Emergence and Dissemination of Extraintestinal Pathogenic High-Risk International Clones of Escherichia coli

Multiresistant Escherichia coli has been disseminated worldwide, and it is one of the major causative agents of nosocomial infections. E. coli has a remarkable and complex genomic plasticity for taking up and accumulating genetic elements; thus, multiresistant high-risk clones can evolve. In this review, we summarise all available data about internationally disseminated extraintestinal pathogenic high-risk E. coli clones based on whole-genome sequence (WGS) data and confirmed outbreaks. Based on genetic markers, E. coli is clustered into eight phylogenetic groups. Nowadays, the E. coli ST131 clone from phylogenetic group B2 is the predominant high-risk clone worldwide. Currently, strains of the C1-M27 subclade within clade C of ST131 are circulating and becoming prominent in Canada, China, Germany, Hungary and Japan. The C1-M27 subclade is characterised by blaCTX-M-27. Recently, the ST1193 clone has been reported as an emerging high-risk clone from phylogenetic group B2. ST38 clone carrying blaOXA-244 (a blaOXA-48-like carbapenemase gene) caused several outbreaks in Germany and Switzerland. Further high-risk international E. coli clones include ST10, ST69, ST73, ST405, ST410, ST457. High-risk E. coli strains are present in different niches, in the human intestinal tract and in animals, and persist in environment. These strains can be transmitted easily within the community as well as in hospital settings. WGS analysis is a useful tool for tracking the dissemination of resistance determinants, the emergence of high-risk mulitresistant E. coli clones and to analyse changes in the E. coli population on a genomic level.


Introduction
Escherichia coli is a Gram-negative rod-shaped commensal bacterium in the human intestine; however, it is also a major causative agent of several infections. Extraintestinal pathogenic E. coli (ExPEC) is responsible for a wide range of severe community-and hospital-acquired infections, such as neonatal meningitis, peritonitis, and bloodstream and urinary tract infections (UTI) [1,2]. Furthermore, multiresistant E. coli strains are responsible for a high number of hospital outbreaks worldwide that are associated with longer hospital stays, increased health care costs and high mortality rates [3][4][5].

ST101
VYQD00000000 (E. coli strain EC121) [77] Recently, the most significant clinical problems have been related to clade C. It originates from clade B, and consists of two major subclades, namely C1/H30-R and C2/H30-Rx ( Figure 1). Their evolution has been demonstrated, as they arose from an early common fluoroquinolone-susceptible ancestor C/H30 subclone with type 1 fimbrial adhesin gene (fimH30). Initially, H30 was the most prevalent among them, emerging in the 1980s. In the course of clonal expansion, it obtained high-level fluoroquinolone resistance by sequential chromosomal mutations of gyrA and parC genes, then it also became resistant against beta-lactams by acquisition of plasmid-mediated ESBLs, as well as carbapenemases [15,29,45,52,53,58]. The self-transmissible plasmids of ST131 are characterised by a remarkable genetic diversity (plasmidome), they belong in particular to incompatibility group F (IncF type). They may possess FIA or FII replicon types, which aid in the successful uptake and rapid dissemination of resistance genes. The most frequently reported plasmid MLST types are F1:A2:B20 in multidrug-resistant (MDR) clade C1 and F2:A1:B of MDR clade C2 [15,78,79]. A recent in-depth analysis showed that by a novel subset of C2, the plasmidome was not uniform; it had a combined pattern of certain plasmid types, and it showed a homogeneous replicon structure of F31/F36:A4:B1 [58].
In general, a common feature of strains in clade C is the carriage of bla TEM . However, subclade C1 presents bla CTX-M-14 or bla CTX-M-27 ESBL genes, while on the other hand, subclade C2, which has a single nucleotide polymorphism (SNP) at fimH30, is mainly associated with bla CTX-M-15 . The bla CTX-M-27 positive subset of C1, referred to as subclade C1-M27, recently became prominent in Japan, Canada, Germany and China [20,46,[80][81][82]. In Iran, a comparative study on MDR ST131 and non-ST-131 clones reported that both were associated with bla TEM , bla SHV , bla CTX-M , bla OXA-48 genes, as well as with plasmid-mediated quinolone resistance (PMQR) determinants (bifunctional aminoglycoside acetyltransferase-Ib-cr [aac6 -Ib-cr] and Qnr protective proteins [qnrB, qnrS] [83]. A genomic epidemiological investigation of ESBL producer E. coli isolates was also performed in Dhaka, Bangladesh. Not surprisingly, the predominant clone from clinical urine and pus samples was ST131, as this clone accounted for 46% of the isolates. The whole-genome sequences (WGS) of these strains were deposited in GenBank under accession numbers from JACHQR000000000.1 to JACHPB000000000.1 [39]. In Brazil a CTX-M-27-producing E. coli ST131 strain that belonged to clade C1-M27 was reported in oysters. This E. coli strain was recovered from an aquatic area impacted by intensive maritime traffic and transoceanic shipping activities [66]. WGS information is shown in Table 1.
