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Zhong Y, Guo S, Thong S, Schlundt J, Kwa AL. First report of environmental bla PAC-1-carrying Aeromonas enteropelogenes. Microbiol Spectr 2023; 11:e0139123. [PMID: 37909756 PMCID: PMC10714797 DOI: 10.1128/spectrum.01391-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 09/25/2023] [Indexed: 11/03/2023] Open
Abstract
The bla PAC-1 has been reported in Central Asia and Europe countries like Afghanistan and France in Aeromonas caviae and Pseudomonas aeruginosa strains from animals and patients, respectively. However, there is no record of bla PAC-1-carrying strain from the natural environment, and bla PAC-1-carrying Aeromonas has not been reported in the Asia Pacific. Here, we report the first known enviromental bla PAC-1-carrying Aeromonas enteropelogenes in the world from reservoir water in Singapore. We have performed a comprehensive genetic environment alignment and comparison of bla PAC-1 between our strain and other strains from different countries and sources and found the bla PAC-1 located on a highly conserved gene cluster. We suggest that environmental Aeromonas strains may act as a hidden reservoir involved in the circulating of bla PAC-1. The finding of conserved bla PAC-1 cluster also suggested the existence of multiple transmission pathways of bla PAC-1 in the Asia-Pacific region, involving multiple sources and different species.
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Affiliation(s)
- Yang Zhong
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
- Department of Clinical Translational Research, Singapore General Hospital, Singapore, Singapore
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
| | - Siyao Guo
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
| | - Shuhua Thong
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
| | - Joergen Schlundt
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
| | - Andrea L. Kwa
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
- Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
- SingHealth Duke-NUS Medicine Academic Clinical Programme, Singapore, Singapore
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2
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Canellas ALB, Laport MS. The biotechnological potential of Aeromonas: a bird's eye view. Crit Rev Microbiol 2023; 49:543-555. [PMID: 35687715 DOI: 10.1080/1040841x.2022.2083940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/18/2022] [Accepted: 05/25/2022] [Indexed: 11/03/2022]
Abstract
The genus Aeromonas comprises Gram-negative bacilli widely distributed in aquatic habitats that can also be found in the terrestrial environment and in close association with humans and animals. Aeromonas spp. are particularly versatile bacteria, with high genomic plasticity and notable capacity to adapt to different environments and extreme conditions. On account of being mostly associated with their pathogenic potential, research on the biotechnological potentialities of Aeromonas spp. is considerably scarce when compared to other bacterial groups. Nonetheless, studies over the years have been hinting at several interesting hidden potentialities in this bacterial group, especially with the recent advances in whole-genome sequencing, unveiling Aeromonas spp. as interesting candidates for the discovery of novel industrial biocatalysts, bioremediation strategies, and biopolyester production. In this context, the present study aims to provide an overview of the main biotechnological applications reported in the genus Aeromonas and provide new insights into the further exploration of these frequently overlooked, yet fascinating, bacteria.
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Affiliation(s)
- Anna Luiza Bauer Canellas
- Laboratório de Bacteriologia Molecular e Marinha, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Marinella Silva Laport
- Laboratório de Bacteriologia Molecular e Marinha, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
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3
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Verhaegen M, Bergot T, Liebana E, Stancanelli G, Streissl F, Mingeot-Leclercq MP, Mahillon J, Bragard C. On the use of antibiotics to control plant pathogenic bacteria: a genetic and genomic perspective. Front Microbiol 2023; 14:1221478. [PMID: 37440885 PMCID: PMC10333595 DOI: 10.3389/fmicb.2023.1221478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/08/2023] [Indexed: 07/15/2023] Open
Abstract
Despite growing attention, antibiotics (such as streptomycin, oxytetracycline or kasugamycin) are still used worldwide for the control of major bacterial plant diseases. This raises concerns on their potential, yet unknown impact on antibiotic and multidrug resistances and the spread of their genetic determinants among bacterial pathogens. Antibiotic resistance genes (ARGs) have been identified in plant pathogenic bacteria (PPB), with streptomycin resistance genes being the most commonly reported. Therefore, the contribution of mobile genetic elements (MGEs) to their spread among PPB, as well as their ability to transfer to other bacteria, need to be further explored. The only well-documented example of ARGs vector in PPB, Tn5393 and its highly similar variants (carrying streptomycin resistance genes), is concerning because of its presence outside PPB, in Salmonella enterica and Klebsiella pneumoniae, two major human pathogens. Although its structure among PPB is still relatively simple, in human- and animal-associated bacteria, Tn5393 has evolved into complex associations with other MGEs and ARGs. This review sheds light on ARGs and MGEs associated with PPB, but also investigates the potential role of antibiotic use in resistance selection in plant-associated bacteria.
