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

Predictive phage therapy for Escherichia coli urinary tract infections: Cocktail selection for therapy based on machine learning models

This study supports the development of predictive bacteriophage (phage) therapy: the concept of phage cocktail selection to treat a bacterial infection based on machine learning (ML) models. For this purpose, ML models were trained on thousands of measured interactions between a panel of phage and sequenced bacterial isolates. The concept was applied to Escherichia coli associated with urinary tract infections. This is an important common infection in humans and companion animals from which multidrug-resistant (MDR) bloodstream infections can originate. The global threat of MDR infection has reinvigorated international efforts into alternatives to antibiotics including phage therapy. E. coli exhibit extensive genome-level variation due to horizontal gene transfer via phage and plasmids. Associated with this, phage selection for E. coli is difficult as individual isolates can exhibit considerable variation in phage susceptibility due to differences in factors important to phage infection including phage receptor profiles and resistance mechanisms. The activity of 31 phage was measured on 314 isolates with growth curves in artificial urine. Random Forest models were built for each phage from bacterial genome features, and the more generalist phage, acting on over 20% of the bacterial population, exhibited F1 scores of >0.6 and could be used to predict phage cocktails effective against previously untested strains. The study demonstrates the potential of predictive ML models which integrate bacterial genomics with phage activity datasets allowing their use on data derived from direct sequencing of clinical samples to inform rapid and effective phage therapy.

Escherichia coli sequence type 410 with carbapenemases: a paradigm shift within E. coli toward multidrug resistance

Escherichia coli sequence type ST410 is an emerging carbapenemase-producing multidrug-resistant (MDR) high-risk One-Health clone with the potential to significantly increase carbapenem resistance among E. coli. ST410 belongs to two clades (ST410-A and ST410-B) and three subclades (ST410-B1, ST410-B2, and ST410-B3). After a fimH switch between clades ST410-A and ST410-B1, ST410-B2 and ST410-B3 subclades showed a stepwise progression toward developing MDR. (i) ST410-B2 initially acquired fluoroquinolone resistance (via homologous recombination) in the 1980s. (ii) ST410-B2 then obtained CMY-2, CTX-M-15, and OXA-181 genes on different plasmid platforms during the 1990s. (iii) This was followed by the chromosomal integration of blaCMY-2, fstl YRIN insertion, and ompC/ompF mutations during the 2000s to create the ST410-B3 subclade. (iv) An IncF plasmid "replacement" scenario happened when ST410-B2 transformed into ST410-B3: F36:31:A4:B1 plasmids were replaced by F1:A1:B49 plasmids (both containing blaCTX-M-15) followed by blaNDM-5 incorporation during the 2010s. User-friendly cost-effective methods for the rapid identification of ST410 isolates and clades are needed because limited data are available about the frequencies and global distribution of ST410 clades. Basic mechanistic, evolutionary, surveillance, and clinical studies are urgently required to investigate the success of ST410 (including the ability to acquire successive MDR determinants). Such information will aid with management and prevention strategies to curb the spread of carbapenem-resistant E. coli. The medical community can ill afford to ignore the spread of a global E. coli clone with the potential to end the carbapenem era.

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

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.

Resistome-based surveillance identifies ESKAPE pathogens as the predominant gram-negative organisms circulating in veterinary hospitals

Introduction

Healthcare-associated infections (HCAIs) associated with extended-spectrum cephalosporin-resistant gram-negative (ESC-R GN) bacteria are an emerging concern in veterinary hospitals, especially in companion animal intensive care units (ICUs).

Methods

To understand the molecular epidemiology of ESC-R GN isolates in two veterinary hospitals (equine and small animal), a 6-month pilot study was performed during which fecal and environmental samples were obtained twice from selected patients, upon ICU admission and after 48 h of hospitalization. In total, 295 ESC-R GNs were analyzed using the Acuitas Resistome® Test (OpGen, Maryland, US), a PCR-based assay screening for 50 antimicrobial resistance gene families encoding for production of extended-spectrum beta-lactamase (ESBLs), TEM/SHV/OXA or AmpC beta-lactamases and carbapenemases. Combining organism identification and antimicrobial susceptibility data to genotyping results, unique "Acuitas profiles" were generated that can be used for fast typing the isolates and tracking transmission events.

Results

ESKAPE GN pathogens were the most prevalent ESC-R GN isolates circulating in both the small animal and equine hospitals, consisting of Enterobacter cloacae complex (21.7%), Pseudomonas aeruginosa (20%), Klebsiella pneumoniae (15.9%), and Acinetobacter baumannii complex (13.6%) followed by Escherichia coli (12.2%), most harboring a combination of genes encoding for beta-lactamases and ESBLs. Some ESKAPE genotypes showed likely intra-hospital transmission, including E. cloacae (two genotypes, one carrying SHV4, SHV5, and TEM7 and the other TEM1, TEM3, and TEM7 enzymes) in the equine and K. pneumoniae (SHV1, SHV5, and DHA1-positive) in the small animal ICUs, respectively. Furthermore, P. aeruginosa (carrying OXA-50), A. baumannii complex (OXA-51), and E. coli (CTX-M-1) genotypes were isolated across both hospitals, suggesting possible transfer mediated via movement of staff and students. Importantly, isolates carrying transmissible resistance to last-resort antimicrobials (i.e. carbapenems) were identified within the hospital environments, consisting of three environmental Acinetobacter spp. harboring blaOXA - 23 and one clinical E. coli with blaOXA - 48.

Conclusion

We describe the widespread occurrence of ESKAPE gram-negative organisms in veterinary ICU patients and hospital environments. Findings from this project provide baseline data on the epidemiology of ESKAPE pathogens in veterinary settings, which can inform infection control policies to aid in patient management and prevent transmission of nosocomial infections associated with these pathogens.

Rapid identification of canine uropathogens by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry and the clinical factors that correlated bacterial species and antimicrobial resistance

Using the matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) method for bacterial diagnosis, rapid urine sample preparation can reduce time relapsing of diagnosis and improve discriminatory power in coinfection cases. We aimed to evaluate rapid urine preparation procedures before MALDI-TOF MS application using dog clinical urine samples in comparison with standard microbiological diagnostic methods by agreement analysis. We determined the frequency and distribution of bacteria and bacterial resistance and their correlations to clinical history. Three experimental procedures comprising direct centrifugation, 10% sodium dodecyl sulfate digestion, and ultrasonic preparation were performed for method validation and sensitivity. Sterile urine containing Escherichia coli and/or Staphylococcus aureus were used as simulated samples. By ultrasonic preparation, the microorganisms could be detected 1.46-1.51 × 105 CFU, which was considered the most suitable technique. This preparation was significantly consistent with the routine method based on data from Hospital Information Systems for 50 urine samples from canine cystitis. By standard protocol, Enterobacteriaceae and Staphylococcus pseudintermedius were found in most of the 155 urine samples with cystitis. Extended-spectrum beta-lactamase-producing Enterobacteriaceae was found in 25-30% of the samples. Imipenem resistance was found in 70% of Acinetobacter baumannii cases; almost all were resistant to second-generation fluoroquinolones and tetracyclines. The most efficient antibiotic for treating bacterial urinary tract infection was amoxicillin plus clavulanic acid. A. baumannii and Pseudomonas aeruginosa were susceptible to pradofloxacin. Prolonged urine catheterization was linked to lower urinary tract infections by Enterobacter spp., which also correlated with chronic kidney disease.

