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Husťáková B, Trundová M, Adámková K, Kovaľ T, Dušková J, Dohnálek J. A highly active S1-P1 nuclease from the opportunistic pathogen Stenotrophomonas maltophilia cleaves c-di-GMP. FEBS Lett 2023; 597:2103-2118. [PMID: 37309731 DOI: 10.1002/1873-3468.14683] [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: 01/19/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/14/2023]
Abstract
A number of multidrug-resistant bacterial pathogens code for S1-P1 nucleases with a poorly understood role. We have characterized a recombinant form of S1-P1 nuclease from Stenotrophomonas maltophilia, an opportunistic pathogen. S. maltophilia nuclease 1 (SmNuc1) acts predominantly as an RNase and is active in a wide range of temperatures and pH. It retains a notable level of activity towards RNA and ssDNA at pH 5 and 9 and about 10% of activity towards RNA at 10 °C. SmNuc1 with very high catalytic rates outperforms S1 nuclease from Aspergillus oryzae and other similar nucleases on all types of substrates. SmNuc1 degrades second messenger c-di-GMP, which has potential implications for its role in the pathogenicity of S. maltophilia.
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Affiliation(s)
- Blanka Husťáková
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, Biocev, Vestec, Czech Republic
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - Mária Trundová
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, Biocev, Vestec, Czech Republic
| | - Kristýna Adámková
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, Biocev, Vestec, Czech Republic
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - Tomáš Kovaľ
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, Biocev, Vestec, Czech Republic
| | - Jarmila Dušková
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, Biocev, Vestec, Czech Republic
| | - Jan Dohnálek
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, Biocev, Vestec, Czech Republic
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Lee HW, Yoon SR, Dang YM, Kang M, Lee K, Ha JH, Bae JW. Presence of an ultra-small microbiome in fermented cabbages. PeerJ 2023; 11:e15680. [PMID: 37483986 PMCID: PMC10358336 DOI: 10.7717/peerj.15680] [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: 02/14/2023] [Accepted: 06/13/2023] [Indexed: 07/25/2023] Open
Abstract
Background Ultramicrobacteria (UMB), also known as ultra-small bacteria, are tiny bacteria with a size less than 0.1 µm3. They have a high surface-to-volume ratio and are found in various ecosystems, including the human body. UMB can be classified into two types: one formed through cell contraction and the other that maintains a small size. The ultra-small microbiome (USM), which may contain UMB, includes all bacteria less than 0.2 µm in size and is difficult to detect with current methods. However, it poses a potential threat to food hygiene, as it can pass through sterilization filters and exist in a viable but non-culturable (VBNC) state. The data on the USM of foods is limited. Some bacteria, including pathogenic species, are capable of forming UMB under harsh conditions, making it difficult to detect them through conventional culture techniques. Methods The study described above focused on exploring the diversity of USM in fermented cabbage samples from three different countries (South Korea, China, and Germany). The samples of fermented cabbage (kimchi, suancai, and sauerkraut) were purchased and stored in chilled conditions at approximately 4 °C until filtration. The filtration process involved two steps of tangential flow filtration (TFF) using TFF cartridges with different pore sizes (0.2 µm and 100 kDa) to separate normal size bacteria (NM) and USM. The USM and NM isolated via TFF were stored in a refrigerator at 4 °C until DNA extraction. The extracted DNA was then amplified using PCR and the full-length 16S rRNA gene was sequenced using single-molecule-real-time (SMRT) sequencing. The transmission electron microscope (TEM) was used to confirm the presence of microorganisms in the USM of fermented cabbage samples. Results To the best of our knowledge, this is the first study to identify the differences between USM and NM in fermented cabbages. Although the size of the USM (average 2,171,621 bp) was smaller than that of the NM (average 15,727,282 bp), diversity in USM (average H' = 1.32) was not lower than that in NM (average H' = 1.22). In addition, some members in USM probably underwent cell shrinkage due to unfavorable environments, while others maintained their size. Major pathogens were not detected in the USM in fermented cabbages. Nevertheless, several potentially suspicious strains (genera Cellulomonas and Ralstonia) were detected. Our method can be used to screen food materials for the presence of USM undetectable via conventional methods. USM and NM were efficiently separated using tangential flow filtration and analyzed via single-molecule real-time sequencing. The USM of fermented vegetables exhibited differences in size, diversity, and composition compared with the conventional microbiome. This study could provide new insights into the ultra-small ecosystem in fermented foods, including fermented cabbages.
