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Riedel R, Meißner K, Kaschubowski A, Benndorf D, Martienssen M, Braun B. Laundry Isolate Delftia sp. UBM14 Capable of Biodegrading Industrially Relevant Aminophosphonates. Microorganisms 2024; 12:1664. [PMID: 39203506 PMCID: PMC11356716 DOI: 10.3390/microorganisms12081664] [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: 07/19/2024] [Revised: 08/08/2024] [Accepted: 08/12/2024] [Indexed: 09/03/2024] Open
Abstract
Phosphonates such as ethylenediaminetetra (methylenephosphonic acid) (EDTMP) and aminotris (methylenephosphonic acid) (ATMP) are used every day in water treatment processes or in household products. Their consumption is still increasing, regardless of the debates on their environmental impact. Here, the microbial characterisation and determination of the biodegradation potential of selected industrially relevant phosphonates for the isolate Delftia sp. UMB14 is reported. The opportunistic strain was isolated from a biofilm that was derived from a conventional washing machine using conventional detergents containing phosphonates. In antimicrobial susceptibility testing, the strain was only susceptible to sulfonamide, tetracycline, and chloramphenicol. Physiological and biochemical characteristics were determined using the BIOLOG EcoPlate assay. Most importantly, the strain was shown to convert D-malic acid and D-mannitol, as confirmed for strains of Delftia lacustris, and thus the new isolate could be closely related. Biodegradation tests with different phosphonates showed that the strain preferentially degrades ATMP and EDTMP but does not degrade glyphosate (GS) and amino (methylphosphonic acid) (AMPA). A specific gene amplification confirmed the presence of phnX (phosphonoacetaldehyde hydrolase) and the absence of PhnJ (the gene for the core component of C-P lyase). The presence of PhnCDE is strongly suggested for the strain, as it is common in Delftia lacustris species.
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Affiliation(s)
- Ramona Riedel
- Chair of Biotechnology of Water Treatment Brandenburg, Institute of Environmental Science and Environmental Technology, BTU Cottbus-Senftenberg, 03046 Cottbus, Germany;
| | - Karsten Meißner
- German Environment Agency (UBA), Section II 3.3, 14195 Berlin, Germany;
- Department of Environmental Microbiomics, University of Technology Berlin, 10587 Berlin, Germany; (A.K.); (B.B.)
| | - Arne Kaschubowski
- Department of Environmental Microbiomics, University of Technology Berlin, 10587 Berlin, Germany; (A.K.); (B.B.)
| | - Dirk Benndorf
- Applied Biosciences and Process Engineering, Anhalt University of Applied Sciences, 06366 Köthen, Germany;
- Chair of Bioprocess Engineering, Otto von Guericke University, 39106 Magdeburg, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
| | - Marion Martienssen
- Chair of Biotechnology of Water Treatment Brandenburg, Institute of Environmental Science and Environmental Technology, BTU Cottbus-Senftenberg, 03046 Cottbus, Germany;
| | - Burga Braun
- Department of Environmental Microbiomics, University of Technology Berlin, 10587 Berlin, Germany; (A.K.); (B.B.)
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2
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Zhang L, Zhang X, Bai H, Li T, Zhang Z, Zong X, Shang X, Liu Z, Fan L. Characterization and Genome Analysis of the Delftia lacustris Strain LzhVag01 Isolated from Vaginal Discharge. Curr Microbiol 2024; 81:232. [PMID: 38898312 PMCID: PMC11186869 DOI: 10.1007/s00284-024-03758-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024]
Abstract
Delftia has been separated from freshwater, sludge, and soil and has emerged as a novel opportunistic pathogen in the female vagina. However, the genomic characteristics, pathogenicity, and biotechnological properties still need to be comprehensively investigated. In this study, a Delftia strain was isolated from the vaginal discharge of a 43-year-old female with histologically confirmed cervical intraepithelial neoplasm (CIN III), followed by whole-genome sequencing. Phylogenetic analysis and average nucleotide identity (ANI) analysis demonstrated that it belongs to Delftia lacustris, named D. lacustris strain LzhVag01. LzhVag01 was sensitive to β-lactams, macrolides, and tetracyclines but exhibited resistance to lincoamines, nitroimidazoles, aminoglycosides, and fluoroquinolones. Its genome is a single, circular chromosome of 6,740,460 bp with an average GC content of 66.59%. Whole-genome analysis identified 16 antibiotic resistance-related genes, which match the antimicrobial susceptibility profile of this strain, and 11 potential virulence genes. These pathogenic factors may contribute to its colonization in the vaginal environment and its adaptation and accelerate the progression of cervical cancer. This study sequenced and characterized the whole-genome of Delftia lacustris isolated from vaginal discharge, which provides investigators and clinicians with valuable insights into this uncommon species.
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Affiliation(s)
- Li Zhang
- Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100026, China
| | - Xin Zhang
- Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100026, China
| | - Huihui Bai
- Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100026, China
| | - Ting Li
- Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100026, China
| | - Zhan Zhang
- Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100026, China
| | - Xiaonan Zong
- Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100026, China
| | - Xiang Shang
- Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100026, China
| | - Zhaohui Liu
- Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100026, China.
| | - Linyuan Fan
- Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100026, China.
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Andriyanov PA, Kashina DD, Menshikova AN. Genomic analysis of multidrug-resistant Delftia tsuruhatensis isolated from raw bovine milk. Front Microbiol 2024; 14:1321122. [PMID: 38239723 PMCID: PMC10794605 DOI: 10.3389/fmicb.2023.1321122] [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: 10/13/2023] [Accepted: 12/06/2023] [Indexed: 01/22/2024] Open
Abstract
Delftia tsuruhatensis is a gram-negative, aerobic bacterium mostly known as an organic pollutant degrading and growth-promoting microorganism. However, it recently emerged as an opportunistic human pathogen. To date, the source of D. tsuruhatensis infection is not clear. The majority of studies of D. tsuruhatensis have focused on environmental or clinical strains, while investigations of D. tsuruhatensis strains isolated from food sources are limited. In the present study, we report the case of D. tsuruhatensis isolation from raw bovine milk. Classical bacteriology approaches, as well as next-generation sequencing and comparative genomics, were used to characterize the features of the D. tsuruhatensis MR-6/3H strain. The MR-6/3H strain was resistant to 19 antimicrobials among 23 tested, including all aminoglycosides, phenicol, trimethoprim-sulfamethoxazole, and almost all β-lactams. Phylogenetically, the MR-6/3H was close to clinical origin strains, including those previously isolated in Russia. Comparative genomics revealed the presence of putative antimicrobial resistance genes in the MR-6/3H isolate, mostly associated with efflux systems. Notably, genus-specific OXA-926-like β-lactamase was also detected. In all, 27 putative virulence factors were predicted, the majority of which were associated with motility, adherence, stress survival, siderophore synthesis, and immunomodulation. In the MR-6/3H genome, the five prophage regions were identified, including two with intact levels. Integrons and CRISPR-Cas systems were not detected in the MR-6/3H isolate. Thus, our findings suggest that raw milk can be the potential source of and transmission route for the dissemination of multidrug-resistant D. tsuruhatensis.