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Affiliation(s)
- Marie Verhaegen
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Catholic University of Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - Thomas Bergot
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Catholic University of Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | | | | | | | - Marie-Paule Mingeot-Leclercq
- Cellular and Molecular Pharmacology Unit, Louvain Drug Research Institute, UCLouvain, Woluwe-Saint-Lambert, Belgium
| | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Catholic University of Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - Claude Bragard
- Plant Health Laboratory, Earth and Life Institute, UCLouvain, Louvain-la-Neuve, Belgium
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Dubey S, Ager-Wick E, Kumar J, Karunasagar I, Karunasagar I, Peng B, Evensen Ø, Sørum H, Munang’andu HM. Aeromonas species isolated from aquatic organisms, insects, chicken, and humans in India show similar antimicrobial resistance profiles. Front Microbiol 2022; 13:1008870. [PMID: 36532495 PMCID: PMC9752027 DOI: 10.3389/fmicb.2022.1008870] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/14/2022] [Indexed: 01/07/2024] Open
Abstract
Aeromonas species are Gram-negative bacteria that infect various living organisms and are ubiquitously found in different aquatic environments. In this study, we used whole genome sequencing (WGS) to identify and compare the antimicrobial resistance (AMR) genes, integrons, transposases and plasmids found in Aeromonas hydrophila, Aeromonas caviae and Aeromonas veronii isolated from Indian major carp (Catla catla), Indian carp (Labeo rohita), catfish (Clarias batrachus) and Nile tilapia (Oreochromis niloticus) sampled in India. To gain a wider comparison, we included 11 whole genome sequences of Aeromonas spp. from different host species in India deposited in the National Center for Biotechnology Information (NCBI). Our findings show that all 15 Aeromonas sequences examined had multiple AMR genes of which the Ambler classes B, C and D β-lactamase genes were the most dominant. The high similarity of AMR genes in the Aeromonas sequences obtained from different host species point to interspecies transmission of AMR genes. Our findings also show that all Aeromonas sequences examined encoded several multidrug efflux-pump proteins. As for genes linked to mobile genetic elements (MBE), only the class I integrase was detected from two fish isolates, while all transposases detected belonged to the insertion sequence (IS) family. Only seven of the 15 Aeromonas sequences examined had plasmids and none of the plasmids encoded AMR genes. In summary, our findings show that Aeromonas spp. isolated from different host species in India carry multiple AMR genes. Thus, we advocate that the control of AMR caused by Aeromonas spp. in India should be based on a One Health approach.
