Comparative genomic analyses of pathogenic bacteria and viruses and antimicrobial resistance genes in an urban transportation canal

Krittayapong Jantharadej; Akechai Kongprajug; Wuttichai Mhuantong; Tawan Limpiyakorn; Benjaporn Boonchayaanant Suwannasilp; Skorn Mongkolsuk; Kwanrawee Sirikanchana

doi:10.1016/j.scitotenv.2022.157652

Comparative genomic analyses of pathogenic bacteria and viruses and antimicrobial resistance genes in an urban transportation canal

Krittayapong Jantharadej, Akechai Kongprajug, Wuttichai Mhuantong, Tawan Limpiyakorn, Benjaporn Boonchayaanant Suwannasilp, Skorn Mongkolsuk, Kwanrawee Sirikanchana

Randall Centre of Cell & Molecular Biophysics

Research output: Contribution to journal › Article › peer-review

3 Citations (Scopus)

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Abstract

Water commuting is a major urban transportation method in Thailand. However, urban boat commuters risk exposure to microbially contaminated bioaerosols or splash. We aimed to investigate the microbial community structures, identify bacterial and viral pathogens, and assess the abundance of antimicrobial resistance genes (ARGs) using next-generation sequencing (NGS) at 10 sampling sites along an 18 km transportation boat route in the Saen Saep Canal, which traverses cultural, commercial, and suburban land-based zones. The shotgun metagenomic (Illumina HiSeq) and 16S rRNA gene amplicon (V4 region) (Illumina MiSeq) sequencing platforms revealed diverse microbial clusters aligned with the zones, with explicit segregation between the cultural and suburban sites. The shotgun metagenomic sequencing further identified bacterial and viral pathogens, and ARGs. The predominant bacterial pathogens (>0.5 % relative abundance) were the Burkholderia cepacia complex, Arcobacter butzleri, Burkholderia vietnamiensis, Klebsiella pneumoniae, and the Enterobacter cloacae complex. The viruses (0.28 %–0.67 % abundance in all microbial sequences) comprised mainly vertebrate viruses and bacteriophages, with encephalomyocarditis virus (33.3 %–58.2 % abundance in viral sequences), hepatitis C virus genotype 1, human alphaherpesvirus 1, and human betaherpesvirus 6A among the human viral pathogens. The 15 ARG types contained 611 ARG subtypes, including those resistant to beta-lactam, which was the most diverse and abundant group (206 subtypes; 17.0 %–27.5 %), aminoglycoside (94 subtypes; 9.6 %–15.3 %), tetracycline (80 subtypes; 15.6 %–20.2 %), and macrolide (79 subtypes; 14.5 %–32.1 %). Interestingly, the abundance of ARGs associated with resistance to beta-lactam, trimethoprim, and sulphonamide, as well as A. butzleri and crAssphage, at the cultural sites was significantly different from the other sites (p < 0.05). We demonstrated the benefits of using NGS to deliver insights into microbial communities, and antimicrobial resistance, both of which pose a risk to human health. Using NGS may facilitate microbial risk mitigation and management for urban water commuters and proximal residents.

Original language	English
Article number	157652
Pages (from-to)	157652
Journal	Science of the Total Environment
Volume	848
Early online date	2 Aug 2022
DOIs	https://doi.org/10.1016/j.scitotenv.2022.157652
Publication status	Published - 20 Nov 2022

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https://linkinghub.elsevier.com/retrieve/pii/S0048969722047507

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Jantharadej, K., Kongprajug, A., Mhuantong, W., Limpiyakorn, T., Suwannasilp, B. B., Mongkolsuk, S., & Sirikanchana, K. (2022). Comparative genomic analyses of pathogenic bacteria and viruses and antimicrobial resistance genes in an urban transportation canal. Science of the Total Environment, 848, 157652. Article 157652. https://doi.org/10.1016/j.scitotenv.2022.157652

