The co-occurrence of antibiotic resistance genes between dogs and their owners in families

Application of phylodynamics to identify spread of antimicrobial-resistant Escherichia coli between humans and canines in an urban environment

The transmission of antimicrobial resistant bacteria in the urban environment is poorly understood. We utilized genomic sequencing and phylogenetics to characterize the transmission dynamics of antimicrobial resistant Escherichia coli (AMR-Ec) cultured from putative canine (caninep) and human feces present on urban sidewalks in San Francisco, California. We isolated a total of fifty-six AMR-Ec isolates from human (n = 20) and caninep (n = 36) fecal samples from the Tenderloin and South of Market (SoMa) neighborhoods of San Francisco. We then analyzed phenotypic and genotypic antimicrobial resistance (AMR) of the isolates, as well as clonal relationships based on cgMLST and single nucleotide polymorphisms (SNPs) of the core genomes. Using Bayesian inference, we reconstructed the transmission dynamics between humans and caninesp from multiple local outbreak clusters using the marginal structured coalescent approximation (MASCOT). Our results provide evidence for multiple sharing events of AMR-Ec between humans and caninesp. In particular, we found one instance of likely transmission from caninesp to humans as well as an additional local outbreak cluster consisting of one caninep and one human sample. Based on this analysis, it appears that non-human feces act as an important reservoir of clinically relevant AMR-Ec within the urban environment for this study population. This work showcases the utility of genomic epidemiology to reconstruct potential pathways by which antimicrobial resistance spreads.

Characterization of the semen microbiota of healthy stud dogs using 16S RNA sequencing

The reproductive microbiota of male dogs has never been investigated using culture-independent sequencing techniques. The purpose of the present study was to get seminal knowledge on the microbiota of the ejaculate. Specifically, factors as the fraction of the ejaculate, the sperm quality (normospermia, teratozoospermia), and the living environment were evaluated. The sperm-rich and the prostatic fractions of the ejaculate were collected from healthy stud dogs. Following the sperm analysis, samples from twenty animals (normospermic n = 10 and teratozoospermic n = 10) were stored at - 80 °C until further processing including DNA extraction and 16S rRNA sequencing. Alpha- (Shannon index) and beta- (Bray-Curtis, Unweighted UniFrac) diversities were assessed and compared (PERMANOVA) based on the group of samples (biological samples from the ejaculate and controls), the fraction of the ejaculate (sperm-rich and prostatic fractions), the animal group (normospermia and teratozoospermia), and the living environment of the animal (kennel or pet living in-house). The most abundant bacterial phyla in canine semen samples were Proteobacteria, Firmicutes, and Actinobacteria. Overall, the dominant bacterial family was that of Pasteurellaceae The genus Mycoplasma was never detected. No differences in terms of bacterial composition were found based on the fraction of the ejaculate and based on the animal group (P > 0.05). On the other hand, differences in alpha and beta diversities were highlighted based on the living environment (P = 0.001). Overall, the results of the present study provide preliminary insights on dog semen microbiota, opening a new chapter in the field of canine andrology. Our results suggest that the environment may play a role in influencing the reproductive microbiota of male dogs and that the prostatic fraction of the ejaculate can be used for further research as a representative of the semen microbiota.

Carbamazepine facilitated horizontal transfer of antibiotic resistance genes by enhancing microbial communication and aggregation

Antimicrobial resistance is a global health security issue of widespread concern. Recent studies have unveiled the potential contribution of non-antibiotics to the emergence of antimicrobial resistance. This study investigated the effect of carbamazepine, a non-antibiotic pharmaceutical, on the fate of antibiotic resistance genes (ARGs) during anaerobic digestion. The results, as revealed by both metagenomic sequencing and absolute quantification, demonstrated that carbamazepine induced the enrichment of ARGs and increased the abundance of ARGs hosts by 1.2-2.1 times. Carbamazepine facilitated microbial aggregation and intercellular communication by upregulating functional genes associated with two-component systems, quorum sensing and type IV secretion systems, thereby increasing the frequency of ARGs conjugation. Furthermore, carbamazepine induced the acquisition of ARGs by pathogens and elevated the overall pathogenic abundance. This study revealed the mechanisms of microbial self-regulation and ARGs transmission under carbamazepine stress, highlighting the potential health risks posed by non-antibiotic pharmaceuticals during the safe disposal of sludge.

