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Serna C, Calderón Bernal JM, Torre-Fuentes L, García Muñoz Á, Díez Guerrier A, Hernández M, Fernández-Garayzábal JF, Vela AI, Cid D, Alvarez J. Integrative and conjugative elements associated with antimicrobial resistance in multidrug resistant Pasteurella multocida isolates from bovine respiratory disease (BRD)-affected animals in Spanish feedlots. Vet Q 2025; 45:1-15. [PMID: 40055923 PMCID: PMC11892046 DOI: 10.1080/01652176.2025.2474220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2024] [Revised: 12/16/2024] [Accepted: 02/24/2025] [Indexed: 05/13/2025] Open
Abstract
The emergence of multidrug-resistance (MDR) in Pasteurella multocida, a major contributor to bovine respiratory disease (BRD) is being increasingly reported, often linked to the carriage of antimicrobial resistance genes (ARGs) on integrative and conjugative elements (ICEs). The resistance phenotype for 19 antimicrobials was determined using broth microdilution in 75 Pasteurella multocida isolates from healthy and BRD-affected cattle from five feedlots. The genomes of 32 isolates were sequenced to identify ARG) and mobile genetic elements (MGEs) and assess their genetic diversity. MDR isolates (with phenotypic resistance to aminoglycosides, macrolides, fluoroquinolones and/or tetracyclines) were primarily found among BRD-affected compared to healthy animals. Non-susceptible isolates, belonging to ST79 and ST13, harbored point mutations and four to nine ARGs, including rarely reported mechanisms in Europe (mph(E), msr(E) and aadA31 ARGs and newly described mutations in the gyrA/parC genes). All ARGs were linked to the presence of MGEs including two ICEs, Tn7407 and the novel Tn7809, a prophage and a putative composite transposon. Clonally related isolates were found in different batches from the same feedlot, suggesting maintenance of MDR strains. Our findings demonstrate the diverse genetic basis of AMR in P. multocida from BRD-affected cattle in Spain, emphasizing the role of MGEs in the ARG dissemination.
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Affiliation(s)
- Carlos Serna
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
| | | | - Laura Torre-Fuentes
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET,), Universidad Complutense, Madrid, Spain
| | - Ángel García Muñoz
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Alberto Díez Guerrier
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET,), Universidad Complutense, Madrid, Spain
| | - Marta Hernández
- Laboratorio de Biología Molecular y Microbiología, Instituto Tecnológico Agrario de Castilla y León, Valladolid, Spain
| | - José Francisco Fernández-Garayzábal
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET,), Universidad Complutense, Madrid, Spain
| | - Ana Isabel Vela
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET,), Universidad Complutense, Madrid, Spain
| | - Dolores Cid
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
| | - Julio Alvarez
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET,), Universidad Complutense, Madrid, Spain
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Lu J, Wang J, Gao M, Zhou K, Liang J, Song C, He X, Liu C, Feng H, Pan W, Bao Q, Yan C, Huang D. Identification of a novel aminoglycoside nucleotidyltransferase gene in Morganella morganii from farm sewage. BMC Microbiol 2025; 25:161. [PMID: 40119290 PMCID: PMC11927176 DOI: 10.1186/s12866-025-03844-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Accepted: 02/24/2025] [Indexed: 03/24/2025] Open
Abstract
BACKGROUND Aminoglycosides are important broad-spectrum antimicrobial agents. When combined with β-lactam drugs, these agents can be used to treat severe infections such as those causing sepsis. Identifying additional resistance mechanisms will guarantee the successful application of aminoglycoside agents in clinical practice. METHODS The isolate Morganella morganii A19 was obtained from a sewage sample from an animal farm by means of agar plate streaking. The agar dilution method was used to determine the minimum inhibitory concentrations (MICs) of the antimicrobial agents. Cloning of the predicted resistance gene was conducted, and its resistance function was assessed through MIC testing. The protein was expressed in E. coli, and the kinetic parameters were quantified. The analysis of novel resistance gene-related sequences, including their structures and evolutionary relationships, was performed using bioinformatic tools. RESULTS In Morganella morganii A19, a newly discovered chromosome-encoded aminoglycoside resistance gene named aadA37 was identified and characterized. The protein AadA37 exhibited the highest amino acid identity (57.14%) with the functionally characterized aminoglycoside adenylyltransferase AadA33. aadA37 confers resistance to spectinomycin, streptomycin and ribostamycin, and enzyme kinetic analysis also demonstrated that it had adenosine transfer activities against spectinomycin and streptomycin, with kcat/Km values of 0.66 × 103 M- 1 s- 1 and 1.63 × 103 M- 1 s- 1, respectively. The aadA37 gene and its homologs were not related to any mobile genetic element (MGE), and they were all found to be encoded on the chromosomes of the M. morganii strains. CONCLUSION A novel aminoglycoside resistance gene was identified from an environmental bacterium and characterized in this work. Identifying new resistance mechanisms will aid in the effective clinical use of antimicrobial agents for treating infectious diseases caused by pathogens harboring the same resistance genes.
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Affiliation(s)
- Junwan Lu
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua University of Vocational Technology, Jinhua, 321000, China
| | - Jing Wang
- Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mengdi Gao
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Kexin Zhou
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Jialei Liang
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Chunhan Song
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua University of Vocational Technology, Jinhua, 321000, China
| | - Xuying He
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua University of Vocational Technology, Jinhua, 321000, China
| | - Chaoqun Liu
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua University of Vocational Technology, Jinhua, 321000, China
| | - Huiyue Feng
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua University of Vocational Technology, Jinhua, 321000, China
| | - Wei Pan
- The People's Hospital of Yuhuan, Yuhuan, 317600, China
| | - Qiyu Bao
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Chunxia Yan
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua University of Vocational Technology, Jinhua, 321000, China.
| | - Dawei Huang
- The People's Hospital of Yuhuan, Yuhuan, 317600, China.