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Affiliation(s)
- Pavel A. Andriyanov
- Federal Research Center for Virology and Microbiology, Branch in Nizhny Novgorod, Nizhny Novgorod, Russia
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Manara S, Beghini F, Masetti G, Armanini F, Geat D, Galligioni G, Segata N, Farina S, Cristofolini M. Thermal Therapy Modulation of the Psoriasis-Associated Skin and Gut Microbiome. Dermatol Ther (Heidelb) 2023; 13:2769-2783. [PMID: 37768448 PMCID: PMC10613183 DOI: 10.1007/s13555-023-01036-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
INTRODUCTION Psoriasis is a systemic immune-mediated disease primarily manifesting as skin redness and inflammation. Balneotherapy proved to be a successful non-pharmacological option to reduce the skin areas affected by the disease, but the specific mechanisms underlying this effect have not been elucidated yet. Here we test the hypothesis that the effect of thermal treatments on psoriatic lesions could be partially mediated by changes in the resident microbial population, i.e., the microbiome. METHODS In this study, we enrolled patients with psoriasis and monitored changes in their skin and gut microbiome after a 12-bath balneotherapy course with a combination of 16S rRNA amplicon sequencing and metagenomics. Changes in the resident microbiome were then correlated with thermal therapy outcomes evaluated as changes in Psoriasis Area and Severity Index (PASI) and Body Surface Area index (BSA). RESULTS The amplicon sequencing analysis of the skin microbiome showed that after thermal treatment the microbiome composition of affected areas improved to approach that typical of unaffected skin. We moreover identified some low-abundance bacterial biomarkers indicative of disease status and treatment efficacy, and we showed via metagenomic sequencing that thermal treatments and thermal water drinking affect the fecal microbiome to host more species associated with favorable metabolic health. CONCLUSIONS Changes in lower-abundance microbial taxa presence and abundance could be the basis for the positive effect of thermal water treatment and drinking on the cutaneous and systemic symptomatology of psoriasis.
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Affiliation(s)
- Serena Manara
- Laboratory of Computational Metagenomics, Department CIBIO, University of Trento, Via Sommarive 9, Povo, 38123, Trento, Italy
| | - Francesco Beghini
- Laboratory of Computational Metagenomics, Department CIBIO, University of Trento, Via Sommarive 9, Povo, 38123, Trento, Italy
- Yale Institute for Network Science, Yale University, New Haven, CT, USA
| | - Giulia Masetti
- Laboratory of Computational Metagenomics, Department CIBIO, University of Trento, Via Sommarive 9, Povo, 38123, Trento, Italy
| | - Federica Armanini
- Laboratory of Computational Metagenomics, Department CIBIO, University of Trento, Via Sommarive 9, Povo, 38123, Trento, Italy
| | - Davide Geat
- Department of Dermatology, ASST Spedali Civili Di Brescia, Brescia, Italy
| | - Giulia Galligioni
- Clinical Unit of Occupational Medicine, Health Agency Trento, Trento, Italy
| | - Nicola Segata
- Laboratory of Computational Metagenomics, Department CIBIO, University of Trento, Via Sommarive 9, Povo, 38123, Trento, Italy.
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Alam MS, Ranjan A, Kumar V, Kumar R. Delftia acidovorans sepsis in a neonate with nosocomial pneumonia. BMJ Case Rep 2023; 16:e256439. [PMID: 37827711 PMCID: PMC10583087 DOI: 10.1136/bcr-2023-256439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023] Open
Abstract
A term neonate weighing 2900 g was referred in the first week of life with complaints of abdominal distension since birth. New onset respiratory distress was noted 36 hours prior to referral. Baby required non-invasive respiratory support and intravenous antibiotics as chest X-ray was suggestive of pneumonia. Ultrasound abdomen confirmed low ano-rectal malformation treated with cut-back anoplasty. Blood culture on admission grew a rare organism Delftia acidovorans The antibiotics were tailored as per the sensitivity pattern and continued for a duration of 14 days. Respiratory distress gradually resolved by day 10 of admission. The baby developed pneumonia after 36 hours of stay in the referring hospital; most probably indicating a hospital acquired source of this pathogen. To the best of our knowledge, this is the second reported neonatal case of D. acidovorans sepsis.
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Affiliation(s)
- Md Shahbaz Alam
- Department of Neonatology, Rani Hospital, Ranchi, Jharkhand, India
| | - Ankit Ranjan
- Department of Neonatology, Rani Hospital, Ranchi, Jharkhand, India
| | - Vinod Kumar
- Department of Neonatology, Rani Hospital, Ranchi, Jharkhand, India
| | - Rajesh Kumar
- Department of Neonatology, Rani Hospital, Ranchi, Jharkhand, India
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Bhat SV, Maughan H, Cameron ADS, Yost CK. Phylogenomic analysis of the genus Delftia reveals distinct major lineages with ecological specializations. Microb Genom 2022; 8:mgen000864. [PMID: 36107145 PMCID: PMC9676026 DOI: 10.1099/mgen.0.000864] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/15/2022] [Indexed: 04/01/2024] Open
Abstract
Delftia is a diverse betaproteobacterial genus with many strains having agricultural and industrial relevance, including plant-growth promotion, bioremediation of hydrocarbon-contaminated soils, and heavy metal immobilization. Delftia spp. are broadly distributed in the environment, and have been isolated from plant hosts as well as healthy and diseased animal hosts, yet the genetic basis of this ecological versatility has not been characterized. Here, we present a phylogenomic comparison of published Delftia genomes and show that the genus is divided into two well-supported clades: one 'Delftia acidovorans' clade with isolates from soils and plant rhizospheres, and a second 'Delftia lacustris and Delftia tsuruhatensis' clade with isolates from humans and sludge. The pan-genome inferred from 61 Delftia genomes contained over 28 000 genes, of which only 884 were found in all genomes. Analysis of industrially relevant functions highlighted the ecological versatility of Delftia and supported their role as generalists.
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Affiliation(s)
- Supriya V. Bhat
- Department of Biology, University of Regina, Regina, SK, Canada
- Institute for Microbial Systems and Society, University of Regina, Regina, SK, Canada
| | | | - Andrew D. S. Cameron
- Department of Biology, University of Regina, Regina, SK, Canada
- Institute for Microbial Systems and Society, University of Regina, Regina, SK, Canada
| | - Christopher K. Yost
- Department of Biology, University of Regina, Regina, SK, Canada
- Institute for Microbial Systems and Society, University of Regina, Regina, SK, Canada
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7
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Pan-Genome Analysis of Delftia tsuruhatensis Reveals Important Traits Concerning the Genetic Diversity, Pathogenicity, and Biotechnological Properties of the Species. Microbiol Spectr 2022; 10:e0207221. [PMID: 35230132 PMCID: PMC9045143 DOI: 10.1128/spectrum.02072-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Delftia tsuruhatensis strains have long been known to promote plant growth and biological control. Recently, it has become an emerging opportunistic pathogen in humans. However, the genomic characteristics of the genetic diversity, pathogenicity, and biotechnological properties have not yet been comprehensively investigated. Here, a comparative pan-genome analysis was constructed. The open pan-genome with a large and flexible gene repertoire exhibited a high degree of genetic diversity. The purifying selection was the main force to drive pan-genome evolution. Significant differences were observed in the evolutionary relationship, functional enrichment, and degree of selective pressure between the different components of the pan-genome. A high degree of genetic plasticity was characterized by the determinations of diverse mobile genetic elements (MGEs), massive genomic rearrangement, and horizontal genes. Horizontal gene transfer (HGT) plays an important role in the genetic diversity of this bacterium and the formation of genomic traits. Our results revealed the occurrence of diverse virulence-related elements associated with macromolecular secretion systems, virulence factors associated with multiple nosocomial infections, and antimicrobial resistance, indicating the pathogenic potential. Lateral flagellum, T1SS, T2SS, T6SS, Tad pilus, type IV pilus, and a part of virulence-related genes exhibited general properties, whereas polar flagellum, T4SS, a part of virulence-related genes, and resistance genes presented heterogeneous properties. The pan-genome also harbors abundant genetic traits related to secondary metabolism, carbohydrate active enzymes (CAZymes), and phosphate transporter, indicating rhizosphere adaptation, plant growth promotion, and great potential uses in agriculture and biological control. This study provides comprehensive insights into this uncommon species from the genomic perspective. IMPORTANCED. tsuruhatensis is considered a plant growth-promoting rhizobacterium (PGPR), an organic pollutant degradation strain, and an emerging opportunistic pathogen to the human. However, the genetic diversity, the evolutionary dynamics, and the genetic basis of these remarkable traits are still little known. We constructed a pan-genome analysis for D. tsuruhatensis and revealed extensive genetic diversity and genetic plasticity exhibited by open pan-genome, diverse mobile genetic elements (MGEs), genomic rearrangement, and horizontal genes. Our results highlight that horizontal gene transfer (HGT) and purifying selection are important forces in D. tsuruhatensis genetic evolution. The abundant virulence-related elements associated with macromolecular secretion systems, virulence factors, and antimicrobial resistance could contribute to the pathogenicity of this bacterium. Therefore, clinical microbiologists need to be aware of D. tsuruhatensis as an opportunistic pathogen. The genetic profiles of secondary metabolism, carbohydrate active enzymes (CAZymes), and phosphate transporter could provide insight into the genetic armory of potential applications for agriculture and biological control of D. tsuruhatensis in general.
