The role of wildlife (wild birds) in the global transmission of antimicrobial resistance genes

Antibiotic-resistant Escherichia coli from treated municipal wastewaters and Black-headed Gull nestlings on the recipient river

Wastewaters belong among the most important sources of environmental pollution, including antibiotic-resistant bacteria. The aim of the study was to evaluate treated wastewaters as a possible transmission pathway for bacterial colonisation of gulls occupying the receiving river. A collection of antibiotic-resistant Escherichia coli originating both from treated municipal wastewaters discharged to the river Svratka (Czech Republic) and nestlings of Black-headed Gull (Chroicocephalus ridibundus) living 35 km downstream of the outlet was obtained using selective cultivation. Isolates were further characterised by various phenotyping and genotyping methods. From a total of 670 E. coli isolates (450 from effluents, 220 from gulls), 86 isolates (41 from effluents, 45 from gulls) showed identical antibiotic resistance phenotype and genotype and were further analysed for clonal relatedness using pulsed-field gel electrophoresis (PFGE). Despite the overall high diversity of the isolates, 21 isolates from both sources showed similar PFGE profiles. Isolates belonging to epidemiologically important sequence types (ST131, 15 isolates; ST23, three isolates) were subjected to whole-genome sequencing. Subsequent phylogenetic analysis did not reveal any close clonal relationship between the isolates from the effluents and gulls' nestlings with the closest strains showing 90 SNPs difference. Although our study did not provide direct evidence of transmission of antibiotic-resistant E. coli to wild gulls via treated wastewaters, we observed gull chicks as carriers of diverse multi-resistant E. coli, including high-risk clones, posing risk of further bacterial contamination of the surrounding environment.

Comparative metagenomics of microbial communities and resistome in southern farming systems: implications for antimicrobial stewardship and public health

Agricultural practices significantly influence microbial diversity and the distribution of virulence and antimicrobial resistance (AMR) genes, with implications for ecosystem health and food safety. This study used metagenomic sequencing to analyze 60 samples (30 per state) including water, soil, and manure (10 each) from Alabama (a mix of cattle and poultry sources) and Tennessee (primarily from cattle). The results highlighted a rich microbial diversity, predominantly comprising Bacteria (67%) and Viruses (33%), with a total of over 1,950 microbial species identified. The dominant bacterial phyla were Proteobacteria, Cyanobacteria, Actinobacteria, Firmicutes, and Bacteroidetes, with the viral communities primarily represented by Phixviricota and Uroviricota. Distinct state-specific microbial profiles were evident, with Alabama demonstrating a higher prevalence of viral populations and unique bacterial phyla compared to Tennessee. The influence of environmental and agricultural practices was reflected in the microbial compositions: soil samples were notably rich in Actinobacteria, water samples were dominated by Proteobacteria and Cyanobacteria, and manure samples from Alabama showed a predominance of Actinobacteria. Further analyses, including diversity assessment and enterotype clustering, revealed complex microbial structures. Tennessee showed higher microbial diversity and phylogenetic complexity across most sample types compared to Alabama, with poultry-related samples displaying distinct diversity trends. Principal Coordinate Analysis (PCoA) highlighted notable state-specific variations, particularly in manure samples. Differential abundance analysis demonstrated elevated levels of Deinococcus and Ligilactobacillus in Alabama, indicating regional effects on microbial distributions. The virulome analysis revealed a significant presence of virulence genes in samples from Alabama. The community resistome was extensive, encompassing 109 AMR genes across 18 antibiotic classes, with manure samples displaying considerable diversity. Ecological analysis of the interactions between AMR gene subtypes and microbial taxa revealed a sophisticated network, often facilitated by bacteriophages. These findings underscore the critical role of agricultural practices in shaping microbial diversity and resistance patterns, highlighting the need for targeted AMR mitigation strategies in agricultural ecosystems to protect both public health and environmental integrity.

Comparative Genomic Analyses of E. coli ST2178 Strains Originated from Wild Birds in Pakistan

The emergence and spread of multidrug-resistance (MDR) pathogenic Escherichia coli due to horizontal gene transfer of antibiotic resistance genes (ARGs) and virulence factors (VFs) is a global health concern, particularly in developing countries. While numerous studies have focused on major sequence types (STs), the implication of minor STs in ARG dissemination and their pathogenicity remains crucial. In this study, two E. coli strains (PEC1011 and PEC1012) were isolated from wild bird feces in Pakistan and identified as ST2178 based on their complete genome sequences. To understand this minor ST, 204 genome assemblies of ST2178 were comparatively analyzed with the isolates' genomes. The phylogenetic analyses revealed five subclades of ST2178. Subclade E strains were predominantly isolated from human specimens, whereas subclades A and B strains including strains PEC1011 and PEC1012, respectively, were frequently isolated from animal. Mobile genetic elements (MGEs) exhibited the positive correlation with ARGs but not with VFs in this ST. Plasmid-borne ARGs exhibited higher correlation with plasmid-borne MGEs, indicating the role of diverse mobile plasmid structures in ARG transmission. Subclade E exhibited diverse plasmid-borne ARG repertoires correlated with MGEs, marking it as a critical surveillance target. In the case of VFs, they exhibited phylogeny-dependent profiles. Strain PEC1012 harbored various plasmid-borne ARGs, which are similar with conserved ARG repertoires in subclade A. The presence of unique ARG insertion in pPEC1012 highlights the importance of subclade A in ARG dissemination. This study comprehensively elucidates the landscape of ST2178, identifying critical phylogenetic subclades and their characteristics in ARG and VF occurrence.

Global Trends of Antibiotic Resistance Genes in Staphylococcus aureus: A Comprehensive Genomic Analysis

Staphylococcus aureus (S. aureus) is a pathogen capable of causing severe diseases and exhibiting resistance to multiple antibiotics. However, there is a significant lack of comprehensive research on the global prevalence of its antibiotic resistance genes (ARGs). This study provided a comprehensive analysis of ARGs in S. aureus, using 113,842 S. aureus genome sequences from the National Center for Biotechnology Information database. The results revealed that a significant majority (84%) of these genomes harbored at least one ARG, with a total of 389,464 ARG sequences identified across 19 major types and 103 subtypes. These ARGs exhibited varied abundances and diversities, linked primarily to clinical cases worldwide. ARGs for fluoroquinolones, multidrug resistance, bacitracin, tetracyclines, beta-lactams, and aminoglycosides were notably abundant, ranging from 3.16 × 10-5 to 1.49 copies of ARG per million bp. Variations in the abundance and diversity of ARGs were observed between countries, with middle- and low-income countries showing higher gene abundance but lower diversity compared with high-income countries. Temporal analysis over 30 years showed a fluctuating decline in ARG abundance alongside an increase in diversity, suggesting evolving resistance mechanisms. The study also explored the role of mobile genetic elements in ARG dissemination, finding a substantial proportion of ARG subtypes associated with plasmids and insertion sequence elements, indicating their potential for spread across borders. The global distribution of mobile ARGs was further analyzed, revealing the extensive reach of certain ARGs across countries. This research provides valuable insights into the prevalence and dissemination of antibiotic resistance in S. aureus on a global scale, aiding in the development of effective monitoring and control strategies to combat ARGs in S. aureus and other pathogens.

A comparison of antibiotic resistance genes and mobile genetic elements in wild and captive Himalayan vultures

As the most widely distributed scavenger birds on the Qinghai-Tibetan Plateau, Himalayan vultures (Gyps himalayensis) feed on the carcasses of various wild and domestic animals, facing the dual selection pressure of pathogens and antibiotics and are suitable biological sentinel species for monitoring antibiotic resistance genes (ARGs). This study used metagenomic sequencing to comparatively investigate the ARGs and mobile genetic elements (MGEs) of wild and captive Himalayan vultures. Overall, the resistome of Himalayan vultures contained 414 ARG subtypes resistant to 20 ARG types, with abundances ranging from 0.01 to 1,493.60 ppm. The most abundant resistance type was beta-lactam (175 subtypes), followed by multidrug resistance genes with 68 subtypes. Decreases in the abundance of macrolide-lincosamide-streptogramin (MLS) resistance genes were observed in the wild group compared with the zoo group. A total of 75 genera (five phyla) of bacteria were predicted to be the hosts of ARGs in Himalayan vultures, and the clinical (102 ARGs) and high-risk ARGs (35 Rank I and 56 Rank II ARGs) were also analyzed. Among these ARGs, twenty-two clinical ARGs, nine Rank I ARG subtypes, sixteen Rank II ARG subtypes were found to differ significantly between the two groups. Five types of MGEs (128 subtypes) were found in Himalayan vultures. Plasmids (62 subtypes) and transposases (44 subtypes) were found to be the main MGE types. Efflux pump and antibiotic deactivation were the main resistance mechanisms of ARGs in Himalayan vultures. Decreases in the abundance of cellular protection were identified in wild Himalayan vultures compared with the captive Himalayan vultures. Procrustes analysis and the co-occurrence networks analysis revealed different patterns of correlations among gut microbes, ARGs, and MGEs in wild and captive Himalayan vultures. This study is the first step in describing the characterization of the ARGs in the gut of Himalayan vultures and highlights the need to pay more attention to scavenging birds.

KPC-2-producing Pseudomonas aeruginosa isolated from wild animals in Brazil

Pseudomonas aeruginosa an opportunistic pathogen that causes infections in hospitals and has high morbidity and mortality rates. In addition, it is a widely distributed environmental bacterium that can colonise a variety of habitats. Although wild animals do not have access to antibiotics, antibacterial resistance in these animals has increasingly been reported worldwide. Although the presence of Klebsiella pneumoniae carbapenemase (KPC) is uncommon in P. aeruginosa, it has been increasingly reported. This study examined KPC-2-producing P. aeruginosa in wild animals. A total of 27 P. aeruginosa isolates were obtained from clinical cases treated at the Microbiology Laboratory of the Veterinary Hospital of UFMT, Brazil. P. aeruginosa and blaKPC-2 carbapenemase resistance genes were identified using PCR. Antimicrobial susceptibility of KPC-producing P. aeruginosa was evaluated using the disk diffusion method. The blaKPC-2 gene was detected in 40.7% of the isolates (11/27). The rates of antimicrobial resistance and intermediate sensitivity were as follows: piperacillin/tazobactam (44.4%), imipenem (29.6%), meropenem (51.8%), amikacin (77.8%), cefepime (85.2%), and ciprofloxacin (70.4%). Twelve isolates were classified as Multidrug-resistant (MDR). This study presents the first report of P. aeruginosa with the blaKPC-2 gene in wild animals in Brazil, highlighting the importance of molecular research on resistance genes in P. aeruginosa from a One-Health perspective.

