Antimicrobial Resistance in Animals

A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Animal System and Management".

Deadline for manuscript submissions: closed (31 March 2022) | Viewed by 31174

Special Issue Editor

Special Issue Information

Dear Colleagues,

Antimicrobial resistance is a greatly increasing problem worldwide. The rapid adaptability of microorganisms leads to the development of resistance mechanisms against many compounds. In particular, among bacteria, resistance has been described against almost all available molecules. The discovery of truly new “antibiotics” is now rarer than in the past and, in many cases, is rapidly followed by the emergence of resistant strains. Furthermore, the possibility of acquiring resistance to multiple compounds has the potential to generate so-called “superbugs”. As consequence, many authors speculate about the possibility of returning to the “pre-antibiotic” era in the near future.

Animals and veterinary practices could play an important role in this scenario. The uncontrolled and abundant use of antibiotics in animals has contributed abundantly to the development and spread of this problem. Domestic animals could be a source of antimicrobial-resistant microorganisms not only directly to owners, workers, and practitioners, but also indirectly to the entire human population via contaminated foods. Wildlife could act as a reservoir of antimicrobial-resistant microbes or genes and contribute to keeping, spreading and transferring them to humans or domestic animals. Migratory wildlife and the global commerce of animals and animal products could contribute to the dissemination of antimicrobial-resistant microorganisms across long distances.

The aim of this Special Issue is to provide new information about the status of antimicrobial resistance in domestic and wild animals. Investigation of the diffusion of antimicrobial resistance among microorganisms collected from animals is the primary objective, and studies on the role of animals as a reservoir for antimicrobial-resistant microbes are also of interest. Both phenotypic and molecular approaches are encouraged. Manuscripts focusing on emerging problems in human health, such as methicillin or vancomycin resistance as well as the production of carbapenemases and Extended Spectyumβ Lactamases (ESBLs), are welcome. Finally, new approaches leading to the possible reduction or alternatives to the use of antimicrobial agents will be considered.

Dr. Fabrizio Bertelloni
Guest Editor

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Keywords

  • antimicrobial resistance
  • domestic animals
  • wildlife
  • reservoir
  • epidemiology
  • spread
  • resistance genes

Published Papers (9 papers)

