First report of a blaNDM-5-carrying Escherichia coli sequence type 12 isolated from a dog with pyometra in Japan.

Carbapenemase-producing Enterobacterales (CPE) are a serious concern in human clinical settings. Companion animal-origin CPE have been only rarely identified in several countries, but they have not yet been identified in Japan. In this study, we present the first case of a canine infected with CPE in Japan. The patient was hospitalized due to pyometra. The pus discharged from the patient's uterus was subjected to bacteriological analysis. As a result, E. coli was identified in the pus and exhibited resistance to piperacillin, amoxicillin-clavulanic acid, cefazolin, ceftazidime, cefepime, meropenem, amikacin, and sulfamethoxazole-trimethoprim and susceptibility to aztreonam, minocycline, and levofloxacin. Results of the sodium mercaptoacetic acid double-disk synergy test showed that the E. coli isolate was positive for metallo-ß-lactamases. Next-generation sequencing identified the blaNDM-5 gene, which was located in the IncFII-type plasmid together with blaTEM-1b, rmtB, aadA2, bleMBL, sul1, qacE, and dfrA12. The case was treated successfully with doxycycline and orbifloxacin. Our finding emphasizes that close attention should be paid to the significance of CPE harboring multidrug-resistance plasmid in companion animals, based on the perspective of One Health approach in Japan as well as in other countries.

Antimicrobial resistance in Enterobacteriaceae isolated from arthropods in Gifu City, Japan.

The wide occurrence of antimicrobial-resistant (AMR) bacteria in various environments is of great concern. Here, we examined the prevalence and antimicrobial susceptibility of Enterobacteriaceae isolated from 88 wild arthropods, collected in Gifu city, Japan. In total, 168 isolates of Enterobacteriaceae were obtained from 61 arthropods. All isolates were susceptible to all the antimicrobial agents tested, except colistin (31 isolates) and kanamycin (one isolate). The aph(3')-Ia gene, responsible for kanamycin resistance, was detected in Klebsiella oxytoca. Although synanthropic arthropods (houseflies and cockroaches) serve as vectors for AMR Enterobacteriaceae, other wild arthropods are not crucial carriers of Enterobacteriaceae resistant to antimicrobial agents.

Persistence of extended-spectrum ß-lactamase plasmids among Enterobacteriaceae in commercial broiler farms.

To clarify the persistence of extended-spectrum ß-lactamase (ESBL) producers, 13 plasmids from two broiler farms were analyzed. On the farm not using antimicrobials, one plasmid from Klebsiella pneumoniae isolated from a day-old chick was similar to that from Escherichia coli isolated a year later, with the deletion of two transposons. On the farm using antimicrobials, most circulating plasmids (eight out of nine) in a flock of 40-days-old chicks were identical, although one from K. pneumoniae had a deletion of a transposon carrying a class 1 integron containing aadA2 and dfrA12. Thus, ESBL plasmids persisted in the farms with or without antimicrobial agent use.

Isolation and Characterization of Antimicrobial-Resistant Escherichia coli from Retail Meats from Roadside Butcheries in Uganda.

Retail meats are one of the main routes for spreading antimicrobial-resistant bacteria (ARB) from livestock to humans through the food chain. In African countries, retail meats are often sold at roadside butcheries without chilling or refrigeration. Retail meats in those butcheries are suspected to be contaminated by ARB, but it was not clear. In this study, we tested for the presence of antimicrobial-resistant Escherichia coli from retail meats (n = 64) from roadside butcheries in Kampala, Uganda. The meat surfaces were swabbed and inoculated on PetriFilm SEC agar to isolate E. coli. We successfully isolated E. coli from 90.6% of these retail meat samples. We identified the phylogenetic type, antimicrobial susceptibility, and antimicrobial resistance genes prevalence between retail meat isolates (n = 89). Phylogenetic type B1 was identified from 70.8% of the retail meat isolates, suggesting that the isolates originated primarily from fecal contamination during meat processing. Tetracycline (TET)-resistant isolates with tetA and/or tetB gene(s) were the most frequently detected (28.1%), followed by ampicillin (AMP) resistance genes with blaTEM (15.7%,) and sulfamethoxazole-trimethoprim (SXT) resistance genes with sul2 (15.7%). No extended-spectrum beta-lactamase-producing isolates were detected. A conjugation assay showed that resistance to AMP, TET, and SXT could be simultaneously transferred to recipients. These findings suggest that antimicrobial-resistant E. coli can easily be transferred from farms to tables from retail meats obtained from roadside butcheries.