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Affiliation(s)
- Hae-Won Lee
- Hygienic Safety ⋅ Materials Research Group, World Institute of Kimchi, Gwangju, Republic of Korea
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - So-Ra Yoon
- Hygienic Safety ⋅ Materials Research Group, World Institute of Kimchi, Gwangju, Republic of Korea
| | - Yun-Mi Dang
- Hygienic Safety ⋅ Materials Research Group, World Institute of Kimchi, Gwangju, Republic of Korea
| | - Miran Kang
- Practical Technology Research Group, World Institute of Kimchi, Gwangju, Republic of Korea
| | - Kwangho Lee
- Center for Research Facilities, Chonnam National University, Gwangju, Republic of Korea
| | - Ji-Hyung Ha
- Hygienic Safety ⋅ Materials Research Group, World Institute of Kimchi, Gwangju, Republic of Korea
| | - Jin-Woo Bae
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
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3
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Chauviat A, Meyer T, Favre-Bonté S. Versatility of Stenotrophomonas maltophilia: Ecological roles of RND efflux pumps. Heliyon 2023; 9:e14639. [PMID: 37089375 PMCID: PMC10113797 DOI: 10.1016/j.heliyon.2023.e14639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
S. maltophilia is a widely distributed bacterium found in natural, anthropized and clinical environments. The genome of this opportunistic pathogen of environmental origin includes a large number of genes encoding RND efflux pumps independently of the clinical or environmental origin of the strains. These pumps have been historically associated with the uptake of antibiotics and clinically relevant molecules because they confer resistance to many antibiotics. However, considering the environmental origin of S. maltophilia, the ecological role of these pumps needs to be clarified. RND efflux systems are highly conserved within bacteria and encountered both in pathogenic and non-pathogenic species. Moreover, their evolutionary origin, conservation and multiple copies in bacterial genomes suggest a primordial role in cellular functions and environmental adaptation. This review is aimed at elucidating the ecological role of S. maltophilia RND efflux pumps in the environmental context and providing an exhaustive description of the environmental niches of S. maltophilia. By looking at the substrates and functions of the pumps, we propose different involvements and roles according to the adaptation of the bacterium to various niches. We highlight that i°) regulatory mechanisms and inducer molecules help to understand the conditions leading to their expression, and ii°) association and functional redundancy of RND pumps and other efflux systems demonstrate their complex role within S. maltophilia cells. These observations emphasize that RND efflux pumps play a role in the versatility of S. maltophilia.
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Weig AR, Löder MGJ, Ramsperger AFRM, Laforsch C. In situ Prokaryotic and Eukaryotic Communities on Microplastic Particles in a Small Headwater Stream in Germany. Front Microbiol 2021; 12:660024. [PMID: 34912303 PMCID: PMC8667586 DOI: 10.3389/fmicb.2021.660024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 11/04/2021] [Indexed: 01/04/2023] Open
Abstract
The ubiquitous use of plastic products in our daily life is often accompanied by improper disposal. The first interactions of plastics with organisms in the environment occur by overgrowth or biofilm formation on the particle surface, which can facilitate the ingestion by animals. In order to elucidate the colonization of plastic particles by prokaryotic and eukaryotic microorganisms in situ, we investigated microbial communities in biofilms on four different polymer types and on mineral particles in a small headwater stream 500 m downstream of a wastewater treatment plant in Germany. Microplastic and mineral particles were exposed to the free-flowing water for 4 weeks in spring and in summer. The microbial composition of the developing biofilm was analyzed by 16S and 18S amplicon sequencing. Despite the expected seasonal differences in the microbial composition of pro- and eukaryotic communities, we repeatedly observed polymer type-specific differentiation in both seasons. The order of polymer type-specific prokaryotic and eukaryotic community distances calculated by Robust Aitchison principal component analysis (PCA) was the same in spring and summer samples. However, the magnitude of the distance differed considerably between polymer types. Prokaryotic communities on polyethylene particles exhibited the most considerable difference to other particles in summer, while eukaryotic communities on polypropylene particles showed the most considerable difference to other spring samples. The most contributing bacterial taxa to the polyethylene-specific differentiation belong to the Planctomycetales, Saccharimonadales, Bryobacterales, uncultured Acidiomicrobia, and Gemmatimonadales. The most remarkable differences in eukaryotic microorganism abundances could be observed in several distinct groups of Ciliophora (ciliates) and Chlorophytes (green algae). Prediction of community functions from taxonomic abundances revealed differences between spring and summer, and – to a lesser extent – also between polymer types and mineral surfaces. Our results show that different microplastic particles were colonized by different biofilm communities. These findings may be used for advanced experimental designs to investigate the role of microorganisms on the fate of microplastic particles in freshwater ecosystems.
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Affiliation(s)
- Alfons R Weig
- Genomics and Bioinformatics, Bayreuth Center of Ecology and Environmental Research, University of Bayreuth, Bayreuth, Germany
| | - Martin G J Löder
- Animal Ecology, Bayreuth Center of Ecology and Environmental Research, University of Bayreuth, Bayreuth, Germany
| | - Anja F R M Ramsperger
- Animal Ecology, Bayreuth Center of Ecology and Environmental Research, University of Bayreuth, Bayreuth, Germany.,Biological Physics, University of Bayreuth, Bayreuth, Germany
| | - Christian Laforsch
- Animal Ecology, Bayreuth Center of Ecology and Environmental Research, University of Bayreuth, Bayreuth, Germany
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The Potential of Phage Therapy against the Emerging Opportunistic Pathogen Stenotrophomonas maltophilia. Viruses 2021; 13:v13061057. [PMID: 34204897 PMCID: PMC8228603 DOI: 10.3390/v13061057] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 12/22/2022] Open
Abstract
The isolation and characterization of bacteriophages for the treatment of infections caused by the multidrug resistant pathogen Stenotrophomonas maltophilia is imperative as nosocomial and community-acquired infections are rapidly increasing in prevalence. This increase is largely due to the numerous virulence factors and antimicrobial resistance genes encoded by this bacterium. Research on S. maltophilia phages to date has focused on the isolation and in vitro characterization of novel phages, often including genomic characterization, from the environment or by induction from bacterial strains. This review summarizes the clinical significance, virulence factors, and antimicrobial resistance mechanisms of S. maltophilia, as well as all phages isolated and characterized to date and strategies for their use. We further address the limited in vivo phage therapy studies conducted against this bacterium and discuss the future research needed to spearhead phages as an alternative treatment option against multidrug resistant S. maltophilia.
