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Bortolami L, Barberio A, Schiavon E, Martignago F, Littamè E, Sturaro A, Gagliazzo L, De Lucia A, Ostanello F. Surveillance of Antimicrobial Resistance of Escherichia coli Isolates from Intestinal Contents of Dairy and Veal Calves in the Veneto Region, Northeaster Italy. Animals (Basel) 2024; 14:1429. [PMID: 38791647 PMCID: PMC11117218 DOI: 10.3390/ani14101429] [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: 04/05/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
This surveillance study aimed to estimate the proportion of antimicrobial resistant strains and antimicrobial resistance (AMR) profiles of E. coli isolates detected from the intestinal contents of veal and dairy calves in the Veneto Region, Northeaster Italy. Additionally, we investigated the differences in AMR profiles between dairy and veal calves over the period 2017-2022. Overall 1150 E. coli isolates were tested from calves exhibiting enteric disease, with 868 from dairy and 282 from veal calves. The percentage of resistant isolates to nine antimicrobials was notably higher in veal calves compared to dairy calves, except for ampicillin. Throughout the study period, we observed a significant increase in the proportion of resistant isolates to florfenicol, gentamycin, paromomycin, tetracycline and trimethoprim/sulfamethoxazole in dairy calves, while we did not detect any significant increase in the proportion of resistant isolates among veal calves. A substantial proportion (75.9%) of the isolated E. coli exhibited multi-drug resistance (MDR). The proportion of multi-drug resistant isolates was significantly higher in veal calves (91.7%) compared to dairy calves (74.3%) all through the surveillance period (2017-2022), with no significant variation in MDR proportion among veal calves between 2017 and 2022 but a significant increase among dairy calves.
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Affiliation(s)
- Laura Bortolami
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università, 10, Legnaro, 35020 Padova, Italy; (L.B.); (A.B.); (E.S.); (F.M.); (E.L.); (A.S.); (L.G.)
| | - Antonio Barberio
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università, 10, Legnaro, 35020 Padova, Italy; (L.B.); (A.B.); (E.S.); (F.M.); (E.L.); (A.S.); (L.G.)
| | - Eliana Schiavon
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università, 10, Legnaro, 35020 Padova, Italy; (L.B.); (A.B.); (E.S.); (F.M.); (E.L.); (A.S.); (L.G.)
| | - Federico Martignago
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università, 10, Legnaro, 35020 Padova, Italy; (L.B.); (A.B.); (E.S.); (F.M.); (E.L.); (A.S.); (L.G.)
| | - Erica Littamè
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università, 10, Legnaro, 35020 Padova, Italy; (L.B.); (A.B.); (E.S.); (F.M.); (E.L.); (A.S.); (L.G.)
| | - Anna Sturaro
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università, 10, Legnaro, 35020 Padova, Italy; (L.B.); (A.B.); (E.S.); (F.M.); (E.L.); (A.S.); (L.G.)
| | - Laura Gagliazzo
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università, 10, Legnaro, 35020 Padova, Italy; (L.B.); (A.B.); (E.S.); (F.M.); (E.L.); (A.S.); (L.G.)
| | | | - Fabio Ostanello
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra, 50, Ozzano dell’Emilia, 40064 Bologna, Italy
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Joddha HB, Mathakiya RA, Joshi KV, Khant RB, Golaviya AV, Hinsu AT, Desai MR, Jakhesara SJ, Koringa PG. Profiling of Antimicrobial Resistance Genes and Integron from Escherichia coli Isolates Using Whole Genome Sequencing. Genes (Basel) 2023; 14:1212. [PMID: 37372392 DOI: 10.3390/genes14061212] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
This study is designed to investigate Escherichia coli for the antibiotic resistance genes (ARGs) and integrons from healthy as well as diarrhoeic/diseased animals/birds' faecal samples. A total of eight samples were selected for the study; from each animal, two samples were taken, one from healthy animals/birds and one from diarrhoeic/diseased animals/birds. Antibiotic sensitivity testing (AST) and whole genome sequencing (WGS) was performed for selected isolates. The E. coli isolates showed resistance to moxifloxacin, followed by erythromycin, ciprofloxacin, pefloxacin, tetracycline, levofloxacin, ampicillin, amoxicillin, and sulfadiazine (4/8, 50.00% each). The E. coli isolates were 100% sensitive to amikacin, followed by chloramphenicol, cefixime, cefoperazone, and cephalothin. A total of 47 ARGs from 12 different antibiotic classes were detected among the eight isolates by WGS. The different classes of antibiotics included aminoglycoside, sulphonamide, tetracycline, trimethoprim, quinolone, fosfomycin, phenicol, macrolide, colistin, fosmidomycin, and multidrug efflux. The class 1 integrons were detected in 6/8 (75.00%) isolates with 14 different gene cassettes.
