Prevalence and characterization of Staphylococcus aureus in wastewater treatment plants by whole genomic sequencing

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Water Research


Infections with Staphylococcus aureus are being spread through contact with the community environment, but the role of wastewater treatment plants in the transmission routes is not defined. This study investigated the prevalence, types, genetic elements, and potential for transmission of S. aureus by these engineered systems. Synchronized sampling events at two wastewater treatment plants were conducted with isolates of S. aureus obtained by a selective enrichment method using acriflavine that suppressed Staphylococcus epidermidis growth. DNA was extracted from a subset of the S. aureus isolates, checked by PCR to assure the absence of S. epidermidis, and sequenced to determine the multilocus sequence type, spa type, and carriage of the methicillin resistance and Panton–Valentine leukocidin genetic elements. Sequences were analyzed for single nucleotide polymorphism differences in pairwise comparison of isolates. There were two dominant S. aureus clonal complexes identified in the isolates, one commonly identified as hospital-related (CC5) and one community-related (CC8). Both types of isolates were found at both treatment facilities, even though only one facility had significant hospital sewage inputs. The presence of S. aureus persisted through treatment, with some isolates recovered from the final processes showing genetic diversity. The presence of the Panton–Valentine leukocidin genetic element was greater than the 1–5% expected from global reports. Our results suggest that treatment provides an opportunity for genetic shift, while the persistence and release of evolved strains of S. aureus may provide an environmentally relevant pathway to new hosts in the environment.

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The work was partially supported by the National Science Foundation grant #1547080 supplemented by funds from the University of Kentucky, College of Engineering, Civil Engineering Department. We thank Wesley Harrod and Kasandra Lambert, former graduate students of the University of Kentucky, for assistance with initial method assessment for environmental staphylococcus and Trish Coakley, Laboratory Manager of the University of Kentucky Environmental Research and Training Laboratories for assistance with DNA extraction techniques and student training. Thanks to Dr. Norman Pace and his labs at the University of Colorado for advice and training in PCR and sequencing. This work would not have been possible without the assistance of Dr. David Price, Laboratory Supervisor of the Town Branch Laboratory and the generosity of the WWTP operators.