Virulence genes, antibiotic resistance and integrons in Escherichia coli strains isolated from synanthropic birds from Spain

First Insights on Resistance and Virulence Potential of Escherichia coli from Captive Birds of Prey in Portugal

Captive birds of prey are often used for pest control in urban areas, while also participating in falconry exhibitions. Traveling across the country, these birds may represent a public health concern as they can host pathogenic and zoonotic agents and share the same environment as humans and synanthropic species. In this work, Escherichia coli from the cloacal samples of 27 captive birds of prey were characterized to determine their pathogenic potential. Isolates were clustered through ERIC-PCR fingerprinting, and the phylogenetic groups were assessed using a quadruplex PCR method. Their virulence and resistance profile against nine antibiotics were determined, as well as the isolates' ability to produce extended-spectrum β-lactamases (ESBLs). The 84 original isolates were grouped into 33 clonal types, and it was observed that more than half of the studied isolates belonged to groups D and B2. Most isolates presented gelatinase activity (88%), almost half were able to produce biofilm (45%), and some were able to produce α-hemolysin (18%). The isolates presented high resistance rates towards piperacillin (42%), tetracycline (33%), and doxycycline (30%), and 6% of the isolates were able to produce ESBLs. The results confirm the importance of these birds as reservoirs of virulence and resistance determinants that can be disseminated between wildlife and humans, stressing the need for more studies focusing on these animals.

Characterisation of typical enteropathogenic Escherichia coli (tEPEC) lineages and novel bfpA variants detected in Australian fruit bats (Pteropus poliocephalus)

Enteropathogenic Escherichia coli (EPEC) is an important cause of diarrhoeal disease in human infants. EPEC strains are defined by the presence of specific virulence factors including intimin (encoded by the eae gene) and bundle forming pili (Bfp). Bfp is encoded by the bfp operon and includes the bfpA gene for the major pilus subunit. By definition, Bfp are only present in typical EPEC (tEPEC), for which, humans are considered to be the only known natural host. This study detected tEPEC in faecal samples from a wild Australian fruit bat species, the grey-headed flying-fox (Pteropus poliocephalus). Whole genome sequencing of 61 E. coli isolates from flying-foxes revealed that 21.3 % (95%CI: 13 %-33 %) were tEPEC. Phylogenetic analyses showed flying-fox tEPEC shared evolutionary lineages with human EPEC, but were predominantly novel sequence types (9 of 13) and typically harboured novel bfpA variants (11 of 13). HEp-2 cell adhesion assays showed adherence to human-derived epithelial cells by all 13 flying-fox tEPEC, indicating that they all carried functional Bfp. Using an EPEC-specific duplex PCR, it was determined that tEPEC comprised 17.4 % (95%CI: 13 %-22 %) of 270 flying-fox E. coli isolates. Furthermore, a tEPEC-specific multiplex PCR detected the eae and bfpA virulence genes in 18.0 % (95%CI: 8.0 %-33.7 %) of 506 flying-fox faecal DNA samples, with occurrences ranging from 1.3 % to 87.0 % across five geographic areas sampled over a four-year period. The identification of six novel tEPEC sequence types and five novel bfpA variants suggests flying-foxes carry bat-specific tEPEC lineages. However, their close relationship with human EPEC and functional Bfp, indicates that flying-fox tEPEC have zoonotic potential and that dissemination of flying-fox tEPEC into urban environments may pose a public health risk. The consistent detection of tEPEC in flying-foxes over extensive geographical and temporal scales indicates that both wild grey-headed flying-foxes and humans should be regarded as natural tEPEC hosts.

Infectious agents present in monk parakeet (Myiopsitta monachus) and rose-ringed parakeet (Psittacula krameri) invasive species in the parks of Madrid and Seville, Spain

Introduction

The introduction of invasive species into an ecosystem could result in biodiversity loss and the spread of infectious agents that could cause re-emergent or emergent zoonotic diseases. Monk parakeets (Myiopsitta monachus) and rose-ringed parakeets (Psittacula krameri) are considered widespread invasive exotic species in urban habitats from the Iberian Peninsula. The aim of this study was to assess the presence of relevant infectious agents in wild parakeets captured in urban parks in Madrid and Seville (Spain).

Methods

A total of 81 cloacal samples were collected and analysed using molecular techniques.

Results

The prevalence of infectious agents varied between parakeet species: 9.5% of monk parakeets and 15% of rose-ringed parakeets were positive for enteropathogenic E. coli (EPEC), 13.3% of rose-ringed parakeets for avian influenza virus (AIV), 3.3% of rose-ringed parakeets for Newcastle disease virus (NDV), and a 23.8% of monk parakeets for Chlamydia psittaci.

Discussion

All C. psittaci-identified isolates were classified as B, E, or E/B genotypes, indicating transmission from wild urban pigeons to parakeets. These results highlight the need for monitoring parakeet populations due to the implications for human and animal health.

