Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2024 Dec 26;71(1):1.
doi: 10.1007/s00294-024-01305-6.

Metagenomic surveillance of microbial community and antibiotic resistant genes associated with Malaysian wastewater during the COVID-19 pandemic

Umama Shahid  1 , Suet Li Hooi  1 , Shu Yong Lim  2 , Alijah Mohd Aris  3 , Bee Chin Khor  3 , Qasim Ayub  1   2 , Hock Siew Tan  4
Affiliations

Metagenomic surveillance of microbial community and antibiotic resistant genes associated with Malaysian wastewater during the COVID-19 pandemic

Umama Shahid et al. Curr Genet. .

Abstract

Wastewater is a reservoir of pathogens and hotspots for disseminating antibiotic resistance genes across species. The metagenomic surveillance of wastewater provides insight into the native microbial community, antibiotic-resistance genes (ARGs) and mobile genetic elements. t. The COVID-19 pandemic has caused wider dissemination of ARGs and resistant bacteria in wastewater. Although immensely significant, no research has been performed on the Malaysian wastewater microbial community and ARGs or their correlation with COVID-19 infections. This study utilised a 16S metagenomics approach to characterise the microbial community in Malaysian wastewater during high and low-case phases of the pandemic. Bacteria belonging to Bacteriodales, Bacillales, Actinomycetales and opportunistic pathogens-Arcobacters, Flavobacteria, and Campylobacterales, Neisseriales, were enriched during higher COVID-19 pandemic (active cases). Additionally, copy number profiling of ARGs in water samples showed the prevalence of elements conferring resistance to antibiotics like sulphonamides, cephalosporins, and colistin. The high prevalence of intI1 and other ion-based transporters in samples highlights an extensive risk of horizontal gene transfer to previously susceptible species. Our study emphasises the importance of wastewater surveillance in understanding microbial community dynamics and ARG dissemination, particularly during public health crises like the COVID-19 pandemic.

Keywords: 16S rRNA gene resequencing; Antimicrobial resistance genes; Microbial diversity; Multi-drug resistance; Wastewater treatment.

PubMed Disclaimer

Conflict of interest statement

Declarations. Ethical approval: No ethical approvals were required for this study. Competing interests: The authors declare no competing interests.

Similar articles

See all similar articles

References

    1. Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu Y-X, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG (2019) Nat Biotechnol 37(9):1091–1091 ‘Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2’. https://doi.org/10.1038/s41587-019-0252-6
    1. Bor B, Bedree JK, Shi W, McLean JS, He X (2019) Saccharibacteria (TM7) in the human oral Microbiome. J Dent Res 98(5):500–509. https://doi.org/10.1177/0022034519831671 - DOI - PubMed - PMC
    1. Caucci S, Karkman A, Cacace D, Rybicki M, Timpel P, Voolaid V, Gurke R, Virta M, Berendonk TU (2016) Seasonality of antibiotic prescriptions for outpatients and resistance genes in sewers and wastewater treatment plant outflow. FEMS Microbiol Ecol 92(5):fiw060. https://doi.org/10.1093/femsec/fiw060 - DOI - PubMed
    1. Chahal C, van den Akker B, Young F, Franco C, Blackbeard J, Monis P (2016) Chapter Two - Pathogen and Particle associations in Wastewater: significance and implications for treatment and disinfection processes. In: Sariaslani S, Michael Gadd G (eds) Advances in Applied Microbiology. Academic. https://doi.org/10.1016/bs.aambs.2016.08.001 .
    1. Chang S-C, Kao M-R, Saldivar RK, Díaz-Moreno SM, Xing X, Furlanetto V, Yayo J, Divne C, Vilaplana F, Abbott DW, Hsieh YSY (2023) The Gram-positive bacterium Romboutsia Ilealis harbors a polysaccharide synthase that can produce (1,3;1,4)-β-D-glucans. Nat Commun 14(1):4526. https://doi.org/10.1038/s41467-023-40214-z - DOI - PubMed - PMC

LinkOut - more resources