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He K, Lin J, Liang Y, Cui J, Chen Q, Dong Y, Ma X, He D, Yuan L. Coexistence of a nonresistance-conferring IncI1 plasmid favors persistence of the blaCTX-M-bearing IncFII plasmid in Escherichia coli. Microbiol Spectr 2024; 12:e0424023. [PMID: 38687059 PMCID: PMC11237657 DOI: 10.1128/spectrum.04240-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/28/2024] [Indexed: 05/02/2024] Open
Abstract
The interaction between coexisting plasmids can affect plasmid-carried resistance gene persistence and spread. However, whether the persistence of the blaCTX-M gene in clinical Enterobacteriaceae is related to the interaction of coresident nonresistance-conferring plasmids has not been reported. This study was initiated to elucidate how a nonresistance-conferring IncI1 plasmid affected the blaCTX-M-bearing IncFII plasmid colocated on the same cell. Herein, we constructed three isogenic derivatives of E. coli C600, designated as C600FII, C600I1, and C600FII+I1, which harbored the blaCTX-M-IncFII plasmid and/or the nonresistance-IncI1 one. We discovered that strain C600FII+I1 conferred higher fitness advantages than strain C600FII; also, the stability of the blaCTX-M-IncFII plasmid was noticeably improved in an antibiotic-free environment when it coexisted with the IncI1 plasmid. To further explore why the IncI1 plasmid enhanced the persistence of the blaCTX-M-IncFII plasmid, we assessed the blaCTX-M-IncFII plasmid's copy numbers, conjugation frequencies, and rep gene expressions in strains C600FII and C600FII+I1. The results demonstrated that the rep expressions of the blaCTX-M-IncFII plasmid in strain C600FII+I1 was greatly decreased, along with the plasmid's copy numbers and mating efficiencies, compared to those in strain C600FII. Moreover, further study revealed that the intracellular ATP levels of strain C600FII+I1 were far lower than those of strain C600FII. Our findings confirmed that coexistence of the nonresistance-IncI1 plasmid can keep the blaCTX-M-IncFII plasmid more stable by increasing the fitness advantages of the host bacteria, which will pose a threat to preventing the long-term presence of the plasmid-carried blaCTX-M gene in clinical Enterobacteriaceae. IMPORTANCE So far, plasmid-carried blaCTX-M is still the most common extended-spectrum beta-lactamase (ESBL) genotype in clinical settings worldwide. Except for the widespread use of third-generation cephalosporins, the interaction between coexisting plasmids can also affect the long-term stable existence of the blaCTX-M gene; however, the study on that is still sparse. In the present study, we assess the interaction of coinhabitant plasmids blaCTX-M-IncFII and nonresistance-IncI1. Our results confirmed that the increased fitness advantages of strain C600FII+I1 were attributable to the cohabitant nonresistance-IncI1 plasmid, which largely reduced the intracellular ATP levels of host bacteria, thus decreasing the rep gene expression of the blaCTX-M-IncFII plasmid, its copy numbers, and mating efficiencies, while the higher fitness advantages of strain C600FII+I1 enhanced the persistence of the blaCTX-M-IncFII plasmid. The results indicate that the nonresistance-IncI1 plasmid contributes to the long-term existence of the blaCTX-M-IncFII plasmid, implying a potentially new strategy for controlling the spread of resistance plasmids in clinical settings by targeting nonresistance plasmids.
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Affiliation(s)
- Kun He
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Jiayu Lin
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Yulei Liang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Junling Cui
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Qiuru Chen
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Yanbin Dong
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Xiaoyuan Ma
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Dandan He
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Li Yuan
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
- Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, Zhengzhou, China
- Zhengzhou Key Laboratory of Research and Evaluation of Traditional Chinese Veterinary Medicine, Zhengzhou, China
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Núñez-Samudio V, Pimentel-Peralta G, De La Cruz A, Landires I. Multidrug-resistant phenotypes of genetically diverse Escherichia coli isolates from healthy domestic cats. Sci Rep 2024; 14:11260. [PMID: 38755240 PMCID: PMC11099059 DOI: 10.1038/s41598-024-62037-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024] Open
Abstract
Β-lactamases-producing Escherichia coli are a widely distributed source of antimicrobial resistance (AMR), for animals and humans. Little is known about the sensitivity profile and genetic characteristics of E. coli strains isolated from domestic cats. We report a cross-sectional study that evaluated E. coli strains isolated from domestic cats in Panama. For this study the following antibiotics were analyzed: ampicillin, amoxicillin-clavulanate cefepime, cefotaxime, cefoxitin, ceftazidime, aztreonam, imipenem, gentamicin, kanamycin, streptomycin, tetracycline, ciprofloxacin, nalidixic acid, trimethoprim-sulfamethoxazole, and chloramphenicol. The data obtained were classified as resistant, intermediate, or sensitive. MDR strains were established when the strain presented resistance to at least one antibiotic from three or more antimicrobial classes. Forty-eight E. coli isolates were obtained, of which 80% presented resistance to at least one of the antibiotics analyzed, while only 20% were sensitive to all (p = 0.0001). The most common resistance was to gentamicin (58%). Twenty-nine percent were identified as multidrug-resistant isolates and 4% with extended spectrum beta-lactamase phenotype. The genes blaTEM (39%), blaMOX(16%), blaACC (16%) and blaEBC (8%) were detected. Plasmid-mediated resistance qnrB (25%) and qnrA (13%) are reported. The most frequent sequence types (STs) being ST399 and we reported 5 new STs. Our results suggest that in intestinal strains of E. coli isolated from domestic cats there is a high frequency of AMR.
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Affiliation(s)
- Virginia Núñez-Samudio
- Instituto de Ciencias Médicas, PO Box 0710-00043, Las Tablas, Los Santos, Panama.
- Sección de Epidemiología, Departamento de Salud Pública, Región de Salud de Herrera, Ministry of Health, Chitré, Herrera, Panama.
| | | | - Alexis De La Cruz
- Laboratorio de Calidad de Agua, Ministry of Health, Chitré, Herrera, Panama
| | - Iván Landires
- Instituto de Ciencias Médicas, PO Box 0710-00043, Las Tablas, Los Santos, Panama.
- Hospital Regional Dr. Joaquín Pablo Franco Sayas, Región de Salud de Los Santos, Ministry of Health, Las Tablas, Los Santos, Panama.
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Oliveira RP, da Silva JS, da Silva GC, Rosa JN, Bazzolli DMS, Mantovani HC. Prevalence and characteristics of ESBL-producing Escherichia coli in clinically healthy pigs: implications for antibiotic resistance spread in livestock. J Appl Microbiol 2024; 135:lxae058. [PMID: 38444193 DOI: 10.1093/jambio/lxae058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/31/2024] [Accepted: 03/04/2024] [Indexed: 03/07/2024]
Abstract
AIM This study aimed to compare and characterize the resistance profile and the presence of extended-spectrum beta-lactamase (ESBL) related genes in Escherichia coli isolated from healthy finishing pigs fed with or without antibiotics in their diets. METHODS AND RESULTS A total of 27 ceftiofur-resistant E. coli isolates were obtained from 96 healthy pigs. The antibiotic resistance profile was tested, and all 27 isolates were classified as multidrug-resistant (MDR). A high proportion of isolates were resistant to cephalosporins, ampicillin, ciprofloxacin, and tetracyclines. The ESBL production was observed in 85% of isolates by double-disc synergy test. The MDR-E. coli isolates harbored ESBL genes, such as blaTEM, blaCTX-M-1, blaCTX-M-2, and blaCTX-M-8,25. In addition, other antibiotics resistance genes (ARGs) were also detected, such as sul2, ant(3″)-I, tetA, and mcr-1. The mobilization of the blaCTX-M gene was confirmed for nine E. coli isolates by conjugation assays. The presence of blaCTX-M on mobile genetic elements in these isolates was demonstrated by Southern blot hybridization, and the resistance to cephalosporins was confirmed in the transconjugants. Our results indicate the prevalence of CTX-M-producing E. coli strains harboring mobile genetic elements in the normal microbiota of healthy pigs. CONCLUSIONS These findings highlight the significance of ESBL genes as a global health concern in livestock and the potential spread of antimicrobial resistance to other members of the gastrointestinal tract microbiota.