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Wang Y, Ma L, He J, He Z, Wang M, Liu Z, Li Z, Wang L, Weng S, Guo C, He J. Environmental risk characteristics of bacterial antibiotic resistome in Antarctic krill. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 232:113289. [PMID: 35144128 DOI: 10.1016/j.ecoenv.2022.113289] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/02/2022] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Antibiotic resistance genes (ARGs) are ubiquitous in nature, especially in the current era of antibiotic abuse, and their existence is a global concern. In the present study, we discovered that Antarctic krill-related culturable bacteria are resistant to β-lactam, tetracyclines, aminoglycosides, and sulphamethoxazole/trimethoprim based on the antibiotic efflux mechanism. In addition, the co-occurrence of ARGs with insertion sequence (IS) (tnpA, IS91) and Intl1 on the isolates and the phylogenetic analysis results of the whole-genome revealed low-frequency ARG transfer events, implying the transferability of these ARGs. These findings provide an early warning for the wide assessment of Antarctic microbiota in the spread of ARGs. Our work provides novel insights into understanding ARGs in culturable host-associated microorganisms, and their ecological risks and has important implications for future risk assessments of antibiotic resistance in extreme environments.
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Affiliation(s)
- Yuanyuan Wang
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, PR China
| | - Lingbo Ma
- Key Laboratory of the East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Shanghai 116023, PR China
| | - Jian He
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, PR China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Muhua Wang
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, PR China
| | - Zixuan Liu
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, PR China
| | - Zhimin Li
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, PR China
| | - Lumin Wang
- Key Laboratory of the East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Shanghai 116023, PR China
| | - Shaoping Weng
- Guangdong Provincial Key Laboratory of Marine Resources, and Coastal Engineering and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, PR China
| | - Changjun Guo
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Marine Resources, and Coastal Engineering and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, PR China.
| | - Jianguo He
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Marine Resources, and Coastal Engineering and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, PR China.
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Yu Y, Kim YH, Cho WH, Son BS, Yeo HJ. Biofilm microbiome in extracorporeal membrane oxygenator catheters. PLoS One 2021; 16:e0257449. [PMID: 34529734 PMCID: PMC8445415 DOI: 10.1371/journal.pone.0257449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 09/01/2021] [Indexed: 12/18/2022] Open
Abstract
Despite the formation of biofilms on catheters for extracorporeal membrane oxygenation (ECMO), some patients do not show bacteremia. To elucidate the specific linkage between biofilms and bacteremia in patients with ECMO, an improved understanding of the microbial community within catheter biofilms is necessary. Hence, we aimed to evaluate the biofilm microbiome of ECMO catheters from adults with (n = 6) and without (n = 15) bacteremia. The microbiomes of the catheter biofilms were evaluated by profiling the V3 and V4 regions of bacterial 16s rRNA genes using the Illumina MiSeq sequencing platform. In total, 2,548,172 reads, with an average of 121,341 reads per sample, were generated. Although alpha diversity was slightly higher in the non-bacteremic group, the difference was not statistically significant. In addition, there was no difference in beta diversity between the two groups. We found 367 different genera, of which 8 were present in all samples regardless of group; Limnohabitans, Flavobacterium, Delftia, Massilia, Bacillus, Candidatus, Xiphinematobacter, and CL0-1 showed an abundance of more than 1% in the sample. In particular, Arthrobacter, SMB53, Neisseria, Ortrobactrum, Candidatus Rhabdochlamydia, Deefgae, Dyella, Paracoccus, and Pedobacter were highly abundant in the bacteremic group. Network analysis indicated that the microbiome of the bacteremic group was more complex than that of the non-bacteremic group. Flavobacterium and CL0.1, which were abundant in the bacteremic group, were considered important genera because they connected different subnetworks. Biofilm characteristics in ECMO catheters varied according to the presence or absence of bacteremia. There were no significant differences in diversity between the two groups, but there were significant differences in the community composition of the biofilms. The biofilm-associated community was dynamic, with the bacteremic group showing very complex network connections within the microbiome.
