Escherichia coli (E. coli) strains are normal flora of human gastrointestinal tract. The evolution encoded by horizontally-transferred genetic (HGT) elements has been perceived in several species. E. coli strains have acquired virulence potential factors by attainment of particular loci through HGT, transposons or phages. The heterogeneous nature of these strains is because of HGT through mobile genetic elements. These genetic exchanges that occur in bacteria provide the genetic diversity.
- Escherichia coli (E. coli)
- horizontal gene transfer (HGT)
- pathogenicity islands (PAIs)
Genome evolution is the process by which the content and organization of genetic information of a species change over time. This process includes different forms of changes: point mutation and gene conversions, rearrangement (inversion or translocation), and deletion and insertion of foreign DNA (plasmid integration and transposition). These mechanisms seem to be the primary forces behind the genetic adaptation of bacterial organisms to novel environments and by which bacterial populations diverge and form separate, evolutionarily distinct species. Mechanisms of horizontal gene flux include the transmission of mobile genetic elements such as conjugative plasmids, bacteriophages, transposons, insertion elements, and genomic islands, as well as the mechanism of recombination of foreign DNA into host DNA .
Point mutations and genetic rearrangements only lead to evolutionary development, primarily without creation of novel genetic determinants, while horizontal gene transfer (HGT) produces extremely dynamic genomes. Thus, HGT can effectively alter the life‐style of bacterial species. This is particularly true for bacterial pathogens, where virulence is linked to acquisition of virulence determinants by HGT .
A major driving force of evolution and diversification in pathogenic bacteria compared with modification of the existing DNA is the acquisition of virulence determinants through successive horizontal gene transfer . The evolution of pathogenic bacteria with a strong lineage dependency often results from integration, retention, and expression of foreign DNA with a specific genomic background. In fact, parallel evolution from strains with the same genomic pathotype has occasionally emerged from multiple lineages, although the genetic mechanisms are not fully understood .
The modification of old functions and the development of new ones are required for bacterial evolution. The most frequent events are nucleotide exchange, insertion, and deletion. Mutation rates, per nucleotide per generation, are generally in the range of 10−6–10−9 in bacteria. Moreover, gene disruption, deletions, and module exchange between different genes occur at appreciable frequency. These mechanisms are common in all living organisms. They allow modification of existing functions for optimizing in a niche or adapting to a new niche. Bacteria have no sexual life cycles, in contrast to higher organisms, to facilitate the exchange of alleles within a population. This function is fulfilled by horizontal gene transfer in bacteria; in this way the entire functional genomic unit can be imported from other sources that are not restricted by species. The DNA is transferred from less than 1 to more than 100 kb, in size. It can encode entire metabolic pathways or complex surface structures. These genes can be taken up as naked DNA or transferred in the form of plasmids, transposons, or phages .
2. Horizontal gene transfer (HGT)
2.1. Horizontal gene transfer (HGT) and pathogenicity islands
Subgroups of genomic islands which have a pivotal role in HGT are pathogenicity islands (PAIs). The concept of PAI was founded in the late 1980s by Jörg Hacker and colleagues in Werner Goebel’s group at the University of Würzburg, Germany [2, 3].
2.1.1. The genetic features of PAIs
One or more virulence genes are carried by PAIs. There are also genomic or metabolic islands with genomic elements and characteristics similar to PAI, but lacking virulence genes. They are not present in the genome of a nonpathogenic species or a closely related species, but they are present in the genome of the same pathogenic bacterium .
Large genomic regions are relatively occupied by PAIs. They often differ from the core genome and the majority of PAIs are in the range of 10–200 kb in their base compositions and they also show different codon usage. It is considered that the horizontally acquired PAI still has the base composition of the donor species. On the other hand, it is also observed that the horizontally acquired DNA base composition will tend to the base composition of the recipient’s genome during evolution. Further factors such as DNA topology or specific codon usage of the virulence genes in PAI may also account for the maintenance of the divergent base composition .