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Affiliation(s)
- Rúzivia Pimentel Oliveira
- Department of Microbiology, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
- Laboratory of Molecular Genetics of Bacteria, Instituto de Biotecnologia Aplicada à Agropecuária (Bioagro), Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Juliana Soares da Silva
- Department of Microbiology, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Giarlã Cunha da Silva
- Department of Microbiology, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Jéssica Nogueira Rosa
- Department of Microbiology, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Denise Mara Soares Bazzolli
- Department of Microbiology, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
- Laboratory of Molecular Genetics of Bacteria, Instituto de Biotecnologia Aplicada à Agropecuária (Bioagro), Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Hilario C Mantovani
- Department of Microbiology, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, 53706, Madison, WI, United States
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Dankittipong N, Broek JVD, de Vos CJ, Wagenaar JA, Stegeman JA, Fischer EAJ. Transmission rates of veterinary and clinically important antibiotic resistant Escherichia coli: A meta- ANALYSIS. Prev Vet Med 2024; 225:106156. [PMID: 38402649 DOI: 10.1016/j.prevetmed.2024.106156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 02/05/2024] [Accepted: 02/13/2024] [Indexed: 02/27/2024]
Abstract
The transmission rate per hour between hosts is a key parameter for simulating transmission dynamics of antibiotic-resistant bacteria, and might differ for antibiotic resistance genes, animal species, and antibiotic usage. We conducted a Bayesian meta-analysis of resistant Escherichia coli (E. coli) transmission in broilers and piglets to obtain insight in factors determining the transmission rate, infectious period, and reproduction ratio. We included blaCTX-M-1, blaCTX-M-2, blaOXA-162, catA1, mcr-1, and fluoroquinolone resistant E. coli. The Maximum a Posteriori (MAP) transmission rate in broilers without antibiotic treatment ranged from 0.4∙10-3 to 2.5∙10-3 depending on type of broiler (SPF vs conventional) and inoculation strains. For piglets, the MAP in groups without antibiotic treatment were between 0.7∙10-3 and 0.8∙10-3, increasing to 0.9∙10-3 in the group with antibiotic treatment. In groups without antibiotic treatment, the transmission rate of resistant E. coli in broilers was almost twice the transmission rate in piglets. Amoxicillin increased the transmission rate of E. coli carrying blaCTX-M-2 by three-fold. The MAP infectious period of resistant E. coli in piglets with and without antibiotics is between 971 and 1065 hours (40 - 43 days). The MAP infectious period of resistant E. coli in broiler without antibiotics is between 475 and 2306 hours (20 - 96 days). The MAP infectious period of resistant E. coli in broiler with antibiotics is between 2702 and 3462 hours (113 - 144 days) which means a lifelong colonization. The MAP basic reproduction ratio in piglets of infection with resistant E. coli when using antibiotics is 27.70, which is higher than MAP in piglets without antibiotics between 15.65 and 18.19. The MAP basic reproduction ratio in broilers ranges between 3.46 and 92.38. We consider three possible explanations for our finding that in the absence of antibiotics the transmission rate is higher among broilers than among piglets: i) due to the gut microbiome of animals, ii) fitness costs of bacteria, and iii) differences in experimental set-up between the studies. Regarding infectious period and reproduction ratio, the effect of the resistance gene, antibiotic treatment, and animal species are inconclusive due to limited data.
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Affiliation(s)
- Natcha Dankittipong
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - Jan Van den Broek
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - Clazien J de Vos
- Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, Lelystad, the Netherlands
| | - Jaap A Wagenaar
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands; Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, Lelystad, the Netherlands
| | - J Arjan Stegeman
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - Egil A J Fischer
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands.
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5
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Mounsey O, Marchetti L, Parada J, Alarcón LV, Aliverti F, Avison MB, Ayala CS, Ballesteros C, Best CM, Bettridge J, Buchamer A, Buldain D, Carranza A, Corti Isgro M, Demeritt D, Escobar MP, Gortari Castillo L, Jaureguiberry M, Lucas MF, Madoz LV, Marconi MJ, Moiso N, Nievas HD, Ramirez Montes De Oca MA, Reding C, Reyher KK, Vass L, Williams S, Giraudo J, De La Sota RL, Mestorino N, Moredo FA, Pellegrino M. Genomic epidemiology of third-generation cephalosporin-resistant Escherichia coli from Argentinian pig and dairy farms reveals animal-specific patterns of co-resistance and resistance mechanisms. Appl Environ Microbiol 2024; 90:e0179123. [PMID: 38334306 PMCID: PMC10952494 DOI: 10.1128/aem.01791-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 12/14/2023] [Indexed: 02/10/2024] Open
Abstract
Control measures are being introduced globally to reduce the prevalence of antibiotic resistance (ABR) in bacteria on farms. However, little is known about the current prevalence and molecular ecology of ABR in bacterial species with the potential to be key opportunistic human pathogens, such as Escherichia coli, on South American farms. Working with 30 dairy cattle farms and 40 pig farms across two provinces in central-eastern Argentina, we report a comprehensive genomic analysis of third-generation cephalosporin-resistant (3GC-R) E. coli, which were recovered from 34.8% (cattle) and 47.8% (pigs) of samples from fecally contaminated sites. Phylogenetic analysis revealed substantial diversity suggestive of long-term horizontal and vertical transmission of 3GC-R mechanisms. CTX-M-15 and CTX-M-2 were more often produced by isolates from dairy farms, while CTX-M-8 and CMY-2 and co-carriage of amoxicillin/clavulanate resistance and florfenicol resistance were more common in isolates from pig farms. This suggests different selective pressures for antibiotic use in these two animal types. We identified the β-lactamase gene blaROB, which has previously only been reported in the family Pasteurellaceae, in 3GC-R E. coli. blaROB was found alongside a novel florfenicol resistance gene, ydhC, also mobilized from a pig pathogen as part of a new composite transposon. As the first comprehensive genomic survey of 3GC-R E. coli in Argentina, these data set a baseline from which to measure the effects of interventions aimed at reducing on-farm ABR and provide an opportunity to investigate the zoonotic transmission of resistant bacteria in this region. IMPORTANCE Little is known about the ecology of critically important antibiotic resistance among bacteria with the potential to be opportunistic human pathogens (e.g., Escherichia coli) on South American farms. By studying 70 pig and dairy cattle farms in central-eastern Argentina, we identified that third-generation cephalosporin resistance (3GC-R) in E. coli was mediated by mechanisms seen more often in certain species and that 3GC-R pig E. coli were more likely to be co-resistant to florfenicol and amoxicillin/clavulanate. This suggests that on-farm antibiotic usage is key to selecting the types of E. coli present on these farms. 3GC-R E. coli and 3GC-R plasmids were diverse, suggestive of long-term circulation in this region. We identified the de novo mobilization of the resistance gene blaROB from pig pathogens into E. coli on a novel mobile genetic element, which shows the importance of surveying poorly studied regions for antibiotic resistance that might impact human health.
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Affiliation(s)
- Oliver Mounsey
- University of Bristol, School of Cellular and Molecular Medicine, Bristol, United Kingdom
| | - Laura Marchetti
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
| | - Julián Parada
- Universidad Nacional de Río Cuarto, Facultad de Agronomía y Veterinaria, Río Cuarto, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Laura V. Alarcón
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
| | - Florencia Aliverti
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
| | - Matthew B. Avison
- University of Bristol, School of Cellular and Molecular Medicine, Bristol, United Kingdom
| | - Carlos S. Ayala
- University of Bristol Veterinary School, Langford, United Kingdom
| | | | - Caroline M. Best
- University of Bristol Veterinary School, Langford, United Kingdom
| | - Judy Bettridge
- University of Bristol Veterinary School, Langford, United Kingdom
- Natural Resources Institute, University of Greenwich, Chatham, United Kingdom
| | - Andrea Buchamer
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
| | - Daniel Buldain
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Alicia Carranza
- Universidad Nacional de Río Cuarto, Facultad de Agronomía y Veterinaria, Río Cuarto, Argentina
| | - Maite Corti Isgro
- Universidad Nacional de Río Cuarto, Facultad de Agronomía y Veterinaria, Río Cuarto, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - David Demeritt
- Department of Geography, King’s College London, London, United Kingdom
| | | | - Lihuel Gortari Castillo
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - María Jaureguiberry
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Mariana F. Lucas
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
- Universidad del Salvador, Facultad de Ciencias Agrarias y Veterinarias, Pilar, Argentina
| | - L. Vanina Madoz
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - María José Marconi
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Nicolás Moiso
- Universidad Nacional de Río Cuarto, Facultad de Agronomía y Veterinaria, Río Cuarto, Argentina
| | - Hernán D. Nievas
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
| | | | - Carlos Reding
- University of Bristol, School of Cellular and Molecular Medicine, Bristol, United Kingdom
| | | | - Lucy Vass
- University of Bristol Veterinary School, Langford, United Kingdom
| | - Sara Williams
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
| | - José Giraudo
- Universidad Nacional de Río Cuarto, Facultad de Agronomía y Veterinaria, Río Cuarto, Argentina
| | - R. Luzbel De La Sota
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Nora Mestorino
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
| | - Fabiana A. Moredo
- Universidad Nacional de La Plata, Facultad de Ciencias Veterinarias, La Plata, Argentina
| | - Matías Pellegrino
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Universidad Nacional de Río Cuarto, Facultad de Ciencias Exactas, Físico Químicas y Naturales, Río Cuarto, Argentina
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Sauget M, Atchon AK, Valot B, Garch FE, de Jong A, Moyaert H, Hocquet D. Genome analysis of third-generation cephalosporin-resistant Escherichia coli and Salmonella species recovered from healthy and diseased food-producing animals in Europe. PLoS One 2023; 18:e0289829. [PMID: 37883425 PMCID: PMC10602299 DOI: 10.1371/journal.pone.0289829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/26/2023] [Indexed: 10/28/2023] Open
Abstract
The animal reservoir of Enterobacterales producing Extended-Spectrum-β-Lactamases (ESBL) and plasmid-borne cephalosporinases (pAmpC) is a global concern. Using genome data, we analyzed a population of Escherichia coli and Salmonella species resistant to third-generation cephalosporins (3GC-R) recovered from healthy food animals (HA) and diseased food animals (DA) across Europe. Among the isolates collected from HA (n = 4,498) and DA (n = 833) in up to twelve European countries, 62 (1.4%) and 45 (5.4%) were 3GC-R, respectively. The genomes of these 3GC-R 107 isolates were sequenced to identify blaESBL and blaAmpC, sequence types (STs), virulence-associated genes, and Salmonella serovars. We also assessed their population structure using core genome multilocus sequence typing. The 78 3GC-R Escherichia coli originated from poultry (n = 27), swine (n = 26), and cattle (n = 25). Almost all (n = 77; 98.7%) harbored at least one blaESBL or blaAmpC, with blaCTX-M-1 predominating. We identified 51 STs, with ST10 and ST101 being the most frequent. The population of 3GC-R E. coli was polyclonal. The 29 3GC-R Salmonella spp. were mostly retrieved from healthy broiler (96.5%). blaCMY-2 dominated in this population. We found two clusters of CMY-2-producing Salmonella spp. in Germany: one with 15 isolates of S. Heidelberg isolates and another with six S. Minnesota, all of them with blaCMY-2. Our results confirm the low prevalence of 3GC-R E. coli and Salmonella spp. in HA and DA. blaCTX-M-1 was dominating in a highly diverse population of E. coli. 3GC-R E.coli isolated from HA and DA were genetically unrelated, with high clonal diversity suggesting multiple origins of contamination. This contrasted with the clonal population of 3GC-R Salmonella spp. in which blaCMY-2 dominated through two dominant serovars in this collection.