Molecular genotyping of Salmonella spp. isolated from cheese samples of local stores in Al-Diwaniyah city, Iraq

Background

Food safety is an important subject that the global cheese industry increases awareness of. This urges these economic sectors to elevate the level of research to minimize cheese contamination with pathogenic bacteria, such as Salmonella.

Aim

Based on these merits, this study was conducted to genotype Salmonella spp. isolated from cheese samples of local stores in Al-Diwaniyah City, Iraq.

Methods

The study used 41 samples of local fresh unsalted white cheese in a selective-growth-based isolation of Salmonella. These isolates were confirmed utilizing a slide-agglutination (SA) test and VITEK® 2 system (V2S). Then, the isolates were subjected to conventional PCR and sequencing techniques that both targeted the 16S rRNA gene. For subtyping, the Salmonella isolates were subjected to a random amplified polymorphic DNA (RAPD)-PCR method.

Results

The results of both SA and V2S revealed the presence of 14 (34.2%) isolates of Salmonella spp. in the cheese samples. The PCR confirmed 6 (42.9%) of these isolates, which further were defined with close nucleotide similarity (98.03%) and (97.88%) to different world isolates, such as Salmonella enterica subsp. Arizonae and Salmonella enterica subsp. enterica serovar Typhi, respectively. The RAPD-PCR findings showed different fragments for all the tested isolates.

Conclusion

The present study indicates that the samples of the local fresh unsalted white cheese contain different Salmonella genotypes, which could be originated from different contamination sources.

Zoonotic sources and the spread of antimicrobial resistance from the perspective of low and middle-income countries

BACKGROUND

Antimicrobial resistance is an increasing challenge in low and middle-income countries as it is widespread in these countries and is linked to an increased mortality. Apart from human and environmental factors, animal-related drivers of antimicrobial resistance in low- and middle-income countries have special features that differ from high-income countries. The aim of this narrative review is to address the zoonotic sources and the spread of antimicrobial resistance from the perspective of low- and middle-income countries.

MAIN BODY

Contamination with extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli is highest in poultry (Africa: 8.9-60%, Asia: 53-93%) and there is a risk to import ESBL-producing E. coli through poultry meat in Africa. In aquacultures, the proportion of ESBL-producers among E. coli can be high (27%) but the overall low quality of published studies limit the general conclusion on the impact of aquacultures on human health. ESBL-producing E. coli colonization of wildlife is 1-9% in bats or 2.5-63% birds. Since most of them are migratory animals, they can disperse antimicrobial resistant bacteria over large distances. So-called 'filth flies' are a relevant vector not only of enteric pathogens but also of antimicrobial resistant bacteria in settings where sanitary systems are poor. In Africa, up to 72.5% of 'filth flies' are colonized with ESBL-producing E. coli, mostly conferred by CTX-M (24.4-100%). While methicillin-resistant Staphylococcus aureus plays a minor role in livestock in Africa, it is frequently found in South America in poultry (27%) or pork (37.5-56.5%) but less common in Asia (poultry: 3%, pork: 1-16%).

CONCLUSIONS

Interventions to contain the spread of AMR should be tailored to the needs of low- and middle-income countries. These comprise capacity building of diagnostic facilities, surveillance, infection prevention and control in small-scale farming.

The global profile of antibiotic resistance in bacteria isolated from goats and sheep: A systematic review

Background and Aim

Antibiotic resistance has become an issue of global importance due to increasing levels of bacterial infections worldwide. Farm management and usage of antibiotics in livestock are known risk factors associated with the increase in global levels of antibiotic resistance. Goats and sheep are examples of livestock with large populations. Although antibiotic resistance in bacteria from livestock negatively affects both human health and the economy, the global data regarding this issue in goats and sheep are limited. Therefore, this study aimed to provide information on the antibiotic-resistance profile of bacteria isolated from goats and sheep worldwide (Asia, Europe, and Africa).

Materials and Methods

We performed a systematic review of articles published on this topic without any restriction on the year of publication. We searched the Directory of Open Access Journals, PubMed, Google Scholar, and Scopus using Boolean logic through various keywords. The search generated a total of 1325 articles, and after screening for duplicates and implementing inclusion and exclusion criteria, qualitative synthesis (i.e., qualitative systematic review) was performed on 37 articles.

Results

The synthesized information indicated that 18 Gram-positive and 13 Gram-negative bacterial species from goats and sheep were resistant to ten antibiotics, namely penicillin, ampicillin, amoxicillin, chloramphenicol, streptomycin, tetracycline, cephalothin, gentamicin, ciprofloxacin (CIP), and sulfamethoxazole. The prevalence of antibiotic resistance ranged from 0.4% to 100%. However, up to 100% of some bacteria, namely, Salmonella Dublin, Aeromonas caviae, and Aeromonas sobria, were susceptible to CIP. Staphylococcus aureus and Escherichia coli were highly resistant to all antibiotics tested. Moreover, eight of the ten antibiotics tested were critically important antibiotics for humans.

Conclusion

Antibiotic-resistant bacteria in goats and sheep are a potential risk to animal and human health. Collaboration between all stakeholders and further research is needed to prevent the negative impacts of antibiotic resistance.

Characterization of a Tigecycline-Resistant and blaCTX-M-Bearing Klebsiella pneumoniae Strain from a Peacock in a Chinese Zoo

In Chinese zoos, there are usually specially designed bird parks, similar to petting zoos, that allow children and adults to interact with diverse birds. However, such behaviors present a risk for the transmission of zoonotic pathogens. Recently, we isolated eight strains of Klebsiella pneumoniae and identified two blaCTX-M-positive strains from 110 birds, including parrots, peacocks, and ostriches, using anal or nasal swabs in a bird park of a zoo in China. There, K. pneumoniae LYS105A was obtained from a diseased peacock with chronic respiratory diseases by a nasal swab, which harbored the blaCTX-M-3 gene and exhibited resistance to amoxicillin, cefotaxime, gentamicin, oxytetracycline, doxycycline, tigecycline, florfenicol, and enrofloxacin. According to an analysis by whole-genome sequencing, K. pneumoniae LYS105A belongs to serotype ST859 (sequence type 859)-K19 (capsular serotype 19) and contains two plasmids, of which pLYS105A-2 can be transferred by electrotransformation and harbors numerous resistance genes such as blaCTX-M-3, aac(6')-Ib-cr5, and qnrB91. The above-mentioned genes are located in a novel mobile composite transposon, Tn7131, which makes horizontal transfer more flexible. Although no known genes were identified in the chromosome, a significant increase in SoxS upregulated the expression levels of phoPQ, acrEF-tolC, and oqxAB, which contributed to strain LYS105A acquiring resistance to tigecycline (MIC = 4 mg/L) and intermediate resistance to colistin (MIC = 2 mg/L). Altogether, our findings show that bird parks in zoos may act as important vehicles for the spread of multidrug-resistant bacteria from birds to humans and vice versa. IMPORTANCE A multidrug-resistant ST859-K19 K. pneumoniae strain, LYS105A, was obtained from a diseased peacock in a Chinese zoo. In addition, multiple resistance genes such as blaCTX-M-3, aac(6')-Ib-cr5, and qnrB91 were located in a novel composite transposon, Tn7131, of a mobile plasmid, implying that most of the resistance genes in strain LYS105A can be moved easily via horizontal gene transfer. Meanwhile, an increase in SoxS can further positively regulate the expression of phoPQ, acrEF-tolC, and oqxAB, which is the key factor for strain LYS105A to develop resistance to tigecycline and colistin. Taken together, these findings enrich our understanding of the horizontal cross-species spread of drug resistance genes, which will help us curb the development of bacterial resistance.

The potential role of migratory birds in the transmission of pathogenic Campylobacter species to broiler chickens in broiler poultry farms and live bird markets

BACKGROUND

Campylobacter species (spp.) are one of the most important zoonotic bacteria possessing potential hazards for animal and human health worldwide. Migratory birds are implicated as significant carriers for microbes and a play very important role in the dissemination of Campylobacter to broiler chickens and their environment. The purpose of this investigation was to detect the prevalence, antibiotic resistant patterns, virulence and diversity of pathogenic Campylobacter spp. in 7 migratory bird species (Northern shoveler, Common pochard, Common teal, Northern pintail, Eared Grebe, Great Crested Grebe and Garganey) and broiler chickens that were collected from broiler poultry farms and live bird markets.

RESULTS

The prevalence of Campylobacter was 12.5% (25/200), of which 15% (15/100) was recovered from 5 migratory bird species only and 10% (10/100) from broiler chickens. At the level of migratory birds, eight isolates (53.3%) were Campylobacter jejuni (C. jejuni) and 7 isolates (46.7%) were Campylobacter coli (C. coli) meanwhile, in broiler chickens C. jejuni and C. coli were 50% (5/10) for each. All isolated strains had phenotypic resistance to doxycycline, while all of the isolates were susceptible to amikacin. The multidrug resistance to three, four or five antimicrobial classes was found in 72% (18/25) of the isolated strains. The multiantibiotic resistance index between the examined isolates was 0.22-0.77, with 10 antibiotic resistance patterns. The virulence of isolated Campylobacter strains (from both migratory birds and broiler chicken birds) was detected by targeting the VirB11, ciaB and iam genes which were recorded at 16%, 52% and 100%, respectively. Additionally, 100% and 84% of the antibiotic resistance genes were identified as tetA and BlaOXA-61, respectively.

CONCLUSIONS

The results of this study revealed the diversity between all the isolated strains from migratory birds and their similarity to broiler chicken isolates. The findings of the present study highlight the impact of migratory birds visiting Egypt and other countries on pathogenic Campylobacter spp. carrying pathogenic virulence and resistance genes, necessitating the application of biosecurity measures to prevent migratory birds from entering farms during their migration period.