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Affiliation(s)
- Yeuni Yu
- Interdisciplinary Program of Genomic Science, Pusan National University, Yagnsan, Republic of Korea
| | - Yun Hak Kim
- Department of Anatomy and Department of Biomedical Informatics, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Woo Hyun Cho
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Pusan National University Yangsan Hospital, Yagnsan, Republic of Korea
| | - Bong Soo Son
- Department of Thoracic and Cardiovascular Surgery, Pusan National University Yangsan Hospital, Yangsan, Republic of Korea
| | - Hye Ju Yeo
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Pusan National University Yangsan Hospital, Yagnsan, Republic of Korea
- Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yagnsan, Republic of Korea
- * E-mail:
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10
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Cho SM, Hong SG, Lee Y, Song W, Yong D, Jeong SH, Lee K, Chong Y. First Identification of IMP-1 Metallo-β-Lactamase in Delftia tsuruhatensis Strain CRS1243 Isolated From a Clinical Specimen. Ann Lab Med 2021; 41:436-438. [PMID: 33536365 PMCID: PMC7884188 DOI: 10.3343/alm.2021.41.4.436] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/23/2020] [Accepted: 01/04/2021] [Indexed: 12/31/2022] Open
Affiliation(s)
- Sun-Mi Cho
- Department of Laboratory Medicine, CHA Bundang Medical Center, CHA University, Seongnam, Korea
| | - Seong Geun Hong
- Department of Laboratory Medicine, CHA Bundang Medical Center, CHA University, Seongnam, Korea,Corresponding author: Seong Geun Hong, M.D., Ph.D. Department of Laboratory Medicine, CHA Bundang Medical Center, CHA University, 59 Yatap-ro, Bundang-gu, Seongnam 13496, Korea Tel: +82-31-780-5463, Fax: +82-31-780-5476 E-mail:
| | - Yangsoon Lee
- Department of Laboratory Medicine, Hanyang University College of Medicine, Seoul, Korea
| | - Wonkeun Song
- Department of Laboratory Medicine, Hallym University College of Medicine, Seoul, Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Kyungwon Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Yunsop Chong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
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Cheng C, Zhou W, Dong X, Zhang P, Zhou K, Zhou D, Qian C, Lin X, Li P, Li K, Bao Q, Xu T, Lu J, Ying J. Genomic Analysis of Delftia tsuruhatensis Strain TR1180 Isolated From A Patient From China With In4-Like Integron-Associated Antimicrobial Resistance. Front Cell Infect Microbiol 2021; 11:663933. [PMID: 34222039 PMCID: PMC8248536 DOI: 10.3389/fcimb.2021.663933] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/31/2021] [Indexed: 12/04/2022] Open
Abstract
Delftia tsuruhatensis has become an emerging pathogen in humans. There is scant information on the genomic characteristics of this microorganism. In this study, we determined the complete genome sequence of a clinical D. tsuruhatensis strain, TR1180, isolated from a sputum specimen of a female patient in China in 2019. Phylogenetic and average nucleotide identity analysis demonstrated that TR1180 is a member of D. tsuruhatensis. TR1180 exhibited resistance to β-lactam, aminoglycoside, tetracycline and sulphonamide antibiotics, but was susceptible to phenicols, fluoroquinolones and macrolides. Its genome is a single, circular chromosome measuring 6,711,018 bp in size. Whole-genome analysis identified 17 antibiotic resistance-related genes, which match the antimicrobial susceptibility profile of this strain, as well as 24 potential virulence factors and a number of metal resistance genes. Our data showed that Delftia possessed an open pan-genome and the genes in the core genome contributed to the pathogenicity and resistance of Delftia strains. Comparative genomics analysis of TR1180 with other publicly available genomes of Delftia showed diverse genomic features among these strains. D. tsuruhatensis TR1180 harbored a unique 38-kb genomic island flanked by a pair of 29-bp direct repeats with the insertion of a novel In4-like integron containing most of the specific antibiotic resistance genes within the genome. This study reports the findings of a fully sequenced genome from clinical D. tsuruhatensis, which provide researchers and clinicians with valuable insights into this uncommon species.
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Affiliation(s)
- Cong Cheng
- Vocational and Technical College, Lishui University, Lishui, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Wangxiao Zhou
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xu Dong
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Peiyao Zhang
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Kexin Zhou
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Danying Zhou
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Changrui Qian
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xi Lin
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Peizhen Li
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Kewei Li
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Qiyu Bao
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Teng Xu
- Institute of Translational Medicine, Baotou Central Hospital, Baotou, China
| | - Junwan Lu
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Jun Ying
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
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12
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Mao YC, Chuang HN, Shih CH, Hsieh HH, Jiang YH, Chiang LC, Lin WL, Hsiao TH, Liu PY. An investigation of conventional microbial culture for the Naja atra bite wound, and the comparison between culture-based 16S Sanger sequencing and 16S metagenomics of the snake oropharyngeal bacterial microbiota. PLoS Negl Trop Dis 2021; 15:e0009331. [PMID: 33857127 PMCID: PMC8078740 DOI: 10.1371/journal.pntd.0009331] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 04/27/2021] [Accepted: 03/25/2021] [Indexed: 01/11/2023] Open
Abstract
Naja atra is a major venomous snake found in Taiwan. The bite of this snake causes extensive wound necrosis or necrotizing soft tissue infection. Conventional microbial culture-based techniques may fail to identify potential human pathogens and render antibiotics ineffective in the management of wound infection. Therefore, we evaluated 16S Sanger sequencing and next-generation sequencing (NGS) to identify bacterial species in the oropharynx of N. atra. Using conventional microbial culture methods and the VITEK 2 system, we isolated nine species from snakebite wounds. On the basis of the 16S Sanger sequencing of bacterial clones from agar plates, we identified 18 bacterial species in the oropharynx of N. atra, including Morganella morganii, Proteus vulgaris, and Proteus mirabilis, which were also present in the infected bite wound. Using NGS of 16S metagenomics, we uncovered more than 286 bacterial species in the oropharynx of N. atra. In addition, the bacterial species identified using 16S Sanger sequencing accounted for only 2% of those identified through NGS of 16S metagenomics. The bacterial microbiota of the oropharynx of N. atra were modeled better using NGS of 16S metagenomics compared to microbial culture-based techniques. Stenotrophomonas maltophilia, Acinetobacter baumannii, and Proteus penneri were also identified in the NGS of 16S metagenomics. Understanding the bacterial microbiota that are native to the oropharynx of N. atra, in addition to the bite wound, may have additional therapeutic implications regarding empiric antibiotic selection for managing N. atra bites. Naja atra bites induce extensive wound necrotizing soft tissue infections in a substantial proportion of patients. Empiric antibiotic administration in snakebite patients is a common practice, but clinical reports indicate that this treatment was ineffective in preventing secondary infection given that the microbiota of the infected wound and oropharynx of the culprit snake were not properly established. In this study, only 9 species were detected in cobra bites using a conventional microbial culture method and the VITEK 2 system, whereas 18 species were detected in the cobra oropharynx using microbial culture-based 16S Sanger sequencing. Among these, Morganella morganii, Proteus vulgaris, and Proteus mirabilis were identified as common bacteria. Compared to microbial culture-based 16S Sanger sequencing, NGS-based 16S metagenomic sequencing detected more than 286 bacterial species. Stenotrophomonas maltophilia, Acinetobacter baumannii, and Proteus penneri only appeared with 16S metagenomic sequencing. These results suggest that NGS-based 16S metagenomic sequencing is a better tool for uncovering the bacterial microbiota of the N. atra oropharynx, which may help in developing a proper therapeutic strategy for patients with N. atra bites.