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6
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Govender R, Amoah ID, Kumari S, Bux F, Stenström TA. Detection of multidrug resistant environmental isolates of acinetobacter and Stenotrophomonas maltophilia: a possible threat for community acquired infections? JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2020; 56:213-225. [PMID: 33378222 DOI: 10.1080/10934529.2020.1865747] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 12/10/2020] [Accepted: 12/12/2020] [Indexed: 06/12/2023]
Abstract
Acinetobacter spp. and Stenotrophomonas maltophilia are bacteria commonly associated with infections at the clinical settings. Reports of infections caused by environmental isolates are rare. Therefore, this study focused on determination of the antibiotic resistance patterns, antibiotic resistance genes, efflux pumps and virulence signatures of Acinetobacter spp. and S. maltophilia recovered from river water, plant rhizosphere and river sediment samples. The isolates were identified and confirmed using biochemical tests and PCR. The antimicrobial resistance profiles of the isolates were determined using Kirby Bauer disk diffusion assay and presence of antibiotic resistance and virulence genes were detected using PCR. S. maltophilia was more frequent in plant rhizosphere and sediment samples than the water samples. Acinetobacter spp. were mostly resistant to trimethoprim-sulfamethoxazole (96% of isolates), followed by polymyxin b (86%), cefixime (54%), colistin (42%), ampicillin (35%) and meropenem (19%). The S. maltophilia isolates displayed total resistance (100%) to trimethoprim- sulfamethoxazole, meropenem, imipenem, ampicillin and cefixime, while 80% of the isolates were resistant to ceftazidime. Acinetobacter spp. contained different antibiotic resistance genes such as sul1 (24% of isolates), sul2 (29%), blaOXA 23/51 (21%) and blaTEM (29%), while S. maltophilia harbored sul1 (8%) and blaTEM (20%). Additionally, efflux pump genes were present in all S. maltophilia isolates. The presence of multidrug resistant Acinetobacter spp. and Stenotrophomonas maltophilia in surface water raises concerns for community-acquired infections as this water is directly been used by the community for various purposes. Therefore, there is the need to institute measures aimed at reducing the risks of these infections and the resulting burden this may have on the health care system within the study area.
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Affiliation(s)
- Reshme Govender
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, South Africa
| | - Isaac D Amoah
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, South Africa
| | - Sheena Kumari
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, South Africa
| | - Faizal Bux
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, South Africa
| | - Thor A Stenström
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, South Africa
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Gomes IB, Querido MM, Teixeira JP, Pereira CC, Simões LC, Simões M. Prolonged exposure of Stenotrophomonas maltophilia biofilms to trace levels of clofibric acid alters antimicrobial tolerance and virulence. CHEMOSPHERE 2019; 235:327-335. [PMID: 31265978 DOI: 10.1016/j.chemosphere.2019.06.184] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/13/2019] [Accepted: 06/24/2019] [Indexed: 06/09/2023]
Abstract
The presence of pharmaceuticals in water sources, including in drinking water (DW), is increasingly being recognized as an emerging and global concern for the environment and public health. Based on the principles of the "One Health" initiative, the present work aims to understand the effects of clofibric acid (CA), a lipid regulator, on the behavior of a selected bacterium isolated from drinking water (DW). Biofilms of the opportunistic pathogen Stenotrophomonas maltophilia were exposed to CA for 12 weeks at 170 and 17000 ng/L. The effects of CA were evaluated on planktonic S. maltophilia susceptibility to chlorine and antibiotics (amoxicillin, ciprofloxacin, erythromycin, kanamycin, levofloxacin, oxacillin, spectinomycin, tetracycline and trimethoprim-sulfamethoxazole), biofilm formation, motility, siderophores production and on the adhesion and internalization of the human colon adenocarcinoma cell line (HT-29). It was found that CA did not affect planktonic S. maltophilia tolerance to chlorine exposure. Additionally, no effects were observed on biofilm formation, motility and siderophores production. However, biofilms formed after CA exposure were more tolerant to chlorine disinfection and lower CFU reductions were obtained. Of additional concern was the effect of CA exposure on S. maltophilia increased tolerance to erythromycin. CA exposure also slightly reduced S. maltophilia ability to invade HT-29 cells. In conclusion, this work reinforces the importance of studying the effects of non-antibiotic contaminants on the behavior of environmental microorganisms, particularly their role as drivers affecting resistance evolution and selection.
