Detection of antibiotic resistant enterococci and Escherichia coli in free range Iberian Lynx (Lynx pardinus)

American crocodiles (Crocodylus acutus: Reptilia: Crocodilidae) visiting the facilities of a freshwater aquaculture of the Northern Pacific region, Costa Rica, carry tetracycline-resistant Escherichia coli

Apex predators are exposed to antimicrobial compounds and resistant microbes, which accumulate at different trophic levels of the related ecosystems. The study aimed to characterize the presence and the antimicrobial resistance patterns of fecal Escherichia coli isolated from cloacal swab samples obtained from wild-living American crocodiles (Crocodylus acutus) (n = 53). Sampling was conducted within the distinctive context of a freshwater-intensive aquaculture farm in Costa Rica, where incoming crocodiles are temporarily held in captivity before release. Phenotypic antimicrobial susceptibility profiles were determined in all isolates, while resistant isolates were subjected to whole-genome sequencing and bioinformatics analyses. In total, 24 samples contained tetracycline-resistant E. coli (45.3%). Isolates carried either tet(A), tet(B), or tet(C) genes. Furthermore, genes conferring resistance to ß-lactams, aminoglycosides, fosfomycin, sulfonamides, phenicol, quinolones, trimethoprim, and colistin were detected in single isolates, with seven of them carrying these genes on plasmids. Genome sequencing further revealed that sequence types, prevalence of antibiotic resistance carriage, and antibiotic resistance profiles differed between the individuals liberated within the next 24 h after their capture in the ponds and those liberated from enclosures after longer abodes. The overall presence of tetracycline-resistant E. coli, coupled with potential interactions with various anthropogenic factors before arriving at the facilities, hinders clear conclusions on the sources of antimicrobial resistance for the studied individuals. These aspects hold significant implications for both the aquaculture farm's biosecurity and the planning of environmental monitoring programs using such specimens. Considering human-crocodile conflicts from the One Health perspective, the occurrence of antimicrobial resistance underscores the importance of systematical surveillance of antibiotic resistance development in American crocodiles.

Antibiotic-Resistant Bacteria Dissemination in the Wildlife, Livestock, and Water of Maiella National Park, Italy

Antimicrobial resistance (AMR) is a global health concern that has been linked to humans, animals, and the environment. The One Health approach highlights the connection between humans, animals, and the environment and suggests that a multidisciplinary approached be used in studies investigating AMR. The present study was carried out to identify and characterize the antimicrobial resistance profiles of bacteria isolated from wildlife and livestock feces as well as from surface water samples in Maiella National Park, Italy. Ecological and georeferenced data were used to select two sampling locations, one where wildlife was caught within livestock grazing areas (sympatric group) and one where wildlife was caught outside of livestock grazing areas (non-sympatric group). Ninety-nine bacterial isolates from 132 feces samples and seven isolates from five water samples were collected between October and December 2019. The specimens were examined for species identification, antibiotic susceptibility and molecular detection of antibiotic resistance. Forty isolates were identified as Escherichia coli, forty-eight as Enterococcus spp., eight as Streptococcus spp. and ten as other gram-negative bacteria. Phenotypic antibiotic resistance to at least one antimicrobial agent, including some antibiotics that play a critical role in human medicine, was detected in 36/106 (33.9%, 95% CI: 25-43) isolates and multidrug resistance was detected in 9/106 isolates (8.49%, 95% CI: 3.9-15.5). In addition, genes associated with antibiotic resistance were identified in 61/106 (57.55%, 95% CI: 47.5-67) isolates. The samples from sympatric areas were 2.11 (95% CI: 1.2-3.5) times more likely to contain resistant bacterial isolates than the samples from non-sympatric areas. These data suggest that drug resistant bacteria may be transmitted in areas where wildlife and livestock cohabitate. This emphasizes the need for further investigations focusing on the interactions between humans, wildlife, and the environment, the results of which can aid in the early detection of emerging AMR profiles and possible transmission routes.