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Affiliation(s)
- Saurabh Dubey
- Section of Experimental Biomedicine, Department of Production Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Eirill Ager-Wick
- Section of Experimental Biomedicine, Department of Production Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Jitendra Kumar
- College of Fisheries, Acharya Narendra Deva University of Agriculture and Technology, Uttar Pradesh, India
| | - Indrani Karunasagar
- Nitte University Centre for Science Education and Research, Mangaluru, India
| | - Iddya Karunasagar
- Nitte University Centre for Science Education and Research, Mangaluru, India
| | - Bo Peng
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Higher Education Mega Center, Guangzhou, China
| | - Øystein Evensen
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Henning Sørum
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Hetron M. Munang’andu
- Section of Experimental Biomedicine, Department of Production Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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Bujak K, Decewicz P, Kitowicz M, Radlinska M. Characterization of Three Novel Virulent Aeromonas Phages Provides Insights into the Diversity of the Autographiviridae Family. Viruses 2022; 14:1016. [PMID: 35632757 PMCID: PMC9145550 DOI: 10.3390/v14051016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/29/2022] [Accepted: 05/05/2022] [Indexed: 11/17/2022] Open
Abstract
In this study, we isolated and characterized three novel virulent Autographiviridae bacteriophages, vB_AspA_Bolek, vB_AspA_Lolek, and vB_AspA_Tola, which infect different Aeromonas strains. These three host-pathogen pairs were derived from the same sampling location-the arsenic-containing microbial mats of the Zloty Stok gold mine. Functional analysis showed they are psychrotolerant (4-25 °C), albeit with a much wider temperature range of propagation for the hosts (≤37 °C). Comparative genomic analyses revealed a high nucleotide and amino acid sequence similarity of vB_AspA_Bolek and vB_AspA_Lolek, with significant differences exclusively in the C-terminal region of their tail fibers, which might explain their host range discrimination. The protein-based phage network, together with a phylogenetic analysis of the marker proteins, allowed us to assign vB_AspA_Bolek and vB_AspA_Lolek to the Beijerinckvirinae and vB_AspA_Tola to the Colwellvirinae subfamilies, but as three novel species, due to their low nucleotide sequence coverage and identity with other known phage genomes. Global comparative analysis showed that the studied phages are also markedly different from most of the 24 Aeromonas autographiviruses known so far. Finally, this study provides in-depth insight into the diversity of the Autographiviridae phages and reveals genomic similarities between selected groups of this family as well as between autographiviruses and their relatives of other Caudoviricetes families.
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Affiliation(s)
| | | | | | - Monika Radlinska
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (K.B.); (P.D.); (M.K.)
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6
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Bacterial Hosts and Genetic Characteristics of Antibiotic Resistance Genes in Wastewater Treatment Plants of Xinjiang (China) Revealed by Metagenomics. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12063100] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Antibiotic resistance genes (ARGs) pose a widespread concern for human health and wastewater treatment plants (WWTPs) are considered to be a major source of ARG transmission. In this paper, the potential hosts and genetic characteristics of ARGs in the influent, activated sludge and effluent of WWTPs in Xinjiang were studied by metagenomics. Bacitracin resistance gene (bacA), beta-lactamase gene (class A beta-lactamase), multidrug resistance genes (mexD, qacEdelta1), and sulfonamide resistance genes (sul1, and sul2) are persistent antibiotic resistance genes (PARGs). The potential hosts of ARGs were mainly pathogens, with Escherichia coli (12.9%), Acinetobacter johnsonii (8.94%), and Klebsiella pneumoniae (5.30%) accounting for the highest proportions. Chromosomal sequences and plasmid sequences accounted for 42.0% and 22.6% of ARG-carrying contigs (ACCs) in the influent, respectively. Meanwhile, the effluent contained 58.3% of ACCs in plasmids and 8.30% in chromosomes. Bacitracin resistance genes and multidrug resistance genes were mainly carried by chromosomes, while resistance genes for macrolide–lincosamide–streptogramin (MLS), vancomycin, sulfonamide, beta-lactam, tetracycline, chloramphenicol, and aminoglycoside were mainly carried by plasmids. ICEPae690-sul1-qacEdelta1 and ICEPmiChn3-sul2 were stable coexistence structures and heighten the transfer potential of ARGs in the environment. This study provided a clearer picture of host bacterial sources and genetic context of ARGs in the environment.