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Affiliation(s)
- I B Gomes
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465, Porto, Portugal
| | - M M Querido
- Department of Environmental Health, Portuguese National Institute of Health DR. Ricardo Jorge, Rua Alexandre Herculano, 321, 4000-055, Porto, Portugal; EPIUnit - Institute of Public Health, University of Porto, Rua das Taipas, 135, 4050-600, Porto, Portugal
| | - J P Teixeira
- Department of Environmental Health, Portuguese National Institute of Health DR. Ricardo Jorge, Rua Alexandre Herculano, 321, 4000-055, Porto, Portugal; EPIUnit - Institute of Public Health, University of Porto, Rua das Taipas, 135, 4050-600, Porto, Portugal
| | - C C Pereira
- Department of Environmental Health, Portuguese National Institute of Health DR. Ricardo Jorge, Rua Alexandre Herculano, 321, 4000-055, Porto, Portugal; EPIUnit - Institute of Public Health, University of Porto, Rua das Taipas, 135, 4050-600, Porto, Portugal
| | - L C Simões
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - M Simões
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465, Porto, Portugal.
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Liu J, Li B, Wang Y, Zhang G, Jiang X, Li X. Passage and community changes of filterable bacteria during microfiltration of a surface water supply. ENVIRONMENT INTERNATIONAL 2019; 131:104998. [PMID: 31330365 DOI: 10.1016/j.envint.2019.104998] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/06/2019] [Accepted: 07/07/2019] [Indexed: 06/10/2023]
Abstract
The omnipresence of filterable bacteria that can pass through 0.22-μm membrane filters demands a change in the sterile filtration practice. In this study, we identified that filterable bacteria enriched from a surface water are members of the Bacteroidetes, Proteobacteria, Spirochaetae, Firmicutes, and Actinobacteria. Filterable bacteria displayed superior filterability during the entire bacterial growth phase, especially at the exponential phase. Maximal passage percentages were comparable at different cell densities, and achieved earlier at high cell density. Furthermore, filter retention for the investigated bacteria is independent of liquid temperature. However, cultivation temperature could affect the growth of some specific filterable bacteria and lead to variability in the passage percentage. Additionally, membrane materials, pore size and filtering flux greatly affected the passage of filterable bacteria. The majority of filterable Hylemonella and SAR324 could pass through 0.1-μm polyvinylidene fluoride and polyethersulfone filters but could not pass through 0.1-μm polycarbonate and mixed cellulose esters filters. Taken together, our results demonstrated that the ultra-small size of filterable bacteria, membrane characteristics and filtration operational conditions could challenge the validity of the 0.22/0.1-μm sterilizing grade filters in providing bio-safety barriers.
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Affiliation(s)
- Jie Liu
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, China
| | - Bing Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, China.
| | - Yingying Wang
- College of Environmental Science and Engineering, Nankai University, China
| | - Guijuan Zhang
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, China
| | - Xiaotao Jiang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Hong Kong, China
| | - Xiaoyan Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, China; Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, China.
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Liu J, Zhao R, Zhang J, Zhang G, Yu K, Li X, Li B. Occurrence and Fate of Ultramicrobacteria in a Full-Scale Drinking Water Treatment Plant. Front Microbiol 2018; 9:2922. [PMID: 30568635 PMCID: PMC6290093 DOI: 10.3389/fmicb.2018.02922] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 11/14/2018] [Indexed: 12/23/2022] Open
Abstract
Ultramicrobacteria (UMB) are omnipresent and numerically dominate in freshwater, as microbes can present in drinking water systems, however, the UMB communities that occur and their removal behaviors remain poorly characterized in drinking water treatment plants (DWTPs). To gain insights into these issues, we profiled bacterial cell density, community structure and functions of UMB and their counterpart large bacteria (LB) using flow cytometry and filtration paired with 16S rRNA gene high-throughput sequencing in a full-scale DWTP. Contrary to the reduction of bacterial density and diversity, the proportion of UMB in the total bacteria community increased as the drinking water treatment process progressed, and biological activated carbon facilitated bacterial growth. Moreover, UMB were less diverse than LB, and their community structure and predicted functions were significantly different. In the DWTP, UMB indicator taxa were mainly affiliated with α/β/γ-Proteobacteria, Deinococcus-Thermus, Firmicutes, Acidobacteria, and Dependentiae. In particular, the exclusive clustering of UMB at the phylum level, e.g., Parcubacteria, Elusimicrobia, and Saccharibacteria, confirmed the fact that the ultra-small size of UMB is a naturally and evolutionarily conserved trait. Additionally, the streamlined genome could be connected to UMB, such as candidate phyla radiation (CPR) bacteria, following a symbiotic or parasitic lifestyle, which then leads to the observed high connectedness, i.e., non-random intra-taxa co-occurrence patterns within UMB. Functional prediction analysis revealed that environmental information processing and DNA replication and repair likely contribute to the higher resistance of UMB to drinking water treatment processes in comparison to LB. Overall, the study provides valuable insights into the occurrence and fate of UMB regarding community structure, phylogenetic characteristics and potential functions in a full-scale DWTP, and it is a useful reference for beneficial manipulation of the drinking water microbiome.