Dissemination of antimicrobial-resistant isolates of Salmonella spp. in wild boars and its relationship with management practices

Antimicrobial resistance (AMR) is a global concern and controlling its spread is critical for the effectiveness of antibiotics. Members of the genus Salmonella are broadly distributed, and wild boar may play an important role in its circulation between peri-urban areas and the environment, due to its frequent interactions both with livestock or human garbage. As the population of these animals is rising due to management on certain hunting estates or the absence of natural predators, the aim of the present work is to identify the mechanisms of AMR present and/or expressed in Salmonella spp. from wild boar populations and to determine the possible role of management-related factors applied to different game estates located in central Spain. The detection of Salmonella spp. was carried out in 121 dead wild boar from 24 game estates, and antimicrobial resistance traits were determined by antibiotic susceptibility testing and screening for their genetic determinants. The effects of feeding supplementation, the proximity of livestock, the existence of a surrounding fence and the density of wild boar on the AMR of the isolates were evaluated. The predominant subspecies and serovar found were S. enterica subsp. enterica (n = 69) and S. choleraesuis (n = 33), respectively. The other subspecies found were S. enterica subsp. diarizonae, S. enterica subsp. salamae and S. enterica subsp. houtenae. AMR was common among isolates (75.2%) and 15.7% showed multi drug resistance (MDR). Resistance to sulphonamides was the most frequent (85.7%), as well as sul1 which was the AMR determinant most commonly found. Plasmids appeared in 38.8% of the isolates, with IncHI1 being the replicon detected with the highest prevalence. The AMR of the isolates increased when the animals were raised with feeding supplementation and enclosed by fences around the estates.

PREVALENCE AND ANTIMICROBIAL RESISTANCE PATTERNS OF SALMONELLA SPP. IN TWO FREE-RANGING POPULATIONS OF EASTERN BOX TURTLES (TERRAPENE CAROLINA CAROLINA)

Salmonellosis is an important zoonotic infection, and exposure to pet reptiles has been implicated in several human outbreaks. Although several studies report a low prevalence of salmonellae in free-ranging chelonians, they may serve as a reservoir. In spring and summer of 2013 and 2019, free-ranging eastern box turtles (Terrapene carolina carolina) from populations in Illinois (rural) and Tennessee (urban) were collected through canine and visual search. Cloacal swab samples were collected from each turtle, selectively enriched with tetrathionate broth, then plated on selective and differential media to isolate Salmonella spp. Genus was confirmed via MALDI-TOF MS and antibiotic sensitivities were performed. Isolates were serotyped by the National Veterinary Services Laboratory. Of the 341 turtles sampled, Salmonella spp. were detected in nine individuals (2.64%; 95% CI: 1.2-5.0%). The isolates included five different serovars: Anatum (n = 2), Newport (n = 2), Thompson (n = 1), Bareilly (n = 2), and Hartford (n = 2). Salmonella spp. were detected from six animals in 2013 (3.19%, 95% CI: 1.2-6.8%) and three in 2019 (1.96%, 95% CI: 0.4-5.6%). There was no significant difference in prevalence between state, (P = 0.115), Illinois locations (P = 0.224), season (P = 0.525), year (P = 0.297), sex (P = 0.435), or age class (P = 0.549). The health of Salmonella-positive and -negative turtles was not significantly different, as assessed through hematology and plasma biochemistry (P > 0.05), indicating asymptomatic carrier status. The low prevalence detected in this study likely concludes that free-ranging eastern box turtles play a minimal role in the spread of salmonellae. However, the identified serotypes are potentially human- and animal-pathogenic. Documenting the prevalence of Salmonella serotypes in animal indicators furthers our understanding of their spread between humans, animal agriculture, and the environment.