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Rattanapanadda P, Ramsay D, Butters A, Booker CW, Hannon SJ, Hendrick S, Van Donkersgoed J, Warr BN, Gow SP, Morley PS. The prevalence and antimicrobial resistance of respiratory pathogens isolated from feedlot cattle in Canada. Front Microbiol 2025; 16:1497402. [PMID: 39935643 PMCID: PMC11810952 DOI: 10.3389/fmicb.2025.1497402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2024] [Accepted: 01/03/2025] [Indexed: 02/13/2025] Open
Abstract
Objectives The purpose of this study was to characterize the prevalence of antimicrobial resistance in Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni isolated from healthy feedlot cattle over 2 years, and investigate factors potentially associated with recovery of resistant isolates. Methods Deep-guarded nasopharyngeal (NP) swabs were used to sample feedlot cattle in multiple randomly selected feedlots (2019 n = 21, 2020 n = 26) at 2 timepoints. NP swabs were collected from 16 animals in each enrolled group upon entry processing and later in the feeding period. Cattle from the same groups (not necessarily the same animals) were sampled at both timepoints. Susceptibility testing was performed using the broth microdilution. Results A total of 1,392 cattle within 47 housing groups were sampled over 2 years, providing 625 bacterial isolates for investigation. Pasteurella multocida (27.4%) was the most frequently isolated BRD organism, followed by H. somni (9%) and M. haemolytica (8.5%). Resistance to ≥3 antimicrobial classes was detected in 2.4% of M. haemolytica, 3.4% of H. somni, and 21.3% of P. multocida isolates. Potential associations were investigated between recovery of resistant organisms and time of year at sampling (quarter), sampling timepoint (arrival or second sample), days on feed (DOF) at sampling, animal age categories, and BRD risk categories. There was a significant (p < 0.05) increase in resistance prevalence after arrival for macrolide drugs in M. haemolytica, and for ampicillin, danofloxacin, enrofloxacin, spectinomycin, gamithromycin, tildipirosin, tulathromycin and tetracycline in P. multocida isolates. Resistance was higher in calves than in yearlings for tulathromycin in H. somni, and for gamithromycin, spectinomycin, tulathromycin, tildipirosin, and tetracycline for P. multocida (p < 0.05) Resistance to tetracycline, tildipirosin, and tulathromycin decreased between 61-80 DOF and 81-100 DOF when compared to 20-40 DOF, whereas for spectinomycin, resistance was lower in cattle sampled between 61-80 DOF than those sampled at 20-40 DOF for P. multocida. Discussion The diversity of AMR profiles and associated risk factors between the BRD pathogens studied, underscores the importance of including all three organisms in future AMR studies in beef cattle.
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Affiliation(s)
- Porjai Rattanapanadda
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
- Department of Livestock Development, Ministry of Agriculture and Cooperatives, Bangkok, Thailand
| | - Dana Ramsay
- Department of Large Animal Clinical Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Alyssa Butters
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | | | | | | | | | - Brian N. Warr
- Veterinary Agri Health Services, Rocky View, AB, Canada
| | - Sheryl P. Gow
- Canadian Integrated Program for Antimicrobial Resistance Surveillance, Public Health Agency of Canada, Saskatoon, SK, Canada
| | - Paul S. Morley
- Veterinary Education, Research and Outreach (VERO) Program, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Canyon, TX, United States
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Chang TH, Pourtois JD, Haddock NL, Furkuawa D, Kelly KE, Amanatullah DF, Burgener E, Milla C, Banaei N, Bollyky PL. Prophages are Infrequently Associated With Antibiotic Resistance in Pseudomonas aeruginosa Clinical Isolates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.06.02.595912. [PMID: 38895396 PMCID: PMC11185549 DOI: 10.1101/2024.06.02.595912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Lysogenic bacteriophages can integrate their genome into the bacterial chromosome in the form of a prophage and can promote genetic transfer between bacterial strains in vitro . However, the contribution of lysogenic phages to the incidence of antimicrobial resistance (AMR) in clinical settings is poorly understood. Here, in a set of 186 clinical isolates of Pseudomonas aeruginosa collected from respiratory cultures from 82 patients with cystic fibrosis (CF), we evaluate the links between prophage counts and both genomic and phenotypic resistance to six anti-pseudomonal antibiotics: tobramycin, colistin, ciprofloxacin, meropenem, aztreonam, and piperacillin-tazobactam. We identified 239 different prophages in total. We find that P. aeruginosa isolates contain on average 3.06 +/- 1.84 (SD) predicted prophages. We find no significant association between the number of prophages per isolate and the minimum inhibitory concentration (MIC) for any of these antibiotics. We then investigate the relationship between particular prophages and AMR. We identify a single lysogenic phage associated with phenotypic resistance to the antibiotic tobramycin and, consistent with this association, we observe that AMR genes associated with resistance to tobramycin are more likely to be found when this prophage is present. However we find that they are not encoded directly on prophage sequences. Additionally, we identify a single prophage statistically associated with ciprofloxacin resistance but do not identify any genes associated with ciprofloxacin phenotypic resistance. These findings suggest that prophages are only infrequently associated with the AMR genes in clinical isolates of P. aeruginosa . Importance Antibiotic-resistant infections of Pseudomonas aeruginosa , a leading pathogen in patients with Cystic Fibrosis (CF) are a global health threat. While lysogenic bacteriophages are known to facilitate horizontal gene transfer, their role in promoting antibiotic resistance in clinical settings remains poorly understood. In our analysis of 186 clinical isolates of P. aeruginosa from CF patients, we find that prophage abundance does not predict phenotypic resistance to key antibiotics but that specific prophages are infrequently associated with tobramycin resistance genes. In addition, we do not find antimicrobial resistance (AMR) genes encoded directly on prophages. These results highlight that while phages can be associated with AMR, phage-mediated AMR transfer may be rare in clinical isolates and difficult to identify. This work is important for future efforts on mitigating AMR in Cystic Fibrosis and other vulnerable populations affected by Pseudomonas aeruginosa infections and advances our understanding of bacterial-phage dynamics in clinical infections.
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Tyagi I, Tyagi K, Gupta V, Dutta R, Singhvi N, Kumar V, Bhutiani R, Prakash O. Microbial diversity characterizations, associated pathogenesis and antimicrobial resistance profiling of Najafgarh drain. ENVIRONMENTAL RESEARCH 2023; 238:117140. [PMID: 37716389 DOI: 10.1016/j.envres.2023.117140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/30/2023] [Accepted: 09/13/2023] [Indexed: 09/18/2023]
Abstract
The Najafgarh drain plays a significant role in the pollution of the Yamuna River, accounting for 40% of the total pollution. Therefore, it is crucial to investigate and analyze the microbial diversity, metabolic functional capacity, and antibiotic resistance genes (ARGs) present in the Najafgarh drain. Additionally, studying the water quality and its relationship with the proliferation of microorganisms in the drain is of utmost importance. Results obtained confirmed the deteriorated water quality as physico-chemical parameters such as biochemical oxygen demand (BOD), chemical oxygen demand (COD), dissolved oxygen (DO), and total suspended solids (TSS) in the range of 125-140, 400-460, 0-0.2, 25-140.4 mg/l respectively violated the standard permissible national and global standards. In addition, the next generation sequencing (NGS) analysis confirm the presence of genus such as Thauera, Arcobacter, Pseudomonas, Geobacter, Dechloromonas, Tolumonas, Sulfurospirullum, Desulfovibrio, Aeromonas, Bacteroides, Prevotella, Cloacibacterium, Bifidobacterium, Clostridium etc. along with 864 ARGs in the wastewater obtained from the Najafgarh drain. Findings confirm that the pathogenic species reported from this dataset possess severe detrimental impact on faunal and human health. Further, Pearson's r correlation analysis indicated that environmental variables, mainly total dissolved solids (TDS) and chemical oxygen demand (COD), play a pivotal role in driving microbial community structure of this heavily polluted drain. Thus, the poor water quality, presence of a microbial nexus, pathogenic markers, and ARGs throughout this drain confirmed that it would be one potential contributor to the dissemination of disease-causing agents (pathogens) to the household and drinking water supplies in the near future.
