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Article

Genotypic Characterization of Uropathogenic Escherichia coli from Companion Animals: Predominance of ST372 in Dogs and Human-Related ST73 in Cats

by
Sophie Aurich
1,*,
Silver Anthony Wolf
2,
Ellen Prenger-Berninghoff
1,
Lakshmipriya Thrukonda
2,
Torsten Semmler
2 and
Christa Ewers
1
1
Institute of Hygiene and Infectious Diseases of Animals, Faculty of Veterinary Medicine, Justus Liebig University Giessen, 35392 Giessen, Germany
2
Genome Competence Centre, Robert Koch Institute, 13353 Berlin, Germany
*
Author to whom correspondence should be addressed.
Antibiotics 2024, 13(1), 38; https://doi.org/10.3390/antibiotics13010038
Submission received: 9 November 2023 / Revised: 13 December 2023 / Accepted: 26 December 2023 / Published: 30 December 2023
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Abstract

:
Extraintestinal pathogenic Escherichia coli (ExPEC) account for over 80% and 60% of bacterial urinary tract infections (UTIs) in humans and animals, respectively. As shared uropathogenic E. coli (UPEC) strains have been previously reported among humans and pets, our study aimed to characterize E. coli lineages among UTI isolates from dogs and cats and to assess their overlaps with human UPEC lineages. We analysed 315 non-duplicate E. coli isolates from the UT of dogs (198) and cats (117) collected in central Germany in 2019 and 2020 utilizing whole genome sequencing and in silico methods. Phylogroup B2 (77.8%), dog-associated sequence type (ST) 372 (18.1%), and human-associated ST73 (16.6%), were predominant. Other STs included ST12 (8.6%), ST141 (5.1%), ST127 (4.8%), and ST131 (3.5%). Among these, 58.4% were assigned to the ExPEC group and 51.1% to the UPEC group based on their virulence associated gene (VAG) profile (ExPEC, presence of ≥VAGs: papAH and/or papC, sfa/focG, afaD/draBC, kpsMTII, and iutA; UPEC, additionally cnf1 or hlyD). Extended-spectrum cephalosporin (ESC) resistance mediated by extended-spectrum β-lactamases (ESBL) and AmpC-β-lactamase was identified in 1.9% of the isolates, along with one carbapenemase-producing isolate and one isolate carrying a mcr gene. Low occurrence of ESC-resistant or multidrug-resistant (MDR) isolates (2.9%) in the two most frequently detected STs implies that E. coli isolated from UTIs of companion animals are to a lesser extent associated with resistance, but possess virulence-associated genes enabling efficient UT colonization and carriage. Detection of human-related pandemic lineages suggests interspecies transmission and underscores the importance of monitoring companion animals.

1. Introduction

Extraintestinal pathogenic Escherichia coli (ExPEC) are recognized as the leading cause of community-acquired and hospital-acquired urinary tract infections (UTIs) in both humans and companion animals [1,2,3,4]. Other significant pathogens commonly found include Staphylococcus pseudintermedius, Enterococcus faecalis, and various Enterobacterales, such as Proteus sp., Klebsiella sp., and Enterobacter sp. Additionally, Streptococcus canis and Pseudomonas aeruginosa have been described as being responsible for UTI infections in companion animals [2]. UTI caused by E. coli is one of the most common indications for which antibiotic treatment is initiated [5]. These treatments, however, have faced significant challenges due to the increase of multidrug-resistant (MDR) bacteria, including extended-spectrum β-lactamase (ESBL)-producing bacteria and isolates carrying plasmid-mediated cephalosporinases [6,7,8]. ESBL-producing E. coli show resistance to extended-spectrum cephalosporins (ESCs) but are still susceptible to β-lactam/β-lactamase inhibitor combinations [9]. In contrast, plasmid-mediated cephalosporinases remain unaffected by β-lactam/β-lactamase inhibitor combinations [10]. Moreover, fluoroquinolone resistance further narrows the choice of antimicrobial treatment of UTIs caused by E. coli or other bacterial pathogens. Fluoroquinolone resistance mechanisms include mutations in the quinolone resistance-determining region of bacterial type-II topoisomerase genes gyrA and parC or the presence of plasmid-encoded genes qnr and aac(6′)-Ib-cr [11]. As a result, the efficacy of commonly utilized antimicrobials like enro- and pradofloxacin, cefovecin, and amoxicillin/clavulanic acid is frequently impaired [12,13].
The majority of UTIs in humans and animals are caused by ExPEC, particularly the uropathogenic E. coli pathotype (UPEC). Both can cause extraintestinal disease in otherwise healthy individuals, including meningitis, intra-abdominal infection, pneumonia, and UTI, while being able to persist in the gut without causing inflammation [1,14,15,16,17]. Due to the presence of a distinctive set of virulence associated genes (VAGs), these pathotypes possess an enhanced ability to overcome host defences. VAGs coding for adhesins, toxins, and protectins allow ExPEC and UPEC to successfully colonize the urinary bladder, damage epithelial cells, and survive in the urinary tract. Additionally, they have evolved metabolic adaptations, such as enhanced iron acquisition systems, in order to survive across nutrient-scarce environments [18,19,20,21]. The distinction of ExPEC and UPEC from other E. coli pathotypes is based on the presence of these VAGs, which follow different classification schemes [22,23,24]. In 2000, Cermont et al. identified four phylogenetic groups within E. coli strains using PCR based on the presence of specific genes [25]. Currently, eight distinct phylogroups (A, B1, B2, C, D, E, F, and G) and various E. coli clades are recognized [26]. ExPEC and UPEC have mainly been associated with phylogroup B2, and to a lesser extent with phylogroups D and F [27,28].
Studies on the population structure of UPEC in dogs predominantly revealed multilocus sequence type ST372, as well as ST12, ST73, ST127, ST131, and ST141 [29,30,31]. Notably, all of these STs, with the exception of ST372, have also been associated with UTI in humans [32,33]. Few studies are available on the population structure of UPEC in cats, which mainly identified ST73 and ST83 [6,8,34,35]. Certain clonal linages appear to be more successful in causing extraintestinal infections and disseminating among certain host populations. Some clonal lineages have also been associated with the carriage of ESBLs and/or with fluoroquinolone resistance, such as O25b:H4-B2-ST131 or O6:H1-B2-ST73 [36]. With pets increasingly becoming integrated into human households, the risk of cross-transferring antimicrobial-resistant (AMR) bacteria and/or AMR genes between pets and their owners has emerged as a public health concern [37,38,39]. Monitoring the spread of these clones might essentially contribute to combating the global spread of ExPEC.
Therefore, we performed an in-depth analysis of UTI-causing E. coli isolated from routine diagnostic specimens of dogs and cats with symptoms of UTIs. We provide data on the pathotypes, phylogroups, serotypes, and clonal structure, and insights into the distribution of the VAG and AMR genes.

2. Results

2.1. Bacterial Isolates

We obtained 315 unique E. coli isolates from 195 dogs (63.3%) and 113 cats (36.7%) from 33 veterinary clinics during routine microbiological diagnostics. All samples were submitted with a preliminary report of suspected bacterial urinary tract infection. The sample pool consisted of urine samples (98.1% [cystocentesis, 17.5% midstream voided samples, 5.2% catheter specimens, 50.5% unspecified sampling procedure]) and, to a lesser extent (1.9%), of bladder tissue, uricult tests, uroliths, and kidney swabs. Notably, 48.9% of the isolates were provided by only three distinct veterinary clinics. A haemolytic phenotype was identified in 194 (61.6%) isolates. In 28.9% of the cases, the isolates were obtained from mixed infections, i.e., together with other specific uropathogens or nonspecific bacteria in low bacterial counts. The remaining 71.1% of isolates were obtained from monoinfections in pure culture.

2.2. Clonal Typing of E. coli Isolates

Phylogenetic group B2, which is associated with extraintestinal and uropathogenic E. coli infections in humans and animals, was the most frequently identified phylogroup (77.8%) (Table 1). Phylogroups D and F, also associated with extraintestinal infections, accounted for 2.2% and 0.6%, respectively.
Based on multilocus sequence typing (MLST), 315 isolates were assigned to 82 distinct sequence types (STs), with ST372 (17.5%), ST73 (15.9%), ST12 (8.6%), ST141 (4.8%), ST127 (4.8%), and ST131 (3.5%) being the most prevalent. Ten allele profiles (3.2%) could not be assigned to existing STs and were submitted to Enterobase (https://enterobase.warwick.ac.uk/; accessed on 19 September 2023) for further characterization (Supplementary Table S1). The distribution of ST372 and ST73 differed significantly between dogs and cats: ST372 was more prevalent in dogs (26.8%) compared to cats (1.7%) (p < 0.001), while ST73 was more common in cats (27.4%) than in dogs (9.1%) (p = 0.0002). ST73 (p < 0.001), ST372 (p = 0.018), ST12 (p = 0.001), and ST127 (p = 0.006) were positively associated with the haemolytic phenotype. A total of 32 different O-serogroups were identified among the E. coli isolates. Among the type I fimbrial adhesion gene alleles, fimH9 was the most frequently detected fimH type (20.3%) predominantly linked with ST372 (85.4%) (p < 0.0001). In cases of the second most common ST73, both fimH9 (28.0%) and fimH102 (18.0%) were the predominant fimH types.
Based on the presence of the VAGs papAH and/or papC, sfa/focG, afaD/draBC, kpsMTII, and iutA, 58.4% of the isolates were assigned to the ExPEC group. Among all isolates, 51.1% were classified as UPEC as they additionally possessed cnf1 or hlyD. Nearly all (98.1%) UPEC isolates were assigned to phylogroup B2 (Figure 1). In cases of mixed infections, E. coli isolates were less frequently classified as ExPEC (p = 0.04). The results of the sero(geno)typing and typing of fimH are displayed in Table 1.