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7
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Frequency and diversity of small plasmids in mesophilic Aeromonas isolates from fish, water and sediment. Plasmid 2021; 118:102607. [PMID: 34800545 DOI: 10.1016/j.plasmid.2021.102607] [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: 05/29/2021] [Revised: 11/10/2021] [Accepted: 11/14/2021] [Indexed: 11/21/2022]
Abstract
Plasmids are autonomous genetic elements ubiquitously present in bacteria. In addition to containing genetic determinants responsible for their replication and stability, some plasmids may carry genes that help bacteria adapt to different environments, while others without a known function are classified as cryptic. In this work we identified and characterized plasmids from a collection of mesophilic Aeromonas spp. (N = 90) isolated from water, sediments and fish. A total of 15 small plasmids ranging from 2287 to 10,558 bp, with an incidence of 16.7% (15/90) was found. Plasmids were detected in A. hydrophila (6), A. veronii (4), A. taiwanensis (2), A. jandaei (1), A. media (1) and Aeromonas sp. (1). There were no large or megaplasmids in the strains studied in this work. Analysis of coding sequences identified proteins associated to replication, mobilization, antibiotic resistance, virulence and stability. A considerable number of hypothetical proteins with unknown functions were also found. Some strains shared identical plasmid profiles, however, only two of them were clones. Small plasmids could be acting as a gene repositories as suggested by the presence of a gene encoding for a putative zonula occludens toxin (Zot) that causes diarrhea and the qnrB gene involved in quinolone resistance harbored in plasmids pAerXII and pAerXIII respectively.
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8
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Liang Z, Zhang Y, He T, Yu Y, Liao W, Li G, An T. The formation mechanism of antibiotic-resistance genes associated with bacterial communities during biological decomposition of household garbage. JOURNAL OF HAZARDOUS MATERIALS 2020; 398:122973. [PMID: 32492618 DOI: 10.1016/j.jhazmat.2020.122973] [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: 03/08/2020] [Revised: 05/17/2020] [Accepted: 05/17/2020] [Indexed: 06/11/2023]
Abstract
Food wastes are significant reservoir of antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) available for exchange with clinical pathogens. However, food wastes-related changes of antibiotic resistance in long-period decomposition have been overlooked. Here, we evaluated the comprehensive ARG profile and its association with microbial communities, explained how this might vary with household garbage decomposition. Average of 128, 150 and 91 ARGs were detected in meat, vegetable and fruit wastes, respectively, with multidrug and tetracycline as the predominant ARG types. ARG abundance significantly increased at initial stage of waste fermentation and then decreased. High abundance of Eubacterium-coprostanoligenes, Sporanaerobacter, Peptoniphilus, Peptostreptococcus might be explained for the high relative abundance of ARGs in meat, while high abundance of Advenella, Prevotella, Solobacterium was attributed to the high diversity of ARGs in vegetables. Significant correlations were observed among volatile organic compounds, mobile genetic elements and ARGs, implying that they might contribute to transfer and transport of ARGs. Network analysis revealed that aph(2')-Id-01, acrA-05, tetO-1 were potential ARG indicators, while Hathewaya, Paraclostridium and Prevotellaceae were possible hosts of ARGs. Our work might unveil underlining mechanism of the effects of food wastes decomposition on development and spread of ARGs in environment and also clues to ARG mitigation.
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Affiliation(s)
- Zhishu Liang
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China
| | - Yuna Zhang
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China
| | - Tao He
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China
| | - Yun Yu
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China
| | - Wen Liao
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, 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, Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China.