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Affiliation(s)
- Inderjeet Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, 700 053, West Bengal, India.
| | - Koamud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, 700 053, West Bengal, India
| | - Vipin Gupta
- Ministry of Environment Forest and Climate Change, Integrated Regional Office-Dehradun, India, 248001, Uttarakhand, India
| | - Ritesh Dutta
- Kiit School of Biotechnology, Bhubaneswar, 751024, Odisha, India
| | - Nirjara Singhvi
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, 248007, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, 700 053, West Bengal, India.
| | - Rakesh Bhutiani
- Limnology and Ecological Modelling Lab, Department of Zoology and Environmental Science, Gurukul Kangri (Deemed to be University), Haridwar, 249404, UK, India
| | - Om Prakash
- Symbiosis Centre for Climate Change and Sustainability (SCCCS), Symbiosis International (Deemed University), Lavale, Pune, 412115, Maharastra, India
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Nascimento APA, de Farias BO, Gonçalves-Brito AS, Magaldi M, Flores C, Quidorne CS, Montenegro KS, Bianco K, Clementino MM. Phylogenomics analysis of multidrug-resistant Elizabethkingia anophelis in industrial wastewater treatment plant. J Appl Microbiol 2023; 134:lxad215. [PMID: 37715335 DOI: 10.1093/jambio/lxad215] [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: 05/23/2023] [Revised: 08/31/2023] [Accepted: 09/13/2023] [Indexed: 09/17/2023]
Abstract
AIMS This study investigated the phylogenetic relatedness of multidrug-resistant Elizabethkingia anophelis recovered from an industrial wastewater treatment plant (WWTPi). METHODS AND RESULTS The wastewater samples were plated in brain heart infusion agar (4 mg/L ceftazidime, 8 mg/L meropenem, and 2 mg/L polimixin). Four isolates recovered from four stages of WWTPi (influent, aeration, decantation, and treated effluent) were identified and evaluated of susceptibility profiles in the VITEK 2 system. These strains identified as E. meningoseptica were confirmed to be E. anophelis by whole genomic sequencing (Miseq-Illumina) and showed antimicrobial resistance genes of β-lactams, aminoglycosides, and tetracycline's classes. The ribosomal multilocus sequence typing showed that they belong to the rST 65620 together with clinical strains. The phylogenomic tree revealed the similarity of our strains to those belonging to sublineage 11 and the single nucleotide polymorphism analysis confirmed that they belong to a single clade. CONCLUSIONS To the best of our knowledge, this is the first study reporting the persistence of multidrug-resistant E. anophelis sublineage 11 along the wastewater treatment.
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Affiliation(s)
- Ana Paula Alves Nascimento
- National Institute of Quality Control in Health-INCQS, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil
| | - Beatriz Oliveira de Farias
- National Institute of Quality Control in Health-INCQS, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil
- Fiocruz Genomic Network, Oswaldo Cruz Foundation-FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil
| | - Andressa Silva Gonçalves-Brito
- National Institute of Quality Control in Health-INCQS, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil
- Fiocruz Genomic Network, Oswaldo Cruz Foundation-FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil
| | - Mariana Magaldi
- National Institute of Quality Control in Health-INCQS, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil
- Fiocruz Genomic Network, Oswaldo Cruz Foundation-FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil
| | - Claudia Flores
- National Institute of Quality Control in Health-INCQS, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil
| | - Camila Silva Quidorne
- National Institute of Quality Control in Health-INCQS, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil
| | - Kaylanne S Montenegro
- National Institute of Quality Control in Health-INCQS, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil
| | - Kayo Bianco
- National Institute of Quality Control in Health-INCQS, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil
- Fiocruz Genomic Network, Oswaldo Cruz Foundation-FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil
- COVID-19 Monitoring Network in Wastewater, Santo André, São Paulo, 09210-580, Brazil
| | - Maysa Mandetta Clementino
- National Institute of Quality Control in Health-INCQS, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil
- Fiocruz Genomic Network, Oswaldo Cruz Foundation-FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil
- COVID-19 Monitoring Network in Wastewater, Santo André, São Paulo, 09210-580, Brazil
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Javvadi Y, Mohan SV. Understanding the distribution of antibiotic resistance genes in an urban community using wastewater-based epidemiological approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 868:161419. [PMID: 36623646 DOI: 10.1016/j.scitotenv.2023.161419] [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: 10/01/2022] [Revised: 01/02/2023] [Accepted: 01/02/2023] [Indexed: 06/17/2023]
Abstract
The study aimed to evaluate the community-wide antimicrobial resistance (AMR) profile of an urban setting using the culture-independent wastewater-based epidemiological surveillance (WBE) approach. The domestic wastewater sample was collected at the converging point of the drain connecting the Sewage Treatment Plant (STP). The collected water sample was evaluated for the presence of 125 antibiotic resistance genes (ARGs) and 13 mobile genetic elements (MGEs, 5 integrons and 8 transposons). Antibiotic residues and the composition of bacterial communities were also examined. Community's sewage showed a diverse resistance pattern, with the positive detection of targeted ARGs, notably aph, aadA1, and strB being particularly abundant. Resistance to aminoglycoside and trimethoprim classes was prevalent, followed by chloramphenicol, sulfonamide, and β-lactams. According to the microbial diversity assessment, Proteobacteria, Bacteroidetes, Firmicutes, and Chloroflexi were abundant phyla observed, while Helicobacteraceae, Pseudomonadaceae, and Moraxellaceae were prevalent families. The study provided comprehensive baseline information of ARGs on a community scale and will be of use for ARG prevention and management.