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Research

12 pages, 288 KiB  
Article
Resistance Patterns, mcr-4 and OXA-48 Genes, and Virulence Factors of Escherichia coli from Apennine Chamois Living in Sympatry with Domestic Species, Italy
by Camilla Smoglica, Alberto Vergara, Simone Angelucci, Anna Rita Festino, Antonio Antonucci, Lorenzo Moschetti, Muhammad Farooq, Fulvio Marsilio and Cristina Esmeralda Di Francesco
Animals 2022, 12(2), 129; https://doi.org/10.3390/ani12020129 - 06 Jan 2022
Cited by 5 | Viewed by 1817
Abstract
The aim of this study was to determine and characterize potential resistance mechanisms against selected Critically Important Antibiotics in Escherichia coli isolates collected from wild and domestic ruminants living in the Maiella National Park, in Central Italy. A total of 38 isolates were [...] Read more.
The aim of this study was to determine and characterize potential resistance mechanisms against selected Critically Important Antibiotics in Escherichia coli isolates collected from wild and domestic ruminants living in the Maiella National Park, in Central Italy. A total of 38 isolates were obtained from red deer, Apennine chamois, cattle, sheep, and goats grazing in lands with different levels of anthropic pressure. Antimicrobial susceptibility was determined by Minimal Inhibitory Concentration testing, showing phenotypic resistance to colistin, meropenem, or ceftazidime in 9 isolates along with one bacterial strain being resistant to three of the tested antibiotics. In addition, the biomolecular assays allowed the amplification of the genes conferring the colistin (mcr-4), the carbapenems (OXA-48), penicillins and cephalosporins (TEM, SHV, CMY-1, CMY-2) resistance. In order to describe the potential pathogenicity of isolates under study, virulence genes related to Shiga toxin-producing (STEC) and enteropathogenic (EPEC) pathovars were identified. This study is the first report of mcr-4 and OXA-48 genes in resistant E. coli harboring virulence genes in Italian wildlife, with special regard to Apennine chamois and red deer species. The multidisciplinary approach used in this study can improve the early detection of emerging antibiotic resistance determinants in human-animal-environment interfaces by means of wildlife monitoring. Full article
(This article belongs to the Special Issue Antimicrobial Resistance in Animals)
17 pages, 822 KiB  
Article
Characterization and Comparison of Enterococcus spp. Isolates from Feces of Healthy Dogs and Urine of Dogs with UTIs
by Dagmara Stępień-Pyśniak, Fabrizio Bertelloni, Marta Dec, Giulia Cagnoli, Dorota Pietras-Ożga, Renata Urban-Chmiel and Valentina Virginia Ebani
Animals 2021, 11(10), 2845; https://doi.org/10.3390/ani11102845 - 29 Sep 2021
Cited by 18 | Viewed by 2717
Abstract
Enterococcus spp. are opportunistic pathogens of both humans and animals characterized by high resistance to antimicrobials. Dogs could be intestinal carriers or suffer from Enterococcus infections, mainly urinary tract infections (UTIs). This study aimed to analyze and compare Enterococcus spp. isolated from healthy [...] Read more.
Enterococcus spp. are opportunistic pathogens of both humans and animals characterized by high resistance to antimicrobials. Dogs could be intestinal carriers or suffer from Enterococcus infections, mainly urinary tract infections (UTIs). This study aimed to analyze and compare Enterococcus spp. isolated from healthy dog stools and sick dog urine. Overall, 51 isolates (29 from stools and 22 from UTI) were characterized at species level and tested for antimicrobial resistance, biofilm production and presence of resistance and virulence genes. E. faecium and E. faecalis resulted as equally distributed in stools samples, while E. faecalis predominated among UTI isolates. HLAR phenotype was detected in 47.1% isolates; 64.7% isolates were resistant to ampicillin (47.1% with a MIC ≥ 64 µg/mL). High levels of resistance were recorded for fluoroquinolones (enrofloxacin 74.5%, ciprofloxacin 66.7%), clindamycin (84.3%), tetracycline (78.4%) and quinupristin–dalfopristin (78.4%). No vancomycin resistant strains were detected. All but one isolate were multidrug-resistant. Most detected resistance genes were tetM (70.5%), pbp4 (52.9%) and aph(3′)-IIIa (39.2%). All isolates were able to produce biofilm, but isolates from UTIs and belonging to E. faecalis more frequently resulted in strong biofilm producers. Most detected virulence genes were asa1 (52.9%), gelE (41.2%), cylA (37.3%) and esp (35.3%); all of them resulted as more frequently associated to E. faecalis. No particular differences emerged between isolates from feces and UTI, considering all evaluated aspects. Our results confirm pet dogs as carriers of multidrug-resistant enterococci; stool microflora could be considered as the most probable source of enterococcal UTI and E. faecalis carried by dogs seems to be more virulent than E. faecium, justifying its more frequent involvement in urinary tract infections. Full article
(This article belongs to the Special Issue Antimicrobial Resistance in Animals)
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13 pages, 1245 KiB  
Article
Antimicrobial Resistance of Escherichia coli in Dairy Calves: A 15-Year Retrospective Analysis and Comparison of Treated and Untreated Animals