Past and future: Urbanization and the avian endocrine system

Urban environments are evolutionarily novel and differ from natural environments in many respects including food and/or water availability, predation, noise, light, air quality, pathogens, biodiversity, and temperature. The success of organisms in urban environments requires physiological plasticity and adjustments that have been described extensively, including in birds residing in geographically and climatically diverse regions. These studies have revealed a few relatively consistent differences between urban and non-urban conspecifics. For example, seasonally breeding urban birds often develop their reproductive system earlier than non-urban birds, perhaps in response to more abundant trophic resources. In most instances, however, analyses of existing data indicate no general pattern distinguishing urban and non-urban birds. It is, for instance, often hypothesized that urban environments are stressful, yet the activity of the hypothalamus-pituitary-adrenal axis does not differ consistently between urban and non-urban birds. A similar conclusion is reached by comparing blood indices of metabolism. The origin of these disparities remains poorly understood, partly because many studies are correlative rather than aiming at establishing causality, which effectively limits our ability to formulate specific hypotheses regarding the impacts of urbanization on wildlife. We suggest that future research will benefit from prioritizing mechanistic approaches to identify environmental factors that shape the phenotypic responses of organisms to urbanization and the neuroendocrine and metabolic bases of these responses. Further, it will be critical to elucidate whether factors affect these responses (a) cumulatively or synergistically; and (b) differentially as a function of age, sex, reproductive status, season, and mobility within the urban environment. Research to date has used various taxa that differ greatly not only phylogenetically, but also with regard to ecological requirements, social systems, propensity to consume anthropogenic food, and behavioral responses to human presence. Researchers may instead benefit from standardizing approaches to examine a small number of representative models with wide geographic distribution and that occupy diverse urban ecosystems.

Understanding the role of insects in the acquisition and transmission of antibiotic resistance

Antibiotic resistance (AR) is a global healthcare threat that requires a comprehensive assessment. Poorly regulated antibiotic stewardship in clinical and non-clinical settings has led to a horizontal dissemination of AR. A variety of often neglected elements facilitate the circulation of AR from antibiotic sinks like concentrated animal feeding operations and healthcare settings to other environments that include healthy human communities. Insects are one of those elements that have received underwhelming attention as vectors of AR, despite their well-known role in transmitting clinically relevant pathogens. We here make an exhaustive attempt to highlight the role of insects as zoonotic reservoirs of AR by discussing the available literature and deriving realistic inferences. We review the AR associated with insects housing various human-relevant environments, namely, animal farm industry, edible-insects enterprise, healthcare institutes, human settlements, agriculture settings and the wild. We also provide evidence-based accounts of the events of the transmission of AR from insects to humans. We evaluate the clinical threats associated with insect-derived AR and propose the adoption of more sophisticated strategies to understand and mitigate future AR concerns facilitated by insects. Future works include a pan-region assessment of insects for AR in the form of AR bacteria (ARB) and AR determinants (ARDs) and the introduction of modern techniques like whole-genome sequencing, metagenomics, and in-silico modelling.

Antimicrobial resistance patterns of bacteria isolated from chicks of Canarian Egyptian vultures (Neophron percnopterus majorensis): A "one health" problem?

Antimicrobial resistance in Gram-negative bacteria isolated from cloacal samples of chicks of Canarian Egyptian vultures was investigated. Prevalence of Salmonella was also studied. Forty-seven isolates, obtained from 23 animals, were analysed. Escherichia coli (n = 29), Proteus mirabilis (n = 17) and Salmonella spp. (n = 1) were identified using API 20E system. Antimicrobial susceptibility to 13 antibiotics included in nine different categories was determined using disk-diffusion technique. The higher percentages of susceptible E. coli isolates were found for aminoglycosides and cefoxitin, and the lower ones were found for ampicillin, enrofloxacin and tetracycline. Proteus mirabilis isolates were susceptible to most of antimicrobials tested. Multidrug resistance patterns were found in 13 E. coli and four Proteus mirabilis. Salmonella spp. was detected in one chick (4.37%), and the isolate was also resistant to ampicillin and tetracycline. Thirteen E. coli isolates and four Proteus isolates showed a multidrug-resistance pattern, being resistant at least to one antibiotic in three or more different antimicrobial categories. This high level of antibiotic resistance in chickens of an endangered bird may be a limitation for possible treatments of infections in this species, as well as representing a source of resistant bacteria for animal care staff and for other animals in wildlife recovery centres. A "One Health" approach to this problem is necessary to reduce the levels of antimicrobial resistance in wild birds.

High Rates of Multidrug-Resistant Escherichia coli in Great Cormorants (Phalacrocorax carbo) of the German Baltic and North Sea Coasts: Indication of Environmental Contamination and a Potential Public Health Risk

Antimicrobial-resistant bacteria pose a serious global health risk for humans and animals, while the role of wildlife in the dynamic transmission processes of antimicrobial resistance in environmental settings is still unclear. This study determines the occurrence of antimicrobial-resistant Escherichia coli in the free-living great cormorants (Phalacrocorax carbo) of the North and Baltic Sea coasts of Schleswig-Holstein, Germany. For this, resistant E.coli were isolated from cloacal or faecal swabs and their antimicrobial resistance pheno- and genotypes were investigated using disk diffusion tests and PCR assays. The isolates were further assigned to the four major phylogenetic groups, and their affiliation to avian pathogenic E. coli (APEC) was tested. Resistant E. coli were isolated from 66.7% of the 33 samples, and 48.9% of all the resistant isolates showed a multidrug resistance profile. No spatial differences were seen between the different sampling locations with regard to the occurrence of antimicrobial resistance or multidrug resistance. Most commonly, resistance percentages occurred against streptomycin, followed by tetracycline and sulfonamides. More than half of the isolates belonged to the phylogenetic group B1. Of all the isolates, 24.4% were classified as APEC isolates, of which almost 82% were identified as multidrug-resistant. These results add information on the dispersal of antimicrobial-resistant bacteria in wild birds in Germany, thereby allowing conclusions on the degree of environmental contamination and potential public health concerns.

