Urban monitoring of antimicrobial resistance during a COVID-19 surge through wastewater surveillance

Harrington, Anthony; Vo, Van; Papp, Katerina; Tillett, Richard L.; Chang, Ching-Lan; Baker, H. Kent; Shen, Shirley; Amei, Amei; Lockett, Cassius; Gerrity, Daniel; Oh, Edwin C.

doi:10.1016/j.scitotenv.2022.158577

Cited by 25 publications

(10 citation statements)

References 60 publications

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“…Other alternatives to culture enrichment prior to metagenomic analysis consist of using commercially available AMR target enrichment NGS panels (Harrington et al 2022).…”

Section: Discussionmentioning

confidence: 99%

“…WBS provides an integrated view of ARG burden across a population that is objective, comprehensive and inclusive. Furthermore, it can be performed serially, and at a tiny fraction of the cost of serial active surveillance to monitor for changes in the prevalence of specific ARG, as might occur in the context of an outbreak (Harrington et al 2022; Li et al 2022). Despite the great potential of this technology, its application to hospitals has been limited to date.…”

Section: Discussionmentioning

confidence: 99%

“…They observed that cephalosporin and carbapenem resistant Enterobacterales only after culture enrichment and not in raw soil samples (Marano et al 2021). Other alternatives to culture enrichment prior to metagenomic analysis consist of using commercially available AMR target enrichment NGS panels (Harrington et al 2022).…”

Section: Discussionmentioning

confidence: 99%

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Metagenomic analysis after selective culture enrichment of wastewater demonstrates increased burden of antibiotic resistant genes in hospitals relative to the community

Acosta

Lee

Bautista

et al. 2023

Preprint

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Antimicrobial resistance (AMR) is an ever-increasing threat to global health. Wastewater-based surveillance is an emerging methodology that objectively enables an inclusive and comprehensive assessment of population AMR in an observed sewershed. Here we compared the resistome of two tertiary-care hospitals with two separate neighborhoods, using complimentary targeted qPCR and metagenomics of wastewater before and after selective culture enrichment for clinically important Gram negatives. In total 26 ARG-type (1225 ARG-subtypes) were found across all samples, in which beta-lactam ARG was the richest (the number of different ARG-subtypes found) followed by multidrug, fluoroquinolone, macrolide-lincosamide-streptogramin (MLS) and aminoglycoside. The composition of ARGs in wastewater differed between raw wastewater pellets and culture-enriched wastewater samples and the resistomes clustered based on the type of location (Hospitals vs neighborhoods). Hospital wastewater was found to have higher diversity and greater abundance of ARGs compared to neighborhood wastewater when the composition profiles of ARGs in both raw and culture-enriched wastewater pellets. Clinically relevant ARG (i.e., VIM, NDM metallo-beta-lactamases) were detected in culture enrichment samples that were not identified in raw samples, despite a lower targeted sequencing depth. Wastewater-based surveillance is an effective, and potentially extremely important and powerful tool that could be developed to augment hospital-based infection control and antimicrobial stewardship programs, creating a safer space for those receiving care.

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“…Other alternatives to culture enrichment prior to metagenomic analysis consist of using commercially available AMR target enrichment NGS panels (Harrington et al 2022).…”

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Metagenomic analysis after selective culture enrichment of wastewater demonstrates increased burden of antibiotic resistant genes in hospitals relative to the community

Acosta

Lee

Bautista

et al. 2023

Preprint

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show abstract

“…The study used a combination of qPCR and metagenomic sequencing for analyzing the samples. 31 Using metagenomics, a positive correlation was also observed between the macrolide, tetracycline, sulfonamide, and some beta-lactamase ARG classes and time over three months in hospital wastewater from Saudi Arabia. 32 Likewise, a study from India noted significant increases in antidrug resistance of E. coli in 2020 compared to 2018 using the culture-based Kirby-Bauer disk diffusion method.…”

Section: Introductionmentioning

confidence: 95%

“…A wastewater surveillance study from Las Vegas, Nevada demonstrated that the abundance of ARGs belonging to fluoroquinolone and beta-lactam classes increased during a COVID-19 surge in December 2020 compared to November 2020. The study used a combination of qPCR and metagenomic sequencing for analyzing the samples . Using metagenomics, a positive correlation was also observed between the macrolide, tetracycline, sulfonamide, and some beta-lactamase ARG classes and time over three months in hospital wastewater from Saudi Arabia .…”

Section: Introductionmentioning

confidence: 99%

Changes in Prevalence but Not Hosts of Antibiotic Resistance Genes during the COVID-19 Pandemic versus Prepandemic in Wastewater Influent

Deshpande,

Ehasz,

Eramo

et al. 2023

ACS EST Water

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The COVID-19 pandemic offered a unique opportunity to study shifts in environmental antibiotic resistance that could be associated with the changes in disinfectant and/or antibiotic usage patterns, coinfections, or other behaviors. The aim of this study was to document temporal changes (pre-, early-, versus later-pandemic) in antibiotic resistance genes (ARGs), ARG hosts, biomarkers of potential coinfections, and the total microbiome in municipal wastewater influent from one separate sanitary and one combined sewer system. The 16S rRNA gene copy normalized concentration of qacE was higher in early- than prepandemic samples, and sul1 and tet(G) were higher in early- than later-pandemic samples. Metagenomics revealed significant changes in the abundance of the macrolide and sulfonamide ARG classes. COVID-19 cases positively correlated with the disinfectants/antiseptics group of ARGs and negatively correlated with the sulfonamide and aminoglycoside resistance classes. Discussion is provided regarding the correspondence of these observations with antibiotic prescription pattern changes during the study period. Putative waterborne pathogens were identified, which is of potential interest for understanding the prevalence of community coinfections. No changes in host-ARG associations were observed. Overall, the results of this study may help in understanding the impact of the pandemic and/or lack thereof on another public health crisis: antibiotic resistance.

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Antimicrobial Resistance Ignited by COVID-19 Pandemic: SOS for Antimicrobial Stewardship

Mazumder,

Kumar

2023

The Handbook of Environmental Chemistry

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Urban monitoring of antimicrobial resistance during a COVID-19 surge through wastewater surveillance

Cited by 25 publications

References 60 publications

Metagenomic analysis after selective culture enrichment of wastewater demonstrates increased burden of antibiotic resistant genes in hospitals relative to the community

Metagenomic analysis after selective culture enrichment of wastewater demonstrates increased burden of antibiotic resistant genes in hospitals relative to the community

Changes in Prevalence but Not Hosts of Antibiotic Resistance Genes during the COVID-19 Pandemic versus Prepandemic in Wastewater Influent

Antimicrobial Resistance Ignited by COVID-19 Pandemic: SOS for Antimicrobial Stewardship

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