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Phu DH, Wongtawan T, Wintachai P, Nhung NT, Yen NTP, Carrique-Mas J, Turni C, Omaleki L, Blackall PJ, Thomrongsuwannakij T. Molecular characterization of Campylobacter spp. isolates obtained from commercial broilers and native chickens in Southern Thailand using whole genome sequencing. Poult Sci 2024; 103:103485. [PMID: 38335668 PMCID: PMC10869288 DOI: 10.1016/j.psj.2024.103485] [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: 11/05/2023] [Revised: 01/12/2024] [Accepted: 01/17/2024] [Indexed: 02/12/2024] Open
Abstract
Chickens are the primary reservoirs of Campylobacter spp., mainly C. jejuni and C. coli, that cause human bacterial gastrointestinal infections. However, genomic characteristics and antimicrobial resistance of Campylobacter spp. in low- to middle-income countries need more comprehensive exploration. This study aimed to characterize 21 C. jejuni and 5 C. coli isolates from commercial broilers and native chickens using whole genome sequencing and compare them to 28 reference Campylobacter sequences. Among the 26 isolates, 13 sequence types (ST) were identified in C. jejuni and 5 ST in C. coli. The prominent ST was ST 2274 (5 isolates, 19.2%), followed by ST 51, 460, 2409, and 6455 (2 isolates in each ST, 7.7%), while all remaining ST (464, 536, 595, 2083, 6736, 6964, 8096, 10437, 828, 872, 900, 8237, and 13540) had 1 isolate per ST (3.8%). Six types of antimicrobial resistance genes (ant(6)-Ia, aph(3')-III, blaOXA, cat, erm(B), and tet(O)) and one point mutations in the gyrA gene (Threonine-86-Isoleucine) and another in the rpsL gene (Lysine-43-Arginine) were detected. The blaOXA resistance gene was present in all isolates, the gyrA mutations was in 95.2% of C. jejuni and 80.0% of C. coli, and the tet(O) resistance gene in 76.2% of C. jejuni and 80.0% of C. coli. Additionally, 203 virulence-associated genes linked to 16 virulence factors were identified. In terms of phenotypic resistance, the C. jejuni isolates were all resistant to ciprofloxacin, enrofloxacin, and nalidixic acid, with lower levels of resistance to tetracycline (76.2%), tylosin (52.3%), erythromycin (23.8%), azithromycin (22.2%), and gentamicin (11.1%). Most C. coli isolates were resistant to all tested antimicrobials, while 1 C. coli was pan-susceptible except for tylosin. Single-nucleotide polymorphisms concordance varied widely, with differences of up to 13,375 single-nucleotide polymorphisms compared to the reference Campylobacter isolates, highlighting genetic divergence among comparative genomes. This study contributes to a deeper understanding of the molecular epidemiology of Campylobacter spp. in Thai chicken production systems.
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Affiliation(s)
- Doan Hoang Phu
- Akkhraratchakumari Veterinary College, Walailak University, Nakhon Si Thammarat 80160, Thailand; Doctoral Program in Health Sciences, College of Graduate Studies, Walailak University, Nakhon Si Thammarat 80160, Thailand; Faculty of Animal Science and Veterinary Medicine, Nong Lam University, Ho Chi Minh City 70000, Vietnam
| | - Tuempong Wongtawan
- Akkhraratchakumari Veterinary College, Walailak University, Nakhon Si Thammarat 80160, Thailand; Centre for One Health, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | | | - Nguyen Thi Nhung
- Oxford University Clinical Research Unit, Ho Chi Minh City 70000, Vietnam
| | | | - Juan Carrique-Mas
- Food and Agriculture Organization of the United Nations, Ha Noi 10000, Vietnam
| | - Conny Turni
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Lida Omaleki
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Patrick J Blackall
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Thotsapol Thomrongsuwannakij
- Akkhraratchakumari Veterinary College, Walailak University, Nakhon Si Thammarat 80160, Thailand; Centre for One Health, Walailak University, Nakhon Si Thammarat 80160, Thailand.
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Barragán-Mayet KF, García-Espinosa G, Sánchez-González MG, Miranda-Antonio L, Maldonado-Reséndiz RI. Antimicrobial Sensitivity Profile in Psittacine Birds at an Avian Teaching Hospital: A Retrospective Study, 2015-2022. J Avian Med Surg 2024; 38:15-20. [PMID: 38686884 DOI: 10.1647/avianms-d-23-00027] [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] [Indexed: 07/11/2024]
Abstract
Veterinary hospitals house patient populations with diverse infectious statuses, microbiota, and histories of prior antibiotic therapy. Choanal swabs are commonly used for assessing the upper respiratory tract of birds for bacterial disease, with the samples submitted for cytologic testing and/or culture and antimicrobial sensitivity testing. The aim of this retrospective study was to identify and quantify bacteria isolated from choanal swabs collected from psittacine patients at a veterinary teaching hospital in Mexico City, Mexico. Data regarding bacterial isolates from choanal swabs were obtained from the medical records of companion psittacines suspected of upper respiratory bacterial disease that presented between November 2015 and December 2022. A total of 47.8% (175 of 366) of the bacterial isolates were from specimens obtained from red-lored Amazons (Amazona autumnalis). Gram-negative bacteria predominated, with 27 different genera identified. Klebsiella, Staphylococcus, and Escherichia were the most frequently isolated genera. A total of 90.4% (331 of 366) of the isolates were resistant to at least 1 antibiotic tested in the sensitivity panel, and a single Klebsiella isolate was resistant to 13 different antibiotics. Gentamicin had a high percentage of efficacy (79.5%; 182 of 229) against the bacterial isolates, whereas isolates tested against sulfonamide-trimethoprim (46.7%, 98 of 210), streptomycin (43.8%; 88 of 201), and clindamycin (12.9%; 15 of 116) had susceptibilities <50%. This is the first study to report common bacterial isolates and their antimicrobial susceptibility patterns from choanal swab samples collected from companion psittacines suspected of upper respiratory disease in Mexico. Clinicians can use the information presented in this study as a guide for therapeutic decision-making when managing upper respiratory bacterial infections in companion psittacine patients.
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Affiliation(s)
- Kevin Fernando Barragán-Mayet
- Zoological Medicine and Surgery Internship, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Circuit of Scientific Research S/N, Ciudad Universitaria, Coyoacán, Mexico City, CP 04360, Mexico
| | - Gary García-Espinosa
- Avian Medicine and Husbandry Department, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Circuit of Scientific Research S/N, Ciudad Universitaria, Coyoacán, Mexico City, CP 04360, Mexico
| | - María Guadalupe Sánchez-González
- Genetics and Biostatistics Department, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Circuit of Scientific Research S/N, Ciudad Universitaria, Coyoacán, Mexico City, CP 04360, Mexico
| | - Lizbeth Miranda-Antonio
- Avian Medicine and Husbandry Department, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Circuit of Scientific Research S/N, Ciudad Universitaria, Coyoacán, Mexico City, CP 04360, Mexico
| | - Ricardo Itzcóatl Maldonado-Reséndiz
- Ethology, Wildlife, and Laboratory Animal Department, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Circuit of Scientific Research S/N, Ciudad Universitaria, Coyoacán, Mexico City, CP 04360, Mexico,
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3
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Hu K, Meyer F, Deng ZL, Asgari E, Kuo TH, Münch PC, McHardy AC. Assessing computational predictions of antimicrobial resistance phenotypes from microbial genomes. Brief Bioinform 2024; 25:bbae206. [PMID: 38706320 PMCID: PMC11070729 DOI: 10.1093/bib/bbae206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 04/08/2024] [Accepted: 04/11/2024] [Indexed: 05/07/2024] Open
Abstract
The advent of rapid whole-genome sequencing has created new opportunities for computational prediction of antimicrobial resistance (AMR) phenotypes from genomic data. Both rule-based and machine learning (ML) approaches have been explored for this task, but systematic benchmarking is still needed. Here, we evaluated four state-of-the-art ML methods (Kover, PhenotypeSeeker, Seq2Geno2Pheno and Aytan-Aktug), an ML baseline and the rule-based ResFinder by training and testing each of them across 78 species-antibiotic datasets, using a rigorous benchmarking workflow that integrates three evaluation approaches, each paired with three distinct sample splitting methods. Our analysis revealed considerable variation in the performance across techniques and datasets. Whereas ML methods generally excelled for closely related strains, ResFinder excelled for handling divergent genomes. Overall, Kover most frequently ranked top among the ML approaches, followed by PhenotypeSeeker and Seq2Geno2Pheno. AMR phenotypes for antibiotic classes such as macrolides and sulfonamides were predicted with the highest accuracies. The quality of predictions varied substantially across species-antibiotic combinations, particularly for beta-lactams; across species, resistance phenotyping of the beta-lactams compound, aztreonam, amoxicillin/clavulanic acid, cefoxitin, ceftazidime and piperacillin/tazobactam, alongside tetracyclines demonstrated more variable performance than the other benchmarked antibiotics. By organism, Campylobacter jejuni and Enterococcus faecium phenotypes were more robustly predicted than those of Escherichia coli, Staphylococcus aureus, Salmonella enterica, Neisseria gonorrhoeae, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, Streptococcus pneumoniae and Mycobacterium tuberculosis. In addition, our study provides software recommendations for each species-antibiotic combination. It furthermore highlights the need for optimization for robust clinical applications, particularly for strains that diverge substantially from those used for training.
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Affiliation(s)
- Kaixin Hu
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Fernando Meyer
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Zhi-Luo Deng
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Ehsaneddin Asgari
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
- Molecular Cell Biomechanics Laboratory, Department of Bioengineering and Mechanical Engineering, University of California, Berkeley, USA
| | - Tzu-Hao Kuo
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Philipp C Münch
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner site Hannover Braunschweig, Braunschweig, Germany
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Alice C McHardy
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
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4
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Yaikhan T, Chukamnerd A, Singkhamanan K, Nokchan N, Chintakovid N, Chusri S, Pomwised R, Wonglapsuwan M, Surachat K. Genomic Characterization of Mobile Genetic Elements Associated with Multidrug-Resistant Acinetobacter Non- baumannii Species from Southern Thailand. Antibiotics (Basel) 2024; 13:149. [PMID: 38391535 PMCID: PMC10886146 DOI: 10.3390/antibiotics13020149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/23/2024] [Accepted: 01/31/2024] [Indexed: 02/24/2024] Open
Abstract
This study investigated the genetic diversity, antimicrobial resistance profiles, and virulence characteristics of Acinetobacter non-baumannii isolates obtained from four hospitals in southern Thailand. Clinical data, genome information, and average nucleotide identity (ANI) were analyzed for eight isolates, revealing diverse genetic profiles and novel sequence types (STs). Minimum spanning tree analysis indicated potential clonal spread of certain STs across different geographic regions. Antimicrobial resistance genes (ARGs) were detected in all isolates, with a high prevalence of genes conferring resistance to carbapenems, highlighting the challenge of antimicrobial resistance in Acinetobacter spp. infections. Mobile genetic elements (MGEs) carrying ARGs were also identified, emphasizing the role of horizontal gene transfer in spreading resistance. Evaluation of virulence-associated genes revealed a diverse range of virulence factors, including those related to biofilm formation and antibiotic resistance. However, no direct correlation was found between virulence-associated genes in Acinetobacter spp. and specific clinical outcomes, such as infection severity or patient mortality. This complexity suggests that factors beyond gene presence may influence disease progression and outcomes. This study emphasizes the importance of continued surveillance and molecular epidemiological studies to combat the spread of multidrug-resistant (MDR) Acinetobacter non-baumannii strains. The findings provide valuable insights into the epidemiology and genetic characteristics of this bacteria in southern Thailand, with implications for infection control and antimicrobial management efforts.
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Affiliation(s)
- Thunchanok Yaikhan
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Arnon Chukamnerd
- Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Kamonnut Singkhamanan
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Natakorn Nokchan
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Nutwadee Chintakovid
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Sarunyou Chusri
- Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Rattanaruji Pomwised
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand
| | - Monwadee Wonglapsuwan
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand
| | - Komwit Surachat
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
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5
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Yang Z, Lan T, Luo H, Li P, Wang M, Jia R, Chen S, Liu M, Zhao X, Yang Q, Wu Y, Zhang S, Huang J, Ou X, Mao S, Gao Q, Sun D, Tian B, Cheng A, Zhu D. Emergence and mobilization of a novel lincosamide resistance gene lnu(I): From environmental reservoirs to pathogenic bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167400. [PMID: 37769725 DOI: 10.1016/j.scitotenv.2023.167400] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 09/09/2023] [Accepted: 09/25/2023] [Indexed: 10/03/2023]
Abstract
Antimicrobial resistance remains an utmost concern in human and veterinary medicine, impacting humans, animals, and the environment while significantly influencing the principles of One Health. While Riemerella anatipestifer (R. anatipestifer) is recognized as a waterfowl pathogen with multidrug-resistant properties, the specifics of its lincosamide resistance mechanism are inadequately understood. In this study, we identified a novel lincosamide resistance gene, lnu(I), in R. anatipestifer RCAD0121, and investigated its potential origin, transfer mechanisms, and dissemination status through genomic epidemiology. This exhibited 74.80 % amino acid identity with a previously reported gene, lnu(H). PCR analysis revealed lnu(I) prevalence in at least 44 R. anatipestifer isolates collected from multiple provinces in China. Furthermore, genomic mining unveiled 56 lnu(I) sequences within publicly available databases, primarily originating from environmental sources. In addition, members of the family Flavobacteriaceae were the dominant (16/56, 28.57 %) bacteria carrying the lnu(I) gene, with Flavobacterium exhibiting a similar GC content as lnu(I). Notably, specific instances of the lnu(I) gene were linked to mobile genetic elements within human and animal pathogenic bacteria. These findings suggest that Flavobacterium species within the environment could serve as potential ancestral sources of the novel lnu(I) gene, which has undergone mobilization events toward pathogenic bacteria.
