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Eladawy M, Thomas JC, Hoyles L. Phenotypic and genomic characterization of Pseudomonas aeruginosa isolates recovered from catheter-associated urinary tract infections in an Egyptian hospital. Microb Genom 2023; 9:001125. [PMID: 37902186 PMCID: PMC10634444 DOI: 10.1099/mgen.0.001125] [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: 07/20/2023] [Accepted: 10/12/2023] [Indexed: 10/31/2023] Open
Abstract
Catheter-associated urinary tract infections (CAUTIs) represent one of the major healthcare-associated infections, and Pseudomonas aeruginosa is a common Gram-negative bacterium associated with catheter infections in Egyptian clinical settings. The present study describes the phenotypic and genotypic characteristics of 31 P. aeruginosa isolates recovered from CAUTIs in an Egyptian hospital over a 3 month period. Genomes of isolates were of good quality and were confirmed to be P. aeruginosa by comparison to the type strain (average nucleotide identity, phylogenetic analysis). Clonal diversity among the isolates was determined; eight different sequence types were found (STs 244, 357, 381, 621, 773, 1430, 1667 and 3765), of which ST357 and ST773 are considered to be high-risk clones. Antimicrobial resistance (AMR) testing according to European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines showed that the isolates were highly resistant to quinolones [ciprofloxacin (12/31, 38.7 %) and levofloxacin (9/31, 29 %) followed by tobramycin (10/31, 32.5 %)] and cephalosporins (7/31, 22.5 %). Genotypic analysis of resistance determinants predicted all isolates to encode a range of AMR genes, including those conferring resistance to aminoglycosides, β-lactamases, fluoroquinolones, fosfomycin, sulfonamides, tetracyclines and chloramphenicol. One isolate was found to carry a 422 938 bp pBT2436-like megaplasmid encoding OXA-520, the first report from Egypt of this emerging family of clinically important mobile genetic elements. All isolates were able to form biofilms and were predicted to encode virulence genes associated with adherence, antimicrobial activity, anti-phagocytosis, phospholipase enzymes, iron uptake, proteases, secretion systems and toxins. The present study shows how phenotypic analysis alongside genomic analysis may help us understand the AMR and virulence profiles of P. aeruginosa contributing to CAUTIs in Egypt.
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Affiliation(s)
- Mohamed Eladawy
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Jonathan C. Thomas
- 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
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Peng W, Lin S, Deng Z, Liang R. Bioaugmentation removal and microbiome analysis of the synthetic estrogen 17α-ethynylestradiol from hostile conditions and environmental samples by Pseudomonas citronellolis SJTE-3. CHEMOSPHERE 2023; 317:137893. [PMID: 36690257 DOI: 10.1016/j.chemosphere.2023.137893] [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: 07/08/2022] [Revised: 01/05/2023] [Accepted: 01/15/2023] [Indexed: 06/17/2023]
Abstract
Synthetic estrogens are emerging environmental contaminants with great estrogenic activities and stable structures that are widespread in various ecological systems and significantly threaten the health of organisms. Pseudomonas citronellolis SJTE-3 is reported to degrade the synthetic estrogen 17α-ethynylestradiol (EE2) efficiently in laboratory conditions. In this work, the environmental adaptability, the EE2-degrading properties, and the ecological effects of P. citronellolis SJTE-3 under different hostile conditions (heavy metals and surfactants) and various natural environment samples (solid soil, lake water, and pig manure) were studied. Strain SJTE-3 can tolerate high concentrations of Zn2+ and Cr3+, but is relatively sensitive to Cu2+. Tween 80 of low concentration can significantly promote EE2 degradation by strain SJTE-3, different from the repressing effect of Triton X-100. High concentration of Tween 80 prolonged the lagging phase of EE2-degrading process, while the final EE2 removal efficiency was improved. More importantly, strain SJTE-3 can grow normally and degrade estrogen stably in various environmental samples. Inoculation of strain SJTE-3 removed the intrinsic synthetic and natural estrogens (EE2 and estrone) in lake water samples in 4 days, and eliminated over 90% of the amended 1 mg/L EE2 in 2 days. Bioaugmentation of strain SJTE-3 in EE2-supplied solid soil and pig manure samples achieved a removal rate of over 55% and 70% of 1 mg/kg EE2 within 2 weeks. Notably, the bioaugmentation of extrinsic strain SJTE-3 had a slight influence on indigenous bacterial community in pig manure samples, and its relative abundance decreased significantly after EE2 removal. Amendment of EE2 or strain SJTE-3 in manure samples enhanced the abundance of Proteobacteria and Actinobacteria, implying their potential in utilizing EE2 or its metabolites. These findings not only shed a light on the environment adaptability and degradation efficiency of strain SJTE-3, but also provide insights for bioremediation application in complex and synthetic estrogen polluted environments.