Novel alphaherpesvirus in a wild South American sea lion (Otaria byronia) with pulmonary tuberculosis

In 2017, an adult male South American sea lion (Otaria byronia), presenting emaciation and a cervical abscess, stranded alive in Florianópolis, southern Brazil. The animal was directed to a rehabilitation center, dying a few days later. On necropsy, the main gross findings were necrotizing lymphadenitis of the right prescapular lymph node and nodular bronchopneumonia. A novel alphaherpesvirus, tentatively named Otariid alphaherpesvirus 1, was amplified in several tissue samples. No histopathologic findings associated with viral infection were observed. Additionally, pulmonary tuberculosis by Mycobacterium pinnipedii was diagnosed by histopathological, immunohistochemical, and molecular techniques. Several bacteria were cultured from antemortem and postmortem samples, including Proteus mirabilis from the cervical abscess and cardiac blood, and Escherichia coli from the cervical abscess and pericardial effusion. Flavivirus, morbillivirus, and Apicomplexa were not detected by molecular techniques. Herein, we report a novel alphaherpesvirus in a pinniped species of the family Otariidae. Although previously described in Southern Hemisphere pinniped species, including South American sea lions, there is limited information regarding M. pinnipedii impact over this group. Further research is required to determine the associated pathogenesis of this novel herpesvirus, and prevalence of Otariid alphaherpesvirus 1 and M. pinnipedii in the reproductive colonies.

Antibiotic Resistance and Virulence Profiles of Escherichia coli Strains Isolated from Wild Birds in Poland

Wild animals are increasingly reported as carriers of antibiotic-resistant and pathogenic bacteria including Enterobacteriaceae. However, the role of free-living birds as reservoirs for potentially dangerous microbes is not yet thoroughly understood. In our work, we examined Escherichia coli strains from wild birds in Poland in relation to their antimicrobial agents susceptibility, virulence and phylogenetic affiliation. Identification of E. coli was performed using MALDI-TOF mass spectrometry. The antibiotic susceptibility of the isolates was determined by the broth microdilution method, and resistance and virulence genes were detected by PCR. E. coli bacteria were isolated from 32 of 34 samples. The strains were most often classified into phylogenetic groups B1 (50%) and A (25%). Resistance to tetracycline (50%), ciprofloxacin (46.8%), gentamicin (34.3%) and ampicillin (28.1%) was most frequently reported, and as many as 31.2% of E. coli isolates exhibited a multidrug resistance phenotype. Among resistance genes, sul2 (31.2% of isolates) and bla_TEM (28.1%) were identified most frequently, while irp-2 (31.2%) and ompT (28.1%) were the most common virulence-associated genes. Five strains were included in the APEC group. The study indicates that wild birds can be carriers of potentially dangerous E. coli strains and vectors for the spread of resistant bacteria and resistance determinants in the environment.

First isolation of atypical enteropathogenic Escherichia coli from geese (Anser anser domestica) and first description of atypical EPEC from turkeys and pigeons in Hungary

Background

Escherichia coli is a bacterial species widely distributed among mammals and avian species, and also a member of the normal intestinal microbiota. However, some E. coli strains of different pathotypes can cause disease in both humans and animals. Atypical enteropathogenic E. coli (aEPEC) can infect both animals and humans or influence the severity of other ongoing infections.

Results

In the present study, a total of 332 samples were collected from ducks, geese, turkeys, chickens, and pigeons from the Hungarian Veterinary Diagnostic Directorate, two slaughterhouses, two pigeon keepers and one backyard chicken farm. E. coli was isolated and verified from 319 samples. The isolates were screened by PCR for diarrheagenic E. coli pathotypes. Altogether seven atypical enteropathogenic E. coli (aEPEC) strains were identified: two from four-week-old dead turkeys, two from force-fed geese, and three from pigeons. No further pathotypes were identified in the collection. The atypical EPEC strains were classified phylogenetically to B1, B2, and F, and four out of the seven aEPEC isolates proved to be multidrug resistant. Serotypes of aEPEC strains were uniform collected from same farms and showed diversity between their origins with O76, O145, O109 serogroups.

Conclusions

This is the first report in the literature about aEPEC in goose (Anser anser domestica). Furthermore, this is the first isolation of aEPEC from turkeys and pigeons in Hungary. The uneven distribution of aEPEC in different age groups of poultry suggests that aEPEC disappears with growing up, but stress (e.g.: force-feeding) and concurrent diseases might promote its reappearance in the intestine.

Pigeons as Carriers of Clinically Relevant Multidrug-Resistant Pathogens-A Clinical Case Report and Literature Review

Pigeons are widespread bird species in urban regions (Columba livia forma urbana) and may carry pathogens with zoonotic potential. In recent years, more and more data indicate that these zoonotic pathogens are multidrug resistant. Our results confirmed that global trend. Three different multidrug-resistant pathogens were isolated from an oral cavity of a racing pigeon with lesions typical for pigeon pox virus infection. Staphylococcus aureus was recognized as methicillin resistant, thus resistant to all beta-lactams. Additionally, it was also resistant to many other classes of antibiotics, namely: aminoglycosides, tetracyclines, phenicols, lincosamides, and macrolides. Escherichia coli showed resistance to all antimicrobials tested, and it was classified as intermediate to amikacin. Moreover, Candida albicans resistant to clotrimazole, natamycin, flucytosine, and amphotericin and intermediate to ketoconazole, nystatin, and econazole was also isolated. This raises the question how pigeons acquire such highly resistant strains. Therefore, more data are needed concerning the resistance to antibiotics in strains from domestic and wild pigeons in Poland. Until the problem is fully understood, it will be challenging to implement adequate planning of any control measures and check their effectiveness.