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Affiliation(s)
- Zhishuang Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Tianjing Lan
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Hongyan Luo
- College of Veterinary Medicine, Southwest University, Beibei, Chongqing, China
| | - Pei Li
- College of Veterinary Medicine, Southwest University, Beibei, Chongqing, China
| | - Mingshu Wang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Renyong Jia
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Shun Chen
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Mafeng Liu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Xinxin Zhao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Qiao Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Ying Wu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Shaqiu Zhang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Juan Huang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Xumin Ou
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Sai Mao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Qun Gao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Di Sun
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Bin Tian
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Anchun Cheng
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China.
| | - Dekang Zhu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China.
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Wanyan R, Pan M, Mai Z, Xiong X, Wang S, Han Q, Yu Q, Wang G, Wu S, Li H. Fate of high-risk antibiotic resistance genes in large-scale aquaculture sediments: Geographical differentiation and corresponding drivers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167068. [PMID: 37714353 DOI: 10.1016/j.scitotenv.2023.167068] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/22/2023] [Accepted: 09/12/2023] [Indexed: 09/17/2023]
Abstract
Antibiotic resistance genes (ARGs), emerging environmental contaminants, have become challenges of public health security. However, the distribution and drivers of ARGs, especially high-risk ARGs, in large-scale aquaculture sediments remain unknown. Here, we collected sediment samples from 40 crayfish ponds in seven main crayfish culture provinces in China and then investigated the distribution and risk of ARGs based on high-throughput sequencing and quantitative PCR techniques. Our results suggested that aquaculture sediment was potential reservoir of ARGs and the abundance of aadA-02 was the highest. High-risk ARG (floR) was also prevalent in the sediment and was the most abundant in Jiangsu Province, where opportunistic pathogens were also enriched. The abundance of floR was positively correlated with different environmental factors, such as total phosphorus in water and total carbon in sediment. In addition, Mycobacterium sp., opportunistic pathogenic bacteria, might be potential host for floR. Furthermore, the potential propagation pathway of ARGs was from sediment to crayfish gut, and Bacteroidetes and Proteobacteria might be the main bacterial groups responsible for the proliferation of ARGs. Generally, our results illustrate that pond sediment may be an ARG reservoir of aquatic animals. Meanwhile, our study helps develop valuable strategies for accessing risks and managing ARGs.
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Affiliation(s)
- Ruijun Wanyan
- School of Public Health, Lanzhou University, Lanzhou 730000, China; Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Meijing Pan
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhan Mai
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiong Xiong
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sijie Wang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Qian Han
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Qiaoling Yu
- State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Gansu 730000, China
| | - Guitang Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shangong Wu
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Gansu 730000, China.
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7
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Hyun JC, Monk JM, Szubin R, Hefner Y, Palsson BO. Global pathogenomic analysis identifies known and candidate genetic antimicrobial resistance determinants in twelve species. Nat Commun 2023; 14:7690. [PMID: 38001096 PMCID: PMC10673929 DOI: 10.1038/s41467-023-43549-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Surveillance programs for managing antimicrobial resistance (AMR) have yielded thousands of genomes suited for data-driven mechanism discovery. We present a workflow integrating pangenomics, gene annotation, and machine learning to identify AMR genes at scale. When applied to 12 species, 27,155 genomes, and 69 drugs, we 1) find AMR gene transfer mostly confined within related species, with 925 genes in multiple species but just eight in multiple phylogenetic classes, 2) demonstrate that discovery-oriented support vector machines outperform contemporary methods at recovering known AMR genes, recovering 263 genes compared to 145 by Pyseer, and 3) identify 142 AMR gene candidates. Validation of two candidates in E. coli BW25113 reveals cases of conditional resistance: ΔcycA confers ciprofloxacin resistance in minimal media with D-serine, and frdD V111D confers ampicillin resistance in the presence of ampC by modifying the overlapping promoter. We expect this approach to be adaptable to other species and phenotypes.
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Affiliation(s)
- Jason C Hyun
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Jonathan M Monk
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Richard Szubin
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Ying Hefner
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Bernhard O Palsson
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kongens, Lyngby, Denmark.
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8
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English J, Newberry F, Hoyles L, Patrick S, Stewart L. Genomic analyses of Bacteroides fragilis: subdivisions I and II represent distinct species. J Med Microbiol 2023; 72. [PMID: 37910167 DOI: 10.1099/jmm.0.001768] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
Introduction. Bacteroides fragilis is a Gram-negative anaerobe that is a member of the human gastrointestinal microbiota and is frequently found as an extra-intestinal opportunistic pathogen. B. fragilis comprises two distinct groups - divisions I and II - characterized by the presence/absence of genes [cepA and ccrA (cfiA), respectively] that confer resistance to β-lactam antibiotics by either serine or metallo-β-lactamase production. No large-scale analyses of publicly available B. fragilis sequence data have been undertaken, and the resistome of the species remains poorly defined.Hypothesis/Gap Statement. Reclassification of divisions I and II B. fragilis as two distinct species has been proposed but additional evidence is required.Aims. To investigate the genomic diversity of GenBank B. fragilis genomes and establish the prevalence of division I and II strains among publicly available B. fragilis genomes, and to generate further evidence to demonstrate that B. fragilis division I and II strains represent distinct genomospecies.Methodology. High-quality (n=377) genomes listed as B. fragilis in GenBank were included in pangenome and functional analyses. Genome data were also subject to resistome profiling using The Comprehensive Antibiotic Resistance Database.Results. Average nucleotide identity and phylogenetic analyses showed B. fragilis divisions I and II represent distinct species: B. fragilis sensu stricto (n=275 genomes) and B. fragilis A (n=102 genomes; Genome Taxonomy Database designation), respectively. Exploration of the pangenome of B. fragilis sensu stricto and B. fragilis A revealed separation of the two species at the core and accessory gene levels.Conclusion. The findings indicate that B. fragilis A, previously referred to as division II B. fragilis, is an individual species and distinct from B. fragilis sensu stricto. The B. fragilis pangenome analysis supported previous genomic, phylogenetic and resistome screening analyses collectively reinforcing that divisions I and II are two separate species. In addition, it was confirmed that differences in the accessory genes of B. fragilis divisions I and II are primarily associated with carbohydrate metabolism and suggest that differences other than antimicrobial resistance could also be used to distinguish between these two species.
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Affiliation(s)
- Jamie English
- Institute for Global Food Security, School of Biological Sciences, Queen's University, Belfast, UK
| | - Fiona Newberry
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Lesley Hoyles
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Sheila Patrick
- Institute for Global Food Security, School of Biological Sciences, Queen's University, Belfast, UK
- Wellcome Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | - Linda Stewart
- Institute for Global Food Security, School of Biological Sciences, Queen's University, Belfast, UK
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9
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Resci I, Cilia G. The use of honey bee (Apis mellifera L.) as biological monitors for pathogenic bacteria and antimicrobial resistance: A systematic review. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 333:122120. [PMID: 37385360 DOI: 10.1016/j.envpol.2023.122120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 06/06/2023] [Accepted: 06/26/2023] [Indexed: 07/01/2023]
Abstract
The phenomenon of antimicrobial resistance (AMR) is an increasingly real and relevant health problem. It is essential to verify the spread of this phenomenon in the environment. The European honey bee, Apis mellifera L., is a globally managed pollinator continuously used for biomonitoring thanks to its morphological and behavioural characteristics. During their foraging activities, a large number of honey bees move in the area surrounding the hive within a 1.5 km of radius. Besides, their body covered with hair and bristles are able to intercept pollen and minute particles, such as atmospheric particles, contaminants and microorganisms. For these reasons, A. mellifera L. is widely used as an environmental sentinel, especially for detecting pollutants, pesticides, microorganisms, and AMR. This systematic review aimed to collect and summarize the role of honey bee colonies as a biological monitor of AMR pathogenic bacteria and the environmental spread of antimicrobial resistance genes (ARGs). From honey bees were isolated a wide range of pathogenic and environmental bacteria strains, harbouring AMR and ARGs. However, AMR and ARGs were detected not only in environmental bacteria but also in symbiotic bacteria colonizing the bee gut. This systematic review highlights the employment of potential use of honey bees as AMR sentinel helpful for ecosystem health to implement possible control measures for humans, animals and plants, in the context of the "One-Health" approach.
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Affiliation(s)
- Ilaria Resci
- Research Centre for Agriculture and Environment (CREA-AA), Council for Agricultural Research and Agricultural Economics Analysis, Via di Corticella 133, 40128, Bologna, Italy
| | - Giovanni Cilia
- Research Centre for Agriculture and Environment (CREA-AA), Council for Agricultural Research and Agricultural Economics Analysis, Via di Corticella 133, 40128, Bologna, Italy.
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10
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Hu S, Fu Y, Xue M, Lan Y, Xi W, Xu Z, Han W, Wu D, Cheng C. Simultaneous removal of antibiotic-resistant Escherichia coli and its resistance genes by dielectric barrier discharge plasma. ENVIRONMENTAL RESEARCH 2023; 231:116163. [PMID: 37217128 DOI: 10.1016/j.envres.2023.116163] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/04/2023] [Accepted: 05/14/2023] [Indexed: 05/24/2023]
Abstract
As emerging contaminants, antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) have been widely detected in various aqueous environments. For antibiotic resistance to be inhibited in the environment, it is essential to control ARB and ARGs. In this study, dielectric barrier discharge (DBD) plasma was used to inactivate antibiotic resistant Escherichia coli (AR E. coli) and remove ARGs simultaneously. Within 15 s of plasma treatment, 108 CFU/mL of AR E. coli were inactivated by 97.9%. The rupture of the bacterial cell membrane and the increase of intracellular ROS are the main reasons for the rapid inactivation of bacteria. Intracellular ARGs (i-qnrB, i-blaCTX-M, i-sul2) and integron gene (i-int1) decreased by 2.01, 1.84, 2.40, and 2.73 log after 15 min of plasma treatment, respectively. In the first 5 min of discharge, extracellular ARGs (e-qnrB, e-blaCTX-M, e-sul2) and integron gene (e-int1) decreased by 1.99, 2.22, 2.66, and 2.80 log, respectively. The results of the ESR and quenching experiments demonstrated that ·OH and 1O2 played important roles in the removal of ARGs. This study shows that DBD plasma is an effective technique to control ARB and ARGs in waters.
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Affiliation(s)
- Shuheng Hu
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui Province 230009, PR China
| | - Yuhang Fu
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui Province 230009, PR China; Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031, China
| | - Muen Xue
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui Province 230009, PR China; Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031, China
| | - Yan Lan
- Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031, China; Institute of Energy, Hefei Comprehensive National Science Center, Hefei 230031, People's Republic of China
| | - Wenhao Xi
- Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031, China
| | - Zimu Xu
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui Province 230009, PR China.
| | - Wei Han
- Institute of Health and Medical Technology/Anhui Province Key Laboratory of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, People's Republic of China
| | - Danzhou Wu
- Anhui Engineering Consulting Institute, Hefei 230001, People's Republic of China
| | - Cheng Cheng
- Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031, China; Institute of Energy, Hefei Comprehensive National Science Center, Hefei 230031, People's Republic of China.
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11
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Michaux C, Gerovac M, Hansen EE, Barquist L, Vogel J. Grad-seq analysis of Enterococcus faecalis and Enterococcus faecium provides a global view of RNA and protein complexes in these two opportunistic pathogens. MICROLIFE 2022; 4:uqac027. [PMID: 37223738 PMCID: PMC10117718 DOI: 10.1093/femsml/uqac027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 12/24/2022] [Indexed: 05/25/2023]
Abstract
Enterococcus faecalis and Enterococcus faecium are major nosocomial pathogens. Despite their relevance to public health and their role in the development of bacterial antibiotic resistance, relatively little is known about gene regulation in these species. RNA-protein complexes serve crucial functions in all cellular processes associated with gene expression, including post-transcriptional control mediated by small regulatory RNAs (sRNAs). Here, we present a new resource for the study of enterococcal RNA biology, employing the Grad-seq technique to comprehensively predict complexes formed by RNA and proteins in E. faecalis V583 and E. faecium AUS0004. Analysis of the generated global RNA and protein sedimentation profiles led to the identification of RNA-protein complexes and putative novel sRNAs. Validating our data sets, we observe well-established cellular RNA-protein complexes such as the 6S RNA-RNA polymerase complex, suggesting that 6S RNA-mediated global control of transcription is conserved in enterococci. Focusing on the largely uncharacterized RNA-binding protein KhpB, we use the RIP-seq technique to predict that KhpB interacts with sRNAs, tRNAs, and untranslated regions of mRNAs, and might be involved in the processing of specific tRNAs. Collectively, these datasets provide departure points for in-depth studies of the cellular interactome of enterococci that should facilitate functional discovery in these and related Gram-positive species. Our data are available to the community through a user-friendly Grad-seq browser that allows interactive searches of the sedimentation profiles (https://resources.helmholtz-hiri.de/gradseqef/).
