COVID-19 surveillance in wastewater: An epidemiological tool for the monitoring of SARS-CoV-2

Maryam, Sajida; Haq, Ihtisham Ul; Yahya, Galal; Haq, Mehboob Ul; Algammal, Abdelazeem; Saber, Sameh; Cavalu, Simona

doi:10.3389/fcimb.2022.978643

Cited by 37 publications

(21 citation statements)

References 250 publications

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“…On a few occasions, we identified strains from distinct patients that were closely related ( i.e., < 30 SNPs) consistent with hospital acquisition, but most strains were genetically diverse suggesting a community source. Given the recent success of wastewater surveillance in identifying SARS-CoV-2 and influenza transmission dynamics (40, 41), we envision that a similar approach could be used to improve understanding of how community prevalence of ESC-R pathogens impacts subsequent infections.…”

Section: Discussionmentioning

confidence: 99%

Temporal Dynamics of Genetically Heterogeneous Extended-Spectrum Cephalosporin ResistantEscherichia coliBloodstream Infections

Shropshire

Strope

Anand

et al. 2023

Preprint

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Extended-spectrum cephalosporin resistant (ESC-R) Escherichia coli (ESC-R-Ec) is an urgent public health threat with clonal complex (CC) 131, phylogroup B2 strains being particularly concerning as the dominant cause of ESC-R-Ec infections. To address the paucity of recent ESC-R-Ec molecular epidemiology data in the United States (US), we used whole genome sequencing (WGS) to fully characterize a large cohort of invasive ESC-R-Ec at a tertiary care cancer center in Houston, Texas collected from 2016-2020. During the study timeframe, there were 1154 index E. coli bloodstream infections (BSIs) of which 389 (33.7%) were ESC-R. Using time series analyses, we identified a temporal dynamic of ESC-R E. coli BSIs (Ec-BSIs), distinct from ESC-susceptible Ec-BSIs, with cases peaking in the last 6 months of the calendar year. WGS of 297 ESC-R Ec-BSI strains revealed that while CC131 strains accounted for ~45% of total infections, the proportion of CC131 strains remained stable across the time-period, and infection peaks were driven by genetically diverse, non-CC131 isolates. BlaCTX-M variants accounted for most beta-lactamases conferring the ESC-R phenotype (89%; 220/248 index ESC-R Ec-BSIs), and amplification of blaCTX-M genes was widely detected in ESC-R Ec-BSI strains, particularly in carbapenem non-susceptible strains and in strains causing recurrent BSIs. BlaCTX-M-55 was significantly enriched within phylogroup A strains, and we identified blaCTX-M-55 plasmid-to-chromosome transmission occurring across non-B2 strains. Our data provide important information regarding the current molecular epidemiology of invasive ESC-R E. coli and provide novel insights into the genetic basis of observed temporal variability for these clinically important pathogens.

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Section: Discussionmentioning

confidence: 99%

Temporal Dynamics of Genetically Heterogeneous Extended-Spectrum Cephalosporin ResistantEscherichia coliBloodstream Infections

Shropshire

Strope

Anand

et al. 2023

Preprint

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“…SARS-CoV-2 is a rapidly evolving virus [ 54 , 55 , 56 , 57 , 58 ], and in the last two years, many variants of the virus have been observed; thus, vaccination alone is insufficient to overcome this pandemic, and thereby cost-effective and reliable methods to understand the mechanisms of viral pathogenicity and immunogenicity in the host are crucial. In a recent study, the SARS-CoV-2 spike S1, the protein’s phage mimotopes which resemble the shape of the viral receptor-binding (RB) sites, were created.…”

Section: Bacteriophages: a Tool For The Expression And Presentation O...mentioning

confidence: 99%

The Breadth of Bacteriophages Contributing to the Development of the Phage-Based Vaccines for COVID-19: An Ideal Platform to Design the Multiplex Vaccine

Haq

Krukiewicz

Yahya

et al. 2023

IJMS

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Phages are highly ubiquitous biological agents, which means they are ideal tools for molecular biology and recombinant DNA technology. The development of a phage display technology was a turning point in the design of phage-based vaccines. Phages are now recognized as universal adjuvant-free nanovaccine platforms. Phages are well-suited for vaccine design owing to their high stability in harsh conditions and simple and inexpensive large-scale production. The aim of this review is to summarize the overall breadth of the antiviral therapeutic perspective of phages contributing to the development of phage-based vaccines for COVID-19. We show that phage vaccines induce a strong and specific humoral response by targeted phage particles carrying the epitopes of SARS-CoV-2. Further, the engineering of the T4 bacteriophage by CRISPR (clustered regularly interspaced short palindromic repeats) presents phage vaccines as a valuable platform with potential capabilities of genetic plasticity, intrinsic immunogenicity, and stability.

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“…Wastewater‐based surveillance has proven to be a successful tool for the monitoring of SARS‐CoV‐2 within populations (Maryam et al, 2023; Pang et al, 2022; Prado et al, 2021). Wastewater sampling allows objective information about the virus circulation, independent of individual willingness and diagnostic testing (Pellegrinelli et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

Development of a reverse transcriptase digital droplet polymerase chain reaction‐based approach for SARS‐CoV‐2 variant surveillance in wastewater

Van Poelvoorde,

Gobbo,

Nauwelaerts

et al. 2024

Water Environment Research

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An urgent need for effective surveillance strategies arose due to the global emergence of the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). Although vaccines and antivirals are available, concerns persist about the evolution of new variants with potentially increased infectivity, transmissibility, and immune evasion. Therefore, variant monitoring is crucial for public health decision‐making. Wastewater‐based surveillance has proven to be an effective tool to monitor SARS‐CoV‐2 variants within populations. Specific SARS‐CoV‐2 variants are detected and quantified in wastewater in this study using a reverse transcriptase digital droplet polymerase chain reaction (RT‐ddPCR) approach. The 11 designed assays were first validated in silico using a substantial dataset of high‐quality SARS‐CoV‐2 genomes to ensure comprehensive variant coverage. The assessment of the sensitivity and specificity with reference material showed the capability of the developed assays to reliably identify target mutations while minimizing false positives and false negatives. The applicability of the assays was evaluated using wastewater samples from a wastewater treatment plant in Ghent, Belgium. The quantification of the specific mutations linked to the variants of concern present in these samples was calculated using these assays based on the detection of single mutations, which confirms their use for real‐world variant surveillance. In conclusion, this study provides an adaptable protocol to monitor SARS‐CoV‐2 variants in wastewater with high sensitivity and specificity. Its potential for broader application in other viral surveillance contexts highlights its added value for rapid response to emerging infectious diseases.Practitioner Points Robust RT‐ddPCR methodology for specific SARS‐CoV‐2 variants of concern detection in wastewater. Rigorous validation that demonstrates high sensitivity and specificity. Demonstration of real‐world applicability using wastewater samples. Valuable tool for rapid response to emerging infectious diseases.

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COVID-19 surveillance in wastewater: An epidemiological tool for the monitoring of SARS-CoV-2

Cited by 37 publications

References 250 publications

Temporal Dynamics of Genetically Heterogeneous Extended-Spectrum Cephalosporin ResistantEscherichia coliBloodstream Infections

Temporal Dynamics of Genetically Heterogeneous Extended-Spectrum Cephalosporin ResistantEscherichia coliBloodstream Infections

The Breadth of Bacteriophages Contributing to the Development of the Phage-Based Vaccines for COVID-19: An Ideal Platform to Design the Multiplex Vaccine

Development of a reverse transcriptase digital droplet polymerase chain reaction‐based approach for SARS‐CoV‐2 variant surveillance in wastewater

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