Molecular diversity and conjugal transferability of class 2 integrons among Escherichia coli isolates from food, animal and human sources
Introduction
Escherichia coli is a Gram-negative member of the Enterobacteriaceae family that has a nearly ubiquitous distribution among humans, animals and the open environment. Although it naturally colonises the intestines of a wide range of animals, E. coli can also act as an opportunistic pathogen associated with community-acquired and nosocomial infections. The extensive use, and misuse, of antimicrobials both in clinical and farm animal settings has led to the selection and global spread of multidrug-resistant E. coli isolates [1], [2].
Integrons are genetic platforms able to excise, integrate and express multiple gene cassettes (GCs), which are mobile genetic elements (MGEs) containing a promoterless coding sequence and a recombination site (attC). The basic structure of an integron includes the integrase gene (intI), a proximal recombination site (attI), and a promoter (Pc) that drives the expression of the GC [3]. Integrons are classified either as sedentary chromosomal integrons, located in the chromosome of different bacterial species and usually carrying multiple GCs encoding a wide range of functions, or as mobile integrons, embedded within MGEs such as transposons or conjugative elements [4]. Mobile integrons comprise five different classes based on the sequence of the integrase gene and usually harbour GCs conferring resistance to antibiotics [5]. Class 1 to 3 integrons differentially contribute to the global threat of antimicrobial resistance owing to their capability to capture and spread antibiotic resistance GCs (intragenomic gene transfer) and to be transferred via MGEs to other bacteria of the same or even different species (horizontal gene transfer) [3], [4], [5].
Class 1 and class 2 integrons are the most frequently detected integrons in Enterobacteriaceae. However, compared with class 1 integrons, class 2 integrons are less diverse in GC content, less prevalent and also less studied [6], [7]. Class 2 integrons usually carry in their variable region (VR) the dfrA1–sat2–aadA1–orfX array (which confers resistance to trimethoprim, streptothricin and streptomycin/spectinomycin), followed by three additional genes (ybfA, ybfB and ybgA) embedded in the Tn7 transposition module (tnsABCDE). orfX, also known as ybeA, is considered a pseudo-GC of unknown function. The intI2 gene is frequently interrupted by a premature stop codon, encoding a non-functional integrase. Most class 2 integrons are associated with Tn7 derivatives. The Tn7 transposon uses two alternative transposition pathways mediated by different target selecting proteins, TnsD and TnsE [8]. TnsD recognises a unique site located within the 3′-end of the essential glmS gene in the bacterial chromosome (attTn7), whilst TnsE directs Tn7 transposition to conjugative/mobilisable plasmids [9].
Insertion sequence (IS) elements are small DNA segments that act as autonomous transposable elements. They can disrupt and inactivate a gene, affect the expression of neighbouring genes and/or promote genome rearrangements. By interacting with other types of genetic platforms, such as integrons, ISs may form large assemblies with higher-order biological properties [10].
Here we investigated the complete genetic organisation, genetic environment, location and conjugative transferability of a collection of class 2 integrons carried by E. coli strains isolated from different sources in Spain, Tunisia and Mexico.
Section snippets
Bacterial collection
A total of 35 E. coli isolates carrying class 2 integrons from different sources [meat products, n = 15 (poultry, n = 14; pork, n = 1); chickens, n = 6; pets, n = 5; humans, n = 5; wild animals, n = 4] and origins (Spain, Mexico and Tunisia) were selected and were included in the present work. E. coli from wild animals (gull, stork, genet and roe deer), pets (dogs and turtles) and chickens were recovered from faeces and were processed as described previously [11], [12], [13] (Supplementary
Class 2 integrons are evolving by integration of insertion sequence elements
The current study focused on the full molecular characterisation of 35 class 2 integrons carried by E. coli strains recovered from different sources and geographical origins (Supplementary Table S1). In contrast to the wide variety of GCs reported among class 1 integrons and even among class 2 integrons from specific sources, such as wastewater environments [19], only three genetic arrangements regarding antibiotic resistance GCs were identified in the present study: dfrA1–sat2–aadA1; estX–sat2–
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2020, Environmental PollutionCitation Excerpt :Therefore, a continuous reporting of integrons is required for monitoring and minimizing MDR, in order to understand the spread of resistant gene spectrum, especially among emerging bacterial pathogens. In the subject matter, advanced techniques such as PCR, sequencing, and PCR cartography have enabled us to understand the emergence of novel mobile genetic elements (Gillings, 2014; Alonso et al., 2018; Zhang et al., 2019). The survival of bacteria is mainly based upon their potential to adapt to the surrounding environment.
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