Emergence and Spread of Cephalosporinases in Wildlife: A Review

Antimicrobial resistance and phylogenetic relatedness of extended-spectrum ß-lactamase (ESBL)-producing Escherichia coli in peridomestic rats (Rattus norvegicus and Rattus tanezumi) linked to city areas and animal farms in Hong Kong

Extended-spectrum β-lactamase-producing Escherichia (E.) coli (ESBL-EC) in the clinical setting have emerged as a major threat to public and animal health. Wildlife, including Rattus spp. may serve as reservoirs and spreaders of ESBL-EC in the environment. Peridomestic rats are well adapted to living in proximity to humans and animals in a variety of urban and agricultural environments and may serve as sentinels to identify variations of ESBL-EC within their different habitats. In this study, a set of 221 rats (Rattus norvegicus, R. tanezumi, R. andamanensis, and Niviventer huang) consisting of 104 rats from city areas, 44 from chicken farms, 52 from pig farms, and 21 from stables of horse-riding schools were screened for ESBL-EC. Overall, a total of 134 ESBL-EC were isolated from the caecal samples of 130 (59%) rats. The predominant blaESBL genes were blaCTX-M-14, blaCTX-M-15, blaCTX-M-55, and blaCTX-M-65. Phylogenetic analysis revealed a total of 62 sequence types (STs) and 17 SNP clusters. E. coli ST10 and ST155 were common to ESBL-EC from city areas and chicken farms, and ST44 were found among ESBL-EC from city areas and pig farms. Extra-intestinal pathogenic E. coli (ExPEC) ST69, ST131 and ST1193 were found exclusively among rats from city areas, and avian pathogenic E. coli (APEC) ST177 was restricted to ESBL-EC originating from chicken farms. Phylogenetic analysis showed that the populations of rodent ESBL-EC from city areas, chicken farms and pig farms were genetically different, suggesting a certain degree of partitioning between the human and animal locations. This study contributes to current understanding of ESBL-EC occurring in rats in ecologically diverse locations.

Resistant Escherichia coli isolated from wild mammals from two rescue and rehabilitation centers in Costa Rica: characterization and public health relevance

This study aimed to characterize the antimicrobial resistance (AMR) and virulence profiles of 67 Escherichia coli isolates obtained from faecal samples of 77 wild mammals from 19 different species, admitted in two rescue and rehabilitation centers in Costa Rica. It was possible to classify 48% (n = 32) of the isolates as multidrug-resistant, and while the highest resistance levels were found towards commonly prescribed antimicrobials, resistance to fluoroquinolones and third generation cephalosporins were also observed. Isolates obtained from samples of rehabilitated animals or animals treated with antibiotics were found to have significantly higher AMR levels, with the former also having a significant association with a multidrug-resistance profile. Additionally, the isolates displayed the capacity to produce α-haemolysins (n = 64, 96%), biofilms (n = 51, 76%) and protease (n = 21, 31%). Our results showed that AMR might be a widespread phenomenon within Costa Rican wildlife and that both free-ranging and rehabilitated wild mammals are potential carriers of bacteria with important resistance and virulence profiles. These results highlight the need to study potential sources of resistance determinants to wildlife, and to determine if wild animals can disseminate resistant bacteria in the environment, potentially posing a significant threat to public health and hindering the implementation of a "One Health" approach.

Genomic insights into ESBL-producing Escherichia coli isolated from non-human primates in the Peruvian Amazon

Introduction

Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae are on the WHO priority pathogens list because they are associated with high mortality, health-care burden, and antimicrobial resistance (AMR), a serious problem that threatens global public health and should be addressed through the One Health approach. Non-human primates (NHP) have a high risk of acquiring these antibiotic-resistant bacteria due to their close phylogenetic relationship with humans and increased anthropogenic activities in their natural environments. This study aimed to detect and analyze the genomes of ESBL-producing Escherichia coli (ESBL-producing E. coli) in NHP from the Peruvian Amazon.

Materials and methods

We collected a total of 119 fecal samples from semi-captive Saguinus labiatus, Saguinus mystax, and Saimiri boliviensis, and captive Ateles chamek, Cebus unicolor, Lagothrix lagothricha, and Sapajus apella in the Loreto and Ucayali regions, respectively. Subsequently, we isolated and identified E. coli strains by microbiological methods, detected ESBL-producing E. coli through antimicrobial susceptibility tests following CLSI guidelines, and analyzed their genomes using previously described genomic methods.

Results

We detected that 7.07% (7/99) of E. coli strains: 5.45% (3/55) from Loreto and 9.09% (4/44) from Ucayali, expressed ESBL phenotype. Genomic analysis revealed the presence of high-risk pandemic clones, such as ST10 and ST117, carrying a broad resistome to relevant antibiotics, including three blaCTX-M variants: blaCTX-M-15, blaCTX-M-55, and blaCTX-M-65. Phylogenomic analysis confirmed the clonal relatedness of high-risk lineages circulating at the human-NHP interface. Additionally, two ESBL-producing E. coli strains were identified as EPEC (eae) and ExPEC according to their virulence profiles, and one more presented a hypermucoviscous phenotype.

Discussion

We report the detection and genomic analysis of seven ESBL-producing E. coli strains carrying broad resistome and virulence factors in NHP from two regions of the Peruvian Amazon. Some of these strains are closely related to high-risk pandemic lineages previously reported in humans and domestic animals, highlighting the negative impact of anthropogenic activities on Amazonian wildlife. To our knowledge, this is the first documentation of ESBL-producing E. coli in NHP from the Amazon, underscoring the importance of adopting the One Health approach to AMR surveillance and minimizing the potential transmission risk of antibiotic-resistant bacteria at the human-NHP interface.

