A survey of antimicrobial resistance in Escherichia coli isolated from wild sika deer (Cervus nippon) in Japan

Circulation of Antibiotic-Resistant Escherichia coli in Wild and Domestic Waterfowl in Ukraine

Background: Antibiotic resistance is becoming an increasingly urgent problem for human and animal health due to the widespread use of antibiotics in medicine, veterinary medicine, and agriculture. At the same time, the natural reservoirs of antibiotic-resistant pathogens remain unclear. Wild birds may play a role in this due to their biology. Escherichia coli is a representative indicator pathogen for antibiotic resistance studies. Materials and Methods: In 2020-2021, sampling of feces and cloacal swabs from six species of wild waterfowl (Eurasian wigeon Anas penelope, Eurasian teal Anas crecca, white-fronted goose Anser albifrons, red-breasted goose Rufibrenta ruficollis, graylag goose Anser anser, shelduck Tadorna tadorna) and from two species of domestic waterfowl (ducks and geese) was conducted in the Kherson, Zaporizhzhia, Odesa, Kharkiv, and Cherkasy regions of Ukraine. Biological material was collected, stored, and transported in cryotubes with transport medium (brain heart infusion broth [BHIB] with the addition of 15% glycerol) in liquid nitrogen. Bacteriological studies were carried out according to standard methods for the isolation and identification of microorganisms. Drug resistance of E. coli was carried out by a standard disk diffusion method. Results: Bacteria representing six families (Enterobacteriaceae, Yersiniaceae, Morganellaceae, Bacillaceae, Pseudomonadaceae, Staphylococcaceae) were isolated from clinically healthy wild birds (wigeon, Eurasian teal, white-fronted goose, red-breasted goose, mallard, graylag goose, shelduck) in the southern regions of Ukraine with isolation rates ranging from 26.7% to 100%. A total of 19 E. coli isolates were cultured from 111 samples from wild birds, and 30 isolates of E. coli were cultured from 32 poultry samples. E. coli was isolated from birds of all species. The prevalence of E. coli ranged from 5.0% to 33.3% in wild waterfowl and from 90.9% to 100% in domestic waterfowl. The prevalence of multidrug-resistant (MDR) E. coli ranged from 10.0% to 31.8% in wild and domestic waterfowl: 3 of 15 (20%) specimens from wild mallard were MDR in the Kherson region, as well as 7 of 22 domestic ducks (31.8%) and 1 of 10 geese (10%) in the Kharkiv and Cherkasy regions. Isolates from wild birds were the most resistant to ampicillin (AMP), amoxiclav (AMC), amoxicillin (AMX), doxycycline (DO), and chloramphenicol (C). Isolates from poultry were resistant to ampicillin, amoxiclav, doxycycline, amoxicillin, chloramphenicol, and enrofloxacin (EX). Most of the other E. coli isolates from wild waterfowl were classified as non-multidrug-resistant (non-MDR) forms. Analysis of antibiotic sensitivity phenotypes showed that only four antibiotic-resistant phenotypes were detected among non-MDR bacteria, whereas among the MDR bacteria, two antibiotic-resistant phenotypes were detected in mallards and six in domestic waterfowl. Conclusion: The results of this study showed that wild waterfowl in Ukraine, which live in natural conditions and do not receive any antimicrobial drugs, are carriers of E. coli that are resistant to a number of antibiotics that are actively used in industrial poultry.

Distribution and associations for antimicrobial resistance and antibiotic resistance genes of Escherichia coli from musk deer (Moschus berezovskii) in Sichuan, China

This study aimed to investigate the antimicrobial resistance (AMR), antibiotic resistance genes (ARGs) and integrons in 157 Escherichia coli (E. coli) strains isolated from feces of captive musk deer from 2 farms (Dujiang Yan and Barkam) in Sichuan province. Result showed that 91.72% (144/157) strains were resistant to at least one antimicrobial and 24.20% (38/157) strains were multi-drug resistant (MDR). The antibiotics that most E. coli strains were resistant to was sulfamethoxazole (85.99%), followed by ampicillin (26.11%) and tetracycline (24.84%). We further detected 13 ARGs in the 157 E. coli strains, of which blaTEM had the highest occurrence (91.72%), followed by aac(3')-Iid (60.51%) and blaCTX-M (16.56%). Doxycycline, chloramphenicol, and ceftriaxone resistance were strongly correlated with the presence of tetB, floR and blaCTX-M, respectively. The strongest positive association among AMR phenotypes was ampicillin/cefuroxime sodium (OR, 828.000). The strongest positive association among 16 pairs of ARGs was sul1/floR (OR, 21.667). Nine pairs positive associations were observed between AMR phenotypes and corresponding resistance genes and the strongest association was observed for CHL/floR (OR, 301.167). Investigation of integrons revealed intl1 and intl2 genes were detected in 10.19% (16/157) and 1.27% (2/157) E. coli strains, respectively. Only one type of gene cassettes (drA17-aadA5) was detected in class 1 integron positive strains. Our data implied musk deer is a reservoir of ARGs and positive associations were common observed among E. coli strains carrying AMRs and ARGs.

