Genome Analysis of Enterobacter asburiae and Lelliottia spp. Proliferating in Oligotrophic Drinking Water Reservoirs and Lakes

Abstract

Surface waters are one of the main sources for drinking water production, and thus microbial contamination should be as minimal as possible. However, high concentrations of coliform bacteria were detected in reservoirs and lakes used for drinking water production during summer months due to autochthonous proliferation processes. Here, we present the genomic analyses of 17 strains of Enterobacter asburiae and Lelliottia spp. proliferating in reservoirs and lakes with special focus on the hygienic relevance, antibiotic resistance, and adaptations to the oligotrophic environments. The genomes contain neither genes for the type III secretion system nor cytotoxins or hemolysins, which are considered typical virulence factors. Examination of antibiotic resistance genes revealed mainly efflux pumps and β-lactamase class C (ampC) genes. Phenotypically, single isolates of Enterobacter asburiae showed resistance to fosfomycin and ceftazidime. The genome analyses further suggest adaptations to oligotrophic and changing environmental conditions in reservoirs and lakes, e.g., genes to cope with low nitrate and phosphate levels and the ability to utilize substances released by algae, like amino acids, chitin, alginate, rhamnose, and fucose. This leads to the hypothesis that the proliferation of the coliform bacteria could occur at the end of summer due to algae die-off. IMPORTANCE Certain strains of coliform bacteria have been shown to proliferate in the oligotrophic water of drinking water reservoirs and lakes, reaching values above 10⁴ per 100 mL. Such high concentrations challenge drinking water treatment, and occasionally the respective coliform bacteria have been detected in the treated drinking water. Thus, the question of their hygienic relevance is of high importance for water suppliers and authorities. Our genomic analyses suggest that the strains are not hygienically relevant, as typical virulence factors are absent and antibiotic resistance genes in the genomes most likely are of natural origin. Furthermore, their presence in the water is not related to fecal contamination. The proliferation in reservoirs and lakes during stable summer stratification is an autochthonic process of certain E. asburiae and Lelliottia strains that are well adapted to the surrounding oligotrophic environment.

Keywords: Enterobacter; Lelliottia; drinking water; hygienic relevance; lakes; oligotrophic waters; reservoir.

FIG 1

Taxonomic analysis of Enterobacter and Lelliottia strains. (A) Phylogenetic analysis, with PATRIC (phylogenetic tree calculated based on 958 genes, outgroup: Xenorhabdus nematophila AN6/1). (B) Plot of average nucleotide identity (ANI; %) between sequenced reservoir strains and the reference strains: E. asburiae ATCC 3595^T (GCA_001521715), E. cloacae subsp. cloacae ATCC 13047^T (GCA_000025565), L. amnigena LMG 2784^T (GCA_002553545), and L. aquatilis 6331-17^T (GCA_002923025). Colors of the source describe where strains were isolated from, with T, type strain; BB, Breitenbach; KB, Klingenberg; KK, Kleine Kinzig; LC, Lake Constance; OR, Obersee (Rur); RB, Rappbode; SÖ, Söse; WB, Wahnbach.

FIG 2

Functional pathway classification using KEGG with the mean number of gene copies in the categories A09100, metabolism, A09120, genetic information processing, A09130, environmental information processing, and A09140, cellular processes. EA, E. asburiae; EC, E. cloacae; LA, L. amnigena/L. aquatilis; PE, pathogen Enterobacterales; Res, reservoir strains; Ref, reference strains.

FIG 3

Overview of the main metabolic pathways in Enterobacter and Lelliottia. Membrane transport proceeds via various transporters, such as ABC transporter, secretion system, phosphotransferase system (PTS), two-component system, and efflux pumps. In addition, the genera are capable of dissimilatory nitrate reduction and assimilatory sulfate reduction. Some systems are present only in individual genera; these are shown with backgrounded circles, in red (Enterobacter) and blue (Lelliottia).

FIG 4

Model of the mass proliferation of coliform bacteria in reservoirs. (A) Situation in the reservoir during summer stratification. Algae die-off and release of dissolved organic matter (DOM) might lead to chemotaxis, quorum sensing, and fast growth of coliform bacteria. (B) Differences between the genera Lelliottia and Enterobacter. Lelliottia spp. have the potential to utilize fucose, rhamnose, and alginate, whereas E. asburiae might use chitin and taurine. Lelliottia spp. might be able to handle lower nitrate levels than E. asburiae.