Occurrence and Quantification of Antimicrobial Resistance Genes in the Gastrointestinal Microbiome of Two Wild Seabird Species With Contrasting Behaviors

Antimicrobial resistance genes (ARGs) are environmental pollutants and anthropization indicators. We evaluated human interference in the marine ecosystem through the ocurrence and quantification (real-time PCRs) of 21 plasmid-mediated ARGs in enema samples of 25 wild seabirds, upon admission into rehabilitation: kelp gull (Larus dominicanus, n = 14) and Magellanic penguin (Spheniscus magellanicus, n = 11). Overall, higher resistance values were observed in kelp gulls (non-migratory coastal synanthropic) in comparison with Magellanic penguins (migratory pelagic non-synanthropic). There were significant differences between species (respectively, kelp gull and Magellanic penguin): ARGs occurrence (bla _TEM [p = 0.032]; tetM [p = 0.015]; tetA [p = 0.003]; and sulII [p = 0.007]), mean number of ARGs per sample (p = 0.031), ARGs mean load percentage (aadA [p = 0.045], tetA [p = 0.031], tetM [p = 0.016], bla _TEM [p = 0.032], sulII [p = 0.008]), percentage of genes conferring resistance to an antimicrobial class (betalactams [p = 0.036] and sulfonamides [p = 0.033]), mean number of genes conferring resistance to one or more antimicrobial classes (p = 0.024]), percentage of multiresistant microbiomes (p = 0.032), and clustering (p = 0.006). These differences are likely due to these species' contrasting biology and ecology - key factors in the epidemiology of ARGs in seabirds. Additionally, this is the first report of mecA in seabirds in the Americas. Further studies are necessary to clarify the occurrence and diversity of ARGs in seabirds, and their role as potential sources of infection and dispersal within the One Health chain of ARGs.

European Starlings (Sturnus vulgaris) as Vectors and Reservoirs of Pathogens Affecting Humans and Domestic Livestock

European starlings are an abundant, widespread avian species frequently found in close association with human development and agriculture. The ability of starlings to carry and disperse pathogens of humans and domesticated livestock has received considerable attention, including studies of enteric bacteria, viruses, and some fungi. To investigate the importance of European starlings as disease vectors, I reviewed and assessed the available literature, comprising several hundred published papers. Although a wide variety of potential pathogens have been reported in starlings, the strongest evidence suggests that they may be responsible for harboring and dispersing some species of enteric bacteria, with Escherichia coli and Campylobacter jejuni of perhaps greatest interest, and primarily in the context of dairies, concentrated animal feeding operations, and other intensive livestock agriculture.

Seabirds as anthropization indicators in two different tropical biotopes: A One Health approach to the issue of antimicrobial resistance genes pollution in oceanic islands

Antimicrobial resistance is a quintessential One Health issue, among the most serious 21st century global threats to human health. Seabirds may act as sentinels of natural and anthropogenic changes in the marine ecosystem health, including pollution by antimicrobial resistance genes (ARGs). We used real time PCR to identify and quantify 22 plasmid-mediated ARGs in the gastrointestinal microbiome of six wild seabird species, comparing an anthropized (Fernando de Noronha Archipelago - FNA) and a pristine biotope (Rocas Atoll - ROA), Brazil. Of 257 birds, 218 (84.8%) were positive to at least one ARG. ARG classes encoding resistance to tetracyclines (75.1%), quinolones (10.5%) and phenicols (10.5%) were the most prevalent, with tetracyclines significantly greater than the remaining classes (p < 0.05). Genes tet(S) (29.2%), tet(A) (28.8%), and tet(B) (24.9%) were the most commonly found and had a significantly greater prevalence when compared to the remaining ARGs (p < 0.05). The anthropized biotope presented statistically significant higher prevalence of sulfonamide- and quinolone-encoding ARGs in comparison with the pristine (respectively, p = 0.01 and p = 0.03), and higher sulII gene prevalence (p = 0.04), consistent with anthropogenic pressure. Migratory species (only present in ROA) showed statistically significant higher mcr-1 (polymyxins) and bla_TEM (betalactam) prevalences (respectively, p = 0.009 and p = 0.02), and mcr-1 percentage load (p = 0.0079) in comparison with non-migratory. To our knowledge, this is the largest ARGs survey based on direct detection and quantification in seabirds worldwide, and the first to evaluate non-synanthropic species in oceanic islands. This is the first detection of mcr-1 in wild free-ranging seabirds in Brazil and in free-ranging migratory non-synanthropic seabirds worldwide. Our findings show the importance of biological and ecological factors, highlighting the role of seabirds as anthropization sentinels and ARGs-pollution environmental indicators (even in a pristine biotope), and their involvement in the One Health epidemiological chain of ARGs.