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Affiliation(s)
- Harshrajsinh B Joddha
- Department of Veterinary Microbiology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India
| | - Rafiyuddin A Mathakiya
- Department of Veterinary Microbiology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India
| | - Kuldip V Joshi
- Department of Veterinary Microbiology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India
| | - Ravindra B Khant
- Department of Veterinary Microbiology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India
| | - Akash V Golaviya
- Department of Veterinary Microbiology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India
| | - Ankit T Hinsu
- Department of Animal Biotechnology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India
| | - Mansi R Desai
- Department of Animal Biotechnology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India
| | - Subhash J Jakhesara
- Department of Animal Biotechnology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India
| | - Prakash G Koringa
- Department of Animal Biotechnology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India
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Wójcicki M, Chmielarczyk A, Świder O, Średnicka P, Strus M, Kasperski T, Shymialevich D, Cieślak H, Emanowicz P, Kowalczyk M, Sokołowska B, Juszczuk-Kubiak E. Bacterial Pathogens in the Food Industry: Antibiotic Resistance and Virulence Factors of Salmonella enterica Strains Isolated from Food Chain Links. Pathogens 2022; 11:1323. [PMID: 36365074 PMCID: PMC9692263 DOI: 10.3390/pathogens11111323] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 10/13/2023] Open
Abstract
Salmonella is one of the most important foodborne pathogens. Fifty-three strains of Salmonella deposited in the Culture Collection of Industrial Microorganisms-Microbiological Resources Center (IAFB) were identified using molecular and proteomic analyses. Moreover, the genetic similarity of the tested strains was determined using the PFGE method. Main virulence genes were identified, and phenotypical antibiotic susceptibility profiles and prevalence of resistance genes were analyzed. Subsequently, the occurrence of the main mechanisms of β-lactam resistance was determined. Virulence genes, invA, fimA, and stn were identified in all tested strains. Phenotypic tests, including 28 antibiotics, showed that 50.9% of the strains were MDR. The tet genes associated with tetracyclines resistance were the most frequently identified genes. Concerning the genes associated with ESBL-producing Salmonella, no resistance to the TEM and CTX-M type was identified, and only two strains (KKP 1597 and KKP 1610) showed resistance to SHV. No strains exhibited AmpC-type resistance but for six Salmonella strains, the efflux-related resistance of PSE-1 was presented. The high number of resistant strains in combination with multiple ARGs in Salmonella indicates the possible overuse of antibiotics. Our results showed that it is necessary to monitor antimicrobial resistance profiles in all food chain links constantly and to implement a policy of proper antibiotic stewardship to contain or at least significantly limit the further acquisition of antibiotic resistance among Salmonella strains.