2.3. Distribution of Virulence-Associated Genes

Virulence genotyping revealed a high number of VAGs required for colonizing the urinary tract, overcoming host immunity responses, and persisting in the urinary tract. The most abundant VAGs were genes encoding type 1 fimbriae (fimACDH, 98.7%), flagella (flgBCDEFGHIJ, 99.7%), and curli (csgABC/DEFG, 100%). Those factors play a crucial role in E. coli biofilm formation by mediating attachment to epithelial cells in the urinary tract [20]. In addition, genes related to the pathogenicity island marker MalX, which possesses glucose and maltose transporting activity, and the outer membrane protein OmpA, which promotes persistence of UPEC in the bladder, were present throughout the isolate collection (100%, each) [40]. Genes coding for the siderophore systems enterobactin (ent/fep/fes; 99.7%), yersiniabactin (irp/fyuA; 85.4%), and salmochelin (iroBCDE/N; 86.8%) were highly abundant, while aerobactin genes (iuc/iutA; 15.2%) occurred less frequently. Certain VAGs, such as the P fimbriae adhesion gene papG allele III, hemolysin gene hly, and cytotoxic necrotizing factor gene cnf1, have previously been associated with canine and feline UTIs and were accordingly detected in 45.1%, 46.3%, and 57.8% of our isolates, respectively [41]. A detailed distribution of the ExPEC-associated VAGs is provided in Table 2. In addition, a comprehensive listing of the VAG distribution among the bacterial isolates is shown in Table S2.
Positive correlations between the presence of UPEC-specific VAGs and STs were most frequently observed for the prevailing B2-STs, namely ST73, ST372, ST141, ST127, and ST12 (Figure 2). Conversely, B1-ST162 and B1-ST297, along with C-ST88, revealed negative associations with UPEC-specific VAGs. In contrast to other phylogenetic groups, B2 isolates more frequently revealed virulence factors that contribute to colonization and pathology of the urinary tract and to bacterial persistence, suggesting that B2 isolates are generally more successful in causing UTIs.

2.4. Distribution of AMR Genes

Among the 315 E. coli isolates, only 89 isolates, obtained from 51 dogs and 38 cats, possessed AMR genes. In total, 373 different AMR genes were identified (Table 3). Of these, blaTEM-1B represented the most common one (49.4%), followed by sul2 (41.6%) and tet(A) (32.6%). A detailed distribution of the resistance genes is shown in Table S3. There was no correlation between the occurrence of AMR genes and animal species. However, a lower number of AMR genes was present in the most prevalent phylogroup B2 compared with other phylogenetic groups. This was particularly notable concerning folate pathway inhibitors, including sul1, sul2, sul3, and different variants of dfrA (Table 3).
Non-susceptibility to fluoroquinolones (FQ) was demonstrated in 26 (8.2%) of the isolates. Susceptibility testing was conducted during a previous study (see [2] for the methodology). Genotyping revealed plasmid-located genes qnrS1, aac(6’)-Ib-c, qnrS2, qnrB19, and qnrB4 (Table 2) in five of these isolates. Furthermore, all FQ non-susceptible isolates showed mutations in the quinolone resistance-determining region, namely S83L in gyrA (7.7%), and S83L and D87N in gyrA (92.3%). In 96.2% of the FQ resistant isolates, an additional mutation in parC (S80I) was observed (Table S3).
Resistance to ESC was also demonstrated in a previous study: 2.9% (n = 9) of the 315 isolates were non-susceptible to cefovecin, a third-generation cephalosporin [2]. Genotypic analysis revealed that four of these isolates carried an ESBL (3 × CTX-M-15 and 1 × CTX-M-27), and two carried an AmpC-β-lactamase (1 × CMY-2 and 1 × DHA-1). Additionally, one canine ST58 ESC-resistant isolate showed chromosomal mutations that resulted in amino acid substitutions of the ampC promotor region (C → T at position −42). This is the most frequently reported promotor mutation; it is associated with a 20-fold increase in enzyme production [42]. The same isolate also harboured a chromosomally encoded ES class C beta-lactamase blaEC gene, which was closely related to blaEC11 (99.2%) and its encoded protein (98.7%) [43]. One isolate carried ES class C beta-lactamase blaEC-6 [43]. An overview of the ESC-resistant isolates is provided in Table 4.
Multi-drug resistant (MDR) isolates, i.e., isolates non-susceptible to at least one antibiotic agent in three or more categories, were identified in 11.7% of 315 UTI isolates in our previous study [2]. MDR isolates were obtained in nearly equal proportions from dogs (n = 25; 12.6%) and cats (n = 12; 10.3%) (Figure 1). Only two STs significantly more often displayed MDR isolates: ST162 (p < 0.001; 66.7%; dog, n = 4; cat, n = 2) and ST88 (p = 0.002; 50.0%; dog, n = 2; cat, n = 1). Of the dominant ST372 and ST73 isolates in this study, only one and two, respectively, showed an MDR phenotype. The single ST14 isolate exhibited MDR, while ST1193, which is a single-locus variant of ST14, was only FQ- and ampicillin-resistant. Of 11 ST131 isolates, three isolates (27.3%) were MDR. A detailed comparison of the AMR genes and the corresponding phenotypic resistance is provided in Supplementary Table S3. A combination of serogroup O25b:H4 and ST131 was identified in 3.5% of our isolates. Generally, ST131 is divided into three clades with different fimH allelic variants, i.e., A/H41, B/H22, and C/H30, with clade C being by far the most represented among human and animal ExPEC isolates. Within clade C, two subclades are defined: C1/H30R1, associated with fluoroquinolone resistance conferred by mutations in the chromosomal genes gyrA and parC, and C2/H30Rx, associated additionally with ESC resistance [44,45]. Only two isolates from our study displayed fluoroquinolone resistance, and they possessed the fimH allelic variant H30 and were therefore assigned to clade C. As none of them showed additional ESC resistance, they were grouped into subclade C1/H30R1. Four of the ST131 isolates possessed fimH22 and another four isolates harboured fimH298, which differs from fimH22 by only a single nucleotide [46]. Thus, these eight isolates can be assigned to clade B.

3. Discussion

In order to investigate the population structure of E. coli isolates causing clinical symptoms of UTIs in dogs and cats, we conducted a comprehensive genomic analysis of 315 isolates (198 of canine and 117 of feline origin). The isolates were collected from submissions to our diagnostic department, due to diagnosis of suspected bacterial UTI. As to be expected, the majority of the isolates (77.8%) was assigned to phylogroup B2. This phylogroup has been frequently associated with ExPEC, and especially with isolates from the urinary tract of humans and animals [31,33,47,48,49]. We demonstrated a positive correlation between phylogroup B2 and the VAG-based categorisation of isolates as ExPEC. In detail, 69.1% of E. coli group B2 isolates from dogs and 77.4% from cats were classified as ExPEC (p < 0.001). Additionally, regarding the B2 isolates, 59.2% from dogs and 72.0% from cats were further identified as UPEC (p < 0.001), which corroborates previous data obtained by comparable methods [31,47].
Based on the presence of specific VAGs, only 51.1% and 57.8% of the isolates were categorized as UPEC and ExPEC, respectively [22,23]. The relatively low number might be considered somewhat surprising given that all isolates were obtained from the urinary tract of animals exhibiting symptoms of UTIs. It has to be considered though, that in cases of underlying comorbidities or the use of medical devices such as urinary catheters, opportunistic E. coli isolates, lacking a specific set of VAGs, might likewise be capable of causing UTIs. Notably, when E. coli was classified as ExPEC, it was often the sole causative agent obtained from the site of infection. In contrast, isolates were less frequently classified as ExPEC in cases of mixed infections.
The distribution of UPEC-associated papG alleles, which encode for the adhesin of P fimbriae, showed a clear predominance of papGIII (45.1%), which is commonly associated with acute cystitis in both humans and dogs. In contrast, papGII, which has been linked to human pyelonephritis, was less prevalent [41]. Interestingly, papGIII showed a positive association with the presence of cnf1 and hlyA genes (p < 0.001), indicating a potential correlation between these VAGs. On the other hand, papGII did not exhibit any association with hlyA and was negatively associated with cnf1 (p = 0.008). Furthermore, we demonstrated that B2 isolates harbour fewer AMR genes but are more prone to carry UPEC associated VAGs. These data substantiate the hypothesis previously established by various authors: that the acquisition of AMR genes may induce the loss of virulence factors [21,50]. For example, mutations in the chromosomal coded gyrA gene of UPEC have been associated with reduced bacterial virulence. One explanation is that during the development of FQ resistance, increased deletion and transposition of DNA regions, such as pathogenicity islands (PAIs), is achieved [51]. PAIs consist typically of VAGs encoded within chromosomal regions and are capable of being exchanged via horizontal gene transfer [52]. Among our isolates, we detected malX and usp, located on PAI ICFT073 and PAIusp, in 100% and 75.9% of the isolates, respectively [53,54]. Usp has been associated with UTI isolates and is suggested as a potential VAG for use as a molecular epidemiological marker specific for UPEC. MalX, although located on the same PAI as genes encoding α-haemolysin, P-fimbriae, and aerobactin, which are established contributors to virulence, currently lacks a known role in virulence [54,55].
Another explanation for the hypothesis that the acquisition of AMR genes induces loss of virulence is the concept of plasmid competition, wherein plasmids carrying resistance or virulence factors compete with each other [56]. However, it is important to note that the acquisition of AMR genes does not necessarily equate to the loss of VAGs. This phenomenon can vary depending on the mechanism of resistance and the antibiotic studied [50].
With 2.5% ESBL- or AmpC-producing isolates, we observed a lower prevalence than found in most previous studies [57,58,59,60]. However, the studies cited investigated not only isolates from UTI but also from other sites of infection. Only four isolates harboured a CTX-M-type enzyme, namely CTX-M-15 (3×) and CTX-M-27 (1×). CTX-M-15 is the predominant ESBL type in E. coli isolated from companion animals in Europe and the American continent [38,60]. The AmpC-β-lactamase CMY-2, which is considered the most common AmpC type currently encountered in humans and animals, was only isolated once [10,38,60]. We also found one blaDHA-1 and two blaEC genes. It remains unclear whether blaEC confers ESC resistance since additional mutations in the ampC promoter (IHIT42298, −42C > T, −18G > A, −1C > T; IHIT44091, −28G > A) were observed in both isolates. Whilst blaDHA has been found in E. coli obtained from urine samples of companion animals, there have been no studies describing the presence of blaEC in uropathogenic E. coli [60].
MDR isolates (dog, n = 25; cat, n = 11) were found more often in non-B2 phylogroup isolates than in B2 isolates (dog, 40.0%; cat, 27.3%; p < 0.001), namely phylogroup A (dog, 16.0%; cat, 9.1%), B1 (dog, 28.0%; cat, 54.6%), and C (dog, 16.0%; cat, 9.1%). These findings may favour more effective antimicrobial therapy of UTIs and/or reduced treatment failures, considering that the majority of UTI cases are caused by B2 isolates.
The occurrence of the carbapenem (CP) resistance gene blaOXA-48 in E. coli from companion animals, particularly in cats, has been rarely documented. In Germany, few cases of OXA-48-producing E. coli in dogs have been reported and, to date, only one OXA-48 positive isolate has been published from a cat [61,62,63]. However, our group has identified additional OXA-48-positive clinical E. coli isolates from cats along with another study (unpublished data). Since carbapenems are not approved for veterinary use, it has been hypothesized that the occurrence of CP resistant Enterobacterales in animals may be attributed to a zoonotic transmission of bacteria and/or genetic determinants from humans to animals [61,64]. The mobile colistin resistance gene mcr-4.6 was identified in the canine ST73 isolate IHIT43641, located on a ColE10 plasmid. To date, only a limited number of MCR-carrying bacteria have been detected in companion animals in Europe. Colistin (polymyxin E), a cationic antimicrobial peptide that entered clinical use in 1959, was abandoned in the 1980s because of its neurotoxic and nephrotoxic effects [65]. However, with the emergence of MDR gram-negative bacteria, colistin was reintroduced in the human domain. In veterinary medicine, it has been widely used, particularly for the treatment of neonatal and post-weaning diarrhoea in pigs and gastrointestinal infections of calves [66,67,68]. Several studies suggest the origin of these resistance genes in the easily transferable mobile elements originating from isolates in the environment and from farm animals, since the treatment of companion animals with colistin is not common in Europe (reviewed in [69]).
The most frequently identified STs, namely ST372 and ST73, displayed an animal species-specific distribution pattern: ST372 was almost exclusively isolated from dogs, whereas a particularly high prevalence of ST73 was observed among isolates from cats. This host-specific distribution has also been documented by other researchers, suggesting that there might be an adaptation of certain lineages to UTI infections in either dogs or cats [29,30,31,70,71]. Similar to Zogg at al., 2018, we found no correlation between the two most common STs and MDR isolates or strains carrying ESBL or AmpC-β-lactamase [8]. The association of ST372 with dogs has recently been mentioned in the context of commercially available dog food. Elankumuran et al., 2023, identified the genes of the propanediol utilization (pdu) operon as accessory genes in ST372 E. coli isolates from dogs. This operon was originally described for its role in microcompartment-mediated metabolism of glycerol and 1,2-propanediol in Salmonella enterica serovar Typhimurium and has been associated with gastrointestinal colonization and pathogenicity. The authors raised the question of whether the high prevalence of ST372 isolates in dogs could be attributed to the presence of glycerol and 1,2-propanediol, which are common additives in semi-moist commercially available dog food [71]. However, it remains unclear why cats, which are also fed commercially available food, predominantly exhibit a high number of ST73 isolates and are rarely infected with ST372 isolates.
Despite the heterogeneity of STs observed in the majority of isolates, a notable finding is the presence of several STs typically associated with humans, indicating a significant overlap between species. The success of certain clonal lineages isolated from humans and animals alike, such as the ESBL-producing E. coli strain O25b:H4-ST131 or the emerging high-risk clone ST410, have been well documented [72,73,74]. O25b:H4-ST131 was identified in 3.5% of our isolates; two of them were assigned to subclade C1/H30R1 and eight isolates to clade B. Three of these isolates showed an MDR phenotype. Interestingly, none of the them harboured an ESBL, although the emergence of ST131 possessing a CTX-M gene has been reported frequently among humans and companion animals lately [44,46,72,75]. Two isolates were assigned to ST1193, previously determined as the FQ-resistant B2 E. coli group, which is referred to as a pandemic ST by Kidsley et al., 2020 [75]. Tchesnokova et al., 2019, identified this ST in one quarter of human clinical urine isolates in the USA, and also in Germany, ST1193 was increasingly detected over the last years in humans [76,77]. In our study, ST1193 was relatively rare, accounting for only 0.6% of isolates. Fluoroquinolone-resistant E. coli assigned to ST410, an “international high-risk clone” for AMR, were found in three dogs [74,78]. One ST410 additionally carried the ESBL CTX-M-15. The overall low occurrence of pandemic AMR clones, such as ST410, ST1193, and ST131 in our study population, and in companion animals in general, may suggest that the primary source of these STs are humans. Companion animals may be more likely to serve as spillover hosts than the original source of these STs known for their increased resistance [75].
Limitations of this study include the missing data on antibiotic treatment prior to sampling. Since a large proportion of the samples originated from only three veterinary clinics (specialist referral clinics), it cannot be ruled out that our data are biased towards complicated cases of cystitis. A separate study with a detailed preliminary report concerning symptoms and treatments would be beneficial to get an even deeper insight into the relevance of distinct pathovars, STs, and VAGs of E. coli isolates associated with complicated and uncomplicated urinary tract infections.

