multi-country and intersectoral assessment of cluster congruence between different bioinformatics pipelines for genomics surveillance of foodborne bacterial pathogens

medRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июль 25, 2024

Food and waterborne disease (FWD) surveillance requires Whole-Genome Sequencing (WGS)-based systems following a One Health approach. However, different laboratories employ WGS pipelines in their routine activities, casting doubt on the comparability of results hindering optimal communication at intersectoral international levels. Through collaborative effort involving eleven European institutes across seven countries spanning food, animal human health sectors, we aimed to assess inter-laboratory clustering for four important foodborne pathogens: Listeria monocytogenes, Salmonella enterica, Escherichia coli Campylobacter jejuni. Each participating institute (n=9) applied its pipeline over same datasets (>2000 isolates per species), and, each pipeline, genetic clusters were identified possible allele/SNP distance threshold. Inter-pipeline congruence was assessed by calculating Congruence Score (relying Adjusted Wallace Rand coefficients) all resolution levels, followed an in-depth comparative analysis cluster composition outbreak level. An additional assessment performed between traditional typing, which, depending species, included Sequence Type (ST), Clonal Complex (CC) and/or serotype. Our revealed general high concordance allele-based levels except C. jejuni, where power available schemas led marked discrepancies. Still, this study non-negligible differences performance detection, suggesting that threshold flexibilization is detection similar signals laboratories. These results, together with observation STs, CCs serotypes exhibit remarkably diversity, should inform future selections case definitions. In conclusion, provides valuable insights into commonly used genomics surveillance, reinforces need, while demonstrating feasibility, conducting continuous comprehensive assessments. Ultimately, it opens good perspectives smoother cooperation towards sustainable efficient FWD surveillance.

Язык: Английский

---

The impact of COVID-19 on antimicrobial use and resistant bacteria in the Nordics: a regression modeling approach

Research Square (Research Square), Год журнала: 2024, Номер unknown

Опубликована: Сен. 11, 2024

Background Coronavirus disease 2019 (COVID-19) pandemic constituted the largest global health crisis in recent generations and led to economic fallout. It may also have disrupted pattern of antimicrobial use (AMU) which subsequently affected development resistance (AMR). The AMR remains a grave human concern. This study aimed evaluate impact COVID-19 on AMU Nordics. Methods Nordic data (2017-2022) were extracted from national annual reports (for both humans animals) European Surveillance System (TESSy) only). TESSy. Multilevel linear regression negative binomial models used fit TESSy data. Data between 2017 categorised as pre-COVID-19 time, while 2020 2022 post-COVID-19 time. Results Denmark had remarkably greater animals (about 10 times greater) than Norway, Sweden, Finland over 6-year span (2017-2022). Iceland highest AMU, Sweden lowest. Fitting multilevel model showed that all variables, except for significant predictors, including drug categories, countries, sectors (p-values < 0.05). Negative resistant Gram-negative Gram-positive isolates results species, categories statistically predictors. time was only fitting isolate Moreover, there significantly fewer those (p = 0.003, 95% CI: -0.42, -0.09). Among Nordics, lowest number isolates; however, lack surveillance high still remain great concern Iceland. Conclusions an finding underscores need establish standardized at regional levels Such standard protocol would facilitate timely information sharing will improve our preparedness response future pandemics and/or large-scale outbreaks.

Язык: Английский

---