Into the sea: Antimicrobial resistance determinants in the microbiota of little penguins (Eudyptula minor)

Terrestrial and aquatic birds have been proposed as sentinels for the spread of antimicrobial resistant bacteria, but few species have been investigated specifically in the context of AMR in the marine ecosystem. This study contrasts the occurrence of class 1 integrons and associated antimicrobial resistance genes in wild and captive little penguins (Eudyptula minor), an Australian seabird with local population declines. PCR screening of faecal samples (n = 448) revealed a significant difference in the prevalence of class 1 integrons in wild and captive groups, 3.2% and 44.7% respectively, with genes that confer resistance to streptomycin, spectinomycin, trimethoprim and multidrug efflux pumps detected. Class 1 integrons were not detected in two clinically relevant bacterial species, Klebsiella pneumoniae or Escherichia coli, isolated from penguin faeces. The presence of class 1 integrons in the little penguin supports the use of marine birds as sentinels of AMR in marine environments.

Raccoons (Procyon lotor) in the Madrid region of Spain are carriers of antimicrobial-resistant Escherichia coli and enteropathogenic E. coli

The role of wildlife in the epidemiology of antimicrobial resistance is unclear. Raccoons in North America can carry a variety of enteric bacteria, with associated antimicrobial resistance, that could infect humans and livestock. The potential for raccoons to carry these bacteria in Europe, where they are an invasive species, has not been explored. Our objectives were to determine the prevalence of Escherichia coli with associated antimicrobial resistance in raccoons from the Madrid region of Spain and to determine whether they are carriers of potential human pathogens, including verotoxin-producing E. coli (VTEC) and enteropathogenic E. coli (EPEC). In total, we tested 237 E. coli isolates from the faeces of 83 euthanized raccoons for susceptibility to 14 antimicrobial agents and the presence of VTEC and EPEC. Antimicrobial resistance to at least one antimicrobial was detected in the faeces of 51% (42/83; 95% CI, 40.1-61.1) of the raccoons tested. A high percentage of raccoons carried, in their faeces, E. coli isolates resistant to ampicillin (33%), streptomycin (33%), tetracycline (30%), sulphafurazole (31%) and trimethoprim-sulphamethoxazole (23%). We detected one isolate of extended-spectrum β-lactamase-producing E. coli from the faeces of one raccoon. We detected VTEC in the faeces of one raccoon, and EPEC in the faeces of 12% (10/83) of the raccoons. Of the raccoons that carried EPEC in their faeces, 60% (6/10) carried EPEC isolates that exhibited characteristics associated with pathogenicity in humans. Raccoons in Madrid can carry pathogenic and antimicrobial-resistant E. coli in their faeces and may be a risk to public health because of their potential to contaminate food and the environment with their faeces.

Dissemination of antibiotic resistance genes (ARGs) via integrons in Escherichia coli: A risk to human health

With the induction of various emerging environmental contaminants such as antibiotic resistance genes (ARGs), environment is considered as a key indicator for the spread of antimicrobial resistance (AMR). As such, the ARGs mediated environmental pollution raises a significant public health concern worldwide. Among various genetic mechanisms that are involved in the dissemination of ARGs, integrons play a vital role in the dissemination of ARGs. Integrons are mobile genetic elements that can capture and spread ARGs among environmental settings via transmissible plasmids and transposons. Most of the ARGs are found in Gram-negative bacteria and are primarily studied for their potential role in antibiotic resistance in clinical settings. As one of the most common microorganisms, Escherichia coli (E. coli) is widely studied as an indicator carrying drug-resistant genes, so this article aims to provide an in-depth study on the spread of ARGs via integrons associated with E. coli outside clinical settings and highlight their potential role as environmental contaminants. It also focuses on multiple but related aspects that do facilitate environmental pollution, i.e. ARGs from animal sources, water treatment plants situated at or near animal farms, agriculture fields, wild birds and animals. We believe that this updated study with summarized text, will facilitate the readers to understand the primary mechanisms as well as a variety of factors involved in the transmission and spread of ARGs among animals, humans, and the environment.

Antimicrobial susceptibility and detection of virulence-associated genes of Escherichia coli and Salmonella spp. isolated from domestic pigeons (Columba livia) in Brazil

Overpopulation of domestic pigeons is considered to be one of the major problems of urban centers, as these birds are responsible for the dissemination of relevant pathogens to animal and human health. The aim of this study was to detect potentially pathogenic Escherichia coli and Salmonella spp. in domestic pigeons captured in areas near silos used for grain and feed storage, analyzing the antimicrobial sensitivity and the presence of virulence-associated genes. We evaluated 41 pigeons. From each bird, cecal contents and a pool of viscera (heart, spleen, and liver) were collected. Fifty strains of E. coli and three strains of S. Typhimurium were isolated. The antimicrobial susceptibility assay showed that 2% of the isolates of E. coli were resistant to chloramphenicol and the combination of sulfamethoxazole + trimethoprim and 4% to tetracycline, doxycycline, and sulfonamide. The three S. Typhimurium strains were sensitive to all antimicrobials tested. The pathogenicity profile demonstrated that no E. coli isolates showed a STEC compatible profile. Regarding the APEC pathotype, all genes were observed in 8% of E. coli, 6% had only the iss gene and 4% presented ompT, hlyF, and iutA genes. invA, hilA, avrA, and lpfA genes were detected in 100% of Salmonella isolates. The sitC and pefA genes were only present in one strain and the remaining genes were detected in two. In conclusion, it was found that pigeons living in the vicinity of silos are carriers of important pathogens, and control measures should be taken to minimize animal and human health risks.