Genomic Evidence of mcr-1.26 IncX4 Plasmid Transmission between Poultry and Humans

Colistin is still commonly used and misused in animal husbandry driving the evolution and dissemination of transmissible plasmid-mediated colistin resistance (mcr). mcr-1.26 is a rare variant and, so far, has only been detected in Escherichia coli obtained from a hospitalized patient in Germany in 2018. Recently, it was also notified in fecal samples from a pigeon in Lebanon. We report on the presence of 16 colistin-resistant, mcr-1.26-carrying extended-spectrum beta-lactamase (ESBL)-producing and commensal E. coli isolated from poultry samples in Germany, of which retail meat was the most common source. Short- and long-read genome sequencing and bioinformatic analyses revealed the location of mcr-1.26 exclusively on IncX4 plasmids. mcr-1.26 was identified on two different IncX4 plasmid types of 33 and 38 kb and was associated with an IS6-like element. Based on the genetic diversity of E. coli isolates, transmission of the mcr-1.26 resistance determinant is mediated by horizontal transfer of IncX4 plasmids, as confirmed by conjugation experiments. Notably, the 33-kb plasmid is highly similar to the plasmid reported for the human sample. Furthermore, we identified the acquisition of an additional beta-lactam resistance linked to a Tn2 transposon on the mcr-1.26 IncX4 plasmids of three isolates, indicating progressive plasmid evolution. Overall, all described mcr-1.26-carrying plasmids contain a highly conserved core genome necessary for colistin resistance development, transmission, replication, and maintenance. Variations in the plasmid sequences are mainly caused by the acquisition of insertion sequences and alteration in intergenic sequences or genes of unknown function. IMPORTANCE Evolutionary events causing the emergence of new resistances/variants are usually rare and challenging to predict. Conversely, common transmission events of widespread resistance determinants are quantifiable and predictable. One such example is the transmissible plasmid-mediated colistin resistance. The main determinant, mcr-1, has been notified in 2016 but has successfully established itself in multiple plasmid backbones in diverse bacterial species across all One Health sectors. So far, 34 variants of mcr-1 are described, of which some can be used for epidemiological tracing-back analysis to identify the origin and transmission dynamics of these genes. Here, we report the presence of the rare mcr-1.26 gene in E. coli isolated from poultry since 2014. Based on the temporal occurrence and high similarity of the plasmids between poultry and human isolates, our study provides first indications for poultry husbandry as the primary source of mcr-1.26 and its transmission between different niches.

Genetic Diversity and New Sequence Types of Escherichia coli Coharboring β-Lactamases and PMQR Genes Isolated from Domestic Dogs in Central Panama

Background: β-lactamase-producing Escherichia coli are a widely distributed source of antimicrobial resistance for animals and humans. Little is known about the susceptibility profile and genetic characteristics of E. coli strains isolated from domestic dogs in Latin America. Methods: We report on a cross-sectional study that evaluated E. coli strains isolated from fecal samples of domestic dogs in central Panama. The extended-spectrum β-lactamase (ESBL), AmpC genes, and plasmid-mediated quinolone resistance were investigated. Molecular typing using Pasteur’s multilocus sequence typing (MLST) was conducted. Results: A total of 40 E. coli isolates were obtained, of which 80% (32/40) were resistant to at least one of the antibiotics tested, while 20% (8/40) were sensitive to all antibiotics analyzed in this study (p < 0.001). Forty percent of the strains were resistant to three or more antibiotics. The most common resistance was to tetracycline (45%) and ampicillin (30%) while 2.5% showed an ESBL phenotype. Antibiotic resistance genes were detected for one β-lactamase (blaTEM-1) and two plasmid-mediated quinolone resistance (PMQR) enzymes (qnrS and qnrB). In addition, mutations in the chromosomal AmpC gene were observed at positions −35, −28, −18, −1, and +58. Fourteen different sequence types (STs) were identified; the most frequent were ST399 and ST425 (12% each). ST3 and ST88, which have been previously identified in human clinical isolates, were also evidenced. Three new STs were found for the first time: ST1015, ST1016 (carrier of the blaTEM-1 gene), and ST1017 (carrier of the blaTEM-1, qnrS, and qnrB genes). Conclusions: In the intestinal strains of E. coli isolated from domestic dogs, there was a high frequency of resistance to antibiotics. The presence of genes from plasmids and chromosomal mutations that conferred antibiotic resistance, the identification of isolates previously reported in humans, and the genetic diversity of STs (including three that were newly identified) confirmed the determinants of resistance to antibiotics in the domestic dogs from central Panama.

Isolation of Escherichia coli and Klebsiella pneumoniae strains producing extended spectrum β-lactamases from dog urine of the Metropolitan Area of the Aburrá Valley Antioquia-Colombia

Escherichia coli and Klebsiella pneumoniae are the most common pathogens causing urinary tract infections in humans and animals. Close contact between humans and companion animals can facilitate the spread of multidrugresistant pathogens between both species. Objective: To characterize extended-spectrum β-lactamases (ESBL) -producing E. coli and K. pneumoniae isolated from dogs with urinary tract infections in the metropolitan area of Valle del Aburrá (Antioquia, Colombia). Methods: Three-hundred seventy-one urine samples collected from March 2018 to March 2019 in a veterinary clinical laboratory were analyzed. E. coli and K. pneumoniae isolates were detected in chromogenic agar and identified by biochemical tests. Susceptibility testing was performed by disc diffusion and ESBL production was evaluated by the double disk test in all isolates. MIC determination of ESBL-positive isolates were performed on the automated VITEK®2 system. Multiple PCR was used for the detection of CTX-M beta-lactamases (group 1, 2, 9 and 8/25), SHV, TEM and AmpC of plasmid origin in ESBL-positive isolates. Results: In total 22 out 371 isolates were positive for ESBL production by double disc test, 11 E. coli (ESBL-Ec) and 11 K. pneumoniae (ESBL-Kp). The multiple PCR detected CTX-M group 1 in the 22 ESBL-positive isolates. Multi-drug resistance was observed in all ESBL-producing isolates Conclusions:  A high frequency of antibiotic multi-resistance was found in ESBL-Ec and ESBL-Kp. The main ESBL detected was CTX-M group 1, which also prevails in human isolates.

The Role of Outer Membrane Proteins in UPEC Antimicrobial Resistance: A Systematic Review

Uropathogenic Escherichia coli (UPEC) are one of the most common agents of urinary tract infection. In the last decade, several UPEC strains have acquired antibiotic resistance mechanisms and some have become resistant to all classes of antibiotics. UPEC outer membrane proteins (OMPs) seem to have a decisive role not only in the processes of invasion and colonization of the bladder mucosa, but also in mechanisms of drug resistance, by which bacteria avoid killing by antimicrobial molecules. This systematic review was performed according to the PRISMA guidelines, aiming to characterize UPEC OMPs and identify their potential role in antimicrobial resistance. The search was limited to studies in English published during the last decade. Twenty-nine studies were included for revision and, among the 76 proteins identified, seven were associated with antibiotic resistance. Indeed, OmpC was associated with β-lactams resistance and OmpF with β-lactams and fluoroquinolone resistance. In turn, TolC, OmpX, YddB, TosA and murein lipoprotein (Lpp) were associated with fluoroquinolones, enrofloxacin, novobiocin, β-lactams and globomycin resistances, respectively. The clinical implications of UPEC resistance to antimicrobial agents in both veterinary and human medicine must propel the implementation of new strategies of administration of antimicrobial agents, while also promoting the development of improved antimicrobials, protective vaccines and specific inhibitors of virulence and resistance factors.

Phylogenetic Groups, Pathotypes and Antimicrobial Resistance of Escherichia coli Isolated from Western Lowland Gorilla Faeces (Gorilla gorilla gorilla) of Moukalaba-Doudou National Park (MDNP)

(1) Background: Terrestrial mammals in protected areas have been identified as a potential source of antimicrobial-resistant bacteria. Studies on antimicrobial resistance in gorillas have already been conducted. Thus, this study aimed to describe the phylogroups, pathotypes and prevalence of antimicrobial resistance of Escherichia coli isolated from western lowland gorilla's faeces living in MDNP. (2) Materials and Methods: Ninety-six faecal samples were collected from western lowland gorillas (Gorilla gorilla gorilla) during daily monitoring in the MDNP. Sixty-four E. coli isolates were obtained and screened for phylogenetic and pathotype group genes by polymerase chain reaction (PCR) after DNA extraction. In addition, antimicrobial susceptibility was determined by the disk diffusion method on Mueller Hinton agar. (3) Results: Sixty-four (64%) isolates of E. coli were obtained from samples. A high level of resistance to the beta-lactam family, a moderate rate for fluoroquinolone and a low rate for aminoglycoside was obtained. All E. coli isolates were positive in phylogroup PCR with a predominance of A (69% ± 11.36%), followed by B2 (20% ± 19.89%) and B1 (10% ± 8.90%) and low prevalence for D (1% ± 3.04%). In addition, twenty E. coli isolates (31%) were positive for pathotype PCR, such as EPEC (85% ± 10.82%) and EPEC/EHEC (15% ± 5.18%) that were obtained in this study. The majority of these MDR E. coli (DECs) belonged to phylogenetic group A, followed by MDR E. coli (DECs) belonging to group B2. (4) Conclusion: This study is the first description of MDR E. coli (DECs) assigned to phylogroup A in western lowland gorillas from the MDNP in Gabon. Thus, wild gorillas in MDNP could be considered as asymptomatic carriers of potential pathogenic MDR E. coli (DECs) that may present a potential risk to human health.