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title = "Comparative genomic analyses of pathogenic bacteria and viruses and antimicrobial resistance genes in an urban transportation canal",

abstract = "Water commuting is a major urban transportation method in Thailand. However, urban boat commuters risk exposure to microbially contaminated bioaerosols or splash. We aimed to investigate the microbial community structures, identify bacterial and viral pathogens, and assess the abundance of antimicrobial resistance genes (ARGs) using next-generation sequencing (NGS) at 10 sampling sites along an 18 km transportation boat route in the Saen Saep Canal, which traverses cultural, commercial, and suburban land-based zones. The shotgun metagenomic (Illumina HiSeq) and 16S rRNA gene amplicon (V4 region) (Illumina MiSeq) sequencing platforms revealed diverse microbial clusters aligned with the zones, with explicit segregation between the cultural and suburban sites. The shotgun metagenomic sequencing further identified bacterial and viral pathogens, and ARGs. The predominant bacterial pathogens (>0.5 % relative abundance) were the Burkholderia cepacia complex, Arcobacter butzleri, Burkholderia vietnamiensis, Klebsiella pneumoniae, and the Enterobacter cloacae complex. The viruses (0.28 %–0.67 % abundance in all microbial sequences) comprised mainly vertebrate viruses and bacteriophages, with encephalomyocarditis virus (33.3 %–58.2 % abundance in viral sequences), hepatitis C virus genotype 1, human alphaherpesvirus 1, and human betaherpesvirus 6A among the human viral pathogens. The 15 ARG types contained 611 ARG subtypes, including those resistant to beta-lactam, which was the most diverse and abundant group (206 subtypes; 17.0 %–27.5 %), aminoglycoside (94 subtypes; 9.6 %–15.3 %), tetracycline (80 subtypes; 15.6 %–20.2 %), and macrolide (79 subtypes; 14.5 %–32.1 %). Interestingly, the abundance of ARGs associated with resistance to beta-lactam, trimethoprim, and sulphonamide, as well as A. butzleri and crAssphage, at the cultural sites was significantly different from the other sites (p < 0.05). We demonstrated the benefits of using NGS to deliver insights into microbial communities, and antimicrobial resistance, both of which pose a risk to human health. Using NGS may facilitate microbial risk mitigation and management for urban water commuters and proximal residents.",

author = "Krittayapong Jantharadej and Akechai Kongprajug and Wuttichai Mhuantong and Tawan Limpiyakorn and Suwannasilp, {Benjaporn Boonchayaanant} and Skorn Mongkolsuk and Kwanrawee Sirikanchana",

note = "Funding Information: This work was financially supported by the Thailand Science Research and Innovation (TSRI) , Chulabhorn Research Institute (grant no. 2536702/43410 ). Publisher Copyright: {\textcopyright} 2022 Elsevier B.V.",

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doi = "10.1016/j.scitotenv.2022.157652",

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AU - Jantharadej, Krittayapong

AU - Kongprajug, Akechai

AU - Mhuantong, Wuttichai

AU - Limpiyakorn, Tawan

AU - Suwannasilp, Benjaporn Boonchayaanant

AU - Mongkolsuk, Skorn

AU - Sirikanchana, Kwanrawee

N1 - Funding Information: This work was financially supported by the Thailand Science Research and Innovation (TSRI) , Chulabhorn Research Institute (grant no. 2536702/43410 ). Publisher Copyright: © 2022 Elsevier B.V.