A recent study in Hungary investigated ESBL-producing E. coli isolates obtained from a tertiary care hospital in Budapest. Whole-genome sequence analysis showed that five E. coli isolates belonged to the ST131 clone: two to the C1-M27 subclade with bla CTX-M-27 Life 2022, 12, 2077 6 of 23 and three to the C2/H30Rx subclade with bla CTX-M-15 . Based on core genome MLST, all C2/H30Rx isolates formed a cluster (≤6 allele differences), while the bla CTX-M-27 -producing C1-M27 isolates differed from each other with respect to at least 35 alleles. This study indicates that the C2/H30Rx and C1-M27 subclades of the ST131 are currently circulating among Hungarian clinical isolates [84].
Carbapenem resistance among ST131 strains is based on plasmid-acquired carbapenemase enzymatic activity [82]. According to a recent genomic epidemiological study that investigated clinical isolates from 62 countries between 2015 and 2017, many subtypes of carbapenemases were carried by ST131. During these studies, ST131 was mainly isolated from UTI and bacteraemia. From two different isolates, bla KPC-3-and bla OXA-48 -producer ST131-A clade has been reported in USA and Lebanon, respectively. A subclade C1-M27 was also present, which showed positivity for bla NDM-1 from Russia and Philippines, and bla OXA-232 from Thailand. From the C1 subclade, a non-M27 subtype was detected as well, and these strains carried bla KPC-2 in Guatemala, Israel and USA, bla KPC-3 in Italy and bla KPC-18 in the USA. The globally predominant ST131-C2 subclade carried bla KPC-2 in Puerto Rico, bla KPC-3 in Italy, bla NDM-1 in Egypt and bla NDM-5 in Canada. Ambler class D carbapenemase, namely bla OXA-48 and bla OXA-181 , production was also described in Egypt and Iran. Additionally, a ST131-C2 strain showed positivity for co-expression of bla NDM-1 and bla VIM-1. [40,82]. Located on plasmids with sequence similarities (95-100%), different carbapenemases of ST131 have been detected in other international clones as well [84][85][86]. Additionally, the co-carriage of bla OXA-1 , bla CTX-M-15 , aac6-Ib-cr and aac3-IIa has also been detected in strains of C2 clade [58,87].
Another recent survey found CC131 subclones in 10 hospitals in different cities in Argentina. The observed samples were mainly blood, urine and abdominal fluids. The majority (7 of 10 samples) belonged to the C2 subclade, and they carried bla KPC-2 , and one strain showed positivity for bla VIM-1 . The C1 subclade was also found, and expressed bla CTX-M−2 . Furthermore, the so called ECO112 KPC-2-producer strain of clade B was fluoroquinolone-susceptible and carried bla FOX−5 . The other isolates of CC131 were resistant to fluoroquinolones based on chromosomal mutations of gyrA, parC or parE, and, additionally, PMQR determinants, namely, qnrB and qnrS1, were also detected. As an interesting result, a strain referenced as ECO14 of ST131 exhibited resistance to colistin (MIC ≥ 4 µg/mL), but it lacked mcr. It developed colistin resistance due to seven chromosomal mutations in the pmrB and pmrA genes (phosphoetanolamin transferase coding genes) [20].
Moreover, in certain cases, O16:H5 ST131 and rare, even non-typeable relatives were also found. These subclones were compared to the most successful O25b:H4 serotype, and studies detected that the so-called O16 subclone has a higher rate of trimethoprimsulfamethoxazole and gentamicin resistance, but a lower prevalence of fluoroquinolone and ceftriaxone resistance, than O25b [88]. In addition, a study in Kyoto, Japan described a separated O75:H30 cluster within the C1 subclade, which was characterised by an extraordinary Phi-like region (M27PP1). Subsequently, this ExPEC subtype was reported not only in Japan, but also in Thailand, Australia, Canada and in the USA, so its prevalence has been significantly increased [15,80,89].