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Affiliation(s)
- Marlène Sauget
- Service D’hygiène Hospitalière, Centre Hospitalier Universitaire, Besançon, France
| | - Alban K. Atchon
- Bioinformatique et Big Data au Service de la Santé, UFR Santé, Université de Bourgogne Franche-Comté, Besançon, France
- UMR 6249 CNRS Chrono-Environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | - Benoît Valot
- Bioinformatique et Big Data au Service de la Santé, UFR Santé, Université de Bourgogne Franche-Comté, Besançon, France
- UMR 6249 CNRS Chrono-Environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | - Farid El Garch
- Vétoquinol SA, Global Drug Development Center, Lure, France
- EASSA and VetPath Study Group, CEESA, Brussels, Belgium
| | - Anno de Jong
- EASSA and VetPath Study Group, CEESA, Brussels, Belgium
| | - Hilde Moyaert
- EASSA and VetPath Study Group, CEESA, Brussels, Belgium
- Zoetis Belgium SA, Veterinary Medicine Research and Development, Zaventem, Belgium
| | - Didier Hocquet
- Service D’hygiène Hospitalière, Centre Hospitalier Universitaire, Besançon, France
- Bioinformatique et Big Data au Service de la Santé, UFR Santé, Université de Bourgogne Franche-Comté, Besançon, France
- UMR 6249 CNRS Chrono-Environnement, Université de Bourgogne Franche-Comté, Besançon, France
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7
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Marangoni-Ghoreyshi YG, Franca T, Esteves J, Maranni A, Pereira Portes KD, Cena C, Leal CRB. Multi-resistant diarrheagenic Escherichia coli identified by FTIR and machine learning: a feasible strategy to improve the group classification. RSC Adv 2023; 13:24909-24917. [PMID: 37608796 PMCID: PMC10440836 DOI: 10.1039/d3ra03518b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/14/2023] [Indexed: 08/24/2023] Open
Abstract
The identification of multidrug-resistant strains from E. coli species responsible for diarrhea in calves still faces many laboratory limitations and is necessary for adequately monitoring the microorganism spread and control. Then, there is a need to develop a screening tool for bacterial strain identification in microbiology laboratories, which must show easy implementation, fast response, and accurate results. The use of FTIR spectroscopy to identify microorganisms has been successfully demonstrated in the literature, including many bacterial strains; here, we explored the FTIR potential for multi-resistant E. coli identification. First, we applied principal component analysis to observe the group formation tendency; the first results showed no clustering tendency with a messy sample score distribution; then, we improved these results by adequately selecting the main principal components which most contribute to group separation. Finally, using machine learning algorithms, a predicting model showed 75% overall accuracy, demonstrating the method's viability as a screaming test for microorganism identification.
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Affiliation(s)
| | - Thiago Franca
- UFMS - Universidade Federal de Mato Grosso do Sul, Optics and Photonic Lab (SISFOTON-UFMS) Campo Grande MS Brazil
| | - José Esteves
- UFMS - Universidade Federal de Mato Grosso do Sul, Optics and Photonic Lab (SISFOTON-UFMS) Campo Grande MS Brazil
| | - Ana Maranni
- UFMS - Universidade Federal de Mato Grosso do Sul, Optics and Photonic Lab (SISFOTON-UFMS) Campo Grande MS Brazil
| | | | - Cicero Cena
- UFMS - Universidade Federal de Mato Grosso do Sul, Optics and Photonic Lab (SISFOTON-UFMS) Campo Grande MS Brazil
| | - Cassia R B Leal
- UFMS - Universidade Federal de Mato Grosso do Sul, Graduate Program in Veterinary Science (CIVET) Campo Grande MS Brazil
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8
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Sierra TAO, Acosta AC, de Melo RPB, de Oliveira PRF, de Moraes Peixoto R, Cavalcanti EFTSF, Junior JWP, Mota RA. Occurrence of extended-spectrum β-lactamase-producing Enterobacteriaceae in raw milk from cows with subclinical mastitis in northeast Brazil. Braz J Microbiol 2023; 54:1303-1307. [PMID: 36964326 PMCID: PMC10235308 DOI: 10.1007/s42770-023-00955-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 03/21/2023] [Indexed: 03/26/2023] Open
Abstract
Extended-spectrum β-lactamase (ESBL)-producing Gram negative bacteria are becoming increasingly important in veterinary and human medicine because they can hydrolyze the third generation β-lactams, penicillins, and monobactams. The aim of this study was to identify ESBL-producing Enterobacteriaceae in raw cow milk samples from northeast Brazil. Twenty-six bacterial isolates belonging to the Enterobacteriaceae family were obtained from milk samples from 257 cows with subclinical mastitis. Using microbiological tests, 53.85% (14/26) were identified as Escherichia coli, 15.38% (4/26) as Proteus mirabilis, 26.92% (7/26) as Klebsiella spp., and 3.85% (1/26) as Citrobacter spp. Of all the isolates, 61.54% (16/26) were positive in the ESBL screening test, of which 12.5% (2/16) were positive in the double-disc synergy test using three types of cephalosporins and amoxicillin/clavulanic acid. The two isolates were identified as Klebsiella spp. Among all the isolates, 53.85% (14/26) were positive for one or both ESBL-encoding genes, blaSHV and blaTEM; among these, 71.43% (10/14) were identified as E. coli. This study demonstrates that ESBL-producing bacteria can be found in raw cow milk from northeast Brazil. Cows with subclinical mastitis should be recognized as reservoirs of these strains, which can propagate to humans.
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Affiliation(s)
| | - Atzel Candido Acosta
- Department of Veterinary Medicine, Federal Rural University of Pernambuco (UFRPE), PE, Recife, 52171-900, Brazil
| | | | | | - Rodolfo de Moraes Peixoto
- Federal Institute of Education, Science and Technology of the Sertão Pernambucano (IF SERTÃO-PE)-R. Maria Luzia de Araújo Gomes Cabral, 791-João de Deus, CEP, Petrolina, PE, 56316-686, Brazil
| | | | - José Wilton Pinheiro Junior
- Department of Veterinary Medicine, Federal Rural University of Pernambuco (UFRPE), PE, Recife, 52171-900, Brazil
| | - Rinaldo Aparecido Mota
- Department of Veterinary Medicine, Federal Rural University of Pernambuco (UFRPE), PE, Recife, 52171-900, Brazil
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9
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Martins JCL, Pintor-Cora A, Alegría Á, Santos JA, Herrera-Arias F. Characterization of ESBL-producing Escherichia spp. and report of an mcr-1 colistin-resistance Escherichia fergusonni strain from minced meat in Pamplona, Colombia. Int J Food Microbiol 2023; 394:110168. [PMID: 36931145 DOI: 10.1016/j.ijfoodmicro.2023.110168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/12/2023]
Abstract
Foods of animal origin are increasingly considered a source of extended spectrum β-lactamase (ESBL) producing bacteria which can disseminate throughout the food chain and become a health concern for humans. This work aimed to evaluate the occurrence of ESBL-producing Escherichia coli in 100 retail minced meat samples taken in markets in Pamplona, Colombia. A total of 19 ESBL-producing isolates were obtained, 18 identified as E. coli and one as E. fergusonii. Fifteen isolates (78.9 %) carried blaCTX-M and blaTEM genes, one (5.2 %) blaSHV and blaTEM genes, one isolate (5.2 %) carried blaCTX-M and one (5.2 %) blaSHV alone. The majority of CTX-M-positive E. coli isolates carried the blaCTX-M-15 gene (13 isolates), being the blaCTX-M-9, blaCTX-M-2, and blaCTX-M-8 (one isolate each) also detected. Two SHV-positive isolates presented the blaSHV-5 and blaSHV-12 allele. The isolate identified as E. fergusonii was positive for blaCTX-M-65 gene and mcr-1 gene. Sixteen isolates (84.2 %) belonged to phylogroups A and B1 and grouped together in the phylogenetic tree obtained by MLST; phylogroups E and F were also detected. Transfer of ESBL resistance was demonstrated for the E. fergusonii isolate. Whole genome sequencing of this isolate revealed the presence of plasmids carrying additional resistance genes. This investigation showed the high prevalence of ESBL-producing E. coli in retail samples of minced meat. Also, the isolation of a strain of E. fergusonii is an additional concern, as some resistance genes are located in mobile elements, which can be transmitted to other bacteria. These evidences support the increasing public health concern considering the spreading of resistance genes through the food chain.