PAIs are frequently adjacent to tRNA genes. tRNA genes serve as anchor points for insertion of foreign DNA that has been acquired by horizontal gene transfer through recombination process. They are frequently associated with mobile genetic elements and they are often flanked by direct repeat (DR) sequences. PAIs delete with distinct frequencies and they are often unstable. PAI virulence functions are lost with a frequency higher than the normal rate of mutation. Integrases, transposases, and insertion sequence (IS) elements have been identified as elements that contribute to the mobilization and instability of PAIs .
PAIs often represent mosaic‐like structures rather than the homogeneous nature of horizontally acquired DNA .
The islands are divided into different subtypes based on their genetic composition and also on their effects in a specific ecological niche, within a particular organism. Therefore, the same islands may have different functions .
2.1.2. Evolution, transfer, regulation, and integration sites of PAIs
The observation that important virulence factors are present in very similar forms in different bacteria may be explained by horizontal gene transfer. PAIs transfer via three major paths, including (i) natural transformation, (ii) plasmids, and (iii) transduction. PAI integration into the bacterial chromosome is a site‐specific process. PAIs are mostly inserted at the 3′ end of tRNA loci. Furthermore, phage attachment sites are frequently located in this region. Specific genes and intergenic regions have been used by PAIs, in operons. For instance,
PAI genes respond to environmental signals by gene expression. PAIs are part of complex regulatory networks that include regulators encoded by the PAI itself or by other PAIs, and other global regulators elsewhere in the chromosome or by plasmids. PAI regulators can be involved in the regulation of genes located outside the PAI. Regulators mostly belong to the AraC/XylS family or to the two‐component response family .
2.2. Horizontal gene transfer and transduction by phages
2.2.1. Evolution of bacterial pathogens by phages
Phages play an important role in the evolution and virulence of many pathogens. From common virulence factors encoded by phages in
The analysis of bacterial genome sequencing revealed that phages affect the bacterial genome architecture . In addition, phages are important vehicles for horizontal gene exchange between different bacterial species and account for a good share of the strain‐to‐strain differences within the same bacterial species. In fact, two‐third of gamma proteobacteria and low G+C Gram‐positive bacteria harbor prophages [4, 5].
The early studies had indicated that some prophages carry additional cargo genes (lysogenic conversion genes) which are not required for the phage life cycle. Instead, a lot of DNA from phages or morons (more DNA) from prophages in pathogenic bacteria encode virulence factors. Lysogenic conversion is thought to have a great impact on the evolution of pathogenic bacteria and results in a very interesting situation of bacterium‐phage coevolution.
2.2.2. Phage‐mediated gene transfer
Phage‐mediated horizontal gene transfer occurs via transduction or lysogenic conversion. In addition, bacterial gene disruption can occur by prophage integration into the bacterial genome.
The phage DNA must be packed, after the phage heads are completed. In a limited frequency, DNA fragments of the host genome are packed instead of the phage DNA; however, the transduction process is quite accurate. In this process, fully functional phage particles can result, which in return deliver the packed DNA into other suitable bacteria. On the one side of transduction, the absence of phage DNA does not harm the bacterium. Instead, the injected foreign bacterial DNA can be incorporated into the genome. This is a typical example of phage‐mediated horizontal gene transfer. These phages have been observed in many bacteria, for instance
220.127.116.11. Lysogenic conversion
Phages can play an important role in the emergence of new pathogens. This was recognized for Shiga toxin of
18.104.22.168. Gene disruption
Acquiring virulence genes is not the only mechanism by which pathogenicity develops. Pathogenic bacteria also develop from commensal bacteria by loss of genes.
