High frequency of B2 phylogroup among non-clonally related fecal Escherichia coli isolates from wild boars, including the lineage ST131

Pathogenic profile and antimicrobial resistance of Escherichia coli, Escherichia marmotae and Escherichia ruysiae detected from hunted wild boars in Sardinia (Italy)

The objective of this study was to evaluate the occurrence of E. coli in hunted wild boars in Sardinia (Italy) and to further characterize the isolates with Whole Genome Sequencing to assess the genetic relatedness and the presence of virulence and antimicrobial resistance (AMR) genes. Samples were taken from 66 wild boars between 2020 and 2022 slaughtered in five hunting houses. A total of 181 samples were tested, including 66 samples from mesenteric lymph nodes, 66 samples from colon content and 49 samples from carcass surface. Isolates referable to Escherichia species were detected in all of the wild boars sampled. On a selection of 61 isolates, sequencing was conducted and antimicrobial susceptibility was tested. Among these, three isolates were confirmed to be two Escherichia marmotae (cryptic clade V) and one Escherichia ruysiae (cryptic clade III). E. coli pathotypes identified were UPEC (13 %), ExPEC-UPEC (5.6 %) and ETEC (3.7 %). Moreover, 3/6 E. marmotae isolates had typical ExPEC genes. Genetic similarity was observed in isolates collected from animals slaughtered in the same hunting house; this suggests epidemiological links deriving from the presence of animals infected with closely related strains or the result of cross-contamination. Antimicrobial resistance genes were detected in three non-pathogenic E. coli isolates: one isolate had sul2, tet(B), aph(6)-ld and aph(3″)-lb resistance genes and two had the fosA7 gene. This study confirmed that wild boars can act as reservoirs and spreaders of pathogenic Escherichia species and it provides information for future comparative genomic analysis in wildlife. Although isolates showed a limited resistome, the detection of resistance in non-pathogenic isolates underlines the need to monitor antimicrobial resistance in the wild boar population. To the best of our knowledge, this is the first detection of E. mamotae and E. ruysiae isolates in wild boars in Italy and the presence of this pathogen in wildlife and livestock need to be investigated further.

Source Control of Gram-Negative Bacteria Using Self-Disinfecting Sinks in a Swedish Burn Centre

Several retrospective studies have identified hospital sinks as reservoirs of Gram-negative bacteria. The aim of this study was to prospectively investigate the bacterial transmission from sinks to patients and if self-disinfecting sinks could reduce this risk. Samples were collected weekly from sinks (self-disinfecting, treated with boiling water, not treated) and patients in the Burn Centre at Linköping University Hospital, Sweden. The antibiotic susceptibility of Gram-negative isolates was tested, and eight randomly chosen patient isolates and their connected sink isolates were subjected to whole genome sequencing (WGS). Of 489 sink samples, 232 (47%) showed growth. The most frequent findings were Stenotrophomonas maltophilia (n = 130), Pseudomonas aeruginosa (n = 128), and Acinetobacter spp. (n = 55). Bacterial growth was observed in 20% of the samplings from the self-disinfecting sinks and in 57% from the sinks treated with boiling water (p = 0.0029). WGS recognized one transmission of Escherichia coli sampled from an untreated sink to a patient admitted to the same room. In conclusion, the results showed that sinks can serve as reservoirs of Gram-negative bacteria and that self-disinfecting sinks can reduce the transmission risk. Installing self-disinfecting sinks in intensive care units is an important measure in preventing nosocomial infection among critically ill patients.

Phylogroup typing and carbapenem resistance of Escherichia coli from agricultural samples in Metro Manila, Philippines

Primary production environment is considered as reservoir of Escherichia coli contamination of produce. E. coli is classified into eight phylogroups which differ in ecological niches, evolutionary history, and phenotypic properties. To understand the population genetic structure and composition of E. coli in primary production environments in Metro Manila, Philippines, a total of 80 E. coli recovered from irrigation water, soil, vegetables, and feces of cat, carabao, chicken, dog, and goat were allocated into distinct phylogroups based on the presence and absence of genetic markers. Results showed that the most prevalent phylogroup was B1 (71.3%), followed by A (18.6%), D (6.3%), B2 (1.3%), E (1.3%), and an unknown phylogroup (1.3%). The most prevalent genetic marker was arpA, followed by TspE4.C2, yjaA, and chuA. The carbapenem resistance of 24 E. coli isolates representing different phylogroups was also evaluated. Intriguingly, all isolates exhibited uniform susceptibility. This is the first report to provide insights into the phylogroup structure and composition, as well as carbapenem resistance of E. coli from primary production in the Philippines, which highlights possible source of and solution for gastrointestinal and enteric diseases.