Finally, the pangenome of clade C is divided into a strongly determined core genome and an additional genetic context with remarkable variability that is responsible for a huge repertoire of virulence factors [83,90]. According to the so-called "perfect storm" theory, acquisition of virulence factors plays an essential role in the clonal expansion of multiresistant bacteria, as the acquirement of these genes is followed by higher antibiotic resistance rates [53]. Based on the PCR-verified presence of certain virulence genes including Afa and Dr adhesins (afa/draBC), operon (afa), catecholate siderophore receptor (iroN), secreted autotransporter toxin (sat), ibeA ('invasion of brain endothelium' gene), allele II and III of papG gene (papGII and papGIII), cytotoxic necrotising factor type 1 (cnf1), alpha-hemolysin (hlyA), cytolethal distending toxin (cdtB) and K1 variant of group II capsule (neuC-K1) virotypes are defined from A to E groups [52]. The current evolution of new virotypes in C2 subclade can also be seen, as a study from Singapore demonstrated a monophyletic subclone from bacteraemia referred to as SEA-C2 [58,91].
Interestingly, a comparative genomic analysis of 99 ST131 strains and 40 genomes of other high-risk clones (ST38, ST405 and ST648) showed that clades A, B, and C of ST131 were more distant relatives than the others. This study could not identify any CC131specific proteins, although the absence of 142 proteins in the core genome of all of the 99 isolates was found. These results suggest that the drive of adaptive strategies of ST131 were mainly loss, exchange, and co-evolution of genes, including that of antimicrobial resistance and virulence [38]. WGS data are available in GenBank (Table 1).
Based on the 'One Health' approach, zoonotic risk, as a novel aspect of MDR CC131 global distribution, has been also suggested. As a common feature, many rapid outbreaks of high-risk international MDR bacteria have originated from the human-animal interface [47]. Due to the similar and overlapping molecular regions between avian pathogenic E. coli and ExPEC, it has previously been hypothesised that avian E. coli may act like a reservoir of virulence and resistance markers. Therefore, it may be responsible for foodborne infections in humans [83,92]. In a study from Iran, ST131 strains from human isolates were compared to isolates obtained from broiler chickens. Half of the isolates from chicken meat belonged to phylogroup A, which exhibited a ciprofloxacin-resistant phenotype, but no ST131 was detected in broilers in that study [83]. On the other hand, studies from Spain, Canada and Arizona confirmed the presence of CC131, mainly clade B, in poultry. Moreover, mcr-5and mcr-9-positive strains were also isolated among these ST131 strains [18,57,93,94].
A genomic surveillance and cell culture-based virulence investigation study demonstrated the co-presence of bla CTX-M-15 -positive Klebsiella pneumoniae ST307 and bla CTX-M-27positive CC131 with other phylogroups of ExPEC MDR clones containing various CTX-M types and AmpC in oysters and mussel specimens from the Atlantic Coast of South America. Marine bivalves are filter-feeding organisms, so they can extract a large amount of material from water, such as human faecal pollution, including MDR bacterial strains. Furthermore, production of thermostable toxin has also been reported among these strains, so a great deal of attention should be paid to seafood as a source of diseases induced by high-risk toxin producer MDR bacterial clones. The whole-genome sequence of this ST131 strain was deposited in GenBank under the accession number NCVZ00000000.1 [47] (Table 1). Furthermore, houseflies have been hypothesised to be vectors of many MDR bacteria, including Pseudomonas aeruginosa, Acinetobacter baumannii, Citrobacter freundii, Enterobacter cloacae, Klebsiella oxytoca and ExPEC clones, such as CC131, in a tertiary hospital in Rwanda, Africa. This clone carried, among others, bla CTX-M-15 , bla OXA-1 , bla TEM-1B and aac(6 )-Ib-cr. In this case, randomly captured flies were observed in fly traps over 4 weeks from different locations of the hospital, for instance, from the surgery operating theatre, gynaecology, paediatrics, the restaurant, the kitchen, and the laboratory. Interestingly, ST131 was identified only from the kitchen, and the vast majority of the other MDR species had a similar resistome. The results demonstrated that almost all of them carried bla CTX-M-15 , bla OXA-1 and some expressed aac(6 )-Ib-cr and qnrB1 [95].