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Affiliation(s)
- Yan-Chiao Mao
- Department of Emergency Medicine, Division of Clinical Toxicology, Taichung Veterans General Hospital, Taichung, Taiwan
- School of Medicine, National Defense Medical Center, Taipei, Taiwan
- Department of Medicine, Division of Clinical Toxicology and Occupational Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- Institute of Environmental and Occupational Health Sciences, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Han-Ni Chuang
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
- Precision Medicine Center, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chien-Hung Shih
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
- Precision Medicine Center, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Han-Hsueh Hsieh
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
- Precision Medicine Center, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yu-Han Jiang
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Liao-Chun Chiang
- Department of Emergency Medicine, Division of Clinical Toxicology, Taichung Veterans General Hospital, Taichung, Taiwan
- School of Medicine, National Defense Medical Center, Taipei, Taiwan
- Department of Medicine, Division of Clinical Toxicology and Occupational Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- Institute of Environmental and Occupational Health Sciences, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- National Tsing Hua University, College of Life Sciences, Hsinchu, Taiwan
| | - Wen-Loung Lin
- Taichung Wildlife Conservation Group, Taichung, Taiwan
| | - Tzu-Hung Hsiao
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
- Precision Medicine Center, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Public Health, Fu Jen Catholic University, New Taipei City, Taiwan
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
- * E-mail: (T-HH); (P-YL)
| | - Po-Yu Liu
- Department of Internal Medicine, Division of Infectious Diseases, Taichung Veterans General Hospital, Taichung, Taiwan
- Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan
- Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung, Taiwan
- * E-mail: (T-HH); (P-YL)
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13
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Brinkmann BW, Koch BEV, Spaink HP, Peijnenburg WJGM, Vijver MG. Colonizing microbiota protect zebrafish larvae against silver nanoparticle toxicity. Nanotoxicology 2020; 14:725-739. [DOI: 10.1080/17435390.2020.1755469] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Bregje W. Brinkmann
- Institute of Environmental Sciences (CML), Leiden University, Leiden, the Netherlands
| | - Bjørn E. V. Koch
- Institute of Biology (IBL), Leiden University, Leiden, the Netherlands
| | - Herman P. Spaink
- Institute of Biology (IBL), Leiden University, Leiden, the Netherlands
| | - Willie J. G. M. Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, Leiden, the Netherlands
- Center for Safety of Substances and Products, National Institute of Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Martina G. Vijver
- Institute of Environmental Sciences (CML), Leiden University, Leiden, the Netherlands
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14
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Wang Y, Xu J, Kong L, Li B, Li H, Huang WE, Zheng C. Raman-activated sorting of antibiotic-resistant bacteria in human gut microbiota. Environ Microbiol 2020; 22:2613-2624. [PMID: 32114713 PMCID: PMC7383503 DOI: 10.1111/1462-2920.14962] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 02/26/2020] [Indexed: 01/12/2023]
Abstract
The antibiotic‐resistant bacteria (ARB) and antibiotic‐resistant genes (ARGs) in human gut microbiota have significant impact on human health. While high throughput metagenomic sequencing reveals genotypes of microbial communities, the functionality, phenotype and heterogeneity of human gut microbiota are still elusive. In this study, we applied Raman microscopy and deuterium isotope probing (Raman–DIP) to detect metabolic active ARB (MA‐ARB) in situ at the single‐cell level in human gut microbiota from two healthy adults. We analysed the relative abundances of MA‐ARB under different concentrations of amoxicillin, cephalexin, tetracycline, florfenicol and vancomycin. To establish the link between phenotypes and genotypes of the MA‐ARB, Raman‐activated cell sorting (RACS) was used to sort MA‐ARB from human gut microbiota, and mini‐metagenomic DNA of the sorted bacteria was amplified, sequenced and analysed. The sorted MA‐ARB and their associated ARGs were identified. Our results suggest a strong relation between ARB in human gut microbiota and personal medical history. This study demonstrates that the toolkit of Raman–DIP, RACS and DNA sequencing can be useful to unravel both phenotypes and genotypes of ARB in human gut microbiota at the single‐cell level.
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Affiliation(s)
- Yi Wang
- School of Environment, Harbin Institute of Technology, Harbin, 150090, China.,Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China.,Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Jiabao Xu
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Lingchao Kong
- School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Bei Li
- The State Key Lab of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, CAS, 130033, Changchun, China.,HOOKE Instruments Ltd., 130033, Changchun, China
| | - Hang Li
- HOOKE Instruments Ltd., 130033, Changchun, China
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Chunmiao Zheng
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
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15
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Aziz G, Zaidi A, Bakht U, Parveen N, Ahmed I, Haider Z, Muhammad T. Microbial safety and probiotic potential of packaged yogurt products in Pakistan. J Food Saf 2019. [DOI: 10.1111/jfs.12741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ghazal Aziz
- National Probiotic LabNational Institute for Biotechnology and Genetic Engineering (NIBGE) Faisalabad Punjab Pakistan
- Dept of BiotechnologyPakistan Institute of Engineering and Applied Sciences (PIEAS) Nilore Islamabad Pakistan
| | - Arsalan Zaidi
- National Probiotic LabNational Institute for Biotechnology and Genetic Engineering (NIBGE) Faisalabad Punjab Pakistan
- Dept of BiotechnologyPakistan Institute of Engineering and Applied Sciences (PIEAS) Nilore Islamabad Pakistan
| | - Urooj Bakht
- Institute of Biotechnology and Molecular BiologyUniversity of Lahore (UoL) Lahore Punjab Pakistan
| | - Naila Parveen
- National Probiotic LabNational Institute for Biotechnology and Genetic Engineering (NIBGE) Faisalabad Punjab Pakistan
| | - Ibrar Ahmed
- R&D Section, Alpha Genomics (Pvt) Ltd Islamabad Pakistan
| | - Zeeshan Haider
- Institute of Biotechnology and Molecular BiologyUniversity of Lahore (UoL) Lahore Punjab Pakistan
| | - Tariq Muhammad
- National Probiotic LabNational Institute for Biotechnology and Genetic Engineering (NIBGE) Faisalabad Punjab Pakistan
- Dept of BiotechnologyPakistan Institute of Engineering and Applied Sciences (PIEAS) Nilore Islamabad Pakistan
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16
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Malešević M, Di Lorenzo F, Filipić B, Stanisavljević N, Novović K, Senerovic L, Polović N, Molinaro A, Kojić M, Jovčić B. Pseudomonas aeruginosa quorum sensing inhibition by clinical isolate Delftia tsuruhatensis 11304: involvement of N-octadecanoylhomoserine lactones. Sci Rep 2019; 9:16465. [PMID: 31712724 PMCID: PMC6848482 DOI: 10.1038/s41598-019-52955-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 10/26/2019] [Indexed: 12/17/2022] Open
Abstract
Pseudomonas aeruginosa is one of the most common opportunistic pathogens that use quorum sensing (QS) system to regulate virulence factors expression and biofilm development. Delftia sp. 11304 was selected among 663 Gram-negative clinical isolates based on its QS inhibitory activity against P. aeruginosa MMA83 clinical isolate. Whole genome sequencing identified this isolate as D. tsuruhatensis and revealed genetic armamentarium of virulence factors and antibiotic resistance determinants. Ethyl acetate extract of D. tsuruhatensis 11304 culture supernatant (QSI extract) prevented biofilm formation of P. aeruginosa MMA83, but was unable to cause biofilm decomposition. QSI extract showed a synergistic effect in combination with meropenem and gentamycin, against P. aeruginosa MMA83. A dose-dependent reduction of the virulence factors: elastase, rhamnolipid and pyocyanin production by P. aeruginosa MMA83 and significant downregulation of lasI, lasR, rhlI, rhlR, pqs and mvfR expression were observed. Matrix-assisted Laser Desorption Ionization (MALDI) mass spectrometry of D. tsuruhatensis 11304 QSI extract revealed the presence of N-acyl homoserine lactones (AHL) with chain lengths of C12 to C18. The main ion peak was identified as N-octadecanoylhomoserine lactone (C18-HSL). Commercial C18-HSL (20 µM) reduced pyocyanin production as well as mRNA level of the lasI gene. A novel AHL species, dihydroxy-N-octadecanoylhomoserine lactone, was also described.
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Affiliation(s)
- Milka Malešević
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, 11010, Serbia
| | - Flaviana Di Lorenzo
- University of Napoli Federico II, Department of Chemical Sciences, Napoli, 80126, Italy
| | - Brankica Filipić
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, 11010, Serbia.,Faculty of Pharmacy, University of Belgrade, Belgrade, 11221, Serbia
| | - Nemanja Stanisavljević
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, 11010, Serbia
| | - Katarina Novović
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, 11010, Serbia
| | - Lidija Senerovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, 11010, Serbia
| | - Natalija Polović
- Faculty of Chemistry, University of Belgrade, Belgrade, 11000, Serbia
| | - Antonio Molinaro
- University of Napoli Federico II, Department of Chemical Sciences, Napoli, 80126, Italy
| | - Milan Kojić
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, 11010, Serbia
| | - Branko Jovčić
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, 11010, Serbia. .,Faculty of Biology, University of Belgrade, Belgrade, 11000, Serbia.