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Affiliation(s)
- Charlotte Michaux
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Straße, 97080, Würzburg, Germany
| | - Milan Gerovac
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Straße, 97080, Würzburg, Germany
| | - Elisabeth E Hansen
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Straße, 97080, Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Josef-Schneider-Straße, 97080, Würzburg, Germany
- Faculty of Medicine, University of Würzburg, Josef-Schneider-Straße, 97080, Würzburg, Germany
| | - Jörg Vogel
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Straße, 97080, Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Josef-Schneider-Straße, 97080, Würzburg, Germany
- Faculty of Medicine, University of Würzburg, Josef-Schneider-Straße, 97080, Würzburg, Germany
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12
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Munk P, Brinch C, Møller FD, Petersen TN, Hendriksen RS, Seyfarth AM, Kjeldgaard JS, Svendsen CA, van Bunnik B, Berglund F, Larsson DGJ, Koopmans M, Woolhouse M, Aarestrup FM. Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance. Nat Commun 2022; 13:7251. [PMID: 36456547 PMCID: PMC9715550 DOI: 10.1038/s41467-022-34312-7] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/20/2022] [Indexed: 12/03/2022] Open
Abstract
Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, evolution, and transmission of individual antibiotic resistance genes (ARGs) is essential to develop sustainable strategies combatting this threat. Here, we use metagenomic sequencing to analyse ARGs in 757 sewage samples from 243 cities in 101 countries, collected from 2016 to 2019. We find regional patterns in resistomes, and these differ between subsets corresponding to drug classes and are partly driven by taxonomic variation. The genetic environments of 49 common ARGs are highly diverse, with most common ARGs carried by multiple distinct genomic contexts globally and sometimes on plasmids. Analysis of flanking sequence revealed ARG-specific patterns of dispersal limitation and global transmission. Our data furthermore suggest certain geographies are more prone to transmission events and should receive additional attention.
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Affiliation(s)
- Patrick Munk
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark.
| | - Christian Brinch
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Frederik Duus Møller
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Thomas N Petersen
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Rene S Hendriksen
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Anne Mette Seyfarth
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Jette S Kjeldgaard
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Christina Aaby Svendsen
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Bram van Bunnik
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK
| | - Fanny Berglund
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - D G Joakim Larsson
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Marion Koopmans
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Mark Woolhouse
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK
| | - Frank M Aarestrup
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
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13
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Huang FY, Zhou SYD, Zhao Y, Zhou XY, Li H, Zhang X, Su JQ. Dissemination of antibiotic resistance genes from landfill leachate to groundwater. JOURNAL OF HAZARDOUS MATERIALS 2022; 440:129763. [PMID: 35985216 DOI: 10.1016/j.jhazmat.2022.129763] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/27/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
Landfill leachate, a highly concentrated organic wastewater containing diverse microorganisms and various heavy metals, has become an important reservoir of antibiotic resistance genes (ARGs). In this study, a total of 203 unique ARGs and 10 mobile genetic elements (MGEs) were identified from collected landfill leachate and groundwater. The number and abundance (normalized and absolute) of antibiotic resistome in effluent of leachate treatment plants decreased significantly compared to influent. The abundance of ARGs in groundwater increased as the distance from the leachate basin decreased. Fast expectation-maximization microbial source tracking (FEAST) showed that up to 96 % of ARGs in groundwater (GW3) may originate from nearby leachate, suggesting that ARGs in leachate can penetrate and spread into the groundwater environment. A significant correlation between ARGs and bacterial communities was identified. Together with network analysis showing the 12 bacterial taxa co-occurring with seven classes of antibiotic-associated ARGs, our results revealed the diverse potential microbial hosts of ARGs in water samples around the landfill sites. Heavy metals, bacterial community and MGEs were the driving factors shaping the ARGs patterns in the water samples, with their interactions explaining 57 % of ARGs variations. Our results provide an understanding of the distribution and dissemination of ARGs from landfill leachate to the nearby groundwater and suggest a comprehensive impact assessment of ARGs in aquatic environments of landfills.
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Affiliation(s)
- Fu-Yi Huang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, No. 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Shu-Yi-Dan Zhou
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, No. 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China
| | - Yi Zhao
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China
| | - Xin-Yuan Zhou
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, No. 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Hu Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, No. 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Xian Zhang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, No. 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, No. 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
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14
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Hiller CX, Schwaller C, Wurzbacher C, Drewes JE. Removal of antibiotic microbial resistance by micro- and ultrafiltration of secondary wastewater effluents at pilot scale. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156052. [PMID: 35598662 DOI: 10.1016/j.scitotenv.2022.156052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/04/2022] [Accepted: 05/15/2022] [Indexed: 05/09/2023]
Abstract
Low-pressure membrane filtration was investigated at pilot scale with regard to its removal of antimicrobial resistance genes (ARGs) in conventional secondary treated wastewater plant effluents. While operating microfiltration (MF) and ultrafiltration (UF) membranes, key operational parameters for antimicrobial resistance (AMR) studies and key factors influencing AMR removal efficiencies of low-pressure membrane filtration processes were examined. The main factor for AMR removal was the pore size of the membrane. The formation of the fouling layer on capillary membranes had only a small additive effect on intra- and extrachromosomal ARG removal and a significant additive effect on mobile ARG removal. Using feeds with different ARGs abundances revealed that higher ARG abundance in the feed resulted in higher ARG abundance in the filtrate. Live-Dead cell counting in UF filtrate showed intact bacteria breaking through the UF membrane. Strong correlations between 16S rRNA genes (as surrogate for bacteria quantification) and the sul1 gene in UF filtrate indicated ARBs likely breaking through UF membranes.
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Affiliation(s)
- Christian X Hiller
- Chair of Urban Water Systems Engineering, Technical University of Munich, Germany
| | - Christoph Schwaller
- Chair of Urban Water Systems Engineering, Technical University of Munich, Germany
| | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering, Technical University of Munich, Germany
| | - Jörg E Drewes
- Chair of Urban Water Systems Engineering, Technical University of Munich, Germany.
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15
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Sanderson H, Gray KL, Manuele A, Maguire F, Khan A, Liu C, Navanekere Rudrappa C, Nash JHE, Robertson J, Bessonov K, Oloni M, Alcock BP, Raphenya AR, McAllister TA, Peacock SJ, Raven KE, Gouliouris T, McArthur AG, Brinkman FSL, Fink RC, Zaheer R, Beiko RG. Exploring the mobilome and resistome of Enterococcus faecium in a One Health context across two continents. Microb Genom 2022; 8. [PMID: 36129737 DOI: 10.1099/mgen.0.000880] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Enterococcus faecium is a ubiquitous opportunistic pathogen that is exhibiting increasing levels of antimicrobial resistance (AMR). Many of the genes that confer resistance and pathogenic functions are localized on mobile genetic elements (MGEs), which facilitate their transfer between lineages. Here, features including resistance determinants, virulence factors and MGEs were profiled in a set of 1273 E. faecium genomes from two disparate geographic locations (in the UK and Canada) from a range of agricultural, clinical and associated habitats. Neither lineages of E. faecium, type A and B, nor MGEs are constrained by geographic proximity, but our results show evidence of a strong association of many profiled genes and MGEs with habitat. Many features were associated with a group of clinical and municipal wastewater genomes that are likely forming a new human-associated ecotype within type A. The evolutionary dynamics of E. faecium make it a highly versatile emerging pathogen, and its ability to acquire, transmit and lose features presents a high risk for the emergence of new pathogenic variants and novel resistance combinations. This study provides a workflow for MGE-centric surveillance of AMR in Enterococcus that can be adapted to other pathogens.
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Affiliation(s)
- Haley Sanderson
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Canada
| | - Kristen L Gray
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Colombia, Canada
| | - Alexander Manuele
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada.,Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Finlay Maguire
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada.,Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada.,Department of Community Health & Epidemiology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Amjad Khan
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada.,Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Chaoyue Liu
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada.,Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada.,Department of Mathematics & Statistics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Chandana Navanekere Rudrappa
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada.,Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - John H E Nash
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph and Toronto, Ontario, Canada
| | - James Robertson
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph and Toronto, Ontario, Canada
| | - Kyrylo Bessonov
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph and Toronto, Ontario, Canada
| | - Martins Oloni
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.,David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
| | - Brian P Alcock
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.,David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
| | - Amogelang R Raphenya
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.,David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | | | - Kathy E Raven
- Department of Medicine, Cambridge University, Cambridge, UK
| | | | - Andrew G McArthur
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.,David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
| | - Fiona S L Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Colombia, Canada
| | - Ryan C Fink
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada.,Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Rahat Zaheer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Robert G Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada.,Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
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16
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Cho S, McMillan EA, Barrett JB, Hiott LM, Woodley TA, House SL, Frye JG, Jackson CR. Distribution and Transfer of Plasmid Replicon Families among Multidrug-Resistant Enterococcus faecalis and Enterococcus faecium from Poultry. Microorganisms 2022; 10:microorganisms10061244. [PMID: 35744761 PMCID: PMC9228330 DOI: 10.3390/microorganisms10061244] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 11/25/2022] Open
Abstract
The presence and transfer of plasmids from commensal bacteria to more pathogenic bacteria may contribute to the dissemination of antimicrobial resistance. However, the prevalence of plasmids from commensal bacteria, such as the enterococci, in food animals remains largely unknown. In this study, the diversity and prevalence of plasmid families from multidrug-resistant (MDR; resistance to three or more antimicrobials) enterococci from poultry carcasses were determined. Plasmid-positive MDR enterococci were also tested for the ability to transfer plasmids to other enterococci using conjugation. MDR Enterococcus faecalis (n = 98) and Enterococcus faecium (n = 696) that were isolated from poultry carcass rinsates between 2004 and 2011 were tested for the presence of 21 plasmid replicon (rep) families using multiplex PCR. Approximately 48% of E. faecalis (47/98) and 16% of E. faecium (110/696) were positive for at least one rep-family. Fourteen rep-families were detected overall, and ten rep-families were shared between E. faecalis and E. faecium. The rep7 and rep17 families were unique to E. faecalis, while the rep5 and rep8 families were unique to E. faecium. The rep9 family was predominant in both E. faecalis and E. faecium for all the years tested. The greatest number of rep-families detected was in 2005 (n = 10), and the least was in 2009 (n = 1). Eight rep-families were transferred from E. faecalis donors to the E. faecalis JH2-2 recipient using conjugation. Results from this study showed that E. faecalis and E. faecium from poultry carcasses contain numerous and diverse rep-families that are capable of conjugal transfer.
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Affiliation(s)
- Sohyun Cho
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, USDA-ARS, U.S. National Poultry Research Center, Athens, GA 30605, USA; (S.C.); (E.A.M.); (J.B.B.); (L.M.H.); (T.A.W.); (S.L.H.); (J.G.F.)
- Oak Ridge Institute for Science and Education, Oak Ridge, TN 37830, USA
| | - Elizabeth A. McMillan
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, USDA-ARS, U.S. National Poultry Research Center, Athens, GA 30605, USA; (S.C.); (E.A.M.); (J.B.B.); (L.M.H.); (T.A.W.); (S.L.H.); (J.G.F.)
| | - John B. Barrett
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, USDA-ARS, U.S. National Poultry Research Center, Athens, GA 30605, USA; (S.C.); (E.A.M.); (J.B.B.); (L.M.H.); (T.A.W.); (S.L.H.); (J.G.F.)
| | - Lari M. Hiott
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, USDA-ARS, U.S. National Poultry Research Center, Athens, GA 30605, USA; (S.C.); (E.A.M.); (J.B.B.); (L.M.H.); (T.A.W.); (S.L.H.); (J.G.F.)
| | - Tiffanie A. Woodley
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, USDA-ARS, U.S. National Poultry Research Center, Athens, GA 30605, USA; (S.C.); (E.A.M.); (J.B.B.); (L.M.H.); (T.A.W.); (S.L.H.); (J.G.F.)
| | - Sandra L. House
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, USDA-ARS, U.S. National Poultry Research Center, Athens, GA 30605, USA; (S.C.); (E.A.M.); (J.B.B.); (L.M.H.); (T.A.W.); (S.L.H.); (J.G.F.)
| | - Jonathan G. Frye
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, USDA-ARS, U.S. National Poultry Research Center, Athens, GA 30605, USA; (S.C.); (E.A.M.); (J.B.B.); (L.M.H.); (T.A.W.); (S.L.H.); (J.G.F.)
| | - Charlene R. Jackson
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, USDA-ARS, U.S. National Poultry Research Center, Athens, GA 30605, USA; (S.C.); (E.A.M.); (J.B.B.); (L.M.H.); (T.A.W.); (S.L.H.); (J.G.F.)