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Affiliation(s)
- Yamini Javvadi
- Bioengineering and Environmental Science Lab, Department of Energy and Environmental Engineering, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - S Venkata Mohan
- Bioengineering and Environmental Science Lab, Department of Energy and Environmental Engineering, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Kang HJ, Lim SK, Lee YJ. Genetic characterization of third- or fourth-generation cephalosporin-resistant avian pathogenic Escherichia coli isolated from broilers. Front Vet Sci 2022; 9:1055320. [PMID: 36504870 PMCID: PMC9732669 DOI: 10.3389/fvets.2022.1055320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/04/2022] [Indexed: 11/26/2022] Open
Abstract
The third- or fourth-generation cephalosporins (3GC or 4 GC) are classified as "critically important antimicrobials for human medicine" by WHO, but resistance to these drugs is increasing rapidly in avian pathogenic E. coli (APEC). This study investigated the distribution and genetic characteristics of 3GC- or 4 GC-resistant APEC isolates from five major integrated broiler operations in Korea. The prevalence of 3GC- or 4GC-resistant APEC isolates in 1-week-old broilers was the highest in farms of operation C (53.3%); however, the highest prevalence of these isolates in 4-week-old broilers was the highest on the farms of operation A (60.0%), followed by operations E (50.0%) and C (35.7%). All 49 3GC- or 4GC-resistant APEC isolates had at least one β-lactamase-encoding gene. The most common β-lactamase-encoding genes was extended-spectrum β-lactamase gene, bla CTX-M-15, detected in 24 isolates (49.0%), followed by bla TEM-1 (32.7%). Sixteen isolates (32.7%) harbored class 1 integrons, and four isolates (8.2%) showed different gene cassette-arrangements. However, only 1 of 26 isolates harboring class 2 integrons carried a gene cassette. Furthermore, both CRISPR 1 and 2 arrays were detected in most isolates (36 isolates; 73.5%), followed by CRISPR 2 (18.4%) and CRISPR 1 (4.1%). Interestingly, CRISPR 2 was significantly more prevalent in multidrug resistant (MDR)-APEC isolates than in non-MDR APEC isolates, whereas CRISPR 3 and 4 were significantly more prevalent in non-MDR APEC isolates (each 11.1%; p < 0.05). None of the protospacers of CRISPR arrays were directly associated with antimicrobial resistance. Our findings indicate that the distribution and characteristics of 3GC or 4GC-resistant APEC isolates differed among the integrated broiler operations; moreover, improved management protocols are needed to control the horizontal transmission of 3GC or 4GC-resistant APEC isolates.
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Affiliation(s)
- Hyo Jung Kang
- College of Veterinary Medicine and Zoonoses Research Institute, Kyungpook National University, Daegu, South Korea
| | - Suk-Kyung Lim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon, South Korea
| | - Young Ju Lee
- College of Veterinary Medicine and Zoonoses Research Institute, Kyungpook National University, Daegu, South Korea
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Wu Z, Che Y, Dang C, Zhang M, Zhang X, Sun Y, Li X, Zhang T, Xia Y. Nanopore-based long-read metagenomics uncover the resistome intrusion by antibiotic resistant bacteria from treated wastewater in receiving water body. WATER RESEARCH 2022; 226:119282. [PMID: 36332295 DOI: 10.1016/j.watres.2022.119282] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Wastewater treatment plant (WWTP) effluent discharge could induce the resistome enrichment in the receiving water environments. However, because of the general lack of a robust antibiotic-resistant bacteria (ARB) identification method, the driving mechanism for resistome accumulation in receiving environment is unclear. Here, we took advantage of the enhanced ARBs recognition by nanopore long reads to distinguish the indigenous ARBs and the accumulation of WWTP-borne ARBs in the receiving water body of a domestic WWTP. A bioinformatic framework (named ARGpore2: https://github.com/sustc-xylab/ARGpore2) was constructed and evaluate to facilitate antibiotic resistance genes (ARGs) and ARBs identification in nanopore reads. ARGs identification by ARGpore2 showed comparable precision and recall to that of the commonly adopt BLASTP-based method, whereas the spectrum of ARBs doubled that of the assembled Illumina dataset. Totally, we identified 33 ARBs genera carrying 65 ARG subtypes in the receiving seawater, whose concentration was in general 10 times higher than clean seawater's. Notably we report a primary resistome intrusion caused by the revival of residual microbes survived from disinfection treatment. These WWTP-borne ARBs, including several animal/human enteric pathogens, contributed up to 85% of the receiving water resistome. Plasmids and class 1 integrons were reckoned as major vehicles facilitating the persistence and dissemination of ARGs. Moreover, our work demonstrated the importance of extensive carrier identification in determining the driving force of multifactor coupled resistome booming in complicated environmental conditions, thereby paving the way for establishing priority for effective ARGs mitigation strategies.
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Affiliation(s)
- Ziqi Wu
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China; Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - You Che
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR
| | - Chenyuan Dang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Miao Zhang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xuyang Zhang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yuhong Sun
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xiang Li
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China; State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR
| | - Yu Xia
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China; State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China.
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10
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Gao M, Feng C, Ji Y, Shi Y, Shi W, Zhang L, Liu S, Li A, Zhang X, Li Q, Lu J, Bao Q, Zhang H. AadA36, a novel chromosomal aminoglycoside nucleotidyltransferase from a clinical isolate of Providencia stuartii. Front Microbiol 2022; 13:1035651. [PMID: 36386671 PMCID: PMC9663854 DOI: 10.3389/fmicb.2022.1035651] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 10/06/2022] [Indexed: 01/25/2023] Open
Abstract
In this study, we characterized a novel chromosome-encoded aminoglycoside nucleotidyltransferase (ANT), AadA36, from the Providencia stuartii strain P14 isolated from the sputum specimen of a burn patient at a hospital in Wenzhou, China. Among the functionally characterized ANTs, AadA36 shared the highest amino acid sequence identity of 51.91% with AadA14. The whole genome of P. stuartii P14 consisted of one chromosome and two plasmids (designated pP14-166 and pP14-114). A total of 19 genes with ≥80% similarity with functionally characterized antimicrobial resistance genes (ARGs) were identified in the whole genome, including aminoglycosides [aac(2')-Ia, aph(6)-Id, aph(3″)-Ib, aac(6')-Ib, ant(3″)-IIa, aph(3')-Ia], β-lactams (bla CMY-2 and bla OXA-10) and so on. Antimicrobial susceptibility testing showed that the aadA36 gene conferred specific resistance to spectinomycin and streptomycin, and the minimum inhibitory concentration (MIC) of these antimicrobials increased 128- and 64-fold compared with the control strain. The kinetic parameters of AadA36 were consistent with the MIC data of spectinomycin and streptomycin, with kcat /Km ratios of (1.07 ± 2.23) × 104 M-1 s-1 and (8.96 ± 1.01) × 103 M-1 s-1, respectively. The identification of a novel aminoglycoside resistance gene will help us further understand the complexity of the resistance mechanisms and provide deep insights into the dissemination of resistance genes in the microbial population.