Characterization of quinolone-resistant and extended-spectrum β-lactamase-producing Escherichia coli derived from sika deer populations of the Nara Prefecture, Japan

Wildlife in urban areas have the potential to disseminate antimicrobial-resistant bacteria (ARB) across a wider environment. Using antimicrobial-supplemented agar plates, we isolated extended-spectrum β-lactamase-producing Escherichia coli (EEC) and quinolone-resistant E. coli (QREC) from 144, 23, and 30 deer feces from Nara Park (NP), rural area neighboring NP (RA), and Mt. Odaigahara (MO), respectively. In NP and RA, the prevalence of EEC was 24.3 and 4.3%, respectively; that of QREC was 11.1 and 17.4%, respectively. Neither EEC nor QREC were detected in MO. The pulsotypes of EEC and QREC isolates differed between NP and RA. Our study suggests that deer of the Nara Prefecture are potential carriers of ARB, but long-distance dissemination is unlikely due to limited deer movement.

Phylogenetic analysis and antibiotic resistance of Escherichia coli isolated from wild and domestic animals at an agricultural land interface area of Salaphra wildlife sanctuary, Thailand

Background and Aim

Domestic and wild animals are important reservoirs for antibiotic-resistant bacteria. This study aimed to isolate Escherichia coli from feces of domestic and wild animals at an agricultural land interface area of Salaphra Wildlife Sanctuary, Thailand, and study the phylogenic characteristics and antibiotic resistance in these isolates.

Materials and Methods

In this cross-sectional, descriptive study, we randomly collected ground feces from free-ranging wild animals (deer and elephants) and domestic animals (cattle and goats). All fecal samples were inoculated onto MacConkey agar plates, and lactose-fermenting colonies were identified as E. coli. Antibiotic susceptibility of the E. coli isolates was determined using the disc diffusion method. Polymerase chain reaction assays were used to detect antibiotic resistance and virulence genes.

Results

We obtained 362 E. coli isolates from the collected fecal samples. The E. coli isolates were categorized into four phylogenetic groups according to the virulence genes (chuA, vjaA, and TspE4C2). Phylogenetic Group D was predominant in the deer (41.67%) and elephants (63.29%), whereas phylogenetic Group B1 was predominant in the cattle (62.31%), and phylogenetic Groups A (36.36%) and B2 (33.33%) were predominant in the goats. Antibiotic susceptibility testing revealed that most antibiotic-resistant E. coli were isolated from domestic goats (96.96%). Among the 362 E. coli isolates, 38 (10.5%) were resistant to at least one antibiotic, 21 (5.8%) were resistant to two antibiotics, and 6 (1.66%) were resistant to three or more antibiotics. Ampicillin (AMP) was the most common antibiotic (48.48%) to which the E. coli were resistant, followed by tetracycline (TET) (45.45%) and trimethoprim-sulfamethoxazole (3.03%). One isolate from an elephant was resistant to five antibiotics: AMP, amoxicillin, sulfisoxazole, TET, and ciprofloxacin. Determination of antibiotic resistance genes confirmed that E. coli isolates carried antibiotic resistance genes associated with phenotypic resistance to antibiotics. Most antibiotic-resistant E. coli belonged to phylogenic Groups A and B1, and most non-resistant E. coli belonged to phylogenic Groups B2 and D.

Conclusion

Monitoring E. coli isolates from wild and domestic animals showed that all four phylogenic groups of E. coli have developed antibiotic resistance and are potential sources of multidrug resistance. High levels of antibiotic resistance have been linked to domestic animals. Our results support strengthening surveillance to monitor the emergence and effects of antibiotic-resistant microorganisms in animals.