Whole-Genome Sequencing and Virulome Analysis of Escherichia coli Isolated from New Zealand Environments of Contrasting Observed Land Use

Generic Escherichia coli is commonly used as an indicator of fecal contamination to assess water quality and human health risk. Where measured E. coli exceedances occur, the presence of other pathogenic microorganisms, such as Shiga toxin-producing E. coli (STEC), is assumed, but confirmatory data are lacking. Putative E. coli isolates (n = 709) were isolated from water, sediment, soil, periphyton, and feces samples (n = 189) from five sites representing native forest and agricultural environments. Ten E. coli isolates (1.41%) were stx₂ positive, 19 (2.7%) were eae positive, and stx₁-positive isolates were absent. At the sample level, stx₂-positive E. coli (5 of 189, 2.6%) and eae-positive isolates (16 of 189, 8.5%) were rare. Using real-time PCR, these STEC-associated virulence factors were determined to be more prevalent in sample enrichments (stx₁, 23.9%; stx₂, 31.4%; eae, 53.7%) and positively correlated with generic E. coli isolate numbers (P < 0.05) determined using culture-based methods. Whole-genome sequencing (WGS) was undertaken on a subset of 238 isolates with assemblies representing seven E. coli phylogroups (A, B1, B2, C, D, E, and F), 22 Escherichia marmotae isolates, and 1 Escherichia ruysiae isolate. Virulence factors, including those from extraintestinal pathogenic E. coli, were extremely diverse in isolates from the different locations and were more common in phylogroup B2. Analysis of the virulome from WGS data permitted the identification of gene repertoires that may be involved in environmental fitness and broadly align with phylogroup. Although recovery of STEC isolates was low, our molecular data indicate that they are likely to be widely present in environmental samples containing diverse E. coli phylogroups. IMPORTANCE This study takes a systematic sampling approach to assess the public health risk of Escherichia coli recovered from freshwater sites within forest and farmland. The New Zealand landscape is dominated by livestock farming, and previous work has demonstrated that "recreational exposure to water" is a risk factor for human infection by Shiga toxin-producing Escherichia coli (STEC). Though STEC isolates were rarely isolated from water samples, STEC-associated virulence factors were identified more commonly from water sample culture enrichments and were associated with increased generic E. coli concentrations. Whole-genome sequencing data from both E. coli and newly described Escherichia spp. demonstrated the presence of virulence factors from E. coli pathotypes, including extraintestinal pathogenic E. coli. This has significance for understanding and interpreting the potential health risk from E. coli where water quality is poor and suggests a role of virulence factors in survival and persistence of E. coli and Escherichia spp.

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.

The Darkest Place Is under the Candlestick-Healthy Urogenital Tract as a Source of Worldwide Disseminated Extraintestinal Pathogenic Escherichia coli Lineages

Since the discovery of the urinary microbiome, including the identification of Escherichia coli in healthy hosts, its involvement in UTI development has been a subject of high interest. We explored the population diversity and antimicrobial resistance of E. coli (n = 22) in the urogenital microbiome of ten asymptomatic women (representing 50% of the sample tested). We evaluated their genomic relationship with extraintestinal pathogenic E. coli (ExPEC) strains from healthy and diseased hosts, including the ST131 lineage. E. coli prevalence was higher in vaginal samples than in urine samples, and occasionally different lineages were observed in the same individual. Furthermore, B2 was the most frequent phylogenetic group, with the most strains classified as ExPEC. Resistance to antibiotics of therapeutic relevance (e.g., amoxicillin-clavulanate conferred by blaTEM-30) was observed in ExPEC widespread lineages sequence types (ST) 127, ST131, and ST73 and ST95 clonal complexes. Phylogenomics of ST131 and other ExPEC lineages revealed close relatedness with strains from gastrointestinal tract and diseased host. These findings demonstrate that healthy urogenital microbiome is a source of potentially pathogenic and antibiotic resistant E. coli strains, including those causing UTI, e.g., ST131. Importantly, diverse E. coli lineages can be observed per individual and urogenital sample type which is relevant for future studies screening for this uropathogen.