| | - Taicheng An
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China
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Massicotte MA, Vincent AT, Schneider A, Paquet VE, Frenette M, Charette SJ. One Aeromonas salmonicida subsp. salmonicida isolate with a pAsa5 variant bearing antibiotic resistance and a pRAS3 variant making a link with a swine pathogen. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 690:313-320. [PMID: 31299566 DOI: 10.1016/j.scitotenv.2019.06.456] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/24/2019] [Accepted: 06/26/2019] [Indexed: 06/10/2023]
Abstract
The Gram-negative bacterium Aeromonas salmonicida subsp. salmonicida is an aquatic pathogen which causes furunculosis to salmonids, especially in fish farms. The emergence of strains of this bacterium exhibiting antibiotic resistance is increasing, limiting the effectiveness of antibiotherapy as a treatment against this worldwide disease. In the present study, we discovered an isolate of A. salmonicida subsp. salmonicida that harbors two novel plasmids variants carrying antibiotic resistance genes. The use of long-read sequencing (PacBio) allowed us to fully characterize those variants, named pAsa5-3432 and pRAS3-3432, which both differ from their classic counterpart through their content in mobile genetic elements. The plasmid pAsa5-3432 carries a new multidrug region composed of multiple mobile genetic elements, including a Class 1 integron similar to an integrated element of Salmonella enterica. With this new region, probably acquired through plasmid recombination, pAsa5-3432 is the first reported plasmid of this bacterium that bears both an essential virulence factor (the type three secretion system) and multiple antibiotic resistance genes. As for pRAS3-3432, compared to the classic pRAS3, it carries a new mobile element that has only been identified in Chlamydia suis. Hence, with the identification of those two novel plasmids harboring mobile genetic elements that are normally encountered in other bacterial species, the present study puts emphasis on the important impact of mobile genetic elements in the genomic plasticity of A. salmonicida subsp. salmonicida and suggests that this aquatic bacterium could be an important reservoir of antibiotic resistance genes that can be exchanged with other bacteria, including human and animal pathogens.
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Affiliation(s)
- Marie-Ange Massicotte
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City G1V 0A6, Quebec, Canada; Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Hôpital Laval, Quebec City, Quebec G1V 4G5, Canada; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval; Quebec City G1V 0A6, Quebec, Canada
| | - Antony T Vincent
- INRS-Institut Armand-Frappier, Bacterial Symbionts Evolution, Laval City H7V 1B7, QC, Canada
| | - Anna Schneider
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City G1V 0A6, Quebec, Canada; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval; Quebec City G1V 0A6, Quebec, Canada
| | - Valérie E Paquet
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City G1V 0A6, Quebec, Canada; Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Hôpital Laval, Quebec City, Quebec G1V 4G5, Canada; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval; Quebec City G1V 0A6, Quebec, Canada
| | - Michel Frenette
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval; Quebec City G1V 0A6, Quebec, Canada; Groupe de Recherche en Écologie Buccale (GREB), Faculté de médecine dentaire; Université Laval; Quebec City G1V 0A6, Quebec, Canada
| | - Steve J Charette
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City G1V 0A6, Quebec, Canada; Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Hôpital Laval, Quebec City, Quebec G1V 4G5, Canada; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval; Quebec City G1V 0A6, Quebec, Canada.
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10
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Argudín MA, Hoefer A, Butaye P. Heavy metal resistance in bacteria from animals. Res Vet Sci 2018; 122:132-147. [PMID: 30502728 DOI: 10.1016/j.rvsc.2018.11.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 11/06/2018] [Accepted: 11/11/2018] [Indexed: 01/19/2023]
Abstract
Resistance to metals and antimicrobials is a natural phenomenon that existed long before humans started to use these products for veterinary and human medicine. Bacteria carry diverse metal resistance genes, often harboured alongside antimicrobial resistance genes on plasmids or other mobile genetic elements. In this review we summarize the current knowledge about metal resistance genes in bacteria and we discuss their current use in the animal husbandry.
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Affiliation(s)
- M A Argudín
- National Reference Centre - Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium
| | - A Hoefer
- Department of Biomedical Sciences, University, School of Veterinary Medicine, Basseterre, PO Box 334, Saint Kitts and Nevis
| | - P Butaye
- Department of Biomedical Sciences, University, School of Veterinary Medicine, Basseterre, PO Box 334, Saint Kitts and Nevis; Department of Pathology, Bacteriology, and Avian Diseases, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium..
