AUTHOR=Ng Charmaine , Tan Boonfei , Jiang Xiao-Tao , Gu Xiaoqiong , Chen Hongjie , Schmitz Bradley William , Haller Laurence , Charles Francis Rathinam , Zhang Tong , Gin Karina 

TITLE=Metagenomic and Resistome Analysis of a Full-Scale Municipal Wastewater Treatment Plant in Singapore Containing Membrane Bioreactors

JOURNAL=Frontiers in Microbiology

VOLUME=10

YEAR=2019

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2019.00172

DOI=10.3389/fmicb.2019.00172

ISSN=1664-302X

ABSTRACT=<p>Reclaimed water provides a water supply alternative to address problems of scarcity in urbanized cities with high living densities and limited natural water resources. In this study, wastewater metagenomes from 6 stages of a wastewater treatment plant (WWTP) integrating conventional and membrane bioreactor (MBR) treatment were evaluated for diversity of antibiotic resistance genes (ARGs) and bacteria, and relative abundance of class 1 integron integrases (<italic>intl1</italic>). ARGs confering resistance to 12 classes of antibiotics (ARG types) persisted through the treatment stages, which included genes that confer resistance to aminoglycoside <italic>[aadA, aph(6)-I, aph(3</italic>′<italic>)-I, aac(6</italic>′<italic>)-I, aac(6</italic>′<italic>)-II, ant(2</italic>″<italic>)-I]</italic>, beta-lactams [class A, class C, class D beta-lactamases (<italic>bla</italic><sub>OXA</sub>)], chloramphenicol (acetyltransferase, exporters, <italic>floR, cmIA</italic>), fosmidomycin (<italic>rosAB</italic>), macrolide-lincosamide-streptogramin (<italic>macAB, ereA, ermFB</italic>), multidrug resistance (subunits of transporters), polymyxin (<italic>arnA</italic>), quinolone (<italic>qnrS</italic>), rifamycin (<italic>arr</italic>), sulfonamide (<italic>sul1, sul2</italic>), and tetracycline (<italic>tetM, tetG, tetE, tet36, tet39, tetR, tet43, tetQ, tetX</italic>). Although the ARG subtypes in sludge and MBR effluents reduced in diversity relative to the influent, clinically relevant beta lactamases (i.e., <italic>bla</italic><sub>KPC</sub>, <italic>bla</italic><sub>OXA</sub>) were detected, casting light on other potential point sources of ARG dissemination within the wastewater treatment process. To gain a deeper insight into the types of bacteria that may survive the MBR removal process, genome bins were recovered from metagenomic data of MBR effluents. A total of 101 close to complete draft genomes were assembled and annotated to reveal a variety of bacteria bearing metal resistance genes and ARGs in the MBR effluent. Three bins in particular were affiliated to <italic>Mycobacterium smegmatis, Acinetobacter Iwoffii</italic>, and <italic>Flavobacterium psychrophila</italic>, and carried aquired ARGs <italic>aac(2</italic>′<italic>)-Ib, bla</italic><sub>OXA−278</sub>, and <italic>tet36</italic> respectively. In terms of indicator organisms, cumulative log removal values (LRV) of <italic>Escherichia coli, Enterococci</italic>, and <italic>P. aeruginosa</italic> from influent to conventional treated effluent was lower (0–2.4), compared to MBR effluent (5.3–7.4). We conclude that MBR is an effective treatment method for reducing fecal indicators and ARGs; however, incomplete removal of <italic>P. aeruginosa</italic> in MBR treated effluents (&lt;8 MPN/100 mL) and the presence of ARGs and <italic>intl1</italic> underscores the need to establish if further treatment should be applied prior to reuse.</p>