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Affiliation(s)
- Mengdi Gao
- Department of Children’s Respiration Disease, The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Chunlin Feng
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yongan Ji
- Department of Children’s Respiration Disease, The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
| | - Yaokai Shi
- Department of Children’s Respiration Disease, The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
| | - Weina Shi
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Lei Zhang
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Shuang Liu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Anqi Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xueya Zhang
- Department of Children’s Respiration Disease, The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Qiaoling Li
- Department of Children’s Respiration Disease, The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Junwan Lu
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Qiyu Bao
- Department of Children’s Respiration Disease, The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China,Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China,*Correspondence: Qiyu Bao,
| | - Hailin Zhang
- Department of Children’s Respiration Disease, The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China,Hailin Zhang,
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11
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Weber J, Borchardt S, Seidel J, Schreiter R, Wehrle F, Donat K, Freick M. Effects of Selective Dry Cow Treatment on Intramammary Infection Risk after Calving, Cure Risk during the Dry Period, and Antibiotic Use at Drying-Off: A Systematic Review and Meta-Analysis of Current Literature (2000-2021). Animals (Basel) 2021; 11:3403. [PMID: 34944180 PMCID: PMC8698164 DOI: 10.3390/ani11123403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/24/2021] [Accepted: 11/26/2021] [Indexed: 01/21/2023] Open
Abstract
The objectives of this paper were (i) to perform a systematic review of the literature over the last 21 yr and (ii) to evaluate the efficacy of selective dry cow treatment (SDCT) vs. blanket dry cow treatment (BDCT) in dairy cows regarding the risk of intramammary infection (IMI) after calving, new IMI risk after calving, cure risk during the dry period, and a reduction in antibiotic use at drying-off by meta-analysis. The systematic search was carried out using the databases PubMed, CAB Direct, and ScienceDirect. A meta-analytical assessment was performed for each outcome of interest using random-effects models, and the relative risk (RR) for IMI and cure or the pooled proportion for antibiotic use was calculated. The final number of included studies was n = 3 for IMI risk after calving and n = 5 for new IMI risk after calving, cure risk during the dry period, and antibiotic use. The RR levels for IMI (RR, 95% confidence interval [CI]: 1.02, 0.94-1.11; p = 0.592), new IMI (RR, 95% CI: 1.06, 0.94-1.20; p = 0.994), and cure (RR, 95% CI: 1.00, 0.97-1.02; p = 0.661) did not differ significantly between SDCT and BDCT. Substantial heterogeneity was observed between the trials regarding the pooled proportion of antibiotic use within the SDCT groups (I2 = 97.7%; p < 0.001). This meta-analysis provides evidence that SDCT seems to be an adequate alternative to BDCT regarding udder health with a simultaneous reduction in antibiotic use. Limitations might arise because of the small number of studies included.
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Affiliation(s)
- Jim Weber
- Veterinary Practice Zettlitz, 09306 Zettlitz, Germany;
| | - Stefan Borchardt
- Clinic for Animal Reproduction, Faculty of Veterinary Medicine, Free University of Berlin, 14163 Berlin, Germany;
| | - Julia Seidel
- Faculty of Agriculture/Environment/Chemistry, HTW Dresden—University of Applied Sciences, 01326 Dresden, Germany;
| | - Ruben Schreiter
- ZAFT e.V., Center for Applied Research and Technology, 01069 Dresden, Germany;
| | - Frederike Wehrle
- Animal Health Service, Thuringian Animal Diseases Fund, 07745 Jena, Germany; (F.W.); (K.D.)
- Clinic for Obstetrics, Gynecology and Andrology of Large and Small Animals with Veterinary Ambulance, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Karsten Donat
- Animal Health Service, Thuringian Animal Diseases Fund, 07745 Jena, Germany; (F.W.); (K.D.)
- Clinic for Obstetrics, Gynecology and Andrology of Large and Small Animals with Veterinary Ambulance, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Markus Freick
- Veterinary Practice Zettlitz, 09306 Zettlitz, Germany;
- Faculty of Agriculture/Environment/Chemistry, HTW Dresden—University of Applied Sciences, 01326 Dresden, Germany;
- ZAFT e.V., Center for Applied Research and Technology, 01069 Dresden, Germany;
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12
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Genomic Characterization of a Proteus sp. Strain of Animal Origin Co-Carrying blaNDM-1 and lnu(G). Antibiotics (Basel) 2021; 10:antibiotics10111411. [PMID: 34827349 PMCID: PMC8615141 DOI: 10.3390/antibiotics10111411] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/10/2021] [Accepted: 11/14/2021] [Indexed: 11/16/2022] Open
Abstract
The emergence of carbapenem-resistant Proteus represents a serious threat to global public health due to limited antibiotic treatment options. Here, we characterize a Proteus isolate NMG38-2 of swine origin that exhibits extensive drug resistance, including carbapenems. Whole-genome sequencing based on Illumina and MinION platforms showed that NMG38-2 contains 24 acquired antibiotic resistance genes and three plasmids, among which, pNDM_NMG38-2, a pPvSC3-like plasmid, is transferable and co-carries blaNDM-1 and lnu(G). Sequence analysis of pPvSC3-like plasmids showed that they share a conserved backbone but have a diverse accessory module with complex chimera structures bearing abundant resistance genes, which are facilitated by transposons and/or homologous recombination. The acquisition of blaNDM-1 in pNDM_NMG38-2 was due to the ISCR1-mediated integration event. Comprehensive analysis of the lnu(G)-bearing cassettes carried by bacterial plasmids or chromosomes revealed a diversification of its genetic contexts, with Tn6260 and ISPst2 elements being the leading contributors to the dissemination of lnu(G) in Enterococcus and Enterobacteriaceae, respectively. In conclusion, this study provides a better understanding of the genetic features of pPvSC3-like plasmids, which represent a novel plasmid group as a vehicle mediating the dissemination of blaNDM-1 among bacteria species. Moreover, our results highlight the central roles of Tn6260 and ISPst2 in the spread of lnu(G).