Faecal microbiota and antibiotic resistance genes in migratory waterbirds with contrasting habitat use

Migratory birds may have a vital role in the spread of antimicrobial resistance across habitats and regions, but empirical data remain scarce. We investigated differences in the gut microbiome composition and the abundance of antibiotic resistance genes (ARGs) in faeces from four migratory waterbirds wintering in South-West Spain that differ in their habitat use. The white stork Ciconia ciconia and lesser black-backed gull Larus fuscus are omnivorous and opportunistic birds that use highly anthropogenic habitats such as landfills and urban areas. The greylag goose Anser anser and common crane Grus grus are herbivores and use more natural habitats. Fresh faeces from 15 individuals of each species were analysed to assess the composition of bacterial communities using 16S rRNA amplicon-targeted sequencing, and to quantify the abundance of the Class I integron integrase gene (intI1) as well as genes encoding resistance to sulfonamides (sul1), beta-lactams (bla_TEM, bla_KPC and bla_NDM), tetracyclines (tetW), fluoroquinolones (qnrS), and colistin (mcr-1) using qPCR. Bacterial communities in gull faeces were the richest and most diverse. Beta diversity analysis showed segregation in faecal communities between bird species, but those from storks and gulls were the most similar, these being the species that regularly feed in landfills. Potential bacterial pathogens identified in faeces differed significantly between bird species, with higher relative abundance in gulls. Faeces from birds that feed in landfills (stork and gull) contained a significantly higher abundance of ARGs (sul1, bla_TEM, and tetW). Genes conferring resistance to last resort antibiotics such as carbapenems (bla_KPC) and colistin (mcr-1) were only observed in faeces from gulls. These results show that these bird species are reservoirs of antimicrobial resistant bacteria and suggest that waterbirds may disseminate antibiotic resistance across environments (e.g., from landfills to ricefields or water supplies), and thus constitute a risk for their further spread to wildlife and humans.

Escherichia coli Antibiotic Resistance Patterns from Co-Grazing and Non-Co-Grazing Livestock and Wildlife Species from Two Farms in the Western Cape, South Africa

Although limited, studies have found conflicting results on whether co-grazing results in significant antibiotic resistance transfer between species. This type of farming system can act as a vector in the geographical spread of antibiotic-resistant bacteria in the environment. The aim of this study was to determine the antibiotic-resistant patterns between co-grazing and non-co-grazing livestock and wildlife species in South Africa. Escherichia coli was isolated from the faeces of various wildlife and livestock species from two farms in South Africa and was tested for antibiotic resistance using the Kirby–Bauer disk diffusion method against chloramphenicol, nalidixic acid, ampicillin, streptomycin, sulphafurazole, and tetracycline. A selection of some common antibiotic-resistant genes (blaCMY, aadA1, sul1, sul2, tetA, and tetB) were detected using PCR. The E. coli isolates from wildlife and livestock that co-grazed showed no significant differences in antibiotic resistance patterns. However, this was not the case for tetracycline resistance as the livestock isolates were significantly more resistant than the co-grazing wildlife isolates. The E. coli isolates from the non-co-grazing livestock and wildlife had significant differences in their antibiotic susceptibility patterns; the wildlife E. coli isolates were significantly more resistant to sulphafurazole and streptomycin than the livestock isolates, whilst those isolated from the cattle were significantly more resistant to ampicillin than the wildlife and sheep isolates. The results of this study suggest that there could be an exchange of antibiotic-resistant bacteria and genes between livestock and wildlife that co-graze.

Multidrug Resistance in Enterococci Isolated From Wild Pampas Foxes (Lycalopex gymnocercus) and Geoffroy's Cats (Leopardus geoffroyi) in the Brazilian Pampa Biome