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Affiliation(s)
- Joana C L Martins
- Department of Food Hygiene and Food Technology, Veterinary Faculty, Universidad de León, 24071 León, Spain
| | - Alberto Pintor-Cora
- Department of Food Hygiene and Food Technology, Veterinary Faculty, Universidad de León, 24071 León, Spain.
| | - Ángel Alegría
- Department of Food Hygiene and Food Technology, Veterinary Faculty, Universidad de León, 24071 León, Spain.
| | - Jesús A Santos
- Department of Food Hygiene and Food Technology, Veterinary Faculty, Universidad de León, 24071 León, Spain.
| | - Fanny Herrera-Arias
- Department of Food Hygiene and Food Technology, Veterinary Faculty, Universidad de León, 24071 León, Spain; Departamento de Microbiología, Facultad de Ciencias Básicas, Universidad de Pamplona, Pamplona, Colombia.
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10
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Núñez-Samudio V, Pimentel-Peralta G, De La Cruz A, Landires I. Genetic Diversity and New Sequence Types of Escherichia coli Coharboring β-Lactamases and PMQR Genes Isolated from Domestic Dogs in Central Panama. Genes (Basel) 2022; 14:73. [PMID: 36672813 PMCID: PMC9859144 DOI: 10.3390/genes14010073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Background: β-lactamase-producing Escherichia coli are a widely distributed source of antimicrobial resistance for animals and humans. Little is known about the susceptibility profile and genetic characteristics of E. coli strains isolated from domestic dogs in Latin America. Methods: We report on a cross-sectional study that evaluated E. coli strains isolated from fecal samples of domestic dogs in central Panama. The extended-spectrum β-lactamase (ESBL), AmpC genes, and plasmid-mediated quinolone resistance were investigated. Molecular typing using Pasteur’s multilocus sequence typing (MLST) was conducted. Results: A total of 40 E. coli isolates were obtained, of which 80% (32/40) were resistant to at least one of the antibiotics tested, while 20% (8/40) were sensitive to all antibiotics analyzed in this study (p < 0.001). Forty percent of the strains were resistant to three or more antibiotics. The most common resistance was to tetracycline (45%) and ampicillin (30%) while 2.5% showed an ESBL phenotype. Antibiotic resistance genes were detected for one β-lactamase (blaTEM-1) and two plasmid-mediated quinolone resistance (PMQR) enzymes (qnrS and qnrB). In addition, mutations in the chromosomal AmpC gene were observed at positions −35, −28, −18, −1, and +58. Fourteen different sequence types (STs) were identified; the most frequent were ST399 and ST425 (12% each). ST3 and ST88, which have been previously identified in human clinical isolates, were also evidenced. Three new STs were found for the first time: ST1015, ST1016 (carrier of the blaTEM-1 gene), and ST1017 (carrier of the blaTEM-1, qnrS, and qnrB genes). Conclusions: In the intestinal strains of E. coli isolated from domestic dogs, there was a high frequency of resistance to antibiotics. The presence of genes from plasmids and chromosomal mutations that conferred antibiotic resistance, the identification of isolates previously reported in humans, and the genetic diversity of STs (including three that were newly identified) confirmed the determinants of resistance to antibiotics in the domestic dogs from central Panama.
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Affiliation(s)
- Virginia Núñez-Samudio
- Instituto de Ciencias Médicas, Las Tablas 0710, Los Santos, Panama
- Sección de Epidemiología, Departamento de Salud Pública, Región de Salud de Herrera, Ministry of Health, Chitré 0601, Herrera, Panama
| | - Gumercindo Pimentel-Peralta
- Instituto de Ciencias Médicas, Las Tablas 0710, Los Santos, Panama
- Escuela de Biología, Facultad de Ciencias Naturales, Exactas y Tecnología, Centro Regional Universitario de Azuero (CRUA), Universidad de Panamá, Chitré 0601, Herrera, Panama
| | - Alexis De La Cruz
- Escuela de Biología, Facultad de Ciencias Naturales, Exactas y Tecnología, Centro Regional Universitario de Azuero (CRUA), Universidad de Panamá, Chitré 0601, Herrera, Panama
- Water Quality Laboratory, Ministry of Health, La Villa 0739, Los Santos, Panama
| | - Iván Landires
- Instituto de Ciencias Médicas, Las Tablas 0710, Los Santos, Panama
- Hospital Joaquín Pablo Franco Sayas, Región de Salud de Los Santos, Ministry of Health, Las Tablas 0710, Los Santos, Panama
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11
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One health clones of multidrug-resistant Escherichia coli carried by synanthropic animals in Brazil. One Health 2022; 16:100476. [PMID: 36691392 PMCID: PMC9860340 DOI: 10.1016/j.onehlt.2022.100476] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
WHO priority pathogens have disseminated beyond hospital settings and are now being detected in urban and wild animals worldwide. In this regard, synanthropic animals such as urban pigeons (Columba livia) and rodents (Rattus rattus, Rattus norvegicus and Mus musculus) are of interest to public health due to their role as reservoirs of pathogens that can cause severe diseases. These animals usually live in highly contaminated environments and have frequent interactions with humans, domestic animals, and food chain, becoming sentinels of anthropogenic activities. In this study, we report genomic data of Escherichia coli strains selected for ceftriaxone and ciprofloxacin resistance, isolated from pigeons and black rats. Genomic analysis revealed the occurrence of international clones belonging to ST10, ST155, ST224 and ST457, carrying a broad resistome to beta-lactams, aminoglycosides, trimethoprim/sulfamethoxazole, fluoroquinolones, tetracyclines and/or phenicols. SNP-based phylogenomic investigation confirmed clonal relatedness with high-risk lineages circulating at the human-animal-environmental interface globally. Our results confirm the dissemination of WHO priority CTX-M-positive E. coli in urban rodents and pigeons in Brazil, highlighting potential of these animals as infection sources and hotspot for dissemination of clinically relevant pathogens and their resistance genes, which is a critical issue within a One Health perspective.
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12
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Dantas Palmeira J, V. Cunha M, Ferreira H, Fonseca C, Tinoco Torres R. Worldwide Disseminated IncX4 Plasmid Carrying mcr-1 Arrives to Wild Mammal in Portugal. Microbiol Spectr 2022; 10:e0124522. [PMID: 36394330 PMCID: PMC9769835 DOI: 10.1128/spectrum.01245-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 10/13/2022] [Indexed: 11/19/2022] Open
Abstract
The mcr-1 gene spread is worldwide recognized as a public health threat at multidrug-resistant infections therapy level. Here, we report for the first time, to the best of our knowledge, the detection of the globally distributed IncX4 plasmid carrying mcr-1 (mcr-1/IncX4) in Escherichia coli isolated from a wild mammal in Portugal and Europe. This plasmid was found in a ST533 E. coli isolate with a multidrug-resistant profile, virulence potential, and possibly phylogenetically related to human isolates. Our work contributes to highlight the importance of antimicrobial resistance (AMR) surveillance in wildlife, an important compartment of the whole ecosystem often overlooked in the fight against AMR. IMPORTANCE Colistin resistance mediated by plasmids is recognized worldwide as an emergency problem connected with the whole ecosystem, since is well described in the interface of the human-animal-environment. The plasmid IncX4 is reported as one of the most prevalent plasmids harboring the gene mcr-1. On an European scale the plasmid IncX4 carrying mcr-1 has been described in humans, the environment, and animals, including wildlife, but only in wild birds. This study shows the first report of the plasmid IncX4 harboring mcr-1 in a wild mammal in Portugal and Europe, identified in a ST533 E. coli commensal that is, curiously, more related to isolates from humans than from livestock. Our findings show that the plasmid IncX4 harboring mcr-1 is well established in a colistin resistance drive embracing the whole ecosystem.