Epidemiologic and molecular characterization of β-lactamase-producing multidrug-resistant uropathogenic Escherichia coli isolated from asymptomatic hospitalized patients

Uropathogenic Escherichia coli (UPECs) are the predominant cause of asymptomatic bacteriuria (ABU) and symptomatic UTI. In this study, multidrug-resistant (MDR) ABU-UPECs from hospitalized patients of Kolkata, India, were characterized with respect to their ESBL phenotype, acquisition of β-lactamase genes, mobile genetic elements (MGEs), phylotype property, ERIC-PCR profile, sequence types (STs), clonal complexes (CCs) and evolutionary and quantitative relationships and compared to the symptomatic ones to understand their epidemiology and evolutionary origin. Statistically significant incidence of ESBL producers, β-lactamase genes, MGEs and novel phylotype property (NPP) among ABU-UPECs similar to the symptomatic ones indicated the probable incidence of chromosomal plasticity on resistance gene acquisition through MGEs due to indiscriminate drug usage. ERIC-PCR typing and MLST analysis showed clonal heterogeneity and predominance of ST940 (CC448) among asymptomatic isolates akin to symptomatic ones along with the evidence of zoonotic transmissions. Minimum spanning tree analysis showed a close association between ABU-UPEC with known and unidentified STs having NPPs with isolates that belonged to phylogroups clade I, D, and B2. This is the first study that reported the occurrence of MGEs and NPPs among ABU-UPECs with the predominance of ESBL production which displayed the deleterious effect of MDR among this pathogen demanding alternative therapeutic interventions. Moreover, this study for the first time attempted to introduce a new approach to ascertain the phylotype property of unassigned UPECs. Withal, increased recognition, proper understanding and characterization of ABU-UPECs with the implementation of appropriate therapeutic measures against them when necessary are the need of the era which otherwise might lead to serious complications in the vulnerable population.

ESBL/AmpC-Producing Escherichia coli in Wild Boar: Epidemiology and Risk Factors

The complex health problem of antimicrobial resistance (AMR) involves many host species, numerous bacteria and several routes of transmission. Extended-spectrum β-lactamase and AmpC (ESBL/AmpC)-producing Escherichia coli are among the most important strains. Moreover, wildlife hosts are of interest as they are likely antibiotics free and are assumed as environmental indicators of AMR contamination. Particularly, wild boar (Sus scrofa) deserves attention because of its increased population densities, with consequent health risks at the wildlife-domestic-human interface, and the limited data available on AMR. Here, 1504 wild boar fecal samples were microbiologically and molecularly analyzed to investigate ESBL/AmpC-producing E. coli and, through generalized linear models, the effects of host-related factors and of human population density on their spread. A prevalence of 15.96% of ESBL/AmpC-producing E. coli, supported by bla_CTX-M (12.3%), bla_TEM (6.98%), bla_CMY (0.86%) and bla_SHV (0.47%) gene detection, emerged. Young animals were more colonized by ESBL/AmpC strains than older subjects, as observed in domestic animals. Increased human population density leads to increased bla_TEM prevalence in wild boar, suggesting that spatial overlap may favor this transmission. Our results show a high level of AMR contamination in the study area that should be further investigated. However, a role of wild boar as a maintenance host of AMR strains emerged.

Genomic Insights into Drug Resistance and Virulence Platforms, CRISPR-Cas Systems and Phylogeny of Commensal E. coli from Wildlife

Commensal bacteria act as important reservoirs of virulence and resistance genes. However, existing data are generally only focused on the analysis of human or human-related bacterial populations. There is a lack of genomic studies regarding commensal bacteria from hosts less exposed to antibiotics and other selective forces due to human activities, such as wildlife. In the present study, the genomes of thirty-eight E. coli strains from the gut of various wild animals were sequenced. The analysis of their accessory genome yielded a better understanding of the role of the mobilome on inter-bacterial dissemination of mosaic virulence and resistance plasmids. The study of the presence and composition of the CRISPR/Cas systems in E. coli from wild animals showed some viral and plasmid sequences among the spacers, as well as the relationship between CRISPR/Cas and E. coli phylogeny. Further, we constructed a single nucleotide polymorphisms-based core tree with E. coli strains from different sources (humans, livestock, food and extraintestinal environments). Bacteria from humans or highly human-influenced settings exhibit similar genetic patterns in CRISPR-Cas systems, plasmids or virulence/resistance genes-carrying modules. These observations, together with the absence of significant genetic changes in their core genome, suggest an ongoing flow of both mobile elements and E. coli lineages between human and natural ecosystems.