4. Conclusions

The majority of E. coli isolates obtained from dogs and cats with symptoms of urinary tract infections were assigned to phylogroup B2. Multidrug-resistant and ESBL/AmpC-producing isolates were less often found in this phylogroup and in general in our study population compared with other studies. Only a small proportion of isolates were assigned to so-called “high-risk clones” for AMR. Nevertheless, pandemic ExPEC lineages ST69, ST73, ST95, ST127, and ST131 were also present among our isolates, indicating the wide distribution of human-related ExPEC/UPEC strains in cats and dogs. Further surveillance of E. coli clonal lineages implicated in UTIs in companion animals is warranted, as the transmission of ESC-resistant E. coli between dogs and humans, particularly within households, has been well-documented [79,80,81,82,83]. Understanding transmission dynamics is crucial to assess the potential impact on public and animal health. Nonetheless, the AMR data gained in this study might be considered as a positive indication in the context of the One Health approach and, in a clinical context, they suggest that a high proportion of UTIs caused by E. coli in companion animals can still be effectively treated with antibiotics.

5. Materials and Methods

5.1. Sampling and Identification of Bacterial Isolates

Escherichia coli isolates were collected from the urinary tract of cats and dogs between November 2019 and November 2020. The isolates were obtained from routine diagnostic submissions to the veterinary diagnostic laboratory of the Institute of Hygiene and Infectious Diseases of Animals, Department of Veterinary Medicine, Justus Liebig University Giessen, Germany. Samples consisted of urine and of bladder swabs/bladder tissue, prostate swabs, uricult tests, uroliths, and kidney swabs. Samples were streaked out on standard nutrient agar (Oxoid, Wesel, Germany) supplemented with 5% defibrinated sheep blood and on water-blue metachrome-yellow lactose agar according to Gassner (sifin diagnostics gmbh, Berlin, Germany) and incubated under aerobic conditions at 37 °C. In cases where multiple samples were submitted for one animal during the study period, all samples were subjected to further phenotypic and genotypic analysis. However, only the first sample was considered for the final analysis, unless changes in the AMR and VAG profile based on whole genome data indicated a non-duplicate strain or the acquisition of additional resistance genes. Generally, a single colony was collected and analysed as representative for the bacterial population causing the infection. The haemolytic phenotype of E. coli was investigated on sheep blood agar. In cases where both haemolytic and non-haemolytic phenotypes were cultured from the same sample, a representative colony of both was collected and further analysed.
Species identification was performed using matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF MS, Microflex, Bruker Daltonics, Bremen, Germany) [84]. Therefore, a single colony was smeared onto a polished steel MALDI target plate (Bruker Daltonics, Bremen, Germany) and allowed to dry at room temperature. The sample was overlaid with 1 µL matrix (Bruker Daltonics). Mass spectra were acquired using a mass range of 2–20 kDa using Biotyper version 3.3.1.0. (Bruker Daltonics). Species identification was considered valid at score values > 2000 according to the manufacturer’s instructions (database v9.0.0.0). Metadata including host species, age, and sex were extracted from the laboratory submission form or from practice management software.

5.2. Isolate Storage, DNA Preparation, and Whole Genome Sequencing

All isolates were stored in Brain Heart Infusion Broth (Oxoid, Wesel, Germany) with 30% glycerol at −70 °C. Genomic DNA was extracted using the Master Pure™ DNA Purification Kit (Biozym Scientific GmbH, Hessisch Oldendorf, Germany). Bacterial genomes were sequenced using an Illumina MiSeq sequencer (MiSeq Reagent Kit V.3; Illumina Inc., San Diego, CA, USA) with multiplexing of 30 samples per flow cell using 2 × 150 bp paired-end reads to obtain an average of 90-fold coverage. Quality control and adapter trimming were performed by an in-house pipeline. De novo assemblies were generated by the SPAdes Genome Assembler (v3.15.5) [85]. The Bakta pipeline (v1.8.2) was employed for genomic annotation of the bacterial genomes [86].

5.3. In Silico Methods

Pathotype assignment was carried out based on published criteria: E. coli isolates harbouring two or more of the VAGs papAH and/or papC, sfaS/focG, afaD/draBC, kpsMTII, and iutA were classified as ExPEC [22]. If toxin and hemolysin genes cnf1 and hlyD were also present, the isolate was assigned to the UPEC pathotype [23]. Virulence genotyping was performed using VirulenceFinder 2.0 hosted by the Center for Genomic Epidemiology (https://cge.food.dtu.dk/services/VirulenceFinder/, accessed on 7 June 2023). Additionally, a custom in-house database was created based on 551 VAGs described for various E. coli pathovars in public databases such as CARD, Institut Pasteur and NCBI (https://www.ncbi.nlm.nih.gov/nucleotide/, https://bigsdb.pasteur.fr/ecoli/, https://card.mcmaster.ca/home, accessed on 22 June 2023). This custom collection was utilized with the ABRicate software (v1.0.1, https://github.com/tseemann/abricate, accessed on 29 June 2023) using a threshold of 80%, or 99% in cases of screening for specific alleles, to profile the corresponding assemblies. MLST 2.0 (https://cge.food.dtu.dk/services/MLST/, accessed on 11 July 2023) was used to determine sequence types (STs) according to the Achtman scheme, employing seven housekeeping genes (adk, fumC, gyrB, icd, mdh, purA, and recA). Sero(geno)typing (O:H) was conducted using SerotypeFinder 2.0 (https://cge.food.dtu.dk/services/SerotypeFinder/, accessed on 14 June 2023). Typing of fimH was achieved by using FimTyper 1.1 (https://cge.food.dtu.dk/services/FimTyper/, accessed on 15 June 2023). AMR genes and chromosomal point mutations were determined using ResFinder 4.1 (https://cge.food.dtu.dk/services/ResFinder/, accessed on 21 June 2023) and BacWGSTdb (http://bacdb.cn/BacWGSTdb/analysis_single.php, accessed on 11 July 2023). All blaTEM and blaSHV genes were further determined by the lactamase engineering database (http://www.laced.uni-stuttgart.de/, accessed on 25 January 2023).
The isolates were also classified into one of the eight E. coli phylogenetic groups (A, B1, B2, C, D, E, F, and G) or a cryptic clade using the refined ClermonTyping method, based on the in vitro PCR assay developed by Clermont et al., 2000, targeting chuA, yjaA, TspE4.C2, arpA, and trpA (http://clermontyping.iame-research.center/, accessed on 12 August 2023).
The population structure of the sample collection was further investigated through phylogenetic reconstruction of a maximum likelihood tree. Here, a gene-by-gene approach was first utilized to establish a shared set of core genes. This was generated using the annotated bacterial assemblies in combination with the roary software (v3.13.0) [87]. A total of 2820 conserved genes were identified using this approach. They were present in at least 99% of the strains (protein sequence similarity min. 95%, sequence coverage min. 90%). This was followed by gene-wise alignments via the Mafft software (v7.520) [88] and subsequent concatenation of the alleles per sample. The resulting alignment was then used to infer a phylogeny through RAxML-NG (v.1.2.0) [89] with a General Time Reversible model and gamma correction for among site rate variation. Finally, iTOL (v6.8.1) [90] was utilized to visualize the population structure in the context of the available metadata.