2.3. Phages, PAIs, and plasmids in the evolution of pathogenic
E. colithrough horizontal gene transfer (HGT)
2.3.1. PAIs and
The best understood genomic islands are PAIs, to date, which carry a cluster of virulence genes. The virulence gene products contribute to the pathogenicity of bacterium. In the case of
LEE (the locus of enterocyte effacement) was initially described in EPEC strains, the causative agents of infant diarrhea in developing and industrial countries. EPEC strains are able to cause attaching‐and‐effacing (A/E) lesions of the microvillus brush border of enterocytes . All of the genes necessary for this phenotype are located on a PAI, termed LEE. LEE is horizontally transferred and contains 41 ORFs, integrated adjacent to either the
HPI (high pathogenicity island) was first described in
Regions encoding hemolysin and P‐fimbriae are named as PAI‐I, ‐II, which are located at centisomes 82 and 97 in
Since most virulence factors must be exposed on the surface of a bacterium or be secreted, many bacteria develop secretion pathways. An example of a T1SS (type 1 secretion system) encoded by a PAI is the
Finally, there are many identified PAIs in different
2.3.2. The role of phages in
E. colipathogenicity and evolution
Phages were acquired through horizontal gene transfer by an old nonpathogenic
22.214.171.124. Shiga toxins
Shiga toxins (Stxs) are a family of related toxins with two major groups, Stx1 and Stx2, which are expressed by genes considered to be horizontally acquired by bacteriophages. Shiga toxin encoded by
The second important factor is T3SS encoded by LEE, a PAI which is adjacent to 933L prophage. Shiga toxin is a causative agent of severe diarrhea, hemorrhagic colitis syndrome (HC), and hemolytic‐uremic syndrome (HUS) in STEC strains. The Shiga toxin released by bacteria residing in the intestinal lumen is thought to be responsible for all of these symptoms. The toxin crosses the intestinal epithelial barrier, and then enters the bloodstream, damages colon vascular cells, kidneys, and the central nervous system [5, 10].
A large number of STEC serotypes are known. Although O157:H7 is the most important, four non‐O157 STEC serotypes such as O26:H11, O103:H2, O145:H28, and O111:H8, have emerged as leading causes of infection. The major virulence factor of STEC is Shiga toxins (Stxs). STEC strains carry Stx1, Stx2, or both. Stx1 and Stx2 are divided into three (a, c, and d) and seven (a–g) subtypes, respectively. Stx phages can insert their DNA into specific chromosomal sites during infection of
Stx phages’ insertion of DNA into genes can be in the basic genetic elements of the
Prophages of non‐O157 EHEC strains were also shown to be remarkably divergent in their structure and integration sites from those of EHEC O157 (Sakai strain). Consequently, among STEC O26:H11 strains isolated from dairy products, cattle, and human patients, a diverse range of genetic patterns was observed. Different
Some outbreaks in the world were noticeable because they highlighted the potential contributions of rapid whole‐genome sequencing for understanding the phylogenetic origins of a new pathogen, its transmission and epidemiology, and the genetic basis for its pathogenicity. One of them is related to
On the whole, investigations have indicated that, the Stx phages provide an example of the rapid exchange of moron cassettes between phages from different
126.96.36.199. Cytolethal distending toxins (CDTs)
First, CDTs were recognized as bacterial toxins that block the eukaryotic cell cycle, suppress cell proliferation, and eventually lead to cell death . The holotoxin is a heterotrimer of three protein subunits, CdtA, CdtB, and CdtC. These are encoded by three adjacent and sometimes overlapping genes. CdtB is the active subunit, possessing DNase activity and sharing homology with the mammalian DNaseI. Genes encoding CDTs are widely disseminated among Gram‐negative pathogenic bacteria, including
Five different CDTs (I–V) have been reported for
CDT‐I and CDT‐II were identified in EPEC serotype O86:H34 and O128: NM strains, respectively. CDT‐III was detected in
CDT‐IV was detected in human and animal pathogenic
The presence of CDT‐V in Shiga‐toxigenic
These findings indicate that during evolution, while the
The presence of
2.3.3. HGT and plasmids harboring virulence genes in pathogenic
It is now evident that some virulent genes are located on a large plasmid (pO157) in pathogenic
EspP can be grouped into the autotransporter proteins family and characterized by catalytically active serine residue in the active center. EspP cleaves pepsin and human coagulation factor V. EspP was detected in EHEC O157 and O26 strains. Catalase‐peroxidase gene (
In pathogenic bacteria, there are S‐fimbriae and P‐fimbriae as different types of fimbriae in uropathogenic
3. Diversity of
The coevolution of bacterial pathogens related to genetic elements, including pathogenicity islands and phages encoding virulence factors, has been observed in several species.
Investigations have revealed,
This evidence further confirms that horizontal gene transfer could occur among pathogenic strains. Moreover, findings indicate that CDT‐producing strains may have originated from a common ancestor during their evolution by HGT, and they departed from each other .
