The Bacterial Urban Resistome: Recent Advances

Abstract

Cities that are densely populated are reservoirs of antibiotic resistant genes (ARGs). The overall presence of all resistance genes in a specific environment is defined as a resistome. Spatial proximity of surfaces and different hygienic conditions leads to the transfer of antibiotic resistant bacteria (ARB) within urban environments. Built environments, public transportation, green spaces, and citizens' behaviors all support persistence and transfer of antimicrobial resistances (AMR). Various unique aspects of urban settings that promote spread and resilience of ARGs/ARB are discussed: (i) the role of hospitals and recreational parks as reservoirs; (ii) private and public transportation as carriers of ARGs/ARB; (iii) the role of built environments as a hub for horizontal gene transfer even though they support lower microbial biodiversity than outdoor environments; (iv) the need to employ ecological and evolutionary concepts, such as modeling the fate of a specific ARG/ARB, to gain enhanced health risk assessments. Our understanding and our ability to control the rise of AMR in an urban setting is linked to our knowledge of the network connecting urban reservoirs and the environment.

Keywords: ARB; ARGs; ARM; antimicrobial resistances; hospitals; pet; recreational water; urban microbiome.

Figure 1

(A) Number of detected antimicrobial resistance markers by city. Colour represents different regions. Clusters of high antimicrobial resistance markers diversity were not evenly distributed across cities. (B) The portion of the Comprehensive Antibiotic Resistance Database (CARD) and antibiotic classes in controlled built environments (CB, microbial confinement and cleaning operations) and naturally unrestricted buildings (UB, houses with a high level of influence from the surrounding outdoor environment). The abundance chart also shows binned genomes and plasmids and for individual binned genomes referring to individual species. Figure modified from [11] (panel A) and [12] (panel B).

Figure 2

Differences between restricted and unrestricted buildings and suggested routes connecting outdoor and indoor settings. Restricted buildings have lower biodiversity when compared with unrestricted buildings. ARGs and ARB present in outdoor environments (dotted lines, high microbial biodiversity) can be transferred into indoor settings (with lower microbial biodiversity), where more resistant forms can be selected through, for example, use of antibiotics. Eventually, these selected and resistant ARGs and ARB can be released outdoors (continuous lines) by different vectors, such as people, pets, and wastewater. In the environment selected ARGs/ARB can find new ways for recombination due to higher biodiversity and integration of ARGs in the environmental microbial communities.

Figure 3

Frequency of papers regarding the top 50 ARG subtypes from 1990. The panels from (A–D) represent ARGs and their respective antibiotic families in different urban contexts. The number of manuscripts identifying the genes were extracted from PubMed [17].

Figure 4

ARGs/ARB contamination routes within the urban environment. Each route discussed in this work is identified with a number and the corresponding supporting references are listed in Table 1. This figure has been prepared using resources from Freepik.com. WWTP: wastewater treatment plants.