- Correspondence: ; Tel.: +1-(706)-546-3604; Fax: +1-(706)-546-3616
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ULUDAĞ AA, ARSLAN AYDOĞDU EÖ, KİMİRAN A. The Determination of Presence of Listeria monocytogenes in Ground Meat Sold in Istanbul. GAZI UNIVERSITY JOURNAL OF SCIENCE 2022. [DOI: 10.35378/gujs.972909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Among the 21 different species of the Listeria genus, Listeria monocytogenes is the most common and listeriosis agent in humans. The mortality rate of L. monocytogenes infection is higher than the other common foodborne pathogens such as Salmonella Enteritidis, Campylobacter and Vibrio species. In the current study, it is aimed to determine the presence of L. monocytogenes bacteria in minced meat samples sold in Istanbul province by using the culture method of the USDA-FSIS. In this study, 100 minced meat samples purchased from different butchers in 11 districts of Istanbul between December 2018 and November 2019 were examined for the presence of L. monocytogenes. The bacteria identified also molecularly verified according to the presence of iap and hlyA gene regions by the polymerase chain reaction (PCR) method. When antibiotic susceptibility tests of 21 strains, identified as L. monocytogenes through biochemical tests, it was found to be resistant to Amoxicillin/Clavulanic acid (14.28%), penicillin (9.52%), cefaclor (9.52%), vancomycin (9.52%), ciprofloxacin (9.52%) and trimethoprim-sulfamethoxazole (9.52%) and susceptible to ampicillin (100%) and tetracycline (100%). In terms of iap and hlyA gene regions, only 16 of 21 isolates, identified as L. monocytogenes as a result of biochemical tests, were found to be L. monocytogenes. In our study with minced meat offered for sale in Istanbul, although, the L. monocytogenes isolation rate (17%) and the incidence of antibiotic resistance of the isolated L. monocytogenes bacteria are low, it was concluded that minced meat may pose a public health risk.
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Affiliation(s)
| | - Elif Özlem ARSLAN AYDOĞDU
- ISTANBUL UNIVERSITY, FACULTY OF SCIENCE, DEPARTMENT OF BIOLOGY, DEPARTMENT OF FUNDAMENTAL AND INDUSTRIAL MICROBIOLOGY
| | - Ayten KİMİRAN
- ISTANBUL UNIVERSITY, FACULTY OF SCIENCE, DEPARTMENT OF BIOLOGY, DEPARTMENT OF FUNDAMENTAL AND INDUSTRIAL MICROBIOLOGY
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18
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Otunba AA, Osuntoki AA, Olukoya DK, Babalola BA. Genomic, biochemical and microbial evaluation of probiotic potentials of bacterial isolates from fermented sorghum products. Heliyon 2021; 7:e08536. [PMID: 34926862 PMCID: PMC8646963 DOI: 10.1016/j.heliyon.2021.e08536] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/11/2021] [Accepted: 11/29/2021] [Indexed: 12/24/2022] Open
Abstract
Fermented products, including Ogi-baba and Pito, provide several health benefits, particularly when probiotics are used in the fermentation process. Probiotic microorganisms exert strain-specific health-promoting activities on humans and animals. The objective of this study was to investigate the probiotic potentials of Lactic-acid bacteria (LAB) isolates from indigenous fermented sorghum products (Ogi-baba and Pito). The LAB isolates were screened for potential probiotic properties by antagonistic activity against eight enteropathogenic clinical bacteria isolates (Escherichia coli, Klebsiella sp., Helicobacter pylori, Bacillus sp., Staphylococcus sp., Salmonella sp., Pseudomonas sp. and Listeria monocytogenes) as indicator organisms using the agar well diffusion technique. The organisms were also screened for acidity, bile tolerance, antibiotic susceptibility, production of lactic acid, diacetyl and hydrogen peroxide. β-galactosidase assay was also done. Genomic DNA was extracted from the two selected LAB isolates; the 16S rRNA were amplified and sequenced. The sequence data were subjected to Basic Local Alignment Search Tool (BLAST) and molecular phylogenetic analyses to identify the isolates. The isolates were identified as strains of Lactobacillus plantarum and Pediococcus pentosaceus. The sequence data for these two isolates were submitted to the Genbank with accession numbers KP883298 and KP883297 respectively. The P. pentosaceus strain (PB2) strain exhibited β-galactosidase activity as well as L. plantrum strain (OB6). The study revealed exceptional probiotic potentials of two LAB namely Lactobacillus plantarum strain (OB6) and Pediococcus pentosaceus strain (PB2) isolated from fermented sorghum products, Ogi-baba and Pito respectively. Hence, the two LAB strains may be potentially used as probiotic to prevent some enteropathogen-induced gastrointestinal disorders; reduce the incidence of respiratory tract infections and for the management of lactose in intolerance.
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Affiliation(s)
| | | | | | - Benjamin Ayodipupo Babalola
- Department of Biological Sciences, College of Basic and Applied Sciences, Mountain Top University, Ogun, Nigeria
- Corresponding author.
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19
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Abstract
Biological rapid sand filtration is a commonly employed method for the removal of organic and inorganic impurities in water which relies on the degradative properties of microorganisms for the removal of diverse contaminants, but their bioremediation capabilities vary greatly across waterworks. Bioaugmentation efforts with degradation-proficient bacteria have proven difficult due to the inability of the exogenous microbes to stably colonize the sand filters. Plasmids are extrachromosomal DNA elements that can often transfer between bacteria and facilitate the flow of genetic information across microbiomes, yet their ability to spread within rapid sand filters has remained unknown. Here, we examine the permissiveness of rapid sand filter communities toward four environmentally transmissible plasmids, RP4, RSF1010, pKJK5, and TOL (pWWO), using a dual-fluorescence bioreporter platform combined with fluorescence-activated cell sorting (FACS) and 16S rRNA gene amplicon sequencing. Our results reveal that plasmids can transfer at high frequencies and across distantly related taxa from rapid sand filter communities, emphasizing their potential suitability for introducing bioremediation determinants in the microbiomes of underperforming water purification plants.
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20
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Yu Y, Liang Z, Liao W, Ye Z, Li G, An T. Contributions of meat waste decomposition to the abundance and diversity of pathogens and antibiotic-resistance genes in the atmosphere. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 784:147128. [PMID: 34088047 DOI: 10.1016/j.scitotenv.2021.147128] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/07/2021] [Accepted: 04/09/2021] [Indexed: 06/12/2023]
Abstract
Airborne transmission of antibiotic-resistance genes (ARGs) in landfill and acquisition of antibiotic resistance by pathogenic bacteria are posing potential threat to human and environmental health. However, little is known about contribution of waste decomposition to airborne ARGs and pathogens during landfilling of household waste. Herein, the dynamic changes of microbial communities and ARGs were comparatively investigated in leachate and bioaerosol during the decomposition of chicken, fish, and pork wastes. Results found that chicken and pork decomposition could result in emitting high abundance of bioaerosol and pathogen, while fish fermentation will lead to high airborne microbial activity. The main pathogens were Bacilli, Burkholderia-Paraburkholderia and Mycobacterium in bioaerosols, but were Wohlfahrtiimonas, Peptoniphilus and Fusobacterium in leachate, suggesting that the ability of aerosolization of bacteria in leachate was independent of their abundance and diversity. Whereas, diversity and relative abundance of ARGs in leachate were significantly higher than bioaerosol. Moreover, the relative abundance of ARGs in leachate and bioaerosols was not completely relevant. The changes of pathogenic community contributed significantly to the prevalence of ARGs in bioaerosol and leachate. The results will define the contribution of household waste decomposition to airborne pathogen and ARG distribution and provide foundation for airborne bacterial exposure risk and control in landfill.
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Affiliation(s)
- Yun Yu
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Institute of Environmental Health and Pollution control, Guangdong University of Technology, Guangzhou 510006, China
| | - Zhishu Liang
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Institute of Environmental Health and Pollution control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green development, Department of Education, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Wen Liao
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Institute of Environmental Health and Pollution control, Guangdong University of Technology, Guangzhou 510006, China
| | - Zikai Ye
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Institute of Environmental Health and Pollution control, Guangdong University of Technology, Guangzhou 510006, China
| | - Guiying Li
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Institute of Environmental Health and Pollution control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green development, Department of Education, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Taicheng An
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Institute of Environmental Health and Pollution control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green development, Department of Education, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China.
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21
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Kaze M, Brooks L, Sistrom M. Antimicrobial resistance in Bacillus-based biopesticide products. MICROBIOLOGY-SGM 2021; 167. [PMID: 34351257 DOI: 10.1099/mic.0.001074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The crisis of antimicrobial resistant bacterial infections is one of the most pressing public health issues. Common agricultural practices have been implicated in the generation of antimicrobial resistant bacteria. Biopesticides, live bacteria used for pest control, are non-pathogenic and considered safe for consumption. Application of bacteria-based pesticides to crops in high concentrations raises the possibility of unintentional contributions to the movement and generation of antimicrobial resistance genes in the environment. However, the presence of clinically relevant antimicrobial resistance genes and their resistance phenotypes are currently unknown. Here we use a combination of multiple bioinformatic and microbiological techniques to define resistomes of widely used biopesticides and determine how the presence of suspected antimicrobial resistance genes translates to observable resistance phenotypes in several biopesticide products. Our results demonstrate that biopesticide products are reservoirs of clinically relevant antimicrobial resistance genes and bear resistance to multiple drug classes.
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Affiliation(s)
- Mo Kaze
- Department of Quantitative and Systems Biology, School of Natural Sciences, University of California Merced, Merced, USA
| | - Lauren Brooks
- Department of Biology, Utah Valley University, Orem, USA
| | - Mark Sistrom
- Department of Quantitative and Systems Biology, School of Natural Sciences, University of California Merced, Merced, USA
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22
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Ubiquitousness of Haloferax and Carotenoid Producing Genes in Arabian Sea Coastal Biosystems of India. Mar Drugs 2021; 19:md19080442. [PMID: 34436281 PMCID: PMC8400781 DOI: 10.3390/md19080442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/26/2021] [Accepted: 07/28/2021] [Indexed: 12/14/2022] Open
Abstract
This study presents a comparative analysis of halophiles from the global open sea and coastal biosystems through shotgun metagenomes (n = 209) retrieved from public repositories. The open sea was significantly enriched with Prochlorococcus and Candidatus pelagibacter. Meanwhile, coastal biosystems were dominated by Marinobacter and Alcanivorax. Halophilic archaea Haloarcula and Haloquandratum, predominant in the coastal biosystem, were significantly (p < 0.05) enriched in coastal biosystems compared to the open sea. Analysis of whole genomes (n = 23,540), retrieved from EzBioCloud, detected crtI in 64.66% of genomes, while cruF was observed in 1.69% Bacteria and 40.75% Archaea. We further confirmed the viability and carotenoid pigment production by pure culture isolation (n = 1351) of extreme halophiles from sediments (n = 410 × 3) sampling at the Arabian coastline of India. All red-pigmented isolates were represented exclusively by Haloferax, resistant to saturated NaCl (6 M), and had >60% G + C content. Multidrug resistance to tetracycline, gentamicin, ampicillin, and chloramphenicol were also observed. Our study showed that coastal biosystems could be more suited for bioprospection of halophiles rather than the open sea.
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23
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Montivipera bornmuelleri Venom: Inhibitory Effect on Staphylococcus epidermidis and Escherichia coli F1F0-ATPases and Cytotoxicity on HCT116 Cancer Cell Lines. SCI 2021. [DOI: 10.3390/sci3030031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In this work, we pursued the biological characterization of the venom of Montivipera bornmuelleri, a viper from the Lebanese mountains. In relation to its antibacterial potential, the inhibitory effect of this venom on the F1F0-ATPase enzymes of Gram-positive Staphylocoocus epidermidis and Gram-negative Escherichia coli bacteria was examined. In order to determine the degree of cytotoxicity of the venom on the HCT116 human colon cancer cell lines, the biological MTT proliferation and cell viability test were implemented. After validation of the enzymatic F1F0-ATPase model by the spectrophotometric method, using quercetin as the reference ligand, results revealed that M. bornmuelleri venom is able to inhibit the activity of the enzyme of these two bacteria with a concentration of the order of 100–150 µg/mL. In addition, a venom concentration of 10 µg/mL was sufficient to kill the totality of HCT116 cell lines cultivated in vitro. These data show that M. bornmuelleri venom is a mixture of diverse molecules presenting activities of interest, and is a potential source to explore in order to discover new drug candidates.