Enterococci are ubiquitous microorganisms present in various environments and within the gastrointestinal tracts of humans and other animals. Notably, fecal enterococci are suitable indicators for monitoring antimicrobial resistance dissemination. Resistant bacterial strains recovered from the fecal samples of wild animals can highlight important aspects of environmental disturbances. In this report, we investigated antimicrobial susceptibility as well as resistance and virulence genes in fecal enterococci isolated from wild Pampas foxes (Lycalopex gymnocercus) (n = 5) and Geoffroy's cats (Leopardus geoffroyi) (n = 4) in the Brazilian Pampa biome. Enterococci were isolated from eight out of nine fecal samples and Enterococcus faecalis was identified in both animals. However, E. faecium and E. durans were only detected in Pampas foxes, while E. hirae was only detected in Geoffroy's cats. Antimicrobial susceptibility analysis showed resistance to rifampicin (94%), erythromycin (72.6%), ciprofloxacin/norfloxacin (40%), streptomycin (38%), and tetracycline (26%). The high frequency of multidrug-resistant enterococci (66%) isolated in this study is a matter of concern since these are wild animals with no history of therapeutic antibiotic exposure. The tetM/tetL and msrC/ermB genes were detected in most tetracycline- and erythromycin-resistant enterococci, respectively. The gelE, ace, agg, esp, and clyA virulence genes were also detected in enterococci. In conclusion, our data suggest that habitat fragmentation and anthropogenic activities in the Pampa biome may contribute to high frequencies of multidrug-resistant enterococci in the gut communities of wild Pampas foxes and Geoffroy's cats. To the best of the authors' knowledge, this is the first report of antimicrobial-resistant enterococci in the Pampa biome.

Temporal and geographical research trends of antimicrobial resistance in wildlife - A bibliometric analysis

Antimicrobial resistance (AMR) is a complex and global problem. Despite the growing literature on AMR in the medical and veterinary settings, there is still a lack of knowledge on the wildlife compartment. The main aim of this study was to report the global trends in AMR research in wildlife, through a bibliometric study of articles found in the Web of Science database. Search terms were "ANTIMICROBIAL" OR "ANTIBIOTIC" AND "RESISTANT" OR "RESISTANCE" and "WILDLIFE" "MAMMAL" "BIRD" "REPTILE" "FERAL" "FREE RANGE". A total of 219 articles were obtained, published between 1979 and 2019. A rising interest in the last decades towards this topic becomes evident. During this period, the scientific literature was distributed among several scientific areas, however it became more multidisciplinary in the last years, focusing on the "One Health" paradigm. There was a geographical bias in the research outputs: most published documents were from the United States, followed by Spain, Portugal and the United Kingdom. The most productive institutions in terms of publication number were located in Portugal and Spain. An important level of international collaboration was identified. An analysis of the main keywords showed an overall dominance of "AMR", "E. coli", "genes", "prevalence", "bacteria", "Salmonella spp." and "wild birds". This is the first study providing a global overview of the spatial and temporal trends of research related to AMR in wildlife. Given the growth tendency over the last years, it is envisaged that scientific production will expand in the future. In addition to offering a broad view of the existing research trends, this study identifies research gaps both in terms of geographical incidence and in relation to unexplored subtopics. Unearthing scientific areas that should be explored in the future is key to designing new strategic research agendas in AMR research in wildlife and to inform funding programs.

Occurrence of ESBL-producing Escherichia coli in soils subjected to livestock grazing in Azores archipelago: an environment-health pollution issue?

Antibiotics are successful drugs used in human and animal therapy; however, they must be considered as environmental pollutants. This study aims to isolate and characterize the extended-spectrum β-lactamase (ESBL) producing Escherichia coli soil from Azores Archipelago subjected to livestock agricultural practices. Twenty-four soil samples were collected from three different pasture systems with different number of cattle heads, and from a control site. Antibiotic susceptibility method was performed by Kirby-Bauer disk diffusion method against 16 antibiotics, and the presence of genes encoding lactamases, antimicrobial resistance genes, virulence factors, and phylogenetic groups was determined by polymerase chain reaction (PCR). Nine ESBLs were recovered from the three grazing sites, and all isolates presented the beta-lactamase genes bla_CTX-M-3 and bla_SHV. E. coli isolates were resistance to tetracycline and streptomycin and harbored the tetB, strA, and strB genes. One isolate also showed resistance to sulfonamides, and the genes sul1 and sul2 were detected. The isolates were grouped into the following phylogenic groups: B1 (n = 6), D (n = 2), and A (n = 1). The presence of antibiotics and resistance genes in soils may be the source to the development of antimicrobial resistance, which may have negative consequences in human and animal health.

