A Pilot Study of Chicago Waterways as Reservoirs of Multidrug-Resistant Enterobacteriaceae (MDR-Ent) in a High-Risk Region for Community-Acquired MDR-Ent Infection in Children

Abstract

Community-acquired multidrug resistant Enterobacteriaceae (MDR-Ent) infections continue to increase in the United States. In prior studies, we identified neighboring regions in Chicago, Illinois, where children have 5 to 6 times greater odds of MDR-Ent infections. To prevent community spread of MDR-Ent, we need to identify the MDR-Ent reservoirs. A pilot study of 4 Chicago waterways for MDR-Ent and associated antibiotic resistance genes (ARGs) was conducted. Three waterways (A1 to A3) are labeled safe for “incidental contact recreation” (e.g., kayaking), and A4 is a nonrecreational waterway that carries nondisinfected water. Surface water samples were collected and processed for standard bacterial culture and shotgun metagenomic sequencing. Generally, A3 and A4 (neighboring waterways which are not hydraulically connected) were strikingly similar in bacterial taxa, ARG profiles, and abundances of corresponding clades and genera within the Enterobacteriaceae. Additionally, total ARG abundances recovered from the full microbial community were strongly correlated between A3 and A4 (R2 = 0.97). Escherichia coli numbers (per 100 ml water) were highest in A4 (783 most probable number [MPN]) and A3 (200 MPN) relative to A2 (84 MPN) and A1 (32 MPN). We found concerning ARGs in Enterobacteriaceae such as MCR-1 (colistin), Qnr and OqxA/B (quinolones), CTX-M, OXA and ACT/MIR (beta-lactams), and AAC (aminoglycosides). We found significant correlations in microbial community composition between nearby waterways that are not hydraulically connected, suggesting cross-seeding and the potential for mobility of ARGs. Enterobacteriaceae and ARG profiles support the hypothesized concerns that recreational waterways are a potential source of community-acquired MDR-Ent.

The role of the plasmid-mediated fluoroquinolone resistance genes as resistance mechanisms in pediatric infections due to Enterobacterales

“…Furthermore, we conducted prior pilot studies using metagenomic sequencing and culture-based approaches to analyze whether waterways in Chicago used for limited contact recreation (e.g., kayaking, boating, and fishing) were potential reservoirs of MDR Enterobacterales. We found multiple antibiotic resistance genes among Enterobacterales in surface waters, including mcr-1 , which was detected in three of the four evaluated waterways ( Logan et al., 2020b ).…”

Spread and persistence of antimicrobial resistance genes in wastewater from human and animal sources in São Paulo, Brazil

“…Class 1 integrases, considered horizontal gene transfer indicators [17,18], were highly frequent in all sampling sites. CTX-M and Qnrencoding genes are endemic worldwide and have already been reported in many human, veterinary, and environmental samples [19][20][21][22][23]. On the other hand, KPC and MCR production are the primary global emergent resistance mechanisms expressed by multidrug-resistant Enterobacterales [16,24], so they were selected for quantification assays.…”

Antibiotic resistance profile of E. coli isolates in 17 municipal wastewater utilities across Oregon

“…Globally, treated or untreated wastewater and biosolids are used for irrigation and soil amendment in agriculture, making soil and food crops potential conduits for human exposure to pathogenic ARB (Mays et al, 2021). Further, there are reports of presence and dissemination of ARB and their determinant genes in environmental reservoirs, such as rivers, lakes, and sediments associated with wastewater discharge (Logan et al, 2020;Quintela-Baluja et al, 2019). Understanding the parameters that impact ARB survival and persistence in wastewater treatment processes will support the development of evidence-based strategies to combat their negative public health impact.…”