5.4. Statistical Analysis

Statistical analysis was carried out using the SAS 9.4 statistical software package [91]. Descriptive statistics were performed for all data. Categorical parameters were compared between groups using a chi-square test. In instances where the chi-square test was not applicable due to low frequencies (more than 20% of the cells had expected frequencies below [92]) a Fisher exact test was employed. The significance level for all statistical analyses was established at p < 0.05.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/antibiotics13010038/s1, Table S1: Newly assigned STs, Table S2: Virulence associated genes, Table S3: Genotypic and phenotypic AMR.

Author Contributions

Conceptualization, C.E. and S.A.; methodology, S.A.; software, S.A.W., L.T. and T.S.; validation, C.E. and S.A.; formal analysis, S.A.; investigation, S.A. and E.P.-B.; resources, C.E. and T.S.; data curation, S.A. and S.A.W.; writing—original draft preparation, S.A. and E.P.-B.; writing—review and editing, C.E. and T.S.; visualization, S.A. and S.A.W.; supervision, C.E. and T.S.; project administration, C.E.; funding acquisition, C.E. and T.S. All authors have read and agreed to the published version of the manuscript.

Funding

This research received no external funding.

Institutional Review Board Statement

Ethical review and approval were waived for this study due to the fact that the urine collection was not for research but for diagnostic purposes, and only the results obtained were used for scientific purposes and no additional pain, suffering, or harm was inflicted on the animals as a result of our study.

Informed Consent Statement

Not applicable.

Data Availability Statement

The raw sequencing data are available under NCBI BioProject PRJNA1031431 (https://www.ncbi.nlm.nih.gov/bioproject/1031431, accessed on 24 October 2023).

Acknowledgments

We would like to thank Ursula Leidner for her excellent technical support. We also thank Kathrin Büttner from the AG Biomathematics and Data Processing of the Justus Liebig University Giessen for statistical analysis and interpretation support.

Conflicts of Interest

The authors declare no conflicts of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of the data; in the writing of the manuscript; or in the decision to publish the results.