Antibiotic Resistance Genes Carried by Commensal Escherichia coli from Shelter Cats in Italy

Antimicrobial resistance is a widespread global health problem. The presence of resistant bacteria and antibiotic resistance genes has been demonstrated not only in humans but also in animals, including pets. Stray cats share the urban environment with people and pets. This may facilitate transmission of resistant bacteria and resistance genes between stray animals, people and domestic animals. Several studies have investigated the role of stray cats as a fecal carrier of ESBL-producing bacteria. However, there are many genes and resistance mechanisms that can be detected in commensal E. coli, which, because of its genetic plasticity, is considered an indicator for monitoring antibiotic resistance. In this study, rectal swabs were collected from stray cats from colonies and shelters in the city of Monza (Monza Brianza, Italy) to isolate commensal E. coli. Phenotypic tests, such as the minimum inhibitory concentration (MIC) and the double disc test (DDST), and molecular analyses to detect antimicrobial resistance genes (ARGs) were used to study the resistance of these isolates. The results obtained confirm that stray cats can carry ESBL-producing E. coli (6.7%) and genes conferring resistance to other important antibiotic classes such as tetracyclines and sulfonamides.

Multidrug-Resistant Escherichia coli Strains to Last Resort Human Antibiotics Isolated from Healthy Companion Animals in Valencia Region

Failure in antibiotic therapies due to the increase in antimicrobial-resistant (AMR) bacteria is one of the main threats to public and animal health. In recent decades, the perception of companion animals has changed, from being considered as a work tool to a household member, creating a family bond and sharing spaces in their daily routine. Hence, the aim of this study is to assess the current epidemiological situation regarding the presence of AMR and multidrug resistance (MDR) in companion animals in the Valencia Region, using the indicator bacteria Escherichia coli as a sentinel. For this purpose, 244 samples of dogs and cats were collected from veterinary centres to assess antimicrobial susceptibility against a panel of 22 antibiotics with public health relevance. A total of 197 E. coli strains were isolated from asymptomatic dogs and cats. The results showed AMR against all the 22 antibiotics studied, including those critically important to human medicine. Moreover, almost 50% of the strains presented MDR. The present study revealed the importance of monitoring AMR and MDR trends in companion animals, as they could pose a risk due to the spread of AMR and its resistance genes to humans, other animals and the environment they cohabit.

Pet cats may shape the antibiotic resistome of their owner's gut and living environment

BACKGROUND

Companion animals can contribute to the physical and mental health of people and often live in very close association with their owners. However, the antibiotic resistome carried by companion animals and the impact they have on their owners and living environment remain unclear. In this study, we compared the ARG profiles of cats, humans, and their living environments using metagenomic analysis to identify the core ARGs in the cat and human gut and explore the potential impact of cats on ARGs in the human gut through the environment.

RESULTS

Results showed that the abundance of ARGs in the cat gut was significantly higher than that in the human gut (P < 0.0001), with aminoglycoside and tetracycline resistance genes being the dominant ARGs in the cat gut. There was no significant difference in the abundance of total ARGs in the guts of cat owners and non-owners (P > 0.05). However, the abundance of aminoglycoside resistance genes including APH(2'')-IIa and AAC(6')-Im was significantly higher in cat owners than that in non-cat owners (P < 0.001). Also, ARG abundance was positively correlated with the frequency of cat activity in the living environment. Enterobacteriaceae was the dominant ARG host co-occurring in the cat gut, human gut, and living environment.

CONCLUSIONS

Our results show that cats may shape the living environment resistome and thus the composition of some ARGs in the human gut, highlighting the importance of companion animal environment health. Video Abstract.

