Insights into the Environmental Resistance Gene Pool from the Genome Sequence of the Multidrug-Resistant Environmental Isolate Escherichia coli SMS-3-5

Abstract

The increasing occurrence of multidrug-resistant pathogens of clinical and agricultural importance is a global public health concern. While antimicrobial use in human and veterinary medicine is known to contribute to the dissemination of antimicrobial resistance, the impact of microbial communities and mobile resistance genes from the environment in this process is not well understood. Isolated from an industrially polluted aquatic environment, Escherichia coli SMS-3-5 is resistant to a record number of antimicrobial compounds from all major classes, including two front-line fluoroquinolones (ciprofloxacin and moxifloxacin), and in many cases at record-high concentrations. To gain insights into antimicrobial resistance in environmental bacterial populations, the genome of E. coli SMS-3-5 was sequenced and compared to the genome sequences of other E. coli strains. In addition, selected genetic loci from E. coli SMS-3-5 predicted to be involved in antimicrobial resistance were phenotypically characterized. Using recombinant vector clones from shotgun sequencing libraries, resistance to tetracycline, streptomycin, and sulfonamide/trimethoprim was assigned to a single mosaic region on a 130-kb plasmid (pSMS35_130). The remaining plasmid backbone showed similarity to virulence plasmids from avian-pathogenic E. coli (APEC) strains. Individual resistance gene cassettes from pSMS35_130 are conserved among resistant bacterial isolates from multiple phylogenetic and geographic sources. Resistance to quinolones was assigned to several chromosomal loci, mostly encoding transport systems that are also present in susceptible E. coli isolates. Antimicrobial resistance in E. coli SMS-3-5 is therefore dependent both on determinants acquired from a mobile gene pool that is likely available to clinical and agricultural pathogens, as well, and on specifically adapted multidrug efflux systems. The association of antimicrobial resistance with APEC virulence genes on pSMS35_130 highlights the risk of promoting the spread of virulence through the extensive use of antibiotics.

Network analyses structure genetic diversity in independent genetic worlds

“…S1) when we investigated the network reconstructed with sequences presenting at least 40% of sequence identity. This is either because of the methodological limit of the method that cannot account for edge weights, or, as it is in agreement with the literature (15)(16)(17)(18), it might be explained if, within the limits of one type of vehicle, DNA molecules obey complex rules of transfers and losses. Yet, the lack of a strong underlying hierarchical structure does not mean that understanding the processes that led to its complexity is out of reach.…”

Diversity of CRISPR loci in Escherichia coli

“…However, such a similarity cannot be due to a common origin, since Shigella species derive from lineages that are independent of B2 (Fricke et al, 2008;Ogura et al, 2009;Pupo et al, 2000;Turner et al 2006). Moreover, the closely related ECOR strains carry a complete CRISPR2/CAS-E system (our unpublished results) and the deletions in CRISPR2.1/CAS-E are unrelated, entailing distinct genes and sequences (Supplementary Fig.…”

WITHDRAWN: Structure genomics of two chimera plasmids p675920-1 and p675920-2 coexisting in a multi-drug resistant Klebsiella pneumoniae isolate

“…Most of IncFII plasmids contain multiple replicons, which are composed of the master IncFII replicon together with one or more other replicons such as IncFIA (rep1A) [2], IncFIB (rep1B) [3], and that (repB) belonging to an uncharacterized incompatibility group [4]; by contrast, there are some IncFII plasmids, such as R100 (accession number AP000342) [5] and R1 [6], which contain the sole IncFII replicon. IncFII plasmids with multiple replicons can overcome the incompatibility barrier with incoming plasmids [1].…”