Contamination of a Water Stream and Water Drainage Reaching Matosinhos Beach by Antibiotic-Resistant Bacteria

Antibiotic-resistant bacteria represent a major public health concern, especially impacting medical care centers and hospitals, thereby challenging the effectiveness of current infection treatment protocols. The emergence and persistence of antimicrobial resistance in the environment have been thoroughly researched, with a focus on the aquatic environment as a potential reservoir of these bacteria in areas with anthropogenic contamination. Having this in mind, this work aims to investigate the water streams of Riguinha and Brito Capelo Street, both of which ultimately flow into Matosinhos Beach in Portugal, to determine the potential presence of fecal contamination. Six water samples were collected and analyzed within twenty-four hours from these two water streams. A phenotypic characterization was performed in various volumes on MacConkey agar with antibiotics. Randomly selected lactose-fermenting gram-negative bacteria underwent antimicrobial susceptibility tests using the agar diffusion method following EUCAST guidelines, covering β-lactam and non-β-lactam antibiotics. The isolates were analyzed through Polymerase Chain Reaction. The findings of this study confirm that both water streams were contaminated by multidrug-resistant bacteria such as Enterobacteriaceae, including Escherichia coli, the KESC group, and Pseudomonas, exhibiting extended-spectrum β-lactamases (ESBL), AmpC β-lactamases, and carbapenemases. These indicate the presence of fecal contamination with relevant antimicrobial-resistant threats.

Rats as sources of multidrug-resistant Enterobacteriaceae in animal production environments

Rattus norvegicus and Rattus rattus are commensal pest rodents, considered reservoirs and vectors of zoonotic pathogens. In livestock farms, the wide use of antimicrobials and their release into the environment lead to high long-term residual concentrations, which may in turn lead to the occurrence of antimicrobial resistance (AMR). Farm environments serve as AMR sources, resulting in the transmission of antimicrobial-resistant bacteria and their AMR genes of livestock origin into wildlife. This study aimed to analyse the profile of enterobacteria carrying AMR determinants in rats captured in livestock farms to determine their potential vectors as for the spread of AMR. To this end, 56 rats (52 R. norvegicus and 4 R. rattus) were live-trapped on 11 farms (pig, dairy, poultry and mixed farms) located in central Argentina, from spring 2016 to autumn 2017. From 50 of the R. norvegicus individuals and three of the R. rattus individuals found in 10 of the farms, we isolated 53 Escherichia coli and five Salmonella strains. Susceptibility to antimicrobials, genotypic profiles, minimal inhibitory concentration of colistin and the presence of mcr-1 and genes encoding extended-spectrum β-lactamase (ESBL) were determined. Of the 58 isolates not susceptible to different antimicrobial classes, 28 of the E. coli strains and two of the Salmonella strains were defined as multi-drug resistant (MDR). S. Westhampton and S. Newport recovered were not susceptible to ampicillin or all the cephems tested. One of the E. coli obtained showed resistance to colistin and harboured the mcr-1 gene, demonstrated by PCR and conjugation. In two ESBL-producing Salmonella isolated from rats, CTX-M-2 genes were responsible for the observed resistance to third-generation cephalosporins. The MDR E. coli isolates showed several different resistance patterns (23), although some of them were the same in different individuals and different farms, with six resistance patterns, evidencing the dispersion of strains. These findings suggest that rats play a role in the dissemination of AMR determinants between animal, humans and environmental reservoirs.

Increased rat-borne zoonotic disease hazard in greener urban areas

Urban greening has benefits for both human and environmental health. However, urban greening might also have negative effects as the abundance of wild rats, which can host and spread a great diversity of zoonotic pathogens, increases with urban greenness. Studies on the effect of urban greening on rat-borne zoonotic pathogens are currently unavailable. Therefore, we investigated how urban greenness is associated with rat-borne zoonotic pathogen prevalence and diversity, and translated this to human disease hazard. We screened 412 wild rats (Rattus norvegicus and Rattus rattus) from three cities in the Netherlands for 18 different zoonotic pathogens: Bartonella spp., Leptospira spp., Borrelia spp., Rickettsia spp., Anaplasma phagocytophilum, Neoehrlichia mikurensis, Spiroplasma spp., Streptobacillus moniliformis, Coxiella burnetii, Salmonella spp., methicillin-resistant Staphylococcus aureus (MRSA), extended-spectrum beta-lactamase (ESBL)/AmpC-producing Escherichia coli, rat hepatitis E virus (ratHEV), Seoul orthohantavirus, Cowpox virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Toxoplasma gondii and Babesia spp. We modelled the relationships between pathogen prevalence and diversity and urban greenness. We detected 13 different zoonotic pathogens. Rats from greener urban areas had a significantly higher prevalence of Bartonella spp. and Borrelia spp., and a significantly lower prevalence of ESBL/AmpC-producing E. coli and ratHEV. Rat age was positively correlated with pathogen diversity while greenness was not related to pathogen diversity. Additionally, Bartonella spp. occurrence was positively correlated with that of Leptospira spp., Borrelia spp. and Rickettsia spp., and Borrelia spp. occurrence was also positively correlated with that of Rickettsia spp. Our results show an increased rat-borne zoonotic disease hazard in greener urban areas, which for most pathogens was driven by the increase in rat abundance rather than pathogen prevalence. This highlights the importance of keeping rat densities low and investigating the effects of urban greening on the exposure to zoonotic pathogens in order to make informed decisions and to take appropriate countermeasures preventing zoonotic diseases.