Antimicrobial Resistance Profile and ExPEC Virulence Potential in Commensal Escherichia coli of Multiple Sources

We recently described the genetic antimicrobial resistance and virulence profile of a collection of 279 commensal E. coli of food-producing animal (FPA), pet, wildlife and human origin. Phenotypic antimicrobial resistance (AMR) and the role of commensal E. coli as reservoir of extra-intestinal pathogenic Escherichia coli (ExPEC) virulence-associated genes (VAGs) or as potential ExPEC pathogens were evaluated. The most common phenotypic resistance was to tetracycline (76/279, 27.24%), sulfamethoxazole/trimethoprim (73/279, 26.16%), streptomycin and sulfisoxazole (71/279, 25.45% both) among the overall collection. Poultry and rabbit were the sources mostly associated to AMR, with a significant resistance rate (p > 0.01) to quinolones, streptomycin, sulphonamides, tetracycline and, only for poultry, to ampicillin and chloramphenicol. Finally, rabbit was the source mostly associated to colistin resistance. Different pandemic (ST69/69*, ST95, ST131) and emerging (ST10/ST10*, ST23, ST58, ST117, ST405, ST648) ExPEC sequence types (STs) were identified among the collection, especially in poultry source. Both ST groups carried high number of ExPEC VAGs (pandemic ExPEC STs, mean = 8.92; emerging ExPEC STs, mean = 6.43) and showed phenotypic resistance to different antimicrobials (pandemic ExPEC STs, mean = 2.23; emerging ExPEC STs, mean = 2.43), suggesting their role as potential ExPEC pathogens. Variable phenotypic resistance and ExPEC VAG distribution was also observed in uncommon ExPEC lineages, suggesting commensal flora as a potential reservoir of virulence (mean = 3.80) and antimicrobial resistance (mean = 1.69) determinants.

Wildlife as Sentinels of Antimicrobial Resistance in Germany?