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Affiliation(s)
- Michał Wójcicki
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland
| | - Agnieszka Chmielarczyk
- Department of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, Czysta 18 Street, 31-121 Cracow, Poland
| | - Olga Świder
- Department of Food Safety and Chemical Analysis, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland
| | - Paulina Średnicka
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland
| | - Magdalena Strus
- Department of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, Czysta 18 Street, 31-121 Cracow, Poland
| | - Tomasz Kasperski
- Department of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, Czysta 18 Street, 31-121 Cracow, Poland
| | - Dziyana Shymialevich
- Culture Collection of Industrial Microorganisms—Microbiological Resources Center, Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland
| | - Hanna Cieślak
- Culture Collection of Industrial Microorganisms—Microbiological Resources Center, Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland
| | - Paulina Emanowicz
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland
| | - Monika Kowalczyk
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland
| | - Barbara Sokołowska
- Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland
| | - Edyta Juszczuk-Kubiak
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland
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Multidrug-Resistant Enteropathogenic Escherichia coli Isolated from Diarrhoeic Calves, Milk, and Workers in Dairy Farms: A Potential Public Health Risk. Antibiotics (Basel) 2022; 11:antibiotics11080999. [PMID: 35892389 PMCID: PMC9332572 DOI: 10.3390/antibiotics11080999] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/21/2022] [Accepted: 07/21/2022] [Indexed: 02/01/2023] Open
Abstract
Enteropathogenic Escherichia coli (EPEC) is a leading cause of diarrhoeagenic diseases in humans and cattle worldwide. The emergence of multidrug-resistant (MDR) EPEC from cattle sources is a public health concern. A total of 240 samples (75 diarrhoeic calves, 150 milk samples, and 15 workers) were examined for prevalence of EPEC in three dairy farms in Egypt. Antimicrobial resistance (AMR) traits were determined by antibiogram and polymerase chain reaction (PCR) detection of β-lactamase-encoding genes, plasmid-mediated quinolone resistance genes, and carbapenemase-encoding genes. The genetic relatedness of the isolates was assessed using repetitive extragenic palindromic sequence-based PCR (REP-PCR). EPEC isolates were detected in 22.7% (17/75) of diarrhoeic calves, 5.3% (8/150) of milk samples, and 20% (3/15) of worker samples. The detected serovars were O26 (5%), O111 (3.3%), O124 (1.6%), O126 (0.8%), and O55 (0.8%). AMR-EPEC (harbouring any AMR gene) was detected in 9.2% of samples. Among isolates, blaTEM was the most detected gene (39.3%), followed by blaSHV (32.1%) and blaCTX-M-1 (25%). The qnrA, qnrB, and qnrS genes were detected in 21.4%, 10.7%, and 7.1% of isolates, respectively. The blaVIM gene was detected in 14.3% of isolates. All EPEC (100%) isolates were MDR. High resistance rates were reported for ampicillin (100%), tetracycline (89.3%), cefazolin (71%), and ciprofloxacin (64.3%). Three O26 isolates and two O111 isolates showed the highest multiple-antibiotic resistance (MAR) indices (0.85–0.92); these isolates harboured blaSHV-12 and blaCTX-M-15 genes, respectively. REP-PCR genotyping showed high genetic diversity of EPEC, although isolates belonging to the same serotype or farm were clustered together. Two worker isolates (O111 and O26) showed high genetic similarity (80–95%) with diarrhoeic calf isolates of matched serotypes/farms. This may highlight potential inter-species transmission within the farm. This study highlights the potential high risk of cattle (especially diarrhoeic calves) as disseminators of MDR-EPEC and/or their AMR genes in the study area. Prohibition of non-prescribed use of antibiotics in dairy farms in Egypt is strongly warranted.
