Enterobacterales high-risk clones and plasmids spreading blaESBL/AmpC and blaOXA-48 genes within and between hospitalized dogs and their environment

Companions in antimicrobial resistance: examining transmission of common antimicrobial-resistant organisms between people and their dogs, cats, and horses

SUMMARYNumerous questions persist regarding the role of companion animals as potential reservoirs of antimicrobial-resistant organisms that can infect humans. While relative antimicrobial usage in companion animals is lower than that in humans, certain antimicrobial-resistant pathogens have comparable colonization rates in companion animals and their human counterparts, which inevitably raises questions regarding potential antimicrobial resistance (AMR) transmission. Furthermore, the close contact between pets and their owners, as well as pets, veterinary professionals, and the veterinary clinic environment, provides ample opportunity for zoonotic transmission of antimicrobial-resistant pathogens. Here we summarize what is known about the transmission of AMR and select antimicrobial-resistant organisms between companion animals (primarily dogs, cats, and horses) and humans. We also describe the global distribution of selected antimicrobial-resistant organisms in companion animals. The impact of interspecies AMR transmission within households and veterinary care settings is critically reviewed and discussed in the context of methicillin-resistant staphylococci, extended-spectrum β-lactamase and carbapenemase-producing bacteria. Key research areas are emphasized within established global action plans on AMR, offering valuable insights for shaping future research and surveillance initiatives.

Fecal carriage of extended-spectrum β-lactamase-, AmpC β-lactamase- and carbapenemase-producing Escherichia coli in stray cats in Italy

The spread of carbapenem-resistant bacteria is a global threat to public health and the role of pets in the rise in antimicrobial resistance is gaining attention worldwide. This study aimed to determine the fecal carriage of extended-spectrum β-lactamase (ESBL)-, AmpC- and carbapenemase (CP)-producing E. coli and associated risk factors in healthy and unhealthy stray cats admitted to the Veterinary Teaching Hospital of Lodi, University of Milan, Italy. Fecal samples collected in, 2020-2022 were microbiologically and molecularly analyzed. Overall, ESBL-/AmpC-/CP-producing E. coli were detected in 18/94 (19.1 %) stray cats. Twelve (12.8 %), 4 (4.3 %) and 7 (7.4 %) stray cats carried ESBL-, AmpC- and CP-producing E. coli phenotypes respectively, supported by the detection of blaCTX-M in all ESBL-producing E. coli, blaCMY-2 in all AmpC-producing E. coli and blaNDM (4/7; 57.1 %) or blaOXA-48 (3/7; 42.9 %) genes in CP-producing E. coli. Multiple combination of resistance genes and phenotypes were detected. MIC results showed that all E. coli were multidrug resistant isolates. Risk factors associated with ESBL-, AmpC- and/or CP-producing E. coli fecal carriage were hospitalization (P < 0.0001), antibiotic treatment during hospitalization (P < 0.0001) and unhealthy status (P < 0.0001). Fecal carriage of CP-producing E. coli is of concern and highlights the need of specific surveillance programs for CP-producing Enterobacteriaceae and antimicrobial stewardship in stray cats to reduce the emergence and spread of resistant bacteria. Limitations of this study suggest a One Health approach to characterize the whole genome of the isolates and the epidemiology of AMR bacteria among stray cats, including additional bacterial species and the environment.

Distinct molecular epidemiology of resistances to extended-spectrum cephalosporins and carbapenems in Enterobacter hormaechei in cats and dogs versus horses in France

BACKGROUND

Enterobacter hormaechei is an important pathogen in humans and animals, which, in addition to its intrinsic AmpC, can acquire a wide variety of genes conferring resistances to extended-spectrum cephalosporins (ESCs) and carbapenems (CPs). In France, human clinical outbreaks of E. hormaechei resistant to ESC or carbapenem were reported.

OBJECTIVES

To study E. hormaechei isolates from cats and dogs (=59) as well as from horses (n = 55) presenting a non-susceptible phenotype to beta-lactams in order to determine which clones, resistance genes and plasmids are circulating in France.

MATERIAL AND METHODS

E. hormaechei isolates (n = 114) were short-read sequenced and five isolates were long-read sequenced to better characterize the plasmids carrying ESC- and CP-resistance determinants. Phenotypes were characterized by antibiograms using the disc diffusion method.