Domestic and game pigeons as reservoirs for Escherichia coli harbouring antimicrobial resistance genes

OBJECTIVES

In Iran, pigeons are kept and bred on the roofs of houses, which indicates the potential significance of pigeons in the dispersal of antimicrobial resistant Escherichia coli strains. Here we characterized antimicrobial resistance genotypes in relation to phenotypic presentations and phylogenetic backgrounds of the E. coli isolates from household pigeons in Kerman in southeast Iran.

METHODS

Totally, 152 faecal E. coli isolates from domestic and household pigeons were screened for 13 antimicrobial resistance genes, bla_TEM, bla_SHV, bla_CTX-M, sulI, sulII, dhfrI, dhfrV, aadA, aac(3)-I, tetA, tetB, floR and qnrA, by conventional polymerase chain reaction (PCR) technique. Clermont phylogenetic background of E. coli strains was studied and antibiotic resistance of all strains was assessed for seven antibiotics.

RESULTS

The antimicrobial resistance genes bla_TEM, tetA, tetB and aadA were detected in 52.6%, 6.5%, 6.5% and 5.9% of the isolates, respectively. PCR phylotyping revealed that a significant number of isolates within A₀ (54%), A₁ (70%), B1 (57.6%), B2₂ (75%) and D1 (87.5%) phylogroups were positive for the studied resistance genes. One phenotypic resistance pattern (trimethoprim-sulfamethoxazole) was associated with the presence of the corresponding gene sul2.

CONCLUSIONS

An alarming rate of phenotypic resistance was observed in this study. Many isolates were positive for the screened resistance genes. According to the phylogenetic background, most resistant isolates belonged to the commensal phylotypes, representing significant role of commensal strains as a source of resistance genes. These findings highlight the role of the pigeon as disseminator of resistant E. coli strains.

Antibiotic resistance genes as landscape anthropization indicators: Using a wild felid as sentinel in Chile

Antimicrobial resistance is a global emerging public health issue whose presence and impact in wildlife are widely unknown. Antimicrobial resistance genes (ARGs) are considered environmental contaminants, suitable to evaluate the degree of anthropic impact on wildlife and the environment. We used a wild felid, the guigna (Leopardus guigna), as a sentinel for the presence of ARGs in anthropized and pristine areas across their entire distribution range in Chile. We evaluated fecal samples from 51 wild guignas, collected between 2009 and 2018. Real-time PCR essays were employed to detect and quantify 22 selected ARGs in their fecal microbiome. All animals (100%) were positive for at least one ARG. The most prevalent ARG families were those that confer resistance to tetracycline (88.2%) and beta-lactamase (68.9%), with tet(Q) (60.8%), tet(W) (60.8%), and bla_TEM (66.7%) as the most prevalent ARGs. Multi-resistance profiles were observed in 43% of the guignas. Statistically significant differences were found between anthropized and pristine areas for tet(Q) (p = 0.014), tet(W) (p = 0.0037), tetracycline family (p = 0.027), multi-resistance profile prevalence (p = 0.043) and tet(W) quantification (p = 0.004). Two animals from anthropized landscapes were positive for mecA, a gene associated with Staphylococcus aureus and other staphylococci resistant to methicillin, while three animals from anthropized areas were positive for bla_CTX-M, that encodes class A extended-spectrum beta-lactamase. Both genes have been identified in bacteria causing relevant nosocomial infections worldwide. This is the first study on ARGs in wild felids from Chile and the first detection of mecA in South American wild felids. We observed an association between the degree of landscape anthropization and ARG prevalence, confirming that ARGs are important indicators of wildlife exposure to human activity/presence, with a widespread distribution.

Are we overestimating risk of enteric pathogen spillover from wild birds to humans?

Enteric illnesses remain the second largest source of communicable diseases worldwide, and wild birds are suspected sources for human infection. This has led to efforts to reduce pathogen spillover through deterrence of wildlife and removal of wildlife habitat, particularly within farming systems, which can compromise conservation efforts and the ecosystem services wild birds provide. Further, Salmonella spp. are a significant cause of avian mortality, leading to additional conservation concerns. Despite numerous studies of enteric bacteria in wild birds and policies to discourage birds from food systems, we lack a comprehensive understanding of wild bird involvement in transmission of enteric bacteria to humans. Here, we propose a framework for understanding spillover of enteric pathogens from wild birds to humans, which includes pathogen acquisition, reservoir competence and bacterial shedding, contact with people and food, and pathogen survival in the environment. We place the literature into this framework to identify important knowledge gaps. Second, we conduct a meta‐analysis of prevalence data for three human enteric pathogens, Campylobacter spp., E. coli, and Salmonella spp., in 431 North American breeding bird species. Our literature review revealed that only 3% of studies addressed the complete system of pathogen transmission. In our meta‐analysis, we found a Campylobacter spp. prevalence of 27% across wild birds, while prevalence estimates of pathogenic E. coli (20%) and Salmonella spp. (6.4%) were lower. There was significant bias in which bird species have been tested, with most studies focusing on a small number of taxa that are common near people (e.g. European starlings Sturnus vulgaris and rock pigeons Columba livia) or commonly in contact with human waste (e.g. gulls). No pathogen prevalence data were available for 65% of North American breeding bird species, including many commonly in contact with humans (e.g. black‐billed magpie Pica hudsonia and great blue heron Ardea herodias), and our metadata suggest that some under‐studied species, taxonomic groups, and guilds may represent equivalent or greater risk to human infection than heavily studied species. We conclude that current data do not provide sufficient information to determine the likelihood of enteric pathogen spillover from wild birds to humans and thus preclude management solutions. The primary focus in the literature on pathogen prevalence likely overestimates the probability of enteric pathogen spillover from wild birds to humans because a pathogen must survive long enough at an infectious dose and be a strain that is able to colonize humans to cause infection. We propose that future research should focus on the large number of under‐studied species commonly in contact with people and food production and demonstrate shedding of bacterial strains pathogenic to humans into the environment where people may contact them. Finally, studies assessing the duration and intensity of bacterial shedding and survival of bacteria in the environment in bird faeces will help provide crucial missing information necessary to calculate spillover probability. Addressing these essential knowledge gaps will support policy to reduce enteric pathogen spillover to humans and enhance bird conservation efforts that are currently undermined by unsupported fears of pathogen spillover from wild birds.