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Affiliation(s)
- Josman Dantas Palmeira
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, Aveiro, Portugal
| | - Mónica V. Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Helena Ferreira
- UCIBIO Applied Molecular Biosciences Unit, REQUIMTE, University of Porto, Porto, Portugal
- Microbiology, Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Carlos Fonseca
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, Aveiro, Portugal
- ForestWISE Collaborative Laboratory for Integrated Forest & Fire Management, Quinta de Prados, Vila Real, Portugal
| | - Rita Tinoco Torres
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, Aveiro, Portugal
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13
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Escherichia coli ST224 and IncF/blaCTX-M-55 plasmids drive resistance to extended-spectrum cephalosporins in poultry flocks in Parana, Brazil. Int J Food Microbiol 2022; 380:109885. [DOI: 10.1016/j.ijfoodmicro.2022.109885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 04/04/2022] [Accepted: 08/19/2022] [Indexed: 11/21/2022]
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14
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Gonzalez C, Oueslati S, Biez L, Dortet L, Naas T. Evaluation of the EasyScreen™ ESBL/CPO Detection Kit for the Detection of ß-Lactam Resistance Genes. Diagnostics (Basel) 2022; 12:diagnostics12092223. [PMID: 36140624 PMCID: PMC9498065 DOI: 10.3390/diagnostics12092223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 11/25/2022] Open
Abstract
Early detection of multidrug resistant bacteria is of paramount importance for implementing appropriate infection control strategies and proper antibacterial therapies. We have evaluated a novel real-time PCR assay using fluorescent probes and 3base® technology, the EasyScreenTM ESBL/CPO Detection Kit (Genetic Signatures, Newtown, Australia), for the detection of 15 β-lactamase genes (blaVIM, blaNDM, blaIMP, blaOXA-48, blaKPC, blaOXA-23, blaOXA-51, blaSME,blaIMI, blaGES,blaTEM,blaSHV, blaCTX-M,blaCMY, blaDHA) and colistin resistance mcr-1 gene from 341 bacterial isolates (219 Enterobacterales, 66 P. aeruginosa and 56 A. baumannii) that were grown on Mueller–Hinton (MH) agar plates. One colony was suspended in provided extraction buffer, which lyses and converts the nucleic acids into a 3base®-DNA form (cytosines are converted into uracil, and subsequently thymine during PCR). The converted bacterial DNA is then added to the 6 PCR mixes, with primers for three targets plus one internal control. The EasyScreenTM ESBL/CPO Detection Kit was able to detect the 5-major (NDM, VIM, IMP, KPC, OXA-48) and 2-minor (IMI, Sme) carbapenemases and their variants irrespective of the species expressing them with nearly 100% sensitivity and specificity. With cephalosporinases CMY (82% of sensitivity) and DHA (87% of sensitivity) detection of chromosomally encoded variants was less efficient. Similarly, the chromosomally encoded OXA-51 variants were not consistently detected in A. baumannii. Despite being capable of efficiently detecting blaCTX-M-, blaTEM-, blaSHV- and blaGES-like genes, the EasyScreen™ ESBL/CPO Detection Kit was not able to distinguish between penicillinases and ESBL-variants of TEM and SHV and between GES-ESBLs and GES-carbapenemases. As GES enzymes are still rare, their detection as an ESBL or a carbapenemase remains important. Detection of mcr-1 was efficient, but none of the other mcr-alleles were detected in the 341 bacterial isolates tested. The EasyScreenTM ESBL/CPO Detection Kit is adapted for the detection of the most prevalent carbapenemases encountered in Gram-negatives isolated worldwide.
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Affiliation(s)
- Camille Gonzalez
- Team “Resist” UMR1184 Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB), INSERM, Faculty of Medicine, University Paris-Saclay, LabEx Lermit, 94270 Le Kremlin-Bicêtre, France
- Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, 94270 Le Kremlin-Bicêtre, France
| | - Saoussen Oueslati
- Team “Resist” UMR1184 Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB), INSERM, Faculty of Medicine, University Paris-Saclay, LabEx Lermit, 94270 Le Kremlin-Bicêtre, France
- Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, 94270 Le Kremlin-Bicêtre, France
| | - Laura Biez
- Team “Resist” UMR1184 Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB), INSERM, Faculty of Medicine, University Paris-Saclay, LabEx Lermit, 94270 Le Kremlin-Bicêtre, France
| | - Laurent Dortet
- Team “Resist” UMR1184 Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB), INSERM, Faculty of Medicine, University Paris-Saclay, LabEx Lermit, 94270 Le Kremlin-Bicêtre, France
- Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, 94270 Le Kremlin-Bicêtre, France
- Associated French National Reference Center for Antibiotic Resistance, Carbapenemase-Producing Enterobacteriaceae, 94270 Le Kremlin-Bicêtre, France
| | - Thierry Naas
- Team “Resist” UMR1184 Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB), INSERM, Faculty of Medicine, University Paris-Saclay, LabEx Lermit, 94270 Le Kremlin-Bicêtre, France
- Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, 94270 Le Kremlin-Bicêtre, France
- Associated French National Reference Center for Antibiotic Resistance, Carbapenemase-Producing Enterobacteriaceae, 94270 Le Kremlin-Bicêtre, France
- Correspondence: ; Tel.: +33-145212986
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15
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Bastidas-Caldes C, Romero-Alvarez D, Valdez-Vélez V, Morales RD, Montalvo-Hernández A, Gomes-Dias C, Calvopiña M. Extended-Spectrum Beta-Lactamases Producing Escherichia coli in South America: A Systematic Review with a One Health Perspective. Infect Drug Resist 2022; 15:5759-5779. [PMID: 36204394 PMCID: PMC9531622 DOI: 10.2147/idr.s371845] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/04/2022] [Indexed: 11/23/2022] Open
Affiliation(s)
- Carlos Bastidas-Caldes
- One Health Research Group, Faculty of Engineering and Applied Sciences, Universidad de las Américas, Quito, Ecuador
- Doctoral Program in Public and Animal Health, Faculty of Veterinary Medicine, University of Extremadura, Cáceres, Spain
- Correspondence: Carlos Bastidas-Caldes, One Health Research Group, Faculty of Engineering and Applied Sciences, Universidad de las Américas, Quito, 170124, Ecuador, Tel +593 983 174949, Email
| | - Daniel Romero-Alvarez
- One Health Reserch Group, Faculty of Medicine, Universidad de las Américas, Quito, Ecuador
- Biodiversity Institute and Department of Ecology & Evolutionary Biology, The University of Kansas, Lawrence, KS, USA
| | - Victor Valdez-Vélez
- One Health Research Group, Faculty of Engineering and Applied Sciences, Universidad de las Américas, Quito, Ecuador
| | - Roberto D Morales
- One Health Research Group, Faculty of Engineering and Applied Sciences, Universidad de las Américas, Quito, Ecuador
| | - Andrés Montalvo-Hernández
- One Health Research Group, Faculty of Engineering and Applied Sciences, Universidad de las Américas, Quito, Ecuador
| | - Cicero Gomes-Dias
- Department of Basic Health Sciences, Federal University of Health Sciences of Porto Alegre, Porto Alegre, Brazil
| | - Manuel Calvopiña
- One Health Reserch Group, Faculty of Medicine, Universidad de las Américas, Quito, Ecuador
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16
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Torres RT, Cunha MV, Araujo D, Ferreira H, Fonseca C, Palmeira JD. A walk on the wild side: Wild ungulates as potential reservoirs of multi-drug resistant bacteria and genes, including Escherichia coli harbouring CTX-M beta-lactamases. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 306:119367. [PMID: 35489528 DOI: 10.1016/j.envpol.2022.119367] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/15/2022] [Accepted: 04/24/2022] [Indexed: 06/14/2023]
Abstract
Extended-spectrum β-lactamases (ESBL)-producing Enterobacterales have been classified as critical priority pathogens by the World Health Organization (WHO). ESBL are universally distributed and, in 2006, were firstly reported on a wild animal. Understanding the relative contributions of wild animals to ESBL circulation in the environment is urgently needed. In this work, we have conducted a nationwide study in Portugal to investigate the occurrence of bacteria carrying clinically significant antimicrobial resistance genes (ARG), using widely distributed wild ungulates as model species. A total of 151 antimicrobial resistant-Enterobacterales isolates were detected from 181 wild ungulates: 50% (44/88) of isolates from wild boar (Sus scrofa), 40.3% (25/62) from red deer (Cervus elaphus), 41.4% (12/29) from fallow deer (Dama dama) and 100% (2/2) from mouflon (Ovis aries subsp. musimon). Selected isolates showed a diversified resistance profile, with particularly high values corresponding to ampicillin (71.5%) and tetracycline (63.6%). Enterobacterales strains carried blaTEM, tetA, tetB, sul2, sul1 or dfrA1 ARG genes. They also carried blaCTX-M-type genes, which are prevalent in human infections, namely CTX-M-14, CTX-M-15 and CTX-M-98. Strikingly, this is the first report of CTX-M-98 in wildlife. Almost 40% (n = 59) of Enterobacterales were multi-drug resistant. The diversity of plasmids carried by ESBL isolates was remarkable, including IncF, K and P. This study highlights the potential role of wild ungulates as environmental reservoirs of CTX-M ESBL-producing E. coli and in the spill-over of AMR bacteria and their determinants. Our findings suggest that wild ungulates are useful as strategic sentinel species of AMR in terrestrial environments, especially in response to potential sources of anthropogenic pollution, providing early warning of potential risks to human, animal and environmental health.