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Affiliation(s)
- Wanli Peng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China; Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China; Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China; Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Rubing Liang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China; Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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Zhang B, Xu X, Song X, Wen Y, Zhu Z, Lv J, Xie X, Chen L, Tang YW, Du H. Emerging and re-emerging KPC-producing hypervirulent Pseudomonas aeruginosa ST697 and ST463 between 2010 and 2021. Emerg Microbes Infect 2022; 11:2735-2745. [DOI: 10.1080/22221751.2022.2140609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Biying Zhang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004 PR China
| | - Xun Xu
- Institute of Active Polymers and Berlin-Brandenburg Center for Regenerative Therapies, Helmholtz-Zentrum Hereon, Kantstr.55, 14513 Teltow, Germany
| | - Xiaomei Song
- Department of Nursing, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004 PR China
| | - Yicheng Wen
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004 PR China
| | - Zhichen Zhu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004 PR China
| | - Jingnan Lv
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004 PR China
| | - Xiaofang Xie
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004 PR China
| | - Liang Chen
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA
| | - Yi-Wei Tang
- Department of Medical Affairs, Danaher Diagnostic Platform/Cepheid (China), New York, NY, USA
| | - Hong Du
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004 PR China
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Fu Y, Peng W, Lin S, Deng Z, Liang R. The 3-Oxoacyl-(Acyl-Carrier-Protein) Reductase HSD-X1 of Pseudomonas Citronellolis SJTE-3 Catalyzes the Conversion of 17β-estradiol to Estrone. Protein Pept Lett 2022; 29:199-207. [PMID: 35049426 DOI: 10.2174/0929866529666220113140721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 12/07/2021] [Accepted: 12/13/2021] [Indexed: 01/12/2023]
Abstract
BACKGROUND Pseudomonas citronellolis SJTE-3 can efficiently degrade 17β-estradiol (E2) and other estrogenic chemicals. However, the enzyme responsible for E2 metabolism within strain SJTE-3 has remained unidentified. OBJECTIVE Here, a novel 3-oxoacyl-(acyl-carrier protein) (ACP) reductase, HSD-X1 (WP_ 009617962.1), was identified in SJTE-3 and its enzymatic characteristics for the transformation of E2 were investigated. METHODS Multiple sequence alignment and homology modelling were used to predict the protein structure of HSD-X1. The concentrations of different steroids in the culture of recombinant strains expressing HSD-X1 were determined by high performance liquid chromatography. Additionally, the transcription of hsd-x1 gene was investigated using reverse transcription and quantitative PCR analysis. Heterologous expression and affinity purification were used to obtain recombinant HSD- X1. RESULTS The transcription of hsd-x1 gene in P. citronellolis SJTE-3 was induced by E2. Multiple sequence alignment (MSA) indicated that HSD-X1 contained the two consensus regions and conserved residues of short-chain dehydrogenase/reductases (SDRs) and 17β-hydroxysteroid dehydrogenases (17β-HSDs). Over-expression of hsd-x1 gene allowed the recombinant strain to degrade E2. Recombinant HSD-X1 was purified with a yield of 22.15 mg/L and used NAD+ as its cofactor to catalyze the oxidization of E2 into estrone (E1) while exhibiting a Km value of 0.025 ± 0.044 mM and a Vmax value of 4.92 ± 0.31 mM/min/mg. HSD-X1 could tolerate a wide range of temperature and pH, while the presence of divalent ions exerted little influence on its activity. Further, the transformation efficiency of E2 into E1 was over 98.03% across 15 min. CONCLUSION Protein HSD-X1 efficiently catalyzed the oxidization of E2 and participated in estrogen degradation by P. citronellolis SJTE-3.