Comparison of Oral Microbial Composition and Determinants Encoding Antimicrobial Resistance in Dogs and Their Owners

Consolidated studies on animal, human, and environmental health have become very important for understanding emerging zoonotic diseases and the spread of antimicrobial resistance (AMR). The aim of this study was to analyse the oral microbiomes of healthy dogs and their owners, including determinants of AMR. Shotgun metagenomic sequencing detected 299 bacterial species in pets and their owners, from which 70 species were carried by dogs and 229 species by humans. Results demonstrated a unique microbial composition of dogs and their owners. At an order level, Bacteroidales were the most prevalent oral microbiota of dogs with significantly lower prevalence in their owners where Actinomycetales and Lactobacillales predominated. Porphyromonas and Corynebacterium were the most prevalent genera in dogs, whereas Streptococcus and Actinomyces were in animal owners. The resistances to macrolides, tetracyclines, lincosamides and Cfx family A class broad-spectrum β-lactamase were detected in both animal and human microbiomes. Resistance determinants to amphenicols, aminoglycosides, sulphonamides, and quaternary ammonium compounds were detected exceptionally in dogs. In conclusion, the study demonstrated different bacterial composition in oral microbiomes of healthy dogs without clinical signs of periodontal disease and their owners. Due to the low numbers of the samples tested, further investigations with an increased number of samples should be performed.

Microbiome Interconnectedness throughout Environments with Major Consequences for Healthy People and a Healthy Planet

Microbiomes have highly important roles for ecosystem functioning and carry out key functions that support planetary health, including nutrient cycling, climate regulation, and water filtration. Microbiomes are also intimately associated with complex multicellular organisms such as humans, other animals, plants, and insects and perform crucial roles for the health of their hosts. Although we are starting to understand that microbiomes in different systems are interconnected, there is still a poor understanding of microbiome transfer and connectivity. In this review we show how microbiomes are connected within and transferred between different habitats and discuss the functional consequences of these connections. Microbiome transfer occurs between and within abiotic (e.g., air, soil, and water) and biotic environments, and can either be mediated through different vectors (e.g., insects or food) or direct interactions. Such transfer processes may also include the transmission of pathogens or antibiotic resistance genes. However, here, we highlight the fact that microbiome transmission can have positive effects on planetary and human health, where transmitted microorganisms potentially providing novel functions may be important for the adaptation of ecosystems.

Characterization of the pig lower respiratory tract antibiotic resistome

Respiratory diseases and its treatments are highly concerned in both the pig industry and human health. However, the composition and distribution of antibiotic resistance genes (ARGs) in swine lower respiratory tract microbiome remain unknown. The relationships of ARGs with mobile genetic elements (MGEs) and lung health are unclear. Here, we characterize antibiotic resistomes of the swine lower respiratory tract microbiome containing 1228 open reading frames belonging to 372 ARGs using 745 metagenomes from 675 experimental pigs. Twelve ARGs conferring resistance to tetracycline are related to an MGE Tn916 family, and multiple types of ARGs are related to a transposase gene tnpA. Most of the linkage complexes between ARGs and MGEs (the Tn916 family and tnpA) are also observed in pig gut microbiomes and human lung microbiomes, suggesting the high risk of these MGEs mediating ARG transfer to both human and pig health. Gammaproteobacteria are the major ARG carriers, within which Escherichia coli harbored >50 ARGs and >10 MGEs. Although the microbial compositions structure the compositions of ARGs, we identify 73 ARGs whose relative abundances are significantly associated with the severity of lung lesions. Our results provide the first overview of ARG profiles in the swine lower respiratory tract microbiome.

Phylodynamics Uncovers the Transmission of Antibiotic-Resistant Escherichia coli between Canines and Humans in an Urban Environment