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17
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Tejman-Yarden N, Robinson A, Davidov Y, Shulman A, Varvak A, Reyes F, Rahav G, Nissan I. Delftibactin-A, a Non-ribosomal Peptide With Broad Antimicrobial Activity. Front Microbiol 2019; 10:2377. [PMID: 31681234 PMCID: PMC6808179 DOI: 10.3389/fmicb.2019.02377] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 09/30/2019] [Indexed: 11/13/2022] Open
Abstract
The rapid emergence of drug resistant bacteria is occurring worldwide, outpacing the development of new antibiotics. It is known that some of the main sources of antibiotics are the bacteria themselves, many of which are secondary metabolites of Gram positive bacteria. Siderophores, which are secondary metabolites, function as natural chelators (e.g., iron). They are produced and secreted by many bacteria and have been experimented on as "carriers" of several types of antibiotics that pass the cell membrane of challenging Gram negative bacteria. Delftibactin A is a non-ribosomal peptide (NRP), which is known to detoxify gold in Delftia spp. and form gold nuggets, and is considered to be a siderophore. In this study we demonstrate that the supernatant from novel environmental isolates of Delftia spp. have antimicrobial activity. We characterized the active fraction and identified delftibactin A as a compound with antimicrobial activity. Delftibactin A exhibits potent antimicrobial activity against Gram positive multi drug resistant (MDR) bacteria like Methicillin-resistant Staphylococcus aureus (MRSA), and Vancomycin resistant Enterococcus (VRE), and also against the Gram negative pathogens Acinetobacter baumannii and Klebsiella pneumoniae. We discovered that the production of delftibactin A is greatly influenced by temperature. Furthermore, we have demonstrated the possibility of utilizing delftibactin A as a siderophore carrier of toxic metals such as gallium into Gram negative bacteria. These findings expose new opportunities of yet unexploited natural products such as delftibactin A, which have been known for other bacterial uses, as potent factors in the battle against MDR bacteria.
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Affiliation(s)
- Noa Tejman-Yarden
- Public Health Regional Laboratory, Southern District, Ministry of Health (Israel), Beer Sheva, Israel.,Laboratory Department, Ministry of Health, Jerusalem, Israel
| | - Ari Robinson
- Infectious Diseases Unit, Sheba Medical Center, Ramat Gan, Israel
| | - Yaakov Davidov
- Infectious Diseases Unit, Sheba Medical Center, Ramat Gan, Israel
| | | | - Alexander Varvak
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | | | - Galia Rahav
- Infectious Diseases Unit, Sheba Medical Center, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Israel Nissan
- Infectious Diseases Unit, Sheba Medical Center, Ramat Gan, Israel.,National Public Health Laboratory, Ministry of Health (Israel), Tel-Aviv, Israel
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18
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Ranc A, Dubourg G, Fournier PE, Raoult D, Fenollar F. Delftia tsuruhatensis, an Emergent Opportunistic Healthcare-Associated Pathogen. Emerg Infect Dis 2019; 24:594-596. [PMID: 29460754 PMCID: PMC5823324 DOI: 10.3201/eid2403.160939] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Delftia tsuruhatensis, which was first isolated in environmental samples, was rarely associated with human infections. We report on pneumonia caused by D. tsuruhatensis in an infant who underwent cardiac surgery. Retrospective analyses detected 9 other isolates from 8 patients. D. tsuruhatensis is an emergent pathogen, at least for immunocompromised patients.
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19
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Bhattacharjee AS, Motlagh AM, Gilcrease EB, Islam MI, Casjens SR, Goel R. Complete genome sequence of lytic bacteriophage RG-2014 that infects the multidrug resistant bacterium Delftia tsuruhatensis ARB-1. Stand Genomic Sci 2017; 12:82. [PMID: 29270250 PMCID: PMC5735904 DOI: 10.1186/s40793-017-0290-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 11/24/2017] [Indexed: 01/10/2023] Open
Abstract
A lytic bacteriophage RG-2014 infecting a biofilm forming multidrug resistant bacterium Delftia tsuruhatensis strain ARB-1 as its host was isolated from a full-scale municipal wastewater treatment plant. Lytic phage RG-2014 was isolated for developing phage based therapeutic approaches against Delftia tsuruhatensis strain ARB-1. The strain ARB-1 belongs to the Comamonadaceae family of the Betaproteobacteria class. RG-2014 was characterized for its type, burst size, latent and eclipse time periods of 150 ± 9 PFU/cell, 10-min, <5-min, respectively. The phage was found to be a dsDNA virus belonging to the Podoviridae family. It has an isometric icosahedrally shaped capsid with a diameter of 85 nm. The complete genome of the isolated phage was sequenced and determined to be 73.8 kbp in length with a G + C content of 59.9%. Significant similarities in gene homology and order were observed between Delftia phage RG-2014 and the E. coli phage N4 indicating that it is a member of the N4-like phage group.
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Affiliation(s)
- Ananda Shankar Bhattacharjee
- Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, UT USA.,Bigelow Laboratory for Ocean Science, 60 Bigelow Dr., East Boothbay, ME USA
| | - Amir Mohaghegh Motlagh
- Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, UT USA.,Department of Civil, Environmental, and Construction Engineering, University of Central Florida, 12800 Pegasus Dr., Room 340, Orlando, FL USA
| | - Eddie B Gilcrease
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Md Imdadul Islam
- Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, UT USA
| | - Sherwood R Casjens
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, UT USA.,Department of Biology, University of Utah, Salt Lake City, UT USA
| | - Ramesh Goel
- Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, UT USA
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20
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Azevedo AS, Almeida C, Gomes LC, Ferreira C, Mergulhão FJ, Melo LF, Azevedo NF. An in vitro model of catheter-associated urinary tract infections to investigate the role of uncommon bacteria on the Escherichia coli microbial consortium. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2016.11.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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21
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Prasannakumar SP, Gowtham HG, Hariprasad P, Shivaprasad K, Niranjana SR. Delftia tsuruhatensis WGR-UOM-BT1, a novel rhizobacterium with PGPR properties from Rauwolfia serpentina (L.) Benth. ex Kurz also suppresses fungal phytopathogens by producing a new antibiotic-AMTM. Lett Appl Microbiol 2015; 61:460-8. [PMID: 26258398 DOI: 10.1111/lam.12479] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 06/30/2015] [Accepted: 07/30/2015] [Indexed: 11/28/2022]
Abstract
UNLABELLED The bacterial strain designated as WGR-UOM-BT1 isolated from rhizosphere of Rauwolfia serpentina exhibited broad-spectrum antifungal activity and also improved early plant growth. Based on morphological, biochemical and 16S rRNA gene sequence analyses, the strain BT1 was identified as Delftia tsuruhatensis (KF727978). Under in vitro conditions, the strain BT1 suppressed the growth of wide range of fungal phytopathogens. Purified antimicrobial metabolite from the strain BT1 was identified as nitrogen-containing heterocyclic compound, 'amino(5-(4-methoxyphenyl)-2-methyl-2-(thiophen-2-yl)-2,3-dihydrofuran-3-yl)methanol' (AMTM), with molecular mass of 340•40 and molecular formula of C17 H19 NO3 S. The strain BT1 was positive for rhizosphere colonization (tomato), IAA production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity and phosphate solubilization. Under laboratory and greenhouse conditions, the strain BT1 promoted plant growth and suppressed foliar and root fungal pathogens of tomato. Therefore, antimicrobial and disease protection properties of strain BT1 could serve as an effective biological control candidate against devastating fungal pathogens of vegetable plants. Besides, the production of IAA, P solubilization and ACC deaminase activity enhance its potential as a biofertilizer and may stabilize the plant performance under fluctuating environmental conditions. SIGNIFICANCE AND IMPACT OF THE STUDY In this study, we reported that Delftia tsuruhatensis WGR-UOM-BT1 strain has the plant growth promotion activities such as rhizosphere colonization (tomato), IAA production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity and phosphate solubilization. This bacterial strain was found producing an antimicrobial nitrogen-containing heterocyclic compound identified as 'amino(5-(4-methoxyphenyl)-2-methyl-2-(thiophen-2-yl)-2,3-dihydrofuran-3-yl)methanol' [C17 H19 NO3 S] (AMTM), which is new to the bacterial world.