Clonal Dissemination of Extended-Spectrum Cephalosporin-Resistant Enterobacterales between Dogs and Humans in Households and Animal Shelters of Romania

Faecal carriage of extended-spectrum cephalosporin-resistant (ESC-R) Enterobacterales in healthy pets is a concerning issue. This study aimed to determine the prevalence, genetic background, and potential for interspecies transmission of these bacteria between dogs and humans within the same household (HH) or shelter environment in Romania. Faecal samples (n = 263) collected from healthy dogs (n = 102), their owners (n = 32), as well as dogs (n = 110) and staff (n = 19) from dog shelters, were screened for ESC-R carriage. Clonal relatedness of canine and human Escherichia coli isolates was established using Fourier Transform Infrared Spectroscopy (FTIR), followed by Illumina WGS of selected isolates. The highest prevalence of ESC-R Enterobacterales faecal carriage was identified in staff working at dog shelters (78.9%), followed by dogs from households (44.11%), dog owners (43.7%), and dogs from shelters (27%). FTIR identified 15 clusters of closely related E. coli isolates, including dog and human isolates from the same environment. Co-carriage of ESC-R isolates in both the dog and owner was identified in 12 HHs (37.5%), with two HHs (6%) having both the owner and dog carrying isolates with identical FTIR spectra, phylogroup, resistance genes, and Inc plasmids. Major ExPEC lineages such as ST127, ST10, ST155, and ST88 were detected in human and dog isolates. Our study revealed a high prevalence of faecal ESC-R E. coli carriage in both dogs and humans from Romanian households and shelters, where bidirectional clonal transmission between humans and dogs is likely. Furthermore, we identified ESC-R Enterobacterales co-carriage in people and dogs sharing the same environment using FTIR, demonstrating its value in AMR surveillance for humans and animals.

Companion Animals as Potential Reservoirs of Antibiotic Resistant Diarrheagenic Escherichia coli in Shandong, China

Antibiotic resistance genes of Escherichia coli (E. coli) from companion animals were still poorly understood. Here, we investigated the extended-spectrum β-lactamases (ESBLs) resistance genes of E. coli from companion animals in Shandong, China. A total of 79 isolates (80.6%) were recovered from 98 healthy or diarrheal companion animals in 2021, among which ESBLs-producing isolates accounted for 43.0% (34/79), and more than half of ESBL E. coli (ESBL-EC) strains (n = 19) were isolated from healthy companion animals. Diarrheagenic E. coli isolates (45.6%, n = 36) were represented by enterotoxigenic (ETEC) (32.9%), enteropathogenic (EPEC) (10.1%) and enteroinvasive (EIEC) (2.6%), 20 isolates of which were from healthy pets. Among tested antibiotics, resistance to tetracycline (64.6%) was the most commonly observed, followed by doxycycline (59.5%) and ampicillin (53.2%). Notably, all isolates were susceptible to meropenem. The multidrug-resistant (MDR) rate was 49.4%, 20 isolates of which were ESBLs producers; moreover, 23.4%, 16.4% of ESBL-EC strains were resistant to 5 or more, 7 or more antibiotics, respectively. Among the 5 β-lactamase resistance genes, the most frequent gene was bla_CTX-M (60.76%), followed by bla_SHV (40.51%). The plasmid-mediated quinolone resistance (PMQR) gene aac(6')-Ib-cr was detected in 35 isolates. Additionally, ESBL-associated genes (i.e., bla_CTX-M, bla_SHV) were found in 76.5% ESBL-EC strains, with six isolates carrying bla_CTX-M and bla_SHV. The marker gene of high-pathogenicity island gene irp2 (encoding iron capture systems) was the most frequency virulence gene. Our results showed that ESBL-EC were widespread in healthy or diarrhea companion animals, especially healthy pets, which may be a potential reservoir of antibiotic resistance, therefore, enhancing a risk to public and animal health.

Fecal Shedding of Multidrug Resistant Escherichia coli Isolates in Dogs Fed with Raw Meat-Based Diets in Brazil

The practice of feeding dogs raw meat-based diets (RMBDs) is growing in several countries, and the risks associated with the ingestion of pathogenic and antimicrobial-resistant Escherichia coli in dogs fed these diets are largely unknown. We characterized E. coli strains isolated from dogs fed either an RMBD or a conventional dry feed, according to the phylogroup, virulence genes, and antimicrobial susceptibility profiles of the bacteria. Two hundred and sixteen E. coli strains were isolated. Dogs fed RMBDs shed E. coli strains from the phylogroup E more frequently and were positive for the E. coli heat-stable enterotoxin 1-encoding gene. Isolates from RMBD-fed dogs were also frequently positive for multidrug-resistant E. coli isolates including extended-spectrum beta-lactamase (ESBL) producers. Whole-genome sequencing of seven ESBL-producing E. coli strains revealed that they predominantly harbored blaCTX-M-55, and two strains were also positive for the colistin-resistant gene mcr-1. These results suggest that feeding an RMBD can affect the dog’s microbiota, change the frequency of certain phylogroups, and increase the shedding of diarrheagenic E. coli. Also, feeding an RMBD seemed to be linked with the fecal shedding of multidrug-resistant E. coli, including the spread of strains harboring mobilizable colistin resistance and ESBL genes. This finding is of concern for both animal and human health.

Massive Spread of OXA-48 Carbapenemase-Producing Enterobacteriaceae in the Environment of a Swiss Companion Animal Clinic

Background: Companion animal clinics contribute to the spread of antimicrobial resistant microorganisms (ARM) and outbreaks with ARM of public health concern have been described. Methods: As part of a project to assess infection prevention and control (IPC) standards in companion animal clinics in Switzerland, a total of 200 swabs from surfaces and 20 hand swabs from employees were collected during four days in a medium-sized clinic and analyzed for extended spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E), carbapenemase-producing Enterobacteriaceae (CPE), vancomycin-resistant enterococci (VRE), and methicillin-resistant staphylococci (MRS). Results: A total of 22 (11.0%) environmental specimen yielded CPE, 14 (7.0%) ESBL-E, and 7 (3.5%) MRS; MR Staphylococcus aureus were isolated from two (10.0%) hand swabs. The CPE isolates comprised Escherichia coli, Klebsiella pneumoniae, Enterobacter hormaechei, Citrobacter braakii, and Serratia marcescens. Whole genome sequencing revealed that all CPE carried closely related bla_OXA-48 plasmids, suggesting a plasmidic spread within the clinic. The clinic exhibited major deficits in surface disinfection, hand hygiene infrastructure, and hand hygiene compliance. CPE were present in various areas, including those without patient contact. The study documented plasmidic dissemination of bla_OXA-48 in a companion animal clinic with low IPC standards. This poses a worrisome threat to public health and highlights the need to foster IPC standards in veterinary clinics to prevent the spread of ARM into the community.

Antibiotic resistance and phylogenetic profiling of Escherichia coli from dairy farm soils; organic versus conventional systems

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First known comparison of antimicrobial resistance traits in E. coli strains from new zealand farms practicing organic and conventional husbandry.

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Potential extended spectrum β-lactamase producing strains isolated from dairy farm environments.

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Organic dairy farms tended to harbour fewer resistant isolates than those recovered from conventionally farmed counterparts.

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Evidence for anthroponotic transmission of resistant strains of human origin to farm environments.

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Implications for the spread of antimicrobial resistance traits from farm environments discussed.

The prevalence and spread of antimicrobial resistance (AMR) as a result of the persistent use and/or abuse of antimicrobials is a key health problem for health authorities and governments worldwide. A study of contrasting farming systems such as organic versus conventional dairy farming may help to authenticate some factors that may contribute to the prevalence and spread of AMR in their soils. A case study was conducted in organic and conventional dairy farms in the South Canterbury region of New Zealand.

A total of 814 dairy farm soil E. coli (DfSEC) isolates recovered over two years were studied. Isolates were recovered from each of two farms practicing organic, and another two practicing conventional husbandries. The E. coli isolates were examined for their antimicrobial resistance (AMR) against cefoxitin, cefpodoxime, chloramphenicol, ciprofloxacin, gentamicin, meropenem, nalidixic acid, and tetracycline. Phylogenetic relationships were assessed using an established multiplex PCR method. The AMR results indicated 3.7% of the DfSEC isolates were resistant to at least one of the eight selected antimicrobials. Of the resistant isolates, DfSEC from the organic dairy farms showed a lower prevalence of resistance to the antimicrobials tested, compared to their counterparts from the conventional farms. Phylogenetic analysis placed the majority (73.7%) of isolates recovered in group B1, itself dominated by isolates of bovine origin. The tendency for higher rates of resistance among strains from conventional farming may be important for future decision-making around farming practices Current husbandry practices may contribute to the prevalence and spread of AMR in the industry.