CDT‐producer strains did not show particular phylogenomic relation and pattern. Indeed, they might carry the same or similar virulence gene sets, but remarkably possess their own divergent genomic structure. This is probably because of their complex and distinct evolutionary pathways, indicating independent acquisition of mobile genetic elements that have driven from their evolution . Furthermore, it was shown that there are different types of CDTs that are encoded by prophages, plasmids, and/or pathogenicity islands that result in different types of CDTs through HGT in different origins [7, 17, 19, 22].
In the recent years, whole‐genome sequences for many bacteria have become accessible. It improves our understanding about virulence‐associated genes and horizontal gene transfer from the emergence of new pathogens aspects. Some pathogens like
Phage‐related and virulence‐associated factors transferred by phages were found to be prevalent signature proteins. The signature proteins identified include several individual phage proteins (holins, nucleases, terminases, and transferases) and multiple members of different protein families (the lambda family, phage‐integrase family, phage‐tail tape protein family, putative membrane proteins, regulatory proteins, restriction‐modification system proteins, tail fiber‐assembly proteins, base plate‐assembly proteins, and other prophage tail‐related proteins).
4. Conclusions and the way forward
The heterogeneous nature of strains could be because of the HGT through mobile genetic elements. The genetic exchanges that occur in bacteria provide genetic diversity and versatility. Plasmids, bacteriophages, and genomic islands belong to the flexible
The accumulating amount of sequence information generated in the era of “genomics” helps to increase our understanding of factors and mechanisms that are involved in diversification of this new bacterial species, as well as in those that may direct host‐specificity. From a comparative genomic aspect, a significant challenge is to utilize bulky amount of datasets to distinguish and conceptualize specific sequence signatures that scientifically or diagnostically are applicable traits. By comparing more sequence data from different strains, new signature biomarkers will be recognized for use as vaccines or as diagnostic factors in future. Signature conserved proteins in a wide range of pathogenic bacterial strains can potentially be used in modern vaccine‐design strategies.
Moriel DG, Rosini R, Seib KL, Serino L, Pizza M, Rappuoli R. Escherichia coli: Great diversity around a common core. MBio. 2012; 3(3):e00118-12
Schmidt H, Hensel M. Pathogenicity islands in bacterial pathogenesis. Clinical Microbiology Reviews. 2004; 17(1):14-56
Schubert S, Darlu P, Clermont O, Wieser A, Magistro G, Hoffmann C, Weinert K, Tenaillon O, Matic I, Denamur E. Role of intraspecies recombination in the spread of pathogenicity islands within the Escherichia colispecies. PLoS Pathogens. 2009; 5(1):e1000257
Ogura Y, Ooka T, Iguchi A, Toh H, Asadulghani M, Oshima K, Kodama T, Abe H, Nakayama K, Kurokawa K, Tobe T, Hattori M, Hayashi T. Comparative genomics reveal the mechanism of the parallel evolution of O157 and non‐O157 enterohemorrhagic Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America. 2009; 106(42):17939-17944
Brüssow H, Canchaya C, Hardt WD. Phages and the evolution of bacterial pathogens: From genomic rearrangements to lysogenic conversion. Microbiology and Molecular Biology Reviews. 2004; 68(3):560-602
Mohammadzadeh M, Oloomi M, Bouzari S. Genetic evaluation of locus of enterocyte effacement pathogenicity island (LEE) in enteropathogenic Escherichia coliisolates (EPEC). Iran Journal of Microbiology. 2013; 5(4):345-349
Oloomi M, Bouzari S. Molecular profile and genetic diversity of cytolethal distending toxin (CDT)‐producing Escherichia coliisolates from diarrheal patients. APMIS. 2008; 116(2):125-132