A survey of antimicrobial-resistant Escherichia coli prevalence in wild mammals in Japan using antimicrobial-containing media

The emergence and spread of antimicrobial-resistant bacteria and resistance genes pose serious human and animal health concerns. Therefore, to control antimicrobial-resistant bacteria in the environment, the status of antimicrobial resistance of Escherichia coli in a variety of wild mammals and their prevalence were examined using antimicrobial-containing media. In total, 750 isolates were obtained from 274/366 (74.9%) wild mammals, and antimicrobial-resistant E. coli was detected in 37/750 isolates (4.9%) from 7 animal species (26/366 [7.1%] individuals). Using antimicrobial-containing media, 14 cefotaxime (CTX)- and 35 nalidixic acid-resistant isolates were obtained from 5 (1.4%) and 17 (4.6%) individuals, respectively. CTX-resistant isolates carried bla_CTX-M-27, bla_CTX-M-55, bla_CTX-M-1, and bla_CMY-2, with multiple resistance genes. Fluoroquinolone-resistant isolates had multiple mutations in the quinolone-resistance determining regions of gyrA and parC or qnrB19. Most resistant isolates exhibited resistance to multiple antimicrobials. The prevalence of antimicrobial-resistant bacteria observed in wild mammals was low; however, it is essential to elucidate the causative factors related to the low prevalence and transmission route of antimicrobial-resistant bacteria/resistance genes released from human activities to wild animals and prevent an increase in their frequency.

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

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

Isolation of extended‐spectrum β‐lactamase‐producing Escherichia coli from Japanese red fox ( Vulpes vulpes japonica )

Antimicrobial resistance is a global concern requiring a one‐health approach. Given wild animals can harbor antimicrobial‐resistant bacteria (ARB), we investigated their presence in 11 fecal samples from wild animals using deoxycholate hydrogen sulfide lactose agar with or without cefotaxime (CTX, 1 mg/L). Thus, we isolated CTX‐resistant Escherichia coli from two Japanese red fox fecal samples. One strain was O83:H42‐ST1485‐fimH58 CTX‐M‐55‐producing E. coli carrying the genes aph(3″)‐Ib, aph(3′)‐Ia, aph(6)‐Id, mdf(A), sitABCD, sul2, tet(A), and tet(B), whereas the other was O25:H4‐ST131‐fimH30 CTX‐M‐14‐producing E. coli carrying mdf(A) and sitABCD and showing fluoroquinolone resistance. Thus, the presence of extended‐spectrum β‐lactamase producers in wild foxes suggests a spillover of ARB from human activities to these wild animals.

Current status and future perspective of antimicrobial-resistant bacteria and resistance genes in animal-breeding environments

The emergence and spread of antimicrobial-resistant bacteria (ARB) and antimicrobial resistance genes (ARGs) are a global public health concern. ARB are transmitted directly or indirectly from animals to humans. The importance of environmental transmission of ARB and ARGs has recently been demonstrated, given the relationships between compost, livestock wastewater, insects, and wildlife. In addition, companion animals and their surrounding environments (veterinary hospitals and homes with companion animals) should be considered owing to their close relationship with humans. This review discusses the current status and future perspectives of ARB and ARGs in animal-breeding environments.

Whole-genome sequence analysis of Shiga toxin-producing Escherichia coli O157 strains isolated from wild deer and boar in Japan

The prevalence of Shiga toxin-producing Escherichia coli O157 (STEC O157) strains in wild deer and boar in Japan was investigated. STEC O157 strains were isolated from 1.9% (9/474) of the wild deer and 0.7% (3/426) of the wild boar examined. Pulsed-field gel electrophoresis (PFGE) analysis classified the wild deer and boar strains into four and three PFGE patterns, respectively. The PFGE pattern of one wild boar strain was similar to that of a cattle strain that had been isolated from a farm in the same area the wild boar was caught, suggesting that a STEC O157 strain may have been transmitted between wild boar and cattle. Clade analysis indicated that, although most of the strains were classified in clade 12, two strains were classified in clade 7. Whole-genome sequence (WGS) analysis indicated that all the strains carried mdfA, a drug resistance gene for macrolide antibiotics, and also pathogenicity-related genes similar to those in the Sakai strain. In conclusion, our study emphasized the importance of food hygiene in processing meat from Japanese wild animals for human consumption.