OUP accepted manuscript

Escherichia coli has a rich history as biology's ‘rock star’, driving advances across many fields. In the wild, E. coli resides innocuously in the gut of humans and animals but is also a versatile pathogen commonly associated with intestinal and extraintestinal infections and antimicrobial resistance—including large foodborne outbreaks such as the one that swept across Europe in 2011, killing 54 individuals and causing approximately 4000 infections and 900 cases of haemolytic uraemic syndrome. Given that most E. coli are harmless gut colonizers, an important ecological question plaguing microbiologists is what makes E. coli an occasionally devastating pathogen? To address this question requires an enhanced understanding of the ecology of the organism as a commensal. Here, we review how our knowledge of the ecology and within-host diversity of this organism in the vertebrate gut has progressed in the 137 years since E. coli was first described. We also review current approaches to the study of within-host bacterial diversity. In closing, we discuss some of the outstanding questions yet to be addressed and prospects for future research.

Hand Hygiene Evaluation Using Two Different Evaluation Tools and Hand Contamination of Veterinary Healthcare Workers in a Swiss Companion Animal Clinic

Hand hygiene (HH) is the most important measure to prevent nosocomial infections. HH compliance in companion animal clinics has been reported to be poor. The present study compared an online application with the WHO evaluation form to assess the WHO five moments of HH in a Swiss companion animal clinic. In 202 hand swabs from 87 staff members, total viable count (TVC) before and after patient contact was evaluated and the swabs were tested for selected antimicrobial resistant microorganisms of public health importance. HH compliance (95% confidence interval) was 36.6% (33.8–39.5%) and was similar when assessed with the two evaluation tools. HH differed between hospital areas (p = 0.0035) and HH indications (p < 0.0001). Gloves were worn in 22.0% (18.0–26.6%) of HH observations and were indicated in 37.2% (27.3–48.3%) of these observations. Mean TVC before patient contact was lower (0.52 log CFU/cm²) than after patient contact (1.02 log CFU/cm²) but was similar before patient contact on gloved and ungloved hands. Three hand swabs (1.5% (0.4–4.3%)) were positive for methicillin-resistant Staphylococcus aureus. Gloving should not be regarded as a substitute for HH. Overall, HH in companion animal medicine should urgently be fostered.

High Occurrence of Shiga Toxin-Producing Escherichia coli in Raw Meat-Based Diets for Companion Animals-A Public Health Issue

Feeding pets raw meat-based diets (RMBDs) is becoming increasingly popular but comes with a risk of pathogenic bacteria, including Shiga toxin-producing Escherichia coli (STEC). In humans, STEC may cause gastrointestinal illnesses, including diarrhea, hemorrhagic colitis (HC), and the hemolytic uremic syndrome (HUS). The aim of this study was to evaluate commercially available RMBDs with regard to the occurrence of STEC. Of 59 RMBD samples, 59% tested positive by real-time PCR for the presence of Shiga toxin genes stx1 and/or stx2. STECs were recovered from 41% of the 59 samples, and strains were subjected to serotyping and virulence gene profiling, using whole genome sequencing (WGS)-based methods. Of 28 strains, 29% carried stx2a or stx2d, which are linked to STEC with high pathogenic potential. Twenty different serotypes were identified, including STEC O26:H11, O91:H10, O91:H14, O145:H28, O146:H21, and O146:H28, which are within the most common non-O157 serogroups associated with human STEC-related illnesses worldwide. Considering the low infectious dose and potential severity of disease manifestations, the high occurrence of STEC in RMBDs poses an important health risk for persons handling raw pet food and persons with close contact to pets fed on RMBDs, and is of concern in the field of public health.

Global prevalence and molecular characterization of extended-spectrum β-lactamase producing-Escherichia coli in dogs and cats - A scoping review and meta-analysis

Antimicrobial resistance (AMR) represents a major threat to human and animal health. Part of the AMR dimension is the circulation of extended-spectrum β-lactamases producing-Escherichia coli (ESBL-E. coli), which is now commonly reported among companion animals. However, the global perspective of the prevalence and population structure of ESBL-E. coli circulating in dogs and cats has not been estimated limiting our understanding of their role in the dissemination of ESBL-E. coli. The aim of this study was to compare the prevalence of ESBL-E. coli between dogs and cats and across countries through meta-analysis. We also performed a scoping review to summarize the current knowledge on ESBL genes and E. coli clones circulating among companion animals. A total of 128 studies published in PubMed, Web of Science, and Scopus up to April 2020 were selected and contained information on prevalence and/or molecular characterization of ESBL genes and ESBL-E. coli clones. Our review shows an increase in the number of publications between 2000 and 2019, concentrated mainly in Europe. Prevalence varied across continents, ranging from 0.63% (Oceania) to 16.56% (Africa) in dogs and from 0% (Oceania) to 16.82% (Asia) in cats. Although there were twice as many studies reporting prevalence on dogs (n = 61) than on cats (n = 32), and only 9 studies focused exclusively on cats, our meta-analysis showed no difference in the global prevalence of ESBL-E. coli between dogs (6.87% [95% CI: 4.46-10.45%]) and cats (5.04% [95% CI: 2.42-10.22%]). A considerable diversity of ESBL genes (n = 60) and sequence types (ST) (n = 171) were recovered from companion animals. ESBL-E. coli encoded by CTX-M-15 (67.5%, 77/114) and SHV-12 (21.9%, 25/114), along with resistant strains of ST38 (22.7%, 15/66) and ST131 (50%, 33/66) were widespread and detected in all continents. While presence of ESBL-E. coli is widespread, the drivers influencing the observed ESBL-E. coli prevalence and the clinical relevance in veterinary medicine and public health along with economic impact of ESBL-E. coli infections among companion animals need to be further investigated.

Animal petting zoos as sources of Shiga toxin-producing Escherichia coli, Salmonella and extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae

Animal petting zoos and farm fairs provide the opportunity for children and adults to interact with animals, but contact with animals carries a risk of exposure to zoonotic pathogens and antimicrobial-resistant bacteria. The aim of this study was to assess the occurrence of Shiga toxin-producing Escherichia coli (STEC), Salmonella, extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae and methicillin-resistant Staphylococcus aureus (MRSA) in animal faeces from six animal petting zoos and one farm fair in Switzerland. Furthermore, hygiene facilities on the venues were evaluated. Of 163 faecal samples, 75 contained stx1, stx2 or stx1/stx2 genes, indicating the presence of STEC. Samples included faeces from sika deer (100%), sheep (92%), goats (88%), mouflons (80%), camels (62%), llamas (50%), yaks (50%), pigs (29%) and donkeys (6%), whereas no stx genes were isolated from faeces of calves, guinea pigs, hens, ostriches, ponies, zebras or zebus. Salmonella enterica subsp. enterica serovar Stourbridge (S. Stourbridge) was detected in faecal samples from camels. A total of four ESBL-producing E. coli strains were isolated from faeces of goats, camels and pigs. PCR and sequencing identified the presence of bla_CTX-M-15 in three and bla_CTX-M-65 in one E. coli. Antimicrobial resistance profiling using the disk diffusion method revealed two multidrug-resistant (MDR) E. coli with resistance to ciprofloxacin, gentamicin and azithromycin, all of which are critically important drugs for human medicine. Multilocus sequence typing identified E. coli ST162, E. coli ST2179, extraintestinal high-risk E. coli ST410 and E. coli ST4553, which belongs to the emerging extraintestinal clonal complex (CC) 648. No MRSA was detected. On all animal petting venues, there were inadequacies with regard to access to hygiene information and handwashing hygiene facilities. This study provides data that underscore the importance of hygiene measures to minimize the risk of transmission of zoonotic pathogens and MDR, ESBL-producing E. coli to visitors of animal petting venues.

Escherichia coli-associated granulomatous colitis in dogs treated according to antimicrobial susceptibility profiling

Background

Eradication of intramucosal Escherichia coli correlates with remission of periodic acid‐Schiff‐positive E coli‐associated granulomatous colitis (GC). Treatment failures attributed to multidrug resistant (MDR) bacteria necessitate alternative approaches.

Hypothesis/objectives

Determine clinical outcome of E coli‐associated GC in dogs treated based on antimicrobial susceptibility profiling and characterize E coli phylogeny and resistance mechanisms.

Animals

Twenty Boxers and 4 French Bulldogs with E coli‐associated GC.