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Affiliation(s)
- Yali Fu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai200240, China
| | - Wanli Peng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai200240, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai200240, China
| | - Rubing Liang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai200240, China
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Peng W, Wang Y, Fu Y, Deng Z, Lin S, Liang R. Characterization of the Tellurite-Resistance Properties and Identification of the Core Function Genes for Tellurite Resistance in Pseudomonas citronellolis SJTE-3. Microorganisms 2022; 10:microorganisms10010095. [PMID: 35056544 PMCID: PMC8779313 DOI: 10.3390/microorganisms10010095] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 12/27/2021] [Accepted: 12/30/2021] [Indexed: 11/16/2022] Open
Abstract
Tellurite is highly toxic to bacteria and commonly used in the clinical screening for pathogens; it is speculated that there is a potential relationship between tellurite resistance and bacterial pathogenicity. Until now, the core function genes of tellurite resistance and their characteristics are still obscure. Pseudomonas citronellolis SJTE-3 was found able to resist high concentrations of tellurite (250 μg/mL) and formed vacuole-like tellurium nanostructures. The terZABCDE gene cluster located in the large plasmid pRBL16 endowed strain SJTE-3 with the tellurite resistance of high levels. Although the terC and terD genes were identified as the core function genes for tellurite reduction and resistance, the inhibition of cell growth was observed when they were used solely. Interestingly, co-expression of the terA gene or terZ gene could relieve the burden caused by the expression of the terCD genes and recover normal cell growth. TerC and TerD proteins commonly shared the conserved sequences and are widely distributed in many pathogenic bacteria, highly associated with the pathogenicity factors.
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Affiliation(s)
- Wanli Peng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (W.P.); (Y.W.); (Y.F.); (Z.D.); (S.L.)
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yanqiu Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (W.P.); (Y.W.); (Y.F.); (Z.D.); (S.L.)
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yali Fu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (W.P.); (Y.W.); (Y.F.); (Z.D.); (S.L.)
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (W.P.); (Y.W.); (Y.F.); (Z.D.); (S.L.)
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (W.P.); (Y.W.); (Y.F.); (Z.D.); (S.L.)
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Rubing Liang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (W.P.); (Y.W.); (Y.F.); (Z.D.); (S.L.)
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Correspondence: ; Tel./Fax: +86-21-34204192
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Harthern-Flint SL, Dolfing J, Mrozik W, Meynet P, Eland LE, Sim M, Davenport RJ. Experimental and Genomic Evaluation of the Oestrogen Degrading Bacterium Rhodococcus equi ATCC13557. Front Microbiol 2021; 12:670928. [PMID: 34276604 PMCID: PMC8281962 DOI: 10.3389/fmicb.2021.670928] [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: 02/22/2021] [Accepted: 05/27/2021] [Indexed: 12/12/2022] Open
Abstract
Rhodococcus equi ATCC13557 was selected as a model organism to study oestrogen degradation based on its previous ability to degrade 17α-ethinylestradiol (EE2). Biodegradation experiments revealed that R. equi ATCC13557 was unable to metabolise EE2. However, it was able to metabolise E2 with the major metabolite being E1 with no further degradation of E1. However, the conversion of E2 into E1 was incomplete, with 11.2 and 50.6% of E2 degraded in mixed (E1-E2-EE2) and E2-only conditions, respectively. Therefore, the metabolic pathway of E2 degradation by R. equi ATCC13557 may have two possible pathways. The genome of R. equi ATCC13557 was sequenced, assembled, and mapped for the first time. The genome analysis allowed the identification of genes possibly responsible for the observed biodegradation characteristics of R. equi ATCC13557. Several genes within R. equi ATCC13557 are similar, but not identical in sequence, to those identified within the genomes of other oestrogen degrading bacteria, including Pseudomonas putida strain SJTE-1 and Sphingomonas strain KC8. Homologous gene sequences coding for enzymes potentially involved in oestrogen degradation, most commonly a cytochrome P450 monooxygenase (oecB), extradiol dioxygenase (oecC), and 17β-hydroxysteroid dehydrogenase (oecA), were identified within the genome of R. equi ATCC13557. These searches also revealed a gene cluster potentially coding for enzymes involved in steroid/oestrogen degradation; 3-carboxyethylcatechol 2,3-dioxygenase, 2-hydroxymuconic semialdehyde hydrolase, 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase, 3-(3-hydroxy-phenyl)propionate hydroxylase, cytochrome P450 monooxygenase, and 3-oxosteroid 1-dehydrogenase. Further, the searches revealed steroid hormone metabolism gene clusters from the 9, 10-seco pathway, therefore R. equi ATCC13557 also has the potential to metabolise other steroid hormones such as cholesterol.