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Zhao R, Feng J, Yin X, Liu J, Fu W, Berendonk TU, Zhang T, Li X, Li B. Antibiotic resistome in landfill leachate from different cities of China deciphered by metagenomic analysis. WATER RESEARCH 2018; 134:126-139. [PMID: 29407646 DOI: 10.1016/j.watres.2018.01.063] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 01/20/2018] [Accepted: 01/25/2018] [Indexed: 05/08/2023]
Abstract
High throughput sequencing-based metagenomic analysis and network analysis were applied to investigate the broad-spectrum profiles of ARGs in landfill leachate from 12 cities in China. In total, 526 ARG subtypes belonging to 21 ARG types were detected with abundances ranging from 1.1 × 10-6 to 2.09 × 10-1 copy of ARG/copy of 16S rRNA gene. 68 ARG subtypes that accounted for 73.4%-93.4% of the total ARG abundances were shared by all leachate samples. The four most abundant ARGs, sul1, sul2, aadA and bacA can be served as ARG indicators to quantitatively predict the total abundances by linear functions (r2 = 0.577-0.819, P < 0.001). No distinct regional distribution pattern of the ARGs was observed among different cities in China, while the ARG compositions of the leachate were clearly distinct from those of other environmental sample types. Nearly 90% ARG subtypes in the anaerobic digestion sludge from sewage treatment plants (STPADS) were shared by the leachate and the abundances of leachate and STPADS ARGs generalists accounted for 84.5% and 87.7% of total abundances in these two types of anaerobic samples, respectively. Furthermore, Procrustes analysis suggested that microbial community composition might be the determining factor of ARG compositions in landfill leachate. ARGs within the same type or among the different types showed higher incidences of non-random co-occurrence and 17 genera might be potential hosts of multiple ARGs. This study highlighted that landfill leachate is an important reservoir of various ARGs and provided a useful reference for the surveillance and risk management of ARGs in landfill environments.
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Affiliation(s)
- Renxin Zhao
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China; School of Environment, Tsinghua University, Beijing 100084, China
| | - Jie Feng
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
| | - Xiaole Yin
- Environmental Biotechnology Laboratory, The University of Hong Kong, Hong Kong, China
| | - Jie Liu
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
| | - Wenjie Fu
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China; School of Environment, Tsinghua University, Beijing 100084, China
| | | | - Tong Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Hong Kong, China
| | - Xiaoyan Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
| | - Bing Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China.
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Pfeiffer F, Zamora-Lagos MA, Blettinger M, Yeroslaviz A, Dahl A, Gruber S, Habermann BH. The complete and fully assembled genome sequence of Aeromonas salmonicida subsp. pectinolytica and its comparative analysis with other Aeromonas species: investigation of the mobilome in environmental and pathogenic strains. BMC Genomics 2018; 19:20. [PMID: 29304740 PMCID: PMC5756416 DOI: 10.1186/s12864-017-4301-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 11/13/2017] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Due to the predominant usage of short-read sequencing to date, most bacterial genome sequences reported in the last years remain at the draft level. This precludes certain types of analyses, such as the in-depth analysis of genome plasticity. RESULTS Here we report the finalized genome sequence of the environmental strain Aeromonas salmonicida subsp. pectinolytica 34mel, for which only a draft genome with 253 contigs is currently available. Successful completion of the transposon-rich genome critically depended on the PacBio long read sequencing technology. Using finalized genome sequences of A. salmonicida subsp. pectinolytica and other Aeromonads, we report the detailed analysis of the transposon composition of these bacterial species. Mobilome evolution is exemplified by a complex transposon, which has shifted from pathogenicity-related to environmental-related gene content in A. salmonicida subsp. pectinolytica 34mel. CONCLUSION Obtaining the complete, circular genome of A. salmonicida subsp. pectinolytica allowed us to perform an in-depth analysis of its mobilome. We demonstrate the mobilome-dependent evolution of this strain's genetic profile from pathogenic to environmental.