Detection of antimicrobial producing Staphylococcus from migratory birds: Potential role in nasotracheal microbiota modulation

A collection of 259 staphylococci of 13 different species [212 coagulase-negative (CoNS) and 47 coagulase-positive (CoPS)] recovered from nasotracheal samples of 87 healthy nestling white storks was tested by the spot-on-lawn method for antimicrobial-activity (AA) against 14 indicator bacteria. Moreover, extracts of AP isolates were obtained [cell-free-supernatants (CFS) both crude and concentrated and butanol extracts] and tested against the 14 indicator bacteria. The microbiota modulation capacity of AP isolates was tested considering: (a) intra-sample AA, against all Gram-positive bacteria recovered in the same stork nasotracheal sample; (b) inter-sample AA against a selection of representative Gram-positive bacteria of the nasotracheal microbiota of all the storks (30 isolates of 29 different species and nine genera). In addition, enzymatic susceptibility test was carried out in selected AP isolates and bacteriocin encoding genes was studied by PCR/sequencing. In this respect, nine isolates (3.5%; seven CoNS and two CoPS) showed AA against at least one indicator bacteria and were considered antimicrobial-producing (AP) isolates. The AP isolates showed AA only for Gram-positive bacteria. Three of these AP isolates (S. hominis X3764, S. sciuri X4000, and S. chromogenes X4620) revealed AA on all extract conditions; other four AP isolates only showed activity in extracts after concentration; the remaining two AP isolates did not show AA in any of extract conditions. As for the microbiota modulation evaluation, three of the nine AP-isolates revealed intra-sample AA. It is to highlight the potent inter-sample AA of the X3764 isolate inhibiting 73% of the 29 representative Gram-positive species of the nasotracheal stork microbiota population. On the other hand, enzymatic analysis carried out in the two highest AP isolates (X3764 and X4000) verified the proteinaceous nature of the antimicrobial compound and PCR analysis revealed the presence of lantibiotic-like encoding genes in the nine AP isolates. In conclusion, these results show that nasotracheal staphylococci of healthy storks, and especially CoNS, produce antimicrobial substances that could be important in the modulations of their nasal microbiota.

Characteristics of Wild Bird Resistomes and Dissemination of Antibiotic Resistance Genes in Interconnected Bird-Habitat Systems Revealed by Similarity of blaTEM Polymorphic Sequences

Wild birds are known to harbor and discharge antibiotic-resistant bacteria (ARB) and their associated antibiotic resistance genes (ARGs). However, assessments of their contribution to the dissemination of antibiotic resistance in the environment are limited to culture-dependent bacterial snapshots. Here, we present a high-throughput sequencing study that corroborates extensive ARG exchange between wild bird feces and their habitats and implies the need to scrutinize high-mobility birds as potential vectors for global propagation of ARGs. We characterized the resistome (281 ARGs) and microbiome of seven wild bird species and their terrestrial and aquatic habitats. The resistomes of bird feces were influenced by the microbial community structure, mobile genetic elements (MGEs), and residual antibiotics. We designated 33 ARGs found in more than 90% of the bird fecal samples as core ARGs of wild bird feces, among which 16 ARGs were shared as core ARGs in both wild bird feces and their habitats; these genes represent a large proportion of both the bird feces (35.0 ± 15.9%) and the environmental resistome (29.9 ± 21.4%). One of the most detected β-lactam resistance genes (bla_TEM, commonly harbored by multidrug resistant "superbugs") was used as molecular marker to demonstrate the high interconnectivity of ARGs between the microbiomes of wild birds and their habitats. Overall, this work provides a comprehensive analysis of the wild bird resistome and underscores the importance to consider genetic exchange between animals and the environment in the One Health approach.

Dissemination and prevalence of plasmid-mediated high-level tigecycline resistance gene tet (X4)

With the large-scale use of antibiotics, antibiotic resistant bacteria (ARB) continue to rise, and antibiotic resistance genes (ARGs) are regarded as emerging environmental pollutants. The new tetracycline-class antibiotic, tigecycline is the last resort for treating multidrug-resistant (MDR) bacteria. Plasmid-mediated horizontal transfer enables the sharing of genetic information among different bacteria. The tigecycline resistance gene tet(X) threatens the efficacy of tigecycline, and the adjacent ISCR2 or IS26 are often detected upstream and downstream of the tet(X) gene, which may play a crucial driving role in the transmission of the tet(X) gene. Since the first discovery of the plasmid-mediated high-level tigecycline resistance gene tet(X4) in China in 2019, the tet(X) genes, especially tet(X4), have been reported within various reservoirs worldwide, such as ducks, geese, migratory birds, chickens, pigs, cattle, aquatic animals, agricultural field, meat, and humans. Further, our current researches also mentioned viruses as novel environmental reservoirs of antibiotic resistance, which will probably become a focus of studying the transmission of ARGs. Overall, this article mainly aims to discuss the current status of plasmid-mediated transmission of different tet(X) genes, in particular tet(X4), as environmental pollutants, which will risk to public health for the "One Health" concept.

Spread and Molecular Characteristics of Enterobacteriaceae Carrying fosA -Like Genes from Farms in China

Here, we report the widespread and complex genetic environments of fosA -like genes in animal-derived strains in China. The fosA7.5 gene was identified in this study and was found to confer resistance to fosfomycin.

Detection of blaTEM, blaCTX-M, blaCMY, and blaSHV Genes Among Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Isolated from Migratory Birds Travelling to Bangladesh

Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli cause severe health hazards. Migratory birds are reservoirs and transmitters of many pathogens including ESBL-producing E. coli. To examine migratory birds as potential carriers of ESBL-producing E. coli and E. coli-carrying antibiotic resistance genes, 55 PCR-positive E. coli isolates were screened using the disk diffusion method, double-disk synergy test, and further polymerase chain reaction (PCR) tests. Genes encoding resistance to tetracycline [tetA, 100% (35/35); tetB, 31.43% (11/35)], fluoroquinolone [qnrA, 35.71% (10/28); qnrB, 25% (7/28)], and streptomycin [aadA1, 90.24% (37/41)] were detected in the isolated E. coli. Of the 55 E. coli isolates, 21 (38.18%) were ESBL producers, and all of them were multidrug resistant. All the ESBL-producing E. coli isolates harbored at least two or more beta-lactamase genes, of which bla_TEM, bla_CMY, bla_CTX-M, and bla_SHV were detected in 95.24%, 90.48%, 85.71%, and 42.86% of isolates, respectively. All the beta-lactamase genes were present in four of the ESBL-producing E. coli isolates. Furthermore, 95.24% of ESBL-producing E. coli isolates were positive for one or more antibiotic resistance genes. To the best of our knowledge, this is the first study to detect E. coli-carrying antibiotic resistance genes including beta-lactamase bla_CMY and bla_SHV originating from migratory birds in Bangladesh. These results suggest that migratory birds are potential carriers of ESBL-producing E. coli along with other clinically important antibiotic resistance genes which may have detrimental impacts on human health.

Antimicrobial susceptibility, plasmid replicon typing, phylogenetic grouping, and virulence potential of avian pathogenic and faecal Escherichia coli isolated from meat chickens in Australia

Globally, avian colibacillosis is a leading cause of morbidity and mortality in poultry, associated with economic losses and welfare problems. Here, clinical avian pathogenic E. coli isolates (CEC; n=50) and faecal E. coli isolates from healthy (FEC; n=187) Australian meat chickens collected between 2006 and 2014 were subjected to antimicrobial susceptibility testing, phylogenetic grouping, plasmid replicon (PR) typing, multilocus sequence typing, and virulence gene (VG) profiling. Extended-spectrum cephalosporin (ESC)- and fluoroquinolone (FQ)-resistant E. coli isolates underwent further genetic characterisation. Significant proportions of CEC and FEC were respectively susceptible (13/50 [26%]; 48/187 [26%],) or MDR (9/50 [18%]; 26/187 [14%]) to 20 tested antimicrobials. Phylogenetic groups A and C, and PR types IncFIB and IncFrep were most commonly represented. Five tested CEC-associated VGs were more prevalent in CEC (≥90%) compared to FEC isolates (≤58%). Some isolates (CEC n=3; FEC n=7) were resistant to ESCs and/or FQs and possessed signature mutations in chromosomal FQ target genes and plasmid-mediated qnrS, bla_CMY-2, and bla_DHA-1 genes. Sequence type 354 (n=4), associated with extraintestinal infections in a broad range of hosts, was prevalent among the ESC- and/or FQ-resistant FEC.This study confirmed the existence of a small reservoir of ESC- and FQ-resistant E. coli in Australian commercial meat chickens despite the absence of use in the industry of these drug classes. Otherwise, a diversity of VGs and PR types in both faecal and clinical E. coli populations were identified. It's hypothesised that the source of ESC- and FQ-resistant E. coli may be external to poultry production facilities.Highlights1. Low-level resistance to older and newer generation antimicrobial drugs detected2. The most common sequence type (ST) associated with FQ resistance was ST354 (4/10)3. A small proportion of CEC (n=3) and FEC (n=7) were resistant to ESCs and/or FQs.

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.

Comparative analysis of antimicrobial resistance and genetic characteristics of Escherichia coli from broiler breeder farms in Korea

Broiler breeder farms could be a reservoir of Escherichia coli, disseminating antimicrobial resistance and virulence factors. We investigated the antimicrobial resistance of E. coli from nine broiler breeder farms and characterised their resistance and virulence genes. A total of 256 E. coli showed a high level of resistance to tetracycline, nalidixic acid, ampicillin, and cephalothin, followed by trimethoprim-sulfamethoxazole and chloramphenicol. The resistance to nalidixic acid, ampicillin, trimethoprim–sulfamethoxazole, and chloramphenicol showed significant differences among the farms. Among 202 β-lactam-resistant E. coli, 138 carried β-lactamase genes. The most prevalent β-lactamase gene was blaTEM-1, of which the presence differed significantly across the farms. Out of 197 tetracycline-resistant E. coli isolates, tetA and tetB were detected in 164 and 50, with significant differences among the farms. Also, 45 of 196 nalidixic acid-resistant E. coli carried qnrS while 67 of 149 trimethoprim–sulfamethoxazole-resistant E. coli carried sul2. Among the five virulence genes tested, ompT was the most prevalent, and all genes except for iutA distributed significantly different among the farms. The phenotypic and genotypic characteristics of E. coli were significantly different among the farms; therefore, management at the breeder level is required to control the vertical transmission of E. coli.