A study from Rwanda investigated 120 ESBL-producing E. coli strains from hospitalised patients. Altogether, 30 different sequence types were detected, including pandemic clonal lineage ST131. Frequently found resistance genes included bla CTX-M-15 , tet (34), and aph(6)-Id. Additionally, a phylogenetic relationship was found among strains from patients and their related community members and animals, indicating transmission of clinically relevant, pathogenic ESBL-producing E. coli among patients, animals, caregivers and the community in Rwanda [96].
In summary, the structure of the E. coli population has changed dramatically, with appearance and global dissemination of the currently dominant multidrug-resistant C2 subclade of ST131. Nevertheless, from the most successful phylogroup B2, other high-risk clones can evolve and cause alarming challenges too [37].

ST1193, a Recently Emerging Pandemic MDR Clone from Phylogroup B2
Although ST1193, a sister clone of ST131, had already been described in Australia in 2012, case reports of this clone have increased considerably in number only in the last few years. The ST1193 clone is also known as the latest pandemic multidrug-resistant clonal group [46,[97][98][99]. A recent study from France described five E. coli strains of ST1193 that were harbouring bla CTX-M-15 and bla CTX-M-27 . These strains were obtained from febrile urinary tract infections in children [100]. A study from China reported that E. coli strains of ST1193 were responsible for more than 20% of neonatal invasive infections in China [100,101]. Furthermore, ST1193 was also found together with clade A ST131 strains in stool samples of healthy children in Changsha, China [46].
One strain of ST1193 was isolated in Dhaka, Bangladesh from a urine sample. It expressed a plasmid-acquired bla CTX-M-15 , and it belonged to the O75:H5 serogroup. The whole-genome sequence data of this strain are available in GenBank under accession number JACHQB000000000.1 [39]. (Table 1).
Altogether, 355 strains of ST1193 were investigated in a study in the USA, and various resistance determinants were detected, namely, bla TEM-1B , bla CMY-2 , bla CTX-M-15 , bla CTX-M-27 , bla CTX-M-55 , bla OXA-1 , aac(6) -Ib-cr, and mutations were detected in genes gyrA, parC and parE. Strains of ST1193 were all lactose non-fermenting and carried fimH64, in particular. Its evolutionary development from K1 to K5 capsular types resulted in genomic changes and uptake of an F-type virulence plasmid were also reported [97]. A study from Hungary recently reported a single E. coli from clinical isolates that belonged to ST1193 and carried bla CTX-M-27 [84].
Carbapenem resistance has occurred in ST1193, and bla KPC-2 and bla NDM-1 have been reported [40]. Moreover, mutations in pmrA and pmrB that confer colistin resistance were also confirmed [102]. The complete ST1193 genome from a neonatal meningitis-associated strain is available in GenBank at accession number: CP030111 [59,97] (Table 1).

ST69 and CC10, the Second and Third Most Common High-Risk Clones
Overall, based on a comparative summary of 169 studies about ExPEC high-risk clones after the predominant ST131, we found ST69 and ST10 to be the second and third most frequent clones, respectively [37]. Initially, ST69 was isolated in the year 2000, from urine samples of 228 women with uncomplicated community-acquired UTIs at a public university campus of California. ST69 belongs to phylogenetic group D, and it is characterised by diverse O-antigen-based serogroups and the common presence of papGII. Since then, most of the reported strains of this clone have been multidrug-resistant, and they typically possess a class I integron that includes a single gene cassette including dihydrofolate reductase and aminoglycoside adenyltransferase (dfrA17-aadA5). In these samples, a trimethoprim-sulphamethoxazole-resistant Clonal Group A (CgA) was also detected, a clone that clusters within ST69 [103]. Interestingly, based on findings of the phylogenetic features of E. coli, it was revealed in England that the E. coli population remained stable over time, but some lineages emerged and were disseminated, including ST69 [104]. In total, 87 of 169 studies describe this clone for the period 1995-2018. ST69 is characterised by the presence of bla KPC-2 , bla NDM-1 [40], co-carriage of bla NDM-1 with bla CMY-6 , [20], bla CTX-M-1,-14,-15,-27 [100], mcr-1 [105], fosA3 [106] and gyrA, parC mutations, leading to fluoroquinolone resistance [107]. During other studies in Italy, this clone has also been identified from various origins, including dairy products, the diaphragms of wild boars, poultry, mussels, clams, and human stool. Aside from human specimens, chicken breast carries a wide spectrum of antimicrobial resistance genes [60,108]. The increasing number of cases of this MDR clone indicates the importance of studies of phylogenetics, population dynamics and molecular epidemiology using the 'One Health' approach [37].
