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Guruge KS, Goswami P, Kanda K, Abeynayaka A, Kumagai M, Watanabe M, Tamamura-Andoh Y. Plastiome: Plastisphere-enriched mobile resistome in aquatic environments. JOURNAL OF HAZARDOUS MATERIALS 2024; 471:134353. [PMID: 38678707 DOI: 10.1016/j.jhazmat.2024.134353] [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: 02/08/2024] [Revised: 03/28/2024] [Accepted: 04/17/2024] [Indexed: 05/01/2024]
Abstract
Aquatic microplastics (MPs) act as reservoirs for microbial communities, fostering the formation of a mobile resistome encompassing diverse antibiotic (ARGs) and biocide/metal resistance genes (BMRGs), and mobile genetic elements (MGEs). This collective genetic repertoire, referred to as the "plastiome," can potentially perpetuate environmental antimicrobial resistance (AMR). Our study examining two Japanese rivers near Tokyo revealed that waterborne MPs are primarily composed of polyethylene and polypropylene fibers and sheets of diverse origin. Clinically important genera like Exiguobacterium and Eubacterium were notably enriched on MPs. Metagenomic analysis uncovered a 3.46-fold higher enrichment of ARGs on MPs than those in water, with multidrug resistance genes (MDRGs) and BMRGs prevailing, particularly within MPs. Specific ARG and BMRG subtypes linked to resistance to vancomycin, beta-lactams, biocides, arsenic, and mercury showed selective enrichment on MPs. Network analysis revealed intense associations between host genera with ARGs, BMRGs, and MGEs on MPs, emphasizing their role in coselection. In contrast, river water exhibited weaker associations. This study underscores the complex interactions shaping the mobile plastiome in aquatic environments and emphasizes the global imperative for research to comprehend and effectively control AMR within the One Health framework.
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Affiliation(s)
- Keerthi S Guruge
- Hygiene Management Group, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan.
| | - Prasun Goswami
- Hygiene Management Group, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | - Kazuki Kanda
- Hygiene Management Group, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | - Amila Abeynayaka
- Pirika Inc., 1 Chome-7-2, Ebisu, Shibuya City, Tokyo 150-6018, Japan; Quantitative Sustainability Assessment, Department of Environmental and Resource Engineering, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Masahiko Kumagai
- Bioinformatics Team, Research Center for Advanced Analysis, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | - Mafumi Watanabe
- Hygiene Management Group, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | - Yukino Tamamura-Andoh
- Enteric Pathogen Group, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
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Lu J, Sha Y, Gao M, Shi W, Lin X, Li K, Bao Q, Feng C. Identification and characterization of a novel aminoglycoside O-nucleotidyltransferase ANT(6)-If from Paenibacillus thiaminolyticus PATH554. Front Microbiol 2023; 14:1184349. [PMID: 37455719 PMCID: PMC10343464 DOI: 10.3389/fmicb.2023.1184349] [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: 03/11/2023] [Accepted: 06/07/2023] [Indexed: 07/18/2023] Open
Abstract
Background Paenibacillus thiaminolyticus, a species of genus Paenibacillus of the family Paenibacillaceae, exists widely in environments and habitats in various plants and worms, and occasionally causes human infections. This work aimed to characterize the function of a novel aminoglycoside O-nucleotidyltransferase resistance gene, designated ant(6)-If, from a P. thiaminolyticus strain PATH554. Methods Molecular cloning, antimicrobial susceptibility testing, enzyme expression and purification, and kinetic analysis were used to validate the function of the novel gene. Whole-genome sequencing and comparative genomic analysis were performed to investigate the phylogenetic relationship of ANT(6)-If and other aminoglycoside O-nucleotidyltransferases, and the synteny of ant(6)-If related sequences. Results The recombinant with the cloned ant(6)-If gene (pMD19-ant(6)-If/DH5α) demonstrated a 128-fold increase of minimum inhibitory concentration level against streptomycin, compared with the control strains (DH5α and pMD19/DH5α). The kinetic parameter kcat/Km of ANT(6)-If for streptomycin was 9.01 × 103 M-1·s-1. Among the function-characterized resistance genes, ANT(6)-If shared the highest amino acid sequence identity of 75.35% with AadK. The ant(6)-If gene was located within a relatively conserved genomic region in the chromosome. Conclusion ant(6)-If conferred resistance to streptomycin. The study of a novel resistance gene in an unusual environmental bacterium in this work contributed to elucidating the resistance mechanisms in the microorganisms.