by Nicoletta Formenti, Chiara Martinelli, Nicoletta Vitale, Stefano Giovannini, Cristian Salogni, Matteo Tonni, Federico Scali, Laura Birbes, Mario D’Incau, Flavia Guarneri, Paolo Pasquali and Giovanni Loris Alborali
Animals 2021, 11(8), 2328; https://doi.org/10.3390/ani11082328 - 06 Aug 2021
Cited by 4 | Viewed by 3034
Abstract
The health problem of antimicrobial resistance (AMR) involves several species. AMR surveillance is essential to identify its development and design control strategies; however, available data are still limited in some contexts. The AMR profiles of 2612 E. coli strains isolated over a period [...] Read more.
The health problem of antimicrobial resistance (AMR) involves several species. AMR surveillance is essential to identify its development and design control strategies; however, available data are still limited in some contexts. The AMR profiles of 2612 E. coli strains isolated over a period of 15 years (2002–2016) from calf enteric cases were analyzed to determine the presence of resistance and their temporal dynamics. Furthermore, the AMR profiles and the presence of the major virulence genes of 505 E. coli strains isolated from 1-week- and 2-week-old calves, 406 treated with antimicrobials and 99 untreated, were analyzed and compared to investigate the potential effects of treatment on AMR and strain pathogenicity. Resistance to tetracycline (90.70%) was the most common, followed by resistance to sulfamethoxazole/trimethoprim (77.70%) and flumequine (72.10%). The significantly higher percentage of AMR and virulence gene expression recorded in treated calves, combined with the statistically higher resistance to sulfamethoxazole/trimethoprim in E. coli with K99, corroborates the notion of resistance being induced by the frequent use of antimicrobials, leading to treatments potentially becoming ineffective. The significantly higher resistance to amoxicillin/clavulanic acid, enrofloxacin, and florfenicol in isolates from 1-week-old calves suggests the role of the environment as a source of contamination that should be investigated further. Full article
(This article belongs to the Special Issue Antimicrobial Resistance in Animals)
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10 pages, 762 KiB  
Article
Prevalence and Characteristics of Multidrug-Resistant Livestock-Associated Methicillin-Resistant Staphylococcus aureus (LA-MRSA) CC398 Isolated from Quails (Coturnix Coturnix Japonica) Slaughtered for Human Consumption
by Vanessa Silva, Madalena Vieira-Pinto, Cândido Saraiva, Vera Manageiro, Lígia Reis, Eugénia Ferreira, Manuela Caniça, José L. Capelo, Gilberto Igrejas and Patrícia Poeta
Animals 2021, 11(7), 2038; https://doi.org/10.3390/ani11072038 - 08 Jul 2021
Cited by 22 | Viewed by 4608
Abstract
Livestock-associated MRSA (LA-MRSA) is a zoonotic pathogen that has been reported in several animals, and it is often associated with clonal complex (CC) 398. We aimed to isolate MRSA from quails and to characterize their antimicrobial resistance and genetic lineages. One hundred swab [...] Read more.
Livestock-associated MRSA (LA-MRSA) is a zoonotic pathogen that has been reported in several animals, and it is often associated with clonal complex (CC) 398. We aimed to isolate MRSA from quails and to characterize their antimicrobial resistance and genetic lineages. One hundred swab samples were recovered from quails at the slaughterhouse. The swabs were inoculated onto CHROMagar™ MRSA agar plates for MRSA isolation. The presence of antimicrobial-resistant genes and virulence factors was investigated by PCR. All strains were typed by MLST, SCCmec-, spa- and agr-typing. From the 100 samples, 29 MRSA were isolated. All strains were resistant to penicillin, cefoxitin, ciprofloxacin, erythromycin and clindamycin and carried the blaZ, mecA, ermB and ermC genes. All strains, except one, showed resistance to tetracycline and harbored the tetM, tetK and tetL genes in different combinations. Twenty strains belonged to ST398 and SCCmec type V, and nine strains belonged to the new ST6831. Twenty-eight out of twenty-nine strains were ascribed to t011 and one to t108. As far as we know, this is the first report of MRSA from quails slaughtered for human consumption. Most strains belonged to ST398-t011, which is the most common LA-MRSA clone found in livestock in Europe. Full article
(This article belongs to the Special Issue Antimicrobial Resistance in Animals)
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10 pages, 624 KiB  
Article
ESBL/AmpC-Producing Escherichia coli in Wild Boar: Epidemiology and Risk Factors
by Nicoletta Formenti, Stefania Calò, Giovanni Parisio, Flavia Guarneri, Laura Birbes, Alessandra Pitozzi, Federico Scali, Matteo Tonni, Federica Guadagno, Stefano Giovannini, Cristian Salogni, Adriana Ianieri, Silvia Bellini, Paolo Pasquali and Giovanni Loris Alborali
Animals 2021, 11(7), 1855; https://doi.org/10.3390/ani11071855 - 22 Jun 2021
Cited by 13 | Viewed by 1842
Abstract
The complex health problem of antimicrobial resistance (AMR) involves many host species, numerous bacteria and several routes of transmission. Extended-spectrum β-lactamase and AmpC (ESBL/AmpC)-producing Escherichia coli are among the most important strains. Moreover, wildlife hosts are of interest as they are likely antibiotics [...] Read more.