Selection of broad-spectrum cephalosporin-resistant Escherichia coli in the feces of healthy dogs after administration of first-generation cephalosporins.

Although antimicrobial products are essential for treating diseases caused by bacteria, antimicrobial treatment selects for antimicrobial-resistant (AMR) bacteria. The aim of this study was to determine the effects of administration of first-generation cephalosporins on development of resistant Escherichia coli in dog feces. The proportions of cephalexin (LEX)-resistant E. coli in fecal samples of three healthy dogs treated i.v. with cefazolin before castration and then orally with LEX for 3 days post-operation (PO) were examined using DHL agar with or without LEX (50 µg/mL). LEX-resistant E. coli were found within 3 days PO, accounted for 100% of all identified E. coli 3-5 days PO in all dogs, and were predominantly found until 12 days PO. LEX-resistant E. coli isolates on DHL agar containing LEX were subjected to antimicrobial susceptibility testing, pulsed-field gel electrophoresis (PFGE) genotyping, ß-lactamase typing and plasmid profiling. All isolates tested exhibited cefotaxime (CTX) resistance (CTX minimal inhibitory concentration ≥4 µg/mL). Seven PFGE profiles were classified into five groups and three ß-lactamase combinations (blaCMY-4 -blaTEM-1 , blaTEM-1 -blaCTX-M-15 and blaTEM-1 -blaCTX-M-15 -blaCMY-4 ). All isolates exhibited identical PFGE profiles in all dogs on four days PO and subsequently showed divergent PFGE profiles. Our results indicate there are two selection periods for AMR bacteria resulting from the use of antimicrobials. Thus, continuing hygiene practices are necessary to prevent AMR bacteria transfer via dog feces after antimicrobial administration.

Molecular Typing of Fluoroquinolone-Resistant Campylobacter jejuni Isolated from Broilers in Japan Using Multilocus Sequence Typing and Pulsed-Field Gel Electrophoresis.

Fluoroquinolone-resistant Campylobacter jejuni isolates from broilers in Japan were characterized using multilocus sequence typing and pulsed-field gel electrophoresis (PFGE) in order to elucidate the genetic relationship between these strains. Forty-three of the isolates were classified into 20 sequence types and were clustered into 21 PFGE types with 70% similarity. The most dominant clonal complex (CC) was CC-21 (41.9%). Diverse PFGE patterns were observed within the same CC, but the combined analysis of PFGE type and CC revealed that the strains with the same combination were isolated from the same district or neighboring districts. On the other hand, strains with the same combination pattern were also isolated from geographically distant districts. Our results elucidate two possible reasons for the prevalence of fluoroquinolone-resistant C. jejuni among broiler farms: (1) the resistant C. jejuni is clonally disseminated within the limited area, and (2) susceptible C. jejuni acquired fluoroquinolone resistance during the use of fluoroquinolone on the farms.

Decreased Resistance to Broad-Spectrum Cephalosporin in Escherichia coli from Healthy Broilers at Farms in Japan After Voluntary Withdrawal of Ceftiofur.

The high prevalence of broad-spectrum cephalosporin (BSC) resistance in Escherichia coli isolates from healthy broilers at farms is a source of grave concern in Japan. In an effort to solve this problem, the off-label use of ceftiofur (CTF) at hatcheries was voluntarily withdrawn around March 2012. The objective of this study was to assess the effect of the voluntary withdrawal on the prevalence of BSC resistance in E. coli from healthy broilers at farms. A total of 693 E. coli isolates collected from 362 fecal samples of healthy broilers at farms between 2010 and 2013 were examined to determine their antimicrobial resistance profiles and ß-lactamase genes. ß-Lactamase genes were characterized by polymerase chain reaction and sequencing. BSC resistance was detected in 84 of the 693 E. coli isolates (12.1%) from healthy broilers between 2010 and 2013. The percentage of BSC-resistant E. coli isolates was significantly decreased: from 16.4% (32/195) in 2010 and 16.8% (27/161) in 2011 to 9.2% (19/206) in 2012 and 4.6% (6/131) in 2013 (2010 versus 2012: p=0.024, 2010 versus 2013: p=0.001, 2011 versus 2012: p=0.038, and 2011 versus 2013: p=0.001). Regarding ß-lactamase genes, 58 of the 84 BSC-resistant E. coli isolates (69.0%) harbored blaCMY-2. The prevalence of BSC resistance in E. coli isolated from healthy broilers at farms was markedly decreased within a year after the voluntary withdrawal from CTF use at hatcheries. This indicates that BSC resistance in E. coli isolates from broilers could be controlled by restricting the use of CTF at the hatchery level.