Molecular characterization of highly prevalent Escherichia coli and Escherichia marmotae resistant to extended-spectrum cephalosporins in European starlings (Sturnus vulgaris) in Tunisia

European starlings are widespread migratory birds that have already been described as carrying bacteria resistant to extended-spectrum cephalosporins (ESC-R). These birds are well known in Tunisia because they spend the wintertime in this country and are hunted for human consumption. The goal of our study was to estimate the proportion of ESC-R in these birds and to characterize the collected isolates using whole-genome sequencing. Results showed that 21.5% (42/200) of the birds carried either an extended-spectrum beta-lactamase (ESBL) or an acquired AmpC gene. Diverse bla CTX-M genes were responsible for the ESBL phenotype, bla CTX-M-14 being the most prevalent, while only bla CMY-2 and one bla CMY-62 were found in AmpC-positive isolates. Likewise, different genetic determinants carried these resistance genes, including IncHI2, and IncF plasmids for bla CTX-M genes and IncI1 plasmids for bla CMY-2 genes. Three chromosomally encoded bla CTX-M-15 genes were also identified. Surprisingly, species identification revealed a large proportion (32.7%) of Escherichia marmotae isolates. This species is phenotypically indistinguishable from Escherichia coli and has obviously the same capacity to acquire ESC-R genes. Our data also strongly suggest that at least the IncHI2/pST3 plasmid can spread equally between E. coli and E. marmotae. Given the potential transmission routes between humans and animals, either by direct contact with dejections or through meat preparation, it is important to closely monitor antimicrobial resistance in European starlings in Tunisia and to set up further studies to identify the sources of contamination of these birds. IMPORTANCE The One Health concept highlighted knowledge gaps in the understanding of the transmission routes of resistant bacteria. A major interest was shown in wild migratory birds since they might spread resistant bacteria over long distances. Our study brings further evidence that wild birds, even though they are not directly submitted to antibiotic treatments, can be heavily contaminated by resistant bacteria. Our results identified numerous combinations of resistance genes, genetic supports, and bacterial clones that can spread vertically or horizontally and maintain a high level of resistance in the bird population. Some of these determinants are widespread in humans or animals (IncHI2/pST3 plasmids and pandemic clones), while some others are less frequent (atypical IncI1 plasmid and minor clones). Consequently, it is essential to be aware of the risks of transmission and to take all necessary measures to prevent the proportions of resistant isolates from increasing uncontrollably.

Epidemiological study of antimicrobial-resistant bacteria in healthy free-ranging bantengs (Bos javanicus) and domestic cattle

Background and Aim

Antimicrobial-resistant microorganisms (ARMs) have been increasing among wild animals. Interactions occurring at the interface between wildlife, humans, and livestock can lead to the transmission of ARMs. Thus, the prevalence of ARMs in wild and domestic animals should be determined to address and prevent this issue. This study aimed to determine the resistance patterns of cefotaxime (CTX)-resistant Escherichia coli and identify the presence of extended-spectrum beta-lactamase (ESBL) genes in ESBL-producing E. coli among a population of wild banteng (Bos javanicus) and domestic cattle kept on farms located close to the Lam Pao non-hunting area, Kalasin province, Thailand.

Materials and Methods

Forty-five fecal samples were taken from wild bantengs inhabiting the Lam Pao non-hunting area in Thailand, alongside 15 samples from domestic cattle. Bacterial culture, triple sugar iron, and motile indole lysine tests were conducted to identify E. coli. A polymerase chain reaction (PCR) was conducted for specific confirmation. MacConkey agar supplemented with 2 μg/mL of CTX was used to identify CTX-resistant E. coli, which would be used to identify ESBL production based on a double-disk synergy test. Extended-spectrum beta-lactamase-producing samples were subjected to disk diffusion tests to determine resistant patterns, and the sizes of PCR bands and DNA sequencing were used to differentiate ESBL gene types.

Results

All samples tested positive for E. coli. Forty-five isolates from 15 banteng samples and three isolates from one domestic cattle sample displayed CTX-resistant and ESBL-producing traits. The banteng and domestic cattle populations exhibited nine and three distinct resistant patterns, respectively. The PCR results indicated that the banteng isolates harbored the following genes: Cefotaxime-M1 (n = 38), CTX-M9 (n = 5), and the SHV group (n = 2). All three isolates from the domestic cattle sample contained the CTX-M1 gene. Classification of ESBL genes based on the DNA sequences of the banteng isolates showed the characteristics of CTX-M15 (n = 20), CTX-M55 (n = 6), CTX-M14 (n = 5), and CTX-M79 (n = 1). The three domestic cattle isolates exhibited the characteristics of CTX-M15, CTX-M55, and CTX-M79.

Conclusion

Despite no previous antibiotic applications, approximately one-third of the banteng samples displayed CTX resistance, indicating ARM contamination within the ecosystem. The similarity in ESBL genes between the banteng and domestic cattle populations suggests potential gene transmissions between these animal groups. However, the initial source of ARMs remains unclear, as the banteng population exhibited more ESBL genes than the domestic cattle, suggesting the possibility of multiple ARM sources. These findings raise concerns because the banteng population inhabits an area that is an important source of freshwater and nourishes the entire north-east region of Thailand and other South-east Asian countries, including Laos, Cambodia, and Southern Vietnam.

Antimicrobial resistance (AMR) as a form of human-wildlife conflict: Why and how nondomesticated species should be incorporated into AMR guidance

The challenge of antimicrobial resistance (AMR) continues to receive significant global attention as common infections become increasingly resistant to the drugs used to treat them. Once an infectious microbe has developed a mechanism of resistance, it can cause longer, more damaging infections which are more costly, time-consuming, and sometimes impossible to treat. Such impacts occur across the health of humans, animals, plants, and the environment. Thus, AMR is considered a One Health issue. However, current narratives on AMR focus on humans, food-producing animals, crops, and their immediate environments. Very little attention is given to wildlife in terms of the impact of AMR on their health, nor their role in the evolution and spread of AMR. This article (1) discusses an absence of wildlife in current AMR guidance, (2) suggests how this absence of wildlife could limit understanding of, and action on, AMR, (3) proposes that considering AMR as a form of human-wildlife conflict could enable AMR guidance to better incorporate wildlife into action planning and create a truly One Health approach to tackle AMR.