The complex health problem of antimicrobial resistance (AMR) involves many host species, numerous bacteria and several routes of transmission. Extended-spectrum β-lactamase and AmpC (ESBL/AmpC)-producing Escherichia coli are among the most important strains. Moreover, wildlife hosts are of interest as they are likely antibiotics free and are assumed as environmental indicators of AMR contamination. Particularly, wild boar (Sus scrofa) deserves attention because of its increased population densities, with consequent health risks at the wildlife–domestic–human interface, and the limited data available on AMR. Here, 1504 wild boar fecal samples were microbiologically and molecularly analyzed to investigate ESBL/AmpC-producing E. coli and, through generalized linear models, the effects of host-related factors and of human population density on their spread. A prevalence of 15.96% of ESBL/AmpC-producing E. coli, supported by blaCTX-M (12.3%), blaTEM (6.98%), blaCMY (0.86%) and blaSHV (0.47%) gene detection, emerged. Young animals were more colonized by ESBL/AmpC strains than older subjects, as observed in domestic animals. Increased human population density leads to increased blaTEM prevalence in wild boar, suggesting that spatial overlap may favor this transmission. Our results show a high level of AMR contamination in the study area that should be further investigated. However, a role of wild boar as a maintenance host of AMR strains emerged. Full article
(This article belongs to the Special Issue Antimicrobial Resistance in Animals)
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16 pages, 3492 KiB  
Article
On Gram-Positive- and Gram-Negative-Bacteria-Associated Canine and Feline Skin Infections: A 4-Year Retrospective Study of the University Veterinary Microbiology Diagnostic Laboratory of Naples, Italy
by Francesca Paola Nocera, Monica Ambrosio, Filomena Fiorito, Laura Cortese and Luisa De Martino
Animals 2021, 11(6), 1603; https://doi.org/10.3390/ani11061603 - 29 May 2021
Cited by 17 | Viewed by 6117
Abstract
A 4-year retrospective study (2016–2019) of selected routine bacteriological examinations of the veterinary microbiology laboratory of the University Veterinary Teaching Hospital of Naples (Italy) was carried out. A total of 189 bacteriological samples were collected from 171 dogs and 18 cats suffering from [...] Read more.
A 4-year retrospective study (2016–2019) of selected routine bacteriological examinations of the veterinary microbiology laboratory of the University Veterinary Teaching Hospital of Naples (Italy) was carried out. A total of 189 bacteriological samples were collected from 171 dogs and 18 cats suffering from skin infections. In dogs, the most common cutaneous infection was otitis externa, while pyoderma was found to be prevalent in cats. The number of recorded Gram-positive strains over the study period did not vary considerably from year to year and was always significantly higher (p-value = 0.0007) in comparison with Gram-negative bacterial isolations. In dogs, Staphylococcus pseudintermedius was the most common identified Gram-positive bacterium (65%), while Pseudomonas aeruginosa (36%) was the one among the isolated Gram-negative bacteria. In cats, coagulase-negative staphylococci were the most predominant isolated bacteria (47%). The phenotypic profiles of antibiotic resistance showed that most of the strains were resistant to amoxicillin–clavulanate, penicillin, clindamycin, and trimethoprim–sulfamethoxazole. Several multi-drug-resistant strains (35%) were detected in canine isolates. An updating of antibiotic resistance profiles of the main Gram-positive and Gram-negative bacteria principally associated with skin infections of pet animals is necessary to improve stewardship programs of veterinary hospitals and clinics. Full article
(This article belongs to the Special Issue Antimicrobial Resistance in Animals)
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13 pages, 813 KiB  
Article
Antimicrobial Resistance of Campylobacter jejuni, Escherichia coli and Enterococcus faecalis Commensal Isolates from Laying Hen Farms in Spain
by Jorge Rivera-Gomis, Pedro Marín, Cristina Martínez-Conesa, Julio Otal, María José Jordán, Elisa Escudero and María José Cubero
Animals 2021, 11(5), 1284; https://doi.org/10.3390/ani11051284 - 29 Apr 2021
Cited by 7 | Viewed by 2334
Abstract
Antimicrobial resistance (AMR) is a global threat for human and animal health. Few studies have been carried out in laying hens. We evaluated the antimicrobial susceptibility of commensal Campylobacter jejuni, Escherichia coli, and Enterococcus faecalis isolates in Spanish laying hens in [...] Read more.
Antimicrobial resistance (AMR) is a global threat for human and animal health. Few studies have been carried out in laying hens. We evaluated the antimicrobial susceptibility of commensal Campylobacter jejuni, Escherichia coli, and Enterococcus faecalis isolates in Spanish laying hens in 2018. The Minimum Inhibitory Concentration (MIC) was used to identify any AMR of the studied isolates by means of a broth microdilution method. C. jejuni was highly resistant to the B category antimicrobials, and 52% of the isolates were susceptible to all the antimicrobials tested. E. coli showed medium and high percentages of resistance to the B and A antibiotic categories, respectively, and 33.33% of the isolates were susceptible to all antimicrobials. The E. faecalis resistance to A category antimicrobials was variable, and 4.62% of the isolates were susceptible to all antimicrobials. In our work, novel data on AMR in laying hen commensal isolates in Spain is provided, and the AMR levels differ from those reported for poultry in the EU. A high resistance to key drugs for human medicine was found, representing a public health risk. Full article