RESULTS

A clear divergence in the molecular epidemiology was observed depending on the host. In cats and dogs, most of the isolates presented an overexpressed ampC gene or the blaCTX-M-15 gene carried by an IncHI2 plasmid, and eight isolates (8/59, 13.6%) presented the blaOXA-48 carbapenemase gene. Thirty-two isolates (32/59, 54.2%) belonged to the human high-risk clones ST78, ST114 and ST171. Contrarily, in horses, ESC resistance was mostly due to the blaSHV-12 and blaCTX-M-15 genes carried by an IncHI2 plasmid, and high-risk clones were rarely identified (5/55, 9.0%).

DISCUSSION

Potential selection by antibiotic use (which is on an increasing trend in France for cats, dogs and horses), the dissemination capacities of both conjugative IncHI2 plasmids and high-risk clones, and possible transfers of resistant bacteria between humans and animals strongly indicate that E. hormaechei should be closely monitored.

Fecal Carriage and Risk Factors Associated with Extended-Spectrum β-Lactamase-/AmpC-/Carbapenemase-Producing Escherichia coli in Dogs from Italy

MDR bacteria are an emerging global threat to public health, and the role of dogs in the rise of antimicrobial resistance is under investigation. This study investigated the fecal shedding of extended-spectrum β-lactamase (ESBL)-, AmpC- and carbapenemase (CP)-producing Escherichia coli and associated risk factors in dogs admitted to the Veterinary Teaching Hospital of Lodi, University of Milan, or other veterinary clinics and kennels in Northen Italy. Feces collected in 2020-2022 were microbiologically and molecularly analyzed. ESBL-/AmpC-/CP-producing E. coli was detected in 14/100 (14%) dogs. Eleven (11%), five (5%) and one (1%) dogs carried ESBL-, AmpC- and CP-producing E. coli phenotypes, respectively, supported by the PCR detection of blaCTX-M and/or blaTEM in ESBL-producing E. coli; blaCMY-2 and the presence of putative low-level AmpC production in AmpC-producing E. coli; and blaOXA-48 in CP-producing E. coli. Different combinations of resistance genes and genetic features were observed. Multidrug resistance was observed in 13/14 (92.9%) E. coli isolates. Binary logistic regression analysis showed that ESBL-/AmpC-/CP-producing E. coli fecal shedding tended to be associated with antibiotic treatment (p = 0.058; OR = 3.87). The detection of ESBL-/AmpC-producing E. coli, along with the presence of a carbapenemase-resistant E. coli isolate from domestic dogs, although still limited, emphasizes the need for antimicrobial stewardship and specific surveillance programs, particularly for CP-producing bacteria in companion animals.

Dissemination and characterization of Escherichia coli resistant to extended-cephalosporins in feedlot lambs: A two-year two-population study

Dissemination of antimicrobial resistance in food animals is a One Health concern, but sheep production has been overlooked. This study aimed to explore the dissemination of Escherichia coli resistant to extended-spectrum cephalosporins (ESC) in feedlot lambs. Two pens were sampled on two occasions, and carcasses and other mammals living around were also tested. E. coli were recovered and antibiotic resistance determined. blaCTX-M/CMY genes and their genetic localization were characterized. Whole genome sequencing (WGS) was performed to confirm clonal relationship. The most prevalent ESC-resistance genes in the 108 E. coli isolates were blaCTX-M-55 (53.7 %), blaCTX-M-2 (14.8 %) and blaCMY-2 (13.9 %). Most blaCTX-M-55 genes were found on the chromosome, but IncA/C, IncHI1, IncHI2 and IncF plasmids were also identified. Genetic diversity was observed even though ST6448 was by far the most frequent ST. WGS analysis showed high similarity among isolates recovered from feedlot lambs, animals in the surroundings and lambs' carcasses, proving the clonal and plasmidic dissemination.

Raw meat diets are a major risk factor for carriage of third-generation cephalosporin-resistant and multidrug-resistant E. coli by dogs in the UK

Introduction

Raw-meat diets (RMD) for dogs, comprising unprocessed or non-heat-treated animal material, are increasingly popular. However, RMDs have been demonstrated to be contaminated with antimicrobial resistant (AMR) bacteria, and there is concern that such diets may pose a zoonotic disease risk. Additionally, dogs fed RMD may shed more AMR- fecal bacteria compared to those fed conventional cooked diets. Data from the UK remain limited; the present study investigated the presence of AMR-Escherichia coli in the feces of RMD and non-RMD (NRMD)-fed dogs in the UK, the E. coli AMR gene complement, and the lifestyle risk factors associated with AMR- E. coli carriage.