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Li K, Zeng Z, Liu J, Pei L, Wang Y, Li A, Kulyar MFEA, Shahzad M, Mehmood K, Li J, Qi D. Effects of Short-Chain Fatty Acid Modulation on Potentially Diarrhea-Causing Pathogens in Yaks Through Metagenomic Sequencing. Front Cell Infect Microbiol 2022; 12:805481. [PMID: 35402298 PMCID: PMC8983862 DOI: 10.3389/fcimb.2022.805481] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 02/25/2022] [Indexed: 12/30/2022] Open
Abstract
Short-chain fatty acids (SCFA) are principal nutrient substrates of intestinal epithelial cells that regulate the epithelial barrier in yaks. Until now, metagenomics sequencing has not been reported in diarrheal yaks. Scarce information is available regarding the levels of fecal SCFA and diarrhea in yaks. So, our study aims to identify the potential pathogens that cause the emerging diarrhea and explore the potential relationship of short-chain fatty acids in this issue. We estimated diarrhea rate in yaks after collecting an equal number of fecal samples from affected animals. Metagenomics sequencing and quantitative analysis of SCFA were performed, which revealed 15%–25% and 5%–10% prevalence of diarrhea in yak’s calves and adults, respectively. Violin box plot also showed a higher degree of dispersion in gene abundance distribution of diarrheal yaks, as compared to normal yaks. We found 366,163 significant differential abundance genes in diarrheal yaks, with 141,305 upregulated and 224,858 downregulated genes compared with normal yaks via DESeq analysis. Metagenomics binning analysis indicated the higher significance of bin 33 (Bacteroidales) (p < 0.05) in diarrheal animals, while bin 10 (p < 0.0001), bin 30 (Clostridiales) (p < 0.05), bin 51 (Lactobacillales) (p < 0.05), bin 8 (Lachnospiraceae) (p < 0.05), and bin 47 (Bacteria) (p < 0.05) were significantly higher in normal yaks. At different levels, a significant difference in phylum (n = 4), class (n = 8), oder (n = 8), family (n = 16), genus (n = 17), and species (n = 30) was noticed, respectively. Compared with healthy yaks, acetic acid (p < 0.01), propionic acid (p < 0.01), butyric acid (p < 0.01), isobutyric acid (p < 0.01), isovaleric acid (p < 0.05), and caproic acid (p < 0.01) were all observed significantly at a lower rate in diarrheal yaks. In conclusion, besides the increased Staphylococcus aureus, Babesia ovata, Anaplasma phagocytophilum, Bacteroides fluxus, viruses, Klebsiella pneumonia, and inflammation-related bacteria, the decrease of SCFA caused by the imbalance of intestinal microbiota was potentially observed in diarrheal yaks.
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Affiliation(s)
- Kun Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Kun Li, ; Jiakui Li, ; Desheng Qi,
| | - Zhibo Zeng
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Juanjuan Liu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Lulu Pei
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yaping Wang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Aoyun Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | | | - Muhammad Shahzad
- Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Khalid Mehmood
- Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Jiakui Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Kun Li, ; Jiakui Li, ; Desheng Qi,
| | - Desheng Qi
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Kun Li, ; Jiakui Li, ; Desheng Qi,
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Zhang X, Yi X, Zhuang H, Deng Z, Ma C. Invited Review: Antimicrobial Use and Antimicrobial Resistance in Pathogens Associated with Diarrhea and Pneumonia in Dairy Calves. Animals (Basel) 2022; 12:ani12060771. [PMID: 35327168 PMCID: PMC8944629 DOI: 10.3390/ani12060771] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 03/16/2022] [Accepted: 03/16/2022] [Indexed: 02/04/2023] Open
Abstract
Antimicrobial use (AMU) is the major driver of antimicrobial resistance (AMR) among bacteria in dairy herds. There have been numerous studies on AMU and AMR in dairy cows; however, studies on AMU and AMR in dairy calves are limited. A comprehensive overview of the current state of knowledge of AMU and AMR among pathogens in dairy calves is important for the development of scientifically supported and applicable measures to curb antimicrobial use and the increasing risk of AMR. Therefore, we performed a systematic review of research on AMU and AMR in dairy calves. A total of 75 publications were included, of which 19 studies reported AMU data for dairy calves and 68 described AMR profiles of the four most prevalent bacteria that are associated with calf diarrhea and calf pneumonia. Large variation in AMU was found among herds across different regions. There seems to be a positive association between exposure to antimicrobials and occurrence of resistance. Most AMU was accounted for by treatment of diseases, while a small proportion of AMU was prophylactic. AMU was more common in treating calf diarrhea than in treating pneumonia, and the resistance rates in bacteria associated with diarrhea were higher than those in pathogens related to pneumonia. Organic farms used significantly fewer antimicrobials to treat calf disease; however, the antimicrobial resistance rates of bacteria associated with calf diarrhea and pneumonia on both types of farms were comparable. Feeding waste or pasteurized milk was associated with a higher risk of AMR in pathogens. Altogether, this review summarizes AMU and AMR data for dairy calves and suggests areas for future research, providing evidence for the design of antimicrobial use stewardship programs in dairy calf farming.
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