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24
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Mukherjee M, Laird E, Gentry TJ, Brooks JP, Karthikeyan R. Increased Antimicrobial and Multidrug Resistance Downstream of Wastewater Treatment Plants in an Urban Watershed. Front Microbiol 2021; 12:657353. [PMID: 34108949 PMCID: PMC8181147 DOI: 10.3389/fmicb.2021.657353] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/27/2021] [Indexed: 01/21/2023] Open
Abstract
Development and spread of antimicrobial resistance (AMR) and multidrug resistance (MDR) through propagation of antibiotic resistance genes (ARG) in various environments is a global emerging public health concern. The role of wastewater treatment plants (WWTPs) as hot spots for the dissemination of AMR and MDR has been widely pointed out by the scientific community. In this study, we collected surface water samples from sites upstream and downstream of two WWTP discharge points in an urban watershed in the Bryan-College Station (BCS), Texas area, over a period of nine months. E. coli isolates were tested for resistance to ampicillin, tetracycline, sulfamethoxazole, ciprofloxacin, cephalothin, cefoperazone, gentamycin, and imipenem using the Kirby-Bauer disc diffusion method. Antimicrobial resistant heterotrophic bacteria were cultured on R2A media amended with ampicillin, ciprofloxacin, tetracycline, and sulfamethoxazole for analyzing heterotrophic bacteria capable of growth on antibiotic-containing media. In addition, quantitative real-time polymerase chain reaction (qPCR) method was used to measure eight ARG – tetA, tetW, aacA, ampC, mecA, ermA, blaTEM, and intI1 in the surface water collected at each time point. Significant associations (p < 0.05) were observed between the locations of sampling sites relative to WWTP discharge points and the rate of E. coli isolate resistance to tetracycline, ampicillin, cefoperazone, ciprofloxacin, and sulfamethoxazole together with an increased rate of isolate MDR. The abundance of antibiotic-resistant heterotrophs was significantly greater (p < 0.05) downstream of WWTPs compared to upstream locations for all tested antibiotics. Consistent with the results from the culture-based methods, the concentrations of all ARG were substantially higher in the downstream sites compared to the upstream sites, particularly in the site immediately downstream of the WWTP effluent discharges (except mecA). In addition, the Class I integron (intI1) genes were detected in high amounts at all sites and all sampling points, and were about ∼20 times higher in the downstream sites (2.5 × 107 copies/100 mL surface water) compared to the upstream sites (1.2 × 106 copies/100 mL surface water). Results suggest that the treated WWTP effluent discharges into surface waters can potentially contribute to the occurrence and prevalence of AMR in urban watersheds. In addition to detecting increased ARG in the downstream sites by qPCR, findings from this study also report an increase in viable AMR (HPC) and MDR (E. coli) in these sites. This data will benefit establishment of improved environmental regulations and practices to help manage AMR/MDR and ARG discharges into the environment, and to develop mitigation strategies and effective treatment of wastewater.
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Affiliation(s)
- Maitreyee Mukherjee
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Long Beach, MS, United States.,Department of Soil and Crop Sciences, Texas A&M University, College Station TX, United States
| | - Edward Laird
- Department of Soil and Crop Sciences, Texas A&M University, College Station TX, United States
| | - Terry J Gentry
- Department of Soil and Crop Sciences, Texas A&M University, College Station TX, United States
| | - John P Brooks
- USDA-ARS, Mississippi State, Starkville, MS, United States
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25
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Pöntinen AK, Top J, Arredondo-Alonso S, Tonkin-Hill G, Freitas AR, Novais C, Gladstone RA, Pesonen M, Meneses R, Pesonen H, Lees JA, Jamrozy D, Bentley SD, Lanza VF, Torres C, Peixe L, Coque TM, Parkhill J, Schürch AC, Willems RJL, Corander J. Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era. Nat Commun 2021; 12:1523. [PMID: 33750782 PMCID: PMC7943827 DOI: 10.1038/s41467-021-21749-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 02/05/2021] [Indexed: 12/20/2022] Open
Abstract
Enterococcus faecalis is a commensal and nosocomial pathogen, which is also ubiquitous in animals and insects, representing a classical generalist microorganism. Here, we study E. faecalis isolates ranging from the pre-antibiotic era in 1936 up to 2018, covering a large set of host species including wild birds, mammals, healthy humans, and hospitalised patients. We sequence the bacterial genomes using short- and long-read techniques, and identify multiple extant hospital-associated lineages, with last common ancestors dating back as far as the 19th century. We find a population cohesively connected through homologous recombination, a metabolic flexibility despite a small genome size, and a stable large core genome. Our findings indicate that the apparent hospital adaptations found in hospital-associated E. faecalis lineages likely predate the "modern hospital" era, suggesting selection in another niche, and underlining the generalist nature of this nosocomial pathogen.
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Affiliation(s)
- Anna K Pöntinen
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Janetta Top
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sergio Arredondo-Alonso
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Ana R Freitas
- UCIBIO/REQUIMTE, Laboratory of Microbiology, Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Carla Novais
- UCIBIO/REQUIMTE, Laboratory of Microbiology, Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Rebecca A Gladstone
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Maiju Pesonen
- Oslo Centre for Biostatistics and Epidemiology (OCBE), Oslo University Hospital Research Support Services, Oslo, Norway
| | - Rodrigo Meneses
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Henri Pesonen
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - John A Lees
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Dorota Jamrozy
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | | | | | - Carmen Torres
- Department of Food and Agriculture, Area of Biochemistry and Molecular Biology, University of La Rioja, Logroño, Spain
| | - Luisa Peixe
- UCIBIO/REQUIMTE, Laboratory of Microbiology, Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Teresa M Coque
- Department of Microbiology, Ramón y Cajal Institute for Health Research Ramón y Cajal University Hospital, Madrid, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Julian Parkhill
- Wellcome Sanger Institute, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Anita C Schürch
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jukka Corander
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway.
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK.
- Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.
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26
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Lambrecht E, Van Coillie E, Boon N, Heyndrickx M, Van de Wiele T. Transfer of Antibiotic Resistance Plasmid from Commensal E. coli Towards Human Intestinal Microbiota in the M-SHIME: Effect of E. coli dosis, Human Individual and Antibiotic Use. Life (Basel) 2021; 11:192. [PMID: 33670965 PMCID: PMC7997361 DOI: 10.3390/life11030192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 01/09/2023] Open
Abstract
Along with (in) direct contact with animals and a contaminated environment, humans are exposed to antibiotic-resistant bacteria by consumption of food. The implications of ingesting antibiotic-resistant commensal bacteria are unknown, as dose-response data on resistance transfer and spreading in our gut is lacking. In this study, transfer of a resistance plasmid (IncF), harbouring several antibiotic resistance genes, from a commensal E. coli strain towards human intestinal microbiota was assessed using a Mucosal Simulator of the Human Intestinal Ecosystem (M-SHIME). More specifically, the effect of the initial E. coli plasmid donor concentration (105 and 107 CFU/meal), antibiotic treatment (cefotaxime) and human individual (n = 6) on plasmid transfer towards lumen coliforms and anaerobes was determined. Transfer of the resistance plasmid to luminal coliforms and anaerobes was observed shortly after the donor strain arrived in the colon and was independent of the ingested dose. Transfer occurred in all six simulated colons and despite their unique microbial community composition, no differences could be detected in antibiotic resistance transfer rates between the simulated human colons. After 72 h, resistant coliform transconjugants levels ranged from 7.6 × 104 to 7.9 × 106 CFUcefotaxime resistant/Ml colon lumen. Presence of the resistance plasmid was confirmed and quantified by PCR and qPCR. Cefotaxime treatment led to a significant reduction (85%) in resistant coliforms, however no significant effect on the total number of cultivable coliforms and anaerobes was observed.
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Affiliation(s)
- Ellen Lambrecht
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Gent, Belgium; (E.L.); (N.B.)
- Flanders Research Institute for Agriculture (ILVO), Fisheries and Food, Brusselsesteenweg 370, 9090 Melle, Belgium; (E.V.C.); (M.H.)
| | - Els Van Coillie
- Flanders Research Institute for Agriculture (ILVO), Fisheries and Food, Brusselsesteenweg 370, 9090 Melle, Belgium; (E.V.C.); (M.H.)
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Gent, Belgium; (E.L.); (N.B.)
| | - Marc Heyndrickx
- Flanders Research Institute for Agriculture (ILVO), Fisheries and Food, Brusselsesteenweg 370, 9090 Melle, Belgium; (E.V.C.); (M.H.)
- Department of Pathology, Bacteriology and Avian Diseases, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Tom Van de Wiele
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Gent, Belgium; (E.L.); (N.B.)
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27
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Abstract
Apramycin is an aminoglycoside antibiotic with the potential to be developed to combat multidrug-resistant pathogens. Its unique structure evades the clinically widespread mechanisms of aminoglycoside resistance that currently compromise the efficacy of other members in this drug class. Of the aminoglycoside-modifying enzymes that chemically alter these antibiotics, only AAC(3)-IVa has been demonstrated to confer resistance to apramycin through N-acetylation. Knowledge of other modification mechanisms is important to successfully develop apramycin for clinical use. Here, we show that ApmA is structurally unique among the previously described aminoglycoside-modifying enzymes and capable of conferring a high level of resistance to apramycin. In vitro experiments indicated ApmA to be an N-acetyltransferase, but in contrast to AAC(3)-IVa, ApmA has a unique regiospecificity of the acetyl transfer to the N2' position of apramycin. Crystallographic analysis of ApmA conclusively showed that this enzyme is an acetyltransferase from the left-handed β-helix protein superfamily (LβH) with a conserved active site architecture. The success of apramycin will be dependent on consideration of the impact of this potential form of clinical resistance.IMPORTANCE Apramycin is an aminoglycoside antibiotic that has been traditionally used in veterinary medicine. Recently, it has become an attractive candidate to repurpose in the fight against multidrug-resistant pathogens prioritized by the World Health Organization. Its atypical structure circumvents most of the clinically relevant mechanisms of resistance that impact this class of antibiotics. Prior to repurposing apramycin, it is important to understand the resistance mechanisms that could be a liability. Our study characterizes the most recently identified apramycin resistance element, apmA We show ApmA does not belong to the protein families typically associated with aminoglycoside resistance and is responsible for modifying a different site on the molecule. The data presented will be critical in the development of apramycin derivatives that will evade apmA in the event it becomes prevalent in the clinic.
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Gwenzi W, Chaukura N, Muisa-Zikali N, Teta C, Musvuugwa T, Rzymski P, Abia ALK. Insects, Rodents, and Pets as Reservoirs, Vectors, and Sentinels of Antimicrobial Resistance. Antibiotics (Basel) 2021; 10:antibiotics10010068. [PMID: 33445633 PMCID: PMC7826649 DOI: 10.3390/antibiotics10010068] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 12/22/2022] Open
Abstract
This paper reviews the occurrence of antimicrobial resistance (AMR) in insects, rodents, and pets. Insects (e.g., houseflies, cockroaches), rodents (rats, mice), and pets (dogs, cats) act as reservoirs of AMR for first-line and last-resort antimicrobial agents. AMR proliferates in insects, rodents, and pets, and their skin and gut systems. Subsequently, insects, rodents, and pets act as vectors that disseminate AMR to humans via direct contact, human food contamination, and horizontal gene transfer. Thus, insects, rodents, and pets might act as sentinels or bioindicators of AMR. Human health risks are discussed, including those unique to low-income countries. Current evidence on human health risks is largely inferential and based on qualitative data, but comprehensive statistics based on quantitative microbial risk assessment (QMRA) are still lacking. Hence, tracing human health risks of AMR to insects, rodents, and pets, remains a challenge. To safeguard human health, mitigation measures are proposed, based on the one-health approach. Future research should include human health risk analysis using QMRA, and the application of in-silico techniques, genomics, network analysis, and ’big data’ analytical tools to understand the role of household insects, rodents, and pets in the persistence, circulation, and health risks of AMR.
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Affiliation(s)
- Willis Gwenzi
- Biosystems and Environmental Engineering Research Group, Department of Agricultural and Biosystems Engineering, University of Zimbabwe, Mount. Pleasant, Harare P.O. Box MP167, Zimbabwe
- Correspondence: or (W.G.); or (A.L.K.A.)
| | - Nhamo Chaukura
- Department of Physical and Earth Sciences, Sol Plaatje University, Kimberley 8300, South Africa;
| | - Norah Muisa-Zikali
- Department of Environmental Sciences and Technology, School of Agricultural Sciences and Technology, Chinhoyi University of Technology, Private Bag, Chinhoyi 7724, Zimbabwe; or
| | - Charles Teta
- Future Water Institute, Faculty of Engineering & Built Environment, University of Cape Town, Cape Town 7700, South Africa;
| | - Tendai Musvuugwa
- Department of Biological and Agricultural Sciences, Sol Plaatje University, Kimberley 8300, South Africa;
| | - Piotr Rzymski
- Department of Environmental Medicine, Poznan University of Medical Sciences, 60-806 Poznan, Poland;
- Integrated Science Association (ISA), Universal Scientific Education and Research Network (USERN), 60-806 Poznań, Poland
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa
- Correspondence: or (W.G.); or (A.L.K.A.)