PY - 2022/11/20

Y1 - 2022/11/20

N2 - Water commuting is a major urban transportation method in Thailand. However, urban boat commuters risk exposure to microbially contaminated bioaerosols or splash. We aimed to investigate the microbial community structures, identify bacterial and viral pathogens, and assess the abundance of antimicrobial resistance genes (ARGs) using next-generation sequencing (NGS) at 10 sampling sites along an 18 km transportation boat route in the Saen Saep Canal, which traverses cultural, commercial, and suburban land-based zones. The shotgun metagenomic (Illumina HiSeq) and 16S rRNA gene amplicon (V4 region) (Illumina MiSeq) sequencing platforms revealed diverse microbial clusters aligned with the zones, with explicit segregation between the cultural and suburban sites. The shotgun metagenomic sequencing further identified bacterial and viral pathogens, and ARGs. The predominant bacterial pathogens (>0.5 % relative abundance) were the Burkholderia cepacia complex, Arcobacter butzleri, Burkholderia vietnamiensis, Klebsiella pneumoniae, and the Enterobacter cloacae complex. The viruses (0.28 %–0.67 % abundance in all microbial sequences) comprised mainly vertebrate viruses and bacteriophages, with encephalomyocarditis virus (33.3 %–58.2 % abundance in viral sequences), hepatitis C virus genotype 1, human alphaherpesvirus 1, and human betaherpesvirus 6A among the human viral pathogens. The 15 ARG types contained 611 ARG subtypes, including those resistant to beta-lactam, which was the most diverse and abundant group (206 subtypes; 17.0 %–27.5 %), aminoglycoside (94 subtypes; 9.6 %–15.3 %), tetracycline (80 subtypes; 15.6 %–20.2 %), and macrolide (79 subtypes; 14.5 %–32.1 %). Interestingly, the abundance of ARGs associated with resistance to beta-lactam, trimethoprim, and sulphonamide, as well as A. butzleri and crAssphage, at the cultural sites was significantly different from the other sites (p < 0.05). We demonstrated the benefits of using NGS to deliver insights into microbial communities, and antimicrobial resistance, both of which pose a risk to human health. Using NGS may facilitate microbial risk mitigation and management for urban water commuters and proximal residents.

AB - Water commuting is a major urban transportation method in Thailand. However, urban boat commuters risk exposure to microbially contaminated bioaerosols or splash. We aimed to investigate the microbial community structures, identify bacterial and viral pathogens, and assess the abundance of antimicrobial resistance genes (ARGs) using next-generation sequencing (NGS) at 10 sampling sites along an 18 km transportation boat route in the Saen Saep Canal, which traverses cultural, commercial, and suburban land-based zones. The shotgun metagenomic (Illumina HiSeq) and 16S rRNA gene amplicon (V4 region) (Illumina MiSeq) sequencing platforms revealed diverse microbial clusters aligned with the zones, with explicit segregation between the cultural and suburban sites. The shotgun metagenomic sequencing further identified bacterial and viral pathogens, and ARGs. The predominant bacterial pathogens (>0.5 % relative abundance) were the Burkholderia cepacia complex, Arcobacter butzleri, Burkholderia vietnamiensis, Klebsiella pneumoniae, and the Enterobacter cloacae complex. The viruses (0.28 %–0.67 % abundance in all microbial sequences) comprised mainly vertebrate viruses and bacteriophages, with encephalomyocarditis virus (33.3 %–58.2 % abundance in viral sequences), hepatitis C virus genotype 1, human alphaherpesvirus 1, and human betaherpesvirus 6A among the human viral pathogens. The 15 ARG types contained 611 ARG subtypes, including those resistant to beta-lactam, which was the most diverse and abundant group (206 subtypes; 17.0 %–27.5 %), aminoglycoside (94 subtypes; 9.6 %–15.3 %), tetracycline (80 subtypes; 15.6 %–20.2 %), and macrolide (79 subtypes; 14.5 %–32.1 %). Interestingly, the abundance of ARGs associated with resistance to beta-lactam, trimethoprim, and sulphonamide, as well as A. butzleri and crAssphage, at the cultural sites was significantly different from the other sites (p < 0.05). We demonstrated the benefits of using NGS to deliver insights into microbial communities, and antimicrobial resistance, both of which pose a risk to human health. Using NGS may facilitate microbial risk mitigation and management for urban water commuters and proximal residents.

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DO - 10.1016/j.scitotenv.2022.157652

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Comparative genomic analyses of pathogenic bacteria and viruses and antimicrobial resistance genes in an urban transportation canal

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