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Affiliation(s)
- Junwan Lu
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Institute of Biomedical Informatics, Ministry of Education, Wenzhou Medical University, Wenzhou, China
| | - Yuning Sha
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Institute of Biomedical Informatics, Ministry of Education, Wenzhou Medical University, Wenzhou, China
| | - Mengdi Gao
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Institute of Biomedical Informatics, Ministry of Education, Wenzhou Medical University, Wenzhou, China
| | - Weina Shi
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Institute of Biomedical Informatics, Ministry of Education, Wenzhou Medical University, Wenzhou, China
| | - Xi Lin
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Institute of Biomedical Informatics, Ministry of Education, Wenzhou Medical University, Wenzhou, China
| | - Kewei Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Institute of Biomedical Informatics, Ministry of Education, Wenzhou Medical University, Wenzhou, China
| | - Qiyu Bao
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Institute of Biomedical Informatics, Ministry of Education, Wenzhou Medical University, Wenzhou, China
| | - Chunlin Feng
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Institute of Biomedical Informatics, Ministry of Education, Wenzhou Medical University, Wenzhou, China
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Li S, Gao H, Zhang H, Wei G, Shu Q, Li R, Jin S, Na G, Shi Y. The fate of antibiotic resistance genes in the coastal lagoon with multiple functional zones. J Environ Sci (China) 2023; 128:93-106. [PMID: 36801045 DOI: 10.1016/j.jes.2022.07.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 07/13/2022] [Accepted: 07/13/2022] [Indexed: 06/18/2023]
Abstract
Coastal lagoons provide many important services to human society, but their year-round use for aquaculture introduces large amounts of sewage. The contamination of antibiotic resistance genes (ARGs) is therefore of great concern. In this study, 50 ARGs subtypes, two integrase genes (intl1, intl2), and 16S rRNA genes were detected by high-throughput quantitative PCR, and standard curves of all target genes were prepared for quantification. The occurrence and distribution of ARGs in a typical coastal lagoon (XinCun lagoon, China) were comprehensively explored. We detected 44 and 38 subtypes of ARGs in the water and sediment, respectively, and discuss the various factors influencing the fate of ARGs in the coastal lagoon. Macrolides-lincosamides-streptogramins B was the primary ARG type, and macB was the predominant subtype. Antibiotic efflux and antibiotic inactivation were the main ARG resistance mechanisms. The XinCun lagoon was divided into eight functional zones. The ARGs showed a distinct spatial distribution owing to the influence of microbial biomass and anthropogenic activity in different functional zones. Fishing rafts, abandoned fish ponds, the town sewage zone, and mangrove wetlands provided a large quantity of ARGs to the XinCun lagoon. Nutrients and heavy metals also significantly correlated with the fate of the ARGs, especially NO2--N and Cu, which cannot be ignored. It is noteworthy that lagoon-barrier systems coupled with persistent pollutant inputs result in coastal lagoons acting as a "buffer pool" for ARGs, which can then accumulate and threaten the offshore environment.
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Affiliation(s)
- Shisheng Li
- National Marine Environmental Monsitoring Center, Dalian 116023, China; College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Hui Gao
- National Marine Environmental Monsitoring Center, Dalian 116023, China
| | - Haibo Zhang
- National Marine Environmental Monsitoring Center, Dalian 116023, China
| | - Guangke Wei
- Laboratory for coastal marine eco-environment process and carbon sink of Hainan provincet/Yazhou Bay Innovation Institute, Hainan Tropical Ocean University, Sanya 572022, China
| | - Qin Shu
- National Marine Environmental Monsitoring Center, Dalian 116023, China; College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Ruijing Li
- National Marine Environmental Monsitoring Center, Dalian 116023, China
| | - Shuaichen Jin
- National Marine Environmental Monsitoring Center, Dalian 116023, China
| | - Guangshui Na
- Laboratory for coastal marine eco-environment process and carbon sink of Hainan provincet/Yazhou Bay Innovation Institute, Hainan Tropical Ocean University, Sanya 572022, China; National Marine Environmental Monsitoring Center, Dalian 116023, China; College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China.
| | - Yali Shi
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China.