A significant number of multi-drug resistant Enterococcus faecalis in wildlife animals; long-term consequences and new or known reservoirs of resistance?

As the last link in the food chain in a complex ecosystem covering at least three different environmental spheres, species of wildlife carnivorous mammals constitute a group accumulating potential pathogens and factors resulting from human activity, including the emergence of drug resistance. Therefore, the aim of this study was to evaluate the level and range of resistance in commensal E. faecalis isolated from wildlife carnivorous mammals and genetic relationships in terms of the source of these strains as well as resistance and virulence genes. Differentiation between strains was performed based on ADSRRS-fingerprinting method. The results showed that almost half of the tested animals (48%) were carriers of at least one multidrug resistant E. faecalis strain. Moreover, 44% of MDR-positive animals showed two or three strains differing in both the genotype and the resistance phenotype. A significant percentage of strains were resistant to high-level aminoglycosides (from 20% to even 57.5%). The resistance and virulence gene profiles showed a rich panel of genes closely related to isolates from nosocomial infection and from livestock animals. The presence of the same genotypes in different hosts reflects not only a possible transfer of genes between E. faecalis strains but also exchange of strains between animals. The obtained results reflect a very high level of contamination of animals that are not subjected to targeted antibiotic therapy, which may suggest the degree of pollution of the environment. Wildlife animals and their environment can be a link closing the circulation cycle of genes and even epidemiologically important strains; therefore, there is a high risk that this pool will never run out and will be maintained at a high level.

Detection of Antibiotic Resistance in Escherichia coli Strains: Can Fish Commonly Used in Raw Preparations such as Sushi and Sashimi Constitute a Public Health Problem?

HIGHLIGHTS

Forty-five E. coli isolates were recovered from fresh fish. Three of the E. coli isolates produced ESBL. ESBL-producing E. coli isolates harbored the bla_CTX-M-1 and bla_TEM genes. The presence of ESBL-producing E. coli may represent a serious public health problem.

Antibiotic Susceptibility and Virulence Factors in Escherichia coli from Sympatric Wildlife of the Apuan Alps Regional Park (Tuscany, Italy)

Today a growing number of studies are focusing on antibiotic resistance in wildlife. This is due to the potential role of wild animals as reservoirs and spreaders of pathogenic and resistant bacteria. This study focused on isolating and identifying Escherichia coli from the feces of wild animals living in the Apuan Alps Regional Park (Tuscany, Italy) and evaluating some of their antibiotic resistance and pathogenicity traits. Eighty-five fecal samples from different species were studied. Seventy-one E. coli were identified by matrix assisted laser desorption ionization-time of flight mass spectrometry analysis, subjected to antibiograms and polymerase chain reaction for the detection of antibiotic resistance genes and pathogenicity factors. The highest resistance rates were found against cephalothin (39.4%) and ampicillin (33.8%), followed by amoxicillin/clavulanic acid (15.5%), streptomycin (12.7%), and tetracycline (5.6%). Regarding resistance genes, 39.4% of the isolates were negative for all tested genes. The remaining isolates were positive for bla_CMY-2, sul2, strA-strB and aadA1, tet(B), and tet(A), encoding resistance to beta-lactams, trimethoprim/sulfamethoxazole, streptomycin, and tetracycline, respectively. With regard to virulence factors, 63.4% of the isolates were negative for all genes; 21.1% carried astA alone, which is associated with different pathotypes, 9.9% carried both escV and eaeA (aEPEC); single isolates (1.4%) harbored escV (aEPEC), escV associated with astA and eaeA (aEPEC), astA with stx2 and hlyA (EHEC) or astA and stx1, stx2, and hlyA (EHEC). These results show that wildlife from nonanthropized environments can be a reservoir for antibiotic-resistant microorganisms and suggest the need for a deeper knowledge on their origin and diffusion mechanisms through different ecological niches.