Methods

Culture, antimicrobial susceptibility profiling, and molecular characterization of E coli were performed and response to treatment was evaluated.

Results

Initial biopsy sample culture yielded fluoroquinolone‐sensitive (FQ‐S) E coli from 9/24 dogs and fluoroquinolone‐resistant (FQ‐R) E coli from 15/24. All but 1 FQ‐R E coli were MDR with susceptibility to macrophage‐penetrating antimicrobials restricted to carbapenems in 13/15 dogs. Of 22/24 treated based on susceptibility profiling, 8/9 FQ‐S dogs had complete initial clinical response (CR) during fluoroquinolone (FQ) treatment, whereas 9/13 FQ‐R dogs had complete or partial response (PR) during meropenem or doxycycline treatment. In 5/9 FQ‐S and 12/13 FQ‐R dogs with follow‐up ≥3 months, CR was sustained in 5/5 FQ‐S (median, 25 months; range, 4‐46) whereas 6/12 FQ‐R had long‐term CR (median, 59 months; range 15‐102), 4/12 PR (median, 19 months; range, 5‐65), and 2/12 had no response (NR). Four dogs with long‐term follow‐up died within 4 years of diagnosis, including 2 euthanized for refractory colitis. Escherichia coli were genetically diverse. Fluoroquinolone resistance was associated with mutations in gyrA and parC, with plasmid‐mediated resistance less common.

Conclusions and Clinical Importance

Antimicrobial treatment guided by susceptibility profiling was associated with positive long‐term outcomes in >80% of cases. Fluoroquinolone‐resistance was widespread and not clonal. Further study is required to optimize treatment for dogs with MDR E coli‐associated GC.

Distinguishing Pathovars from Nonpathovars: Escherichia coli

Escherichia coli is one of the most well-adapted and pathogenically versatile bacterial organisms. It causes a variety of human infections, including gastrointestinal illnesses and extraintestinal infections. It is also part of the intestinal commensal flora of humans and other mammals. Groups of E. coli that cause diarrhea are often described as intestinal pathogenic E. coli (IPEC), while those that cause infections outside of the gut are called extraintestinal pathogenic E. coli (ExPEC). IPEC can cause a variety of diarrheal illnesses as well as extraintestinal syndromes such as hemolytic-uremic syndrome. ExPEC cause urinary tract infections, bloodstream infection, sepsis, and neonatal meningitis. IPEC and ExPEC have thus come to be referred to as pathogenic variants of E. coli or pathovars. While IPEC can be distinguished from commensal E. coli based on their characteristic virulence factors responsible for their associated clinical manifestations, ExPEC cannot be so easily distinguished. IPEC most likely have reservoirs outside of the human intestine but it is unclear if ExPEC represent nothing more than commensal E. coli that breach a sterile barrier to cause extraintestinal infections. This question has become more complicated by the advent of whole genome sequencing (WGS) that has raised a new question about the taxonomic characterization of E. coli based on traditional clinical microbiologic and phylogenetic methods. This review discusses how molecular epidemiologic approaches have been used to address these questions, and how answers to these questions may contribute to our better understanding of the epidemiology of infections caused by E. coli. *This article is part of a curated collection.

Surveillance of OXA-244-producing Escherichia coli and epidemiologic investigation of cases, Denmark, January 2016 to August 2019

Background

Carbapenemase-producing Escherichia coli are increasing worldwide. In recent years, an increase in OXA-244-producing E. coli isolates has been seen in the national surveillance of carbapenemase-producing organisms in Denmark.

Aim

Molecular characterisation and epidemiological investigation of OXA-244-producing E. coli isolates from January 2016 to August 2019.

Methods

For the epidemiological investigation, data from the Danish National Patient Registry and the Danish register of civil registration were used together with data from phone interviews with patients. Isolates were characterised by analysing whole genome sequences for resistance genes, MLST and core genome MLST (cgMLST).

Results

In total, 24 OXA-244-producing E. coli isolates were obtained from 23 patients. Among the 23 patients, 13 reported travelling before detection of the E. coli isolates, with seven having visited countries in Northern Africa. Fifteen isolates also carried an extended-spectrum beta-lactamase gene and one had a plasmid-encoded AmpC gene. The most common detected sequence type (ST) was ST38, followed by ST69, ST167, ST10, ST361 and ST3268. Three clonal clusters were detected by cgMLST, but none of these clusters seemed to reflect nosocomial transmission in Denmark.

Conclusion

Import of OXA-244 E. coli isolates from travelling abroad seems likely for the majority of cases. Community sources were also possible, as many of the patients had no history of hospitalisation and many of the E. coli isolates belonged to STs that are present in the community. It was not possible to point at a single country or a community source as risk factor for acquiring OXA-244-producing E. coli.

Identification and Characterization of Multidrug-Resistant Extended-Spectrum Beta-Lactamase-Producing Bacteria from Healthy and Diseased Dogs and Cats Admitted to a Veterinary Hospital in Brazil

The objective of this study was to identify the main extended-spectrum beta-lactamase (ESBL)-producing bacteria and to detect the frequency of the major genes responsible to trigger this resistance in hospitalized animals. We collected 106 rectal swabs from cats (n = 25) and dogs (n = 81) to detect ESBL-producing isolates. ESBL-positive samples were submitted to the antimicrobial susceptibility test, and polymerase chain reaction was performed to detect TEM, SHV, and CTX-M genes from different groups. We observed that 44.34% of these samples (11 cats and 36 dogs) were positive for ESBL-producing bacteria. Thirteen animals (27.66%-seven cats and six dogs) were hospitalized for elective castration (healthy animals). Only a single animal was positive for ESBL-producing bacteria at hospital admission (the animal also showed an ESBL-positive isolate after leaving the hospital), whereas 11 were positive only at the hospital discharge. Of the 73 ESBL-producing isolates, 13 were isolated from cats (8 sick and 7 healthy) and 60 from dogs (53 sick and 7 healthy). Escherichia coli was the major ESBL-producing bacterium isolated (53.42%), followed by Pseudomonas aeruginosa (15.07%), Salmonella sp., and Proteus mirabilis (5.48% each one). Antimicrobial resistance profile of ESBL-producing isolates showed that 67 isolates (91.78%) were resistant to 3 or more antibiotic classes, while 13 of them (17.81%-2 healthy cats and 11 sick dogs) were resistant to all tested antimicrobial classes. The bla_TEM gene exhibited the highest frequency in ESBL-producing isolates, followed by the bla_CTX-M group 8/25, bla_CTX-M group 1 and bla_CTX-M group 9 genes. These results are useful to assess the predominance of ESBL-producing isolates recovered from dogs and in cats in Brazil. Consequently, we draw attention to these animals, as they can act as reservoirs for these microorganisms, which are the major pathogens of nosocomial infections worldwide.

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

Under a one health perspective and the worldwide antimicrobial resistance concern, we investigated extraintestinal pathogenic Escherichia coli (ExPEC), uropathogenic E. coli (UPEC), and multidrug resistant (MDR) E. coli from 197 isolates recovered from healthy dogs in Spain between 2013 and 2017. A total of 91 (46.2%) isolates were molecularly classified as ExPEC and/or UPEC, including 50 clones, among which (i) four clones were dominant (B2-CH14-180-ST127, B2-CH52-14-ST141, B2-CH103-9-ST372 and F-CH4-58-ST648) and (ii) 15 had been identified among isolates causing extraintestinal infections in Spanish and French humans in 2015 and 2016. A total of 28 (14.2%) isolates were classified as MDR, associated with B1, D, and E phylogroups, and included 24 clones, of which eight had also been identified among the human clinical isolates. We selected 23 ST372 strains, 21 from healthy dogs, and two from human clinical isolates for whole genome sequencing and built an SNP-tree with these 23 genomes and 174 genomes (128 from canine strains and 46 from human strains) obtained from public databases. These 197 genomes were segregated into six clusters. Cluster 1 comprised 74.6% of the strain genomes, mostly composed of canine strain genomes (p < 0.00001). Clusters 4 and 6 also included canine strain genomes, while clusters 2, 3, and 5 were significantly associated with human strain genomes. Finding several common clones and clone-related serotypes in dogs and humans suggests a potentially bidirectional clone transfer that argues for the one health perspective.