References

  1. Stamm, W.E.; Norrby, S.R. Urinary tract infections: Disease panorama and challenges. J. Infect. Dis. 2001, 183 (Suppl. S1), S1–S4. [Google Scholar] [CrossRef] [PubMed]
  2. Aurich, S.; Prenger-Berninghoff, E.; Ewers, C. Prevalence and Antimicrobial Resistance of Bacterial Uropathogens Isolated from Dogs and Cats. Antibiotics 2022, 11, 1730. [Google Scholar] [CrossRef] [PubMed]
  3. Dorsch, R.; Remer, C.; Sauter-Louis, C.; Hartmann, K. Feline lower urinary tract disease in a German cat population. Tierarztl. Prax. 2014, 42, 231–239. [Google Scholar] [CrossRef]
  4. Thompson, M.F.; Litster, A.L.; Platell, J.L.; Trott, D.J. Canine bacterial urinary tract infections: New developments in old pathogens. Vet. J. 2011, 190, 22–27. [Google Scholar] [CrossRef] [PubMed]
  5. Weese, J.S.; Blondeau, J.; Boothe, D.; Guardabassi, L.G.; Gumley, N.; Papich, M.; Jessen, L.R.; Lappin, M.; Rankin, S.; Westropp, J.L.; et al. International Society for Companion Animal Infectious Diseases (ISCAID) guidelines for the diagnosis and management of bacterial urinary tract infections in dogs and cats. Vet. J. 2019, 247, 8–25. [Google Scholar] [CrossRef] [PubMed]
  6. Chen, Y.; Liu, Z.; Zhang, Y.; Zhang, Z.; Lei, L.; Xia, Z. Increasing Prevalence of ESBL-Producing Multidrug Resistance Escherichia coli From Diseased Pets in Beijing, China From 2012 to 2017. Front. Microbiol. 2019, 10, 2852. [Google Scholar] [CrossRef] [PubMed]
  7. Marques, C.; Belas, A.; Franco, A.; Aboim, C.; Gama, L.T.; Pomba, C. Increase in antimicrobial resistance and emergence of major international high-risk clonal lineages in dogs and cats with urinary tract infection: 16 year retrospective study. J. Antimicrob. Chemother. 2018, 73, 377–384. [Google Scholar] [CrossRef] [PubMed]
  8. Zogg, A.L.; Zurfluh, K.; Schmitt, S.; Nüesch-Inderbinen, M.; Stephan, R. Antimicrobial resistance, multilocus sequence types and virulence profiles of ESBL producing and non-ESBL producing uropathogenic Escherichia coli isolated from cats and dogs in Switzerland. Vet. Microbiol. 2018, 216, 79–84. [Google Scholar] [CrossRef]
  9. Paterson, D.L.; Bonomo, R.A. Extended-spectrum beta-lactamases: A clinical update. Clin. Microbiol. Rev. 2005, 18, 657–686. [Google Scholar] [CrossRef]
  10. Jacoby, G.A. AmpC beta-lactamases. Clin. Microbiol. Rev. 2009, 22, 161–182. [Google Scholar] [CrossRef]
  11. Aldred, K.J.; Kerns, R.J.; Osheroff, N. Mechanism of quinolone action and resistance. Biochemistry 2014, 53, 1565–1574. [Google Scholar] [CrossRef] [PubMed]
  12. Weese, J.S.; Webb, J.; Ballance, D.; McKee, T.; Stull, J.W.; Bergman, P.J. Evaluation of antimicrobial prescriptions in dogs with suspected bacterial urinary tract disease. J. Vet. Intern. Med. 2021, 35, 2277–2286. [Google Scholar] [CrossRef] [PubMed]
  13. Weese, J.S.; Stull, J.W.; Evason, M.; Webb, J.; Ballance, D.; McKee, T.; Bergman, P.J. A multicenter study of antimicrobial prescriptions for cats diagnosed with bacterial urinary tract disease. J. Feline Med. Surg. 2022, 24, 806–814. [Google Scholar] [CrossRef] [PubMed]
  14. Wiles, T.J.; Kulesus, R.R.; Mulvey, M.A. Origins and virulence mechanisms of uropathogenic Escherichia coli. Exp. Mol. Pathol. 2008, 85, 11–19. [Google Scholar] [CrossRef] [PubMed]
  15. Russo, T.A.; Stapleton, A.; Wenderoth, S.; Hooton, T.M.; Stamm, W.E. Chromosomal restriction fragment length polymorphism analysis of Escherichia coli strains causing recurrent urinary tract infections in young women. J. Infect. Dis. 1995, 172, 440–445. [Google Scholar] [CrossRef] [PubMed]
  16. Johnson, J.R.; Kaster, N.; Kuskowski, M.A.; Ling, G.V. Identification of urovirulence traits in Escherichia coli by comparison of urinary and rectal E. coli isolates from dogs with urinary tract infection. J. Clin. Microbiol. 2003, 41, 337–345. [Google Scholar] [CrossRef] [PubMed]
  17. Foxman, B. The epidemiology of urinary tract infection. Nat. Rev. Urol. 2010, 7, 653–660. [Google Scholar] [CrossRef] [PubMed]
  18. Mann, R.; Mediati, D.G.; Duggin, I.G.; Harry, E.J.; Bottomley, A.L. Metabolic Adaptations of Uropathogenic E. coli in the Urinary Tract. Front. Cell. Infect. Microbiol. 2017, 7, 241. [Google Scholar] [CrossRef]
  19. Terlizzi, M.E.; Gribaudo, G.; Maffei, M.E. UroPathogenic Escherichia coli (UPEC) Infections: Virulence factors, bladder responses, antibiotic, and non-antibiotic antimicrobial strategies. Front. Microbiol. 2017, 8, 1566. [Google Scholar] [CrossRef]
  20. Flores-Mireles, A.L.; Walker, J.N.; Caparon, M.; Hultgren, S.J. Urinary tract infections: Epidemiology, mechanisms of infection and treatment options. Nat. Rev. Microbiol. 2015, 13, 269–284. [Google Scholar] [CrossRef]
  21. Johnson, J.R.; Russo, T.A. Molecular epidemiology of extraintestinal pathogenic (uropathogenic) Escherichia coli. Int. J. Med. Microbiol. 2005, 295, 383–404. [Google Scholar] [CrossRef] [PubMed]
  22. Johnson, J.R.; Gajewski, A.; Lesse, A.J.; Russo, T.A. Extraintestinal pathogenic Escherichia coli as a cause of invasive nonurinary infections. J. Clin. Microbiol. 2003, 41, 5798–5802. [Google Scholar] [CrossRef] [PubMed]
  23. Johnson, J.R.; Scheutz, F.; Ulleryd, P.; Kuskowski, M.A.; O’Bryan, T.T.; Sandberg, T. Phylogenetic and pathotypic comparison of concurrent urine and rectal Escherichia coli isolates from men with febrile urinary tract infection. J. Clin. Microbiol. 2005, 43, 3895–3900. [Google Scholar] [CrossRef] [PubMed]
  24. Spurbeck, R.R.; Dinh, P.C.; Walk, S.T.; Stapleton, A.E.; Hooton, T.M.; Nolan, L.K.; Kim, K.S.; Johnson, J.R.; Mobley, H.L.T. Escherichia coli isolates that carry vat, fyuA, chuA, and yfcV efficiently colonize the urinary tract. Infect. Immun. 2012, 80, 4115–4122. [Google Scholar] [CrossRef] [PubMed]
  25. Clermont, O.; Bonacorsi, S.; Bingen, E. Rapid and Simple Determination of the Escherichia coli Phylogenetic Group. Appl. Environ. Microbiol. 2000, 66, 4555–4558. [Google Scholar] [CrossRef] [PubMed]
  26. Clermont, O.; Dixit, O.V.A.; Vangchhia, B.; Condamine, B.; Dion, S.; Bridier-Nahmias, A.; Denamur, E.; Gordon, D. Characterization and rapid identification of phylogroup G in Escherichia coli, a lineage with high virulence and antibiotic resistance potential. Environ. Microbiol. 2019, 21, 3107–3117. [Google Scholar] [CrossRef] [PubMed]
  27. Johnson, J.R.; Russo, T.A. Extraintestinal pathogenic Escherichia coli: “the other bad E. coli”. J. Lab. Clin. Med. 2002, 139, 155–162. [Google Scholar] [CrossRef]
  28. Vangchhia, B.; Abraham, S.; Bell, J.M.; Collignon, P.; Gibson, J.S.; Ingram, P.R.; Johnson, J.R.; Kennedy, K.; Trott, D.J.; Turnidge, J.D.; et al. Phylogenetic diversity, antimicrobial susceptibility and virulence characteristics of phylogroup F Escherichia coli in Australia. Microbiology 2016, 162, 1904–1912. [Google Scholar] [CrossRef]
  29. LeCuyer, T.E.; Byrne, B.A.; Daniels, J.B.; Diaz-Campos, D.V.; Hammac, G.K.; Miller, C.B.; Besser, T.E.; Davis, M.A. Population structure and antimicrobial resistance of canine uropathogenic Escherichia coli. J. Clin. Microbiol. 2018, 56, 452–458. [Google Scholar] [CrossRef]
  30. Gilbertie, J.M.; Levent, G.; Norman, K.N.; Vinasco, J.; Scott, H.M.; Jacob, M.E. Comprehensive phenotypic and genotypic characterization and comparison of virulence, biofilm, and antimicrobial resistance in urinary Escherichia coli isolated from canines. Vet. Microbiol. 2020, 249, 108822. [Google Scholar] [CrossRef]
  31. Valat, C.; Drapeau, A.; Beurlet, S.; Bachy, V.; Boulouis, H.-J.; Pin, R.; Cazeau, G.; Madec, J.-Y.; Haenni, M. Pathogenic Escherichia coli in Dogs Reveals the Predominance of ST372 and the Human-Associated ST73 Extra-Intestinal Lineages. Front. Microbiol. 2020, 11, 580. [Google Scholar] [CrossRef] [PubMed]
  32. Fibke, C.D.; Croxen, M.A.; Geum, H.M.; Glass, M.; Wong, E.; Avery, B.P.; Daignault, D.; Mulvey, M.R.; Reid-Smith, R.J.; Parmley, E.J.; et al. Genomic Epidemiology of Major Extraintestinal Pathogenic Escherichia coli Lineages Causing Urinary Tract Infections in Young Women Across Canada. Open Forum Infect. Dis. 2019, 6, ofz431. [Google Scholar] [CrossRef] [PubMed]
  33. Flament-Simon, S.-C.; Nicolas-Chanoine, M.-H.; García, V.; Duprilot, M.; Mayer, N.; Alonso, M.P.; García-Meniño, I.; Blanco, J.E.; Blanco, M.; Blanco, J. Clonal Structure, Virulence Factor-encoding Genes and Antibiotic Resistance of Escherichia coli, Causing Urinary Tract Infections and Other Extraintestinal Infections in Humans in Spain and France during 2016. Antibiotics 2020, 9, 161. [Google Scholar] [CrossRef] [PubMed]
  34. Liu, X.; Thungrat, K.; Boothe, D.M. Multilocus Sequence Typing and Virulence Profiles in Uropathogenic Escherichia coli Isolated from Cats in the United States. PLoS ONE 2015, 10, e0143335. [Google Scholar] [CrossRef] [PubMed]
  35. Huber, H.; Zweifel, C.; Wittenbrink, M.M.; Stephan, R. ESBL-producing uropathogenic Escherichia coli isolated from dogs and cats in Switzerland. Vet. Microbiol. 2013, 162, 992–996. [Google Scholar] [CrossRef] [PubMed]
  36. Manges, A.R.; Johnson, J.R. Reservoirs of Extraintestinal Pathogenic Escherichia coli. Microbiol. Spectr. 2015, 3, 161–177. [Google Scholar] [CrossRef] [PubMed]