Antimicrobial Resistance in Enterococcus spp. of animal origin

Enterococci are natural inhabitants of the intestinal tract in humans and many animals, including food-producing and companion animals. They can easily contaminate the food and the environment, entering the food chain. Moreover, Enterococcus is an important opportunistic pathogen, especially the species E. faecalis and E. faecium, causing a wide variety of infections. This microorganism not only contains intrinsic resistance mechanisms to several antimicrobial agents, but also has the capacity to acquire new mechanisms of antimicrobial resistance. In this review we analyze the diversity of enterococcal species and their distribution in the intestinal tract of animals. Moreover, resistance mechanisms for different classes of antimicrobials of clinical relevance are reviewed, as well as the epidemiology of multidrug-resistant enterococci of animal origin, with special attention given to beta-lactams, glycopeptides, and linezolid. The emergence of new antimicrobial resistance genes in enterococci of animal origin, such as optrA and cfr, is highlighted. The molecular epidemiology and the population structure of E. faecalis and E. faecium isolates in farm and companion animals is presented. Moreover, the types of plasmids that carry the antimicrobial resistance genes in enterococci of animal origin are reviewed.

Antimicrobial Resistance in Escherichia coli

Multidrug resistance in Escherichia coli has become a worrying issue that is increasingly observed in human but also in veterinary medicine worldwide. E. coli is intrinsically susceptible to almost all clinically relevant antimicrobial agents, but this bacterial species has a great capacity to accumulate resistance genes, mostly through horizontal gene transfer. The most problematic mechanisms in E. coli correspond to the acquisition of genes coding for extended-spectrum β-lactamases (conferring resistance to broad-spectrum cephalosporins), carbapenemases (conferring resistance to carbapenems), 16S rRNA methylases (conferring pan-resistance to aminoglycosides), plasmid-mediated quinolone resistance (PMQR) genes (conferring resistance to [fluoro]quinolones), and mcr genes (conferring resistance to polymyxins). Although the spread of carbapenemase genes has been mainly recognized in the human sector but poorly recognized in animals, colistin resistance in E. coli seems rather to be related to the use of colistin in veterinary medicine on a global scale. For the other resistance traits, their cross-transfer between the human and animal sectors still remains controversial even though genomic investigations indicate that extended-spectrum β-lactamase producers encountered in animals are distinct from those affecting humans. In addition, E. coli of animal origin often also show resistances to other-mostly older-antimicrobial agents, including tetracyclines, phenicols, sulfonamides, trimethoprim, and fosfomycin. Plasmids, especially multiresistance plasmids, but also other mobile genetic elements, such as transposons and gene cassettes in class 1 and class 2 integrons, seem to play a major role in the dissemination of resistance genes. Of note, coselection and persistence of resistances to critically important antimicrobial agents in human medicine also occurs through the massive use of antimicrobial agents in veterinary medicine, such as tetracyclines or sulfonamides, as long as all those determinants are located on the same genetic elements.

Study of the spread of antimicrobial-resistant Enterobacteriaceae from wild mammals in the National Park of Aspromonte (Calabria, Italy)