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13
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Andrés-Lasheras S, Ha R, Zaheer R, Lee C, Booker CW, Dorin C, Van Donkersgoed J, Deardon R, Gow S, Hannon SJ, Hendrick S, Anholt M, McAllister TA. Prevalence and Risk Factors Associated With Antimicrobial Resistance in Bacteria Related to Bovine Respiratory Disease-A Broad Cross-Sectional Study of Beef Cattle at Entry Into Canadian Feedlots. Front Vet Sci 2021; 8:692646. [PMID: 34277758 PMCID: PMC8280473 DOI: 10.3389/fvets.2021.692646] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/31/2021] [Indexed: 11/13/2022] Open
Abstract
A broad, cross-sectional study of beef cattle at entry into Canadian feedlots investigated the prevalence and epidemiology of antimicrobial resistance (AMR) in Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasma bovis, bacterial members of the bovine respiratory disease (BRD) complex. Upon feedlot arrival and before antimicrobials were administered at the feedlot, deep nasopharyngeal swabs were collected from 2,824 feedlot cattle in southern and central Alberta, Canada. Data on the date of feedlot arrival, cattle type (beef, dairy), sex (heifer, bull, steer), weight (kg), age class (calf, yearling), source (ranch direct, auction barn, backgrounding operations), risk of developing BRD (high, low), and weather conditions at arrival (temperature, precipitation, and estimated wind speed) were obtained. Mannheimia haemolytica, P. multocida, and H. somni isolates with multidrug-resistant (MDR) profiles associated with the presence of integrative and conjugative elements were isolated more often from dairy-type than from beef-type cattle. Our results showed that beef-type cattle from backgrounding operations presented higher odds of AMR bacteria as compared to auction-derived calves. Oxytetracycline resistance was the most frequently observed resistance across all Pasteurellaceae species and cattle types. Mycoplasma bovis exhibited high macrolide minimum inhibitory concentrations in both cattle types. Whether these MDR isolates establish and persist within the feedlot environment, requires further evaluation.
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Affiliation(s)
- Sara Andrés-Lasheras
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Reuben Ha
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Rahat Zaheer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Catrione Lee
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | | | - Craig Dorin
- Veterinary Agri-Health Systems, Airdrie, AB, Canada
| | | | - Rob Deardon
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada.,Department of Mathematics and Statistics, University of Calgary, Calgary, AB, Canada
| | - Sheryl Gow
- Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada.,Public Health Agency of Canada, Saskatoon, SK, Canada
| | | | | | - Michele Anholt
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada.,POV Inc., Airdrie, AB, Canada
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
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14
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El-Baz AM, Yahya G, Mansour B, El-Sokkary MMA, Alshaman R, Alattar A, El-Ganiny AM. The Link between Occurrence of Class I Integron and Acquired Aminoglycoside Resistance in Clinical MRSA Isolates. Antibiotics (Basel) 2021; 10:488. [DOI: https:/doi.org/10.3390/antibiotics10050488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2025] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of nosocomial infections because of its high resistance. Here, we study the antibiotic resistance in MRSA clinical isolates and their relation to integron I occurrence. A total of 88 clinical Staphylococcusaureus isolates were collected. MRSA were identified by the disk diffusion method (DDM) and confirmed by PCR, and antibiogram was determined by DDM. Integron I, II and the aacA4 gene were investigated by PCR. Integrase-positive strains were analyzed for the presence of resistance gene cassettes by sequencing. All isolates were identified as MRSA by DDM and confirmed by PCR. All isolates were resistant to ampicillin and cefoxitin. Concerning aminoglycosides, the frequency of resistance was reported for streptomycin (60.7%), tobramycin (37.1%) gentamicin (36%), and for amikacin (15.9%). Integron I was detected in 41 isolates (46.6%), while integron II was detected in three isolates (3.4%). Sequencing of the integron I-cassette indicated the exclusive prevalence of addA gene variants mediating aminoglycoside resistance. The aacA4 gene was found in DNA of 31 isolates (35.22%). This study revealed the high existence of MRSA. Furthermore, the AacA4 gene and class I integron harboring aadA gene were predominant in MRSA isolates.
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Affiliation(s)
- Ahmed M. El-Baz
- Microbiology and Biotechnology Department, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa 11152, Egypt
| | - Galal Yahya
- Microbiology and Immunology Department, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
- Department of Molecular Genetics, TU Kaiserlautern, 67663 Kaiserslautern, Germany
| | - Basem Mansour
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa 11152, Egypt
| | - Mohamed M. A. El-Sokkary
- Microbiology and Immunology Department, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Reem Alshaman
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, University of Tabuk, Tabuk 471, Saudi Arabia
| | - Abdullah Alattar
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, University of Tabuk, Tabuk 471, Saudi Arabia
| | - Amira M. El-Ganiny
- Microbiology and Immunology Department, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
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15
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The Link between Occurrence of Class I Integron and Acquired Aminoglycoside Resistance in Clinical MRSA Isolates. Antibiotics (Basel) 2021; 10:antibiotics10050488. [PMID: 33922421 PMCID: PMC8147066 DOI: 10.3390/antibiotics10050488] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 04/18/2021] [Accepted: 04/21/2021] [Indexed: 11/20/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of nosocomial infections because of its high resistance. Here, we study the antibiotic resistance in MRSA clinical isolates and their relation to integron I occurrence. A total of 88 clinical Staphylococcusaureus isolates were collected. MRSA were identified by the disk diffusion method (DDM) and confirmed by PCR, and antibiogram was determined by DDM. Integron I, II and the aacA4 gene were investigated by PCR. Integrase-positive strains were analyzed for the presence of resistance gene cassettes by sequencing. All isolates were identified as MRSA by DDM and confirmed by PCR. All isolates were resistant to ampicillin and cefoxitin. Concerning aminoglycosides, the frequency of resistance was reported for streptomycin (60.7%), tobramycin (37.1%) gentamicin (36%), and for amikacin (15.9%). Integron I was detected in 41 isolates (46.6%), while integron II was detected in three isolates (3.4%). Sequencing of the integron I-cassette indicated the exclusive prevalence of addA gene variants mediating aminoglycoside resistance. The aacA4 gene was found in DNA of 31 isolates (35.22%). This study revealed the high existence of MRSA. Furthermore, the AacA4 gene and class I integron harboring aadA gene were predominant in MRSA isolates.
