A sewage microbiome is dominated by Arcobacter cryaerophilus that expresses multiple drug resistance and virulence genes

A sewage microbiome is dominated by Arcobacter cryaerophilus that expresses multiple drug resistance and virulence genes

 

Background:

Wastewater treatment plants (WWTP) are good indicators of a community’s microbial burden. WWTP are also important hubs for horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) and virulence factors (VFs). Arcobacter, a bacterium commonly found in sewage communities, has become a growing public health concern in the past decade due to its pathogenicity and growing antibiotic resistance. Our study explored the bacterial diversity of a WWTP, and characterized the putative ARGs and VFs present in an Arcobacter species that dominates this microbiome.

 

Methods:

DNA and RNA were extracted from untreated sewage samples from Tucson, AZ over 2 days. Contigs and draft genome were assembled using IDBA and Albertsen et al. 2013. Gene expression was measured in CLC. ARGs and VFs were annotated using PHMMER and the ARDB and PATRIC databases. Putative HGT events were detected using HGTector and phylogenetic analyses.

 

Results:

15 phyla were present and stable across the three samples. We identified 162 ARGs belonging to 60 antibiotic types and 177 VFs belonging to 46 virulence categories. The emerging human pathogen Arcobacter cryaerophilus dominated all samples. Its draft genome contained 48 putative ARGs against 27 antibiotic types, dominant expression belonging to Tetracycline. We also found 74 putative VFs belonging to 22 virulence categories, highest expression relating to Adhesion and Invasion.

The A. cryaerophilus genome also contained genes related to mobile genetic elements (phages, 227; transposases, 58); in sum, about 4% of its genome appears to be horizontally acquired from outside the order of Campylobacterales. Of interest, about 5% of VFs show signs of HGT, mostly relating to Intracellular Survival and Replication.

 

Discussion:

Our results show that even with the continuous influx of sewage, the microbial diversity in a WWTP remained constant across 25 hours, suggesting that the urban population hosts a fairly stable microbial community. Additionally, high levels of expression of ARGs among the sewage microbes indicate the presence of large number of antibiotics in the urban sewage, highlighting the urgent need to better manage antibiotic use. A. cryaerophilus, which contains multiple ARGs, thrive in this environment. As treatment of sewage is not always very effective, this emerging human pathogen could pose a threat to public health.