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Affiliation(s)
| | - Jan Dolfing
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom.,Faculty Engineering and Environment, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Wojciech Mrozik
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom.,Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Gdańsk, Poland
| | - Paola Meynet
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lucy E Eland
- School of Computing Science, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Martin Sim
- School of Computing Science, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Russell J Davenport
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
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Emergence and Expansion of a Carbapenem-Resistant Pseudomonas aeruginosa Clone Are Associated with Plasmid-Borne bla KPC-2 and Virulence-Related Genes. mSystems 2021; 6:6/3/e00154-21. [PMID: 34006625 PMCID: PMC8269210 DOI: 10.1128/msystems.00154-21] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Pseudomonas aeruginosa is a major opportunistic pathogen and one of the leading bacterial species causing health care-associated infections. Carbapenems are the most effective antimicrobial agents for the treatment of severe infections caused by P. aeruginosa However, our recent surveillance demonstrated that the prevalence of carbapenem-resistant P. aeruginosa (CRPA) reached 38.67% in Zhejiang, China. By analyzing CRPA isolates collected from patients from 2006 to 2018, we found that 33% of CRPA isolates carried the gene bla KPC-2, which conferred high-level resistance to carbapenems and other β-lactams. In particular, a CRPA clone, ST463 (sequence type 463), emerged and has become the predominant CRPA clone among the population. Genome sequencing demonstrated that ST463 expansion was associated with plasmid-borne bla KPC-2 The mobile element flanking bla KPC-2, the type IV secretion system, and the successful expansion of clone ST463 might have further favored bla KPC-2 spread in P. aeruginosa Molecular clock analysis dated the emergence of clone ST463 to around 2007. Genome-wide association analysis showed that 567 genes were associated with clone ST463, including several known virulence genes related to the biosynthesis of lipooligosaccharide (LOS) O-antigens and exotoxin. These findings indicate that ST463 is expanding with plasmid-borne bla KPC-2 and virulence-related genes in nosocomial infections, and close surveillance should be undertaken in the future.IMPORTANCE Health care-associated infections, also known as nosocomial infections, are the most frequent adverse events in health care delivery worldwide, causing high rates of morbidity and mortality and high health care costs. Pseudomonas aeruginosa is one of the leading bacterial species causing health care-associated infections. Carbapenems are the most effective antimicrobial agents for the treatment of its severe infections. However, the prevalence of carbapenem-resistant P. aeruginosa (CRPA) has been increasing rapidly in recent years, and our surveillance demonstrated that the prevalence of CRPA reached 38.67% in Zhejiang, China. Genome sequencing of CRPA isolates over a decade showed that a CRPA clone (ST463) emerged recently. The clone is highly resistant to β-lactams, including carbapenems, and fluoroquinolones. Genome-wide association analysis showed that the clone expanded with virulence-related genes and the plasmid-borne carbapenem-resistant gene bla KPC-2 These findings are of significant public health importance, as the information will facilitate the control and minimization of CRPA nosocomial infections.
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Iron-Stimulated Production and Antimicrobial Potential of a Novel Biosurfactant Produced by a Drilling Waste-Degrading Pseudomonas citronellolis Strain. Processes (Basel) 2021. [DOI: 10.3390/pr9040686] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A Pseudomonas citronellolis strain was isolated from drilling waste (DW). This strain utilizes DW as the sole energy and carbon source to produce biosurfactants (BSs). The BS produced was thermally stable, amorphous and includes a peptide structure. FeSO4, FeCl3 and Fe(NO3)3 were supplemented at various concentration levels to assess possible enhancement of BS production and DW biodegradation. The limit concentration of Fe compounds between the increase in BS formation and microbial toxicity was 0.1 mM. FeCl3 enhanced DW biodegradation and more than doubled the BS formation yield, determining an optimization strategy for BS production. The BS was then partially purified and used against several Gram-negative and positive multi-drug resistant bacteria (such as Klebsiella pneumoniae, Pseudomonas aeruginosa, Escherichia coli spp, Acinetobacter baumaniii, Enterococcus faecalis spp, Streptococcus pneumoniae, Staphylococcus aureus, Salmonella enterica). The minimum inhibitory concentration was defined at a range of 0.25 to 10 mg/mL. The antimicrobial properties of the partially purified BS established its effectiveness and suggested a down-stream processing cost reduction, as no additional purification steps were necessary. The study could lead to a sustainable low-cost bioprocess towards a circular bioeconomy because waste, a non-expensive substrate, is used; while the BS holds great potential as a novel compound with antibiotic and disinfectant-like action, following toxicity testing with human cells.