Comparison of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Isolates From Rooks (Corvus frugilegus) and Contemporary Human-Derived Strains: A One Health Perspective

During winter, a large number of rooks gather and defecate at the park of a university clinic. We investigated the prevalence of extended-spectrum beta-lactamase (ESBL)–producing Escherichia coli in these birds and compared recovered isolates with contemporary human isolates. In 2016, fecal samples were collected from 112 trap-captured rooks and investigated for presence of ESBL producers using eosin methylene blue agar supplemented by 2 mg/L cefotaxime; 2,455 contemporary human fecal samples of patients of the clinics sent for routine culturing were tested similarly. In addition, 42 ESBL-producing E. coli isolates collected during the same period from inpatients were also studied. ESBL genes were sought for by PCR and were characterized by sequencing; E. coli ST131 clones were identified. Epidemiological relatedness was determined by pulsed-field gel electrophoresis and confirmed using whole genome sequencing in selected cases. Thirty-seven (33%) of sampled rooks and 42 (1.7%) of human stools yielded ESBL-producing E coli. Dominant genes were blaCTX–M–55 and blaCTX–M–27 in corvid, blaCTX–M–15 and blaCTX–M–27 in human isolates. ST162 was common among rooks. Two rook-derived E. coli belonged to ST131 C1-M27, which was also predominant (10/42) among human fecal and (15/42) human clinical isolates. Another potential link between rooks and humans was a single ST744 rook isolate grouped with one human fecal and three clinical isolates. Despite possible contact, genotypes shared between rooks and humans were rare. Thus, rooks are important as long-distance vectors and reservoirs of ESBL-producing E. coli rather than direct sources of infections to humans in our setting.

Migratory Birds as Vehicle to Transmit Multi Drug Resistant Extended Spectrum β Lactamase Producing Escherichia fergusonii, an Emerging Zoonotic Pathogen

The acquisition of multi-drug resistance (MDR) genes by pathogenic bacterial bugs and their dispersal to different food webs has become a silent pandemic. The multiplied use of different antibacterial therapeutics during COVID-19 pandemic has accelerated the process among emerging pathogens. Wild migratory birds play an important role in the spread of MDR pathogens and MDR gene flow due to the consumption of contaminated food and water. Escherichia fergusonii is an emerging pathogen of family Enterobacteriaceae and commonly causes disease in human and animals. The present study focused on the isolation of E. fergusonii from blood, saliva, and intestine of selected migratory birds of the Hazara Division. The sensitivity of isolated strains was assessed against ten different antibiotics. The isolation frequency of E. fergusonii was 69%. In blood samples, a high rate of resistance was observed against ceftriaxone (80%) followed by ampicillin (76%) whereas, in oral and intestinal samples, ceftriaxone resistant strains were 56% and 57% while ampicillin resistance was 49% and 52% respectively. The overall ceftriaxone and ampicillin-resistant cases in all three sample sources were 71% and 65% respectively. In comparison to oral and intestinal samples, high numbers of ceftriaxone-resistant strains were isolated from the blood of mallard while ampicillin-resistant strains were observed in blood samples of cattle egrets. 16S rRNA-based confirmed strains of E. fergusonii were processed for detection of CTX-M and TEM-1 gene through Polymerase chain reaction (PCR) after DNA extraction. Hundred percent ceftriaxone resistant isolates possessed CTX-M and all ampicillin-resistant strains harbored TEM-1 genes. Amplified products were sequenced by using the Sanger sequencing method and the resulted sequences were checked for similarity in the nucleotide Database through the BLAST program. TEM-1 gene showed 99% and the CTX-M gene showed 98% similar sequences in the Database. The 16S rRNA sequence and nucleotide sequences for TEM-1 and CTX-M genes were submitted to Gene Bank with accession numbers LC521304, LC521306, LC521307 respectively. We posit to combat MDR gene flow among the bacterial pathogens across different geographical locations, regular surveillance of new zoonotic pathogens must be conducted.

Polymyxin E-Resistant Gram-Negative Bacteria in Tunisia and Neighboring Countries: Are There Commonalities?

The current global dissemination of polymyxin E resistance constitutes a real public health threat because of the restricted therapeutic options. This review provides a comprehensive assessment of the epidemiology of polymyxin E-resistant bacteria, with special reference to colistin-resistant Gram-negative bacteria in Tunisia and neighboring countries, based on available published data to January 2020. We aimed to determine their prevalence by species and origin, shedding light on the different genes involved and illustrating their genetic support, genetic environment, and geographic distribution. We found that colistin resistance varies considerably among countries. A majority of the research has focused on Algeria (13 of 32), followed by Tunisia (nine of 32), Egypt (nine of 32), and Libya (one of 32). All these reports showed that colistin-resistant Gram-negative bacteria were dramatically disseminated in these countries, as well as in African wildlife. Moreover, high prevalence of these isolates was recorded from various sources (humans, animals, food products, and natural environments). Colistin resistance was mainly reported among Enterobacteriaceae, particularly Klebsiella pneumoniae and Escherichia coli. It was associated with chromosomal mutations and plasmid-mediated genes (mcr). Four mcr variants (mcr1, mcr2, mcr3, and mcr8), mobilized by several plasmid types (IncHI2, IncP, IncFIB, and IncI2), were detected in these countries and were responsible for their rapid spread. Countrywide dissemination of high-risk clones was also observed, including E. coli ST10 and K. pneumoniae ST101 and ST11. Intensified efforts to raise awareness of antibiotic use and legalization thereon are required in order to monitor and minimize the spread of multidrug-resistant bacteria.

Using whole-genome sequence data to examine the epidemiology of Salmonella, Escherichia coli and associated antimicrobial resistance in raccoons (Procyon lotor), swine manure pits, and soil samples on swine farms in southern Ontario, Canada

To better understand the contribution of wildlife to the dissemination of Salmonella and antimicrobial resistance in Salmonella and Escherichia coli, we examined whole-genome sequence data from Salmonella and E. coli isolates collected from raccoons (Procyon lotor) and environmental sources on farms in southern Ontario. All Salmonella and phenotypically resistant E. coli collected from raccoons, soil, and manure pits on five swine farms as part of a previous study were included. We assessed for evidence of potential transmission of these organisms between different sources and farms utilizing a combination of population structure assessments (using core-genome multi-locus sequence typing), direct comparisons of multi-drug resistant isolates, and epidemiological modeling of antimicrobial resistance (AMR) genes and plasmid incompatibility (Inc) types. Univariable logistic regression models were fit to assess the impact of source type, farm location, and sampling year on the occurrence of select resistance genes and Inc types. A total of 159 Salmonella and 96 resistant E. coli isolates were included. A diversity of Salmonella serovars and sequence types were identified, and, in some cases, we found similar or identical Salmonella isolates and resistance genes between raccoons, soil, and swine manure pits. Certain Inc types and resistance genes associated with source type were consistently more likely to be identified in isolates from raccoons than swine manure pits, suggesting that manure pits are not likely a primary source of those particular resistance determinants for raccoons. Overall, our data suggest that transmission of Salmonella and AMR determinants between raccoons and swine manure pits is uncommon, but soil-raccoon transmission appears to be occurring frequently. More comprehensive sampling of farms, and assessment of farms with other livestock species, as well as additional environmental sources (e.g., rivers) may help to further elucidate the movement of resistance genes between these various sources.

Occurrence of Mycoplasma spp. in wild birds: phylogenetic analysis and potential factors affecting distribution

Different Mycoplasma species have been reported in avian hosts. However, the majority of studies focus on one particular species of Mycoplasma or one host. In our research, we screened a total of 1141 wild birds representing 55 species, 26 families, and 15 orders for the presence of mycoplasmas by conventional PCR based on the 16S rRNA gene. Selected PCR products were sequenced to perform the phylogenetic analysis. All mycoplasma-positive samples were tested for M. gallisepticum and M. synoviae, which are considered the major pathogens of commercial poultry. We also verified the influence of ecological characteristics of the tested bird species including feeding habits, habitat types, and movement patterns. The presence of Mycoplasma spp. was confirmed in 498 birds of 29 species, but none of the tested birds were positive for M. gallisepticum or M. synoviae. We found possible associations between the presence of Mycoplasma spp. and all investigated ecological factors. The phylogenetic analysis showed a high variability of Mycoplasma spp.; however, some clustering of sequences was observed regarding particular bird species. We found that wild migratory waterfowl, particularly the white-fronted goose (Anser albifrons) and mallard (Anas platyrhynchos) could be reservoirs and vectors of mycoplasmas pathogenic to commercial waterfowl.

Antimicrobial Resistance in Loggerhead Sea Turtles (Caretta caretta): A Comparison between Clinical and Commensal Bacterial Isolates

Simple Summary

Gram negative organisms are frequently isolated from Caretta caretta and may contribute to the dissemination of antimicrobial resistance. In this study, commensal bacteria isolated from oral and cloacal samples of 98 healthy C. caretta were compared to clinical isolates isolated from the wounds of 102 injured animals, in order to investigate the presence of antimicrobial resistance bacteria in free-living loggerheads from the Adriatic Sea. A total of 410 bacteria were cultured and differences were noted in the isolated genera, as some of them were isolated only in healthy animals, while others were isolated only from injured animals. When tested for susceptibility to antimicrobials, clinical isolates showed highly significant differences in the antimicrobial resistance rates vs. commensal isolates for all the drugs tested, except for doxycycline. The detection of high antimicrobial resistance rates in loggerhead sea turtles is of clinical and microbiological significance since it impacts both the choice of a proper antibiotic therapy and the implementation of conservation programs.

Abstract

Gram negative organisms are frequently isolated from Caretta caretta turtles, which can act as reservoir species for resistant microorganisms in the aquatic environment. C. caretta, which have no history of treatment with antimicrobials, are useful sentinel species for resistant microbes. In this culture-based study, commensal bacteria isolated from oral and cloacal samples of 98 healthy C. caretta were compared to clinical isolates from the wounds of 102 injured animals, in order to investigate the presence of AMR bacteria in free-living loggerheads from the Adriatic Sea. A total of 410 isolates were cultured. Escherichia coli and genera such as Serratia, Moraxella, Kluyvera, Salmonella were isolated only in healthy animals, while Acinetobacter, Enterobacter, Klebsiella and Morganella were isolated only from the wounds of the injured animals. When tested for susceptibility to ampicillin, amoxicillin + clavulanic acid, ceftazidime, cefuroxime, gentamicin, doxycycline, ciprofloxacin and enrofloxacin, the clinical isolates showed highly significant differences in AMR rates vs. commensal isolates for all the drugs tested, except for doxycycline. The detection of high AMR rates in loggerheads is of clinical and microbiological significance since it impacts both the choice of a proper antibiotic therapy and the implementation of conservation programs.

