ESBL-plasmid carriage in E. coli enhances in vitro bacterial competition fitness and serum resistance in some strains of pandemic sequence types without overall fitness cost

Escherichia coli (E. coli) are among the most common pathogens of extra-intestinal (ExPEC) and intestinal infections (InPEC) in humans and animals [1, 2]. ExPEC cause urinary tract, bloodstream, skin, and soft tissue infections as well as meningitis in humans and are causative agents for colisepticemia and other infections in poultry [1, 3, 4]. Treatment of ExPEC with antimicrobial agents results in an significant economic burden to healthcare facilities and in the poultry industry [5]. In recent years, an increase in resistance towards antimicrobials, including third generation cephalosporins, due to the production of extended-spectrum beta-lactamases (ESBL), has reduced treatment possibilities [6]. Dissemination of ESBL occurs not only through resistance plasmids, in addition certain clones referred to as “high risk clones” (HRC) such as ST131 and ST648 are also responsible for the spread across different niches [7, 8]. ST131 is the predominant clone isolated from E. coli infections reported worldwide, whereas ST648 is an emerging high risk clone reported in recent years from various habitats [3, 9‐12]. For both clones, recent advances in their detection will likely further increase their identification as contributors to E. coli infections [13, 14].

Although ST131 (phylogroup B2) and ST648 (phylogroup D) differ in their phylogenetic background, both lineages show similar epidemiological success, and disseminate resistance traits equally in different populations [11, 15]. Both lineages also often host large ESBL-plasmids carrying CTX-M enzymes, which have also been found integrated into the chromosome [16, 17]. ESBL-plasmids have been reported to confer fitness costs for the host strain [18], but in addition to resistance factors, they also carry a large number of non-resistance genes. These “cargo” genes encode for variety of uncharacterized, hypothetical proteins, and their possible impact on fitness are yet to be explored [19]. Recently, we demonstrated that ESBL-plasmids do not reduce fitness in strains of these pandemic sequence types ST131 and ST648, but rather contributed to virulence in terms of biofilm formation in some strains through interactions between plasmid and host chromosomally-encoded factors [20]. This observation likely contributes to the success of certain HRC worldwide, including environments with low antimicrobial selection pressures.

The majority of ESBL-producing E. coli are ExPEC, capable of causing severe bloodstream infections. Thus, serum survival is an important virulence trait in those pathogens. In this study, we investigated whether E. coli wildtype isolates of two HRC clones, ST131 and ST648, which harbor ESBL-plasmids, demonstrate better serum survival when compared to their isogenic, ESBL-plasmid-free variant (PCV). As the reservoir of ExPEC is mainly the gut of humans and animals, intestinal epithelial adhesion is a preliminary step to colonization and systemic infection in competition with other bacteria. We performed competition assays with commensal, colicin-producing ST10 E. coli strains, alone and in combination with cell culture adhesion assays, to determine the overall competition fitness and adhesion with regard to the presence of the ESBL-plasmids.

The emergence and dissemination of ESBL-producing E. coli are of global concern, as treatment opportunities are now restricted to the use of last resort antibiotics such as carbapenems [28]. This situation has become more precarious, as an increase in carbapenem-resistant strains has been reported worldwide [28, 29]. Although the dissemination is largely driven by resistance plasmids, high risk clones such as ST131 or ST648 also play an important role, as they represent successful lineages which dominate clinical cases across different host and sites [11, 12].

A large number of hypothetical genes from these large plasmids remain unexplored, and their implications with regard to clinical or virulence attributes are still unknown. In a previous study we found that ESBL-plasmids enhance biofilm formation in ST131 and ST648 E. coli [20]. Here, we explored possible impact of different ESBL-plasmids on important virulence characteristics such as competition with commensal microorganisms, and serum-resistance. Five different strains harboring different plasmids (Additional file 1) were chosen based on their original host type, disease association, size of the plasmid, CTX-M variant and inc/rep types. We examined different combinations of plasmids with isolates of ST648 and ST131 to obtain an initial impression as to which virulence traits might be affected by ESBL-plasmid carriage. The differences in genetic content of the plasmids (Additional file 1: Figure S3) may harbor clues to explain the differences in the beneficial effects of plasmid carriage.

The onset of an infection by a pathogen begins with competition against endogenous microorganisms. Commensal strains are believed to act as protective microbiota which compete for both metabolic as well as niche space in the host [30]. We observed that all the strains were equally competitive, and had similar growth kinetics against both the commensal colicin-producing strains, except for the isolate PCV17433, which was out-competed in competition against IMT13858 (Fig. 1 and Additional file 1: Figure S2A–F). This observation suggests a protective role for the ESBL plasmid harbored by IMT17433 against colicin or competition, as both the wild type and re-transformed (T) variant showed similar growth. As both the competitors and wild type strains had similar metabolic capabilities, and all the variants showed similar capabilities to utilize different metabolic substrates, a role for metabolic competition seems unlikely. A similar observation was seen for competitive adhesion against both competitors in a porcine intestinal cell line. However, the PCV variant of IMT17887 belonging to ST648 showed lower colony counts in adhesion competition assays (Fig. 2), suggesting possible roles of ESBL-plasmids in competition or colicin protection.

Serum resistance is an important virulence characteristic of ExPEC. Serum resistance is mediated by large number of factors including the outer membrane proteins and plasmid associated factors [31, 32]. Phan et al. [26] demonstrated 56 genes which were essential for serum survival in EC958 (ST131) strain defining the serum resistome in ST131 dominant lineage. We observed that both PCV variants of IMT17433 and IMT17887 were sensitive to human serum, while PCV17433 was additionally sensitive to chicken serum (Fig. 3). As the ESBL-plasmid and sequence type vary between the two strains, and constituents of human and chicken serum are different this suggest that the PCV17887 variant might harbor additional serum resistance determinants. Nevertheless, these results suggest the possible involvement of ESBL plasmids in serum resistance. Earlier reports had shown that the introduction of ESBL-plasmid in the J53 conjugative strain increased its serum resistance, and ESBL-producing strains had higher serum resistance than non ESBL-producing strains [33, 34]. However, to our knowledge, we have shown for the first time enhanced serum resistance by transfer of an ESBL-plasmid into an isogenic background of the pandemic sequence types ST131 and ST648.

We observed the upregulation of factors like ompA, known to enhance serum resistance in K12 E. coli [27] and nha, dnaJ, acrA, which are the constituents of the serum resistome. Outer membrane proteins are one of the essential components, and are involved in many of the stress related defenses in pathogenic organisms. We observed that the PCV17443 and PCV17887 variants showed reduced viability and/growth in osmotic, salt, and acid stress. In none of the isolate variants did we observe an additional fitness cost due to plasmid carriage in isolates harboring an ESBL-plasmid. As the experiments were performed with unique triplets of wild type, plasmid-cured (PCV) and complemented (T) strains, the observed differences in phenotypes appear to be solely dictated by in presence of the respective plasmids.

The inheritance of ESBL-plasmids in strains of the sequence types ST648 and ST131 does not lead to a general fitness burden in bacterial competition or serum resistance assays. For certain combinations of ESBL-plasmids with different bacterial chromosomal backgrounds, we observed that plasmids could confer beneficial virulence properties in some of strains of pandemic sequence types of ST131 and ST648.