  37. Guardabassi, L.; Schwarz, S.; Lloyd, D.H. Pet animals as reservoirs of antimicrobial-resistant bacteria. J. Antimicrob. Chemother. 2004, 54, 321–332. [Google Scholar] [CrossRef] [PubMed]
  38. Ewers, C.; Bethe, A.; Semmler, T.; Guenther, S.; Wieler, L.H. Extended-spectrum β-lactamase-producing and AmpC-producing Escherichia coli from livestock and companion animals, and their putative impact on public health: A global perspective. Clin. Microbiol. Infect. 2012, 18, 646–655. [Google Scholar] [CrossRef]
  39. Ksiezarek, M.; Novais, Â.; Felga, H.; Mendes, F.; Escobar, M.; Peixe, L. Phylogenomic analysis of a highly virulent Escherichia coli ST83 lineage with potential animal-human transmission. Microb. Pathog. 2021, 155, 104920. [Google Scholar] [CrossRef]
  40. Naziri, Z.; Derakhshandeh, A.; Soltani Borchaloee, A.; Poormaleknia, M.; Azimzadeh, N. Treatment Failure in Urinary Tract Infections: A Warning Witness for Virulent Multi-Drug Resistant ESBL- Producing Escherichia coli. Infect. Drug Resist. 2020, 13, 1839–1850. [Google Scholar] [CrossRef]
  41. Johnson, J.R.; Russo, T.A. Molecular Epidemiology of Extraintestinal Pathogenic Escherichia coli. EcoSal Plus 2018, 8. [Google Scholar] [CrossRef] [PubMed]
  42. Tracz, D.M.; Boyd, D.A.; Hizon, R.; Bryce, E.; McGeer, A.; Ofner-Agostini, M.; Simor, A.E.; Paton, S.; Mulvey, M.R. ampC gene expression in promoter mutants of cefoxitin-resistant Escherichia coli clinical isolates. FEMS Microbiol. Lett. 2007, 270, 265–271. [Google Scholar] [CrossRef] [PubMed]
  43. Mammeri, H.; Poirel, L.; Fortineau, N.; Nordmann, P. Naturally occurring extended-spectrum cephalosporinases in Escherichia coli. Antimicrob. Agents Chemother. 2006, 50, 2573–2576. [Google Scholar] [CrossRef] [PubMed]
  44. Melo, L.C.; Haenni, M.; Saras, E.; Duprilot, M.; Nicolas-Chanoine, M.-H.; Madec, J.-Y. Emergence of the C1-M27 cluster in ST131 Escherichia coli from companion animals in France. J. Antimicrob. Chemother. 2019, 74, 3111–3113. [Google Scholar] [CrossRef] [PubMed]
  45. Price, L.B.; Johnson, J.R.; Aziz, M.; Clabots, C.; Johnston, B.; Tchesnokova, V.; Nordstrom, L.; Billig, M.; Chattopadhyay, S.; Stegger, M.; et al. The epidemic of extended-spectrum-β-lactamase-producing Escherichia coli ST131 is driven by a single highly pathogenic subclone, H30-Rx. mBio 2013, 4, e00377-13. [Google Scholar] [CrossRef] [PubMed]
  46. Boll, E.J.; Overballe-Petersen, S.; Hasman, H.; Roer, L.; Ng, K.; Scheutz, F.; Hammerum, A.M.; Dungu, A.; Hansen, F.; Johannesen, T.B.; et al. Emergence of Enteroaggregative Escherichia coli within the ST131 Lineage as a Cause of Extraintestinal Infections. mBio 2020, 11. [Google Scholar] [CrossRef] [PubMed]
  47. Hutton, T.A.; Innes, G.K.; Harel, J.; Garneau, P.; Cucchiara, A.; Schifferli, D.M.; Rankin, S.C. Phylogroup and virulence gene association with clinical characteristics of Escherichia coli urinary tract infections from dogs and cats. J. Vet. Diagn. Investig. 2018, 30, 64–70. [Google Scholar] [CrossRef] [PubMed]
  48. Nüesch-Inderbinen, M.T.; Baschera, M.; Zurfluh, K.; Hächler, H.; Nüesch, H.; Stephan, R. Clonal Diversity, Virulence Potential and Antimicrobial Resistance of Escherichia coli Causing Community Acquired Urinary Tract Infection in Switzerland. Front. Microbiol. 2017, 8, 2334. [Google Scholar] [CrossRef]
  49. Toval, F.; Köhler, C.-D.; Vogel, U.; Wagenlehner, F.; Mellmann, A.; Fruth, A.; Schmidt, M.A.; Karch, H.; Bielaszewska, M.; Dobrindt, U. Characterization of Escherichia coli isolates from hospital inpatients or outpatients with urinary tract infection. J. Clin. Microbiol. 2014, 52, 407–418. [Google Scholar] [CrossRef]
  50. Cepas, V.; Soto, S.M. Relationship between Virulence and Resistance among Gram-Negative Bacteria. Antibiotics 2020, 9, 719. [Google Scholar] [CrossRef]
  51. Soto, S.M.; Jimenez de Anta, M.T.; Vila, J. Quinolones induce partial or total loss of pathogenicity islands in uropathogenic Escherichia coli by SOS-dependent or -independent pathways, respectively. Antimicrob. Agents Chemother. 2006, 50, S649–S653. [Google Scholar] [CrossRef] [PubMed]
  52. Sabaté, M.; Moreno, E.; Pérez, T.; Andreu, A.; Prats, G. Pathogenicity island markers in commensal and uropathogenic Escherichia coli isolates. Clin. Microbiol. Infect. 2006, 12, 880–886. [Google Scholar] [CrossRef] [PubMed]
  53. Lai, Y.M.; Zaw, M.T.; Shamsudin, S.B.; Lin, Z. Polymerase chain reaction-restriction fragment length polymorphism method for differentiation of uropathogenic specific protein gene types. J. Microbiol. Immunol. Infect. 2016, 49, 591–594. [Google Scholar] [CrossRef] [PubMed]
  54. Johnson, J.R.; Kuskowski, M.A.; O’Bryan, T.T.; Maslow, J.N. Epidemiological correlates of virulence genotype and phylogenetic background among Escherichia coli blood isolates from adults with diverse-source bacteremia. J. Infect. Dis. 2002, 185, 1439–1447. [Google Scholar] [CrossRef] [PubMed]
  55. Kanamaru, S.; Kurazono, H.; Nakano, M.; Terai, A.; Ogawa, O.; Yamamoto, S. Subtyping of uropathogenic Escherichia coli according to the pathogenicity island encoding uropathogenic-specific protein: Comparison with phylogenetic groups. Int. J. Urol. 2006, 13, 754–760. [Google Scholar] [CrossRef] [PubMed]
  56. Göttig, S.; Riedel-Christ, S.; Saleh, A.; Kempf, V.A.J.; Hamprecht, A. Impact of blaNDM-1 on fitness and pathogenicity of Escherichia coli and Klebsiella pneumoniae. Int. J. Antimicrob. Agents 2016, 47, 430–435. [Google Scholar] [CrossRef] [PubMed]
  57. Pepin-Puget, L.; El Garch, F.; Bertrand, X.; Valot, B.; Hocquet, D. Genome analysis of enterobacteriaceae with non-wild type susceptibility to third-generation cephalosporins recovered from diseased dogs and cats in Europe. Vet. Microbiol. 2020, 242, 108601. [Google Scholar] [CrossRef]
  58. Shaheen, B.W.; Nayak, R.; Foley, S.L.; Kweon, O.; Deck, J.; Park, M.; Rafii, F.; Boothe, D.M. Molecular characterization of resistance to extended-spectrum cephalosporins in clinical Escherichia coli isolates from companion animals in the United States. Antimicrob. Agents Chemother. 2011, 55, 5666–5675. [Google Scholar] [CrossRef]
  59. Lo Piccolo, F.; Belas, A.; Foti, M.; Fisichella, V.; Marques, C.; Pomba, C. Detection of multidrug resistance and extended-spectrum/plasmid-mediated AmpC beta-lactamase genes in Enterobacteriaceae isolates from diseased cats in Italy. J. Feline Med. Surg. 2020, 22, 613–622. [Google Scholar] [CrossRef]
  60. Bortolami, A.; Zendri, F.; Maciuca, E.I.; Wattret, A.; Ellis, C.; Schmidt, V.; Pinchbeck, G.; Timofte, D. Diversity, Virulence, and Clinical Significance of Extended-Spectrum β-Lactamase- and pAmpC-Producing Escherichia coli From Companion Animals. Front. Microbiol. 2019, 10, 1260. [Google Scholar] [CrossRef]
  61. Pulss, S.; Stolle, I.; Stamm, I.; Leidner, U.; Heydel, C.; Semmler, T.; Prenger-Berninghoff, E.; Ewers, C. Multispecies and Clonal Dissemination of OXA-48 Carbapenemase in Enterobacteriaceae From Companion Animals in Germany, 2009–2016. Front. Microbiol. 2018, 9, 1265. [Google Scholar] [CrossRef] [PubMed]
  62. Feßler, A.T.; Scholtzek, A.D.; Schug, A.R.; Kohn, B.; Weingart, C.; Hanke, D.; Schink, A.-K.; Bethe, A.; Lübke-Becker, A.; Schwarz, S. Antimicrobial and biocide resistance among canine and feline Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii isolates from diagnostic submissions. Antibiotics 2022, 11, 152. [Google Scholar] [CrossRef] [PubMed]
  63. Stolle, I.; Prenger-Berninghoff, E.; Stamm, I.; Scheufen, S.; Hassdenteufel, E.; Guenther, S.; Bethe, A.; Pfeifer, Y.; Ewers, C. Emergence of OXA-48 carbapenemase-producing Escherichia coli and Klebsiella pneumoniae in dogs. J. Antimicrob. Chemother. 2013, 68, 2802–2808. [Google Scholar] [CrossRef] [PubMed]
  64. Irrgang, A.; Pauly, N.; Tenhagen, B.-A.; Grobbel, M.; Kaesbohrer, A.; Hammerl, A.J.A. Spill-Over from Public Health? First Detection of an OXA-48-Producing Escherichia coli in a German Pig Farm. Microorganisms 2020, 8, 855. [Google Scholar] [CrossRef] [PubMed]
  65. Nation, R.L.; Li, J. Colistin in the 21st century. Curr. Opin. Infect. Dis. 2009, 22, 535–543. [Google Scholar] [CrossRef] [PubMed]
  66. Luppi, A.; Gibellini, M.; Gin, T.; Vangroenweghe, F.; Vandenbroucke, V.; Bauerfeind, R.; Bonilauri, P.; Labarque, G.; Hidalgo, Á. Prevalence of virulence factors in enterotoxigenic Escherichia coli isolated from pigs with post-weaning diarrhoea in Europe. Porcine Health Manag. 2016, 2, 20. [Google Scholar] [CrossRef] [PubMed]
  67. Rhouma, M.; Fairbrother, J.M.; Beaudry, F.; Letellier, A. Post weaning diarrhea in pigs: Risk factors and non-colistin-based control strategies. Acta Vet. Scand. 2017, 59, 31. [Google Scholar] [CrossRef]
  68. Catry, B.; Cavaleri, M.; Baptiste, K.; Grave, K.; Grein, K.; Holm, A.; Jukes, H.; Liebana, E.; Lopez Navas, A.; Mackay, D.; et al. Use of colistin-containing products within the European Union and European Economic Area (EU/EEA): Development of resistance in animals and possible impact on human and animal health. Int. J. Antimicrob. Agents 2015, 46, 297–306. [Google Scholar] [CrossRef]
  69. Hamame, A.; Davoust, B.; Cherak, Z.; Rolain, J.-M.; Diene, S.M. Mobile Colistin Resistance (mcr) Genes in Cats and Dogs and Their Zoonotic Transmission Risks. Pathogens 2022, 11, 698. [Google Scholar] [CrossRef]