Multi-drug resistant, biofilm-producing high-risk clonal lineage of Klebsiella in companion and household animals

Antimicrobial resistance is a global emergency which needs one health approach to address. The present study was conducted to detect the prevalence of beta-lactamase and biofilm-producing Klebsiella strains in rectal swabs (n = 624) collected from healthy dogs, cats, sheep and goats reared as companion or household animals in India. The dogs and cats were frequently exposed to third- or fourth-generation cephalosporins for therapy. The sheep and goats were occasionally exposed to antibiotics and had environmental exposure. Phenotypical ESBL (n = 93) and ACBL (n = 88)-producing Klebsiella were isolated significantly more (P < 0·05) from companion animals than household animals. Majority of the Klebsiella possessed bla_CTX-M-15 . The sequences bla_CTX-M-15.2 , bla_CTX-M-197 and bla_CTX-M-225 are reported first time from the companion animals. All ACBL-producing isolates possessed bla_AmpC . The present study detected 65·8% of Klebsiella strains as biofilm producers possessing the studied biofilm associated genes. The isolates showed phenotypical resistance against chloramphenicol, tetracycline, doxycycline, co-trimoxazole, ampicillin, cefotaxime/clavulanic acid. The present study showed that companion and household animals (dogs, cats, sheep, goats) may act as a carrier of ESBL/biofilm-producing, multi-drug resistant, high-risk clonal lineage of Klebsiella.

Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia

Increasing contact between humans and non-human primates provides an opportunity for the transfer of potential pathogens or antimicrobial resistance between host species. We have investigated genomic diversity and antimicrobial resistance in Escherichia coli isolates from four species of non-human primates in the Gambia: Papio papio (n=22), Chlorocebus sabaeus (n=14), Piliocolobus badius (n=6) and Erythrocebus patas (n=1). We performed Illumina whole-genome sequencing on 101 isolates from 43 stools, followed by nanopore long-read sequencing on 11 isolates. We identified 43 sequence types (STs) by the Achtman scheme (ten of which are novel), spanning five of the eight known phylogroups of E. coli. The majority of simian isolates belong to phylogroup B2 - characterized by strains that cause human extraintestinal infections - and encode factors associated with extraintestinal disease. A subset of the B2 strains (ST73, ST681 and ST127) carry the pks genomic island, which encodes colibactin, a genotoxin associated with colorectal cancer. We found little antimicrobial resistance and only one example of multi-drug resistance among the simian isolates. Hierarchical clustering showed that simian isolates from ST442 and ST349 are closely related to isolates recovered from human clinical cases (differences in 50 and 7 alleles, respectively), suggesting recent exchange between the two host species. Conversely, simian isolates from ST73, ST681 and ST127 were distinct from human isolates, while five simian isolates belong to unique core-genome ST complexes - indicating novel diversity specific to the primate niche. Our results are of planetary health importance, considering the increasing contact between humans and wild non-human primates.

The population genetics of pathogenic Escherichia coli

Escherichia coli is a commensal of the vertebrate gut that is increasingly involved in various intestinal and extra-intestinal infections as an opportunistic pathogen. Numerous pathotypes that represent groups of strains with specific pathogenic characteristics have been described based on heterogeneous and complex criteria. The democratization of whole-genome sequencing has led to an accumulation of genomic data that render possible a population phylogenomic approach to the emergence of virulence. Few lineages are responsible for the pathologies compared with the diversity of commensal strains. These lineages emerged multiple times during E. coli evolution, mainly by acquiring virulence genes located on mobile elements, but in a specific chromosomal phylogenetic background. This repeated emergence of stable and cosmopolitan lineages argues for an optimization of strain fitness through epistatic interactions between the virulence determinants and the remaining genome.

Characteristics of Extended-Spectrum β-Lactamase-Producing Escherichia coli From Dogs and Cats Admitted to a Veterinary Teaching Hospital in Taipei, Taiwan From 2014 to 2017

Extended-spectrum β-lactamases (ESBLs) are enzymes that mediate resistance to newer β-lactam antibiotics, including extended-spectrum cephalosporins and monobactams. The production of ESBL is primarily plasmid mediated, and such plasmids often comprise the genes that encode resistance to other classes of antimicrobials, such as aminoglycosides and fluoroquinolones. Therefore, ESBL-producing microorganisms leave clinicians with limited therapeutic options in both human and veterinary medicine. Compared with human medicine, information regarding ESBL-producing microorganisms is limited in veterinary medicine. We screened for ESBL-producing Escherichia coli in dogs and cats admitted to National Taiwan University Veterinary Hospital, Taipei, from 2014 to 2017 and further analyzed the genotypes and phylogenetic traits of these ESBL producers. Double disk tests specified by the Clinical and Laboratory Standards Institute were performed on 283 E. coli isolates and revealed a total of 65 E. coli (54 from dogs and 11 from cats) with the ESBL phenotype (22.8%). bla_{CTX−M−1group} and bla_{CTX−M−2group} were the most commonly identified ESBL gene groups. bla_CTX−M−55 was the main ESBL gene within the bla_{CTX−M−1group}, whereas the bla_{CTX−M−2group} contained only bla_{CTX−M−124}. The ESBL-producing E. coli were all resistant to ampicillin. The resistance rate to ceftiofur, doxycycline, enrofloxacin, and ciprofloxacin was 93.8, 73.8, 80, and 78.5%, respectively. Of the antibiotics tested, greater sensitivity to imipenem and gentamicin was noted. Multilocus sequence typing indicated that ST457, ST131, and ST648 were the most common sequence types. Our study identified eight ST131/O25b isolates, which is a global zoonotic clone of public health concern. The major ESBL genes of these clones were bla_{CTX−M−174} and bla_{CTX−M−194}. Because companion animals such as dogs and cats are in close contact with humans, the characterization of ESBL producers originating from them is crucial from the perspective of both public health and veterinary medicine.

Genetic diversity, antimicrobial resistance and extended-spectrum β-lactamase type of Escherichia coli isolates from chicken, dog, pig and yak in Gansu and Qinghai Provinces, China

OBJECTIVES

In this study, the genetic diversity, phylogenetic grouping, antimicrobial resistance and extended-spectrum β-lactamase (ESBL) types of Escherichia coli isolates from chickens, dogs, pigs and yaks in six prefectures of Gansu and Qinghai Provinces, China, were investigated.

METHODS

E. coli was isolated from diarrhoeic and healthy faecal samples. Multilocus sequence typing (MLST), phylogenetic grouping, antimicrobial resistance and ESBL profiles were investigated.

RESULTS

A total of 142 MLST sequence types (STs) were identified from 400 E. coli isolates. eBURST clustering analysis resolved the 142 STs into 19 clonal complexes (CCs) and 67 singletons. PCR phylogenetic typing determined the isolation rate of potentially pathogenic B2/D group isolates among all E. coli to be 12.5% from healthy animal samples and 17.5% from diarrhoeic samples. Antimicrobial susceptibility testing revealed 78 antimicrobial resistance patterns. E. coli resistance rates were highest to doxycycline, ampicillin and tetracycline, whereas polymyxin B and meropenem had the lowest resistance rates. All polymyxin B-resistant E. coli isolates were positive for the mcr-1 gene. A total of 62 ESBL-producing isolates were identified. The ESBL prevalence was 55.0% in diarrhoeic samplings and 5.6% in healthy animals. TEM (82.3%) was the predominant ESBL type, followed by CTM (43.5%) and SHV (19.4%).

CONCLUSION

E. coli isolates in the study area have a high diversity of genetic and antimicrobial resistance patterns but a relatively low isolation rate of potentially pathogenic phylogroups. However, the somewhat high isolation rate of multidrug-resistant E. coli, particularly ESBL-producing isolates, requires continual surveillance of E. coli from animals in these areas.

Genomic analysis of phylogenetic group B2 extraintestinal pathogenic E. coli causing infections in dogs in Australia

This study investigated the prevalence of extraintestinal pathogenic E. coli (ExPEC)-associated sequence types (STs) from phylogenetic group B2 among 449 fluoroquinolone-susceptible dog clinical isolates from Australia. Isolates underwent PCR-based phylotyping and random amplified polymorphic DNA analysis to determine clonal relatedness. Of the 317 so-identified group B2 isolates, 77 underwent whole genome sequencing (WGS), whereas the remainder underwent PCR-based screening for ST complexes (STc) STc12, STc73, STc372, and ST131. The predominant ST was ST372 according to both WGS (31 % of 77) and ST-specific PCR (22 % of 240), followed by (per WGS) ST73 (17 %), ST12 (7 %), and ST80 (7 %). A WGS-based phylogenetic comparison of ST73 isolates from dogs, cats, and humans showed considerable overall phylogenetic diversity. Although most clusters were species-specific, some contained closely related human and animal (dog > cat) isolates. For dogs in Australia these findings both confirm ST372 as the predominant E. coli clonal lineage causing extraintestinal infections and clarify the importance of human-associated group B2 lineage ST73 as a cause of UTI, with some strains possibly being capable of bi-directional (i.e., dog-human and human-dog) transmission.