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9
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Urbanowicz P, Bitar I, Izdebski R, Baraniak A, Literacka E, Hrabák J, Gniadkowski M. Epidemic Territorial Spread of IncP-2-Type VIM-2 Carbapenemase-Encoding Megaplasmids in Nosocomial Pseudomonas aeruginosa Populations. Antimicrob Agents Chemother 2021; 65:e02122-20. [PMID: 33526490 PMCID: PMC8097432 DOI: 10.1128/aac.02122-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/25/2021] [Indexed: 11/20/2022] Open
Abstract
In 2003 to 2004, the first five VIM-2 metallo-β-lactamase (MBL)-producing Pseudomonas aeruginosa (MPPA) isolates with an In4-like integron, In461 (aadB-blaVIM-2-aadA6), on conjugative plasmids were identified in three hospitals in Poland. In 2005 to 2015, MPPA expanded much in the country, and as many as 80 isolates in a collection of 454 MPPA (∼18%) had In461, one of the two most common MBL-encoding integrons. The organisms occurred in 49 hospitals in 33 cities of 11/16 main administrative regions. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) classified them into 55 pulsotypes and 35 sequence types (STs), respectively, revealing their remarkable genetic diversity overall, with only a few small clonal clusters. S1 nuclease/hybridization assays and mating of 63 representative isolates showed that ∼85% of these had large In461-carrying plasmids, ∼350 to 550 kb, usually self-transmitting with high efficiency (∼10-1 to 10-2 per donor cell). The plasmids from 19 isolates were sequenced and subjected to structural and single-nucleotide-polymorphism (SNP)-based phylogenetic analysis. These formed a subgroup within a family of IncP-2-type megaplasmids, observed worldwide in pseudomonads from various environments and conferring resistance/tolerance to multiple stress factors, including antibiotics. Their microdiversity in Poland arose mainly from acquisition of different accessory fragments, as well as new resistance genes and multiplication of these. Short-read sequence and/or PCR mapping confirmed the In461-carrying plasmids in the remaining isolates to be the IncP-2 types. The study demonstrated a large-scale epidemic spread of multidrug resistance plasmids in P. aeruginosa populations, creating an epidemiological threat. It contributes to the knowledge on IncP-2 types, which are interesting research objects in resistance epidemiology, environmental microbiology, and biotechnology.
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Affiliation(s)
- Paweł Urbanowicz
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - Ibrahim Bitar
- Biomedical Center, Faculty of Medicine in Plzen, Charles University, Plzen, Czech Republic
| | - Radosław Izdebski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - Anna Baraniak
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - Elżbieta Literacka
- Department of Epidemiology and Clinical Microbiology, The National Reference Centre for Susceptibility Testing, National Medicines Institute, Warsaw, Poland
| | - Jaroslav Hrabák
- Biomedical Center, Faculty of Medicine in Plzen, Charles University, Plzen, Czech Republic
| | - Marek Gniadkowski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
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10
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Cazares A, Moore MP, Hall JPJ, Wright LL, Grimes M, Emond-Rhéault JG, Pongchaikul P, Santanirand P, Levesque RC, Fothergill JL, Winstanley C. A megaplasmid family driving dissemination of multidrug resistance in Pseudomonas. Nat Commun 2020; 11:1370. [PMID: 32170080 PMCID: PMC7070040 DOI: 10.1038/s41467-020-15081-7] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 02/13/2020] [Indexed: 11/10/2022] Open
Abstract
Multidrug resistance (MDR) represents a global threat to health. Here, we used whole genome sequencing to characterise Pseudomonas aeruginosa MDR clinical isolates from a hospital in Thailand. Using long-read sequence data we obtained complete sequences of two closely related megaplasmids (>420 kb) carrying large arrays of antibiotic resistance genes located in discrete, complex and dynamic resistance regions, and revealing evidence of extensive duplication and recombination events. A comprehensive pangenomic and phylogenomic analysis indicates that: 1) these large plasmids comprise an emerging family present in different members of the Pseudomonas genus, and associated with multiple sources (geographical, clinical or environmental); 2) the megaplasmids encode diverse niche-adaptive accessory traits, including multidrug resistance; 3) the accessory genome of the megaplasmid family is highly flexible and diverse. The history of the megaplasmid family, inferred from our analysis of the available database, suggests that members carrying multiple resistance genes date back to at least the 1970s.