(This article belongs to the Special Issue Antimicrobial Resistance in Animals)
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17 pages, 10362 KiB  
Article
Antibiotic-Resistant Escherichia coli and Salmonella from the Feces of Food Animals in the East Province of Rwanda
by Rosine Manishimwe, Paola M. Moncada, Vestine Musanayire, Anselme Shyaka, H. Morgan Scott and Guy H. Loneragan
Animals 2021, 11(4), 1013; https://doi.org/10.3390/ani11041013 - 03 Apr 2021
Cited by 9 | Viewed by 3578
Abstract
In Rwanda, information on antibiotic resistance in food animals is scarce. This study was conducted to detect and phenotypically characterize antibiotic-resistant Escherichia coli and Salmonella in feces of cattle, goats, pigs, and poultry in the East province of Rwanda. We isolated non-type-specific (NTS) [...] Read more.
In Rwanda, information on antibiotic resistance in food animals is scarce. This study was conducted to detect and phenotypically characterize antibiotic-resistant Escherichia coli and Salmonella in feces of cattle, goats, pigs, and poultry in the East province of Rwanda. We isolated non-type-specific (NTS) E. coli and Salmonella using plain culture media. In addition, we used MacConkey agar media supplemented with cefotaxime at 1.0 μg/mL and ciprofloxacin at 0.5 μg/mL to increase the probability of detecting E. coli with low susceptibility to third-generation cephalosporins and quinolones, respectively. Antibiotic susceptibility testing was performed using the disk diffusion test. Among 540 NTS E. coli isolates, resistance to tetracycline was the most frequently observed (35.6%), followed by resistance to ampicillin (19.6%) and streptomycin (16.5%). Percentages of NTS E. coli resistant to all three antibiotics and percentages of multidrug-resistant strains were higher in isolates from poultry. All isolated Salmonella were susceptible to all antibiotics. The sample-level prevalence for resistance to third-generation cephalosporins was estimated at 35.6% with all third-generation cephalosporin-resistant E. coli, expressing an extended-spectrum beta-lactamase phenotype. The sample-level prevalence for quinolone resistance was estimated at 48.3%. These results provided a baseline for future research and the development of integrated surveillance initiatives. Full article
(This article belongs to the Special Issue Antimicrobial Resistance in Animals)
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15 pages, 950 KiB  
Article
Clostridioides difficile in Calves in Central Italy: Prevalence, Molecular Typing, Antimicrobial Susceptibility and Association with Antibiotic Administration
by Francesca Blasi, Carmela Lovito, Elisa Albini, Luca Bano, Gastone Dalmonte, Ilenia Drigo, Carmen Maresca, Francesca Romana Massacci, Serenella Orsini, Sara Primavilla, Eleonora Scoccia, Silvia Tofani, Claudio Forte and Chiara Francesca Magistrali
Animals 2021, 11(2), 515; https://doi.org/10.3390/ani11020515 - 16 Feb 2021
Cited by 16 | Viewed by 2497
Abstract
The emergence of Clostridioides difficile as the main agent of antibiotic-associated diarrhoea has raised concerns about its potential zoonotic role in different animal species. The use of antimicrobials is a major risk factor for C. difficile infection. Here, we provide data on C. [...] Read more.
The emergence of Clostridioides difficile as the main agent of antibiotic-associated diarrhoea has raised concerns about its potential zoonotic role in different animal species. The use of antimicrobials is a major risk factor for C. difficile infection. Here, we provide data on C. difficile infection in dairy and beef calves in Umbria, a region in central Italy. This cross-sectional study focuses on prevalence, risk factors, ribotypes, toxinotypes and antimicrobial resistance profiles of circulating ribotypes. A prevalence of 19.8% (CI95%, 12–27.6%) positive farms was estimated, and the prescription of penicillins on the farms was associated with C. difficile detection (OR = 5.58). Eleven different ribotypes were found, including the ST11 sublineages RT-126 and -078, which are also commonly reported in humans. Thirteen isolates out of 17 showed resistance to at least one of clindamycin, moxifloxacin, linezolid and vancomycin. Among them, multiple-drug resistance was observed in two isolates, belonging to RT-126. Furthermore, RT-126 isolates were positive for tetracycline resistance determinants, confirming that tetracycline resistance is widespread among ST11 isolates from cattle. The administration of penicillins increased the risk of C. difficile in calves: this, together with the recovery of multi-resistant strains, strongly suggests the need for minimising antibiotic misuse on cattle farms. Full article
(This article belongs to the Special Issue Antimicrobial Resistance in Animals)
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