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Gusman VP, Medić DD, Trudić AD, Banović PZ, Nikolić NM. First Isolation of Exiguobacterium aurantiacum in Serbia. Pol J Microbiol 2021; 70:405-407. [PMID: 34584535 PMCID: PMC8458997 DOI: 10.33073/pjm-2021-037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/16/2021] [Accepted: 07/28/2021] [Indexed: 11/21/2022] Open
Abstract
Exiguobacterium aurantiacum is isolated from a variety of environmental samples but rarely from patients. The aim of the study was to represent isolation of unusual bacterial strains that could cause infection in patients. Final identification was performed using matrix-assisted description/ionization time-of-flight mass spectrometry (MALDI-TOF). Two isolates strains of E. aurantiacum were isolated, one isolate from distilled water used during surgical treatment and the second one from a patient with bacteremia after radical prostatectomy, both sensitive to all tested antimicrobials. Environmental strains could cause infection, especially in immunocompromised patients; therefore, rare bacteria testing is required, in which identification special assistance is provided by an automated system MALDI-TOF.
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Affiliation(s)
- Vera P Gusman
- Department of Microbiology, Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia.,Institute of Public Health of Vojvodina, Novi Sad, Serbia
| | - Deana D Medić
- Department of Microbiology, Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia.,Institute of Public Health of Vojvodina, Novi Sad, Serbia
| | - Anika Dj Trudić
- Department of Microbiology, Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia.,Institute for Pulmonary Diseases of Vojvodina, Sremska Kamenica, Serbia
| | - Pavle Z Banović
- Department of Microbiology, Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia.,Pasteur Institute of Novi Sad, Novi Sad, Serbia
| | - Nataša M Nikolić
- Department of Microbiology, Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia.,Institute of Public Health of Vojvodina, Novi Sad, Serbia
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The Resistome and Mobilome of Multidrug-Resistant Staphylococcus sciuri C2865 Unveil a Transferable Trimethoprim Resistance Gene, Designated dfrE, Spread Unnoticed. mSystems 2021; 6:e0051121. [PMID: 34374564 PMCID: PMC8407400 DOI: 10.1128/msystems.00511-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Methicillin-resistant Staphylococcus sciuri (MRSS) strain C2865 from a stranded dog in Nigeria was trimethoprim (TMP) resistant but lacked formerly described staphylococcal TMP-resistant dihydrofolate reductase genes (dfr). Whole-genome sequencing, comparative genomics, and pan-genome analyses were pursued to unveil the molecular bases for TMP resistance via resistome and mobilome profiling. MRSS C2865 comprised a species subcluster and positioned just above the intraspecies boundary. Lack of species host tropism was observed. S. sciuri exhibited an open pan-genome, while MRSS C2865 harbored the highest number of unique genes (75% associated with mobilome). Within this fraction, we discovered a transferable TMP resistance gene, named dfrE, which confers high-level TMP resistance in Staphylococcus aureus and Escherichia coli. dfrE was located in a novel multidrug resistance mosaic plasmid (pUR2865-34) encompassing adaptive, mobilization, and segregational stability traits. dfrE was formerly denoted as dfr_like in Exiguobacterium spp. from fish farm sediment in China but escaped identification in one macrococcal and diverse staphylococcal genomes in different Asian countries. dfrE shares the highest identity with dfr of soil-related Paenibacillus anaericanus (68%). Data analysis discloses that dfrE has emerged from a single ancestor and places S. sciuri as a plausible donor. C2865 unique fraction additionally enclosed novel chromosomal mobile islands, including a multidrug-resistant pseudo-SCCmec cassette, three apparently functional prophages (Siphoviridae), and an SaPI4-related staphylococcal pathogenicity island. Since dfrE seems not yet common in staphylococcal clinical specimens, our data promote early surveillance and enable molecular diagnosis. We evidence the genome plasticity of S. sciuri and highlight its role as a resourceful reservoir for adaptive traits. IMPORTANCE The discovery and surveillance of antimicrobial resistance genes (AMRG) and their mobilization platforms are critical to understand the evolution of bacterial resistance and to restrain further expansion. Limited genomic data are available on Staphylococcus sciuri; regardless, it is considered a reservoir for critical AMRG and mobile elements. We uncover a transferable staphylococcal TMP resistance gene, named dfrE, in a novel mosaic plasmid harboring additional resistance, adaptive, and self-stabilization features. dfrE is present but evaded detection in diverse species from varied sources geographically distant. Our analyses evidence that the dfrE-carrying element has emerged from a single ancestor and position S. sciuri as the donor species for dfrE spread. We also identify novel mobilizable chromosomal islands encompassing AMRG and three unrelated prophages. We prove high intraspecies heterogenicity and genome plasticity for S. sciuri. This work highlights the importance of genome-wide ecological studies to facilitate identification, characterization, and evolution routes of bacteria adaptive features.