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Abdi RD, Gillespie BE, Ivey S, Pighetti GM, Almeida RA, Kerro Dego O. Antimicrobial Resistance of Major Bacterial Pathogens from Dairy Cows with High Somatic Cell Count and Clinical Mastitis. Animals (Basel) 2021; 11:ani11010131. [PMID: 33430135 PMCID: PMC7827620 DOI: 10.3390/ani11010131] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/23/2020] [Accepted: 01/05/2021] [Indexed: 12/25/2022] Open
Abstract
Simple Summary Mastitis is the most prevalent disease of dairy cattle that causes significant economic losses. Different agents cause mastitis which leads to increased somatic cell count (SCC) and low milk quality. Treating mastitis with antimicrobials is essential to reduce SCC and improve milk quality. Excessive use or misuse of antimicrobials in dairy farms leads to the development of antimicrobial resistant bacteria. The objectives of this study were (1) to isolate and identify the causative agent of mastitis and (2) determine antimicrobial resistance profiles of bacterial isolates. A total of 174 quarter milk samples from 151 cows with high SCC and clinical mastitis from 34 dairy farms in Tennessee, Kentucky, and Mississippi were collected. Bacterial causative agents were determined by bacteriological and biochemical tests. Antimicrobial resistance of bacterial isolates against 10 commonly used antimicrobials was tested. A total of 193 bacteria consisting of six bacterial species, which include Staphylococcus aureus, Streptococcus uberis, Streptococcus dysgalactiae, Escherichia coli, Klebsiella oxytoca and Klebsiella pneumoniae were isolated. Staphylococcus aureus was the predominant isolate. The proportion of resistant isolates was relatively higher in Gram-negatives than Gram-positives. Continuous antimicrobial resistance testing and identification of reservoirs of resistance traits in dairy farms are essential to implement proper mitigation measures. Abstract Mastitis is the most prevalent and economically important disease caused by different etiological agents, which leads to increased somatic cell count (SCC) and low milk quality. Treating mastitis cases with antimicrobials is essential to reduce SCC and improve milk quality. Non-prudent use of antimicrobials in dairy farms increased the development of antimicrobial resistant bacteria. This study’s objectives were (1) to isolate and identify etiological agents of mastitis and (2) to determine antimicrobial resistance profiles of bacterial isolates. A total of 174 quarter milk samples from 151 cows with high SCC and clinical mastitis from 34 dairy farms in Tennessee, Kentucky, and Mississippi were collected. Bacterial causative agents were determined by bacteriological and biochemical tests. The antimicrobial resistance of bacterial isolates against 10 commonly used antimicrobials was tested. A total of 193 bacteria consisting of six bacterial species, which include Staphylococcus aureus, Streptococcus uberis, Streptococcus dysgalactiae, Escherichia coli, Klebsiella oxytoca and Klebsiella pneumoniae were isolated. Staphylococcus aureus was the predominant isolate followed by Strep. spp., E. coli, and Klebsiella spp. Results of this study showed that Gram-negatives (E. coli and Klebsiella spp.) were more resistant than Gram-positives (Staph. aureus and Streptococcus spp.). Continuous antimicrobial resistance testing and identification of reservoirs of resistance traits in dairy farms are essential to implement proper mitigation measures.
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Affiliation(s)
- Reta D. Abdi
- Department of Animal Science, Hebert College of Agriculture, The University of Tennessee, Knoxville, TN 37996, USA; (R.D.A.); (B.E.G.); (S.I.); (G.M.P.); (R.A.A.)
- Department of Biomedical Sciences, College of Veterinary Medicine, Long Island University Post, Roth Hall, Brookville, NY 11548, USA
| | - Barbara E. Gillespie
- Department of Animal Science, Hebert College of Agriculture, The University of Tennessee, Knoxville, TN 37996, USA; (R.D.A.); (B.E.G.); (S.I.); (G.M.P.); (R.A.A.)
| | - Susan Ivey
- Department of Animal Science, Hebert College of Agriculture, The University of Tennessee, Knoxville, TN 37996, USA; (R.D.A.); (B.E.G.); (S.I.); (G.M.P.); (R.A.A.)
| | - Gina M. Pighetti
- Department of Animal Science, Hebert College of Agriculture, The University of Tennessee, Knoxville, TN 37996, USA; (R.D.A.); (B.E.G.); (S.I.); (G.M.P.); (R.A.A.)
| | - Raul A. Almeida
- Department of Animal Science, Hebert College of Agriculture, The University of Tennessee, Knoxville, TN 37996, USA; (R.D.A.); (B.E.G.); (S.I.); (G.M.P.); (R.A.A.)
| | - Oudessa Kerro Dego
- Department of Animal Science, Hebert College of Agriculture, The University of Tennessee, Knoxville, TN 37996, USA; (R.D.A.); (B.E.G.); (S.I.); (G.M.P.); (R.A.A.)
- Correspondence: ; Tel.: +1-865-974-9740; Fax: +1-865-974-7297
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Zhelev G. Bacterial resistance to antiseptics and disinfectants – minireview. BULGARIAN JOURNAL OF VETERINARY MEDICINE 2021. [DOI: 10.15547/bjvm.2019-0085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The appearance of bacterial resistance to disinfectants and antiseptics is an issue of substantial health concern, resulting in low efficiency of epidemic control activities and emergence of microorganisms with cross-resistance to antibiotics and biocides. A synopsis of the main mechanisms of development of resistance to biocides is presented. The emphasis is placed to health risks and impact on medical practice. The main methods for detection of resistance, and prevention measures of key importance for its control are outlined.
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Affiliation(s)
- G. Zhelev
- Department of Veterinary Microbiology, Infectious and Parasitic Diseases, Faculty of Veterinary Medicine , Trakia University, 6000 Stara Zagora, Bulgaria
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31
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Michaux C, Hansen EE, Jenniches L, Gerovac M, Barquist L, Vogel J. Single-Nucleotide RNA Maps for the Two Major Nosocomial Pathogens Enterococcus faecalis and Enterococcus faecium. Front Cell Infect Microbiol 2020; 10:600325. [PMID: 33324581 PMCID: PMC7724050 DOI: 10.3389/fcimb.2020.600325] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 10/19/2020] [Indexed: 12/19/2022] Open
Abstract
Enterococcus faecalis and faecium are two major representative clinical strains of the Enterococcus genus and are sadly notorious to be part of the top agents responsible for nosocomial infections. Despite their critical implication in worldwide public healthcare, essential and available resources such as deep transcriptome annotations remain poor, which also limits our understanding of post-transcriptional control small regulatory RNA (sRNA) functions in these bacteria. Here, using the dRNA-seq technique in combination with ANNOgesic analysis, we successfully mapped and annotated transcription start sites (TSS) of both E. faecalis V583 and E. faecium AUS0004 at single nucleotide resolution. Analyzing bacteria in late exponential phase, we capture ~40% (E. faecalis) and 43% (E. faecium) of the annotated protein-coding genes, determine 5′ and 3′ UTR (untranslated region) length, and detect instances of leaderless mRNAs. The transcriptome maps revealed sRNA candidates in both bacteria, some found in previous studies and new ones. Expression of candidate sRNAs is being confirmed under biologically relevant environmental conditions. This comprehensive global TSS mapping atlas provides a valuable resource for RNA biology and gene expression analysis in the Enterococci. It can be accessed online at www.helmholtz-hiri.de/en/datasets/enterococcus through an instance of the genomic viewer JBrowse.
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Affiliation(s)
- Charlotte Michaux
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Elisabeth E Hansen
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Laura Jenniches
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
| | - Milan Gerovac
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany.,Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Jörg Vogel
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany.,Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
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32
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McDermott PF, Davis JJ. Predicting antimicrobial susceptibility from the bacterial genome: A new paradigm for one health resistance monitoring. J Vet Pharmacol Ther 2020; 44:223-237. [PMID: 33010049 DOI: 10.1111/jvp.12913] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 08/25/2020] [Accepted: 09/09/2020] [Indexed: 12/11/2022]
Abstract
The laboratory identification of antibacterial resistance is a cornerstone of infectious disease medicine. In vitro antimicrobial susceptibility testing has long been based on the growth response of organisms in pure culture to a defined concentration of antimicrobial agents. By comparing individual isolates to wild-type susceptibility patterns, strains with acquired resistance can be identified. Acquired resistance can also be detected genetically. After many decades of research, the inventory of genes underlying antimicrobial resistance is well known for several pathogenic genera including zoonotic enteric organisms such as Salmonella and Campylobacter and continues to grow substantially for others. With the decline in costs for large scale DNA sequencing, it is now practicable to characterize bacteria using whole genome sequencing, including the carriage of resistance genes in individual microorganisms and those present in complex biological samples. With genomics, we can generate comprehensive, detailed information on the bacterium, the mechanisms of antibiotic resistance, clues to its source, and the nature of mobile DNA elements by which resistance spreads. These developments point to a new paradigm for antimicrobial resistance detection and tracking for both clinical and public health purposes.
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Affiliation(s)
- Patrick F McDermott
- Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, USA
| | - James J Davis
- Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL, USA.,University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
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33
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Jang HM, Lee J, Shin SG, Shin J, Kim YM. Comparing the fate of antibiotic resistance genes in two full-scale thermophilic anaerobic digestion plants treating food wastewater. BIORESOURCE TECHNOLOGY 2020; 312:123577. [PMID: 32531733 DOI: 10.1016/j.biortech.2020.123577] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 05/21/2023]
Abstract
This study focus on the fate of ARGs in the full-scale AD of food wastewater (FWW). Residue was collected from two different full-scale thermophilic AD treating FWW. Ten selected ARGs, including tetracycline resistance genes (tetM, tetX, tetQ, tetH and tetG), sulfonamide resistance genes (sul1 and sul2), quinolone resistance genes (qnrD) and macrolide resistance genes (ermB and ermC), were amplified using quantitative polymerase chain reaction (qPCR). Furthermore, the class 1 integron-integrase gene (intI1) was selected as a representative mobile gene element. Remarkable reduction in the ARGs and intI1 was observed in two-stage (acidogenic-methanogenic) AD, particularly, tetG, tetH, tetM, tetQ, tetX and intI1 not detected. Additionally, significant positive correlation (p < 0.01) between ARGs and intI1 suggested a strong likelihood of horizontal gene transfer (HGT). Furthermore, stepwise multiple linear regression analysis revealed significant factors related to the fate of individual ARGs and intI1 during AD.
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Affiliation(s)
- Hyun Min Jang
- Department of Environmental Engineering and Soil Environment Research Center, Jeonbuk National University, Jeonju, Jeollabukdo 54896, Republic of Korea
| | - Jangwoo Lee
- Department of Surface Waters-Research and Management, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Seung Gu Shin
- Department of Energy Engineering, Future Convergence Technology Research Institute, Gyeongnam National University of Science and Technology, Jinju 52725, Republic of Korea
| | - Jingyeong Shin
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Young Mo Kim
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-gu, Seoul 04763, Republic of Korea.
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The impact of metal pipe materials, corrosion products, and corrosion inhibitors on antibiotic resistance in drinking water distribution systems. Appl Microbiol Biotechnol 2020; 104:7673-7688. [DOI: 10.1007/s00253-020-10777-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/29/2020] [Accepted: 07/05/2020] [Indexed: 02/07/2023]
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Naidoo Y, Valverde A, Cason ED, Pierneef RE, Cowan DA. A clinically important, plasmid-borne antibiotic resistance gene (β-lactamase TEM-116) present in desert soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 719:137497. [PMID: 32114220 DOI: 10.1016/j.scitotenv.2020.137497] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 02/20/2020] [Accepted: 02/20/2020] [Indexed: 06/10/2023]
Abstract
The exhaustive use of antibiotics in humans, animal farming and other agricultural practices has resulted in the frequent appearance of antibiotic resistant bacteria in human-impacted habitats. However, antibiotic resistance in natural (less-impacted) habitats is less understood. Using shotgun metagenomics we analysed soils from relatively low anthropogenic impact sites across the Namib Desert. We report the presence of a clinically significant extended spectrum β-lactamase (TEM-116), on a ColE1-like plasmid also carrying a metal resistance gene (arsC). The co-occurrence of resistance to antimicrobial drugs and metals encoded on a single mobile genetic element increases the probability of dissemination of these resistance determinants and the potential selection of multiple resistance mechanisms. In addition, the presence of a P7 entero-bacteriophage on the same plasmid, may represent a new vehicle for the propagation of TEM-116 in these soil communities. These findings highlight the role of the environment in the One Health initiative.
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Affiliation(s)
- Yashini Naidoo
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynnwood Road, Pretoria 0002, South Africa
| | - Angel Valverde
- Department of Microbial, Biochemical and Food Technology, University of the Free State, Nelson Mandela Drive, Bloemfontein 9300, South Africa
| | - Errol D Cason
- Department of Animal, Wildlife and Grassland Science, University of the Free State, Nelson Mandela Drive, Bloemfontein 9300, South Africa
| | - Rian E Pierneef
- Biotechnology Platform, Agricultural Research Council, Soutpan Road, Onderstepoort Campus, Pretoria 0110, South Africa
| | - Don A Cowan
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynnwood Road, Pretoria 0002, South Africa.