The presence of bacteria carrying antimicrobial resistance (AMR) genes in wildlife is an indicator that resistant bacteria of human or livestock origin are widespread in the environment. In addition, it could represent an additional challenge for human health, since wild animals could act as efficient AMR reservoirs and epidemiological links between human, livestock and natural environments. The aim of this study was to investigate the occurrence and the antibiotic resistance patterns of several bacterial species in certain wild animals in Germany, including wild boars (Sus scrofa), roe deer (Capreolus capreolus) and wild ducks (family Anatidae, subfamily Anatinae) and geese (family Anatidae, subfamily Anserinae). In the framework of the German National Zoonoses Monitoring Program, samples from hunted wild boars, roe deer and wild ducks and geese were collected nationwide in 2016, 2017, and 2019, respectively. Fecal samples were tested for the presence of Salmonella spp. (in wild boars and wild ducks and geese), Campylobacter spp. (in roe deer and wild ducks and geese), Shiga toxin-producing Escherichia (E.) coli (STEC), commensal E. coli and extended-spectrum beta-lactamase- (ESBL) or ampicillinase class C (AmpC) beta-lactamase-producing E. coli (in wild boars, roe deer and wild ducks and geese). In addition, the presence of methicillin-resistant Staphylococcus aureus (MRSA) was investigated in nasal swabs from wild boars. Isolates obtained in the accredited regional state laboratories were submitted to the National Reference Laboratories (NRLs) for confirmation, characterization and phenotypic resistance testing using broth microdilution according to CLSI. AMR was assessed according to epidemiological cut-offs provided by EUCAST. Salmonella spp. were isolated from 13 of 552 (2.4%) tested wild boar fecal samples, but absent in all 101 samples from wild ducks and geese. Nine of the 11 isolates that were submitted to the NRL Salmonella were susceptible to all tested antimicrobial substances. Campylobacter spp. were isolated from four out of 504 (0.8%) roe deer fecal samples, but not from any of the samples from wild ducks and geese. Of the two isolates received in the NRL Campylobacter, neither showed resistance to any of the substances tested. From roe deer, 40.2% of the fecal samples (144 of 358) yielded STEC compared to 6.9% (37 of 536) from wild boars. In wild ducks and geese, no STEC isolates were found. Of 150 STEC isolates received in the NRL (24 from wild boars and 126 from roe deer), only one from each animal species showed resistance. Of the 219 isolates of commensal E. coli from wild boars tested for AMR, 210 were susceptible to all 14 tested substances (95.9%). In roe deer this proportion was even higher (263 of 269, 97.8%), whereas in wild ducks and geese this proportion was lower (41 of 49, 83.7%). Nevertheless, selective isolation of ESBL-/AmpC-producing E. coli yielded 6.5% (36 of 551) positive samples from wild boars, 2.3% (13 of 573) from roe deer and 9.8% (10 of 102) from wild ducks and geese. Among the 25 confirmed ESBL-/AmpC-producing isolates from wild boars, 14 (56.0%) showed resistance up to five classes of substances. This proportion was lower in roe deer (3 of 12, 25%) and higher in wild ducks and geese (7 of 10, 70%). None of the 577 nasal swabs from wild boars yielded MRSA. Results indicate that overall, the prevalence of resistant bacteria from certain wild animals in Germany is low, which may reflect not only the low level of exposure to antimicrobials but also the low level of resistant bacteria in the areas where these animals live and feed. However, despite this low prevalence, the patterns observed in bacteria from the wild animals included in this study are an indicator for specific resistance traits in the environment, including those to highest priority substances such as 3rd generation cephalosporins, fluoroquinolones and colistin. Therefore, also continuous monitoring of the occurrence of such bacteria in wildlife by selective isolation is advisable. Furthermore, the possible role of wildlife as reservoir and disperser of resistant bacteria would need to be assessed, as wild animals, and in particular wild ducks and geese could become spreaders of resistant bacteria given their capacity for long-range movements.

Resistance to critically important antimicrobials in Australian silver gulls (Chroicocephalus novaehollandiae) and evidence of anthropogenic origins

OBJECTIVES

Antimicrobial resistance (AMR) to critically important antimicrobials (CIAs) amongst Gram-negative bacteria can feasibly be transferred amongst wildlife, humans and domestic animals. This study investigated the ecology, epidemiology and origins of CIA-resistant Escherichia coli carried by Australian silver gulls (Chroicocephalus novaehollandiae), a gregarious avian wildlife species that is a common inhabitant of coastal areas with high levels of human contact.

METHODS

Sampling locations were widely dispersed around the perimeter of the Australian continent, with sites separated by up to 3500 km. WGS was used to study the diversity and molecular characteristics of resistant isolates to ascertain their epidemiological origin.

RESULTS

Investigation of 562 faecal samples revealed widespread occurrence of extended-spectrum cephalosporin-resistant (21.7%) and fluoroquinolone-resistant (23.8%) E. coli. Genome sequencing revealed that CIA-resistant E. coli isolates (n = 284) from gulls predominantly belonged to human-associated extra-intestinal pathogenic E. coli (ExPEC) clones, including ST131 (17%), ST10 (8%), ST1193 (6%), ST69 (5%) and ST38 (4%). Genomic analysis revealed that gulls carry pandemic ExPEC-ST131 clades (O25:H4 H30-R and H30-Rx) and globally emerging fluoroquinolone-resistant ST1193 identified among humans worldwide. Comparative analysis revealed that ST131 and ST1193 isolates from gulls overlapped extensively with human clinical isolates from Australia and overseas. The present study also detected single isolates of carbapenem-resistant E. coli (ST410-blaOXA-48) and colistin-resistant E. coli (ST345-mcr-1).

CONCLUSIONS

The carriage of diverse CIA-resistant E. coli clones that strongly resemble pathogenic clones from humans suggests that gulls can act as ecological sponges indiscriminately accumulating and disseminating CIA-resistant bacteria over vast distances.