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Affiliation(s)
- Jie Liu
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Renxin Zhao
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Jiayu Zhang
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Guijuan Zhang
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Ke Yu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Xiaoyan Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Bing Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
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10
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Adegoke AA, Stenström TA, Okoh AI. Stenotrophomonas maltophilia as an Emerging Ubiquitous Pathogen: Looking Beyond Contemporary Antibiotic Therapy. Front Microbiol 2017; 8:2276. [PMID: 29250041 PMCID: PMC5714879 DOI: 10.3389/fmicb.2017.02276] [Citation(s) in RCA: 185] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/06/2017] [Indexed: 12/21/2022] Open
Abstract
Stenotrophomonas maltophilia is a commensal and an emerging pathogen earlier noted in broad-spectrum life threatening infections among the vulnerable, but more recently as a pathogen in immunocompetent individuals. The bacteria are consistently being implicated in necrotizing otitis, cutaneous infections including soft tissue infection and keratitis, endocarditis, meningitis, acute respiratory tract infection (RTI), bacteraemia (with/without hematological malignancies), tropical pyomyositis, cystic fibrosis, septic arthritis, among others. S. maltophilia is also an environmental bacteria occurring in water, rhizospheres, as part of the animals' microflora, in foods, and several other microbiota. This review highlights clinical reports on S. maltophilia both as an opportunistic and as true pathogen. Also, biofilm formation as well as quorum sensing, extracellular enzymes, flagella, pili/fimbriae, small colony variant, other virulence or virulence-associated factors, the antibiotic resistance factors, and their implications are considered. Low outer membrane permeability, natural MDR efflux systems, and/or resistance genes, resistance mechanisms like the production of two inducible chromosomally encoded β-lactamases, and lack of carefully compiled patient history are factors that pose great challenges to the S. maltophilia control arsenals. The fluoroquinolone, some tetracycline derivatives and trimethoprim-sulphamethaxole (TMP-SMX) were reported as effective antibiotics with good therapeutic outcome. However, TMP-SMX resistance and allergies to sulfa together with high toxicity of fluoroquinolone are notable setbacks. S. maltophilia's production and sustenance of biofilm by quorum sensing enhance their virulence, resistance to antibiotics and gene transfer, making quorum quenching an imperative step in Stenotrophomonas control. Incorporating several other proven approaches like bioengineered bacteriophage therapy, Epigallocatechin-3-gallate (EGCG), essential oil, nanoemulsions, and use of cationic compounds are promising alternatives which can be incorporated in Stenotrophomonas control arsenal.
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Affiliation(s)
- Anthony A Adegoke
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, South Africa.,Applied and Environmental Microbiology Research Group, University of Fort Hare, Alice, South Africa.,SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa
| | - Thor A Stenström
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, South Africa
| | - Anthony I Okoh
- Applied and Environmental Microbiology Research Group, University of Fort Hare, Alice, South Africa.,SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa
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Degand N, Lotte R, Decondé Le Butor C, Segonds C, Thouverez M, Ferroni A, Vallier C, Mély L, Carrère J. Epidemic spread of Pandoraea pulmonicola in a cystic fibrosis center. BMC Infect Dis 2015; 15:583. [PMID: 26705696 PMCID: PMC4691299 DOI: 10.1186/s12879-015-1327-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 12/17/2015] [Indexed: 11/10/2022] Open
Abstract
Background Pandoraea spp. are recently discovered bacteria, mainly recovered from cystic fibrosis (CF) patients, but their epidemiology and clinical significance are not well known. We describe an epidemic spread of Pandoraea pulmonicola from 2009 in our CF center, involving 6 out of 243 CF patients. Methods Bacterial identification used amplified ribosomal DNA restriction analysis (ARDRA), MALDI-TOF mass spectrometry (MALDI-TOF MS) and 16S rDNA gene sequencing. The clonal link between strains was assessed with pulsed field gel electrophoresis (PFGE) using XbaI. Clinical data were gathered for all patients. Results The index case was chronically colonized since 2000. The main hypothesis for this bacterial spread was a droplet cross-transmission, due to preventive measures not being strictly followed. Antibiotic susceptibility testing revealed resistance to beta-lactams, ciprofloxacin and colistin. However, there was susceptibility to trimethoprim-sulfamethoxazole. All patients were chronically colonized with Pseudomonas aeruginosa, and the acquisition of P. pulmonicola resulted in chronic colonization in all patients. Three patients died, and two patients remained clinically stable, whereas one patient had a decline in lung function. Conclusions This study, which is the first to describe an epidemic spread of P. pulmonicola, notes the potential transmissibility of this bacterial species and the need for infection control measures.
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Affiliation(s)
- Nicolas Degand
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Nice, Hôpital Archet II, Nice, France.
| | - Romain Lotte
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Nice, Hôpital Archet II, Nice, France. .,INSERM 1065-Centre Méditerranéen de Médecine moléculaire, « Toxines microbiennes dans la relation hôte-agents pathogènes », Bâtiment Universitaire Archimed, Nice, France. .,Faculté de Médicine, Université de Nice Sophia-Antipolis, Nice, France.
| | - Célia Decondé Le Butor
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Nice, Hôpital Archet II, Nice, France.
| | - Christine Segonds
- Observatoire Burkholderia cepacia, Laboratoire de Bactériologie, Hôpital Purpan, Toulouse, France.
| | | | - Agnès Ferroni
- Laboratoire de Bactériologie, Hôpital Necker-Enfants Malades, Paris, France.
