Identification of new bacteria harboring qnrS and aac(6′)-Ib/cr and mutations possibly involved in fluoroquinolone resistance in raw sewage and activated sludge samples from a full-scale WWTP

• Published in: Water research (Oxford) 2017-03, Vol.110, p.27-37
• Main Authors: Paiva, Magna C., Reis, Mariana P., Costa, Patrícia S., Dias, Marcela F., Bleicher, Lucas, Scholte, Larissa L.S., Nardi, Regina M.D., Nascimento, Andréa M.A.
• Format: Article
• Language: English
• Subjects: aac(6′)Ib; aac(6′)Ib-cr; Activated sludge; Anti-Bacterial Agents - pharmacology; Bacteria; Drug Resistance, Bacterial - genetics; Escherichia coli - isolation & purification; Fluoroquinolones; Microbial Sensitivity Tests; Mutation; Plasmids - drug effects; qnrS; Quinolone; Quinolones; Raw sewage; Sewage
• ISSN: 0043-1354; 1879-2448
• DOI: 10.1016/j.watres.2016.11.056

Wastewater treatment plants (WWTPs) harbor bacteria and antimicrobial resistance genes, favoring gene exchange events and resistance dissemination. Here, a culture-based and metagenomic survey of qnrA, qnrB, qnrS, and aac(6′)-Ib genes from raw sewage (RS) and activated sludge (AS) of a full-scale municipal WWTP was performed. A total of 96 bacterial isolates were recovered from nalidixic acid-enrichment cultures. Bacteria harboring the aac(6′)-Ib gene predominated in RS, whereas qnrS-positive isolates were specific to AS. Novel qnrS- and aac(6′)-Ib-cr positive species were identified: Morganella morganii, Providencia rettgeri, and Pseudomonas guangdongensis (qnrS), and Alcaligenes faecalis and P. rettgeri (aac(6′)-Ib-cr). Analysis of qnrS and aac(6′)-Ib sequences from isolates and clone libraries suggested that the diversity of qnrS is wider than that of aac(6′)-Ib. A large number of amino acid mutations were observed in the QnrS and AAC(6′)-Ib proteins at previously undetected positions, whose structural implications are not clear. An accumulation of mutations at the C72, Q73, L74, A75 and M76 positions of QnrS, and D181 of AAC(6′)-Ib might be important for resistance. These findings add significant information on bacteria harboring qnrS and aac(6′)-Ib genes, and the presence of novel mutations that may eventually emerge in clinical isolates. •Bacteria harboring the aac(6′)-Ib gene predominated in raw sewage.•qnrS-positive bacteria were specific to activated sludge.•First report of the qnrS gene in Providencia rettgeri and Pseudomonas guangdongensis.•aac(6′)-Ib-cr: first report in Alcaligenes faecalis and Providencia rettgeri.•QnrS and AAC(6′)Ib exhibited many amino acids alterations previously undetected.