Methods

Fecal samples from UK-owned dogs (N = 193 RMD, N = 239 NRMD) and questionnaires discussing lifestyle factors, were obtained between October 2020-August 2021. Samples underwent culture and antimicrobial susceptibility testing to determine the presence of AMR-E. coli. Whole genome sequencing determined AMR gene carriage. Risk factors for the presence of AMR-E. coli were determined by multivariable modeling.

Results

RMD dogs carried significantly more fecal AMR E. coli (p < 0.001), including third-generation cephalosporin resistant, extended-spectrum beta-lactamase (ESBL) producing, and multidrug resistant isolates and multivariable modeling confirmed raw-meat diets to be a significant risk factor. The bla CTX-M-15 gene was the most frequently identified bla ESBL gene. The bla CTX-M-55 and bla SHV-66 genes were also prevalent and were only found in RMD dogs. The mobile colistin resistance gene, mcr-4 was identified in one ESBL-producing E. coli isolate from a NRMD-fed dog.

Conclusion

This study has shown that dogs fed RMD in the UK are significantly more likely to shed E. coli which is resistant to highest priority critically important antibiotics, and multidrug resistant E. coli, than dogs fed NRMD. Additionally, AMR-E. coli isolates from RMD-fed dogs harbor multiple, diverse, and novel AMR genes. Therefore, provision of RMD to dogs could pose an important potential threat to human and animal health, especially given the close nature of the relationship many owners share with their pets. Awareness of these findings should be shared with pet owners, veterinary and medical professionals, pet food manufacturers and public health to mitigate potential risks.

Prevalence and molecular epidemiology of carbapenemase-producing Enterobacterales isolated from dog and cat faeces submitted to veterinary laboratories in the USA

AIMS

To estimate the prevalence of carbapenemase-producing Enterobacterales (CPE) carriage among pets using faecal specimens submitted to veterinary diagnostic laboratories throughout the US. A secondary aim was to employ whole-genome sequencing (WGS) to characterize isolates of CPE from companion animals and compare them to publicly available CPE genomes.

METHODS AND RESULTS

To estimate the prevalence of CPE in companion animals in the USA, a multicenter surveillance study including 8 different veterinary diagnostic laboratories from across the USA was conducted. Briefly, remnant faecal specimens from dogs and cats were screened using two selective agar plates (CHROMID Carba and MacConkey with 1 mg/L cefotaxime and 0.125 mg/L meropenem) and presumptive CPE isolates screened by the modified carbapenemase inactivation method for carbapenemase production. A total of 2393 specimens were screened and yielded 196 isolates for carbapenemase screening. A total of 5 isolates from 4 dogs and 1 cat at 3 different veterinary diagnostic laboratories were confirmed to produce a carbapenemase (0.21%). Whole-genome sequencing (WGS) revealed two E. coli (ST167) isolates that both produced an NDM-5 carbapenemase, two Enterobacter hormaechei (ST171) isolates that produced an NDM-5 carbapenemase and a KPC-4 carbapenemase respectively and one Klebsiella oxytoca (ST199) that produced an Oxa-48-type carbapenemase. Both E. coli isolates were found to be within at least 22 SNPs of previously characterized canine and human CPE isolates.

CONCLUSIONS

This study demonstrates that the prevalence of CPE among companion animals is relatively low (0.21%) but that given the genetic relatedness of animal isolates to human isolates, additional surveillance is needed.

Global transmission of extended-spectrum cephalosporin resistance in Escherichia coli driven by epidemic plasmids

BACKGROUND

Extended-spectrum cephalosporins (ESCs) are third and fourth generation cephalosporin antimicrobials used in humans and animals to treat infections due to multidrug-resistant (MDR) bacteria. Resistance to ESCs (ESC-R) in Enterobacterales is predominantly due to the production of extended-spectrum β-lactamases (ESBLs) and plasmid-mediated AmpC β-lactamases (AmpCs). The dynamics of ESBLs and AmpCs are changing across countries and host species, the result of global transmission of ESC-R genes. Plasmids are known to play a key role in this dissemination, but the relative importance of different types of plasmids is not fully understood.