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Mao Y, Zeineldin M, Usmani M, Uprety S, Shisler JL, Jutla A, Unnikrishnan A, Nguyen TH. Distribution and Antibiotic Resistance Profiles of Salmonella enterica in Rural Areas of North Carolina After Hurricane Florence in 2018. GEOHEALTH 2021; 5:e2020GH000294. [PMID: 33709047 PMCID: PMC7892206 DOI: 10.1029/2020gh000294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 12/10/2020] [Accepted: 12/15/2020] [Indexed: 05/07/2023]
Abstract
In this study, water samples were analyzed from a rural area of North Carolina after Hurricane Florence in 2018 and the distribution of the ttrC virulence gene of Salmonella enterica were investigated. We also examined the distribution of culturable S. enterica and determined their antibiotic resistance profiles. Antibiotic resistance genes (ARGs) in the classes of aminoglycoside, beta-lactam, and macrolide-lincosamide-streptogramin B (MLSB) were targeted in this study. The ttrC gene was detected in 23 out of 25 locations. There was a wider and higher range of the ttrC gene in flooded water versus unflooded water samples (0-2.12 × 105 copies/L vs. 0-4.86 × 104 copies/L). Culturable S. enterica was isolated from 10 of 25 sampling locations, which was less prevalent than the distribution of the ttrC gene. The antibiotic resistance profiles were not distinct among the S. enterica isolates. The aminoglycoside resistance gene aac(6')-Iy had the highest relative abundance (around 0.05 copies/16S rRNA gene copy in all isolates) among all ARGs. These findings suggested that the 2018 flooding event led to higher copy numbers of the ttrC genes of S. enterica in some flooded water bodies compared to those in unflooded water bodies. The high ARG level and similar ARG profiles were observed in all S. enterica isolates from both flooded and unflooded samples, suggesting that the antibiotic resistance was prevalent in S. enterica within this region, regardless of flooding.
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Affiliation(s)
- Yuqing Mao
- Department of Civil and Environmental EngineeringUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
| | - Mohamed Zeineldin
- Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
- Animal Medicine DepartmentCollege of Veterinary MedicineBenha UniversityBenhaEgypt
| | - Moiz Usmani
- Environmental Engineering SciencesUniversity of FloridaGainesvilleFLUSA
| | - Sital Uprety
- Department of Civil and Environmental EngineeringUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
| | - Joanna L. Shisler
- Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
- Department of MicrobiologyUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
| | - Antarpreet Jutla
- Environmental Engineering SciencesUniversity of FloridaGainesvilleFLUSA
| | | | - Thanh H. Nguyen
- Department of Civil and Environmental EngineeringUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
- Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
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Zhao Z. Comparison of microbial communities and the antibiotic resistome between prawn mono- and poly-culture systems. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 207:111310. [PMID: 32937228 DOI: 10.1016/j.ecoenv.2020.111310] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/01/2020] [Accepted: 09/05/2020] [Indexed: 06/11/2023]
Abstract
Antibiotic resistance genes (ARGs) in mariculture sediments pose a potential risk to public health due to their ability to transfer from environmental bacteria to human pathogens. Long term, this may reduce pathogen susceptibility to antibiotics in medical settings. In recent years, the poly-culture of multiple species has become a popular mariculture approach in China, thanks to its environmental and economic benefits. However, differences in microbial communities and antibiotic resistome between mono- and poly-culture systems are still unclear. In this study, microbial community composition and profiles of entire (microbial DNA) and mobile (plasmid and phage) ARGs in prawn mono- and poly-culture systems were investigated using metagenomics. The abundance of several viruses and human pathogens were enhanced in prawn poly-culture ponds, when compared to monoculture systems. In contrast, sediments from poly-culture systems had a lower diversity and ARG abundance when compared to mono-culture approaches. These ARG variations were predominantly related to mobile genetic elements. Prawn mariculture activities exerted a unique selectivity for ARGs in plasmids, and this selectivity was not influenced by culture methods. The findings of this study have important implications for the selection of mariculture systems in preventing pollution with ARGs.