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Affiliation(s)
- S P Prasannakumar
- Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | - H G Gowtham
- Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | - P Hariprasad
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - K Shivaprasad
- Manipal Centre for Natural Sciences, Manipal University, Manipal, Udupi, Karnataka, India
| | - S R Niranjana
- Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
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Draft Genome Sequence of Delftia tsuruhatensis MTQ3, a Strain of Plant Growth-Promoting Rhizobacterium with Antimicrobial Activity. GENOME ANNOUNCEMENTS 2015; 3:3/4/e00822-15. [PMID: 26251486 PMCID: PMC4541264 DOI: 10.1128/genomea.00822-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Delftia tsuruhatensis MTQ3 is a plant growth-promoting rhizobacterium (PGPR) isolated from tobacco rhizosphere. Here, we report the draft genome sequence of D. tsuruhatensis MTQ3. Several functional genes related to antimicrobial activity and environment adaption have been found in the genome. This is the first genome sequence of D. tsuruhatensis related to PGPR.
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Bhattacharjee AS, Choi J, Motlagh AM, Mukherji ST, Goel R. Bacteriophage therapy for membrane biofouling in membrane bioreactors and antibiotic-resistant bacterial biofilms. Biotechnol Bioeng 2015; 112:1644-54. [PMID: 25728819 DOI: 10.1002/bit.25574] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 01/06/2015] [Accepted: 02/13/2015] [Indexed: 11/06/2022]
Abstract
To demonstrate elimination of bacterial biofilm on membranes to represent wastewater treatment as well as biofilm formed by antibiotic-resistant bacterial (ARB) to signify medical application, an antibiotic-resistant bacterium and its lytic bacteriophage were isolated from a full-scale wastewater treatment plant. Based on gram staining and complete 16 S rDNA sequencing, the isolated bacterium showed a more than 99% homology with Delftia tsuruhatensis, a gram-negative bacterium belonging to β-proteobacteria. The Delftia lytic phage's draft genome revealed the phage to be an N4-like phage with 59.7% G + C content. No transfer RNAs were detected for the phage suggesting that the phage is highly adapted to its host Delftia tsuruhatensis ARB-1 with regard to codon usage, and does not require additional tRNAs of its own. The gene annotation of the Delftia lytic phage found three different components of RNA polymerase (RNAP) in the genome, which is a typical characteristic of N4-like phages. The lytic phage specific to D. tsuruhatensis ARB-1 could successfully remove the biofilm formed by it on a glass slide. The water flux through the membrane of a prototype lab-scale membrane bioreactor decreased from 47 L/h m(2) to ∼15 L/h m(2) over 4 days due to a biofilm formed by D. tsuruhatensis ARB-1. However, the flux increased to 70% of the original after the lytic phage application. Overall, this research demonstrated phage therapy's great potential to solve the problem of membrane biofouling, as well as the problems posed by pathogenic biofilms in external wounds and on medical instruments.
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Affiliation(s)
| | - Jeongdong Choi
- Department of Environmental Engineering, Korea National University of Transportation, Chungju, South Korea
| | - Amir Mohaghegh Motlagh
- Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, USA
| | - Sachiyo T Mukherji
- Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, USA
| | - Ramesh Goel
- Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, USA.
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Kang H, Xu X, Fu K, An X, Mi Z, Yin X, Peng F, Pei G, Wang Y, Huang Y, Zhang X, Zhang Z, Wang W, Zhou L, Chen J, Tong Y. Characterization and Genomic Analysis of Quinolone-Resistant Delftia sp. 670 Isolated from a Patient Who Died from Severe Pneumonia. Curr Microbiol 2015; 71:54-61. [PMID: 25935202 DOI: 10.1007/s00284-015-0818-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 03/04/2015] [Indexed: 11/29/2022]
Abstract
Antibiotic-resistant opportunistic pathogens have become a serious concern in recent decades, as they are increasingly responsible for hospital-acquired infections. Here, we describe quinolone-resistant Delftia sp. strain 670, isolated from the sputum of a patient who died from severe pulmonary infection. The draft genome sequence of this strain was obtained by whole-genome shotgun sequencing, and was subjected to comparative genome analysis. Genome analysis revealed that one critical mutation (Ser83Ile in gyrA) might play a decisive role in quinolone resistance. The genome of Delftia sp. strain 670 contains both type II and type VI secretion systems, which were predicted to contribute to the virulence of the strain. Phylogenetic analysis, assimilation tests, and comparative genome analysis indicated that strain 670 differed from the four known Delftia species, suggesting this strain could represent a novel species. Although the study could not determine the strain 670 as the pathogen led to mortality, our findings also presented the pathogenic potential of Delftia species, and the increasing severity of antibiotic resistance among emerging opportunistic pathogens. The whole genome sequencing and comparative analysis improved our understanding of genome evolution in the genus Delftia, and provides the foundation for further study on drug resistance and virulence of Delftia strains.
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Affiliation(s)
- Huaixing Kang
- School of Basic Medical Science Central South University, Changsha, 410013, People's Republic of China,
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25
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Khan S, Sistla S, Dhodapkar R, Parija SC. Fatal Delftia acidovorans infection in an immunocompetent patient with empyema. Asian Pac J Trop Biomed 2015; 2:923-4. [PMID: 23569872 DOI: 10.1016/s2221-1691(12)60254-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Revised: 09/27/2012] [Accepted: 11/28/2012] [Indexed: 11/30/2022] Open
Abstract
Delftia acidovorans (earlier known as Comamonas acidovorans) is an aerobic, non-fermentative, Gram negative rod, classified in the Pseudomonas rRNA homology Group III. Reports of isolation of the organism from serious infections like central venous catheter associated bacteremia, corneal ulcers, otitis media exist. The microbiologists can identify this organism based on an orange indole reaction. This reaction demonstrates the organism's ability to produce anthranilic acid from tryptophan on addition of Kovac's reagent; which gives the media its characteristic "pumpkin orange" colour. Here we report the isolation of this organism from the Endotracheal tube aspirate of a 4 year old child. With the increasing use of invasive devices, it has become important to recognize these non fermentative gram negative bacilli as emerging source of infection even in immunocompetent individuals.
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Affiliation(s)
- Sadia Khan
- Department of Microbiology JIPMER Puducherry-605006, India
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26
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Sohn KM, Baek JY. Delftia lacustris septicemia in a pheochromocytoma patient: case report and literature review. Infect Dis (Lond) 2015; 47:349-53. [PMID: 25712727 DOI: 10.3109/00365548.2014.993422] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
We report the first case of true Delftia lacustris bacteremia in a patient with pheochromocytoma. The organism was identified using 16S rRNA gene sequencing and biochemical tests. A peripheral intravenous catheter was the suspected source of infection, and the patient was successfully treated with piperacillin/tazobactam. We also present a review of the literature describing bacteremia caused by Delftia species.