The Role of Gulls as Reservoirs of Antibiotic Resistance in Aquatic Environments: A Scoping Review

The role of wildlife with long-range dispersal such as gulls in the global dissemination of antimicrobial resistance (AMR) across natural and anthropogenic aquatic environments remains poorly understood. Antibiotic-resistant bacteria have been detected in resident and migratory gulls worldwide for more than a decade, suggesting gulls as either sentinels of AMR pollution from anthropogenic sources or independent reservoirs that could maintain and disperse AMR across aquatic environments. However, confirming either of these roles remains challenging and incomplete. In this review, we present current knowledge on the geographic regions where AMR has been detected in gulls, the molecular characterization of resistance genes, and the evidence supporting the capacity of gulls to disperse AMR across regions or countries. We identify several limitations of current research to assess the role of gulls in the spread of AMR including most studies not identifying the source of AMR, few studies comparing bacteria isolated in gulls with other wild or domestic species, and almost no study performing longitudinal sampling over a large period of time to assess the maintenance and dispersion of AMR by gulls within and across regions. We suggest future research required to confirm the role of gulls in the global dispersion of AMR including the standardization of sampling protocols, longitudinal sampling using advanced satellite tracking, and whole-genome sequencing typing. Finally, we discuss the public health implications of the spread of AMR by gulls and potential solutions to limit its spread in aquatic environments.

Clonal spread of Escherichia coli O101: H9-ST10 and O101: H9-ST167 strains carrying fosA3 and bla CTX-M-14 among diarrheal calves in a Chinese farm, with Australian Chroicocephalus as the possible origin of E. coli O101: H9-ST10

During a 2018 antimicrobial resistance surveillance of Escherichia coli isolates from diarrheal calves in Xinjiang Province, China, an unexpectedly high prevalence (48.5%) of fosfomycin resistance was observed. This study aimed to reveal the determinants of fosfomycin resistance and the underlying transmission mechanism. Polymerase chain reaction (PCR) screening showed that all fosfomycin-resistant E. coli carried the fosA3 gene. Pulsed-field gel electrophoresis (PFGE) and southern blot hybridization revealed that the 16 fosA3-positive isolates belonged to four different PFGE patterns (i.e., A, B, C, D). The fosA3 genes of 11 clonally related strains (pattern D) were located on the chromosome, while others were carried by plasmids. Whole-genome and long-read sequencing indicated that the pattern D strains were E. coli O101:H9-ST10, and the pattern C, B, and A strains were O101:H9-ST167, O8:H30-ST1431, and O101:H9 with unknown ST, respectively. Among the pattern C strains, the bla_CTX-M-14 gene was co-localized with the fosA3 gene on the F18:A-:B1 plasmids. Interestingly, phylogenetic analysis based on core genome single nucleotide polymorphisms (cgSNPs) showed that the O101:H9-ST10 strains were closely related to a Australian-isolated Chroicocephalus-origin E. coli O101:H9-ST10 strain producing CTX-M-14 and FosA3, with a difference of only 11 SNPs. These results indicate possible international dissemination of the high-risk E. coli clone O101:H9-ST10 by migratory birds.

Multidrug-Resistant Phenotypes of Escherichia coli Isolates in Wild Canarian Egyptian Vultures (Neophron percnopterus majorensis)

Simple Summary

Increasing antimicrobial resistance is a global problem for both human and animal health. Escherichia coli is frequently used as a “sentinel” for antimicrobial resistance and as an indicator of faecal contamination of the environment. This study is a characterisation of the antimicrobial resistance phenotypes of E. coli isolates obtained from cloacal samples of Canarian Egyptian vultures. A total of 65 chickens and 38 adult and immature birds were studied. Antimicrobial susceptibility to 16 antibiotics of 12 different categories was determined in 103 E. coli isolates. We found a 39.8% prevalence of multidrug-resistant (MDR) E. coli. Almost all MDR phenotypes found included resistance to tetracycline, an antibiotic widely used in veterinary medicine. Resistance has also been found to chloramphenicol (13 MDR phenotypes), imipenem (5 MDR phenotypes) and others. Wild birds can act as reservoirs and disseminators of MDR E. coli, transferring them via faeces to the environment, feed or water. Our results highlight the need to minimise exposure of wild birds to antimicrobials from human activities to avoid the spread of antimicrobial resistance.

Abstract

The presence of multidrug-resistant (MDR) Escherichia coli in cloacal samples from Canarian Egyptian vultures was investigated. Samples were obtained from chicks (n = 65) and from adults and immature birds (n = 38). Antimicrobial susceptibility to 16 antibiotics included in 12 different categories was determined for 103 E. coli isolates. MDR was defined as acquired non-susceptibility to at least one agent in three or more antimicrobial categories. Forty-seven different resistance phenotypes were detected: 31 MDR (41 isolates) and 16 non-MDR (62 isolates). One isolate was resistant to all 12 antimicrobial categories and 2 phenotypes included resistance to 9 antimicrobial categories. Imipenem resistance was included in five MDR phenotypes, corresponding to five different isolates. Statistically significant differences in prevalence of MDR-phenotypes were found between chicks in nests and the rest of the animals, probably due to the shorter exposure time of chicks to antimicrobials. The main risk derived from MDR bacteria in scavengers is that it threatens the treatment of wild animals in rescue centres and could be transferred to other animals in the facilities. In addition to this, it could pose a health risk to veterinarians or other staff involved in wildlife protection programmes.

Presence of β-Lactamase-producing Enterobacterales and Salmonella Isolates in Marine Mammals

Marine mammals have been described as sentinels of the health of marine ecosystems. Therefore, the aim of this study was to investigate (i) the presence of extended-spectrum β-lactamase (ESBL)- and AmpC-producing Enterobacterales, which comprise several bacterial families important to the healthcare sector, as well as (ii) the presence of Salmonella in these coastal animals. The antimicrobial resistance pheno- and genotypes, as well as biocide susceptibility of Enterobacterales isolated from stranded marine mammals, were determined prior to their rehabilitation. All E. coli isolates (n = 27) were screened for virulence genes via DNA-based microarray, and twelve selected E. coli isolates were analyzed by whole-genome sequencing. Seventy-one percent of the Enterobacterales isolates exhibited a multidrug-resistant (MDR) pheno- and genotype. The gene bla_CMY (n = 51) was the predominant β-lactamase gene. In addition, bla_TEM-1 (n = 38), bla_SHV-33 (n = 8), bla_CTX-M-15 (n = 7), bla_OXA-1 (n = 7), bla_SHV-11 (n = 3), and bla_DHA-1 (n = 2) were detected. The most prevalent non-β-lactamase genes were sul2 (n = 38), strA (n = 34), strB (n = 34), and tet(A) (n = 34). Escherichia coli isolates belonging to the pandemic sequence types (STs) ST38, ST167, and ST648 were identified. Among Salmonella isolates (n = 18), S. Havana was the most prevalent serotype. The present study revealed a high prevalence of MDR bacteria and the presence of pandemic high-risk clones, both of which are indicators of anthropogenic antimicrobial pollution, in marine mammals.

Prevalence of 16S rRNA Methylation Enzyme Gene armA in Salmonella From Outpatients and Food

Salmonella is the primary cause of community-acquired foodborne infections, so its resistance to antimicrobials, such as aminoglycosides, is a public health issue. Of concern, aminoglycoside resistance in Salmonella is increasing rapidly. Here, we performed a retrospective study evaluating the prevalence of Salmonella harboring armA-mediated aminoglycoside resistance in community-acquired infections and in food or environmental sources. The prevalence rates of armA-harboring Salmonella strains were 1.1/1,000 (13/12,095) and 8.7/1,000 (32/3,687) in outpatient and food/environmental isolates, respectively. All the armA-harboring Salmonella strains were resistant to multiple drugs, including fluoroquinolone and/or extended-spectrum cephalosporins, and most (34/45) belonged to serovar Indiana. The armA gene of these strains were all carried on plasmids, which spanned five replicon types with IncHI2 being the dominant plasmid type. All the armA-carrying plasmids were transferable into Escherichia coli and Acinetobacter baumannii recipients. The conjugation experiment results revealed that the armA-harboring S. Indiana strains had a relatively higher ability to acquire armA-carrying plasmids. The low similarity of their pulsed field gel electrophoresis patterns indicates that the armA-harboring Salmonella strains were unlikely to have originated from a single epidemic clone, suggesting broad armA spread. Furthermore, the genetic backgrounds of armA-harboring Salmonella strains isolated from outpatients exhibited higher similarity to those isolated from poultry than to those isolated from swine, suggesting that poultry consumption maybe an infection source. These findings highlight an urgent need to monitor the prevalence and transmission of armA-harboring Salmonella, especially S. Indiana, to better understand the potential public health threat and prevent the further spread of these strains.

Characterization of beta-lactam-resistant Escherichia coli from Australian fruit bats indicates anthropogenic origins

Antimicrobial-resistant Escherichia coli, particularly those resistant to critically important antimicrobials, are increasingly reported in wildlife. The dissemination of antimicrobial-resistant bacteria to wildlife indicates the far-reaching impact of selective pressures imposed by humans on bacteria through misuse of antimicrobials. The grey-headed flying fox (GHFF; Pteropus poliocephalus), a fruit bat endemic to eastern Australia, commonly inhabits urban environments and encounters human microbial pollution. To determine if GHFF have acquired human-associated bacteria, faecal samples from wild GHFF (n=287) and captive GHFF undergoing rehabilitation following illness or injury (n=31) were cultured to detect beta-lactam-resistant E. coli. Antimicrobial susceptibility testing, PCR and whole genome sequencing were used to determine phenotypic and genotypic antimicrobial resistance profiles, strain type and virulence factor profiles. Overall, 3.8 % of GHFF carried amoxicillin-resistant E. coli (wild 3.5 % and captive 6.5 %), with 38.5 % of the 13 GHFF E. coli isolates exhibiting multidrug resistance. Carbapenem (blaNDM-5) and fluoroquinolone resistance were detected in one E. coli isolate, and two isolates were resistant to third-generation cephalosporins (blaCTX-M-27 and ampC). Resistance to tetracycline and trimethoprim plus sulfamethoxazole were detected in 69.2% and 30.8 % of isolates respectively. Class 1 integrons, a genetic determinant of resistance, were detected in 38.5 % of isolates. Nine of the GHFF isolates (69.2 %) harboured extraintestinal virulence factors. Phylogenetic analysis placed the 13 GHFF isolates in lineages associated with humans and/or domestic animals. Three isolates were human-associated extraintestinal pathogenic E. coli (ST10 O89:H9, ST73 and ST394) and seven isolates belonged to lineages associated with extraintestinal disease in both humans and domestic animals (ST88, ST117, ST131, ST155 complex, ST398 and ST1850). This study provides evidence of anthropogenic multidrug-resistant and pathogenic E. coli transmission to wildlife, further demonstrating the necessity for incorporating wildlife surveillance within the One Health approach to managing antimicrobial resistance.