Genomic Characterization of Fecal Escherichia coli Isolates with Reduced Susceptibility to Beta-Lactam Antimicrobials from Wild Hogs and Coyotes

This study was carried out to determine the antimicrobial resistance (AMR) genes and mobile genetic elements of 16 Escherichia coli isolates-with reduced susceptibility to ceftazidime and imipenem-that were recovered from the fecal samples of coyotes and wild hogs from West Texas, USA. Whole-genome sequencing data analyses revealed distinct isolates with a unique sequence type and serotype designation. Among 16 isolates, 4 isolates were multidrug resistant, and 5 isolates harbored at least 1 beta-lactamase gene (bla_CMY-2, bla_CTX-M-55, or bla_CTX-M-27) that confers resistance to beta-lactam antimicrobials. Several isolates carried genes conferring resistance to tetracyclines (tet(A), tet(B), and tet(C)), aminoglycosides (aac(3)-IId, ant(3″)-Ia, aph(3')-Ia, aph(3″)-lb, aadA5, and aph(6)-ld), sulfonamides (sul1, sul2, and sul3), amphenicol (floR), trimethoprim (dfrA1 and dfrA17), and macrolide, lincosamide, and streptogramin B (MLSB) agents (Inu(F), erm(B), and mph(A)). Nine isolates showed chromosomal mutations in the promoter region G of ampC beta-lactamase gene, while three isolates showed mutations in gyrA, parC, and parE quinolone resistance-determining regions, which confer resistance to quinolones. We also detected seven incompatibility plasmid groups, with incF being the most common. Different types of virulence genes were detected, including those that enhance bacterial fitness and pathogenicity. One bla_CMY-2 positive isolate (O8:H28) from a wild hog was also a Shiga toxin-producing E. coli and was a carrier of the stx2A virulence toxin subtype. We report the detection of bla_CMY-2, bla_CTX-M-55, and bla_CTX-M-27 beta-lactamase genes in E. coli from coyotes for the first time. This study demonstrates the importance of wildlife as reservoirs of important multi-drug-resistant bacteria and provides information for future comparative genomic analysis with the limited literature on antimicrobial resistance dynamics in wildlife such as coyotes.

Under-Appreciated Phylogroup Diversity of Escherichia coli within and between Animals at the Urban-Wildland Interface

Wild animals have been implicated as reservoirs and even "melting pots" of pathogenic and antimicrobial-resistant bacteria of concern to human health. Though Escherichia coli is common among vertebrate guts and plays a role in the propagation of such genetic information, few studies have explored its diversity beyond humans nor the ecological factors that influence its diversity and distribution in wild animals. We characterized an average of 20 E. coli isolates per scat sample (n = 84) from a community of 14 wild and 3 domestic species. The phylogeny of E. coli comprises 8 phylogroups that are differentially associated with pathogenicity and antibiotic resistance, and we uncovered all of them in one small biological preserve surrounded by intense human activity. Challenging previous assumptions that a single isolate is representative of within-host phylogroup diversity, 57% of individual animals sampled carried multiple phylogroups simultaneously. Host species' phylogroup richness saturated at different levels across species and encapsulated vast within-sample and within-species variation, indicating that distribution patterns are influenced both by isolation source and laboratory sampling depth. Using ecological methods that ensure statistical relevance, we identify trends in phylogroup prevalence associated with host and environmental factors. The vast genetic diversity and broad distribution of E. coli in wildlife populations has implications for biodiversity conservation, agriculture, and public health, as well as for gauging unknown risks at the urban-wildland interface. We propose critical directions for future studies of the "wild side" of E. coli that will expand our understanding of its ecology and evolution beyond the human environment. IMPORTANCE To our knowledge, neither the phylogroup diversity of E. coli within individual wild animals nor that within an interacting multispecies community have previously been assessed. In doing so, we uncovered the globally known phylogroup diversity from an animal community on a preserve imbedded in a human-dominated landscape. We revealed that the phylogroup composition in domestic animals differed greatly from that in their wild counterparts, implying potential human impacts on the domestic animal gut. Significantly, many wild individuals hosted multiple phylogroups simultaneously, indicating the potential for strain-mixing and zoonotic spillback, especially as human encroachment into wildlands increases in the Anthropocene. We reason that due to extensive anthropogenic environmental contamination, wildlife is increasingly exposed to our waste, including E. coli and antibiotics. The gaps in the ecological and evolutionary understanding of E. coli thus necessitate a significant uptick in research to better understand human impacts on wildlife and the risk for zoonotic pathogen emergence.

Building an International One Health Strain Level Database to Characterise the Epidemiology of AMR Threats: ESBL—AmpC Producing E. coli as An Example—Challenges and Perspectives

Antimicrobial resistance (AMR) is one of the top public health threats nowadays. Among the most important AMR pathogens, Escherichia coli resistant to extended spectrum cephalosporins (ESC-EC) is a perfect example of the One Health problem due to its global distribution in animal, human, and environmental sources and its resistant phenotype, derived from the carriage of plasmid-borne extended-spectrum and AmpC β-lactamases, which limits the choice of effective antimicrobial therapies. The epidemiology of ESC-EC infection is complex as a result of the multiple possible sources involved in its transmission, and its study would require databases ideally comprising information from animal (livestock, companion, wildlife), human, and environmental sources. Here, we present the steps taken to assemble a database with phenotypic and genetic information on 10,763 ESC-EC isolates retrieved from multiple sources provided by 13 partners located in eight European countries, in the frame of the DiSCoVeR Joint Research project funded by the One Health European Joint Programme (OH-EJP), along with its strengths and limitations. This database represents a first step to help in the assessment of different geographical and temporal trends and transmission dynamics in animals and humans. The work performed highlights aspects that should be considered in future international efforts, such as the one presented here.