Control of the development and prevalence of antimicrobial resistance in bacteria of food animal origin in Japan: a new approach for risk management of antimicrobial veterinary medicinal products in Japan.

Antimicrobial agents are essential for controlling bacterial disease in food-producing animals and contribute to the stable production of safe animal products. The use of antimicrobial agents in these animals affects the emergence and prevalence of antimicrobial resistance in bacteria isolated from animals and animal products. As disease-causing bacteria are often transferred from food-producing animals to humans, the food chain is considered a route of transmission for the resistant bacteria and/or resistance genes. The Food Safety Commission of Japan (FSC) has been assessing the risk posed to human health by the transmission of antimicrobial-resistant bacteria from livestock products via the food chain. In addition to the FSC's risk assessments, the Japanese Ministry of Agriculture, Forestry and Fisheries has developed risk-management guidelines to determine feasible risk-management options for the use of antimicrobial veterinary medicinal products during farming practices. This report includes information on risk assessment and novel approaches for risk management of antimicrobial veterinary medicinal products for mitigating the risk of development and prevalence of antimicrobial resistance in bacteria originating from food-producing animals in Japan.

Phylogenetic grouping, epidemiological typing, analysis of virulence genes, and antimicrobial susceptibility of Escherichia coli isolated from healthy broilers in Japan.

BACKGROUND: The aim of our study was to investigate the possible etiology of avian colibacillosis by examining Escherichia coli isolates from fecal samples of healthy broilers. FINDINGS: Seventy-eight E. coli isolates from fecal samples of healthy broilers in Japan were subjected to analysis of phylogenetic background, virulence-associated gene profiling, multi-locus sequence typing (MLST), and antimicrobial resistance profiling. Phylogenetic analysis demonstrated that 35 of the 78 isolates belonged to group A, 28 to group B1, one to group B2, and 14 to group D. Virulence-associated genes iutA, iss, cvaC, tsh, iroN, ompT, and hlyF were found in 23 isolates (29.5%), 16 isolates (20.5%), nine isolates (11.5%), five isolates (6.4%), 19 isolates (24.4%), 23 isolates (29.5%), and 22 isolates (28.2%) respectively. Although the genetic diversity of group D isolates was revealed by MLST, the group D isolates harbored iutA (10 isolates, 71.4%), iss (6 isolates, 42.9%), cvaC (5 isolates, 35.7%), tsh (3 isolates, 21.4%), hlyF (9 isolates, 64.3%), iroN (7 isolates, 50.0%), and ompT (9 isolates, 64.3%). CONCLUSIONS: Our results indicated that E. coli isolates inhabiting the intestines of healthy broilers pose a potential risk of causing avian colibacillosis.

Changes in the Phenotypes of Salmonella spp. in Japanese Broiler Flocks.

Salmonella infections represent a leading cause of foodborne illnesses; resistance to third-generation cephalosporins (TGCs), which are a first-choice antimicrobial for treating human Salmonella enteritis, has become a serious public health concern worldwide. Because the consumption of undercooked chicken meat products is a major cause of foodborne salmonellosis in Japan, we conducted three surveys at different periods between 2017 and 2022, with the cooperation of four abattoirs (two in Eastern and two in Western Japan). The first survey was conducted at abattoir A, which is located in Eastern Japan. Salmonella was detected in 84.4% of broiler flocks tested (27/32); among them, all the TGC-resistant isolates obtained from one farm (farm FA) were identified as S. Infantis. Salmonella was recovered from 62.5% of breast meat samples (20/32), with one case suggesting cross-contamination. The second survey was conducted at three other abattoirs to examine the prevalence of TGC-resistant Salmonella, in both Western (abattoirs B and C) and Eastern (abattoir D) Japan. Salmonella was detected in 90.6% of broiler flocks examined (29/32). TGC-resistant S. Infantis was isolated from 2 flocks until 2018 and not thereafter. Subsequently, isolates were identified as TGC-susceptible S. Schwarzengrund in both regions. The third survey was performed at abattoir A to elucidate whether there were changes in the phenotypes. Of the 11 broiler flocks introduced from farm FA, 10 were positive for Salmonella (90.9%); all the isolates were S. Schwarzengrund susceptible to TGC. This study shows that TGC-susceptible S. Schwarzengrund has replaced the resistant phenotypes among broiler flocks in both Eastern and Western Japan. Although chicken meat products could be cross-contaminated with Salmonella during the slaughtering process, reducing the prevalence of Salmonella in broiler flocks remains important to decrease Salmonella enteritis in humans.