CC10 belongs to phylogenetic group A, and it has been detected to be a widely disseminated clone, since it has been reported from food producing animals, free-living birds, plantbased foods, retail meats, wastewater, rivers, urban streams, and clinical settings, as well as being a part of human gut microbiome. Thus, faecal carriage in humans probably played a Life 2022, 12, 2077 9 of 23 significant role in its clonal expansion and dissemination. This clonal complex is composed of ST10 and its further relatives, including, among others ST44, ST48, ST167, ST617, ST410, and ST744 [37,109,110] (Figure 1). During a survey aiming to characterise the molecular epidemiology of carbapenemase-producing ExPEC in Argentina, CC10 was the major one, accounting for more than 20% of the samples. Of them, eight contained ST10, and the others were single-locus variants (ST44, ST744, ST167), double-locus variants (ST746, ST617) and a satellite clone (ST12667). On the other hand, CC10 was the main clone reported among carbapenemase producers, as it demonstrated positivity (in order of decreasing abundance) for bla KPC-2 , bla NDM-1 and bla IMP-8 . As an important finding, two of them showed co-expression of mcr-1; furthermore, another NDM-1-producer isolate was a co-producer of bla PER-2 . On the other hand, the ST617 clone exhibited the co-existence of bla KPC-2 , bla CTX-M-14 and bla CTX-M-27 . The nucleotide sequence information was submitted in GenBank under the BioProject accession number PRJNA784589 [20] (Table 1). In addition to β-lactam resistance, CC10 has also been marked by fluoroquinolone-resistance determinants (e.g., qnrS1, aac(6 )-Ib-cr) and the mcr-1 colistin-resistance gene [7,60,111,112]. In addition, bla OXA-48 associated with ST10; bla NDM-1 related to ST44, ST48, ST167, ST617; bla CTX-M-14,15,55 , fosA3, bla OXA-1 , bla NDM-1,9 , bla NDM-5 together with bla OXA-181 and co-carriage of bla OXA-48 in ST167; as well as bla KPC-2,3 with bla NDM-1 in ST617 have also been reported. Of these high-risk CC10 lineages, in the last few years, ST167 was clustered into subclades, and it was reported to be a predominant clone in China. This clone was also identified from a urine clinical sample as a qepA4 carrier [7,40,61,62,112,113].
Several studies have been reported indicating the high risk potential of ST410 from phylogenetic group A [5] (Figure 1). This clone has been described in many countries, albeit to a lesser extent compared to other high-risk clones. ST410 has been reported to be a clone that is transmitted between different reservoirs, namely, between wildlife, humans, companion animals, and the environment [114,115]. The ST410 clone has been reported as being bla OXA-181 positive in China [116] and Italy [117], as well as hospital outbreaks in Denmark [118]. A study from Dhaka, Bangladesh reported ST410 as being bla CTX-M-15 positive [39].
A whole-genome sequence analysis of E. coli ST410 in Denmark revealed carriage of bla OXA-181 and bla NDM-5 on IncX3 and IncF plasmids, respectively [119].

ST405 and High-Risk CC/ST38 Clones from Phylogenetic Group D
ST405 is a globally reported clone that carries similar variants of virulence genes to O25b:H4 ST131 [65]. Recently, this clone was marked as a potential reservoir for bla NDM-5 [40,62,119]. NDM-5-producing ST405 has been detected in many geographic regions, but it has shown the highest prevalence in the United Kingdom and Italy [63,120,121].
Moreover, an autochthonous case in 2018 was reported in Italy. The isolated strain carried bla NDM-5 , and among others bla CMY-42 , aadA2, mdf(A), sul1 and alterations of gyrA, parC, parE [121]. The presence of bla NDM-5 has also been detected in Japan and Mozambique, Africa [63,64]. This clone in Japan was non-susceptible to fluoroquinolones and β-lactams, including broad-spectrum cephalosporins and carbapenems, but it kept its susceptibility against tigecycline. The complete genome sequence of this strain is available under BioProject number: PRJDB8512 [63] ( Table 1).