Intestinal colonization with multidrug-resistant Enterobacterales: screening, epidemiology, clinical impact, and strategies to decolonize carriers

The clinical impact of infections due to extended-spectrum β-lactamase (ESBL)- and/or carbapenemase-producing Enterobacterales (Ent) has reached dramatic levels worldwide. Infections due to these multidrug-resistant (MDR) pathogens-especially Escherichia coli and Klebsiella pneumoniae-may originate from a prior asymptomatic intestinal colonization that could also favor transmission to other subjects. It is therefore desirable that gut carriers are rapidly identified to try preventing both the occurrence of serious endogenous infections and potential transmission. Together with the infection prevention and control countermeasures, any strategy capable of effectively eradicating the MDR-Ent from the intestinal tract would be desirable. In this narrative review, we present a summary of the different aspects linked to the intestinal colonization due to MDR-Ent. In particular, culture- and molecular-based screening techniques to identify carriers, data on prevalence and risk factors in different populations, clinical impact, length of colonization, and contribution to transmission in various settings will be overviewed. We will also discuss the standard strategies (selective digestive decontamination, fecal microbiota transplant) and those still in development (bacteriophages, probiotics, microcins, and CRISPR-Cas-based) that might be used to decolonize MDR-Ent carriers.

Development of a Method for the Fast Detection of Extended-Spectrum β-Lactamase- and Plasmid-Mediated AmpC β-Lactamase-Producing Escherichia coli and Klebsiella pneumoniae from Dogs and Cats in the USA

Antibiotic resistance, such as resistance to beta-lactams and the development of resistance mechanisms, is associated with multifactorial phenomena and not only with the use of third-generation cephalosporins. Many methods have been recommended for the detection of ESBL and pAmpC β-lactamase production but they are very subjective and the appropriate facilities are not available in most laboratories, especially not in clinics. Therefore, for fast clinical antimicrobial selection, we need to rapidly detect ESBL- and pAmpC β-lactamase-producing bacteria using a simple method with samples containing large amounts of bacteria. For the detection of ESBL- and pAmpC phenotypes and genes, the disk diffusion test, DDST and multiplex PCR were conducted. Of the 109 samples, 99 (90.8%) samples were grown in MacConkey broth containing cephalothin, and 71 samples were grown on MacConkey agar containing ceftiofur. Of the 71 samples grown on MacConkey agar containing ceftiofur, 58 Escherichia coli and 19 Klebsiella pneumoniae isolates, in particular, harbored β-lactamase genes. Of the 38 samples that did not grow in MacConkey broth containing cephalothin or on MacConkey agar containing ceftiofur, 32 isolates were identified as E. coli, and 10 isolates were identified as K. pneumoniae; β-lactamase genes were not detected in these E. coli and K. pneumoniae isolates. Of the 78 ESBL- and pAmpC β-lactamase-producing E. coli and K. pneumoniae, 55 (70.5%) isolates carried one or more ESBL genes and 56 (71.8%) isolates carried one or more pAmpC β-lactamase genes. Our method is a fast, and low-cost tool for the screening of frequently encountered ESBL- and pAmpC β-lactamase-producing bacteria and it would assist in diagnosis and improve therapeutic treatment in animal hospitals.

One health clones of multidrug-resistant Escherichia coli carried by synanthropic animals in Brazil

WHO priority pathogens have disseminated beyond hospital settings and are now being detected in urban and wild animals worldwide. In this regard, synanthropic animals such as urban pigeons (Columba livia) and rodents (Rattus rattus, Rattus norvegicus and Mus musculus) are of interest to public health due to their role as reservoirs of pathogens that can cause severe diseases. These animals usually live in highly contaminated environments and have frequent interactions with humans, domestic animals, and food chain, becoming sentinels of anthropogenic activities. In this study, we report genomic data of Escherichia coli strains selected for ceftriaxone and ciprofloxacin resistance, isolated from pigeons and black rats. Genomic analysis revealed the occurrence of international clones belonging to ST10, ST155, ST224 and ST457, carrying a broad resistome to beta-lactams, aminoglycosides, trimethoprim/sulfamethoxazole, fluoroquinolones, tetracyclines and/or phenicols. SNP-based phylogenomic investigation confirmed clonal relatedness with high-risk lineages circulating at the human-animal-environmental interface globally. Our results confirm the dissemination of WHO priority CTX-M-positive E. coli in urban rodents and pigeons in Brazil, highlighting potential of these animals as infection sources and hotspot for dissemination of clinically relevant pathogens and their resistance genes, which is a critical issue within a One Health perspective.

Finding of extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales in wild game meat originating from several European countries: predominance of Moellerella wisconsensis producing CTX-M-1, November 2021

IntroductionMeat can be a vehicle for food-borne transmission of antimicrobial resistant bacteria and antimicrobial resistance genes. The occurrence of extended-spectrum beta-lactamase (ESBL) producing Enterobacterales has been observed in meat from livestock production but has not been well studied in meat from wild game.AimWe aimed to investigate, particularly in central Europe, to what extent ESBL-producing Enterobacterales may be present in wild game meat.MethodsA total of 111 samples of different types of game meat supplied by butchers, hunters, retail stores and a large game-processing establishment in Europe were screened for ESBL-producing Enterobacterales using a selective culture medium. Isolates were genotypically and phenotypically characterised.ResultsThirty-nine samples (35% of the total) yielded ESBL-producing Enterobacterales, with most (35/39) supplied by the game-processing establishment. Isolates included 32 Moellerella wisconsensis, 18 Escherichia coli and one Escherichia marmotae. PCR screening identified bla CTX-M-1 (n = 31), bla CTX-M-32 (n = 8), bla CTX-M-65 (n = 4), bla CTX-M-15 (n = 3), bla CTX-M-8 (n = 1), bla CTX-M-14 (n = 1), bla CTX-M-55 (n = 1), and bla SHV-12 (n = 2). Most E. coli belonged to phylogenetic group A (n = 7) or B1 (n = 9), but several isolates belonged to extraintestinal pathogenic E. coli (ExPEC) sequence types (ST)58 (n = 4), ST68 (n = 1) and ST540 (n = 1). Whole genome sequencing of six selected isolates localised bla CTX-M-1 on megaplasmids in four M. wisconsensis and bla CTX-M-32 on IncN_1 plasmids in one M. wisconsensis and one E. marmotae. Forty-eight isolates (94%) exhibited a multidrug-resistance phenotype.ConclusionWe found a high occurrence of ESBL-producing Enterobacterales in wild game meat, suggesting wildlife habitat pollution and possible microbial contamination events occurring during skinning or cutting carcasses.