ESBL-Producing Escherichia coli Carrying CTX-M Genes Circulating among Livestock, Dogs, and Wild Mammals in Small-Scale Farms of Central Chile

Antibiotic-resistant bacteria of critical importance for global health such as extended-spectrum beta-lactamases-producing (ESBL)-Escherichia coli have been detected in livestock, dogs, and wildlife worldwide. However, the dynamics of ESBL-E. coli between these animals remains poorly understood, particularly in small-scale farms of low and middle-income countries where contact between species can be frequent. We compared the prevalence of fecal carriage of ESBL-E. coli among 332 livestock (207 cows, 15 pigs, 60 horses, 40 sheep, 6 goats, 4 chickens), 82 dogs, and wildlife including 131 European rabbits, 30 rodents, and 12 Andean foxes sharing territory in peri-urban localities of central Chile. The prevalence was lower in livestock (3.0%) and wildlife (0.5%) compared to dogs (24%). Among 47 ESBL-E. coli isolates recovered, CTX-M-group 1 was the main ESBL genotype identified, followed by CTX-M-groups 2, 9, 8, and 25. ERIC-PCR showed no cluster of E. coli clones by either host species nor locality. To our knowledge, this is the first report of ESBL-E. coli among sheep, cattle, dogs, and rodents of Chile, confirming their fecal carriage among domestic and wild animals in small-scale farms. The high prevalence of ESBL-E. coli in dogs encourages further investigation on their role as potential reservoirs of this bacteria in agricultural settings.

Association between the blaCTX-M-14-harboring Escherichia coli Isolated from Weasels and Domestic Animals Reared on a University Campus

Antimicrobial-resistant (AMR) bacteria affect human and animal health worldwide. Here, CTX-M-14-producing Escherichia coli isolates were isolated from Siberian weasels (Mustela sibirica) that were captured on a veterinary campus. To clarify the source of bacteria in the weasels, we examined the domestic animals reared in seven facilities on the campus. Extended-spectrum β-lactamase (ESBL)-producing E. coli were isolated on deoxycholate hydrogen sulfide lactose agar, containing cephalexin (50 μg/mL) or cefotaxime (2 μg/mL), and were characterized with antimicrobial susceptibility testing, pulsed-field gel electrophoresis (PFGE), replicon typing, and β-lactamase typing analyses. Next-generation sequencing of the ESBL-encoding plasmids was also performed. CTX-M-14 producers isolated from both domestic animals and weasels were classified into six clusters with seven PFGE profiles. The PFGE and antimicrobial resistance profiles were characterized by the animal facility. All CTX-M-14 plasmids belonged to the IncI1 type with a similar size (98.9-99.3 kb), except for one plasmid that was 105.5 kb in length. The unweighted pair group method with arithmetic mean (UPGMA) revealed that the CTX-M-14 plasmid in the weasel isolates might have the same origin as the CTX-M-14 plasmid in the domestic animals. Our findings shed further light on the association of antimicrobial resistance between wild and domestic animals.

Importance of anthropogenic sources at shaping the antimicrobial resistance profile of a peri-urban mesocarnivore

Anthropogenically derived antimicrobial-resistant bacteria (ARB) and antimicrobial resistance genes (ARG) have been detected in wildlife. The likelihood of detecting ARB and ARG in wildlife increases with wildlife exposure to anthropogenic sources of antimicrobial resistance (AMR). Whether anthropogenic sources also increase the risk for AMR to spread in bacteria of wildlife is not well understood. The spread of AMR in bacteria of wildlife can be estimated by examining the richness of ARB and ARG, and the prevalence of ARB that have mobilizable ARG (i.e., ARG that can be transferred across bacteria via plasmids). Here, we investigated whether raccoons (Procyon lotor), with different exposures to anthropogenic sources, differed in prevalence and richness of extended-spectrum cephalosporin-resistant (ESC-R) Escherichia coli, richness of ARG present in ESC-R E. coli, and prevalence of ESC-R E. coli with plasmid-associated ARG. Sampling took place over the course of 10 months at seven sites in Chicago, USA. ESC-R E. coli were isolated from over half of the 211 raccoons sampled and were more likely to be isolated from urban than suburban raccoons. When examining the whole-genome sequences of ESC-R E. coli, 56 sequence types were identified, most of which were associated with the ARG bla_CMY and bla_CTX-M. A greater richness of ESC-R E. coli sequence types was found at sites with a wastewater treatment plant (WWTP) than without, but no difference was detected based on urban context. ARG richness in ESC-R E. coli did not significantly vary by urban context nor with presence of a WWTP. Importantly, ESC-R E. coli carrying plasmid-associated bla_CTX-M and bla_CMY ARG were more likely to be isolated from raccoons sampled at sites with a WWTP than without. Our findings indicate that anthropogenic sources may shape the AMR profile of wildlife, reinforcing the need to prevent dissemination of AMR into the environment.

Antimicrobial Resistance Genes in ESBL-Producing Escherichia coli Isolates from Animals in Greece

The prevalence of multidrug resistant, extended spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is increasing worldwide. The present study aimed to provide an overview of the multidrug resistance phenotype and genotype of ESBL-producing Escherichia coli (E. coli) isolates of livestock and wild bird origin in Greece. Nineteen phenotypically confirmed ESBL-producing E. coli strains isolated from fecal samples of cattle (n = 7), pigs (n = 11) and a Eurasian magpie that presented resistance to at least one class of non β-lactam antibiotics, were selected and genotypically characterized. A DNA-microarray based assay was used, which allows the detection of various genes associated with antimicrobial resistance. All isolates harbored blaCTX-M-1/15, while blaTEM was co-detected in 13 of them. The AmpC gene blaMIR was additionally detected in one strain. Resistance genes were also reported for aminoglycosides in all 19 isolates, for quinolones in 6, for sulfonamides in 17, for trimethoprim in 14, and for macrolides in 8. The intI1 and/or tnpISEcp1 genes, associated with mobile genetic elements, were identified in all but two isolates. This report describes the first detection of multidrug resistance genes among ESBL-producing E. coli strains retrieved from feces of cattle, pigs, and a wild bird in Greece, underlining their dissemination in diverse ecosystems and emphasizing the need for a One-Health approach when addressing the issue of antimicrobial resistance.

Epidemic HI2 Plasmids Mobilising the Carbapenemase Gene blaIMP-4 in Australian Clinical Samples Identified in Multiple Sublineages of Escherichia coli ST216 Colonising Silver Gulls

Escherichia coli ST216, including those that carry bla_KPC-2, bla_FOX-5, bla_CTX-M-15 and mcr-1, have been linked to wild and urban-adapted birds and the colonisation of hospital environments causing recalcitrant, carbapenem-resistant human infections. Here we sequenced 22 multiple-drug resistant ST216 isolates from Australian silver gull chicks sampled from Five Islands, of which 21 carried nine or more antibiotic resistance genes including bla_IMP-4 (n = 21), bla_TEM-1b (n = 21), aac(3)-IId (n = 20), mph(A) (n = 20), catB3 (n = 20), sul1 (n = 20), aph(3”)-Ib (n = 18) and aph(6)-Id (n = 18) on FIB(K) (n = 20), HI2-ST1 (n = 11) and HI2-ST3 (n = 10) plasmids. We show that (i) all HI2 plasmids harbour bla_IMP-4 in resistance regions containing In809 flanked by IS26 (HI2-ST1) or IS15DI (HI2-ST3) and diverse metal resistance genes; (ii) HI2-ST1 plasmids are highly related to plasmids reported in diverse Enterobacteriaceae sourced from humans, companion animals and wildlife; (iii) HI2 were a feature of the Australian gull isolates and were not observed in international ST216 isolates. Phylogenetic analyses identified close relationships between ST216 from Australian gull and clinical isolates from overseas. E. coli ST216 from Australian gulls harbour HI2 plasmids encoding resistance to clinically important antibiotics and metals. Our studies underscore the importance of adopting a one health approach to AMR and pathogen surveillance.

Migratory Wild Birds as a Potential Disseminator of Antimicrobial-Resistant Bacteria around Al-Asfar Lake, Eastern Saudi Arabia

Migratory wild birds acquire antimicrobial-resistant (AMR) bacteria from contaminated habitats and then act as reservoirs and potential spreaders of resistant elements through migration. However, the role of migratory wild birds as antimicrobial disseminators in the Arabian Peninsula desert, which represents a transit point for birds migrating all over Asia, Africa, and Europe not yet clear. Therefore, the present study objective was to determine antimicrobial-resistant bacteria in samples collected from migratory wild birds around Al-Asfar Lake, located in Al-Ahsa Oasis, Eastern Saudi Arabia, with a particular focus on Escherichia coli virulence and resistance genes. Cloacal swabs were collected from 210 migratory wild birds represent four species around Al-Asfar. E. coli, Staphylococcus, and Salmonella spp. have been recovered from 90 (42.9%), 37 (17.6%), and 5 (2.4%) birds, respectively. Out of them, 19 (14.4%) were a mixed infection. All samples were subjected to AMR phenotypic characterization, and results revealed (14-41%) and (16-54%) of E. coli and Staphylococcus spp. isolates were resistant to penicillins, sulfonamides, aminoglycoside, and tetracycline antibiotics. Multidrug-resistant (MDR) E. coli and Staphylococcus spp. were identified in 13 (14.4%) and 7 (18.9%) isolates, respectively. However, none of the Salmonella isolates were MDR. Of the 90 E. coli isolates, only 9 (10%) and 5 (5.6%) isolates showed the presence of eaeA and stx2 virulence-associated genes, respectively. However, both eaeA and stx2 genes were identified in four (4.4%) isolates. None of the E. coli isolates carried the hlyA and stx1 virulence-associated genes. The E. coli AMR associated genes bla_CTX-M, bla_TEM, bla_SHV, aac(3)-IV, qnrA, and tet(A) were identified in 7 (7.8%), 5 (5.6%), 1 (1.1%), 8 (8.9%), 4 (4.4%), and 6 (6.7%) isolates, respectively. While the mecA gene was not detected in any of the Staphylococcus spp. isolates. Regarding migratory wild bird species, bacterial recovery, mixed infection, MDR, and AMR index were relatively higher in aquatic-associated species. Overall, the results showed that migratory wild birds around Al-Asfar Lake could act as a reservoir for AMR bacteria enabling them to have a potential role in maintaining, developing, and disseminating AMR bacteria. Furthermore, results highlight the importance of considering migratory wild birds when studying the ecology of AMR.