The O102:H6 serotype was reported in Mozambique for the first time, possessing an FI:A1:B49 plasmid that co-harboured bla NDM-5 , bla CTX-M-15 , bla TEM-1 , aadA2, sul1 and dfrA12 genes. Additionally, this strain had chromosomal mutations of gyrA, parC and parE, resulting in fluoroquinolone resistance. The WGS data of this strain are available in the EMBL-EBI database, project accession number: ERS4552076 [64] (Table 1).
A study from Algeria reported mcr-1 in ST405 E. coli in environmental samples taken from eight agricultural sites in North West Algeria [122].
Similar to ST405, CC/ST38 was also previously a neglected clone, but nowadays it belongs to the so-called 'significant minority' of ESBL-producer E. coli, accounting for approximately 12% of strains from UTI [37,38,69]. Compared to ST131, the phylogenetic background of ST38 is far less detailed. It has mainly been described, on the basis of various O:H serotypes, as a hybrid uropathogenic-enteroaggregative clone [68,124].
During one study, three multiresistant E. coli strains were detected from rectal samples taken in the course of screening from three patients in Paris, France. Two patients had stayed previously in Egypt, and the third patient had come from Turkey. All three E. coli isolates belonged to the ST38 clone, and showed resistance to penicillins, cefotaxime, sulfonamides, tobramycin, and gentamicin, but remained susceptible to amikacin, tetracycline and fluoroquinolones. They also demonstrated a reduced susceptibility to carbapenems based on the presence of bla OXA-48 -harbouring plasmid. Co-carriage of bla CTX-M-2 , a point mutant variant of CTX-M-14, and bla TEM-1 was reported in that strain. Furthermore, this study demonstrated that these strains were clonally related; the same clonal strain probably circulated in Turkey and Egypt, and was later introduced into France [125].
On the other hand, bla CTX-M-14 and bla CTX-M-27 genes were also found in ST38, including in surveys from Germany, Switzerland and the USA [68,69,128]. Moreover, the bla CTX-M-27 gene was encoded by two distinct plasmid variants. In ST38, it was encoded in an IncF(F2:A-:B10) plasmid; by contrast, in ST131, it was located on IncF(F1:A2:B20) [68,69]. During this study in New York, USA the ST38 strains co-carried bla OXA-48 , bla DHA-1 and bla CTX-M-14 . The sequence information is available under BioProject accession numbers PRJNA692174 and PRJNA510429 [68] (Table 1). Moreover, MDR ST38 strains are often characterised as having a higher number of alterations in nitroreductase genes (nfsA and nfsB), resulting in nitrofurantoin resistance. The accession number for GenBank is RZEE00000000 [69] (Table 1). ST38 has also been detected as a colistin-resistant clone carrying mcr-5 in healthy chickens in a farm in Paraguay [130].
A study from Japan found that the bla NDM-1 gene was embedded between two IS903 elements as a gene cassette in an IncA/C-type plasmid. This transposon region was compared to plant pathogen bacteria, and homologous sequences were identified indicating that these microbes (e.g., Pseudoxanthomonas and Xanthomonas spp.) are potential sources of the bla NDM-1 gene [131]. In addition to the relationship between plant pathogens and ST38, this clone was also identified in Mongolian birds, but the acquired ESBLs (bla CTX-M-14 and bla CTX-M-15 ), independently of the antimicrobial selective pressure, were stably harboured by their chromosome instead of plasmids [132]. In addition, CC38 and CC10 were the predominant pandemic STs in food and among environmental E. coli strains in Brazil during a recent genomic surveillance analysis [112].