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.

Antibiotic resistant bacteria are widespread in songbirds across rural and urban environments

The widespread use of antibiotics in human and veterinary medicine to treat pathogenic bacteria has resulted in the rapid emergence of antibiotic-resistant bacteria (ARB). Wild animals may enable the spread of pathogenic and non-pathogenic ARB when they are exposed to reservoirs (e.g., contaminated soil, water, or crops) and carry ARB in and on their bodies to other environments. We tested for the presence of ARB in four songbird species in southwest Michigan across a gradient of land use. Our specific objectives were to: 1) quantify the prevalence of ARB found in the gut microbiome of birds; 2) identify the specific bacteria exhibiting resistance; 3) assess whether ARB prevalence and identity varied among bird species; and 4) assess whether anthropogenic land use influenced the prevalence and identity of ARB found on birds. We sampled birds across a land use gradient consisting of urban, agricultural, and natural land covers using a randomized, spatially-balanced sampling design and cultured bacteria from fecal samples in the presence of three different antibiotics (amoxicillin, tetracycline, and ciprofloxacin). Overall prevalence of ARB was high, with 88% of total birds carrying ARB resistant to one of three antibiotics that we tested. Resistance to amoxicillin was more common (83% of sampled birds) than resistance to tetracycline (15%) or ciprofloxacin (1%). Identified ARB were diverse, and included 135 isolates representing 5 bacterial phyla and 22 genera. There was no effect of land use on ARB prevalence, with 90% of sampled birds captured in rural sites and 85% of sampled birds in urban sites carrying ARB. We provide the first analysis of ARB prevalence across multiple bird species and land uses utilizing a spatially-balanced, randomized study design. Our results demonstrate that nearly all sampled birds carried at least some ARB, and that they may serve as important dispersal agents of ARB across large spatial scales.

Free-Ranging Synanthropic Birds (Ardea alba and Columba livia domestica) as Carriers of Salmonella spp. and Diarrheagenic Escherichia coli in the Vicinity of an Urban Zoo

The presence of free-ranging urban birds is a risk factor for transmitting pathogens to captive animals and humans alike, including Salmonella spp. and diarrheagenic Escherichia coli. Cloacal swabs from 156 synanthropic Great egrets (Ardea alba) and feral pigeons (Columba livia domestica) that inhabit the surroundings of an urban zoo were processed for the identification of Salmonella spp. and diarrheagenic E. coli pathotypes. Bacterial species identification and genotypic characterization employed the matrix-assisted laser desorption ionization-time of flight mass spectrometry and PCR techniques, respectively, comparing their phylogenetic profiles through amplified fragment length polymorphism (AFLP) analysis. A total of 11 birds were positive for Salmonella Typhimurium (7%) and 9 individuals (5.8%) for diarrheagenic E. coli (enteropathogenic E. coli/Shiga-toxin producing E. coli [EPEC/STEC]) strains. S. Typhimurium strains presented highly similar AFLP profiles (85-100%), whereas EPEC/STEC strains showed more polymorphism. The results show free-ranging birds as carriers for both microorganisms in a zoo environment in Brazil for the first time and suggest these species as possible sources of infection to other animals as well as exposing personnel and visitors to potential zoonotic microorganisms. The presence of carriers highlights the importance of a surveillance system and the need for preventive measures to avoid attracting growing number of synanthropic avian species.

Zoonotic Agents in Feral Pigeons (Columba livia) from Costa Rica: Possible Improvements to Diminish Contagion Risks

Most studies on zoonotic agents in pigeons have been conducted in the Palearctic region, but the scarcity of data is notorious in the Neotropical region, where these birds can breed all year around and are in close contact with humans. In this study, we used a combination of culture-dependent and culture-independent methods to identify infectious agents in 141 fecal samples from pigeons collected at four urban parks from Costa Rica. Of these we identified 34 positive samples for Salmonella enterica subsp. enterica serovar Braenderup (24.1%), 13 for Chlamydophila psittaci (9.2%), 9 for enteropathogenic Escherichia coli (6.4% eaeA, 0% stx-1 and 0% stx-2), and 2 for Campylobacter jejuni (1.4%). These populations of pigeons pose low risk for healthy adult humans, however, they may pose a health risk to immunocompromised patients or children. This study provides scientific data, which can be incorporated into educational programs aiming to reverse the public attitude toward pigeon feeding and to rationally justify population control efforts.