  70. Flament-Simon, S.-C.; de Toro, M.; García, V.; Blanco, J.E.; Blanco, M.; Alonso, M.P.; Goicoa, A.; Díaz-González, J.; Nicolas-Chanoine, M.-H.; Blanco, J. Molecular Characteristics of Extraintestinal Pathogenic E. coli (ExPEC), Uropathogenic E. coli (UPEC), and Multidrug Resistant E. coli Isolated from Healthy Dogs in Spain. Whole Genome Sequencing of Canine ST372 Isolates and Comparison with Human Isolates Causing Extraintestinal Infections. Microorganisms 2020, 8, 1712. [Google Scholar] [CrossRef]
  71. Elankumuran, P.; Browning, G.F.; Marenda, M.S.; Kidsley, A.; Osman, M.; Haenni, M.; Johnson, J.R.; Trott, D.J.; Reid, C.J.; Djordjevic, S.P. Identification of genes influencing the evolution of Escherichia coli ST372 in dogs and humans. Microb. Genom. 2023, 9, mgen.0.000930. [Google Scholar] [CrossRef] [PubMed]
  72. Ewers, C.; Grobbel, M.; Stamm, I.; Kopp, P.A.; Diehl, I.; Semmler, T.; Fruth, A.; Beutlich, J.; Guerra, B.; Wieler, L.H.; et al. Emergence of human pandemic O25:H4-ST131 CTX-M-15 extended-spectrum-beta-lactamase-producing Escherichia coli among companion animals. J. Antimicrob. Chemother. 2010, 65, 651–660. [Google Scholar] [CrossRef] [PubMed]
  73. Elankumaran, P.; Cummins, M.L.; Browning, G.F.; Marenda, M.S.; Reid, C.J.; Djordjevic, S.P. Genomic and Temporal Trends in Canine ExPEC Reflect Those of Human ExPEC. Microbiology Spectrum 2022, 10, e0129122. [Google Scholar] [CrossRef] [PubMed]
  74. Schaufler, K.; Semmler, T.; Wieler, L.H.; Wöhrmann, M.; Baddam, R.; Ahmed, N.; Müller, K.; Kola, A.; Fruth, A.; Ewers, C.; et al. Clonal spread and interspecies transmission of clinically relevant ESBL-producing Escherichia coli of ST410--another successful pandemic clone? FEMS Microbiol. Ecol. 2016, 92, fiv155. [Google Scholar] [CrossRef] [PubMed]
  75. Kidsley, A.K.; White, R.T.; Beatson, S.A.; Saputra, S.; Schembri, M.A.; Gordon, D.; Johnson, J.R.; O’Dea, M.; Mollinger, J.L.; Abraham, S.; et al. Companion Animals Are Spillover Hosts of the Multidrug-Resistant Human Extraintestinal Escherichia coli Pandemic Clones ST131 and ST1193. Front. Microbiol. 2020, 11, 1968. [Google Scholar] [CrossRef]
  76. Tchesnokova, V.L.; Rechkina, E.; Larson, L.; Ferrier, K.; Weaver, J.L.; Schroeder, D.W.; She, R.; Butler-Wu, S.M.; Aguero-Rosenfeld, M.E.; Zerr, D.; et al. Rapid and Extensive Expansion in the United States of a New Multidrug-resistant Escherichia coli Clonal Group, Sequence Type 1193. Clin. Infect. Dis. 2019, 68, 334–337. [Google Scholar] [CrossRef]
  77. Valenza, G.; Werner, M.; Eisenberger, D.; Nickel, S.; Lehner-Reindl, V.; Höller, C.; Bogdan, C. First report of the new emerging global clone ST1193 among clinical isolates of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli from Germany. J. Glob. Antimicrob. Resist. 2019, 17, 305–308. [Google Scholar] [CrossRef]
  78. Roer, L.; Overballe-Petersen, S.; Hansen, F.; Schønning, K.; Wang, M.; Røder, B.L.; Hansen, D.S.; Justesen, U.S.; Andersen, L.P.; Fulgsang-Damgaard, D.; et al. Escherichia coli Sequence Type 410 Is Causing New International High-Risk Clones. mSphere 2018, 3. [Google Scholar] [CrossRef]
  79. Toombs-Ruane, L.J.; Benschop, J.; French, N.P.; Biggs, P.J.; Midwinter, A.C.; Marshall, J.C.; Chan, M.; Drinković, D.; Fayaz, A.; Baker, M.G.; et al. Carriage of Extended-Spectrum-Beta-Lactamase- and AmpC Beta-Lactamase-Producing Escherichia coli Strains from Humans and Pets in the Same Households. Appl. Environ. Microbiol. 2020, 86. [Google Scholar] [CrossRef]
  80. Grönthal, T.; Österblad, M.; Eklund, M.; Jalava, J.; Nykäsenoja, S.; Pekkanen, K.; Rantala, M. Sharing more than friendship—transmission of NDM-5 ST167 and CTX-M-9 ST69 Escherichia coli between dogs and humans in a family, Finland, 2015. Euro Surveill. 2018, 23. [Google Scholar] [CrossRef]
  81. Johnson, J.R.; Davis, G.; Clabots, C.; Johnston, B.D.; Porter, S.; DebRoy, C.; Pomputius, W.; Ender, P.T.; Cooperstock, M.; Slater, B.S.; et al. Household Clustering of Escherichia coli Sequence Type 131 Clinical and Fecal Isolates According to Whole Genome Sequence Analysis. Open Forum Infect. Dis. 2016, 3, ofw129. [Google Scholar] [CrossRef] [PubMed]
  82. Ljungquist, O.; Ljungquist, D.; Myrenås, M.; Rydén, C.; Finn, M.; Bengtsson, B. Evidence of household transfer of ESBL-/pAmpC-producing Enterobacteriaceae between humans and dogs—a pilot study. Infect. Ecol. Epidemiol. 2016, 6, 31514. [Google Scholar] [CrossRef] [PubMed]
  83. Cozma, A.P.; Rimbu, C.M.; Zendri, F.; Maciuca, I.E.; Timofte, D. Clonal Dissemination of Extended-Spectrum Cephalosporin-Resistant Enterobacterales between Dogs and Humans in Households and Animal Shelters of Romania. Antibiotics 2022, 11, 1242. [Google Scholar] [CrossRef] [PubMed]
  84. Schubert, S.; Wieser, A. Einsatz der Matrix-Assisted Laser Desorption/ionisation-Time of Flight Massenspektrometrie (MALDI-TOF MS) in der mikrobiologischen Routinediagnostik/Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) in clinical microbiological routine diagnostics. LaboratoriumsMedizin 2011, 35, 195–203. [Google Scholar] [CrossRef]
  85. Bankevich, A.; Nurk, S.; Antipov, D.; Gurevich, A.A.; Dvorkin, M.; Kulikov, A.S.; Lesin, V.M.; Nikolenko, S.I.; Pham, S.; Prjibelski, A.D.; et al. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 2012, 19, 455–477. [Google Scholar] [CrossRef] [PubMed]
  86. Schwengers, O.; Jelonek, L.; Dieckmann, M.A.; Beyvers, S.; Blom, J.; Goesmann, A. Bakta: Rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb. Genom. 2021, 7. [Google Scholar] [CrossRef]
  87. Page, A.J.; Cummins, C.A.; Hunt, M.; Wong, V.K.; Reuter, S.; Holden, M.T.G.; Fookes, M.; Falush, D.; Keane, J.A.; Parkhill, J. Roary: Rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015, 31, 3691–3693. [Google Scholar] [CrossRef] [PubMed]
  88. Nakamura, T.; Yamada, K.D.; Tomii, K.; Katoh, K. Parallelization of MAFFT for large-scale multiple sequence alignments. Bioinformatics 2018, 34, 2490–2492. [Google Scholar] [CrossRef]
  89. Kozlov, A.M.; Darriba, D.; Flouri, T.; Morel, B.; Stamatakis, A. RAxML-NG: A fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 2019, 35, 4453–4455. [Google Scholar] [CrossRef]
  90. Letunic, I.; Bork, P. Interactive Tree of Life (iTOL) v5: An online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 2021, 49, W293–W296. [Google Scholar] [CrossRef]
  91. SAS® Institute Inc. Base SAS® 9.4 Procedures Guide: Statistical Procedures, 2nd ed.; Statistical Analysis System Institute Inc.: Cary, NC, USA, 2013. [Google Scholar]
  92. Kim, H.-Y. Statistical notes for clinical researchers: Chi-squared test and Fisher’s exact test. Restor. Dent. Endod. 2017, 42, 152–155. [Google Scholar] [CrossRef] [PubMed]
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Figure 1. Core gene-based maximum-likelihood phylogenetic tree of 315 E. coli isolates from the urinary tract of cats and dogs. The inner to outer coloured rings display additional metadata defined by the host species, pathotype, phylogroup, sequence type, putative MDR phenotype, and site of isolation.
Figure 1. Core gene-based maximum-likelihood phylogenetic tree of 315 E. coli isolates from the urinary tract of cats and dogs. The inner to outer coloured rings display additional metadata defined by the host species, pathotype, phylogroup, sequence type, putative MDR phenotype, and site of isolation.
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Figure 2. Correlations among 34 VAGs identified in UPEC isolates and 26 dominant STs: blue coloured cells indicate a significant positive association between VAG and ST (p ≤ 0.05), light grey coloured cells indicate no significant association (p > 0.05), and green coloured cells indicate a significant negative association (p ≤ 0.05) as determined by Chi-square tests.
Figure 2. Correlations among 34 VAGs identified in UPEC isolates and 26 dominant STs: blue coloured cells indicate a significant positive association between VAG and ST (p ≤ 0.05), light grey coloured cells indicate no significant association (p > 0.05), and green coloured cells indicate a significant negative association (p ≤ 0.05) as determined by Chi-square tests.
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Table 1. Results of phenotype, clonal typing, sero(geno)typing, and fimH-typing of 198 canine and 117 feline E. coli isolates.
Table 1. Results of phenotype, clonal typing, sero(geno)typing, and fimH-typing of 198 canine and 117 feline E. coli isolates.
Phylogenetic GroupHaemolytic PhenotypeMultilocus
Sequence Type		PathotypeSero(geno)typeFimH Type
(percentages of positive isolates are given in brackets)
DogA (3.0)
B1 (12.1)
B2 (76.8)
C (4.0)
D (3.0)
E (0.0)
F (0.5)
G (0.5)		non-haemolytic (43.4)
haemolytic (56.6)		ST372 (26.8)
ST73 (9.1)
ST12 (8.1)
ST127 (5.1)
ST141 (4.6)
ST131 (3.0)
ST162 (2.5)
ST80 (1.52)
ST2015 (2.53)
Other (36.9)		ExPEC (8.6 *)
UPEC (46.0)
Other (45.5)		Ont (24.8)
O4 (17.2)
O2 (13.1)
O6 (10.6)
O25 (3.5)
O8 (4.6)
O83 (5.1)
O15 (5.1)
O25b (2.5)
O9 (2.5)
Other (11.1)		fimH9 (25.9)
fimH5 (5.1)
fimH32 (4.6)
fimH2 (3.6)
fimH102 (3.1)
fimH13 (0.5)
fimH27 (2.5)
fimH14 (2.5)
fimH197 (2.5)
fimH1 (2.0)
fimH39 (2.0)
fimH31 (2.6)
Other (44.2)
CatA (1.7)
B1 (12.0)