ST457, a Novel Emerging Clone from Phylogroup F
ST457 was first described in 2008 in the United Kingdom, and it was obtained in a clinical isolate from UTI. However, since then, the E. coli ST457 clone has emerged as a diverse E. coli clone present on all continents and from various samples, even in wild animals from Antarctica [19,133]. As evidence for further possible zoonotic and zooanthroponotic (reverse zoonotic) linkages, close similarities were found between Australian human clinical and silver gull strains among the H45 clade of ST457 [19]. These strains are characterised by carbapenemase production in patients with sepsis, namely bla KPC-2 (from Italy and Mexico), bla KPC-3 (from USA), bla NDM-5 (from Shanghai), and bla IMP-4 were also described in Australia, and interestingly, bla NDM-9 was detected in a poultry specimen. Surprisingly, chromosomally located bla OXA-23 was identified from Australian gull samples too [19,[134][135][136][137]. Additionally, this lineage often carries further beta-lactam resistance genes, the most common of which is bla CMY-2 from AmpC β-lactamases. ESBLs were also detected in ST457, including bla CTX-M-1,-2,-3,-8,-12,-14,-15,-27,-55 [19].
Colistin resistance has been reported in the ST457 clone in many cases. This can be explained by the presence of plasmid-mediated mcr-1 from human clinical isolates in the USA, China, Vietnam, Mexico, and from wildlife and poultry in Asia [138][139][140][141]. Furthermore, an mcr-3 variant was also identified in ST457 from a single domestic duck in China [142]. In addition, located on transferable plasmids, mcr-5, bla CTX-M-8 , bla TEM-1A , co-expression of aph(6)-Id aph-Ib, and sul2 were found among healthy chickens [19,70,130]. GenBank Accession numbers for high-risk international ST457 clones are available in Table 1.
The current dissemination of ST58 and ST101 from phylogenetic group B1 is alarming, because previously, this group was reported to be a cluster of environmental bacteria. However, recently, these clones have been described as causative agents of invasive infections (e.g., bloodstream infections). Interestingly, these clones have not been reported to be carbapenemase producers or as being colistin resistant, yet [76,77]. Currently, there are only a small number of reports available about these clones that explain their emergence and dissemination [20,[37][38][39][40]46,83,112,130,133,[143][144][145]. The related genome-sequence information from published reports is summarised in Table 1.

Discussion
The emergence, expansion, and recent outbreaks of ExPEC high-risk international clones are of great concern worldwide [37, 40,106]. MDR high-risk ExPEC is commonly detected in both nosocomial and community-acquired infections, and these infections are usually difficult to treat, because therapeutic options are limited [37][38][39]. The genome of E. coli has plasticity and high variability, and therefore various resistance and virulence genes can be taken up from different species of Enterobacterales and can be passed on to other species [19,95]. The development of these MDR strains depends significantly on the features of a given geographic area, such as trends of antibiotic consumption, resistance profile among currently circulating pathogens, travelling habits, medical tourism, and previous hospitalisation [64,121,125]. Furthermore, in countries such as Canada, the USA, Korea, Kuwait, Lebanon, France, Switzerland, Portugal, Spain, Germany, Bangladesh, China, and Japan, many lineages (e.g., ST131) circulate with quite similar resistance patterns [8] ( Table 2). Table 2. Overview of the most common resistance genes against beta-lactams, fluoroquinolones and colistin among high-risk international ExPEC clones. The most frequently reported plasmid types are also summarised here.

No data available
bla KPC-2 , bla KPC-3 , and bla  No data available
Fosfomycin is also mentioned as being among the last resort antibiotics that has retained antibacterial efficacy against MDR E. coli strains [10]. Of great concern, however, numerous fosfomycin-resistant E. coli clones have already been reported across the globe [106,112]. In the most common cases, resistance to fosfomycin is based on the enzymatic activity of fosA3. In addition, an ST131 clone was detected among patients of a hospital in China that carried mcr-3 and fosA3 together on an IncP plasmid [106]. Nitrofurantoin has also been considered to be an option for therapy in the case of UTI caused by MDR E. coli. However, resistance to nitrofurantoin has also been reported in ST131 and ST38 [44,69] (Table 3). Although in this study we focused on beta-lactams, fluoroquinolones and colistin, notably, almost all of the studied high-risk clones harboured a multicoloured collection of aminoglycoside-modifying enzymes, sumetrolim, tetracycline resistance genes [107].
Future actions that can be used to investigate and to analyse high-risk extraintestinal E. coli clones include surveillance on a genomic level, and the application of databases to detect new emerging clones and resistance determinants [147][148][149][150][151][152][153][154]. In terms of medical importance, novel antibiotics are needed to treat infections caused by multiresistant E. coli [21].
In conclusion, antibiotic resistance poses as an ongoing challenge worldwide and highrisk E. coli clones play a central role in the dissemination of resistance determinants. Taking