Pathogenic Escherichia coli in Dogs Reveals the Predominance of ST372 and the Human-Associated ST73 Extra-Intestinal Lineages

Escherichia coli is a ubiquitous commensal and pathogen that has also been recognized as a multi-sectoral indicator of antimicrobial resistance (AMR). Given that latter focus, such as on resistances to extended-spectrum cephalosporins (ESC) and carbapenems, the reported population structure of E. coli is generally biased toward resistant isolates, with sequence type (ST)131 being widely reported in humans, and ST410 and ST648 being reported in animals. In this study, we characterized 618 non-duplicate E. coli isolates collected throughout France independently of their resistance phenotype. The B2 phylogroup was over-represented (79.6%) and positively associated with the presence of numerous virulence factors (VFs), including those defining the extra-intestinal pathogenic E. coli isolates (presence of ≥2 VFs: papA, sfaS, focG, afaD, iutA, and kpsMTII) and those more specifically related to uropathogenic E. coli (cnf1, hlyD). The major STs associated with clinical isolates from dogs were by far the dog-associated ST372 (20.7%) and ST73 (20.1%), a lineage that had commonly been considered until now as human-associated. Resistance to ESC was found in 33 isolates (5.3%), along with one carbapenemase-producing isolate, and was mostly restricted to non-B2 isolates. In conclusion, the presence of virulent E. coli lineages may be the issue, rather than the presence of ESC-resistant isolates, and the risk of transmission of such virulent isolates to humans needs to be further studied.

Genomic analysis of fluoroquinolone-susceptible phylogenetic group B2 extraintestinal pathogenic Escherichia coli causing infections in cats

Extraintestinal pathogenic Escherichia coli (ExPEC) can cause urinary tract and other types of infection in cats, but the relationship of cat ExPEC to human ExPEC remains equivocal. This study investigated the prevalence of ExPEC-associated sequence types (STs) from phylogenetic group B2 among fluoroquinolone-susceptible cat clinical isolates. For this, 323 fluoroquinolone-susceptible cat clinical E. coli isolates from Australia underwent PCR-based phylotyping and random amplified polymorphic DNA analysis to determine clonal relatedness. Of the 274 group B2 isolates, 53 underwent whole genome sequencing (WGS), whereas 221 underwent PCR-based screening for (group B2) sequence type complexes (STc) STc12, STc73, ST131, and STc372. Group B2 was the dominant phylogenetic group (274/323, 85 %), whereas within group B2 ST73 dominated, according to both WGS (43 % of 53; followed by ST127, ST12, and ST372 [4/53, 8 % each]) and ST-specific PCR (20 % of 221). In WGS-based comparisons of cat and reference human ST73 isolates, cat isolates had a relatively conserved virulence gene profile but were phylogenetically diverse. Although in the phylogram most cat and human ST73 isolates occupied host species-specific clusters within serotype-specific clades (O2:H1, O6:H1, O25:H1, O50/O2:H1), cat and human isolates were intermingled within two serotype-specific clades: O120:H31 (3 cat and 2 human isolates) and O22:H1 (3 cat and 5 human isolates). These findings confirm the importance of human-associated group B2 lineages as a cause of urinary tract infections in cats. The close genetic relationship of some cat and human ST73 strains suggests bi-directional transmission may be possible.

The Aquatic Ecosystem, a Good Environment for the Horizontal Transfer of Antimicrobial Resistance and Virulence-Associated Factors Among Extended Spectrum β-lactamases Producing E. coli

One of the main public health problems nowadays is the increase of antimicrobial resistance, both in the hospital environment and outside it (animal environment, food and aquatic ecosystems, among others). It is necessary to investigate the virulence-associated factors and the ability of horizontal gene transfer among bacteria for a better understanding of the pathogenicity and the mechanisms of dissemination of resistant bacteria. Therefore, the objective of this work was to detect several virulence factors genes (fimA, papC, papG III, cnf1, hlyA and aer) and to determine the conjugative capacity in a wide collection of extended-spectrum β-lactamases-producing E. coli isolated from different sources (human, food, farms, rivers, and wastewater treatment plants). Regarding virulence genes, fimA, papC, and aer were distributed throughout all the studied environments, papG III was mostly related to clinical strains and wastewater is a route of dissemination for cnf1 and hlyA. Strains isolated from aquatic environments showed an average conjugation frequencies of 1.15 × 10⁻¹ ± 5 × 10⁻¹, being significantly higher than those observed in strains isolated from farms and food (p < 0.05), with frequencies of 1.53 × 10⁻⁴ ± 2.85 × 10⁻⁴ and 9.61 × 10⁻⁴ ± 1.96 × 10⁻³, respectively. The reported data suggest the importance that the aquatic environment (especially WWTPs) acquires for the exchange of genes and the dispersion of resistance. Therefore, specific surveillance programs of AMR indicators in wastewaters from animal or human origin are needed, in order to apply sanitation measures to reduce the burden of resistant bacteria arriving to risky environments as WWTPs.

Mechanistic insights into the action of probiotics against bacterial vaginosis and its mediated preterm birth: An overview

The human body is a reservoir of numerous micro-creatures; whose role is substantial and indispensable in the overall development of human beings. The advances in omic approaches have offered powerful means to decipher the core microbiome and metabolome diversities in a specific organ system. The establishment of lactobacilli in the female reproductive tract is thought to be a paramount prerequisite that maintains homeostatic conditions for a sustainable and healthy pregnancy. Nevertheless, a plethora of such Lactobacillus strains of vaginal source revealed probiotic phenotypes. The plummeting in the occurrence of lactobacilli in the vaginal ecosystem is associated with several adverse pregnancy outcomes (APOs). One such pathological condition is "Bacterial Vaginosis" (BV), a pathogen dominated gynecological threat. In this scenario, the ascending traffic of notorious Gram-negative/variable BV pathogens to the uterus is one of the proposed pathways that give rise to inflammation-related APOs like preterm birth. Since antibiotic resistance is aggravating among urogenital pathogens, the probiotics intervention remains one of the alternative biotherapeutic strategies to overcome BV and its associated APOs. Perhaps, the increased inclination towards the safer and natural biotherapeutic strategies rather than pharmaceutical drugs for maintaining gestational and reproductive health resulted in the use of probiotics in pregnancy diets. In this context, the current review is an attempt to highlight the microbiome and metabolites signatures of BV and non-BV vaginal ecosystem, inflammation or infection-related preterm birth, host-microbial interactions, role and effectiveness of probiotics to fight against aforesaid diseased conditions.

Prevalence of Antimicrobial Resistance Genes and Integrons in Commensal Gram-Negative Bacteria in a College Community

Although the human intestinal microbiome has been shown to harbor antimicrobial drug resistance genes (ARGs), the prevalence of such genes in a healthy population and their impact on extraintestinal infections that occur in that community are not well established. This study sought to identify ARG prevalence and their mobile elements in the intestines of a healthy community population at a California University, and compared these genes to those previously identified among uropathogenic Escherichia coli isolated from patients with urinary tract infection from the same community. We isolated Gram-negative bacteria (GNB) from fecal samples of healthy volunteers and screened them by polymerase chain reaction for class 1 integron cassette sequences and ARGs encoding resistance against ampicillin, trimethoprim-sulfamethoxazole, gentamicin, and colistin. We found antimicrobial-resistant GNB from 83 (81%) of 102 nonredundant rectal swab samples. Seventy-four (72%) of these samples contained β-lactamase genes (bla_TEM, bla_SHV, bla_CTX-M, bla_OXA, and bla_OXY), dihydrofolate reductase (DHFR) genes (dhfr-A17, dhfr-A12, dhfr-A7, dhfr-A5, dhfr-A21, dhfr-A1, dhfr-A13, and dhfr-7), and aminoglycoside resistance genes (aadA5, aadA2, aadA1, and aadB). Integron sequences were found in 37 (36%) fecal samples. These genes were found in 11 different GNB species. The high prevalence of clinically common ARGs and integrons harbored by GNB in the intestine of a healthy population suggest that human intestines may serve as a major reservoir of these mobile ARGs that appear in E. coli strains causing extraintestinal infections in the same community.