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Probiotic Cocktail Identified by Microbial Network Analysis Inhibits Growth, Virulence Gene Expression, and Host Cell Colonization of Vancomycin-Resistant Enterococci. Microorganisms 2020; 8:microorganisms8060816. [PMID: 32486106 PMCID: PMC7357164 DOI: 10.3390/microorganisms8060816] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 05/24/2020] [Accepted: 05/27/2020] [Indexed: 12/16/2022] Open
Abstract
The prevalence of vancomycin resistant enterococcus (VRE) carrier-state has been increasing in patients of intensive care unit and it would be a public health threat. Different research groups conducted decolonizing VRE with probiotic and the results were controversial. Therefore, a systemic approach to search for the probiotic species capable of decolonizing VRE is necessary. Thus, VRE was co-cultured with ten probiotic species. The fluctuations of each bacterial population were analyzed by 16S rRNA sequencing. Microbial network analysis (MNA) was exploited to identify the most critical species in inhibiting the VRE population. The MNA-selected probiotic cocktail was then validated for its efficacy in inhibiting VRE, decolonizing VRE from Caco-2 cells via three approaches: exclusion, competition, and displacement. Finally, the expression of VRE virulence genes after co-incubation with the probiotic cocktail were analyzed with quantitative real-time PCR (qRT-PCR). The MNA-selected probiotic cocktail includes Bacillus coagulans, Lactobacillus rhamnosus GG, Lactobacillus reuteri, and Lactobacillus acidophilus. This probiotic combination significantly reduces the population of co-cultured VRE and prevents VRE from binding to Caco-2 cells by down-regulating several host-adhesion genes of VRE. Our results suggested the potential of this four-strain probiotic cocktail in clinical application for the decolonization of VRE in human gut.
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Heß S, Hiltunen T, Berendonk TU, Kneis D. High variability of plasmid uptake rates in Escherichia coli isolated from sewage and river sediments. PLoS One 2020; 15:e0232130. [PMID: 32353032 PMCID: PMC7192377 DOI: 10.1371/journal.pone.0232130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/07/2020] [Indexed: 12/05/2022] Open
Abstract
The horizontal transfer of plasmids is a key mechanism behind the spread of antibiotic resistance in bacteria. So far, transfer rate constants were measured for a variety of plasmids, donors and recipients. The employed strains typically had a long history in laboratories. Existing data are, therefore, not necessarily representative for real-world environments. Moreover, information on the inter-strain variability of plasmid transfer rates is scarce. Using a high-throughput approach, we studied the uptake of RP4 by various Escherichia coli recipients using Serratia marcescens as the donor. The recipient strains were isolated from human-borne sewage and river sediments. The rate constants of plasmid transfer generally followed a log-normal distribution with considerable variance. The rate constants for good and poor recipients (95 and 5% quantile) differed by more than three orders of magnitude. Specifically, the inter-strain variability of the rate constant was large in comparison to alterations induced by low-level antibiotic exposure. We did not find evidence for diverging efficiencies of plasmid uptake between E. coli recipients of different origin. On average, strains isolated from river bottom sediments were equally efficient in the acquisition of RP4 as isolates extracted from sewage. We conclude that E. coli strains persisting in the aquatic environment and those of direct human origin share a similar intrinsic potential for the conjugative uptake of certain plasmids. In view of the large inter-strain variability, we propose to work towards probabilistic modeling of the environmental spread of antibiotic resistance.
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Affiliation(s)
- Stefanie Heß
- Department of Microbiology, University of Helsinki, Helsinki, Finland
- * E-mail: (SH); (DK)
| | - Teppo Hiltunen
- Department of Microbiology, University of Helsinki, Helsinki, Finland
- Department of Biology, University of Turku, Turku, Finland
| | | | - David Kneis
- Institute of Hydrobiology, TU Dresden, Dresden, Germany
- Helmholtz-Centre for Environmental Research, Magdeburg, Germany
- * E-mail: (SH); (DK)
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Quadros MD, Bugs RCF, Soares RDO, Rossato AM, Rocha LDL, d'Azevedo PA. Identifying gram-positive cocci in dermatoscopes and smartphone adapters using MALDI-TOF MS: a cross-sectional study. An Bras Dermatol 2020; 95:298-306. [PMID: 32303433 PMCID: PMC7253918 DOI: 10.1016/j.abd.2019.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 11/09/2019] [Indexed: 01/15/2023] Open
Abstract
Background The increasingly frequent use of dermoscopy makes us think about the possibility of transfer of microorganisms, through the dermatoscope, between doctor and patients. Objectives To identify the most frequent gram-positive cocci in dermatoscopes and smartphone adapters, as well as the resistance profile, and to evaluate the factors associated with a higher risk of bacterial contamination of the dermatoscopes. Methods A cross-sectional study was carried out with 118 dermatologists from Porto Alegre/Brazil between September 2017 and July 2018. Gram-positive cocci were identified by MALDI-TOF MS and habits of use of the dermatoscope were evaluated through an anonymous questionnaire. Results Of the dermatoscopes analysed, 46.6% had growth of gram-positive cocci on the lens and 37.3% on the on/off button. The microorganisms most frequently found were S. epidermidis, S. hominis and S. warneri. Attending a hospital, using the dermatoscope at the hospital, with inpatients and in the intensive care unit were significantly associated with colonisation by gram-positive cocci. The highest resistance rates were observed for penicillin, erythromycin and sulfamethoxazole-trimethoprim. Study limitations The non-search of gram-negative bacilli, fungi and viruses. Moreover, the small number of adapters did not make it possible to better define if the frequency differences were statistically significant. Conclusion Coagulase-negative staphylococci were frequently identified. S. aureus was detected only on the lens.
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Affiliation(s)
- Maurício de Quadros
- Gram-positive Cocci Laboratory, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS, Brazil; Department of Dermatology, Hospital Santa Casa de Misericórdia de Porto Alegre, Porto Alegre, RS, Brazil.
| | - Roberto Carlos Freitas Bugs
- Gram-positive Cocci Laboratory, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS, Brazil
| | - Renata de Oliveira Soares
- Gram-positive Cocci Laboratory, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS, Brazil
| | - Adriana Medianeira Rossato
- Gram-positive Cocci Laboratory, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS, Brazil
| | - Lisiane da Luz Rocha
- Gram-positive Cocci Laboratory, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS, Brazil
| | - Pedro Alves d'Azevedo
- Gram-positive Cocci Laboratory, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS, Brazil
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Chen QL, Hu HW, Zhu D, Ding J, Yan ZZ, He JZ, Zhu YG. Host identity determines plant associated resistomes. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 258:113709. [PMID: 31838394 DOI: 10.1016/j.envpol.2019.113709] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/12/2019] [Accepted: 11/30/2019] [Indexed: 05/20/2023]
Abstract
Plant microbiome, as the second genome of plant, and the interface between human and environmental microbiome, represents a potential pathway of human exposure to environmental pathogens and resistomes. However, the impact of host identity on the profile of resistomes in plant phyllosphere is unclear and this knowledge is vital for establishing a framework to evaluate the dissemination of antibiotic resistance via the plant microbiome. Here, we explored the phyllosphere microbiome and resistomes in 12 selected plant species. By using High-throughput quantitative PCR, we identified a total of 172 unique resistance genes in plant phyllosphere microbiome, which was significantly divergent from the profile of resistomes in associated soils (Adonis, P < 0.01). Host identity had a significant effect on the plant resistome, which was mainly attributed to the dissimilarity of phyllosphere bacterial phylogeny across different plants. We identified a core set of plant resistomes shared in more than 80% of samples, which accounted for more than 64% of total resistance genes. These plant core resistomes conferred resistance to antibiotics that are commonly administered to humans and animals. Our findings extend our knowledge regarding the resistomes in plant phyllosphere microbiome and highlight the role of host identity in shaping the plant associated antibiotic resistance genes.
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Affiliation(s)
- Qing-Lin Chen
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Dong Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Jing Ding
- School of Environmental and Material Engineering, Yantai University, 30 Qingquan Road, Yantai, 264005, China
| | - Zhen-Zhen Yan
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Ji-Zheng He
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
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Evaluation of two transformation protocols and screening of positive plasmid introduction into Bacillus cereus EB2, a gram-positive bacterium using qualitative analyses. Braz J Microbiol 2020; 51:919-929. [PMID: 32078730 DOI: 10.1007/s42770-020-00241-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 02/05/2020] [Indexed: 10/25/2022] Open
Abstract
Both Gram-positive and Gram-negative bacteria can take up exogenous DNA when they are in a competent state either naturally or artificially. However, the thick peptidoglycan layer in Gram-positive bacteria's cell wall is considered as a possible barrier to DNA uptake. In the present work, two transformation techniques have been evaluated in assessing the protocol's ability to introduce foreign DNA, pBBRGFP-45 plasmid which harbors kanamycin resistance and green fluorescent protein (GFP) genes into a Gram-positive bacterium, Bacillus cereus EB2. B. cereus EB2 is an endophytic bacterium, isolated from oil palm roots. A Gram-negative bacterium, Pseudomonas aeruginosa EB35 was used as a control sample for both transformation protocols. The cells were made competent using respective chemical treatment to Gram-positive and Gram-negative bacteria, and kanamycin concentration in the selective medium was also optimized. Preliminary findings using qualitative analysis of colony polymerase chain reaction (PCR)-GFP indicated that the putative positive transformants for B. cereus EB2 were acquired using the second transformation protocol. The positive transformants were then verified using molecular techniques such as observation of putative colonies on specific media under UV light, plasmid extraction, and validation analyses, followed by fluorescence microscopy. Conversely, both transformation protocols were relatively effective for introduction of plasmid DNA into P. aeruginosa EB35. Therefore, this finding demonstrated the potential of chemically prepared competent cells and the crucial step of heat-shock in foreign DNA transformation process of Gram-positive bacterium namely B. cereus was required for successful transformation.
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DeNegre AA, Myers K, Fefferman NH. Impact of chemorophylaxis policy for AIDS-immunocompromised patients on emergence of bacterial resistance. PLoS One 2020; 15:e0225861. [PMID: 31999715 PMCID: PMC6992000 DOI: 10.1371/journal.pone.0225861] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/13/2019] [Indexed: 12/20/2022] Open
Abstract
Chemoprophylaxis (antibiotic prophylaxis) is a long relied-upon means of opportunistic infection management among HIV/AIDS patients, but its use represents an evolutionary tradeoff: Despite the benefits of chemoprophylaxis, widespread use of antibiotics creates a selective advantage for drug-resistant bacterial strains. Especially in the developing world, with combined resource limitations, antibiotic misuse, and often-poor infection control, the emergence of antibiotic resistance may pose a critical health risk. Extending previous work that demonstrated that this risk is heightened when a significant proportion of the population is HIV/AIDS-immunocompromised, we work to address the relationship between HIV/AIDS patients' use of antibiotic chemoprophylaxis and the emergence of resistance. We apply an SEIR compartmental model, parameterized to reflect varying percentages of chemoprophylaxis use among HIV/AIDS+ patients in a resource-limited setting, to investigate the magnitude of the risk of prophylaxis-associated emergence versus the individual-level benefits it is presumed to provide. The results from this model suggest that, while still providing tangible benefits to the individual, chemoprophylaxis is associated with negligible decreases in population-wide morbidity and mortality from bacterial infection, and may also fail to provide assumed efficacy in reduction of TB prevalence.
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Affiliation(s)
- Ashley A. DeNegre
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, New Jersey, United States of America
- The Command, Control and Interoperability Center for Advanced Data Analysis (CCICADA), Rutgers University, New Brunswick, New Jersey, United States of America
| | - Kellen Myers
- Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, United States of America
- Department of Mathematics, University of Tennessee, Knoxville, Tennessee, United States of America
- National Institute for Mathematical and Biological Synthesis (NIMBioS), University of Tennessee, Knoxville, Tennessee, United States of America
- Department of Mathematics, Tusculum University, Greeneville, Tennessee, United States of America
| | - Nina H. Fefferman
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, New Jersey, United States of America
- The Command, Control and Interoperability Center for Advanced Data Analysis (CCICADA), Rutgers University, New Brunswick, New Jersey, United States of America
- Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, United States of America
- Department of Mathematics, University of Tennessee, Knoxville, Tennessee, United States of America
- National Institute for Mathematical and Biological Synthesis (NIMBioS), University of Tennessee, Knoxville, Tennessee, United States of America
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Cyriaque V, Jacquiod S, Riber L, Abu Al-Soud W, Gillan DC, Sørensen SJ, Wattiez R. Selection and propagation of IncP conjugative plasmids following long-term anthropogenic metal pollution in river sediments. JOURNAL OF HAZARDOUS MATERIALS 2020; 382:121173. [PMID: 31563088 DOI: 10.1016/j.jhazmat.2019.121173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 08/14/2019] [Accepted: 09/05/2019] [Indexed: 06/10/2023]
Abstract
For a century, the MetalEurop foundry released metals into the river "La Deûle". Previous work revealed higher microbial diversity in metal impacted sediments, and horizontal gene transfer mediated by conjugative plasmids was suggested to drive the community adaptation to metals. We used an integrative state-of-the-art molecular approach coupling quantitative PCR, conjugation assays, flow cytometry, fluorescence activated cell sorting and 16S rRNA gene amplicon sequencing to investigate the presence of conjugative plasmids and their propagation patterns in sediment microbiomes. We highlighted the existence of a native broad-host range IncP conjugative plasmid population in polluted sediments, confirming their ecological importance for microbial adaptation. However, despite incompatibilities and decreased transfer frequencies with our own alien IncP plasmid, we evidenced that a wide diversity of bacterial members was still prone to uptake the plasmid, indicating that sediment microbial communities are still inclined to receive conjugative plasmids from the same group. We observed that metal pollution favoured exogenous plasmid transfer to specific metal-selected bacteria, which are likely coming from upstream sources (e.g. wastewater treatment plant, farms…). Altogether, our results suggest that MetalEurop sediments are hotspots for gene transfer via plasmids, acting as an "environmental reservoir" for microbes and mobile elements released by human activities.