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16
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Klima CL, Holman DB, Cook SR, Conrad CC, Ralston BJ, Allan N, Anholt RM, Niu YD, Stanford K, Hannon SJ, Booker CW, McAllister TA. Multidrug Resistance in Pasteurellaceae Associated With Bovine Respiratory Disease Mortalities in North America From 2011 to 2016. Front Microbiol 2020; 11:606438. [PMID: 33240256 PMCID: PMC7682020 DOI: 10.3389/fmicb.2020.606438] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 10/19/2020] [Indexed: 01/20/2023] Open
Abstract
Multidrug-resistant (MDR; resistance to ≥3 antimicrobial classes) members of the Pasteurellaceae family may compromise the efficacy of therapies used to prevent and treat bovine respiratory disease (BRD) in feedlot cattle. This study examined the prevalence of multidrug resistance in strains of Mannheimia haemolytica and Pasteurella multocida collected from BRD cattle mortalities in North America. Isolates of M. haemolytica (n = 147) and P. multocida (n = 70) spanning 69 Alberta feedlots from 2011 to 2016 and two United States feedlots from 2011 to 2012 were examined for antimicrobial resistance (AMR) in association with integrative and conjugative elements (ICEs). Overall, resistance was high in both bacterial species with an increase in the prevalence of MDR isolates between 2011 and 2016. Resistance to >7 antimicrobial drugs occurred in 31% of M. haemolytica and 83% of P. multocida isolates. Resistance to sulfadimethoxine, trimethoprim/sulfamethoxazole, neomycin, clindamycin oxytetracycline, spectinomycin, tylosin, tilmicosin, and tulathromycin was most common. Although >80% of strains harbored three or more ICE-associated genes, only 12% of M. haemolytica and 77% of P. multocida contained all six, reflecting the diversity of ICEs. There was evidence of clonal spread as P. multocida and M. haemolytica isolates with the same pulsed-field gel electrophoresis profile from the United States in 2011 were isolated in Alberta in 2015–2016. This work highlights that MDR strains of Pasteurellaceae containing ICEs are widespread and may be contributing to BRD therapy failure in feedlot cattle. Given the antimicrobial resistance gene profiles identified, these MDR isolates may be selected for by the use of macrolides, tetracyclines, and/or in-feed supplements containing heavy metals.
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Affiliation(s)
- Cassidy L Klima
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Devin B Holman
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Shaun R Cook
- Alberta Agriculture and Forestry, Lethbridge, AB, Canada
| | - Cheyenne C Conrad
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | | | - Nick Allan
- Chinook Contract Research Inc., Airdrie, AB, Canada
| | | | - Yan D Niu
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Kim Stanford
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | | | | | - Tim A McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
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17
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Antimicrobial Resistance in Members of the Bacterial Bovine Respiratory Disease Complex Isolated from Lung Tissue of Cattle Mortalities Managed with or without the Use of Antimicrobials. Microorganisms 2020; 8:microorganisms8020288. [PMID: 32093326 PMCID: PMC7074851 DOI: 10.3390/microorganisms8020288] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/11/2020] [Accepted: 02/17/2020] [Indexed: 02/06/2023] Open
Abstract
Over a two-year period, Mannheimia haemolytica (MH; n = 113), Pasteurella multocida (PM; n = 47), Histophilus somni (HS; n = 41) and Mycoplasma bovis (MB; n = 227) were isolated from bovine lung tissue at necropsy from cattle raised conventionally (CON, n = 29 feedlots) or without antimicrobials [natural (NAT), n = 2 feedlots]. Excluding MB, isolates were assayed by PCR to detect the presence of 13 antimicrobial resistance (AMR) genes and five core genes associated with integrative and conjugative elements (ICEs). Antimicrobial susceptibility phenotypes and minimum inhibitory concentrations (MICs, µg/mL) were determined for a subset of isolates (MH, n = 104; PM, n = 45; HS, n = 23; and MB, n = 61) using Sensititre analyses. A subset of isolates (n = 21) was also evaluated by whole-genome sequencing (WGS) based on variation in AMR phenotype. All five ICE core genes were detected in PM and HS by PCR, but only 3/5 were present in MH. Presence of mco and tnpA ICE core genes in MH was associated with higher MICs (p < 0.05) for all tetracyclines, and 2/3 of all macrolides, aminoglycosides and fluoroquinolones evaluated. In contrast, association of ICE core genes with MICs was largely restricted to macrolides for PM and to individual tetracyclines and macrolides for HS. For MH, the average number of AMR genes markedly increased (p < 0.05) in year 2 of the study due to the emergence of a strain that was PCR positive for all 13 PCR-tested AMR genes as well as two additional AMR genes (aadA31 and blaROB-1) detected by WGS. Conventional management of cattle increased (p < 0.05) MICs of tilmicosin and tulathromycin for MH; neomycin and spectinomycin for PM; and gamithromycin and tulathromycin for MB. The average number of PCR-detected AMR genes in PM was also increased (p < 0.05) in CON mortalities. This study demonstrates increased AMR especially to macrolides by bovine respiratory disease organisms in CON as compared to NAT feedlots and a rapid increase in AMR following dissemination of strain(s) carrying ICE-associated multidrug resistance.
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18
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Cameron A, Zaheer R, McAllister TA. Emerging Variants of the Integrative and Conjugant Element ICE Mh1 in Livestock Pathogens: Structural Insights, Potential Host Range, and Implications for Bacterial Fitness and Antimicrobial Therapy. Front Microbiol 2019; 10:2608. [PMID: 31781082 PMCID: PMC6861422 DOI: 10.3389/fmicb.2019.02608] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 10/28/2019] [Indexed: 11/23/2022] Open
Abstract
Horizontal gene transfer of integrative and conjugative elements (ICE) in bacterial pathogens of the bovine respiratory disease (BRD) complex has emerged as a significant cause of antimicrobial resistance (AMR) and therapeutic failure and mortalities in cattle. The aim of this study was to assess an AMR ICE occurring in Pasteurella multocida from a case of BRD, designated ICEMh1PM22 for its structure and host genome insertion site, and to identify consequences for host fitness and antimicrobial therapy. The modular structure of ICEMh1-like elements found in several related livestock pathogens was compared to ICEMh1PM22, and the repertoire of cargo genes in variable ICE modules was functionally categorized. AMR genes were identified as frequent additions to the variable modules of ICEMh1-like elements. Random PCR-based mapping of ICEMh1PM22-genome junctions in transconjugants provided evidence that ICEMh1PM22 integrates into the tRNA-leu for the UUG codon, and not into tRNA-leu for other codons. This was separately confirmed in the genomes of ICEMh1-like-harboring livestock pathogens. Bacterial genera harboring receptive tRNA-leuUUG were identified to establish the potential host range of ICEMh1-like elements. ICEMh1PM22-carrying transconjugants in P. multocida and Mannheimia haemolytica were less fit than isogenic strains without the ICE when grown without antimicrobial selection. This fitness cost was abrogated in the presence of subinhibitory concentrations of antimicrobials. Despite this cost, ICEMh1PM22 was retained in transconjugants in extended culture. To identify possible therapeutic efficiencies, antimicrobial combinations were screened for synergistic interactions against AMR ICEMh1PM22-carrying transconjugants. No antimicrobial combination tested exhibited synergistic interactions against AMR P. multocida or M. haemolytica harboring ICEMh1PM22. In conclusion, this study provided information on the structural variation of ICEMh1-like elements, refined the ICE insertion site and potential host range, and demonstrated the risk and consequences for AMR following horizontal transfer of ICE into BRD pathogens.