Diversity of plasmid replicons encoding the bla(CMY-2) gene in broad-spectrum cephalosporin-resistant Escherichia coli from livestock animals in Japan.

Broad-spectrum cephalosporin (BSC) resistance has increased in Escherichia coli isolates from broiler chickens in Japan since 2004. The purpose of this study was to understand the epidemiology of BSC-resistant E. coli in livestock animals. Among 3274 E. coli isolates from 1767 feces of apparently healthy animals on 1767 farms between 2004 and 2009, 118 ceftiofur (CTF)-resistant isolates (CTF MIC ≥4 µg/mL) were identified on 74 farms. After elimination of apparently clonal isolates from a single animal, 75 selected CTF-resistant isolates (62 isolates from 61 broiler chickens, 10 isolates from 10 layer chickens, two isolates from two cows, and one isolate from a pig) were characterized. The bla(CMY-2) gene was most frequently detected in 50 isolates, followed by bla(CTX-M) (CTX-M-2: six isolates; CTX-M-14: four isolates; CTX-M-25: two isolates; CTX-M-1: one isolate) and bla(SHV) (SHV-12: seven isolates; SHV-2, SHV-2a, SHV-5: one isolate each). In particular, 42 of 62 broiler chicken isolates harbored bla(CMY-2). Pulsed-field gel electrophoresis analyses using XbaI revealed divergent profiles among the BSC-resistant isolates. The incompatibility groups of bla(CMY-2) plasmids from 34 of the 42 broiler chicken isolates belonged to IncIγ (10 isolates), IncA/C (nine isolates), IncB/O (seven isolates) and IncI1 (six isolates), or were nontypeable (two isolates). Co-transmission of resistance to non-ß-lactam antibiotics was observed in transconjugants with IncA/C plasmids, but not with IncI1, IncIγ, and IncB/O plasmids except for one isolate with IncB/O. Our findings suggest that the bla(CMY-2) gene is a key player in BSC-resistant E. coli isolates and that coselection is unlikely to be associated with the abundance of bla(CMY-2) plasmids, except for IncA/C plasmids.

Antimicrobial usage surveys using electronic medical records in cattle practice in Gifu Prefecture.

As the majority of antimicrobial treatments for cattle in Japan are prescribed by veterinarians, medical record information can be useful in clarifying the amount and purpose of antimicrobial use. In this study, we examined their amount and purpose in cattle practices in Gifu Prefecture. In cattle, approximately 85% of the antimicrobials are used for the treatment of gastrointestinal (50.4%) and respiratory diseases (34.4%). The main antimicrobials were sulfonamides (27.1 kg, 49.2%), followed by amphenicols (11.9 kg, 21.7%). As for second-line antimicrobials for veterinary treatment, fluoroquinolones, a third-generation cephalosporins, and 15 membered-ring macrolides, accounted for 5.6%, 0.1%, and 0.9% of all antimicrobials, respectively. Thus, medical record information may represent the actual situation of not only antimicrobial use, but also the significance of the disease in local regions.

Characterization of quinolone-resistant and extended-spectrum ß-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 ß-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.

Low potential of persistence and dissemination of antimicrobial-resistant Enterobacterales by wild nutria (Myocastor coypus) in a local river of Gifu Prefecture.

Environmental pollution caused by antimicrobial resistance is a global public health concern. To investigate the contribution of nutrias (Myocastor coypus) to the presence of extended-spectrum ß-lactamase (ESBL)-producing Enterobacterales in the Ijira River, prevalence of ESBL-producing Enterobacterales in their feces was examined using deoxycholate-hydrogen sulfide-lactose agar containing cefotaxime. Additionally, the composition of the fecal microbiota of nutria was examined using DNA metabarcoding analysis of the 16S ribosomal RNA gene and compared with that of Amami rabbit, deer, fox, and raccoon dog. The absence of ESBL-producing Enterobacterales and substantially lower abundance of Enterobacterales was observed in the feces of nutrias than in those of other wild mammals. Our results suggest the low potential of antimicrobial-resistant Enterobacterales persistence and dissemination by nutria.