Antimicrobial resistance in Escherichia coli isolates from Japanese raccoon dogs (Nyctereutes viverrinus) in Kanagawa Prefecture, Japan: Emergence of extended-spectrum cephalosporin-resistant human-related clones

Introduction. Wild animals are one of the putative reservoirs of antimicrobial-resistant bacteria, but the significance of raccoon dogs remains to be investigated.Hypothesis. Raccoon dogs can be a reservoir of antimicrobial-resistant bacteria.Aim. This study aimed to explore the prevalence of antimicrobial resistance, mainly extended-spectrum cephalosporins resistance, in Escherichia coli isolates from faeces of 80 Japanese raccoon dogs in Kanagawa Prefecture, Japan.Methodology. All of the 80 faecal samples were streaked onto deoxycholate-hydrogen sulfate-lactose (DHL) and cefotaxime (CTX)-supplemented DHL (DHL-CTX) agars. Susceptibilities to ten antimicrobials were determined using the agar dilution method. Additionally, extended-spectrum β-lactamases (ESBLs) and AmpC-type β-lactamases (ABLs) were identified in addition to sequence types (STs), in ESC-resistant isolates by a polymerase chain reaction and sequencing.Results. Out of all the samples, 75 (93.8 %) and 20 (25.0 %) E. coli isolates were isolated by DHL and DHL-CTX agars, respectively. Significantly higher resistance rates to most of the drugs were found in DHL-CTX-derived isolates than DHL-derived isolates (P<0.01). Genetic analysis identified CTX-M-14 (n=6), CTX-M-2 (n=2), CTX-M-1 (n=1) and CTX-M-55 (n=1) as ESBLs, and CMY-2 (n=8) and DHA-1 (n=1) as ABLs in 20 DHL-CTX-derived isolates. Most of the detected STs were related to Japanese humans (i.e. ST10, ST58, ST69, ST131, ST357, ST648 and ST4038). Notably, this is the first report on ST69, ST131, ST155 and ST648, which are well-known international high-risk clones in Japanese raccoon dogs.Conclusion. Our findings underscore the need to understand the significance of raccoon dogs as an antimicrobial-resistant bacteria reservoir using one health approach.

Extended Spectrum- and Carbapenemase-Based β-Lactam Resistance in the Arabian Peninsula—A Descriptive Review of Recent Years

Antimicrobial resistance (AMR) is a global problem that also includes countries of the Arabian Peninsula. Of particular concern, is the continuing development of extended-spectrum β-lactamases (ESBLs) in the countries of this region. Additionally, antibiotic treatment options for ESBL-producing bacteria are becoming limited, primarily due to the continuing development of carbapenem resistance (CR), carbapenems being frequently used to treat such infections. An overview of recent publications (2018–2021) indicates the presence of ESBL and/or CR in patients and hospitals in most countries of the Arabian Peninsula, although the delay between microbial isolation and publication inevitably makes an accurate analysis of the current situation rather difficult. However, there appears to be greater emphasis on CR (including combined ESBL and CR) in recent publications. Furthermore, although publications from Saudi Arabia are the most prevalent, this may simply reflect the increased interest in ESBL and CR within the country. Enhanced ESBL/CR surveillance is recommended for all countries in the Arabian Peninsula.

CTX-M-Producing Bacteria Isolated from a Highly Polluted River System in Portugal

Enterobacteriaceae resistant to third-generation cephalosporins are a great concern for public health, as these are first-line drugs to treat infections. The production of carbapenemases and extended spectrum beta-lactamases (ESBLs) and/or the overexpression of AmpC β-lactamases are the main mechanisms of resistance to these antibiotics. Among the ESBLs, CTX-M β-lactamases are the most prevalent worldwide. Our aims were to determine the prevalence of cefotaxime-resistant Enterobacteriaceae along a heavily polluted river and characterize bla_CTX-M carriers. River water was collected in 11 sites along the main course and tributaries, in two sampling moments. Water quality was evaluated and a collection of cefotaxime-resistant isolates was obtained. bla_CTX-M carriers were characterized regarding phylogenetic affiliation, clonality, antibiotic susceptibility, gene diversity, and context. Water presented very low quality in all sites. From 147 cefotaxime-resistant isolates, 46% carried bla_CTX-M and were affiliated with Escherichia, Klebsiella, Enterobacter, and Citrobacter. Molecular typing revealed clonal isolates in different sites and over the two years, suggesting survival of the strains in the river or continuous pollution inputs from the same sources. Eight variants of bla_CTX-M were found, with bla_CTX-M-15 being the most prevalent (52.5%). Sites with a lower water quality showed the highest resistance rates and prevalence of bla_CTX-M, suggesting that river water may embody human health risks.