METHODS

In this study, Escherichia coli with the major ESC-R genes blaCTX-M-1, blaCTX-M-15, blaCTX-M-14 (ESBLs) and blaCMY-2 (AmpC), were selected from diverse host species and other sources across Canada, France and Germany, collected between 2003 and 2017. To examine in detail the vehicles of transmission of the ESC-R genes, long- and short-read sequences were generated to obtain complete contiguous chromosome and plasmid sequences (n = 192 ESC-R E. coli). The types, gene composition and genetic relatedness of these plasmids were investigated, along with association with isolate year, source and geographical origin, and put in context with publicly available plasmid sequences.

FINDINGS

We identified five epidemic resistance plasmid subtypes with distinct genetic properties that are associated with the global dissemination of ESC-R genes across multiple E. coli lineages and host species. The IncI1 pST3 blaCTX-M-1 plasmid subtype was found in more diverse sources than the other main plasmid subtypes, whereas IncI1 pST12 blaCMY-2 was more frequent in Canadian and German human and chicken isolates. Clonal expansion also contributed to the dissemination of the IncI1 pST12 blaCMY-2 plasmid in ST131 and ST117 E. coli harbouring this plasmid. The IncI1 pST2 blaCMY-2 subtype was predominant in isolates from humans in France, while the IncF F31:A4:B1 blaCTX-M-15 and F2:A-:B- blaCTX-M-14 plasmid subtypes were frequent in human and cattle isolates across multiple countries. Beyond their epidemic nature with respect to ESC-R genes, in our collection almost all IncI1 pST3 blaCTX-M-1 and IncF F31:A4:B1 blaCTX-M-15 epidemic plasmids also carried multiple antimicrobial resistance (AMR) genes conferring resistance to other antimicrobial classes. Finally, we found genetic signatures in the regions surrounding specific ESC-R genes, identifying the predominant mechanisms of ESC-R gene movement, and using publicly available databases, we identified these epidemic plasmids from widespread bacterial species, host species, countries and continents.

INTERPRETATION

We provide evidence that epidemic resistance plasmid subtypes contribute to the global dissemination of ESC-R genes, and in addition, some of these epidemic plasmids confer resistance to multiple other antimicrobial classes. The success of these plasmids suggests that they may have a fitness advantage over other plasmid types and subtypes. Identification and understanding of the vehicles of AMR transmission are crucial to develop and target strategies and interventions to reduce the spread of AMR.

FUNDING

This project was supported by the Joint Programming Initiative on Antimicrobial Resistance (JPIAMR), through the Medical Research Council (MRC, MR/R000948/1), the Canadian Institutes of Health Research (CFC-150770), and the Genomics Research and Development Initiative (Government of Canada), the German Federal Ministry of Education and Research (BMBF) grant no. 01KI1709, the French Agency for food environmental and occupational health & safety (Anses), and the French National Reference Center (CNR) for antimicrobial resistance. Support was also provided by the Biotechnology and Biological Sciences Research Council (BBSRC) through the BBSRC Institute Strategic Programme Microbes in the Food ChainBB/R012504/1 and its constituent project BBS/E/F/000PR10348 (Theme 1, Epidemiology and Evolution of Pathogens in the Food Chain).

[Development of antibiotic resistance in animals not receiving antibiotic therapy]

The fight against antibiotic resistance in the animal sector over the last ten years in France (Ecoantibio plans) has largely focused on reducing the veterinary use of antibiotics. However, antibiotic resistance in an animal is not necessarily due to antibiotic therapy, but can also result from the transmission of resistant bacteria or resistance plasmids. Several examples illustrate the importance of this transmission of antibiotic resistance in the animal world, which are detailed in this communication. Like in human medicine, this nosocomial transmission can be observed in veterinary care institutions, as well as in animal husbandry. It also explains the presence of antibiotic resistance on the surface of foodstuffs, which by definition are not treated with antibiotics. At the international level, countries that are very virtuous in their use of veterinary antibiotics can display high levels of antibiotic resistance through the importation of carrier animals. Finally, the presence of antibiotic resistance in wildlife is likewise explained by contamination and not by antibiotic treatment. All these situations demonstrate that, in addition to paying attention to antibiotic prescription, an equally important facet of the fight against antibiotic resistance is to control the transmission routes of resistant bacteria.