Antimicrobial-resistant (AMR) bacteria are a threat to global health. Epidemiological studies are necessary to gain a more detailed understanding of the transmission modality of resistant bacteria to wild animals and their diffusion into the environment to ensure a broader evaluation of the epidemiological role of wildlife. The study aimed to identify little-known epidemiological aspects by focusing on the isolation of Enterobacteriaceae in order to bring knowledge on the bacterial flora of wild mammals living in the National Park of Aspromonte (Calabria, Italy). Two hundred twenty-five faecal samples of wild mammals were collected and submitted to standard bacteriological examination for Enterobacteriaceae detection. Isolates were identified by mass spectrometry MALDI-TOF (matrix assisted laser desorption/ionisation - time of fligt mass spectrometry). The 30 isolates showing the highest number of resistances were screened for Extended Spectrum Beta Lactamase (ESBL) production. Antimicrobial susceptibility testing of the bacterial isolates was performed by the disk diffusion method. Two hundred sixty-three strains were isolated. The most frequently recovered bacterial species were Hafnia alvei, Escherichia coli and Citrobacter spp.. Potentially pathogenic species including Salmonella spp., Yersinia enterocolitica and Serratia marcescens have also been identified. Isolates displayed significant frequencies of antibiotic resistance. The resistance to amoxicillin (71.4%) was the most frequent, followed by amoxicillin/clavulanic acid (55.5%), ampicillin (49.8%), streptomycin (35.7%), doxycycline (16.3%), tobramycin (15.2%), tetracycline (13.3%) and gentamicin (10.6%). Nine strains showed resistance to imipenem and 1 to meropenem. All isolates were negative for the presence of ESBL-encoding genes. Wild animals can be regarded as sentinel species and used as environmental health indicators.

A Decade-Long Commitment to Antimicrobial Resistance Surveillance in Portugal

Antimicrobial resistance (AMR) is a worldwide problem with serious health and economic repercussions. Since the 1940s, underuse, overuse, and misuse of antibiotics have had a significant environmental downside. Large amounts of antibiotics not fully metabolized after use in human and veterinary medicine, and other applications, are annually released into the environment. The result has been the development and dissemination of antibiotic-resistant bacteria due to many years of selective pressure. Surveillance of AMR provides important information that helps in monitoring and understanding how resistance mechanisms develop and disseminate within different environments. Surveillance data is needed to inform clinical therapy decisions, to guide policy proposals, and to assess the impact of action plans to fight AMR. The Functional Genomics and Proteomics Unit, based at the University of Trás-os-Montes and Alto Douro in Vila Real, Portugal, has recently completed 10 years of research surveying AMR in bacteria, mainly commensal indicator bacteria such as enterococci and Escherichia coli from the microbiota of different animals. Samples from more than 75 different sources have been accessed, from humans to food-producing animals, pets, and wild animals. The typical microbiological workflow involved phenotypic studies followed by molecular approaches. Throughout the decade, 4,017 samples were collected and over 5,000 bacterial isolates obtained. High levels of AMR to several antimicrobial classes have been reported, including to β-lactams, glycopeptides, tetracyclines, aminoglycosides, sulphonamides, and quinolones. Multi-resistant strains, some relevant to human and veterinary medicine like extended-spectrum β-lactamase-producing E. coli and vancomycin-resistant enterococci, have been repeatedly isolated even in non-synanthropic animal species. Of particular relevance are reports of AMR bacteria in wildlife from natural reserves and endangered species. Future work awaits as this threatening yet unsolved problem persists. GRAPHICAL ABSTRACTSummary diagram of the antimicrobial resistance surveillance work developed by the UTAD Functional Genomics and Proteomics Unit.

Determinants encoding fimbriae type 1 in fecal Escherichia coli are associated with increased frequency of bacteriocinogeny

Background

To screen whether E. coli strains encoding type 1 fimbriae, isolated from fecal microflora, produce bacteriocins more often relative to fimA-negative E. coli strains of similar origin.

Methods

PCR assays were used to detect presence of genes encoding 30 bacteriocin determinants (23 colicin- and 7 microcin-encoding genes) and 18 virulence determinants in 579 E. coli strains of human and animal origin isolated from hospitals and animal facilities in the Czech and Slovak Republic. E. coli strains were also classified into phylogroups (A, B1, B2 and D).

Results

fimA-negative E. coli strains (defined as those possessing none of the 18 tested virulence determinants) were compared to fimA-positive E. coli strains (possessing fimA as the only detected virulence determinant). Strains with identified bacteriocin genes were more commonly found among fimA-positive E. coli strains (35.6 %) compared to fimA-negative E. coli strains (21.9 %, p < 0.01) and this was true for both colicin and microcin determinants (p = 0.02 and p < 0.01, respectively). In addition, an increased number of strains encoding colicin E1 were found among fimA-positive E. coli strains (p < 0.01).