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Affiliation(s)
- Friedhelm Pfeiffer
- Computational Biology Group, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Maria-Antonia Zamora-Lagos
- Computational Biology Group, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Martin Blettinger
- Research Group Chromosome Organization and Dynamics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Assa Yeroslaviz
- Computational Biology Group, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Andreas Dahl
- Biotechnology Center (biotec), Technical University Dresden, Tatzberg 47, 1307 Dresden, Germany
| | - Stephan Gruber
- Research Group Chromosome Organization and Dynamics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Bianca H. Habermann
- Computational Biology Group, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
- Computational Biology Group, Developmental Biology Institute of Marseille (IBDM) UMR 7288, Aix Marseille Universite, Parc Scientifique de Luminy, 163 Avenue de Luminy, 13009 Marseille, France
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Uhrynowski W, Decewicz P, Dziewit L, Radlinska M, Krawczyk PS, Lipinski L, Adamska D, Drewniak L. Analysis of the Genome and Mobilome of a Dissimilatory Arsenate Reducing Aeromonas sp. O23A Reveals Multiple Mechanisms for Heavy Metal Resistance and Metabolism. Front Microbiol 2017; 8:936. [PMID: 28611742 PMCID: PMC5446998 DOI: 10.3389/fmicb.2017.00936] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 05/09/2017] [Indexed: 12/28/2022] Open
Abstract
Aeromonas spp. are among the most ubiquitous microorganisms, as they have been isolated from different environmental niches including waters, soil, as well as wounds and digestive tracts of poikilothermic animals and humans. Although much attention has been paid to the pathogenicity of Aeromonads, the role of these bacteria in environmentally important processes, such as transformation of heavy metals, remains to be discovered. Therefore, the aim of this study was a detailed genomic characterization of Aeromonas sp. O23A, the first representative of this genus capable of dissimilatory arsenate reduction. The strain was isolated from microbial mats from the Zloty Stok mine (SW Poland), an environment strongly contaminated with arsenic. Previous physiological studies indicated that O23A may be involved in both mobilization and immobilization of this metalloid in the environment. To discover the molecular basis of the mechanisms behind the observed abilities, the genome of O23A (∼5.0 Mbp) was sequenced and annotated, and genes for arsenic respiration, heavy metal resistance (hmr) and other phenotypic traits, including siderophore production, were identified. The functionality of the indicated gene modules was assessed in a series of minimal inhibitory concentration analyses for various metals and metalloids, as well as mineral dissolution experiments. Interestingly, comparative analyses revealed that O23A is related to a fish pathogen Aeromonas salmonicida subsp. salmonicida A449 which, however, does not carry genes for arsenic respiration. This indicates that the dissimilatory arsenate reduction ability may have been lost during genome reduction in pathogenic strains, or acquired through horizontal gene transfer. Therefore, particular emphasis was placed upon the mobilome of O23A, consisting of four plasmids, a phage, and numerous transposable elements, which may play a role in the dissemination of hmr and arsenic metabolism genes in the environment. The obtained results indicate that Aeromonas sp. O23A is well-adapted to the extreme environmental conditions occurring in the Zloty Stok mine. The analysis of genome encoded traits allowed for a better understanding of the mechanisms of adaptation of the strain, also with respect to its presumable role in colonization and remediation of arsenic-contaminated waters, which may never have been discovered based on physiological analyses alone.
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Affiliation(s)
- Witold Uhrynowski
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of WarsawWarsaw, Poland
| | - Przemyslaw Decewicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of WarsawWarsaw, Poland
| | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of WarsawWarsaw, Poland
| | - Monika Radlinska
- Department of Virology, Institute of Microbiology, Faculty of Biology, University of WarsawWarsaw, Poland
| | - Pawel S Krawczyk
- Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsaw, Poland
| | - Leszek Lipinski
- Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsaw, Poland
| | - Dorota Adamska
- Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsaw, Poland
| | - Lukasz Drewniak
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of WarsawWarsaw, Poland
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