Co-selection may explain the unexpectedly high prevalence of plasmid-mediated colistin resistance gene mcr-1 in a Chinese broiler farm

The rise of the plasmid-encoded colistin resistance gene mcr-1 is a major concern globally. Here, during a routine surveillance, an unexpectedly high prevalence of Escherichia coli with reduced susceptibility to colistin (69.9%) was observed in a Chinese broiler farm. Fifty-three (63.9%)E. coli isolates were positive for mcr-1. All identified mcr-1-positive E. coli (MCREC) were multidrug resistant and carried other clinically significant resistance genes. Furthermore, the mcr-1 genes were mainly located on the IncI2 and IncHI2 plasmids. Conjugation experiments unraveled the co-transfer of mcr-1 with other antibiotic resistance genes (bla_CTX-M-55, bla_CTX-M-14, floR, and fosA3) via the IncI2 (n=3) and IncHI2 (n=4) plasmids. The stable genetic context mcr-1-pap2 was common in the IncI2 plasmids, whereas ISApl1-mcr-1-pap2-ISApl1 was mainly found in the IncHI2 plasmids. The dominance of mcr-1-bearing IncI2 and IncHI2 plasmids and co-selection of mcr-1with other antimicrobial resistance genes might contribute to the exceptionally high prevalence of mcr-1 in this broiler farm. Our results emphasized the importance of appropriate antibiotic use in animal production.

Prevalence of ESβL, AmpC and Colistin-Resistant E. coli in Meat: A Comparison between Pork and Wild Boar

A global increase in Escherichia coli (E. coli) resistant to cephalosporins (extended-spectrum β-lactamases (ESβLs) and AmpC β-lactamases) has been recorded in the last 20 years. Similarly, several studies have reported the spread of colistin resistance in Enterobacteriaceae isolated from food and the environment. The aim of the present study was to evaluate the prevalence of ESβL, AmpC and colistin-resistant E. coli isolated from pork and wild boar meat products in the Emilia Romagna region (North Italy). The isolates were analysed phenotypically (considering both resistant and intermediate profiles) and genotypically. The prevalence of genotypically confirmed ESβL and AmpC E. coli was higher in pork meat products (ESβL = 11.1% vs. AmpC = 0.3%) compared to wild boar meat (ESβL = 6.5% vs. AmpC = 0%). Intermediate profiles for cefotaxime (CTX) and ceftazidime (CAZ) were genotypically confirmed as ESβL in pork meat isolates but not for wild boar. Four E. coli from wild boar meat were resistant to colistin but did not harbour the mcr-1 gene. E. coli isolated from wild boar meat seem to show aspecific antimicrobial resistance mechanisms for cephalosporins and colistin. The prevalence of resistant isolates found in wild boar is less alarming than in pork from farmed domestic pigs. However, the potential risk to consumers of these meat products will require further investigations.

Molecular characterisation of extended-spectrum ß-lactamase producing Escherichia coli in wild birds and cattle, Ibadan, Nigeria

Background

Antimicrobial resistance (AMR) is an increasing global health concern reducing options for therapy of infections and also for perioperative prophylaxis. Many Enterobacteriaceae cannot be treated anymore with third generation cephalosporins (3GC) due to the production of certain 3GC hydrolysing enzymes (extended spectrum beta-lactamases, ESBLs). The role of animals as carriers and vectors of multi-resistant bacteria in different geographical regions is poorly understood. Therefore, we investigated the occurrence and molecular characteristics of ESBL-producing Escherichia coli (E. coli) in wild birds and slaughtered cattle in Ibadan, Nigeria.

Cattle faecal samples (n = 250) and wild bird pooled faecal samples (cattle egrets, Bubulcus ibis, n = 28; white-faced whistling duck, Dendrocygna viduata, n = 24) were collected and cultured on cefotaxime-eosin methylene blue agar. Antimicrobial susceptibility was determined by agar diffusion assays and all 3GC resistant isolates were genotypically characterised for AMR genes, virulence associated genes (VAGs) and serotypes using DNA microarray-based assays.

Results

All 3GC resistant isolates were E. coli: cattle (n = 53), egrets (n = 87) and whistling duck (n = 4); cultured from 32/250 (12.8%), 26/28 (92.9%), 2/24(8.3%), cattle, egrets and whistling duck faecal samples, respectively. blaCTX-M gene family was prevalent; blaCTX-M15 (83.3%) predominated over blaCTX-M9 (11.8%). All were susceptible to carbapenems. The majority of isolates were resistant to at least one of the other tested antimicrobials; multidrug resistance was highest in the isolates recovered from egrets.

The isolates harboured diverse repositories of other AMR genes (including strB and sul2), integrons (predominantly class 1) and VAGs. The isolates recovered from egrets harboured more AMR genes; eight were unique to these isolates including tetG, gepA, and floR. The prevalent VAGs included hemL and iss; while 14 (including sepA) were unique to certain animal isolates. E. coli serotypes O9:H9, O9:H30 and O9:H4 predominated. An identical phenotypic microarray profile was detected in three isolates from egrets and cattle, indicative of a clonal relationship amongst these isolates.

Conclusion

Wild birds and cattle harbour diverse ESBL-producing E. coli populations with potential of inter-species dissemination and virulence. Recommended guidelines to balance public health and habitat conservation should be implemented with continuous surveillance.

Occurrence of KPC-Producing Escherichia coli in Psittaciformes Rescued from Trafficking in Paraíba, Brazil

The emergence and spread of antimicrobial resistance pose a threat to public health globally. Antibiotic-resistant bacteria and genes can disseminate among environments, animals and humans. Therefore, investigation into potential reservoirs of multidrug-resistant bacteria is of great importance to the understanding of putative transmission routes of resistant bacteria and resistance genes. This study aimed to report the occurrence of Escherichia coli harboring the Klebsiella pneumoniae carbapenemase-producing gene (bla_KPC) in Psittaciformes rescued from wildlife trafficking in Paraíba State, Brazil. Cloacal swabs were collected from thirty birds and cultured by conventional microbiology using MacConkey and serum tryptone glucose glycerol (STGG) media supplemented with selective antimicrobials. E. coli isolates (n = 43) were identified by phenotypic tests and confirmed by MALDI-TOF. Antimicrobial susceptibility profiles were determined by means of Kirby–Bauer test. All isolates were further screened for extended-spectrum beta-lactamase (ESBL) production, and putative genes encoding ESBL were investigated by PCR. Additionally, bla_KPC-harboring strains were genotyped by REP-PCR. A total of 43 E. coli phenotypically resistant isolates were recovered. The highest resistance rate was observed against ciprofloxacin. Among the resistance genes, only bla_KPC was found in seven different birds from three species. According to the genotyping, these seven isolates belonged to four different strains. To date, this is the first report on the occurrence of KPC-E. coli in Psittaciformes rescued from trafficking in Northeastern Brazil. Due to the high clinical importance of KPC-E. coli, our findings suggest that wild animals in captivity at wildlife rescue centers can play a role as reservoirs of bacteria that are resistance to Critically Important antimicrobials in human medicine.

Wide Spread of bla CTX-M-9/mcr-9 IncHI2/ST1 Plasmids and CTX-M-9-Producing Escherichia coli and Enterobacter cloacae in Rescued Wild Animals

Wildlife has recently been pinpointed as one of the drivers of dissemination of genes conferring resistances to clinically important antimicrobials. The presence of both extended-spectrum beta-lactamase- (ESBL) and carbapenemase-encoding genes has notably been reported in wild birds, that can act as sentinels of antimicrobial resistance (AMR) contamination but also as long-distance spreaders in case of migratory birds. Here, 424 wild birds brought to a rescue center in France were sampled over a 6-month period. These birds encompassed 62 different sedentary or migratory species. A further 16 wild mammals present in the center were also investigated. No carbapenemase-producer was found, but we identified a surprisingly high proportion (24.1%) of ESBL-positive isolates. A total of 144 non-duplicate isolates were collected, including Escherichia coli (n = 88), Enterobacter cloacae (n = 51), and Citrobacter freundii (n = 5), of which 123 carried the bla_CTX–M–9 gene. PFGE, phylogroup, and MLST revealed the presence of a limited number of ESBL-positive clones circulating in these animals, all presenting multiple associated resistances. Next-generation sequencing on a subset of isolates, followed by Southern blot hybridization, showed the wide dissemination of an IncHI2/ST1 plasmid carrying the bla_CTX–M–9, bla_SHV–12 and mcr-9 genes. In all, our results undoubtedly reflect cross transmissions of ESC-resistance (ESC-R) Enterobacteriaceae within the rescue center – similarly to nosocomial spreads observed at hospital, rather than the true bacterial flora of birds. We also showed that the spread of ESC-R in this rescue center did not only rely on clonal but also on a highly successful plasmidic transmission. Since most animals are intended to get back to nature after a few days or weeks, this is obviously an issue with regard to ESBL dissemination in natural environments.

Antimicrobial Resistance of Escherichia coli and Pseudomonas aeruginosa from Companion Birds

Antimicrobial resistance is a public health concern worldwide and it is largely attributed to the horizontal exchange of transferable genetic elements such as plasmids carrying integrons. Several studies have been conducted on livestock showing a correlation between the systemic use of antibiotics and the onset of resistant bacterial strains. In contrast, although companion birds are historically considered as an important reservoir for human health threats, little information on the antimicrobial resistance in these species is available in the literature. Therefore, this study was aimed at evaluating the antimicrobial resistance of Escherichia coli and Pseudomonasaeruginosa isolated from 755 companion birds. Cloacal samples were processed for E. coli and P. aeruginosa isolation and then all isolates were submitted to antimicrobial susceptibility testing. P. aeruginosa was isolated in 59/755 (7.8%) samples, whereas E. coli was isolated in 231/755 (30.7%) samples. Most strains showed multidrug resistance. This study highlights that companion birds may act as substantial reservoirs carrying antimicrobial resistance genes which could transfer directly or indirectly to humans and animals, and from a One Health perspective this risk should not be underestimated.