B2 (79.5)
C (3.4)
D (0.8)
E (0.8)
F (0.8)
G (0.8)		non-haemolytic (29.9)
haemolytic (70.1)		ST372 (1.7)
ST73 (27.4)
ST12 (9.4)
ST127 (4.3)
ST141 (5.1)
ST131 (4.3)
ST162 (3.4)
ST80 (3.4)
ST2015 (1.7)
Other (39.3)		ExPEC (5.1 *)
UPEC (59.8)
Other (35.0)		Ont (26.5)
O4 (11.1)
O2 (17.1)
O6 (8.6)
O25 (12.0)
O8 (5.1)
O83 (1.7)
O15 (0.0)
O25b (3.4)
O9 (3.4)
Other (11.1)		fimH9 (11.1)
fimH5 (5.1)
fimH32 (5.1)
fimH2 (6.0)
fimH102 (3.4)
fimH13 (6.0)
fimH27 (2.6)
fimH14 (1.7)
fim197 (1.7)
fimH1 (1.7)
fimH39 (1.7)
fimH31 (2.6)
Other (51.3)
* Indicates the number of isolates that could be assigned to the pathotype ExPEC but were not confirmed as UPEC.
Table 2. Distribution of ExPEC-associated genes among 315 E. coli isolates from 198 dogs and 117 cats.
Table 2. Distribution of ExPEC-associated genes among 315 E. coli isolates from 198 dogs and 117 cats.
CategoryGeneDog
N (%)		Cat
N (%)		Total
N (%)		p-Value 1
Adhesins
Fimbrial papGI1 (0.5)3 (2.6)4 (1.3)0.146
papGII5 (2.5)2 (1.7)7 (2.2)0.483
papGIII92 (46.5)50 (42.7)142 (45.1)0.520
fimACDH194 (98.0)117 (100.0)311 (98.7)0.154
focAC/D70 (35.4)34 (29.1)104 (33.0)0.251
sfaSAF22 (11.1)17 (15.5)39 (12.4)0.373
Non-Fimbrial csgABC/DEFG198 (100.0)117 (100.0)315 (100.0)-
fdeC155 (78.3)96 (82.1)251 (79.7)0.422
iha10 (5.1)13 (11.1)23 (7.3)0.046
afaE-I2 (1.0)-2 (0.6)0.394
draAD3 (1.5)-3 (1.0)0.247
flgBCDEFGHIJ198 (100.0)117 (100.0)315 (100.0)-
Siderophore systems ent/fep/fes197 (99.5)117 (100)314 (99.7)0.629
irp1 + 2/fyuA168/167 (84.8/84.3)101/102 (86.3/87.2)269 (85.4)0.491
iroBCDEN144 (72.7)98 (83.8)242 (76.8)0.025
iuc/iutA28 (14.1)20 (17.1)48 (15.2)0.481
chuA/hma160/110 (80.8/55.6)97/84
(82.9/71.8)		257/194 (81.6/61.6)0.643/0.004
sitABCD114 (54.0)62 (53.0)176 (55.9)0.429
Toxins cnf1107 (54.0)75 (64.1)182 (57.8)0.081
vat144 (72.7)87 (74.4)231 (73.3)0.752
pic41 (20.7)60 (51.3)101 (32.1)<0.001
astA25 (12.6)9 (7.7)31 (9.8)0.173
cdtB13 (6.6)15 (12.8)28 (8.9)0.059
hlyCABD97 (49.0)49 (41.9)146 (46.3)0.221
tosA102 (51.5)63 (53.8)165 (52.4)0.689
Autotransporter
proteins 		agn4377 (38.937 (31.6)114 (36.2)0.195
upaC69 (34.8)69 (59.0)138 (43.8)<0.001
sat9 (4.5)8 (6.8)17 (5.4)0.384
Surface
polysaccharides		kpsMTII80 (40.4)69 (59.0)149 (47.3)<0.001
neuC15 (7.6)7 (6.0)22 (7.0)0.592
neuS1 (0.5)1 (0.9)2 (0.6)0.606
InvasinsompA198 (100.0)117 (100.0)315 (100.0)-
ibeA84 (42.4)30 (25.6)114 (36.2)0.003
traT69 (34.8)41 (35.0)110 (34.9)0.972
Miscellaneous or unknown functionmalX198 (100.0)117 (100.0)315 (100.0)-
ompT174 (87.9)107 (91.5)281 (89.2)0.323
usp149 (75.3)90 (76.9)239 (75.9)0.738
1 The occurrence of VAGs between animal species was assessed using Chi-square tests, and a value of p < 0.05 was seen as statistically significant (bold); papGII/papGIII, P fimbriae; fimACDH, type 1 fimbriae; focAC/D, F1C fimbriae; sfaSAF, S fimbriae (sialic acid-specific); csgABC/DEFG, curli; fdeC, factor adherence E. coli; iha, iron-regulated-gene-homologue adhesin; afaE-I, afimbrial adhesin; draAD, dr antigen-binding adhesin; ent/fep/fes, entero-bactin synthesis/receptor; irp/fyuA, yersiniabactin synthesis/receptor; iroBCDE/N, salmochelin synthesis/receptor; iuc/iutA, aerobactin synthesis/receptor; chuA/hma, heme receptor; sitABCD, salmonella iron transporter; cnf1, cytotoxic necrotizing factor 1; vat, vacuolating autotransporter toxin; pic, serin protease autotransporter; astA, enteroaggregative E. coli toxin; cdtB, cytolethal distending toxin; hlyCABD, hemolysin A; tosA, putative repeat-in-toxin protein; agn43, antigen 43; upaC, uropathogenic E. coli autotransporter; sat, secreted autotransporter toxin; kpsMTII, group II capsule synthesis; neuC/S, K1 capsular polysaccharide; ompA, outer membrane protein A; ibeA, invasion of brain endothelium; traT, serum-resistance associated; malX, pathogenicity island marker; ompT, outer membrane protein T; usp, uropathogenic specific protein.
Table 3. Distribution of AMR genes in 315 E. coli isolates from urine samples of 117 cats and 198 dogs, differentiated by phylogroup B2 (n = 245) and non-B2 (n = 70) isolates.
Table 3. Distribution of AMR genes in 315 E. coli isolates from urine samples of 117 cats and 198 dogs, differentiated by phylogroup B2 (n = 245) and non-B2 (n = 70) isolates.
AntibioticGeneCat
n (%)		Dog
n (%)		p-Value 1B2
n (%)		non-B2
n (%)		p-Value 2All
n (%)
Amino-
glycoside		aac(3)-IId-4 (2.0)0.3013 (1.2)1 (1.4)14 (1.3)
aadA6 (5.1)22 (11.1)0.10013 (5.3)15 (21.4)<0.000128 (8.9)
ant(2″)-Ia1 (0.9)-0.371-1 (1.4)0.2221 (0.3)
aphAI-IAB32 (27.4)52 (26.3)0.89550 (20.4)34 (48.6)<0.000184 (26.7)
Quinoloneaac(6′)-Ib-cr1 (0.9)-0.371-1 (1.4)0.2221 (0.3)
qnrB-2 (1.0)0.532-2 (2.9)0.0492 (0.6)
qnrS1 (0.9)2 (1.0)1-3 (4.3)0.0893 (1.0)
Rifampicinarr-31 (0.9)-0.371-1 (1.4)0.2221 (0.3)
β-LactamsblaTEM23 (19.7)36 (18.2)0.76636 (14.7)23 (32.9)0.00259 (18.8)
blaOXA-12 (1.7)3 (1.5)11 (0.4)4 (5.7)0.0095 (1.6)
blaCTX-M-15-3 (1.5)0.297-3 (4.3)0.0113 (1.0)
blaCTX-M-271 (0.9)-0.371-1 (1.4)0.2221 (0.3)
blaDHA-1-1 (0.5)1-1 (1.4)0.2221 (0.3)
blaCMY-21 (0.9)-0.3711 (0.4)-11 (0.3)
blaOXA-481 (0.9)-0.3711 (0.4)-11 (0.3)
blaSHV-13 (2.6)2 (1.0)0.3645 (2.0)-0.5905 (1.6)
PhenicolscatA1-6 (3.0)0.0884 (1.6)2 (2.9)0.6186 (1.9)
catB31 (0.9)-0.371-1 (1.4)0.2221 (0.3)
cmlA1-2 (1.0)0.5321 (0.4)1 (1.4)0.3962 (0.6)
floR3 (2.6)3 (1.5)0.674-6 (8.6)<0.00016 (1.9)
Folate
pathway inhibitors		sul16 (5.1)14 (7.1)0.49510 (4.1)10 (14.3)0.00220 (6.3)
sul215 (12.8)22 (11.1)0.64918 (7.3)19 (27.1)<0.000137 (11.7)
sul3-4 (2.0)0.3011 (0.4)3 (4.3)0.0364 (1.3)
drfA12 (10.3)28 (14.1)0.38314 (5.7)26 (37.1)<0.000140 (12.7)
Tetracyclinetet(A)8 (6.8)21 (10.6)0.26417 (6.9)12 (17.1)0.00929 (9.2)
tet(B)5 (4.3)7 (3.5)0.7414 (1.6)8 (11.4)<0.000112 (3.8)
tet(D)1 (0.9)-0.3711 (0.4)-11 (0.3)
tet(M)-1 (0.5)11 (0.4)-11 (0.3)
Macrolidesmph(A)1 (0.9)6 (3.0)0.2654 (1.6)3 (4.3)0.1867 (2.2)
mph(B)-1 (0.5)11 (0.4)-11 (0.3)
mph(E)-1 (0.5)1-1 (1.4)0.2221 (0.3)
msr(E)-1 (0.5)1-1 (1.4)0.2221 (0.3)
Colistinmcr-4.6 *-1 (0.5)11 (0.4)-11 (0.3)
FosfomycinfosA73 (2.6)-0.050-3 (4.3)0.0113 (1.0)
AMR genes total 1282450.244287186<0.0001373
The occurrence of AMR genes was compared among animal species 1 and among phylogroups (B2 versus non-B2) 2 by employing Chi-square tests. Significance was set at p = 0.05 (bold). * Mutations in the pmrA and pmrB genes that are known to confer colistin resistance were not detected.
Table 4. Origin, haemolytic phenotype, molecular characteristics, AMR profiles and AMR genes of CP/ESBL/AmpC-positive E. coli isolates.
Table 4. Origin, haemolytic phenotype, molecular characteristics, AMR profiles and AMR genes of CP/ESBL/AmpC-positive E. coli isolates.
Sample IDAnimalHaemolysisSTPhylo-GroupCP/ESBL/
AmpC-Positive Isolate		AMR GenesMutations
ampC PromotorgyrAparCparE
IHIT41651 dog0410CESBLblaCTX-M-15, blaTEM-1B,aadA2, sul1, dfrA12, tet(A), mph(A)-S83L, D87NS80IS458A
IHIT41754 dog01844B1AmpCblaDHA-1, blaTEM-1B,sul1, dfrA17, tet(B), qnrB4, mph(A)−1C > T,
−18G > A		---
IHIT42192 cat0533B1ESBLblaCTX-M-27,sul2, dfrA36, tet(B), sul2−1C > T
−18G > A		D87N, S83LS80I
IHIT42968 dog058B1AmpCblaEC11-like, dfrA5−42C > T *
−18G > A
−1C > T		---
IHIT43081 cat1372B2CPblaOXA-48----
IHIT43540 dog088CESBLblaCTX-M-15,aadA1, sul2, dfrA1, tet(B), qnrS1−18G > A
−1C > T		S83L--
IHIT43661 cat112B2AmpCblaCMY-2----
IHIT43802 dog0361AESBLblaCTX-M-15, blaTEM-32,aph(3″)-Ib, aph(3′)-Ia, aph(6)-Id, sul2, dfrA1-D87N, S83LS80IS458A
IHIT44091 cat1131B2AmpCblaTEM-1B,blaEC-6, aph(3″)-Ib, aph(6)-Id, sul2, dfrA8−28G > A--I529L
AMC: amoxicillin/clavulanic acid; AMP: ampicillin; CFX: cephalexin; CFV: cefovecin; ENR: enrofloxacin; PRA: pradofloxacin; SXT: trimethoprim/sulfamethoxazole; TET: tetracycline; CP: carbapenemase; * associated with phenotypic resistance (ampicillin, ampicillin/clavulanic acid, amoxicillin, amoxicillin/clavulanic acid, cefixime, cefotaxime, cefoxitin, ceftazidime, piperacillin).
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Aurich, S.; Wolf, S.A.; Prenger-Berninghoff, E.; Thrukonda, L.; Semmler, T.; Ewers, C. Genotypic Characterization of Uropathogenic Escherichia coli from Companion Animals: Predominance of ST372 in Dogs and Human-Related ST73 in Cats. Antibiotics 2024, 13, 38. https://doi.org/10.3390/antibiotics13010038

AMA Style

Aurich S, Wolf SA, Prenger-Berninghoff E, Thrukonda L, Semmler T, Ewers C. Genotypic Characterization of Uropathogenic Escherichia coli from Companion Animals: Predominance of ST372 in Dogs and Human-Related ST73 in Cats. Antibiotics. 2024; 13(1):38. https://doi.org/10.3390/antibiotics13010038

Chicago/Turabian Style

Aurich, Sophie, Silver Anthony Wolf, Ellen Prenger-Berninghoff, Lakshmipriya Thrukonda, Torsten Semmler, and Christa Ewers. 2024. "Genotypic Characterization of Uropathogenic Escherichia coli from Companion Animals: Predominance of ST372 in Dogs and Human-Related ST73 in Cats" Antibiotics 13, no. 1: 38. https://doi.org/10.3390/antibiotics13010038

APA Style

Aurich, S., Wolf, S. A., Prenger-Berninghoff, E., Thrukonda, L., Semmler, T., & Ewers, C. (2024). Genotypic Characterization of Uropathogenic Escherichia coli from Companion Animals: Predominance of ST372 in Dogs and Human-Related ST73 in Cats. Antibiotics, 13(1), 38. https://doi.org/10.3390/antibiotics13010038

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