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Affiliation(s)
- Adrian Cazares
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
| | - Matthew P Moore
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - James P J Hall
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool, UK
| | - Laura L Wright
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Macauley Grimes
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | | | | | | | - Roger C Levesque
- Institute for Integrative and Systems Biology (IBIS), University Laval, Quebec City, QC, Canada
| | - Joanne L Fothergill
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Craig Winstanley
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
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11
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Xiong W, Yin C, Wang Y, Lin S, Deng Z, Liang R. Characterization of an efficient estrogen-degrading bacterium Stenotrophomonas maltophilia SJTH1 in saline-, alkaline-, heavy metal-contained environments or solid soil and identification of four 17β-estradiol-oxidizing dehydrogenases. JOURNAL OF HAZARDOUS MATERIALS 2020; 385:121616. [PMID: 31780289 DOI: 10.1016/j.jhazmat.2019.121616] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/28/2019] [Accepted: 11/04/2019] [Indexed: 05/26/2023]
Abstract
The efficient bioremediation of estrogen contamination in complex environments is of great concern. Here the strain Stenotrophomonas maltophilia SJTH1 was found with great and stable estrogen-degradation efficiency even under stress environments. The strain could utilize 17β-estradiol (E2) as a carbon source and degrade 90% of 10 mg/L E2 in a week; estrone (E1) was the first degrading intermediate of E2. Notably, diverse pH conditions (3.0-11.0) and supplements of 4% salinity, 6.25 mg/L of heavy metal (Cd2+ or Cu2+), or 1 CMC of surfactant (Tween 80/ Triton X-100) had little effect on its cell growth and estrogen degradation. The addition of low concentrations of copper and Tween 80 even promoted its E2 degradation. Bioaugmentation of strain SJTH1 into solid clay soil achieved over 80% removal of E2 contamination (10 mg/kg) within two weeks. Further, the whole genome sequence of S. maltophilia SJTH1 was obtained, and a series of potential genes participating in stress-tolerance and estrogen-degradation were predicted. Four dehydrogenases similar to 17β-hydroxysteroid dehydrogenases (17β-HSDs) were found to be induced by E2, and the four heterogenous-expressed enzymes could oxidize E2 into E1 efficiently. This work could promote bioremediation appliance potential with microorganisms and biodegradation mechanism study of estrogens in complex real environments.
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Affiliation(s)
- Weiliang Xiong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Chong Yin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yanqiu Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Rubing Liang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
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12
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Weiser R, Green AE, Bull MJ, Cunningham-Oakes E, Jolley KA, Maiden MCJ, Hall AJ, Winstanley C, Weightman AJ, Donoghue D, Amezquita A, Connor TR, Mahenthiralingam E. Not all Pseudomonas aeruginosa are equal: strains from industrial sources possess uniquely large multireplicon genomes. Microb Genom 2019; 5:e000276. [PMID: 31170060 PMCID: PMC6700666 DOI: 10.1099/mgen.0.000276] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 05/24/2019] [Indexed: 12/13/2022] Open
Abstract
Pseudomonas aeruginosa is a highly versatile, antibiotic-resistant Gram-negative bacterium known for causing opportunistic infections and contamination of industrial products. Despite extensive genomic analysis of clinical P. aeruginosa strains, no genomes exist for preservative-tolerant industrial strains. A unique collection of 69 industrial isolates was assembled and compared to clinical and environmental strains; 16 genetically distinct industrial strains were subjected to array tube genotyping, multilocus sequence typing and whole-genome sequencing. The industrial strains possessed high preservative tolerance and were dispersed widely across P. aeruginosa as a species, but recurrence of strains from the same lineage within specific industrial products and locations was identified. The industrial P. aeruginosa genomes (mean=7.0 Mb) were significantly larger than those of previously sequenced environmental (mean=6.5 Mb; n=19) and clinical (mean=6.6 Mb; n=66) strains. Complete sequencing of the P. aeruginosa industrial strain RW109, which encoded the largest genome (7.75 Mb), revealed a multireplicon structure including a megaplasmid (555 265 bp) and large plasmid (151 612 bp). The RW109 megaplasmid represented an emerging plasmid family conserved in seven industrial and two clinical P. aeruginosa strains, and associated with extremely stress-resilient phenotypes, including antimicrobial resistance and solvent tolerance. Here, by defining the detailed phylogenomics of P. aeruginosa industrial strains, we show that they uniquely possess multireplicon, megaplasmid-bearing genomes, and significantly greater genomic content worthy of further study.