Merging Metagenomics and Spatial Epidemiology To Understand the Distribution of Antimicrobial Resistance Genes from Enterobacteriaceae in Wild Owls

Antimicrobial resistance (AMR) is a well-documented phenomenon in bacteria from many natural ecosystems, including wild animals. However, the specific determinants and spatial distribution of resistant bacteria and antimicrobial resistance genes (ARGs) in the environment remain incompletely understood. In particular, information regarding the importance of anthropogenic sources of AMR relative to that of other biological and ecological influences is lacking. We conducted a cross-sectional study of AMR in great horned owls (Bubo virginianus) and barred owls (Strix varia) admitted to a rehabilitation center in the midwestern United States. A combination of selective culture enrichment and shotgun metagenomic sequencing was used to identify ARGs from Enterobacteriaceae Overall, the prevalence of AMR was comparable to that in past studies of resistant Enterobacteriaceae in raptors, with acquired ARGs being identified in 23% of samples. Multimodel regression analyses identified seasonality and owl age to be important predictors of the likelihood of the presence of ARGs, with birds sampled during warmer months being more likely to harbor ARGs than those sampled during cooler months and with birds in their hatch year being more likely to harbor β-lactam ARGs than adults. Beyond host-specific determinants, ARG-positive owls were also more likely to be recovered from areas of high agricultural land cover. Spatial clustering analyses identified a significant high-risk cluster of tetracycline resistance gene-positive owls in the southern sampling range, but this could not be explained by any predictor variables. Taken together, these results highlight the complex distribution of AMR in natural environments and suggest that both biological and anthropogenic factors play important roles in determining the emergence and persistence of AMR in wildlife.IMPORTANCE Antimicrobial resistance (AMR) is a multifaceted problem that poses a worldwide threat to human and animal health. Recent reports suggest that wildlife may play an important role in the emergence, dissemination, and persistence of AMR. As such, there have been calls for better integration of wildlife into current research on AMR, including the use of wild animals as biosentinels of AMR contamination in the environment. A One Health approach can be used to gain a better understanding of all AMR sources and pathways, particularly those at the human-animal-environment interface. Our study focuses on this interface in order to assess the effect of human-impacted landscapes on AMR in a wild animal. This work highlights the value of wildlife rehabilitation centers for environmental AMR surveillance and demonstrates how metagenomic sequencing within a spatial epidemiology framework can be used to address questions surrounding AMR complexity in natural ecosystems.

Implications of Foraging and Interspecies Interactions of Birds for Carriage of Escherichia coli Strains Resistant to Critically Important Antimicrobials

Globally, gulls have been associated with carriage of high levels of Escherichia coli strains resistant to critically important antimicrobials (CIAs), a major concern, as these antimicrobials are the sole alternative or one among only a few alternatives available to treat severe life-threatening infections in humans. Previous studies of Australian silver gulls demonstrated high levels of resistance to CIAs, particularly fluoroquinolone and extended-spectrum cephalosporins, among E. coli strains (carriage at 24% and 22%, respectively). This study aimed to identify and characterize strains from four distinct bird species inhabiting a common coastal environment, determine the frequency of carriage of CIA-resistant E. coli strains, and examine if these resistant clones and their resistance-encoding mobile genetic elements (MGEs) could be transmitted between species. CIA-resistant E. coli was detected in silver gulls (53%), little penguins (11%), and feral pigeons (10%), but not in bridled terns. In total, 37 different sequence types (STs) were identified, including clinically significant human-associated lineages, such as ST131, ST95, ST648, ST69, ST540, ST93, ST450, and ST10. Five main mobile genetic elements associated with bla _CTX-M-positive E. coli strains isolated from three bird species were detected. Examination of clonal lineages and MGEs provided indirect evidence of transfer of resistance between bird species. The carriage of CIA-resistant E. coli by gulls and pigeons with proximity to humans, and in some instances food-producing animals, increases the likelihood of further bidirectional dissemination.IMPORTANCE It has been shown that 20% of Australian silver gulls carry drug-resistant Escherichia coli strains of anthropogenic origin associated with severe diseases, such as sepsis and urinary tract infections, in humans. To further characterize the dynamics of drug-resistant E. coli in wildlife populations, we investigated the carriage of critically important antimicrobial (CIA) drug-resistant E. coli in four bird species in a common environment. Our results indicated that gulls, pigeons, and penguins carried drug-resistant E. coli strains, and analysis of mobile genetic elements associated with resistance genes indicated interspecies resistance transfer. Terns, representing a bird species that forages on natural food sources at sea and distant from humans, did not test positive for drug-resistant E. coli This study demonstrates carriage of CIA-resistant bacteria in multiple bird species living in areas commonly inhabited by humans and provides further evidence for a leapfrog effect of resistance in wildlife, facilitated by feeding habits.

International clones of extended-spectrum β-lactamase (CTX-M)-producing Escherichia coli in peri-urban wild animals, Brazil

CTX-M-type extended-spectrum β-lactamase (ESBL)-producing Escherichia coli clones have been increasingly reported worldwide. In this regard, although discussions of transmission routes of these bacteria are in evidence, molecular data are lacking to elucidate the epidemiological impacts of ESBL producers in wild animals. In this study, we have screened 90 wild animals living in a surrounding area of São Paulo, the largest metropolitan city in South America, to monitor the presence of multidrug-resistant (MDR) Gram-negative bacteria. Using a genomic approach, we have analysed eight ceftriaxone-resistant E. coli. Resistome analyses revealed that all E. coli strains carried blaCTX-M -type genes, prevalent in human infections, besides other clinically relevant resistance genes to aminoglycosides, β-lactams, phenicols, tetracyclines, sulphonamides, trimethoprim, fosfomycin and quinolones. Additionally, E. coli strains belonged to international sequence types (STs) ST38, ST58, ST212, ST744, ST1158 and ST1251, and carried several virulence-associated genes. Our findings suggest spread and adaptation of international clones of CTX-M-producing E. coli beyond urban settings, including wildlife from shared environments.

Occurrence and Antimicrobial Resistance Traits of Escherichia coli from Wild Birds and Rodents in Singapore

Antimicrobial resistance (AMR) in Escherichia coli (E. coli) poses a public health concern worldwide. Wild birds and rodents, due to their mobility, are potential vehicles for transmission of AMR bacteria to humans. Ninety-six wild birds’ faecal samples and 135 rodents’ droppings samples were collected and analysed in 2017. Forty-six E. coli isolates from wild birds and rodents were subjected to AMR phenotypic and genotypic characterisation. The proportion of E. coli isolates resistant to at least one of the antimicrobials tested from wild birds (80.8%) was significantly higher than that of isolates from rodents (40.0%). The proportion of E. coli isolates resistant to each antimicrobial class for wild birds was 3.8% to 73.1% and that for rodents was 5.0% to 35.0%. Six out of 26 E. coli isolates from wild birds (23.1%) and two out of 20 (10.0%) isolates from rodents were multi-drug resistant (MDR) strains. These MDR E. coli isolates were detected with various antimicrobial resistance genes such as bla_TEM-1B and qnrS1 and could be considered as part of the environmental resistome. Findings in this study suggested that wild birds and rodents could play a role in disseminating antimicrobial resistant E. coli, and this underscores the necessity of environment management and close monitoring on AMR bacteria in wild birds and rodents to prevent spreading of resistant organisms to other wildlife animals and humans.

Escherichia coli Producing Extended-Spectrum β-lactamases (ESBL) from Domestic Camels in the Canary Islands: A One Health Approach

Simple Summary

Extended-spectrum beta-lactamase (ESBL) producing Escherichia coli is an important problem in hospital settings. Camels are known to harbor multidrug-resistant Gram-negative bacteria and to be involved in the transmission of various microorganisms to humans. Fecal samples of 58 camels were recovered in the Canary Islands for detection and characterization of cefotaxime-resistant (CTX^R) and ESBL-producing E. coli isolates. Five samples carried CTX^RE. coli isolates and two of them contained ESBL-positive E. coli (3.4%) with the following characteristics: (ESBL/phylogroup/sequence type): CTX-M-15/A/ST3018 and CTX-M-15/B1/ST69. The three remaining isolates recovered from CTX-supplemented plates were ascribed to phylogroup-B₁. Due to the participation of these animals in touristic activities in the region, the potential transference of ESBL-positive bacteria between humans and animals could happen and should be further monitored.

Abstract

Objective: This work aimed to determine the carriage rate of ESBL-producing Escherichia coli as well as their genetic characteristics in camels from the Canary Islands, Spain. Methods: Fecal samples were recovered from 58 healthy camels from Gran Canaria (n = 32) and Fuerteventura Islands (n = 26) during July 2019. They were seeded on MacConkey (MC) agar no supplemented and supplemented (MC + CTX) with cefotaxime (2 µg/mL). Antimicrobial susceptibility was determined by disk diffusion test (CLSI, 2018). The presence of bla_CTX-M, bla_SHV, bla_TEM,bla_CMY-2 and bla_OXA-1/48 genes was tested by PCR/sequencing. Furthermore, the mcr-1 (colistin resistance), tetA/tetB (tetracycline resistance), int1 (integrase of class 1 integrons) and stx_1,2 genes were analyzed. Phylogenetic groups and sequence types were determined by specific-PCR/sequencing for selected isolates. Results: E. coli was obtained from all the 58 camels in MC media (100%) and in five of them in MC + CTX media (8.6%). Furthermore, 63.8% of E. coli isolates recovered from MC agar were susceptible to all the antibiotics tested. The five E. coli isolates recovered from MC + CTX media were characterized and two of them were ESBL-producers (3.4%). Both ESBL-producer isolates carried the bla_CTX-M-15 gene and belonged to the lineages ST3018 (phylogroup A) and ST69 (phylogroup B1). The 3 ESBL-negative isolates recovered from MC-CTX plates were ascribed to phylogroup-B₁. Conclusions: Camels can be a source of ESBL-producer bacteria, containing the widespread bla_CTX-M-15 gene associated with the lineages ST3018 and ST69.