A walk on the wild side: Wild ungulates as potential reservoirs of multi-drug resistant bacteria and genes, including Escherichia coli harbouring CTX-M beta-lactamases

Extended-spectrum β-lactamases (ESBL)-producing Enterobacterales have been classified as critical priority pathogens by the World Health Organization (WHO). ESBL are universally distributed and, in 2006, were firstly reported on a wild animal. Understanding the relative contributions of wild animals to ESBL circulation in the environment is urgently needed. In this work, we have conducted a nationwide study in Portugal to investigate the occurrence of bacteria carrying clinically significant antimicrobial resistance genes (ARG), using widely distributed wild ungulates as model species. A total of 151 antimicrobial resistant-Enterobacterales isolates were detected from 181 wild ungulates: 50% (44/88) of isolates from wild boar (Sus scrofa), 40.3% (25/62) from red deer (Cervus elaphus), 41.4% (12/29) from fallow deer (Dama dama) and 100% (2/2) from mouflon (Ovis aries subsp. musimon). Selected isolates showed a diversified resistance profile, with particularly high values corresponding to ampicillin (71.5%) and tetracycline (63.6%). Enterobacterales strains carried bla_TEM, tetA, tetB, sul2, sul1 or dfrA1 ARG genes. They also carried bla_CTX-M-type genes, which are prevalent in human infections, namely CTX-M-14, CTX-M-15 and CTX-M-98. Strikingly, this is the first report of CTX-M-98 in wildlife. Almost 40% (n = 59) of Enterobacterales were multi-drug resistant. The diversity of plasmids carried by ESBL isolates was remarkable, including IncF, K and P. This study highlights the potential role of wild ungulates as environmental reservoirs of CTX-M ESBL-producing E. coli and in the spill-over of AMR bacteria and their determinants. Our findings suggest that wild ungulates are useful as strategic sentinel species of AMR in terrestrial environments, especially in response to potential sources of anthropogenic pollution, providing early warning of potential risks to human, animal and environmental health.

Serotype Diversity and Antimicrobial Resistance Profile of Salmonella enterica Isolates From Freshwater Turtles Sold for Human Consumption in Wet Markets in Hong Kong

Chelonians are recognized as a source of human salmonellosis through direct contact or consumption of their meat. Freshwater turtles sold for food are widely available in wet markets in Asia. In this pilot study, 50 turtles belonging to three species were randomly sampled from wet markets throughout Hong Kong. The turtles were humanely euthanised and their feces or the colon were sampled for Salmonella culture. The Salmonella isolates obtained were serotyped and examined for phenotypic antimicrobial resistance and the presence of antimicrobial resistance genes. The study reports a high prevalence (42%, 95% CI: 29.4–55.8) and considerable serotype diversity of Salmonella among turtles sold in wet markets. The most common among the 11 serotypes isolated were S. Oranienburg and S. Thompson, which have been reported in turtles previously. The serotype S. Manhattan is reported in chelonians for the first time. Resistance to streptomycin and chloramphenicol was common, despite the latter being banned from aquaculture in mainland China since 2002. Resistance against fluoroquinolones and third-generation cephalosporins which represent first-line treatment options for salmonellosis was also observed. The multidrug-resistance gene cfr is identified for the first time in Salmonella. This is a worrying finding as it indicates an expansion of the cfr reservoir and potential horizontal spread to other bacteria. The results of this study emphasize the need for close surveillance of Salmonella from turtles sold as food and better regulation of turtle farming to safeguard public health and improve animal welfare.

Wild Boars as an Indicator of Environmental Spread of ESβL-Producing Escherichia coli

Antimicrobial resistance (AMR) represents an increasing issue worldwide, spreading not only in humans and farmed animals but also in wildlife. One of the most relevant problems is represented by Extended-Spectrum Beta-Lactamases (ESβLs) producing Escherichia coli because they are the cause of important infections in human. Wild boars (Sus scrofa) as a source of ESβLs attracted attention due to their increasing density and their habits that lead them to be at the human-livestock-wildlife interface. The aim of this study was to increase the knowledge about the ESβLs E. coli strains carried by wild boars living in a particularly high-density area of Northern Italy. The analysis of 60 animals allowed to isolate 16 ESβL-producing E. coli strains (prevalence 23.3%), which were characterised from a phenotypical and molecular point of view. The overall analysis revealed that the 16 isolates were all not only ESβL producers but also multidrug resistant and carried different types of plasmid replicons. The genome analysis performed on a subset of isolates confirmed the heterogeneity observed with pulsed-field gel electrophoresis (PFGE) and highlighted the presence of two pandemic sequence types, ST131 and ST10, with different collections of virulence factors. The genomic context of ESβL genes further evidenced that all of them were surrounded by transposons and insertion sequences, suggesting the possibility to exchange AMR genes. Overall, this study shows the worrying dissemination of ESβL-producing E. coli in wild boars in Northern Italy, suggesting the role of these animals as a spreader of AMR and their inclusion in surveillance programmes, to shed light on the “One Health” complex interactions.

ESBL-Producing Moellerella wisconsensis—The Contribution of Wild Birds in the Dissemination of a Zoonotic Pathogen

Simple Summary

Moellerella wisconsensis is a potentially zoonotic pathogen that has sporadically been isolated from animals and humans. In the present study, we describe the occurrence of the organism among 445 wild bird and 2000 human fecal samples, in the context of an investigation regarding antimicrobial resistant bacteria in Greece. According to our results, 0.9% (n = 4) of the examined wild birds were found to be colonized by M. wisconsensis, while no human was a carrier of the bacterium. Out of the total number of four M. wisconsensis strains that we detected, three presented resistance to 3rd generation cephalosporins, were phenotypically confirmed to produce extended spectrum beta lactamases (ESBLs) and harbored bla_CTX-M-1. Resistance to tetracyclines, aminoglycosides and trimethoprim/sulfamethoxazole was additionally detected in three, two and one of the ESBL isolates, respectively. This is the first report that presents the dissemination of M. wisconsensis in wild bird from Greece and describes CTX-M-1 production in multidrug resistant wild birds’ isolates of this bacterial species.