CTX-M-15 Producing Escherichia coli Sequence Type 361 and Sequence Type 38 Causing Bacteremia and Umbilical Infection in a Neonate Foal

An eighteen-hour-old Tennessee walking horse foal was referred due to weakness and abdominal pain. Physical examination revealed dehydration, distended abdomen, and uveitis. Blood analysis revealed leukopenia, neutrophils' toxicity and left shift. The foal developed bloody diarrhea, gastric reflux, and was diagnosed with sepsis and enterocolitis. The foal was treated with intravenous fluids, plasma, antibiotics (ceftriaxone and metronidazole), partial parenteral nutrition (dextrose and amino acids), flunixin meglumine, and ophthalmic drops. Umbilical ultrasound revealed a fluid pocket adjacent to the umbilical vein; therefore, omphalectomy was performed. Umbilicus and blood were cultured. Results recovered two multidrug-resistant extended-spectrum β-lactamase (ESBL) producing Escherichia coli clones, identified as ST38 (umbilicus) and ST361 (blood), harboring two different plasmids encoding bla_CTX-M-15. Antibiotic treatment was replaced with imipenem and amikacin, but the foal deteriorated and was euthanized. Postmortem investigation revealed severe ulcerative enteritis, a perforation site and acute renal infarcts. Sepsis due to several different ESBL-producing E. coli strains should be considered, investigated, and treated accordingly.

Occurrence of ESBL-Producing Escherichia coli ST131, Including the H30-Rx and C1-M27 Subclones, Among Urban Seagulls from the United Kingdom

Antimicrobial resistance is a public health concern. Understanding any role that urban seagulls may have as a reservoir of resistant bacteria could be important for reducing transmission. This study investigated fecal Escherichia coli isolates from seagulls (herring gulls and lesser black-backed gulls) to determine the prevalence of extended-spectrum cephalosporin-resistant (ESC-R) and fluoroquinolone-resistant E. coli among gull species from two cities (Taunton and Birmingham) in the United Kingdom (UK). We characterized the genetic background and carriage of plasmid-mediated resistance genes in extended-spectrum β-lactamase (ESBL)-producing E. coli obtained from these birds. Sixty ESC-R E. coli isolates were obtained from 39 seagulls (39/78, 50%), of which 28 (28/60, 46.7%) were positive for plasmid-mediated CTX-M and/or AmpC β-lactamase resistance genes. Among these, bla_CTX-M-15, bla_CTX-M-14, and bla_CMY-2 predominated. Three isolates belonging to the B2-ST131 clone were detected, of which two harbored bla_CTX-M-15 (typed to C2/H30Rx) and one harbored bla_CTX-M-27 and was typed to C1/H30-R (recently described as the C1-M27 sublineage). The plasmid-mediated quinolone resistance (PMQR) gene carriage prevalence (11.7%) consisted of aac(6')-Ib-cr and qnrB genes. No carbapenem or colistin resistance genes were detected. Urban seagulls in the UK are colonized and can spread major antimicrobial-resistant E. coli isolates harboring ESBL and PMQR determinants, including clinically important strains such as the pandemic clone B2-ST131 and the C1-M27 subclade. This is the first report of ST131-C1-M27 subclade in wildlife in the UK and in seagulls worldwide.

A clinical approach to multidrug-resistant urinary tract infection and subclinical bacteriuria in dogs and cats

Multidrug-resistant bacteria are increasingly isolated from the urinary tract of pets, particularly those that suffer from concurrent conditions, have been hospitalised, or were treated with antimicrobials in the recent past. Many of the multidrug-resistant bacteria encountered are resistant to all commonly used oral antibiotics. This poses both a therapeutic dilemma in the individual pet and a threat to public health. This article begins with an overview of multidrug resistance in organisms that are commonly isolated from the urinary tract of pets. This is followed by a proposed clinical approach to managing multidrug-resistant urinary bacteria, which summarises current knowledge regarding appropriate sampling and analysis, reviews the current guidelines regarding appropriate antimicrobial use and discusses treatment options that might be considered. The article highlights several shortcomings of the current knowledge to be considered when planning future clinical research and developing policies.

Raw meat-based diets for companion animals: a potential source of transmission of pathogenic and antimicrobial-resistant Enterobacteriaceae

Feeding pets raw meat-based diets (RMBDs) has become increasingly popular but may constitute a risk due to the contamination with pathogenic and antimicrobial-resistant (AMR) bacteria. The aim of this study was to evaluate commercially available RMBDs with regard to microbiological quality and occurrence of AMR Enterobacteriaceae. Of 51 RMBD samples, 72.5% did not meet the microbiological standards for Enterobacteriaceae set out by EU regulations for animal by-products intended for pet food. Furthermore, Salmonella was detected in 3.9% of the samples. AMR bacteria were found in 62.7% of the samples, the majority thereof were resistant to third-generation cephalosporins due to the production of extended-spectrum β-lactamases (ESBLs) including CTX-M-1, which is widespread in livestock, and CTX-M-15, which is the most common ESBL variant worldwide. Colistin- and aminoglycoside-resistant isolates, producing MCR-1 and RMTB, were identified in 3.9 and 2% of the samples, respectively. The majority of the AMR Escherichia coli belonged to commensal groups A or B1 and were associated with clonal complexes CC155 and CC10. Two belonged to the emerging extraintestinal pathogenic CC648, and one to the globally disseminated uropathogenic E. coli sequence type ST69, suggesting zoonotic potential. The microbiological quality and the high prevalence of AMR producing Enterobacteriaceae in RMBDs raise concerns for animal and public health.

Genetic structure, antimicrobial resistance and frequency of human associated Escherichia coli sequence types among faecal isolates from healthy dogs and cats living in Canberra, Australia

Extraintestinal pathogenic Escherichia coli (ExPEC) cause clinical infections in humans. Understanding the evolution and dissemination of ExPEC strains via potential reservoirs is important due to associated morbidity, health care costs and mortality. To further understanding this survey has examined isolates recovered from the faeces of 221 healthy dogs and 427 healthy cats. The distribution of phylogroups varied with host species, and depended on whether the animal was living in a shelter or a home. The human associated STs 69, 73, 95, 131 and 127 were prevalent, with 30.5% of cat isolates and 10.3% of dog isolates representing these ExPEC sequence types. Resistance to the antibiotics ampicillin and tetracycline was common, but resistance to other antimicrobials was negligible.

Enterobacter cloacae Complex Sequence Type 171 Isolates Expressing KPC-4 Carbapenemase Recovered from Canine Patients in Ohio

Companion animals are likely relevant in the transmission of antimicrobial-resistant bacteria. Enterobacter xiangfangensis sequence type 171 (ST171), a clone that has been implicated in clusters of infections in humans, was isolated from two dogs with clinical disease in Ohio. The canine isolates contained IncHI2 plasmids encoding bla _KPC-4 Whole-genome sequencing was used to put the canine isolates in phylogenetic context with available human ST171 sequences, as well as to characterize their bla _KPC-4 plasmids.

Phenotypic characterization and whole genome analysis of extended-spectrum beta-lactamase-producing bacteria isolated from dogs in Germany

Asymptomatic colonization with extended-spectrum beta-lactamase (ESBL) producing Enterobacteriaceae has been described for humans, various mammal species, and birds. Here, antimicrobial resistant bacteria were recovered from dog feces originating in Germany, Kosovo, Afghanistan, Croatia, and Ukraine, with a subset of mostly E. coli isolates obtained from a longitudinal collection over twelve months. In vitro antimicrobial resistance testing revealed various patterns of resistance against single or all investigated beta-lactam antibiotics, with none of the 101 isolates resistant against two tested carbapenem antibiotics. Whole genome sequence analysis revealed bacteria species-specific patterns for 23 antimicrobial resistance coding DNA sequences (CDS) that were unapparent from the in vitro analysis alone. Phylogenetic analysis of single nucleotide polymorphisms (SNP) revealed clonal bacterial isolates originating from different dogs, suggesting transmission between dogs in the same community. However, individual resistant E. coli clones were not detected over a period longer than seven days. Multi locus sequence typing (MLST) of 85 E. coli isolates revealed 31 different sequence types (ST) with an accumulation of ST744 (n = 9), ST10 (n = 8), and ST648 (n = 6), although the world-wide hospital-associated CTX-M beta-lactamase producing ST131 was not detected. Neither the antimicrobial resistance CDSs patterns nor the phylogenetic analysis revealed an epidemiological correlation among the longitudinal isolates collected from a period longer than seven days. No genetic linkage could be associated with the geographic origin of isolates. In conclusion, healthy dogs frequently carry ESBL-producing bacteria, independent to prior treatment, which may be transmitted between individual dogs of the same community. Otherwise, these antimicrobial resistant bacteria share few commonalities, making their presence eerily unpredictable.