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Affiliation(s)
- Rita Tinoco Torres
- Departament of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
| | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisbon, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Débora Araujo
- Faculty of Engineering of University of Porto, Porto, Portugal
| | - Helena Ferreira
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE - University of Porto, Porto, Portugal; Microbiology, Biological Sciences Department, Faculty of Pharmacy of University of Porto, Porto, Portugal
| | - Carlos Fonseca
- Departament of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal; ForestWISE - Collaborative Laboratory for Integrated Forest & Fire Management, Quinta de Prados, 5001-801, Vila Real, Portugal
| | - Josman Dantas Palmeira
- Departament of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
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17
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Torres RT, Cunha MV, Ferreira H, Fonseca C, Palmeira JD. A high-risk carbapenem-resistant Pseudomonas aeruginosa clone detected in red deer (Cervus elaphus) from Portugal. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 829:154699. [PMID: 35318052 DOI: 10.1016/j.scitotenv.2022.154699] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Pseudomonas aeruginosa is a ubiquitous bacterium, successfully exploiting a variety of environmental niches due to its remarkable metabolic versatility. The World Health Organization classifies P. aeruginosa as a "priority pathogen" due to its a great ability to overcome the action of antimicrobials, including carbapenems. Hitherto, most studies have focused on clinical settings from humans, but much less on animal and environmental settings, particularly on wildlife. In this work, we report the isolation of a carbapenem-resistant Pseudomonas aeruginosa strain recovered from the faeces of a red deer adult female sampled in a humanized area. This isolate was obtained during a nationwide survey on antimicrobial resistance in wildlife aimed to determine the occurrence of carbapenem-resistant bacteria among 181 widely distributed wild ungulates. This P. aeruginosa isolate was found to be a high-risk clone, belonging to the sequence type (ST) 274. The genomic analysis of P. aeruginosa isolate UP4, classified this isolate as belonging to serogroup O3, which was also found to harbour the genes blaPAO, blaPDC-24, blaOXA-486 (encoding resistance to beta-lactams), aph(3')-IIb (aminoglycosides resistance), fosA (fosfomycin resistance) and catB7 (chloramphenicol resistance). Antimicrobial susceptibility screening, according to EUCAST, showed resistance to imipenem and intermediate resistance to meropenem and doripenem. To our knowledge, this is the first description of carbapenem-resistant P. aeruginosa in deer in Europe. Our results highlight the importance of wild ungulates either as victims of human activity or amplifiers of AMR, either way with potential impacts on animal, human and ecosystem health, since excretion of AMR bacteria might directly or indirectly contaminate other animals and the surrounding environment, perpetuating the spill-over and chain dissemination of AMR determinants.
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Affiliation(s)
- Rita Tinoco Torres
- Departamento de Biologia & CESAM, Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal.
| | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Helena Ferreira
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE - University of Porto, Porto, Portugal; Microbiology, Biological Sciences Department, Faculty of Pharmacy of University of Porto, Porto, Portugal
| | - Carlos Fonseca
- Departamento de Biologia & CESAM, Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal; ForestWISE - Collaborative Laboratory for Integrated Forest & Fire Management, Quinta de Prados, 5001-801 Vila Real, Portugal
| | - Josman Dantas Palmeira
- Departamento de Biologia & CESAM, Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
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Torres RT, Cunha MV, Araujo D, Ferreira H, Fonseca C, Palmeira JD. Emergence of colistin resistance genes (mcr-1) in Escherichia coli among widely distributed wild ungulates. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 291:118136. [PMID: 34530238 DOI: 10.1016/j.envpol.2021.118136] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/02/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Abstract
The environment is considered a major reservoir of antimicrobial resistant microorganisms (AMR) and antimicrobial resistance genes (ARG). Colistin, a "last resort" antibiotic, is used for the treatment of severe infections caused by multidrug-resistant Gram-negative bacteria. The global dissemination of mobile colistin resistance genes (mcr) in natural and non-natural environments is a major setback in the fight against antimicrobial resistance. Hitherto, there is a limited number of studies screening this resistance determinant in bacteria from wildlife. In this study, we describe for the first time the detection of plasmid-mediated colistin resistance in Escherichia coli from wild ungulates in Portugal, which are also widely distributed across Europe. This information is critical to identify the importance of ungulates in the dissemination of resistant bacteria, and their corresponding genes, across the environment. Here, 151 resistant-Enterobacteriaceae isolated from 181 samples collected from different wild ungulate species throughout Portugal were screened for mcr genes. Four mcr-1-positive Escherichia coli were detected from four fallow deer individuals that were sampled in the same hunting ground. These four isolates harboured mcr-1-related IncP plasmids belonging to sequencing types ST155, ST533 and ST345 (n = 2), suggesting bacterial and/or plasmid circulation. All mcr-1-positive E. coli also showed other resistance phenotypes, including MDR, including the B1 commensal phylogenetic profile. All mcr-1-positive E. coli show additional resistance phenotypes, including MDR, including the B1 commensal phylogenetic profile. Our findings are upsetting, highlighting the global dissemination of colistin resistance genes in the whole ecosystem, which, under the One Health framework, emphasizes the urgent need for effective implementation of AMR surveillance and control in the human-animal-environment interfaces.
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Affiliation(s)
- Rita Tinoco Torres
- Departamento de Biologia & CESAM, Universidade de Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
| | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisbon, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Débora Araujo
- Faculty of Engineering of University of Porto, Porto, Portugal; UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE - University of Porto, Porto, Portugal
| | - Helena Ferreira
- Faculty of Engineering of University of Porto, Porto, Portugal; Microbiology, Biological Sciences Department, Faculty of Pharmacy of University of Porto, Porto, Portugal
| | - Carlos Fonseca
- Departamento de Biologia & CESAM, Universidade de Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal; ForestWISE - Collaborative Laboratory for Integrated Forest & Fire Management, Quinta de Prados, 5001-801, Vila Real, Portugal
| | - Josman Dantas Palmeira
- Departamento de Biologia & CESAM, Universidade de Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
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Suzuki M, Norizuki C, Wachino JI, Kawamura K, Nagano N, Nagano Y, Hayashi W, Kimura K, Doi Y, Arakawa Y. Dissecting the clonality of I1 plasmids using ORF-based binarized structure network analysis of plasmids (OSNAp). J Infect Chemother 2021; 28:473-479. [PMID: 34916137 DOI: 10.1016/j.jiac.2021.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/18/2021] [Accepted: 12/05/2021] [Indexed: 11/29/2022]
Abstract
OBJECTIVES We aimed to elucidate the relationship among blaCTX-M-carrying plasmids and their transmission between humans and domestic animals. METHODS Phylogenetic relationship of 90 I1 plasmids harboring blaCTX-M genes encoding extended-spectrum β-lactamase (ESBL) was analyzed using the ORF-based binarized structure network analysis of plasmids (OSNAp). RESULTS The majority of plasmids carrying blaCTX-M-1 or blaCTX-M-8 belonged to a single lineage, respectively, and were primarily associated with domestic animals especially chickens. On the other hand, plasmids carrying blaCTX-M-14 or blaCTX-M-15, identified from both humans and domestic animals, were distributed in two or more lineages. CONCLUSION OSNAp has revealed the phylogenetic relationships and diversity of plasmids carrying blaCTX-M more distinctly than pMLST. The findings suggest that circulation of I1 plasmids between humans and animals may contribute to their diversity.
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Affiliation(s)
- Masahiro Suzuki
- Department of Microbiology, Fujita Health University School of Medicine, Aichi, Japan.
| | - Chihiro Norizuki
- Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Jun-Ichi Wachino
- Department of Bacteriology, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Kumiko Kawamura
- Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Noriyuki Nagano
- Department of Medical Sciences, Shinshu University Graduate School of Medicine, Science and Technology, Nagano, Japan
| | - Yukiko Nagano
- Department of Medical Sciences, Shinshu University Graduate School of Medicine, Science and Technology, Nagano, Japan
| | - Wataru Hayashi
- Department of Medical Sciences, Shinshu University Graduate School of Medicine, Science and Technology, Nagano, Japan
| | - Kouji Kimura
- Department of Bacteriology, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Yohei Doi
- Department of Microbiology, Fujita Health University School of Medicine, Aichi, Japan; Department of Infectious Diseases, Fujita Health University School of Medicine, Aichi, Japan; Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yoshichika Arakawa
- Department of Bacteriology, Nagoya University Graduate School of Medicine, Aichi, Japan
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Dantas Palmeira J, Haenni M, Madec JY, Ferreira HMN. First Global Report of Plasmid-Mediated mcr-1 and Extended-Spectrum Beta-Lactamase-Producing Escherichia coli from Sheep in Portugal. Antibiotics (Basel) 2021; 10:antibiotics10111403. [PMID: 34827341 PMCID: PMC8615169 DOI: 10.3390/antibiotics10111403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/08/2021] [Accepted: 11/11/2021] [Indexed: 11/25/2022] Open
Abstract
Resistances to extended-spectrum cephalosporins (ESC) and colistin are One Health issues since genes encoding these resistances can be transmitted between all sectors of the One Health concept, i.e., human, animal, and the environment. Among food-producing animals, sheep farming has long been overlooked. To fill in this knowledge gap, we looked for ESC- and colistin resistance in 21 faecal samples collected from sheep in one farm in the south of Portugal. ESC-resistant isolates were selected on MacConkey agar plates supplemented with cefotaxime. Susceptibility testing was performed by the disk-diffusion method according to CLSI, while colistin MIC was determined by broth microdilution. ESC- and colistin-resistance genes were identified by PCR, and the clonality of all isolates was assessed by XbaI-PFGE. The replicon content was determined by PCR according to the PCR-based replicon typing (PBRT) scheme. Sixty-two non-duplicate ESC-resistant E. coli isolates were identified, which all presented an extended-spectrum beta-lactamase (ESBL) phenotype, mostly due to the presence of CTX-M genes. One CTX-M-1-producing E. coli was concomitantly colistin-resistant and presented the plasmid-mediated mcr-1 gene. Nearly all isolates showed associated resistances to non-beta-lactam antibiotics, which could act as co-selectors, even in the absence of beta-lactam use. The results showed a high proportion of ESBL-producing E. coli in sheep faeces. Their dissemination was very dynamic, with the spread of successful clones between animals, but also a large diversity of clones and plasmids, sometimes residing in the same animal. This study highlights the need for global surveillance in all food-producing sectors, in order to avoid the dissemination of genes conferring resistance to last-resort antibiotics in human medicine.