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Affiliation(s)
- Zelong Zhao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, Liaoning, PR China.
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8
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Han Y, Wang J, Zhao Z, Chen J, Lu H, Liu G. Detecting antibiotic resistance genes and human potential pathogenic Bacteria in fishmeal by culture-independent method. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:8665-8674. [PMID: 30707381 DOI: 10.1007/s11356-019-04303-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/22/2019] [Indexed: 06/09/2023]
Abstract
Fishmeal is a fundamental ingredient of feedstuffs and is used globally in aquaculture. However, there are few data on the antibiotic resistance genes (ARGs) and human pathogenic bacteria in fishmeal and little understanding of the potential risks of fishmeal application in mariculture systems. Here, we investigated the high-throughput profiles of ARGs and human potential pathogenic bacteria (HPPB) in representative fishmeals (n = 5) and the potential impact of fishmeal on mariculture sediments. ARGs were quantified with microbial DNA quantitative PCR arrays and HPPB were analyzed with Illumina sequencing of 16S rRNA genes. The impact of the fishmeal on the aquaculture sediments was assessed in a microcosm study. Twenty-four unique ARGs (3-14 per sample) and 25 HPPB species were detected in the fishmeal samples. The most prevalent ARGs were fluoroquinolone resistance genes. The overall abundance of HPPB was 5.0-25.5%, and the HPPB species were dominated by Vibrio parahaemolyticus, Clostridium novyi, and Escherichia coli. In the mariculture microcosm sediment, fishmeal significantly increased the normalized abundance of the class I integrase gene (25.4-fold), which plays an important role in the dissemination of ARGs. Dosing with fishmeal also contributed to increases in a resident sulfanilamide resistance gene (sulI gene) and the emergence of a macrolide resistance gene (ermB gene) in the sediment. These findings demonstrated that fishmeal itself is an underestimated reservoir and source of ARGs and HPPBs, and that the application of fishmeal facilitates the dissemination of ARGs in aquaculture sediments. Our results extend our knowledge of the ARGs and HPPB within fishmeal and may provide a feasible and effective approach to the detection of ARGs and HPPB in fishmeal during food safety inspection. Graphical abstract ᅟ.
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Affiliation(s)
- Ying Han
- Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, 2#Linggong Road, Ganjingzi District, Dalian, Liaoning, 116024, People's Republic of China
| | - Jing Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, 2#Linggong Road, Ganjingzi District, Dalian, Liaoning, 116024, People's Republic of China.