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Affiliation(s)
- Kyung Mok Sohn
- From the Division of Infectious Diseases, Chungnam National University Hospital, Chungnam National University School of Medicine , Daejeon , Republic of Korea
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27
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Azevedo AS, Almeida C, Melo LF, Azevedo NF. Interaction between atypical microorganisms and E. coli in catheter-associated urinary tract biofilms. BIOFOULING 2014; 30:893-902. [PMID: 25184430 DOI: 10.1080/08927014.2014.944173] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Most biofilms involved in catheter-associated urinary tract infections (CAUTIs) are polymicrobial, with disease causing (eg Escherichia coli) and atypical microorganisms (eg Delftia tsuruhatensis) frequently inhabiting the same catheter. Nevertheless, there is a lack of knowledge about the role of atypical microorganisms. Here, single and dual-species biofilms consisting of E. coli and atypical bacteria (D. tsuruhatensis and Achromobacter xylosoxidans), were evaluated. All species were good biofilm producers (Log 5.84-7.25 CFU cm(-2) at 192 h) in artificial urine. The ability of atypical species to form a biofilm appeared to be hampered by the presence of E. coli. Additionally, when E. coli was added to a pre-formed biofilm of the atypical species, it seemed to take advantage of the first colonizers to accelerate adhesion, even when added at lower concentrations. The results suggest a greater ability of E. coli to form biofilms in conditions mimicking the CAUTIs, whatever the pre-existing microbiota and the inoculum concentration.
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Affiliation(s)
- Andreia S Azevedo
- a Laboratory for Process Engineering, Environment, and Energy and Biotechnology Engineering (LEPABE), Department of Chemical Engineering, Faculty of Engineering , University of Porto , Rua Dr Roberto Frias, 4200-465 Porto , Portugal
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28
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Bacteremia caused by Comamonas kerstersii in a patient with diverticulosis. J Clin Microbiol 2013; 52:1009-12. [PMID: 24371242 DOI: 10.1128/jcm.02942-13] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We report for the first time a case of bacteremia caused by Comamonas kerstersii in a 65-year-old patient with sign of diverticulosis. In addition, we review the isolation of Comamonas sp. and related organisms in our hospital over 25 years.
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29
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Keusch S, Speich R, Treder U, Ulrich Somaini S. Central Venous Catheter Infections in Outpatients with Pulmonary Hypertension Treated with Continuous Iloprost. Respiration 2013; 86:402-6. [DOI: 10.1159/000350441] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 02/13/2013] [Indexed: 11/19/2022] Open
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30
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Wei CL, Chao SH, Tsai WB, Lee PS, Tsau NH, Chen JS, Lai WL, Tu JCY, Tsai YC. Analysis of bacterial diversity during the fermentation of inyu, a high-temperature fermented soy sauce, using nested PCR-denaturing gradient gel electrophoresis and the plate count method. Food Microbiol 2013; 33:252-61. [PMID: 23200659 DOI: 10.1016/j.fm.2012.10.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 07/14/2012] [Accepted: 10/02/2012] [Indexed: 12/14/2022]
Abstract
The diversity of bacteria associated with the fermentation of inyu, also known as black soy sauce, was studied through the nested PCR-denaturing gradient gel electrophoresis (DGGE) of samples collected from the fermentation stages of the inyu production process. The DGGE profiles targeted the bacterial 16S rDNA and revealed the presence of Citrobacter farmeri, Enterobacter cloacae, Enterobacter hormaechei, Enterococcus faecium, Klebsiella pneumoniae, Pantoea agglomerans, Salmonella enterica, Serratia marcescens, Staphylococcus sciuri and Weissella confusa. The bacterial compositions of 4 fermented samples were further elucidated using the plate count method. The bacteria isolated from the koji-making stage exhibited the highest diversity; Brachybacterium rhamnosum, E. hormaechei, K. pneumoniae, Kurthia gibsonii, Pantoea dispersa, Staphylococcus gallinarum, Staphylococcus kloosii and S. sciuri were identified. Koji collected during the preincubation stage presented the largest cell counts, and E. hormaechei, K. pneumoniae, E. cloacae and Enterobacter pulveris were identified. In brine samples aged for 7 and 31 days, the majority of the bacteria isolated belonged to 4 Bacillus species, but 4 Staphylococcus species and Delftia tsuruhatensis were also detected. This study demonstrates the benefits of using a combined approach to obtain a more complete picture of microbial populations and provides useful information for the control or development of bacterial flora during inyu fermentation.
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Affiliation(s)
- Chia-Li Wei
- Department of Biochemical Science and Technology, National Chiayi University, Chiayi City 60004, Taiwan
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31
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Shin SY, Choi JY, Ko KS. Four cases of possible human infections with Delftia lacustris. Infection 2012; 40:709-12. [PMID: 23055149 DOI: 10.1007/s15010-012-0339-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 09/12/2012] [Indexed: 12/01/2022]
Abstract
We report four cases of possible human infections with Delftia lacustris. D. lacustris isolates, which were isolated from blood cultures and bile fluid of patients with underlying diseases such as empyema, renal injury, hepatocellular carcinoma, and renal infarction, were identified using 16S rRNA gene sequencing and biochemical tests. Four D. lacustris isolates did not show the same antimicrobial susceptibility profiles and enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) patterns, indicating their non-clonality.
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Affiliation(s)
- S Y Shin
- Korea Medical Institute, Seoul, South Korea
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32
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Chen S, Hickey WJ. Development of Tools for Genetic Analysis of Phenanthrene Degradation and Nanopod Production by Delftia sp. Cs1-4. Front Microbiol 2011; 2:187. [PMID: 22016746 PMCID: PMC3191457 DOI: 10.3389/fmicb.2011.00187] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 08/22/2011] [Indexed: 11/16/2022] Open
Abstract
The bacterium Delftia sp. Cs1-4 produces novel extracellular structures (nanopods) in conjunction with its growth on phenanthrene. While a full genome sequence is available for strain Cs1-4, genetic tools that could be applied to study phenanthrene degradation/nanopod production have not been reported. Thus, the objectives of this study were to establish such tools, and apply them for molecular analysis of nanopod formation or phenanthrene degradation. Three types of tools were developed or validated. First, we developed a new expression system based on a strong promoter controlling expression of a surface layer protein (NpdA) from Delftia sp. Cs1-4, which was ca. 2,500-fold stronger than the widely used lactose promoter. Second, the Cre-loxP system was validated for generation of markerless, in-frame, gene deletions, and for in-frame gene insertions. The gene deletion function was applied to examine potential roles in nanopod formation of three genes (omp32, lasI, and hcp), while the gene insertion function was used for reporter gene tagging of npdA. Lastly, pMiniHimar was modified to enhance gene recovery and mutant analysis in genome-wide transposon mutagenesis. Application of the latter to strain Cs1-4, revealed several new genes with potential roles in phenanthrene degradation or npdA expression. Collectively, the availability of these tools has opened new avenues of investigation in Delftia sp. Cs1-4 and other related genera/species with importance in environmental toxicology.
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Affiliation(s)
- Shicheng Chen
- O.N. Allen Laboratory for Soil Microbiology, Department of Soil Science, University of Wisconsin-Madison Madison, WI, USA
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