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Affiliation(s)
- Rebecca Weiser
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, UK
| | - Angharad E. Green
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, UK
- University of Liverpool, Institute of Infection and Global Health, Liverpool, UK
| | - Matthew J. Bull
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, UK
| | - Edward Cunningham-Oakes
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, UK
| | - Keith A. Jolley
- Department of Zoology, The Tinbergen Building, University of Oxford, Oxford, UK
| | - Martin C. J. Maiden
- Department of Zoology, The Tinbergen Building, University of Oxford, Oxford, UK
| | - Amanda J. Hall
- University of Liverpool, Institute of Infection and Global Health, Liverpool, UK
| | - Craig Winstanley
- University of Liverpool, Institute of Infection and Global Health, Liverpool, UK
| | - Andrew J. Weightman
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, UK
| | - Denise Donoghue
- Unilever Research and Development, Port Sunlight, Wirral, UK
| | - Alejandro Amezquita
- Unilever Research and Development, Safety and Environmental Assurance Centre, Colworth House, Sharnbrook, Bedford, UK
| | - Thomas R. Connor
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, UK
| | - Eshwar Mahenthiralingam
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, UK
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13
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Williams G. First report of infection with Pseudomonas citronellolis: a case of urosepsis. New Microbes New Infect 2019; 30:100531. [PMID: 31080622 PMCID: PMC6505106 DOI: 10.1016/j.nmni.2019.100531] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 11/24/2022] Open
Abstract
This is the first case report of infection with the environmental bacterium Pseudomonas citronellolis, presented here as a urinary tract and bloodstream infection that occurred shortly after a transrectal ultrasound-guided prostate biopsy.
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Affiliation(s)
- G Williams
- Pathology and Laboratory Medicine Service, VA Central Western Massachusetts, Leeds, MA 01053, USA
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14
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Wang P, Zheng D, Liang R. Isolation and characterization of an estrogen-degrading Pseudomonas putida strain SJTE-1. 3 Biotech 2019; 9:61. [PMID: 30729085 DOI: 10.1007/s13205-018-1537-z] [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: 08/06/2018] [Accepted: 12/14/2018] [Indexed: 01/19/2023] Open
Abstract
In this report, Pseudomonas putida SJTE1 isolated from an enrichment culture of sludge was confirmed to degrade natural estrogens (17β-estradiol, estrone, estriol), estrogenic chemicals (naphthalene and phenanthrene) and testosterone. The strain completely degraded 1 mg/L 17β-estradiol in 24 h and transformed it into estrone; 90% and 75% of 50 mg/L and 100 mg/L 17β-estradiol were utilized in 7 days, respectively. The transformation efficiency of this strain against natural estrogens was much higher than that against other estrogenic chemicals. Organic carbon sources, lipopolysaccharide and surfactants could enhance the degradation efficiency of strain SJTE-1 against 17β-estradiol. The adsorption of 17β-estradiol onto the biomass was the premise for transmembrane and cellular utilization of this chemical. This work has the potential to bioremediate the environmental estrogens.