| | - Zelong Zhao
- Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, 2#Linggong Road, Ganjingzi District, Dalian, Liaoning, 116024, People's Republic of China
| | - Jingwen Chen
- Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, 2#Linggong Road, Ganjingzi District, Dalian, Liaoning, 116024, People's Republic of China
| | - Hong Lu
- Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, 2#Linggong Road, Ganjingzi District, Dalian, Liaoning, 116024, People's Republic of China
| | - Guangfei Liu
- Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, 2#Linggong Road, Ganjingzi District, Dalian, Liaoning, 116024, People's Republic of China
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9
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The evolution of substrate discrimination in macrolide antibiotic resistance enzymes. Nat Commun 2018; 9:112. [PMID: 29317655 PMCID: PMC5760710 DOI: 10.1038/s41467-017-02680-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 12/19/2017] [Indexed: 12/13/2022] Open
Abstract
The production of antibiotics by microbes in the environment and their use in medicine and agriculture select for existing and emerging resistance. To address this inevitability, prudent development of antibiotic drugs requires careful consideration of resistance evolution. Here, we identify the molecular basis for expanded substrate specificity in MphI, a macrolide kinase (Mph) that does not confer resistance to erythromycin, in contrast to other known Mphs. Using a combination of phylogenetics, drug-resistance phenotypes, and in vitro enzyme assays, we find that MphI and MphK phosphorylate erythromycin poorly resulting in an antibiotic-sensitive phenotype. Using likelihood reconstruction of ancestral sequences and site-saturation combinatorial mutagenesis, supported by Mph crystal structures, we determine that two non-obvious mutations in combination expand the substrate range. This approach should be applicable for studying the functional evolution of any antibiotic resistance enzyme and for evaluating the evolvability of resistance enzymes to new generations of antibiotic scaffolds. New antibiotics with reduced potential for resistance are urgently needed. Here, the authors use a multidisciplinary approach to characterize substrate discrimination in macrolide resistance kinases and present a strategy for the prediction of mutations that expand the substrate range of antibiotic-inactivating enzymes.
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Cong M, Jiang Q, Xu X, Huang L, Su Y, Yan Q. The complete genome sequence of Exiguobacterium arabatum W-01 reveals potential probiotic functions. Microbiologyopen 2017; 6. [PMID: 28589562 PMCID: PMC5635162 DOI: 10.1002/mbo3.496] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 04/01/2017] [Accepted: 04/10/2017] [Indexed: 12/27/2022] Open
Abstract
Shrimp is extensively cultured worldwide. Shrimp farming is suffering from a variety of diseases. Probiotics are considered to be one of the effective methods to prevent and cure shrimp diseases. Exiguobacterium arabatum W‐01, a gram‐positive and orange‐pigmented bacterium, was isolated from the intestine of a healthy Penaeus vannamei specimen. Whole‐genome sequencing revealed a genome of 2,914,854 bp, with 48.02% GC content. In total, 3,083 open reading frames (ORFs) were identified, with an average length of 843.98 bp and a mean GC content of 48.11%, accounting for 89.27% of the genome. Among these ORFs, 2,884 (93.5%) genes were classified into Clusters of Orthologous Groups (COG) families comprising 21 functional categories, and 1,650 ORFs were classified into 83 functional Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. A total of 27 rRNA operons and 68 tRNAs were identified, with all 20 amino acids represented. In addition, 91 genomic islands, 68 potential prophages, and 33 tandem repeats, but no clustered regularly interspaced short palindromic repeats (CRISPRs), were found. No resistance genes and only one virulence gene were identified. Among the 150 secreted proteins of E. arabatum W‐01, a variety of transport system substrate‐binding proteins, enzymes, and biosynthetic proteins, which play important roles in the uptake and metabolism of nutrients, were found. Two adherence‐related protein genes and 31 flagellum‐related protein genes were also identified. Taken together, these results indicate potential probiotic functions for E. arabatum W‐01.
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Affiliation(s)
- Meinan Cong
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, Fujian, China
| | - Qingling Jiang
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, Fujian, China
| | - Xiaojin Xu
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, Fujian, China
| | - Lixing Huang
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, Fujian, China
| | - Yongquan Su
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde, Fujian, China.,College of Ocean & Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Qingpi Yan
- Fisheries College, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, Fujian, China.,State Key Laboratory of Large Yellow Croaker Breeding, Ningde, Fujian, China
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Draft Genome Sequence of Alkaliphilic Exiguobacterium sp. Strain HUD, Isolated from a Polymicrobial Consortia. GENOME ANNOUNCEMENTS 2015; 3:3/1/e01451-14. [PMID: 25614564 PMCID: PMC4319586 DOI: 10.1128/genomea.01451-14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
An alkaliphilic microorganism from the genus Exiguobacterium, Exiguobacterium sp. strain HUD was isolated from a fermentative, methanogenic polymicrobial microcosm operating at pH 10. The draft genome shows the presence of genes encoding for the metabolism of a range of carbohydrates under both aerobic and anaerobic conditions.