Pathotypes and Antimicrobial Susceptibility of Escherichia Coli Isolated from Wild Boar (Sus scrofa) in Tuscany

Wild boar are among the most widespread wild mammals in Europe. Although this species can act as a reservoir for different pathogens, data about its role as a carrier of pathogenic and antimicrobial-resistant Escherichia coli are still scarce. The aim of this study was to evaluate the occurrence of antimicrobial-resistant and pathogenic Escherichia coli in wild boar in the Tuscany region of Italy. During the hunting season of 2018-2019, E. coli was isolated from 175 of 200 animals and subjected to antimicrobial resistance tests and PCR for detection of resistance and virulence factor genes. The highest resistance rates were against cephalothin (94.3%), amoxicillin-clavulanic acid (87.4%), ampicillin (68.6%), and tetracycline (44.6%). The most detected resistance genes were blaCMY-2 (54.3%), sul1 (38.9%), sul2 (30.9%), and tetG (24.6%). Concerning genes encoding virulence factors, 55 of 175 isolates (31.4%) were negative for all tested genes. The most detected genes were hlyA (47.4%), astA (29.1%), stx2 (24.6%), eaeA (17.1%), and stx1 (11.4%). E. coli was classified as Shiga toxin-producing E. coli (STEC) (21.7%), enterohemorrhagic E. coli (EHEC) (6.3%), enteroaggregative E. coli (EAEC) (5.1%), and atypical enteropathogenic E. coli (aEPEC) (3.4%). Enterotoxigenic E. coli (ETEC), enteroinvasive E. coli (EIEC), and typical enteropathogenic E. coli (tEPEC) were not detected. Our results show that wild boars could carry pathogenic and antimicrobial-resistant E. coli, representing a possible reservoir of domestic animal and human pathogens.

The Aquatic Ecosystem, a Good Environment for the Horizontal Transfer of Antimicrobial Resistance and Virulence-Associated Factors Among Extended Spectrum β-lactamases Producing E. coli

One of the main public health problems nowadays is the increase of antimicrobial resistance, both in the hospital environment and outside it (animal environment, food and aquatic ecosystems, among others). It is necessary to investigate the virulence-associated factors and the ability of horizontal gene transfer among bacteria for a better understanding of the pathogenicity and the mechanisms of dissemination of resistant bacteria. Therefore, the objective of this work was to detect several virulence factors genes (fimA, papC, papG III, cnf1, hlyA and aer) and to determine the conjugative capacity in a wide collection of extended-spectrum β-lactamases-producing E. coli isolated from different sources (human, food, farms, rivers, and wastewater treatment plants). Regarding virulence genes, fimA, papC, and aer were distributed throughout all the studied environments, papG III was mostly related to clinical strains and wastewater is a route of dissemination for cnf1 and hlyA. Strains isolated from aquatic environments showed an average conjugation frequencies of 1.15 × 10⁻¹ ± 5 × 10⁻¹, being significantly higher than those observed in strains isolated from farms and food (p < 0.05), with frequencies of 1.53 × 10⁻⁴ ± 2.85 × 10⁻⁴ and 9.61 × 10⁻⁴ ± 1.96 × 10⁻³, respectively. The reported data suggest the importance that the aquatic environment (especially WWTPs) acquires for the exchange of genes and the dispersion of resistance. Therefore, specific surveillance programs of AMR indicators in wastewaters from animal or human origin are needed, in order to apply sanitation measures to reduce the burden of resistant bacteria arriving to risky environments as WWTPs.

Metagenomic Analysis of Acquired Antibiotic Resistance Determinants in the Gut Microbiota of Wild Boars (Sus Scrofa) - Preliminary Results

Introduction

Land application of manure that contains antibiotics and resistant bacteria may facilitate the establishment of an environmental reservoir of antibiotic-resistant microbes, promoting their dissemination into agricultural and natural habitats. The main objective of this study was to search for acquired antibiotic resistance determinants in the gut microbiota of wild boar populations living in natural habitats.

Material and Methods

Gastrointestinal samples of free-living wild boars were collected in the Zemplén Mountains in Hungary and were characterised by culture-based, metagenomic, and molecular microbiological methods. Bioinformatic analysis of the faecal microbiome of a hunted wild boar from Japan was used for comparative studies. Also, shotgun metagenomic sequencing data of two untreated sewage wastewater samples from North Pest (Hungary) from 2016 were analysed by bioinformatic methods. Minimum spanning tree diagrams for seven-gene MLST profiles of 104 E. coli strains isolated in Europe from wild boars and domestic pigs were generated in Enterobase.