The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2021-2022

This report by the European Food Safety Authority and the European Centre for Disease prevention and Control, provides an overview of the main findings of the 2021-2022 harmonised Antimicrobial Resistance (AMR) monitoring in Salmonella spp., Campylobacter jejuni and C. coli from humans and food-producing animals (broilers, laying hens and fattening turkeys, fattening pigs and cattle under one year of age) and relevant meat thereof. For animals and meat thereof, AMR data on indicator commensal Escherichia coli, presumptive extended-spectrum beta-lactamases (ESBL)-/AmpC beta-lactamases (AmpC)-/carbapenemase (CP)-producing E. coli, and the occurrence of methicillin-resistant Staphylococcus aureus (MRSA) are also analysed. Generally, resistance levels differed greatly between reporting countries and antimicrobials. Resistance to commonly used antimicrobials was frequently found in Salmonella and Campylobacter isolates from humans and animals. In humans, increasing trends in resistance to one of two critically antimicrobials (CIA) for treatment was observed in poultry-associated Salmonella serovars and Campylobacter, in at least half of the reporting countries. Combined resistance to CIA was however observed at low levels except in some Salmonella serovars and in C. coli from humans and animals in some countries. While CP-producing Salmonella isolates were not detected in animals in 2021-2022, nor in 2021 for human cases, in 2022 five human cases of CP-producing Salmonella were reported (four harbouring bla OXA-48 or bla OXA-48-like genes). The reporting of a number of CP-producing E. coli isolates (harbouring bla OXA-48, bla OXA-181, bla NDM-5 and bla VIM-1 genes) in fattening pigs, cattle under 1 year of age, poultry and meat thereof by a limited number of MSs (5) in 2021 and 2022, requires a thorough follow-up. The temporal trend analyses in both key outcome indicators (rate of complete susceptibility and prevalence of ESBL-/AmpC-producers in E. coli) showed an encouraging progress in reducing AMR in food-producing animals in several EU MSs over the last 7 years.

Emergence of OXA-48-producing Enterobacter hormaechei in a Swiss companion animal clinic and their genetic relationship to clinical human isolates

BACKGROUND

Enterobacter hormaechei producing the carbapenemase OXA-48 was identified repeatedly in infections in companion animals hospitalized at a Swiss veterinary clinic where OXA-48-producing Klebsiella pneumoniae was previously reported.

OBJECTIVES

To determine the genetic relatedness of animal and human E. hormaechei strains collected in Switzerland during 2017-22 and their mobile genetic elements.

METHODS

Hybrid assemblies for phylogenetic and comparative analysis of animal (n = 9) and human (n = 25) isolates were obtained by sequencing with Illumina, PacBio and Oxford Nanopore Technologies. Antimicrobial susceptibility was tested by broth microdilution.

RESULTS

The animal strains were identified as E. hormaechei subsp. xiangfangensis ST114 (n = 6) and ST418 (n = 2), and E. hormaechei subsp. hoffmannii ST78 (n = 1). Human E. hormaechei belonged to subspecies steigerwaltii (n = 10), xiangfangensis (n = 13), hoffmannii (n = 1) and hormaechei (n = 1), with a heterogeneous ST distribution differing from the animal strains, except for two ST114. Core-gene SNP analysis confirmed the clonality of the animal ST114 and ST418 isolates (0 to 10 SNPs), and close relatedness of animal and human ST114 strains (80-120 SNPs). The strains harboured the blaOXA-48 gene on ca. 63 kb IncL-type plasmids (n = 27); on ca. 72 kb IncL plasmids co-harbouring blaCTX-M-14 (n = 2); and on ca. 150-180 kb IncFIB (n = 4) or hybrid IncFIB/IncL (n = 1) plasmids. The blaOXA-48-harbouring plasmids and the blaDHA-1-carrying ISCR1 element in one animal ST114 and both ST418 clones were likely acquired from previously spreading K. pneumoniae strains.

CONCLUSIONS

Common ecological niches favour the spread of plasmid-borne carbapenemases among Enterobacterales and the emergence of MDR E. hormaechei clones.