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Schaumann S, Staufenbiel I, Scherer R, Schilhabel M, Winkel A, Stumpp SN, Eberhard J, Stiesch M. Pyrosequencing of supra- and subgingival biofilms from inflamed peri-implant and periodontal sites. BMC Oral Health 2014; 14:157. [PMID: 25518856 PMCID: PMC4298060 DOI: 10.1186/1472-6831-14-157] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 12/15/2014] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND To investigate the microbial composition of biofilms at inflamed peri-implant and periodontal tissues in the same subject, using 16S rRNA sequencing. METHODS Supra- and submucosal, and supra- and subgingival plaque samples were collected from 7 subjects suffering from diseased peri-implant and periodontal tissues. Bacterial DNA was isolated and 16S rRNA genes were amplified, sequenced and aligned for the identification of bacterial genera. RESULTS 43734 chimera-depleted, denoised sequences were identified, corresponding to 1 phylum, 8 classes, 10 orders, 44 families and 150 genera. The most abundant families or genera found in supramucosal or supragingival plaque were Streptoccocaceae, Rothia and Porphyromonas. In submucosal plaque, the most abundant family or genera found were Rothia, Streptococcaceae and Porphyromonas on implants. The most abundant subgingival bacteria on teeth were Prevotella, Streptococcaceae, and TG5. The number of sequences found for the genera Tannerella and Aggregatibacter on implants differed significantly between supra- and submucosal locations before multiple testing. The analyses demonstrated no significant differences between microbiomes on implants and teeth in supra- or submucosal and supra- or subgingival biofilms. CONCLUSION Diseased peri-implant and periodontal tissues in the same subject share similiar bacterial genera and based on the analysis of taxa on a genus level biofilm compositions may not account for the potentially distinct pathologies at implants or teeth.
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Affiliation(s)
- Simone Schaumann
- />Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Hannover, Germany
| | - Ingmar Staufenbiel
- />Department of Conservative Dentistry, Periodontology and Preventive Dentistry, Hannover Medical School, Hannover, Germany
| | - Ralph Scherer
- />Institute for Biometry, Hannover Medical School, Hannover, Germany
| | - Markus Schilhabel
- />Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Andreas Winkel
- />Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Hannover, Germany
| | - Sascha Nico Stumpp
- />Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Hannover, Germany
| | - Jörg Eberhard
- />Peri-implant and Oral Infections, Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Meike Stiesch
- />Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Hannover, Germany
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Wang C, Sui Z, Leclercq SO, Zhang G, Zhao M, Chen W, Feng J. Functional characterization and phylogenetic analysis of acquired and intrinsic macrolide phosphotransferases in theBacillus cereusgroup. Environ Microbiol 2014; 17:1560-73. [DOI: 10.1111/1462-2920.12578] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 07/21/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Chao Wang
- State Key Laboratory of Microbial Resources; Institute of Microbiology; Chinese Academy of Sciences; Beijing 100101 China
| | - Zhihai Sui
- State Key Laboratory of Microbial Resources; Institute of Microbiology; Chinese Academy of Sciences; Beijing 100101 China
| | - Sébastien Olivier Leclercq
- State Key Laboratory of Microbial Resources; Institute of Microbiology; Chinese Academy of Sciences; Beijing 100101 China
| | - Gang Zhang
- State Key Laboratory of Microbial Resources; Institute of Microbiology; Chinese Academy of Sciences; Beijing 100101 China
| | - Meilin Zhao
- School of Food and Biological Engineering; Jiangsu University; Zhenjiang Jiangsu 212013 China
| | - Weiqi Chen
- Department of Environmental and Biological Pharmaceutical; Beijing Industrial Technician College; Beijing 100023 China
| | - Jie Feng
- State Key Laboratory of Microbial Resources; Institute of Microbiology; Chinese Academy of Sciences; Beijing 100101 China
- Beijing Key Laboratory of Microbial Drug Resistance and Resistome; Beijing 100101 China
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