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Affiliation(s)
- Josman Dantas Palmeira
- Microbiology, Biological Sciences Department, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal;
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE—University of Porto, 4050-313 Porto, Portugal
- Departamento de Biologia & CESAM, Campus de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal
- PICTIS—International Platform for Science, Technology and Innovation in Health, Universidade de Aveiro (Portugal) & FIOCRUZ, Rio de Janeiro 21040-360, Brazil
- Correspondence:
| | - Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, Anses Laboratoire de Lyon, Université de Lyon, 69007 Lyon, France; (M.H.); (J.-Y.M.)
| | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, Anses Laboratoire de Lyon, Université de Lyon, 69007 Lyon, France; (M.H.); (J.-Y.M.)
| | - Helena Maria Neto Ferreira
- Microbiology, Biological Sciences Department, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal;
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE—University of Porto, 4050-313 Porto, Portugal
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Chemical Composition and Antimicrobial Activity of a New Olive Pomace Functional Ingredient. Pharmaceuticals (Basel) 2021; 14:ph14090913. [PMID: 34577612 PMCID: PMC8471359 DOI: 10.3390/ph14090913] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/04/2021] [Accepted: 09/06/2021] [Indexed: 12/13/2022] Open
Abstract
Olive pomace, an olive oil processing byproduct, can be upcycled and meet the current demand for natural and sustainable food ingredients. In this work, a patented process was used to obtain a functional ingredient from different olive pomaces. The nutritional, chemical and antioxidant profiles, as well as the antimicrobial activity against S. aureus, E. coli and C. albicans, were investigated for the first time. The amount of phenolics ranged between 3.1 and 3.8 g gallic acid eq./100 g in all samples and flavonoids between 2.0 and 3.2 g catechin eq/100 g. No significant differences were found regarding the antioxidant activity. The total fat varied between 5 and 11%, α-tocopherol being the major vitamer and oleic acid the main fatty acid. The protein and ash contents were 1–4% and 10–17%, respectively. The functional ingredient with a higher hydroxytyrosol content (220 mg/100 g) also presented the best minimal inhibitory concentration against the tested bacteria. No activity against C. albicans was verified. This new functional ingredient presents the potential to be used as a natural preservative or as a nutritional profile enhancer. Moreover, it can be an advantageous ingredient in food products, since it comprises specific lipid and hydrophilic bioactive compounds usually not present in other plant extracts.
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Emergence and Spread of Cephalosporinases in Wildlife: A Review. Animals (Basel) 2021; 11:ani11061765. [PMID: 34204766 PMCID: PMC8231518 DOI: 10.3390/ani11061765] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 12/21/2022] Open
Abstract
Simple Summary Antimicrobial resistance (AMR) is one of the global public health challenges nowadays. AMR threatens the effective prevention and treatment of an ever-increasing range of infections, being present in healthcare settings but also detected across the whole ecosystem, including wildlife. This work compiles the available information about an important resistance mechanism that gives bacteria the ability to inactivate cephalosporin antibiotics, the cephalosporinases (extended-spectrum beta-lactamase (ESBL) and AmpC beta-lactamase), in wildlife. Through a rigorous systematic literature review in the Web of Science database, the available publications on this topic in the wildlife sphere were analysed. The emergence and spread of cephalosporinases in wildlife has been reported in 46 countries from all continents (52% in Europe), with descriptions mainly in birds and mammals. The most widely disseminated cephalosporinases in human-related settings (e.g. CTX-M-1, CTX-M-14, CTX-M-15 and CMY-2) are also the most reported in wildlife, suggesting that anthropogenic pressure upon natural environments have a strong impact on antimicrobial resistance spread, including the dissemination of genes encoding these enzymes. Our work highlights the urgence and importance of public and ecosystem health policies, including improved surveillance and control strategies that breakdown AMR transmission chains across wildlife, as part of an integrated strategy of the One Health approach. Abstract In the last decade, detection of antibiotic resistant bacteria from wildlife has received increasing interest, due to the potential risk posed by those bacteria to wild animals, livestock or humans at the interface with wildlife, and due to the ensuing contamination of the environment. According to World Health Organization, cephalosporins are critically important antibiotics to human health. However, acquired resistance to β-lactams is widely distributed and is mainly mediated by extended-spectrum beta-lactamase and AmpC beta-lactamases, such as cephalosporinases. This work thus aimed to compile and analyse the information available on the emergence and dissemination of cephalosporinases in wildlife worldwide. Results suggest a serious scenario, with reporting of cephalosporinases in 46 countries from all continents (52% in Europe), across 188 host species, mainly birds and mammals, especially gulls and ungulates. The most widely reported cephalosporinases, CTX-M-1, CTX-M-14, CTX-M-15 and CMY-2, were also the most common in wild animals, in agreement with their ubiquity in human settings, including their association to high-risk clones of Escherichia coli (E. coli), such as the worldwide distributed CTX-M-15/ST131 E. coli. Altogether, our findings show that anthropogenic activities affect the whole ecosystem and that public policies promoting animal and environmental surveillance, as well as mitigation measures to avoid antimicrobial misuse and AMR spread, are urgently needed to be out in practise.
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Burgess SA, Aplin J, Biggs PJ, Breckell G, Benschop J, Fayaz A, Toombs-Ruane LJ, Midwinter AC. Characterisation of AmpC and extended-spectrum beta-lactamase producing E. coli from New Zealand dairy farms. Int Dairy J 2021. [DOI: 10.1016/j.idairyj.2021.104998] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Homeier-Bachmann T, Heiden SE, Lübcke PK, Bachmann L, Bohnert JA, Zimmermann D, Schaufler K. Antibiotic-Resistant Enterobacteriaceae in Wastewater of Abattoirs. Antibiotics (Basel) 2021; 10:antibiotics10050568. [PMID: 34065908 PMCID: PMC8150771 DOI: 10.3390/antibiotics10050568] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/08/2021] [Accepted: 05/09/2021] [Indexed: 11/16/2022] Open
Abstract
Antibiotic-resistant Enterobacteriaceae are regularly detected in livestock. As pathogens, they cause difficult-to-treat infections and, as commensals, they may serve as a source of resistance genes for other bacteria. Slaughterhouses produce significant amounts of wastewater containing antimicrobial-resistant bacteria (AMRB), which are released into the environment. We analyzed the wastewater from seven slaughterhouses (pig and poultry) for extended-spectrum β-lactamase (ESBL)-carrying and colistin-resistant Enterobacteriaceae. AMRB were regularly detected in pig and poultry slaughterhouse wastewaters monitored here. All 25 ESBL-producing bacterial strains (19 E. coli and six K. pneumoniae) isolated from poultry slaughterhouses were multidrug-resistant. In pig slaughterhouses 64% (12 of 21 E. coli [57%] and all four detected K. pneumoniae [100%]) were multidrug-resistant. Regarding colistin, resistant Enterobacteriaceae were detected in 54% of poultry and 21% of pig water samples. Carbapenem resistance was not detected. Resistant bacteria were found directly during discharge of wastewaters from abattoirs into water bodies highlighting the role of slaughterhouses for environmental surface water contamination.
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Affiliation(s)
- Timo Homeier-Bachmann
- Friedrich-Loeffler-Institut, Institute of Epidemiology, 17493 Greifswald-Insel Riems, Germany;
- Correspondence: ; Tel.: +49-38351-7-1505
| | - Stefan E. Heiden
- Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany; (S.E.H.); (K.S.)
| | - Phillip K. Lübcke
- Friedrich-Loeffler-Institut, Institute of Epidemiology, 17493 Greifswald-Insel Riems, Germany;
- Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany; (S.E.H.); (K.S.)
| | - Lisa Bachmann
- Leibniz-Institut für Nutztierbiologie, Institute of Nutritional Physiology “Oskar Kellner”, 18196 Dummerstorf, Germany;
| | - Jürgen A. Bohnert
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, 17475 Greifswald, Germany;
| | | | - Katharina Schaufler
- Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany; (S.E.H.); (K.S.)
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ESBL-Producing Escherichia coli Carrying CTX-M Genes Circulating among Livestock, Dogs, and Wild Mammals in Small-Scale Farms of Central Chile. Antibiotics (Basel) 2021; 10:antibiotics10050510. [PMID: 33946277 PMCID: PMC8145412 DOI: 10.3390/antibiotics10050510] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/22/2021] [Accepted: 04/24/2021] [Indexed: 12/11/2022] Open
Abstract
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.