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Moulton-Meissner H, Noble-Wang J, Gupta N, Hocevar S, Kallen A, Arduino M. Laboratory replication of filtration procedures associated with Serratia marcescens bloodstream infections in patients receiving compounded amino acid solutions. Am J Health Syst Pharm 2015. [PMID: 26195654 DOI: 10.2146/ajhp150141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
PURPOSE Specific deviations from United States Pharmacopeia standards were analyzed to investigate the factors allowing an outbreak of Serratia marcescens bloodstream infections in patients receiving compounded amino acid solutions. METHODS Filter challenge experiments using the outbreak strain of S. marcescens were compared with those that used the filter challenge organism recommended by ASTM International (Brevundimonas diminuta ATCC 19162) to determine the frequency and degree of organism breakthrough. Disk and capsule filters (0.22- and 0.2-μm nominal pore size, respectively) were challenged with either the outbreak strain of S. marcescens or B. diminuta ATCC 19162. The following variables were compared: culture conditions in which organisms were grown overnight or cultured in sterile water (starved), solution type (15% amino acid solution or sterile water), and filtration with or without a 0.5-μm prefilter. RESULTS Small-scale, syringe-driven, disk-filtration experiments of starved bacterial cultures indicated that approximately 1 in every 1,000 starved S. marcescens cells (0.12%) was able to pass through a 0.22-μm nominal pore-size filter, and about 1 in every 1,000,000 cells was able to pass through a 0.1-μm nominal pore-size filter. No passage of the B. diminuta ATCC 19162 cells was observed with either filter. In full-scale experiments, breakthrough was observed only when 0.2-μm capsule filters were challenged with starved S. marcescens in 15% amino acid solution without a 0.5-μm prefiltration step. CONCLUSION Laboratory simulation testing revealed that under certain conditions, bacteria can pass through 0.22- and 0.2-μm filters intended for sterilization of an amino acid solution. Bacteria did not pass through 0.2-μm filters when a 0.5-μm prefilter was used.
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Affiliation(s)
- Heather Moulton-Meissner
- Heather Moulton-Meissner, Ph.D., is Associate Service Fellow, Division of Healthcare Quality Promotion (DHQP); Judith Noble-Wang, Ph.D., is Supervisory Microbiologist, DHQP; LCDR Neil Gupta, USPHS, M.D., is Medical Officer, DHQP; LCDR Susan Hocevar, USPHS, M.D., is Medical Officer, DHQP; CDR Alex Kallen, USPHS, M.D., is Medical Officer, DHQP; and Matthew Arduino, Dr.P.H., is Branch Chief, Clinical Environmental Microbiology, DHQP, Centers for Disease Control and Prevention, Atlanta, GA.
| | - Judith Noble-Wang
- Heather Moulton-Meissner, Ph.D., is Associate Service Fellow, Division of Healthcare Quality Promotion (DHQP); Judith Noble-Wang, Ph.D., is Supervisory Microbiologist, DHQP; LCDR Neil Gupta, USPHS, M.D., is Medical Officer, DHQP; LCDR Susan Hocevar, USPHS, M.D., is Medical Officer, DHQP; CDR Alex Kallen, USPHS, M.D., is Medical Officer, DHQP; and Matthew Arduino, Dr.P.H., is Branch Chief, Clinical Environmental Microbiology, DHQP, Centers for Disease Control and Prevention, Atlanta, GA
| | - Neil Gupta
- Heather Moulton-Meissner, Ph.D., is Associate Service Fellow, Division of Healthcare Quality Promotion (DHQP); Judith Noble-Wang, Ph.D., is Supervisory Microbiologist, DHQP; LCDR Neil Gupta, USPHS, M.D., is Medical Officer, DHQP; LCDR Susan Hocevar, USPHS, M.D., is Medical Officer, DHQP; CDR Alex Kallen, USPHS, M.D., is Medical Officer, DHQP; and Matthew Arduino, Dr.P.H., is Branch Chief, Clinical Environmental Microbiology, DHQP, Centers for Disease Control and Prevention, Atlanta, GA
| | - Susan Hocevar
- Heather Moulton-Meissner, Ph.D., is Associate Service Fellow, Division of Healthcare Quality Promotion (DHQP); Judith Noble-Wang, Ph.D., is Supervisory Microbiologist, DHQP; LCDR Neil Gupta, USPHS, M.D., is Medical Officer, DHQP; LCDR Susan Hocevar, USPHS, M.D., is Medical Officer, DHQP; CDR Alex Kallen, USPHS, M.D., is Medical Officer, DHQP; and Matthew Arduino, Dr.P.H., is Branch Chief, Clinical Environmental Microbiology, DHQP, Centers for Disease Control and Prevention, Atlanta, GA
| | - Alex Kallen
- Heather Moulton-Meissner, Ph.D., is Associate Service Fellow, Division of Healthcare Quality Promotion (DHQP); Judith Noble-Wang, Ph.D., is Supervisory Microbiologist, DHQP; LCDR Neil Gupta, USPHS, M.D., is Medical Officer, DHQP; LCDR Susan Hocevar, USPHS, M.D., is Medical Officer, DHQP; CDR Alex Kallen, USPHS, M.D., is Medical Officer, DHQP; and Matthew Arduino, Dr.P.H., is Branch Chief, Clinical Environmental Microbiology, DHQP, Centers for Disease Control and Prevention, Atlanta, GA
| | - Matthew Arduino