The role of canines in transmitting antibiotic resistant bacteria to humans in the urban environment is poorly understood. To elucidate this role, we utilized genomic sequencing and phylogenetics to characterize the burden and transmission dynamics of antibiotic resistant Escherichia coli (ABR-Ec) cultured from canine and human feces present on urban sidewalks in San Francisco, California. We collected a total of fifty-nine ABR-Ec from human (n=12) and canine (n=47) fecal samples from the Tenderloin and South of Market (SoMa) neighborhoods of San Francisco. We then analyzed phenotypic and genotypic antibiotic resistance (ABR) of the isolates, as well as clonal relationships based on cgMLST and single nucleotide polymorphisms (SNPs) of the core genomes. Using Bayesian inference, we reconstructed the transmission dynamics between humans and canines from multiple local outbreak clusters using the marginal structured coalescent approximation (MASCOT). Overall, we found human and canine samples to carry similar amounts and profiles of ABR genes. Our results provide evidence for multiple transmission events of ABR-Ec between humans and canines. In particular, we found one instance of likely transmission from canines to humans as well as an additional local outbreak cluster consisting of one canine and one human sample. Based on this analysis, it appears that canine feces act as an important reservoir of clinically relevant ABR-Ec within the urban environment. Our findings support that public health measures should continue to emphasize proper canine feces disposal practices, access to public toilets and sidewalk and street cleaning. Importance: Antibiotic resistance in E. coli is a growing public health concern with global attributable deaths projected to reach millions annually. Current research has focused heavily on clinical routes of antibiotic resistance transmission to design interventions while the role of alternative reservoirs such as domesticated animals remain less well understood. Our results suggest canines are part of the transmission network that disseminates high-risk multidrug resistance in E. coli within the urban San Francisco community. As such, this study highlights the need to consider canines, and potentially domesticated animals more broadly, when designing interventions to reduce the prevalence of antibiotic resistance in the community. Additionally, it showcases the utility of genomic epidemiology to reconstruct the pathways by which antimicrobial resistance spreads.

Correction

[This corrects the article DOI: 10.1002/imt2.21.].

Urbanization-land-use interactions predict antibiotic contamination in soil across urban-rural gradients

Antibiotics ubiquitously occur in soils and pose a potential threat to ecosystem health. Concurrently, urbanization and land-use intensification have transformed soil ecosystems, but how they affect antibiotic contamination remain largely unknown. Therefore, we profiled a broad-scale pattern of antibiotics in soil from agricultural lands and green spaces across urbanization gradients, and explored the hypothetical models to verify the effects of urbanization and land-use intensity on antibiotic contamination. The results showed that antibiotic concentrations and seasonality were higher in agricultural soil than in green spaces, which respectively showed linear or hump-shaped declines along with the increasing distance to urban centers. However, the response of antibiotic pollution to land-use intensity depended strongly on the urbanization level. More importantly, interactions between urbanization and land-use explained, on average, 59.6 % of the variation in antibiotic concentrations in soil across urbanization gradients. The proposed interactions can predict the non-linear changes in soil vulnerability to antibiotic contamination. Our study revealed that the urbanization can modulate the effects of land-use intensity on antibiotic concentration and seasonality in the soil environment, and that there is high stress on peri-urban soil ecosystems due to ongoing land-use changes arising from rapid urbanization processes.

First Belgian Report of Ertapenem Resistance in an ST11 Klebsiella Pneumoniae Strain Isolated from a Dog Carrying blaSCO-1 and blaDHA-1 Combined with Permeability Defects

Klebsiella pneumoniae of sequence type (ST) 11 is a hyper-epidemic nosocomial clone, which is spreading worldwide among humans and emerging in pets. This is the first report, to the best of our knowledge, of multidrug-resistant (MDR) K. pneumoniae ST11 carrying blaSCO-1 and blaDHA-1, isolated from a four-month-old dog in Belgium. Antimicrobial susceptibility testing (AST) of the isolate, performed via broth microdilution following the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines, revealed resistance to eight different classes of antimicrobials, including carbapenems, in particular ertapenem, third-generation cephalosporins and fluoroquinolones. A hybrid approach, combining long- and short-read sequencing, was employed for in silico plasmid characterization, multi-locus sequence typing (MLST) and the identification and localization of antimicrobial resistance (AMR) and virulence-associated genes. Three plasmids were reconstructed from the whole-genome sequence (WGS) data: the conjugative IncFIB(K), the non-mobilizable IncR and the mobilizable but unconjugative ColRNAI. The IncFIB(K) plasmid carried the blaSCO-1 gene, whereas IncR carried blaDHA-1, both alongside several other antimicrobial resistance genes (ARGs). No virulence genes could be detected. Here, we suggest that the resistance to ertapenem associated with susceptibility to imipenem and meropenem in K. pneumoniae could be related to the presence of blaSCO-1 and blaDHA-1, combined with permeability defects caused by point mutations in an outer membrane porin (OmpK37). The presence of the blaSCO-1 gene on a conjugative IncFIB(K) plasmid is worrisome as it can increase the risk of transmission to humans, to animals and to the environment.