Abstract

Moellerella wisconsensis is an Enterobacteriaceae with unclarified dispersion and pathogenicity. During an ongoing investigation about antimicrobial resistance in Greece, the occurrence of M. wisconsensis was evaluated among wild birds and humans. A total of 445 wild bird and 2000 human fecal samples were collected and screened for the presence of the organism. Subsequently, all M. wisconsensis strains were phenotypically and molecularly characterized regarding their antimicrobial resistance characteristics. Four M. wisconsensis were isolated from a common pheasant (Phasianus colchicus), two Eurasian magpies (Pica pica) and a great white-fronted goose (Anser albifrons). Among these four strains, the three latter presented resistance to 3rd generation cephalosporins, were phenotypically confirmed to produce ESBLs and were found to harbor bla_CTX-M-1. The three ESBL isolates additionally exhibited resistance to tetracyclines, while resistance to aminoglycosides was detected in two of them and to trimethoprim/sulfamethoxazole in one. No Moellerella wisconsensis strains were retrieved from the human samples tested. This is the first report that provides evidence of M. wisconsensis dissemination among wild birds in Greece, describing CTX-M-1 production in multidrug resistant wild birds’ isolates of this bacterial species.

Resistance Patterns, mcr-4 and OXA-48 Genes, and Virulence Factors of Escherichia coli from Apennine Chamois Living in Sympatry with Domestic Species, Italy

The aim of this study was to determine and characterize potential resistance mechanisms against selected Critically Important Antibiotics in Escherichia coli isolates collected from wild and domestic ruminants living in the Maiella National Park, in Central Italy. A total of 38 isolates were obtained from red deer, Apennine chamois, cattle, sheep, and goats grazing in lands with different levels of anthropic pressure. Antimicrobial susceptibility was determined by Minimal Inhibitory Concentration testing, showing phenotypic resistance to colistin, meropenem, or ceftazidime in 9 isolates along with one bacterial strain being resistant to three of the tested antibiotics. In addition, the biomolecular assays allowed the amplification of the genes conferring the colistin (mcr-4), the carbapenems (OXA-48), penicillins and cephalosporins (TEM, SHV, CMY-1, CMY-2) resistance. In order to describe the potential pathogenicity of isolates under study, virulence genes related to Shiga toxin-producing (STEC) and enteropathogenic (EPEC) pathovars were identified. This study is the first report of mcr-4 and OXA-48 genes in resistant E. coli harboring virulence genes in Italian wildlife, with special regard to Apennine chamois and red deer species. The multidisciplinary approach used in this study can improve the early detection of emerging antibiotic resistance determinants in human-animal-environment interfaces by means of wildlife monitoring.

Extended-Spectrum β-Lactam Resistant Klebsiella pneumoniae and Escherichia coli in Wild European Hedgehogs (Erinaceus europeus) Living in Populated Areas

Simple Summary

The alarming emergence of antimicrobial resistance (AMR) in human and veterinary medicine has activated awareness for monitoring the levels of AMR pollution in the environment and wildlife. European hedgehogs (Erinaceus europaeus) are common wild species habiting urban areas in Europe. In this study, the occurrence and distribution of extended-spectrum β-lactam (ESBL) resistant enterobacteria and AMR genes were assessed in wild European hedgehogs in Catalonia, NE Spain. The results showed that 36.8% of the animals were detected as carriers of β-lactamase/carbapenemase resistance genes, with a special occurrence of human nosocomial bacteria such as Klebsiella pneumoniae, Escherichia coli, and Citrobacter freundii. In addition, more than half of the enterobacteria presented a multidrug resistance (MDR) phenotype and 31% of the isolates had an extended XDR profile. No differences in the spatial distribution of animals with AMR genes were observed within the study region. The results of this study suggest that the close contact with human areas predispose the transmission of AMR genes to wild hedgehogs because they either inhabit and/or feed in an anthropogenic environment. In conclusion, hedgehogs could be good sentinels or bioindicators of AMR environmental pollution, especially in highly populated areas with high human activity.

Abstract

Wildlife has been suggested to be a good sentinel of environmental health because of its close interaction with human populations, domestic animals, and natural ecosystems. The alarming emergence of antimicrobial resistance (AMR) in human and veterinary medicine has activated/triggered the awareness of monitoring the levels of AMR pollution in wildlife. European hedgehogs (Erinaceus europaeus) are common wild species habiting urban areas in Europe. However, there are few studies conducted in hedgehogs as reservoirs of AMR bacteria or genes. The aim of this study was to assess the occurrence and distribution of ESBL, AmpC, and carbapenem-resistant enterobacteria and AMR genes in wild European hedgehogs in Catalonia, a densely populated region of NE Spain. A total of 115 hedgehogs admitted at the Wildlife Rehabilitation Center of Torreferrussa were studied. To our knowledge, this is the first description of β-lactam resistant enterobacteria in wild hedgehogs. Interestingly, 36.8% (42/114) of the animals were detected as carriers of β-lactamase/carbapenemase resistance genes. Klebsiella spp. (59.6%), and specifically K. pneumoniae (84.6%), were the bacteria with the highest proportion of resistance genes, followed by E. coli (34.6%) and C. freundii (5.8%). The most frequently detected genetic variants were blaCTX-M-15 (19.3%), blaSHV-28 (10.5%), blaCMY-1 (9.7%), blaCMY-2 (8.8%), and blaOXA-48 (1.7%). In addition, 52% (27/52) of the isolates presented a multidrug resistance (MDR) phenotype and 31% had an extended drug resistance (XDR) profile. No clustering of animals with AMR genes within the study region was shown in the spatial analysis, nor differences in the proportion of positive animals among regions, were detected. The results of this study suggest that wild European hedgehogs could be good sentinels of AMR environmental pollution, especially in areas with a high human population density, because they either inhabit and/or feed in an anthropogenic environment. In conclusion, it is crucial to raise awareness of the strong interconnection between habitats and compartments, and therefore this implies that AMR issues must be tackled under the One Health approach.