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Affiliation(s)
- Pingping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 China
| | - Daning Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 China
| | - Rubing Liang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 China
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15
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Wang Y, Shao H, Zhu S, Tian K, Qiu Q, Huo H. Degradation of 17β-estradiol and products by a mixed culture of Rhodococcus equi DSSKP-R-001 and Comamonas testosteroni QYY20150409. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1568913] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Yu Wang
- College of Life Sciences, Northeast Normal University, Jilin, PR China
| | - Huanhuan Shao
- College of Environment, Northeast Normal University, Jilin, PR China
| | - Suiyi Zhu
- College of Environment, Northeast Normal University, Jilin, PR China
| | - Kejian Tian
- College of Environment, Northeast Normal University, Jilin, PR China
| | - Qing Qiu
- College of Life Sciences, Northeast Normal University, Jilin, PR China
| | - Hongliang Huo
- College of Environment, Northeast Normal University, Jilin, PR China
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16
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Xiong W, Peng W, Liang R. Identification and genome analysis of Deinococcus actinosclerus SJTR1, a novel 17β-estradiol degradation bacterium. 3 Biotech 2018; 8:433. [PMID: 30306002 DOI: 10.1007/s13205-018-1466-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/26/2018] [Indexed: 12/20/2022] Open
Abstract
Biodegradation with microorganisms is considered as an efficient strategy to remove the environmental pollutants. In this work, Deinococcus actinosclerus SJTR1 isolated from the wastewater was confirmed with great degradation capability to 17β-estradiol, one typical estrogen chemical. It could degrade nearly 90% of 17β-estradiol (10 mg/L) in 5 days and transform it into estrone; its degradation kinetics fitted for the first-order kinetic equation. The whole genome sequence of D. actinosclerus SJTR1 was obtained and annotated, containing one chromosome (3,315,586 bp) and four plasmids (ranging from 17,267 bp to 460,244 bp). A total of 3913 CDSs and 73 RNA genes (including 12 rRNA genes, 50 tRNA genes, and 11 ncRNA genes) were identified in its whole genome sequence. On this basis, a series of potential genes involved in steroid metabolism and stress responses of D. actinosclerus SJTR1 were predicted. It is the first report of Deinococcus strain with the degradation capability to estrogens. This work could enrich the genome sources of the estrogen-degrading strains and promote the degradation mechanism study of 17β-estradiol in bacteria.
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Affiliation(s)
- Weiliang Xiong
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 China
| | - Wanli Peng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 China
| | - Rubing Liang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 China
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17
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Metagenomes Reveal Global Distribution of Bacterial Steroid Catabolism in Natural, Engineered, and Host Environments. mBio 2018; 9:mBio.02345-17. [PMID: 29382738 PMCID: PMC5790920 DOI: 10.1128/mbio.02345-17] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Steroids are abundant growth substrates for bacteria in natural, engineered, and host-associated environments. This study analyzed the distribution of the aerobic 9,10-seco steroid degradation pathway in 346 publically available metagenomes from diverse environments. Our results show that steroid-degrading bacteria are globally distributed and prevalent in particular environments, such as wastewater treatment plants, soil, plant rhizospheres, and the marine environment, including marine sponges. Genomic signature-based sequence binning recovered 45 metagenome-assembled genomes containing a majority of 9,10-seco pathway genes. Only Actinobacteria and Proteobacteria were identified as steroid degraders, but we identified several alpha- and gammaproteobacterial lineages not previously known to degrade steroids. Actino- and proteobacterial steroid degraders coexisted in wastewater, while soil and rhizosphere samples contained mostly actinobacterial ones. Actinobacterial steroid degraders were found in deep ocean samples, while mostly alpha- and gammaproteobacterial ones were found in other marine samples, including sponges. Isolation of steroid-degrading bacteria from sponges confirmed their presence. Phylogenetic analysis of key steroid degradation proteins suggested their biochemical novelty in genomes from sponges and other environments. This study shows that the ecological significance as well as taxonomic and biochemical diversity of bacterial steroid degradation has so far been largely underestimated, especially in the marine environment. Microbial steroid degradation is a critical process for biomass decomposition in natural environments, for removal of important pollutants during wastewater treatment, and for pathogenesis of bacteria associated with tuberculosis and other bacteria. To date, microbial steroid degradation was mainly studied in a few model organisms, while the ecological significance of steroid degradation remained largely unexplored. This study provides the first analysis of aerobic steroid degradation in diverse natural, engineered, and host-associated environments via bioinformatic analysis of an extensive metagenome data set. We found that steroid-degrading bacteria are globally distributed and prevalent in wastewater treatment plants, soil, plant rhizospheres, and the marine environment, especially in marine sponges. We show that the ecological significance as well as the taxonomic and biochemical diversity of bacterial steroid degradation has been largely underestimated. This study greatly expands our ecological and evolutionary understanding of microbial steroid degradation.
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