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Multi-Drug Resistant Plasmids with ESBL/AmpC and mcr-5.1 in Paraguayan Poultry Farms: The Linkage of Antibiotic Resistance and Hatcheries. Microorganisms 2021; 9:microorganisms9040866. [PMID: 33920558 PMCID: PMC8072826 DOI: 10.3390/microorganisms9040866] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 11/16/2022] Open
Abstract
Poultry represents a common source of bacteria with resistance to antibiotics including the critically important ones. Selective cultivation using colistin, cefotaxime and meropenem was performed for 66 chicken samples coming from 12 farms in Paraguay while two breeding companies supplied the farms. A total of 62 Escherichia coli and 22 Klebsiella pneumoniae isolates were obtained and representative isolates were subjected to whole-genome sequencing. Relatively high prevalence of phylogenetic group D and F was observed in E. coli isolates and several zoonotic sequence types (STs) including ST457 (14 isolates), ST38 (5), ST10 (2), ST117 (2) or ST93 (4) were detected. Isolates from three farms, which purchased chicken from a Paraguayan hatchery showed higher prevalence of mcr-5.1 and blaCTX-M-8 compared to the other nine farms, which purchased chickens from a Brazilian hatchery. Moreover, none of the K. pneumoniae isolates were linked to the Paraguayan hatchery. ESBL/AmpC and mcr-5-carrying multi-drug resistant (MDR) plasmids were characterized, and complete sequences were obtained for eight plasmids. The study shed light on Paraguayan poultry farms as a reservoir of antibiotic resistance commonly conferred via MDR plasmids and showed linkage between resistance and origin of the chickens at the hatcheries level.
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Ewers C, de Jong A, Prenger-Berninghoff E, El Garch F, Leidner U, Tiwari SK, Semmler T. Genomic Diversity and Virulence Potential of ESBL- and AmpC-β-Lactamase-Producing Escherichia coli Strains From Healthy Food Animals Across Europe. Front Microbiol 2021; 12:626774. [PMID: 33868190 PMCID: PMC8047082 DOI: 10.3389/fmicb.2021.626774] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 03/02/2021] [Indexed: 01/07/2023] Open
Abstract
The role of livestock animals as a putative source of ESBL/pAmpC E. coli for humans is a central issue of research. In a large-scale pan-European surveillance, 2,993 commensal Escherichia spp. isolates were recovered from randomly collected fecal samples of healthy cattle, pigs and chickens in various abattoirs. One-hundred Escherichia spp. isolates (0.5% from cattle, 1.3% pigs, 8.0% chickens) fulfilled the criteria for cefotaxime and ceftazidime non-wildtype (EUCAST). In silico screening of WGS data of 99 isolates (98 E. coli and 1 E. fergusonii) revealed blaSHV–12 (32.3%), blaCTX–M–1 (24.2%), and blaCMY–2 (22.2%) as predominant ESBL/pAmpC types. Other types were blaSHV–2 (1.0%), blaCTX–M–2/–14/–15 (1.0/6.1/1.0%), and blaTEM–52 (5.1%). Six isolates revealed AmpC-promoter mutations (position −42 (C > T) and one carried mcr-1. The majority (91.3%) of ESBL/pAmpC genes were located on plasmids. SHV-12 was mainly (50%) encoded on IncI1α plasmids (pST-3/-26/-95), followed by IncX3 (12.5%) and IncK2 (3.1%). The blaTEM–52 genes were located on IncI1α-pST-36 (60%) and IncX1 plasmids (20%). The dominant plasmid lineage among CTX-M-1 isolates was IncI1α (pST-3/-295/-317) (87.5%), followed by IncN-pST-1 (8.3%). CMY-2 was mostly identified on IncI1α (pST-12/-2) (54.5%) and IncK2 (31.8%) plasmids. Several plasmids revealed high similarity to published plasmids from human and animal Enterobacteriaceae. The isolates were assigned to phylogroups A/C (34.7/7.1%), B1 (27.6%), B2 (3.1%), D/F (9.2/10.2%), E (5.1%), and to E. clades (3.0%). With 51 known and 2 novel MLST types, a wide variety of STs was found, including STs previously observed in human isolates (ST10/38/117/131/648). ESBL/AmpC types or STs were rarely correlated with the geographic origin of the isolates or animal species. Virulence gene typing identified extraintestinal pathogenic E. coli (ExPEC; 2.0%), avian pathogenic E. coli (APEC; 51.5%), and atypical enteropathogenic E. coli (EPEC; 6.1%). In conclusion, the high diversity of STs and phylogenetic groups provides hardly any hint for clonal spread of single lineages but hints toward the dissemination of cephalosporin resistance genes in livestock via distinct, globally successful plasmid lineages. Even though a number of isolates could not be assigned to a distinct pathotype, our finding of combined multidrug-resistance and virulence in this facultative pathogen should be considered an additional threat to public health.
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Affiliation(s)
- Christa Ewers
- Department of Veterinary Medicine, Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
| | - Anno de Jong
- European Antimicrobial Susceptibility Surveillance in Animals (EASSA) Study Group, Executive Animal Health Study Center (CEESA), Brussels, Belgium
| | - Ellen Prenger-Berninghoff
- Department of Veterinary Medicine, Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
| | - Farid El Garch
- European Antimicrobial Susceptibility Surveillance in Animals (EASSA) Study Group, Executive Animal Health Study Center (CEESA), Brussels, Belgium
| | - Ursula Leidner
- Department of Veterinary Medicine, Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
| | - Sumeet K Tiwari
- NG1 Microbial Genomics, Robert Koch Institute, Berlin, Germany
| | - Torsten Semmler
- NG1 Microbial Genomics, Robert Koch Institute, Berlin, Germany
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Nobrega DB, Calarga AP, Nascimento LC, Chande Vasconcelos CG, de Lima EM, Langoni H, Brocchi M. Molecular characterization of antimicrobial resistance in Klebsiella pneumoniae isolated from Brazilian dairy herds. J Dairy Sci 2021; 104:7210-7224. [PMID: 33773789 DOI: 10.3168/jds.2020-19569] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 01/16/2021] [Indexed: 11/19/2022]
Abstract
In this observational study, phenotypic and genotypic patterns of antimicrobial resistance (AMR) in Klebsiella pneumoniae isolated from intramammary infections, clinical mastitis, fresh feces, rectal swabs, animal hindlimbs, and bulk tank milk samples from Brazilian dairy herds were investigated. In addition, we identified specific genetic variants present among extended-spectrum β-lactamase (ESBL) producers. We obtained 169 isolates of K. pneumoniae from 2009 to 2011 on 24 Brazilian dairy farms located in 4 Brazilian states. The AMR profile of all isolates was determined using disk-diffusion assays. The antimicrobial panel included drugs commonly used as mastitis treatment in Brazilian dairy herds (gentamicin, cephalosporins, sulfamethoxazole-trimethoprim, tetracycline) as well as antimicrobials of critical importance for human health (meropenem, ceftazidime, fluoroquinolones). The K. pneumoniae isolates resistant to tetracycline, fluoroquinolones, sulfamethoxazole-trimethoprim, or chloramphenicol were screened for presence of drug-specific AMR genes [tet, qnr, aac(6')-Ib, floR, catA2, cm1A, dfr, sul] using PCR. In addition, we identified ESBL genes present among ESBL-producers by using whole genome sequencing. Genomes were assembled and annotated, and patterns of AMR genes were investigated. Resistance was commonly detected against tetracycline (22.5% of all isolates), streptomycin (20.7%), and sulfamethoxazole-trimethoprim (9.5%). Antimicrobial resistance rates were higher in K. pneumoniae isolated from intramammary infections in comparison with isolates from feces (19.2 and 0% of multidrug resistance in intramammary and fecal isolates, respectively). In contrast, no difference in AMR rates was observed when contrasting hind limbs and isolates from intramammary infections. The genes tetA, sul2, and floR were the most frequently observed AMR genes in K. pneumoniae resistant to tetracycline, sulfamethoxazole-trimethoprim, and chloramphenicol, respectively. The tetA gene was present exclusively in isolates from milk. The genes blaCTX-M8 and blaSHV-108 were present in 3 ESBL-producing K. pneumoniae, including an isolate from bulk tank milk. The 3 isolates were of sequence type 281 and had similar mobile genetic elements and virulence genes. Our study reinforced the epidemiological importance and dissemination of blaCTX-M-8 pST114 plasmid in food-producing animals in Brazil.
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Affiliation(s)
- Diego Borin Nobrega
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON, N1G 2W1, Canada; Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), 13083-650, Campinas, São Paulo, Brazil.
| | - Aline Parolin Calarga
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), 13083-650, Campinas, São Paulo, Brazil
| | - Leandro Costa Nascimento
- Central Laboratory for High Performance Technologies (LaCTAD), University of Campinas (UNICAMP), 13083-886, Campinas, São Paulo, Brazil
| | | | | | - Helio Langoni
- Department of Veterinary Hygiene and Public Health, São Paulo State University (UNESP), 16618-681, Botucatu, São Paulo, Brazil
| | - Marcelo Brocchi
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), 13083-650, Campinas, São Paulo, Brazil.
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