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 blaCTX-M-27, blaCTX-M-55, blaCTX-M-1, and blaCMY-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.

Prevalence of Antimicrobial-Resistant Escherichia coli in Migratory Greater White-Fronted Geese (Anser albifrons) and their Habitat in Miyajimanuma, Japan

The spread of antimicrobial-resistant bacteria (ARB) in natural environments including wild animals is a concern for public health. Birds cover large areas, and some fly across borders to migrate in large flocks. As a migratory bird, the Greater White-fronted Goose (Anser albifrons) travels to Miyajimanuma, North Japan, each spring and autumn. To investigate the ARB in migratory birds and their surroundings, we collected 110 fecal samples of A. albifrons and 18 water samples from Miyajimanuma in spring and autumn of 2019. Isolation of Escherichia coli was performed using selective agars with or without antimicrobials (cefazolin and nalidixic acid). Isolates of E. coli were recovered from 56 fecal samples (50.9%) and five water samples (27.8%) on agars without antimicrobials. No isolates were recovered on agars with antimicrobials. One E. coli isolate derived from a fecal sample exhibited resistance to β-lactams (ampicillin and cefazolin), whereas all other isolates exhibited susceptibility to all tested antimicrobials. The resistant isolate harbored blaACC, which could be transferred to other bacteria and confer resistance to β-lactams. These results suggest a low prevalence of antimicrobial resistance in wild migratory birds and their living environments; however, wild migratory birds sometimes carry ARB harboring transferrable antimicrobial resistance genes and therefore present a risk of spreading antimicrobial resistance.

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

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

Prevalence of antimicrobial resistance in bacteria isolated from Great Cormorants (Phalacrocorax carbo hanedae) in Japan

Wild birds are recognized as disseminators of antimicrobial-resistant (AMR) bacteria into the environment. Here, we isolated AMR indicator bacteria from 198 Great Cormorant cloacal swabs collected in Shiga (n=90), Oita (n=52), Gifu (n=29), and Gunma (n=27) Prefectures, Japan, in 2018 and 2019. In total, 198 Aeromonas spp. and 194 Escherichia spp. were isolated, and their antimicrobial susceptibility was examined. Aeromonas spp. were resistant to colistin (8.6%), nalidixic acid (4%), and other antimicrobials (<2%), with 3.0% positivity for mcr-3. Escherichia spp. showed resistance to colistin (3.1%), ampicillin (2.6%), tetracycline (2.1%), and other antimicrobials (<2%). This study shows the presence of AMR bacteria in Great Cormorants, indicating that these birds potentially disseminate AMR bacteria.

Antimicrobial susceptibility of Escherichia coli isolates obtained from wild mammals between 2013 and 2017 in Japan

The emergence and prevalence of antimicrobial-resistant bacteria in wild animals are a great concern for public health. A total of 963 Escherichia coli isolates from 475 wild mammals (242 sika deers, 112 wild boars, 113 small mammals, 4 Japanese badger, 2 Tokara cows, and 2 Amani rabbits), collected between 2013 and 2017, were examined for antimicrobial susceptibility. Resistance to at least one antimicrobial was observed in 92 of 963 isolates (9.3%). No isolates exhibited resistance to carbapenem (meropenem). Resistance to third-generation cephalosporin (cefotaxime) and fluoroquinolone (ciprofloxacin) was observed in less than 1% of the isolates. Thus, low prevalence of bacterial antimicrobial resistance was observed in wild mammals between 2013 and 2017 in Japan.

Prevalence of antimicrobial-resistant Escherichia coli in endangered Okinawa rail (Gallirallus okinawae) inhabiting areas around a livestock farm

Antimicrobial resistance (AMR) is an important issue for public, animal and environmental health. It has been suggested that livestock farms could be a source origin of AMR, and some wild animals that inhabit this area may play an important role in the spread of AMR in the natural environment. The prevalence of AMR in Escherichia coli was examined from Okinawa rails (Gallirallus okinawae), an endemic bird in Okinawa Main Island, Japan. Forty‐eight faecal samples of wild Okinawa rails were collected from around a livestock farm area (LA), near human settlements, in which a population of the Okinawa rail had newly inhabited for feeding, and a forest area (FA), their natural habitat. Among 16 E. coli‐positive faecal samples collected around LA, 11/16 (69%) showed antimicrobial resistance and five multiple drug resistance patterns were identified. However, among 15 E. coli‐positive faecal samples from FA, 3/15 (20%) showed antimicrobial resistance, and three multiple drug resistance patterns were identified. These results indicate that the endangered Okinawa rail may also play an important role as a potential vector for the spread of AMR in the natural environment. To maintain ecological health, it is imperative that in situ/ex situ conservation projects that include translocation plans for endangered species are aware of these data.

We identified antimicrobial‐resistant bacteria in Okinawa rails living near a livestock farm and in forest areas in Okinawa Main Island, suggesting that Okinawa rails play a role in spreading antimicrobial resistance between areas of human habitation and the natural environment.

Surveillance of antibiotic resistance in Escherichia coli isolated from wild cranes on the Izumi plain in Kagoshima prefecture, Japan

The prevalence of antibiotic resistance in 376 Escherichia coli (E. coli) isolates from fecal samples of Hooded and White-naped cranes was investigated on the Izumi plain in Kagoshima prefecture, Japan, during winter 2016 and 2017. Resistance to oxytetracycline, ampicillin, and nalidixic acid were observed in 10.9%, 3.1–4.4%, and 2.1–7.7% of isolates, respectively. Since the previous surveillance in 2007, isolation rates of antibiotic-resistant E. coli recovered from wild cranes have remained at significantly low levels compared with those in Japanese livestock. Our results indicate that surveillance of antibiotic-resistant E. coli from wild cranes wintering in the Izumi plain could be a useful strategy to indicate natural environmental pollution by antibiotic-resistant bacteria in the environment.

Multidrug-resistant pathogens in the food supply

Antimicrobial resistance, including multidrug resistance (MDR), is an increasing problem globally. MDR bacteria are frequently detected in humans and animals from both more- and less-developed countries and pose a serious concern for human health. Infections caused by MDR microbes may increase morbidity and mortality and require use of expensive drugs and prolonged hospitalization. Humans may be exposed to MDR pathogens through exposure to environments at health-care facilities and farms, livestock and companion animals, human food, and exposure to other individuals carrying MDR microbes. The Centers for Disease Control and Prevention classifies drug-resistant foodborne bacteria, including Campylobacter, Salmonella Typhi, nontyphoidal salmonellae, and Shigella, as serious threats. MDR bacteria have been detected in both meat and fresh produce. Salmonellae carrying genes coding for resistance to multiple antibiotics have caused numerous foodborne MDR outbreaks. While there is some level of resistance to antimicrobials in environmental bacteria, the widespread use of antibiotics in medicine and agriculture has driven the selection of a great variety of microbes with resistance to multiple antimicrobials. MDR bacteria on meat may have originated in veterinary health-care settings or on farms where animals are given antibiotics in feed or to treat infections. Fresh produce may be contaminated by irrigation or wash water containing MDR bacteria. Livestock, fruits, and vegetables may also be contaminated by food handlers, farmers, and animal caretakers who carry MDR bacteria. All potential sources of MDR bacteria should be considered and strategies devised to reduce their presence in foods. Surveillance studies have documented increasing trends in MDR in many pathogens, although there are a few reports of the decline of certain multidrug pathogens. Better coordination of surveillance programs and strategies for controlling use of antimicrobials need to be implemented in both human and animal medicine and agriculture and in countries around the world.