Involved Member: Prof. Tong ZHANG

Antibiotic resistance is a global crisis of public health. Surveillance of antibiotic resistance genes (ARGs) has been increasingly conducted in environmental sectors. Prof. Tong Zhang’s team established methods and strategies towards standardization in environmental ARG surveillance. A cellular spike-in method integrated with metagenomics sequencing was developed for ARG absolute quantification. This spike-in method was employed to evaluate the ARG removal efficiencies across various anaerobic digestion systems. The team also developed a viable cell absolute quantification workflow by a combination of propidium monoazide (PMA) and cellular spike-in method to address the limitations of the culture-based enumeration method.

The team quantified the microbial profiling variations arising from common technical variables associated with metagenomic workflows, and developed an environment reference material, sequencing a well-homogenized environmental sample composed of activated sludge to facilitate accurate and reproducible environmental metagenomics-based studies. From the perspective of the quantification unit for profiling ARGs, Prof. Tong Zhang’s team and their international collaborators (comprising more than 40 co-authors from 30 institutions in 19 countries) proposed a universal unit (ARG copy per cell) for reporting biological measurements in research and regulation.

To disentangle the source-sink connectivity and understand the transfer of ARGs in the environment, a broad range of resistome profiles including 13 different habitats spanning most continents and oceans was collected to benchmark the global resistome features under standardized bioinformatic workflow. Based on the habitat specialty of resistome, a robust source tracking model was constructed to decipher the resistome attributions of various sources for targeted sinks.

References:

Yang, Y., Deng, Y., Shi, X., Liu, L., Yin, X., Zhao, W., Li, S., Yang, C., Zhang, T., (2023). QMRA of beach water by Nanopore sequencing-based viability-metagenomics absolute quantification. Water Research, 235, 119858. (impact factor: 12.8)

Yang, Y., Deng, Y., Liu, L., Yin, X., Xu, X., Wang, D., Zhang, T., (2023). Establishing reference material for the quest towards standardization in environmental microbial metagenomic studies. Water Research, 245, 120641. (impact factor: 12.8)

Yin, X., Chen, X., Jiang, X.T., Yang, Y., Li, B., Shum, M.H., Lam, T.T., Leung, G.M., Rose, J., Sanchez-Cid, C., Vogel, T.M., Walsh, F., Berendonk, T.U., Midega, J., Uchea, C., Frigon, D., Wright, G.D., Bezuidenhout, C., Picão, R.C., Ahammad, S.Z., Nielsen, P.H., Hugenholtz, P., Ashbolt, N.J., Corno, G., Fatta-Kassinos, D., Bürgmann, H., Schmitt, H., Cha, C.J., Pruden, A., Smalla, K., Cytryn, E., Zhang, Y., Yang, M., Zhu, Y.G., Dechesne, A., Smets, B.F., Graham, D.W., Gillings, M.R., Gaze, W.H., Manaia, C.M., van Loosdrecht, M.C.M., Alvarez, P.J.J., Blaser, M.J., Tiedje, J.M., Topp, E., Zhang, T., (2023). Toward a universal unit for quantification of antibiotic resistance genes in environmental samples. Environmental Science & Technology, 57(26), 9713-9721. (impact factor: 11.4)

Yin, X., Li, L., Chen, X., Liu, Y.Y., Lam, T.T., Topp, E., Zhang, T., (2023). Global environmental resistome: Distinction and connectivity across diverse habitats benchmarked by metagenomic analyses. Water research, 235, 119875. (impact factor: 12.8)