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Affiliation(s)
- Andrew Cameron
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada.,Lethbridge Research and Development Centre, Lethbridge, AB, Canada
| | - Rahat Zaheer
- Lethbridge Research and Development Centre, Lethbridge, AB, Canada
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Lethbridge, AB, Canada
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Cheng G, Ning J, Ahmed S, Huang J, Ullah R, An B, Hao H, Dai M, Huang L, Wang X, Yuan Z. Selection and dissemination of antimicrobial resistance in Agri-food production. Antimicrob Resist Infect Control 2019; 8:158. [PMID: 31649815 PMCID: PMC6805589 DOI: 10.1186/s13756-019-0623-2] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 10/09/2019] [Indexed: 12/14/2022] Open
Abstract
Public unrest about the use of antimicrobial agents in farming practice is the leading cause of increasing and the emergences of Multi-drug Resistant Bacteria that have placed pressure on the agri-food industry to act. The usage of antimicrobials in food and agriculture have direct or indirect effects on the development of Antimicrobial resistance (AMR) by bacteria associated with animals and plants which may enter the food chain through consumption of meat, fish, vegetables or some other food sources. In addition to antimicrobials, recent reports have shown that AMR is associated with tolerance to heavy metals existing naturally or used in agri-food production. Besides, biocides including disinfectants, antiseptics and preservatives which are widely used in farms and slaughter houses may also contribute in the development of AMR. Though the direct transmission of AMR from food-animals and related environment to human is still vague and debatable, the risk should not be neglected. Therefore, combined global efforts are necessary for the proper use of antimicrobials, heavy metals and biocides in agri-food production to control the development of AMR. These collective measures will preserve the effectiveness of existing antimicrobials for future generations.
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Affiliation(s)
- Guyue Cheng
- 1MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jianan Ning
- 1MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070 China
| | - Saeed Ahmed
- 1MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070 China
| | - Junhong Huang
- 1MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070 China
| | - Rizwan Ullah
- 3State key laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 China
| | - Boyu An
- 1MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070 China
| | - Haihong Hao
- 1MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070 China
| | - Menghong Dai
- 1MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070 China
| | - Lingli Huang
- 2National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xu Wang
- 1MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070 China
| | - Zonghui Yuan
- 1MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070 China.,2National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, 430070 China
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López-Ochoa AJ, Sánchez-Alonso P, Vázquez-Cruz C, Horta-Valerdi G, Negrete-Abascal E, Vaca-Pacheco S, Mejía R, Pérez-Márquez M. Molecular and genetic characterization of the pOV plasmid from Pasteurella multocida and construction of an integration vector for Gallibacterium anatis. Plasmid 2019; 103:45-52. [PMID: 31022414 DOI: 10.1016/j.plasmid.2019.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 04/18/2019] [Accepted: 04/21/2019] [Indexed: 11/16/2022]
Abstract
BACKGROUND The pOV plasmid isolated from the Pasteurella multocida strain PMOV is a new plasmid, and its molecular characterization is important for determining its gene content and its replicative properties in Pasteurellaceae family bacteria. METHODS Antimicrobial resistance mediated by the pOV plasmid was tested in bacteria. Purified pOV plasmid DNA was used to transform E. coli DH5α and Gallibacterium anatis 12656-12, including the pBluescript II KS(-) plasmid DNA as a control for genetic transformation. The pOV plasmid was digested with EcoRI for cloning fragments into the pBluescript II KS(-) vector to obtain constructs and to determine the full DNA sequence of pOV. RESULTS The pOV plasmid is 13.5 kb in size; confers sulfonamide, streptomycin and ampicillin resistance to P. multocida PMOV; and can transform E. coli DH5α and G. anatis 12656-12. The pOV plasmid was digested for the preparation of chimeric constructs and used to transform E. coli DH5α, conferring resistance to streptomycin (plasmid pSEP3), ampicillin (pSEP4) and sulfonamide (pSEP5) on the bacteria; however, similar to pBluescript II KS(-), the chimeric plasmids did not transform G. anatis 12656-12. A 1.4 kb fragment of the streptomycin cassette from pSEP3 was amplified by PCR and used to construct pSEP7, which in turn was used to interrupt a chromosomal DNA locus of G. anatis by double homologous recombination, introducing strA-strB into the G. anatis chromosome. CONCLUSION The pOV plasmid is a wide-range, low-copy-number plasmid that is able to replicate in some gamma-proteobacteria. Part of this plasmid was integrated into the G. anatis 12656-12 chromosome. This construct may prove to be a useful tool for genetic studies of G. anatis.
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Affiliation(s)
- Ana Jaqueline López-Ochoa
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Universidad Autónoma de Puebla, 72570 Puebla, Pue, México
| | - Patricia Sánchez-Alonso
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Universidad Autónoma de Puebla, 72570 Puebla, Pue, México
| | - Candelario Vázquez-Cruz
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Universidad Autónoma de Puebla, 72570 Puebla, Pue, México.
| | - Guillermo Horta-Valerdi
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Universidad Autónoma de Puebla, 72570 Puebla, Pue, México
| | - Erasmo Negrete-Abascal
- Carrera de Biología, Facultad de Estudios Superiores de Iztacala UNAM, Tlalnepantla, Edo de México 54090, México
| | - Sergio Vaca-Pacheco
- Carrera de Biología, Facultad de Estudios Superiores de Iztacala UNAM, Tlalnepantla, Edo de México 54090, México
| | - Ricardo Mejía
- Carrera de Biología, Facultad de Estudios Superiores de Iztacala UNAM, Tlalnepantla, Edo de México 54090, México
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