Captive wild birds as reservoirs of enteropathogenic E. coli (EPEC) and Shiga-toxin producing E. coli (STEC)

Psittacine birds have been identified as reservoirs of diarrheagenic Escherichia coli, a subset of pathogens associated with mortality of children in tropical countries. The role of other orders of birds as source of infection is unclear. The aim of this study was to perform the molecular diagnosis of infection with diarrheagenic E. coli in 10 different orders of captive wild birds in the state of São Paulo, Brazil. Fecal samples were analyzed from 516 birds belonging to 10 orders: Accipitriformes, Anseriformes, Columbiformes, Falconiformes, Galliformes, Passeriformes, Pelecaniformes, Piciformes, Psittaciformes and Strigiformes. After isolation, 401 E. coli strains were subjected to multiplex PCR system with amplification of genes eae and bfp (EPEC), stx1 and stx2 for STEC. The results of these tests revealed 23/401 (5.74%) positive strains for eae gene, 16/401 positive strains for the bfp gene (3.99%) and 3/401 positive for stx2 gene (0.75%) distributed among the orders of Psittaciformes, Strigiformes and Columbiformes. None of strains were positive for stx1 gene. These data reveal the infection by STEC, typical and atypical EPEC in captive birds. The frequency of these pathotypes is low and restricted to few orders, but the data suggest the potential public health risk that these birds represent as reservoirs of diarrheagenic E. coli.

Environmental Factors and Zoonotic Pathogen Ecology in Urban Exploiter Species

Knowledge of pathogen ecology, including the impacts of environmental factors on pathogen and host dynamics, is essential for determining the risk that zoonotic pathogens pose to people. This review synthesizes the scientific literature on environmental factors that influence the ecology and epidemiology of zoonotic microparasites (bacteria, viruses and protozoa) in globally invasive urban exploiter wildlife species (i.e., rock doves [Columba livia domestica], European starlings [Sturnus vulgaris], house sparrows [Passer domesticus], Norway rats [Rattus norvegicus], black rats [R. rattus] and house mice [Mus musculus]). Pathogen ecology, including prevalence and pathogen characteristics, is influenced by geographical location, habitat, season and weather. The prevalence of zoonotic pathogens in mice and rats varies markedly over short geographical distances, but tends to be highest in ports, disadvantaged (e.g., low income) and residential areas. Future research should use epidemiological approaches, including random sampling and robust statistical analyses, to evaluate a range of biotic and abiotic environmental factors at spatial scales suitable for host home range sizes. Moving beyond descriptive studies to uncover the causal factors contributing to uneven pathogen distribution among wildlife hosts in urban environments may lead to targeted surveillance and intervention strategies. Application of this knowledge to urban maintenance and planning may reduce the potential impacts of urban wildlife-associated zoonotic diseases on people.

Antimicrobial Resistance Genes in Pigeons from Public Parks in Costa Rica

Antimicrobial resistance is known to be an emerging problem, but the extent of the issue remains incomplete. The aim of this study was to determine the presence or absence of nine resistance genes (bla_TEM , catI, mecA, qnrS, sulI, sulII, tet(A), tet(Q), vanA) in the faeces of 141 pigeons from four urban parks in Alajuela, Guadalupe, Tres Ríos and San José in Costa Rica. The genes were identified by real-time PCR directly from enema samples. About 30% of the samples were positive for genes catI and sulI; between 13% and 17% were positive for qnrS, sulII, tet(A) and tet(Q); and 4% were positive for bla_TEM . The mecA and vanA genes were not detected. The average of antimicrobial resistance genes detected per pigeon was 2. Eight different patterns of resistance were identified, without differences in the sampling areas, being the most common pattern 2 (sulII positive samples). During rainy season, the genes more frequently found were sulI and tet(A). In conclusion, the urban inhabiting pigeons tested are currently carrying antimicrobial resistance genes, potentially acting as reservoirs of resistant bacteria and vectors to humans. To the authors' knowledge, this is the first study carried out on direct detection of resistance genes in the digestive metagenomes of pigeons.

ISOLATION AND MOLECULAR IDENTIFICATION OF POTENTIALLY PATHOGENIC Escherichia coli AND Campylobacter jejuni IN FERAL PIGEONS FROM AN URBAN AREA IN THE CITY OF LIMA, PERU

Feral pigeons (Columbia livia) live in close contact with humans and other animals. They can transmit potentially pathogenic and zoonotic agents. The objective of this study was to isolate and detect strains of diarrheagenic Escherichia coli and Campylobacter jejuni of urban feral pigeons from an area of Lima, Peru. Fresh dropping samples from urban parks were collected for microbiological isolation of E. coli strains in selective agar, and Campylobacter by filtration method. Molecular identification of diarrheagenic pathotypes of E.coli and Campylobacter jejuni was performed by PCR. Twenty-two parks were sampled and 16 colonies of Campylobacter spp. were isolated. The 100% of isolates were identified as Campylobacter jejuni. Furthermore, 102 colonies of E. coliwere isolated and the 5.88% resulted as Enteropathogenic (EPEC) type and 0.98% as Shiga toxin-producing E. coli (STEC). The urban feral pigeons of Lima in Peru can act as a reservoir or carriers of zoonotic potentially pathogenic enteric agents.