Antimicrobial resistance profiles of Campylobacter jejuni and Salmonella spp. isolated from enteritis patients in Japan.

Understanding the antimicrobial resistance of Campylobacter jejuni and Salmonella spp. isolated from patients with enteritis will aid in therapeutic decision-making. This study aimed to characterize C. jejuni and Salmonella spp. isolates from patients with enteritis. For C. jejuni, the resistance rates against ampicillin, tetracycline, and ciprofloxacin were 17.2%, 23.8%, and 46.4%, respectively. All the C. jejuni isolates were susceptible to erythromycin, which is recommended as a first-choice antimicrobial if Campylobacter enteritis is strongly suspected. C. jejuni was classified into 64 sequence types (STs), and the five major STs were ST22, ST354, ST21, ST918, and ST50. The ciprofloxacin-resistance rate of ST22 was 85.7%. For Salmonella, the resistance rates against ampicillin, cefotaxime, streptomycin, kanamycin, tetracycline, and nalidixic acid were 14.7%, 2.0%, 57.8%, 10.8%, 16.7%, and 11.8%, respectively. All the Salmonella spp. isolates were susceptible to ciprofloxacin. Therefore, fluoroquinolones are the recommended antimicrobials against Salmonella enteritis. S. Thompson, S. Enteritidis, and S. Schwarzengrund were the three most prevalent serotypes. The two cefotaxime-resistant isolates were serotyped as S. Typhimurium and were found to harbor blaCMY-2. The results of this study would help select antimicrobials for treating patients with Campylobacter and Salmonella enteritis.

Unique genomic sequences in a novel Mycobacterium avium subsp. hominissuis lineage enable fine scale transmission route tracing during pig movement.

Mycobacterium avium subsp. hominissuis (MAH) is one of the most prevalent mycobacteria causing non-tuberculous mycobacterial disease in humans and animals. Of note, MAH is a major cause of mycobacterial granulomatous mesenteric lymphadenitis outbreaks in pig populations. To determine the precise source of infection of MAH in a pig farm and to clarify the epidemiological relationship among pig, human and environmental MAH lineages, we collected 50 MAH isolates from pigs reared in Japan and determined draft genome sequences of 30 isolates. A variable number of tandem repeat analysis revealed that most pig MAH isolates in Japan were closely related to North American, European and Russian human isolates but not to those from East Asian human and their residential environments. Historical recombination analysis revealed that most pig isolates could be classified into SC2/4 and SC3, which contain MAH isolated from pig, European human and environmental isolates. Half of the isolates in SC2/4 had many recombination events with MAH lineages isolated from humans in East Asia. To our surprise, four isolates belonged to a new lineage (SC5) in the global MAH population. Members of SC5 had few footprints of inter-lineage recombination in the genome, and carried 80 unique genes, most of which were located on lineage specific-genomic islands. Using unique genetic features, we were able to trace the putative transmission route via their host pigs. Together, we clarify the possibility of species-specificity of MAH in addition to local adaptation. Our results highlight two transmission routes of MAH, one exposure on pig farms from the environment and the other via pig movement. Moreover, our study also warns that the evolution of MAH in pigs is influenced by MAH from patients and their residential environments, even if the MAH are genetically distinct.

First detection of Lake Sinai virus in honeybees (Apis mellifera) and wild arthropods in Japan.

Lake Sinai virus (LSV), an RNA virus, is suspected to be associated with poor health in honeybees (Apis mellifera). We examined LSV in 26 specimens of healthy honeybees and 44 specimens of wild arthropods in the Gifu Prefecture, Japan. LSV was found more frequently in honeybee specimens (11/26, 42.3%) than in wild arthropod specimens (1/44, 2.3%) (P<0.01). Phylogenetic and nucleotide sequence analysis revealed two lineages: LSV3 in honeybees, and LSV4 in both honeybees and wild arthropods. To our knowledge, this is the first report of LSV prevalence in honeybees and wild arthropods in Japan.

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.

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.