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Affiliation(s)
- Valentine Cyriaque
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, 20 place du parc, Mons, Belgium; Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, 1, Bygning, 1-1-215, Denmark.
| | - Samuel Jacquiod
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, 1, Bygning, 1-1-215, Denmark; Agroécologie, UMR 1347, INRA Centre Dijon, Dijon, France
| | - Leise Riber
- Section of Functional Genomics, Department of Biology, University of Copenhagen, Ole Maaløesvej 5, 2200 Copenhagen N, Denmark
| | - Waleed Abu Al-Soud
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, 1, Bygning, 1-1-215, Denmark; Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Jouf University, Qurayyat, Saudi Arabia
| | - David C Gillan
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, 20 place du parc, Mons, Belgium
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, 1, Bygning, 1-1-215, Denmark
| | - Ruddy Wattiez
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, 20 place du parc, Mons, Belgium
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Alanber MN, Alharbi NS, Khaled JM. Evaluation of multidrug-resistant Bacillus strains causing public health risks in powdered infant milk formulas. J Infect Public Health 2019; 13:1462-1468. [PMID: 31870631 DOI: 10.1016/j.jiph.2019.11.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/27/2019] [Accepted: 11/10/2019] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Antibiotic-resistant bacteria are one of the major global health issues that can affect humans, animals, and the environment. Antibiotic-resistant bacteria have emerged as opportunistic pathogenic bacteria that are frequently isolated from both clinical patients and healthy individuals. The aim of this study was to characterize the antibiotic-resistant bacteria isolated from powdered infant formulas marketed in Riyadh, Saudi Arabia. METHODS Infant powdered milk formulas were purchased from different pharmacies located within Riyadh, and ten products of powdered milk formulas designed for children of various ages were then transferred to the laboratory in the Department of Botany and Microbiology at King Saud University, Riyadh. Isolation and purification of Bacillus species were both performed according to standard protocols. The identification test was performed using the automated Vitek 2 system (BioMerieux, France), and antibiotic sensitivity tests were performed using the disk-diffusion method incorporating standard antibiotic disks foramikacin (30μg/disk), gentamicin (10μg/disk), imipenem (10μg/disk), moxifloxacin (5μg/disk), cefoperazone (75μg/disk), cefpodoxime (10μg/disk), ceftazidime (30μg/disk), and cefepime (30μg/disk). Statistical analysis was performed using Ward's method to obtain antibiotic resistance of the isolates. RESULTS The results obtained from the milk samples indicated that all isolates were sensitive to amikacin, gentamicin, and moxifloxacin. A group of isolates obtained from milk was resistant to cefoperazone by 6.49%, cefpodoxime by 25.9%, ceftazidime by 14.28%, and cefepime by 19.48%. CONCLUSIONS Based on these findings, we concluded that the powdered infant formula marketed in Riyadh City may act as a source of bacterial isolates that are resistant to several standard antibiotics.
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Affiliation(s)
- Mohamed N Alanber
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Naiyf S Alharbi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia.
| | - Jamal M Khaled
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia.
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Lambrecht E, Van Coillie E, Van Meervenne E, Boon N, Heyndrickx M, Van de Wiele T. Commensal E. coli rapidly transfer antibiotic resistance genes to human intestinal microbiota in the Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME). Int J Food Microbiol 2019; 311:108357. [DOI: 10.1016/j.ijfoodmicro.2019.108357] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 08/28/2019] [Accepted: 09/06/2019] [Indexed: 12/16/2022]
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Phage Transduction is Involved in the Intergeneric Spread of Antibiotic Resistance-Associated bla CTX-M, mel, and tetM Loci in Natural Populations of Some Human and Animal Bacterial Pathogens. Curr Microbiol 2019; 77:185-193. [PMID: 31754824 DOI: 10.1007/s00284-019-01817-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/15/2019] [Indexed: 12/16/2022]
Abstract
The horizontal genetic transfer (HGT) of antibiotic resistance genes (ARGs) mediated by species-specific bacteriophages contributes to the emergence of antibiotic-resistant strains in natural populations of human and animal bacterial pathogens posing a significant threat to global public health. However, it is unclear and needs to be determined whether polyvalent bacteriophages play any role in the intergeneric transmission of ARGs. In this study, we examined the genome sequences of 2239 bacteriophages from different sources for the presence of ARGs. The identified ARG-carrying bacteriophages were then analyzed by PHACTS, PHAST, and HostPhinder programs to determine their lifestyles, genes coding for bacterial cell lysis, recombinases, and a spectrum of their potential host species, respectively. We employed the SplitsTree, RDP4 and SimPlot software packages in recombination tests to identify HGT events of ARGs between these bacteriophages and bacteria. In our analyses, some ARG-carrying bacteriophages exhibited temperate and/or polyvalent patterns. The bootstrap values (97-100) for the SplitsTree-generated parallelograms, fit values (97-100) for splits networks, Phi P values (< 10-17 to 3.9 × 10-16), RDP4 P values (≤ 7.8 × 10-03), and the SimPlot results, provided strong statistical evidence for the phage transduction events of blaCTX-M, mel, and tetM loci on inter-species level. These events involved several host species such as Escherichia coli, Salmonella enterica, Shigella sonnei, Streptococcus pneumoniae and Bacillus coagulans. HGT of mel loci between Erysipelothrix and Streptococcus phages were also detected. These results firmly suggest that certain bacteriophages possibly with temperate properties induce the intergeneric dissemination of blaCTX-M, mel and tetM in the above species.
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He P, Yu Z, Shao L, Zhou Y, Lü F. Fate of antibiotics and antibiotic resistance genes in a full-scale restaurant food waste treatment plant: Implications of the roles beyond heavy metals and mobile genetic elements. J Environ Sci (China) 2019; 85:17-34. [PMID: 31471024 DOI: 10.1016/j.jes.2019.04.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 04/08/2019] [Indexed: 06/10/2023]
Abstract
Is our food safe and free of the crisis of antibiotics and antibiotic resistance (AR)? And will the derived food waste (FW) impose AR risk to the environment after biological treatment? This study used restaurant FW leachates flowing through a 200 tons-waste/day biological treatment plant as a window to investigate the fate of antibiotics and antibiotic-resistance genes (ARGs) during the acceptance and treatment of FW. Sulfonamides (sulfamethazine, sulfamethoxazole) and quinolones (ciprofloxacin, enrofloxacin, ofloxacin) were detected during FW treatment, while tetracyclines, macrolides and chloramphenicols were not observable. ARGs encoding resistance to sulfonamides, tetracyclines and macrolides emerged in FW leachates. Material flow analysis illustrated that the total amount of antibiotics (except sulfamethazine) and ARGs were constant during FW treatment processes. Both the concentration and total amount of most antibiotics and ARGs fluctuated during treatment, physical processes (screening, centrifugation, solid-liquid and oil-water separation) did not decrease antibiotic or ARGs concentrations or total levels permanently; the affiliated wastewater treatment plant appeared to remove sulfonamides and most ARGs concentrations and total amount. Heavy metals Ni, Co and Cu were important for disseminating antibiotics concentrations and MGEs for distributing ARGs concentrations. Humic substances (fulvic acids, hydrophilic fractions), C-associated and N-associated contents were essential for the distribution of the total amounts of antibiotics and ARGs. Overall, this study implied that human food might not be free of antibiotics and ARGs, and FW was an underestimated AR pool with various determinants. Nonetheless, derived hazards of FW could be mitigated through biological treatment with well-planned daily operations.
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Affiliation(s)
- Pinjing He
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China; Institute of Waste Treatment and Reclamation, Tongji University, Shanghai 200092, China; Centre for the Technology Research and Training on Household Waste in Small Towns & Rural Area, Ministry of Housing and Urban-Rural Development of PR China (MOHURD), China
| | - Zhuofeng Yu
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Liming Shao
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai 200092, China; Centre for the Technology Research and Training on Household Waste in Small Towns & Rural Area, Ministry of Housing and Urban-Rural Development of PR China (MOHURD), China
| | - Yizhou Zhou
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Fan Lü
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
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Hiller CX, Hübner U, Fajnorova S, Schwartz T, Drewes JE. Antibiotic microbial resistance (AMR) removal efficiencies by conventional and advanced wastewater treatment processes: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 685:596-608. [PMID: 31195321 DOI: 10.1016/j.scitotenv.2019.05.315] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 05/15/2019] [Accepted: 05/20/2019] [Indexed: 05/27/2023]
Abstract
The World Health Organization (WHO) has identified the spread of antibiotic resistance as one of the major risks to global public health. An important transfer route into the aquatic environment is the urban water cycle. In this paper the occurrence and transport of antibiotic microbial resistance in the urban water cycle are critically reviewed. The presence of antibiotic resistance in low impacted surface water is being discussed to determine background antibiotic resistance levels, which might serve as a reference for treatment targets in the absence of health-based threshold levels. Different biological, physical and disinfection/oxidation processes employed in wastewater treatment and their efficacy regarding their removal of antibiotic resistant bacteria and antibiotic resistance geness (ARGs) were evaluated. A more efficient removal of antibiotic microbial resistance abundances from wastewater effluents can be achieved by advanced treatment processes, including membrane filtration, ozonation, UV-irradiation or chlorination, to levels typically observed in urban surface water or low impacted surface water.
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Affiliation(s)
- C X Hiller
- Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, 85748 Garching, Germany
| | - U Hübner
- Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, 85748 Garching, Germany
| | - S Fajnorova
- Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, 85748 Garching, Germany; Department of Water Technology and Environmental Engineering, University of Chemistry and Technology, Prague, Technická 5, 166 28 Praha, Czech Republic
| | - T Schwartz
- Karlsruhe Institute of Technology (KIT) - Campus North, Institute of Functional Interfaces (IFG), Microbiology at Natural and Technical Interfaces Department, 76021 Karlsruhe, Germany
| | - J E Drewes
- Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, 85748 Garching, Germany.
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Abstract
While the description of resistance to quinolones is almost as old as these antimicrobial agents themselves, transferable mechanisms of quinolone resistance (TMQR) remained absent from the scenario for more than 36 years, appearing first as sporadic events and afterward as epidemics. In 1998, the first TMQR was soundly described, that is, QnrA. The presence of QnrA was almost anecdotal for years, but in the middle of the first decade of the 21st century, there was an explosion of TMQR descriptions, which definitively changed the epidemiology of quinolone resistance. Currently, 3 different clinically relevant mechanisms of quinolone resistance are encoded within mobile elements: (i) target protection, which is mediated by 7 different families of Qnr (QnrA, QnrB, QnrC, QnrD, QnrE, QnrS, and QnrVC), which overall account for more than 100 recognized alleles; (ii) antibiotic efflux, which is mediated by 2 main transferable efflux pumps (QepA and OqxAB), which together account for more than 30 alleles, and a series of other efflux pumps (e.g., QacBIII), which at present have been sporadically described; and (iii) antibiotic modification, which is mediated by the enzymes AAC(6')Ib-cr, from which different alleles have been claimed, as well as CrpP, a newly described phosphorylase.
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Jacukowicz-Sobala I, Kociołek-Balawejder E, Stanisławska E, Dworniczek E, Seniuk A. Antimicrobial activity of anion exchangers containing cupric compounds against Enterococcus faecalis. Colloids Surf A Physicochem Eng Asp 2019. [DOI: 10.1016/j.colsurfa.2019.05.040] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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50
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Narendrakumar L, Gupta SS, Johnson JB, Ramamurthy T, Thomas S. Molecular Adaptations and Antibiotic Resistance inVibrio cholerae: A Communal Challenge. Microb Drug Resist 2019; 25:1012-1022. [DOI: 10.1089/mdr.2018.0354] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Lekshmi Narendrakumar
- Cholera and Biofilm Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Kerala, India
- Research Scholar, University of Kerala, Kerala, India
| | | | - John B. Johnson
- Viral Disease Biology, Rajiv Gandhi Centre for Biotechnology, Kerala, India
| | | | - Sabu Thomas
- Cholera and Biofilm Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Kerala, India
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