Conclusions

fimA-positive E. coli strains produced bacteriocins (colicins and microcins) more often compared to fimA-negative strains of similar origin. Since type 1 fimbriae of E. coli have been shown to mediate adhesion to epithelial host cells and help colonize the intestines, bacteriocin synthesis appears to be an additional feature of colonizing E. coli strains.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-015-0530-5) contains supplementary material, which is available to authorized users.

Lack of dissemination of acquired resistance to β-lactams in small wild mammals around an isolated village in the Amazonian forest

In this study, we quantitatively evaluated the spread of resistance to β-lactams and of integrons in small rodents and marsupials living at various distances from a point of antibiotic's use. Rectal swabs from 114 animals were collected in Trois-Sauts, an isolated village in French Guiana, and along a 3 km transect heading through the non-anthropized primary forest. Prevalence of ticarcillin-resistant enterobacteria was 36% (41/114). Klebsiella spp., naturally resistant to ticarcillin, were found in 31.1% (23/73) of animals from the village and in an equal ratio of 31.7% (13/41) of animals trapped along the transect. By contrast Escherichia coli with acquired resistance to ticarcillin were found in 13.7% (10/73) of animals from the village and in only 2.4% (1/41) of those from the transect (600 m from the village). There was a huge diversity of E. coli and Klebsiella pneumoniae strains with very unique and infrequent sequence types. The overall prevalence of class 1 integrons carriage was 19.3% (22/114) homogenously distributed between animals from the village and the transect, which suggests a co-selection by a non-antibiotic environmental factor. Our results indicate that the anthropogenic acquired antibiotic resistance did not disseminate in the wild far from the point of selective pressure.

Acquired antibiotic resistance among wild animals: the case of Iberian Lynx (Lynx pardinus)

The selective pressure generated by the clinical misuse of antibiotics has been the major driving force leading to the emergence of antibiotic resistance among bacteria. Antibiotics or even resistant bacteria are released into the environment and contaminate the surrounding areas. Human and animal populations in contact with these sources are able to become reservoirs of these resistant organisms. Then, due to the convergence between habitats, the contact of wild animals with other animals, humans, or human sources is now more common and this leads to an increase in the exchange of resistance determinants between their microbiota. Indeed, it seems that wildlife populations living in closer proximity to humans have higher levels of antibiotic resistance. Now, the Iberian Lynx (Lynx pardinus) is a part of this issue, being suggested as natural reservoir of acquired resistant bacteria. The emerging public health concern regarding microbial resistance to antibiotics is becoming true: the bacteria are evolving and are now affecting unintentional hosts.

Erythromycin- and copper-resistant Enterococcus hirae from marine sediment and co-transfer of erm(B) and tcrB to human Enterococcus faecalis

An erythromycin-, copper- and cadmium-resistant isolate of Enterococcus hirae from marine sediment was shown to harbor the plasmid pRE25 and to co-transfer erm(B) and tcrB to Enterococcus faecalis JH2-2. These data highlight the scope for antibiotic resistance selection by the marine environment through heavy metals and its possible involvement in antibiotic-resistant enterococcal infections.

Potential impact of antimicrobial resistance in wildlife, environment and human health

Given the significant spatial and temporal heterogeneity in antimicrobial resistance distribution and the factors that affect its evolution, dissemination, and persistence, it is important to highlight that antimicrobial resistance must be viewed as an ecological problem. Monitoring the resistance prevalence of indicator bacteria such as Escherichia coli and enterococci in wild animals makes it possible to show that wildlife has the potential to serve as an environmental reservoir and melting pot of bacterial resistance. These researchers address the issue of antimicrobial-resistant microorganism proliferation in the environment and the related potential human health and environmental impact.