Bidet P, Bonacorsi S, Clermont O, De Montille C, Brahimi N, Bingen E. Multiple insertional events, restricted by the genetic background, have led to acquisition of pathogenicity island IIJ96‐like domains among Escherichia colistrains of different clinical origins. Infection and Immunity. 2005; 73(7):4081-4087
Taneike I, Zhang HM, Wakisaka‐Saito N, Yamamoto T. Enterohemolysin operon of Shiga toxin‐producing Escherichia coli: A virulence function of inflammatory cytokine production from human monocytes. FEBS Letters. 2002; 524(1-3):219-224
Gyles CL. Shiga toxin‐producing Escherichia coli: An overview. Journal of Animal Sciences. 2007; 85(13 Suppl):E45-62
Kyle JL, Cummings CA, Parker CT, Quiñones B, Vatta P, Newton E, Huynh S, Swimley M, Degoricija L, Barker M, Fontanoz S, Nguyen K, Patel R, Fang R, Tebbs R, Petrauskene O, Furtado M, Mandrell RE. Escherichia coliserotype O55:H7 diversity supports parallel acquisition of bacteriophage at Shiga toxin phage insertion sites during evolution of the O157:H7 lineage. Journal of Bacteriology. 2012; 194(8):1885-1896
Bonanno L, Loukiadis E, Mariani‐Kurkdjian P, Oswald E, Garnier L, Michel V, Auvray F. Diversity of Shiga toxin‐producing Escherichia coli(STEC) O26:H11 strains examined via Stx subtypes and insertion sites of Stx and EspK bacteriophages. Applied Environmental Microbiology. 2015; 81(11):3712-3721
Grad YH, Godfrey P, Cerquiera GC, Mariani‐Kurkdjian P, Gouali M, Bingen E, Shea TP, Haas BJ, Griggs A, Young S, Zeng Q, Lipsitch M, Waldor MK, Weill FX, Wortman JR, Hanage WP. Comparative genomics of recent Shiga toxin‐producing Escherichia coliO104:H4: Short‐term evolution of an emerging pathogen. MBio. 2013; 4(1):e00452-12
Sváb D, Horváth B, Maróti G, Dobrindt U, Tóth I. Sequence variability of P2‐like prophage genomes carrying the cytolethal distending toxin V operon in Escherichia coliO157. Applied Environmental Microbiology. 2013; 79(16):4958-4964
Tóth I, Nougayrède JP, Dobrindt U, Ledger TN, Boury M, Morabito S, Fujiwara T, Sugai M, Hacker J, Oswald E. Cytolethal distending toxin type I and type IV genes are framed with lambdoid prophage genes in extraintestinal pathogenic Escherichia coli. Infection and Immunity. 2009; 77(1):492-500
Asakura M, Hinenoya A, Alam MS, Shima K, Zahid SH, Shi L, Sugimoto N, Ghosh AN, Ramamurthy T, Faruque SM, Nair GB, Yamasaki S. An inducible lambdoid prophage encoding cytolethal distending toxin (Cdt‐I) and a type III effector protein in enteropathogenic Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America. 2007; 104(36):14483-14488
Javadi M, Oloomi M, Bouzari S. Genotype cluster analysis in pathogenic Escherichia coliisolates producing different CDT types. Journal of Pathogens. 2016; 2016:9237127
Brunder W, Khan AS, Hacker J, Karch H. Novel type of fimbriae encoded by the large plasmid of sorbitol‐fermenting enterohemorrhagic Escherichia coliO157:H(−). Infections and Immunity. 2001; 69(7):4447-4457
Oloomi M, Javadi M, Bouzari S. Presence of pathogenicity island‐related and plasmid encoded virulence genes in cytolethal distending toxin producing Escherichia coliisolates from diarrheal cases. International Journal of Applied Basic Medical Research. 2015; 5(3):181-186
Brunder W, Schmidt H, Karch H. KatP, a novel catalase‐peroxidase encoded by the large plasmid of enterohaemorrhagic Escherichia coliO157:H7. Microbiology. 1996; 142(Pt11):3305-3315
Brunder W, Schmidt H, Karch H. EspP, a novel extracellular serine protease of enterohaemorrhagic Escherichia coliO157:H7 cleaves human coagulation factor V. Molecular Microbiology. 1997; 4(4):767-778
Bouzari S, Oloomi M, Oswald E. Detection of the cytolethal distending toxin locus cdtB among diarrheagenic Escherichia coliisolates from humans in Iran. Research in Microbiology. 2005; 156(2):137-144