- Heather Moulton-Meissner, Ph.D., is Associate Service Fellow, Division of Healthcare Quality Promotion (DHQP); Judith Noble-Wang, Ph.D., is Supervisory Microbiologist, DHQP; LCDR Neil Gupta, USPHS, M.D., is Medical Officer, DHQP; LCDR Susan Hocevar, USPHS, M.D., is Medical Officer, DHQP; CDR Alex Kallen, USPHS, M.D., is Medical Officer, DHQP; and Matthew Arduino, Dr.P.H., is Branch Chief, Clinical Environmental Microbiology, DHQP, Centers for Disease Control and Prevention, Atlanta, GA
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Buse HY, Lu J, Lu X, Mou X, Ashbolt NJ. Microbial diversities (16S and 18S rRNA gene pyrosequencing) and environmental pathogens within drinking water biofilms grown on the common premise plumbing materials unplasticized polyvinylchloride and copper. FEMS Microbiol Ecol 2014; 88:280-95. [PMID: 24490699 DOI: 10.1111/1574-6941.12294] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 01/08/2014] [Accepted: 01/23/2014] [Indexed: 11/29/2022] Open
Abstract
Drinking water (DW) biofilm communities influence the survival of opportunistic pathogens, yet knowledge about the microbial composition of DW biofilms developed on common in-premise plumbing material is limited. Utilizing 16S and 18S rRNA gene pyrosequencing, this study characterized the microbial community structure within DW biofilms established on unplasticized polyvinyl chloride (uPVC) and copper (Cu) surfaces and the impact of introducing Legionella pneumophila (Lp) and Acanthamoeba polyphaga. Mature (> 1 year old) biofilms were developed before inoculation with sterilized DW (control, Con), Lp, or Lp and A. polyphaga (LpAp). Comparison of uPVC and Cu biofilms indicated significant differences between bacterial (P = 0.001) and eukaryotic (P < 0.01) members attributable to the unique presence of several family taxa: Burkholderiaceae, Characeae, Epistylidae, Goniomonadaceae, Paramoebidae, Plasmodiophoridae, Plectidae, Sphenomonadidae, and Toxariaceae within uPVC biofilms; and Enterobacteriaceae, Erythrobacteraceae, Methylophilaceae, Acanthamoebidae, and Chlamydomonadaceae within Cu biofilms. Introduction of Lp alone or with A. polyphaga had no effect on bacterial community profiles (P > 0.05) but did affect eukaryotic members (uPVC, P < 0.01; Cu, P = 0.001). Thus, established DW biofilms host complex communities that may vary based on substratum matrix and maintain consistent bacterial communities despite introduction of Lp, an environmental pathogen.
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Lacombe A, Li RW, Klimis-Zacas D, Kristo AS, Tadepalli S, Krauss E, Young R, Wu VCH. Lowbush wild blueberries have the potential to modify gut microbiota and xenobiotic metabolism in the rat colon. PLoS One 2013; 8:e67497. [PMID: 23840722 PMCID: PMC3696070 DOI: 10.1371/journal.pone.0067497] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 05/19/2013] [Indexed: 12/12/2022] Open
Abstract
The gastrointestinal tract is populated by an array of microbial species that play an important role in metabolic and immune functions. The composition of microorganisms is influenced by the components of the host's diet and can impact health. In the present study, dietary enrichment of lowbush wild blueberries (LWB) was examined to determine their effect on colon microbial composition and their potential in promoting gut health. The microbial composition and functional potential of the colon microbiota from Sprague Dawley rats fed control diets (AIN93) and LWB-enriched diets (AIN93+8% LWB powder substituting for dextrose) for 6 weeks were assessed using Illumina shotgun sequencing and bioinformatics tools. Our analysis revealed an alteration in the relative abundance of 3 phyla and 22 genera as representing approximately 14 and 8% of all phyla and genera identified, respectively. The LWB-enriched diet resulted in a significant reduction in the relative abundance of the genera Lactobacillus and Enterococcus. In addition, hierarchal analysis revealed a significant increase in the relative abundance of the phylum Actinobacteria, the order Actinomycetales, and several novel genera under the family Bifidobacteriaceae and Coriobacteriaceae, in the LWB group. Functional annotation of the shotgun sequences suggested that approximately 9% of the 4709 Kyoto Encyclopaedia of Gene and Genome (KEGG) hits identified were impacted by the LWB-diet. Open Reading Frames (ORFs) assigned to KEGG category xenobiotics biodegradation and metabolism were significantly greater in the LWB-enriched diet compared to the control and included the pathway for benzoate degradation [PATH:ko00362] and glycosaminoglycan degradation [PATH:ko00531]. Moreover, the number of ORFs assigned to the bacterial invasion of epithelial cells [PATH:ko05100] pathway was approximately 8 fold lower in the LWB group compared to controls. This study demonstrated that LWBs have the potential to promote gut health and can aid in the development of optimal diets.