Results

In the ileum of a diarrhoeic boar, a dominant E. coli O112ab:H2 strain with intermediate resistance to gentamicin, tobramycin, and amikacin was identified, displaying sequence type ST388 and harbouring the EAST1 toxin astA gene. Metagenomic analyses of the colon and rectum digesta revealed the presence of the tetQ, tetW, tetO, and mefA antibiotic resistance genes that were also detected in the gut microbiome of four other wild boars from the mountains. Furthermore, the tetQ and cfxA genes were identified in the faecal microbiome of a hunted wild boar from Japan.

Conclusion

The gastrointestinal microbiota of the free-living wild boars examined in this study carried acquired antibiotic resistance determinants that are highly prevalent among domestic livestock populations.

Diversity, Virulence, and Clinical Significance of Extended-Spectrum β-Lactamase- and pAmpC-Producing Escherichia coli From Companion Animals

Escherichia coli are opportunistic pathogens with the potential to cause a variety of infections in both humans and animals and in many cases have developed antimicrobial resistance. In this study, we characterized extended-spectrum cephalosporin resistant (ESCR) E. coli isolates from diseased companion animals (dogs, cats, and horses) and related the results to clinical findings. ESCR E. coli clinical isolates obtained over a 6-year period were screened for extended-spectrum β-lactamase (ESBL) and/or plasmid mediated AmpC (pAmpC) and virulence markers likely to be associated with extraintestinal pathogenic E. coli (ExPEC). ESBL and/or pAmpC genetic determinants were identified in 79.9% of the ESCR E. coli isolates with bla CTX-M genes being the most common ESBL genotype of which bla CTX-M-15, bla CTX-M-14, and bla CTX-M-55 were the most prevalent. In addition, bla CMY -2 was the most common genotype identified amongst pAmpC producing isolates. Phylogenetic group typing showed that B2 was the most prevalent phylogroup among the ESCR E. coli isolates, followed by the closely related phylogroups D and F which are also associated with extra-intestinal infections. ESCR was also identified in phylogroups commonly regarded as commensals (B1, A, and C). Virulence factor (VF) scores >2 were mostly present amongst isolates in phylogroup B2. Higher virulence scores were found in isolates lacking ESBL/pAmpC resistance genes compared with those carrying both genes (p < 0.05). Five of phylogroup B2 isolates, were typed to the pandemic virulent O25b-ST131 clone and three ST131 isolates carrying bla CTX-M-15 belonged to the subclade C2/H30Rx whilst one isolate carrying bla CTX-M-27 typed to the recently described sub-clade C1-M27. MLST typing also identified other sequence types commonly associated with infections in humans (ST410, ST10, and ST648). Most ESCR E. coli isolates obtained in pure growth were cultured from normally sterile body sites (mostly from urinary tract infections, UTIs) whilst only a small proportion were obtained from body sites populated with commensal flora (p < 0.0001). Our study has shown that ExPEC ESBL/pAmpC producing E. coli isolates are common amongst companion animal isolates and are associated with colonization and infection. In addition, their isolation from a normally sterile site is likely to be clinically significant and warrants antimicrobial treatment.

Bats as reservoirs of antibiotic resistance determinants: A survey of class 1 integrons in Grey-headed Flying Foxes (Pteropus poliocephalus)

Increasing reports of antimicrobial resistance in wildlife highlight the significance of a One Health approach to managing resistance. We investigated the prevalence and diversity of class 1 integrons, a genetic determinant of resistance, in grey-headed flying foxes, a large fruit bat species belonging to the order Chiroptera. Class 1 integrons were detected in both wild flying foxes (5.3%) and captive flying foxes (41.2%) housed in wildlife rehabilitation facilities. Genes encoding resistance to aminoglycosides, trimethoprim and beta-lactams, and Qac efflux pumps were detected. Analysis of conserved integron elements and gene cassette arrays indicate the direction of integron transfer is from humans to flying foxes. The detection of two novel gene cassette arrays (5'CS-qacH-aacA34-bla_OXA-21-3'CS and 5'CS-qacF-3'CS strongly suggests acquisition of genes from the environmental resistome into class 1 integrons within the flying fox microbiota. The dynamics of class 1 integrons in flying foxes indicates bats have a role in the emergence of novel antibiotic resistance determinants.