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Affiliation(s)
- Alison Lacombe
- Department of Food Science and Human Nutrition, The University of Maine, Orono, Maine, United States of America
| | - Robert W. Li
- United States Department of Agriculture ARS, BARC, Bovine Functional Genomics Laboratory, Beltsville, Maryland, United States of America
| | - Dorothy Klimis-Zacas
- Department of Food Science and Human Nutrition, The University of Maine, Orono, Maine, United States of America
| | - Aleksandra S. Kristo
- Department of Food Science and Human Nutrition, The University of Maine, Orono, Maine, United States of America
| | - Shravani Tadepalli
- Department of Food Science and Human Nutrition, The University of Maine, Orono, Maine, United States of America
| | - Emily Krauss
- Department of Food Science and Human Nutrition, The University of Maine, Orono, Maine, United States of America
| | - Ryan Young
- Department of Molecular and Biomedical Sciences, The University of Maine, Orono, Maine, United States of America
| | - Vivian C. H. Wu
- Department of Food Science and Human Nutrition, The University of Maine, Orono, Maine, United States of America
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Belova SE, Fedotova AV, Dedysh SN. Prokaryotic ultramicroforms in a Sphagnum peat bog of upper Volga catchment. Microbiology (Reading) 2012. [DOI: 10.1134/s0026261712050050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Duda VI, Suzina NE, Polivtseva VN, Boronin AM. Ultramicrobacteria: Formation of the concept and contribution of ultramicrobacteria to biology. Microbiology (Reading) 2012. [DOI: 10.1134/s0026261712040054] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Abstract
Stenotrophomonas maltophilia is an emerging multidrug-resistant global opportunistic pathogen. The increasing incidence of nosocomial and community-acquired S. maltophilia infections is of particular concern for immunocompromised individuals, as this bacterial pathogen is associated with a significant fatality/case ratio. S. maltophilia is an environmental bacterium found in aqueous habitats, including plant rhizospheres, animals, foods, and water sources. Infections of S. maltophilia can occur in a range of organs and tissues; the organism is commonly found in respiratory tract infections. This review summarizes the current literature and presents S. maltophilia as an organism with various molecular mechanisms used for colonization and infection. S. maltophilia can be recovered from polymicrobial infections, most notably from the respiratory tract of cystic fibrosis patients, as a cocolonizer with Pseudomonas aeruginosa. Recent evidence of cell-cell communication between these pathogens has implications for the development of novel pharmacological therapies. Animal models of S. maltophilia infection have provided useful information about the type of host immune response induced by this opportunistic pathogen. Current and emerging treatments for patients infected with S. maltophilia are discussed.
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Affiliation(s)
- Joanna S Brooke
- Department of Biological Sciences, DePaul University, Chicago, Illinois, USA.
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Thomas V, McDonnell G, Denyer SP, Maillard JY. Free-living amoebae and their intracellular pathogenic microorganisms: risks for water quality. FEMS Microbiol Rev 2010; 34:231-59. [DOI: 10.1111/j.1574-6976.2009.00190.x] [Citation(s) in RCA: 208] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Park SK, Hu JY. Assessment of the extent of bacterial growth in reverse osmosis system for improving drinking water quality. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2010; 45:968-977. [PMID: 20512722 DOI: 10.1080/10934521003772386] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
This study was carried out to assess reverse osmosis (RO) treatment efficacy of drinking water in terms of biological stability in the distribution system. Two flat-sheet RO membranes were used in this study. Experiments were designed to investigate the growth of biofilm and bulk phase bacteria for the RO-treated water flowing through a model distribution system under controlled conditions without disinfectants. RO membranes improved the water quality of drinking water in terms of inorganic, organic and bacterial contents. Organic matter including the fraction available for microbes was efficiently removed by the RO membranes tested. More than 99% of bacterial cells in the tap water was retained by the RO membranes, leaving <50 cells/mL in the permeate water. In spite of the low nutrient contents and few cells in the RO permeates, monitoring of the model distribution systems receiving the RO permeates showed that remarkable biofilm accumulation and bulk cell growth occurred in the RO permeate water. In quasi-steady state, the total cell numbers in the biofilm and bulk water were of order 10(3) cells/cm(2) and 10(3) cells/mL, respectively, which were about 2 orders of magnitude lower than those grown in the tap water produced from conventional water treatment. The culturable heterotrophic bacteria constituted a significant part of the total cells (20.7-32.1% in biofilms and 21.3-46.3% in bulk waters). Biofilm maximum density and production rate were of the order 10(4) cells/cm(2) and 10(2) cells/cm(2)/day, respectively. The specific cell growth rate of bacteria in the biofilms was found to be much lower than those in the bulk waters (0.04-0.05 day(-1) versus 0.28-0.36 day(-1)). The overall specific cell growth rate which indicates the growth potential in the whole system was calculated as 0.07-0.08 day(-1), representing a doubling time of 9.1-10.1 days. These observations can be indicative of possibilities for bacterial growth in the RO permeate water with easily assimilable organic carbon concentrations below values proposed for biostability. RO permeate water does not appear to be biologically stable water. Therefore, efforts to minimize bacterial growth in the RO permeate water and in the distribution system must consider post-disinfection.
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Affiliation(s)
- Se-keun Park
- Division of Environmental Science and Engineering, National University of Singapore, Singapore.
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