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Ekwanzala MD, Abia ALK, Ubomba-Jaswa E, Keshri J, Momba NBM. Genetic relatedness of faecal coliforms and enterococci bacteria isolated from water and sediments of the Apies River, Gauteng, South Africa. AMB Express 2017; 7:20. [PMID: 28063147 PMCID: PMC5218955 DOI: 10.1186/s13568-016-0319-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 12/26/2016] [Indexed: 11/15/2022] Open
Abstract
To date, the microbiological quality of river sediments and its impact on water resources are not included in the water quality monitoring assessment. Therefore, the aim of this study was to establish genetic relatedness between faecal coliforms and enterococci isolated from the river water and riverbed sediments of Apies River to better understand the genetic similarity of microorganisms between the sediment and water phases. Indicator bacteria were subjected to a molecular study, which consisted of PCR amplification and sequence analysis of the 16S rRNA and 23S rRNA gene using specific primers for faecal coliforms and enterococci, respectively. Results revealed that the Apies River had high faecal pollution levels with enterococci showing low to moderate correlation coefficient (r2 values ranged from 0.2605 to 0.7499) compared to the faecal coliforms which showed zero to low correlation (r2 values ranged from 0.0027 to 0.1407) indicating that enterococci may be better indicator than faecal coliforms for detecting faecal contamination in riverbed sediments. The phylogenetic tree of faecal coliforms revealed a 98% homology among their nucleotide sequences confirming the close genetic relatedness between river water and riverbed sediment isolates. The phylogenetic tree of the enterococci showed that Enterococcus faecalis and Enterococcus faecium are the predominant species found in both river water and riverbed sediments with bootstrap values of ≥99%. A high degree of genetic relatedness between sediment and water isolates indicated a possible common ancestry and transmission pathway. We recommend the microbial monitoring of riverbed sediments as it harbours more diverse microbial community and once resuspended may cause health and environmental problems.
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Lau P, Cordey S, Brito F, Tirefort D, Petty TJ, Turin L, Guichebaron A, Docquier M, Zdobnov EM, Waldvogel-Abramowski S, Lecompte T, Kaiser L, Preynat-Seauve O. Metagenomics analysis of red blood cell and fresh-frozen plasma units. Transfusion 2017; 57:1787-1800. [PMID: 28497550 DOI: 10.1111/trf.14148] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 01/19/2017] [Accepted: 02/19/2017] [Indexed: 12/14/2022]
Abstract
BACKGROUND Although the risk of transmitting infectious agents by blood transfusion is dramatically reduced after donor selection, leukoreduction, and laboratory testing, some could still be present in donor's blood. A description of metagenomes in blood products eligible for transfusion represents relevant information to evaluate the risk of pathogen transmission by transfusion. STUDY DESIGN AND METHODS Detection of viruses, bacteria, and fungi genomes was made by high-throughput sequencing (HTS) of 600 manufactured blood products eligible for transfusion: 300 red blood cell (RBC) and 300 fresh-frozen plasma (FFP) units. RESULTS Anelloviruses and human pegivirus, frequent in the blood of healthy individuals, were found. Human papillomavirus type 27 and Merkel cell polyomavirus, present on the skin, were also detected. Unexpectedly, astrovirus MLB2 was identified and characterized in a FFP unit. The presence of astrovirus MLB2 was confirmed in donor's blood and corresponded to an asymptomatic acute viremia. Sequences of bacteria and fungi were also detected; they are likely the result of environmental contamination. CONCLUSION This study demonstrates that HTS is a promising tool for detecting common and less frequent infectious pathogens in blood products.
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Affiliation(s)
- Pierre Lau
- Department of Medical Specialties, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva, Geneva.,Department of Human Protein Sciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Samuel Cordey
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva, Geneva
| | - Francisco Brito
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Diderik Tirefort
- Department of Medical Specialties, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva, Geneva
| | - Thomas J Petty
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Lara Turin
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva, Geneva
| | - Arthur Guichebaron
- Department of Medical Specialties, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva, Geneva.,Department of Human Protein Sciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Mylène Docquier
- iGE3 Genomics Platform, University of Geneva, Geneva, Switzerland
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Sophie Waldvogel-Abramowski
- Department of Medical Specialties, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva, Geneva
| | - Thomas Lecompte
- Department of Medical Specialties, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva, Geneva
| | - Laurent Kaiser
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva, Geneva
| | - Olivier Preynat-Seauve
- Department of Medical Specialties, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva, Geneva.,Department of Human Protein Sciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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Propionibacterium acnes: Disease-Causing Agent or Common Contaminant? Detection in Diverse Patient Samples by Next-Generation Sequencing. J Clin Microbiol 2016; 54:980-7. [PMID: 26818667 PMCID: PMC4809928 DOI: 10.1128/jcm.02723-15] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 01/16/2016] [Indexed: 01/01/2023] Open
Abstract
Propionibacterium acnes is the most abundant bacterium on human skin, particularly in sebaceous areas. P. acnes is suggested to be an opportunistic pathogen involved in the development of diverse medical conditions but is also a proven contaminant of human clinical samples and surgical wounds. Its significance as a pathogen is consequently a matter of debate. In the present study, we investigated the presence of P. acnes DNA in 250 next-generation sequencing data sets generated from 180 samples of 20 different sample types, mostly of cancerous origin. The samples were subjected to either microbial enrichment, involving nuclease treatment to reduce the amount of host nucleic acids, or shotgun sequencing. We detected high proportions of P. acnes DNA in enriched samples, particularly skin tissue-derived and other tissue samples, with the levels being higher in enriched samples than in shotgun-sequenced samples. P. acnes reads were detected in most samples analyzed, though the proportions in most shotgun-sequenced samples were low. Our results show that P. acnes can be detected in practically all sample types when molecular methods, such as next-generation sequencing, are employed. The possibility of contamination from the patient or other sources, including laboratory reagents or environment, should therefore always be considered carefully when P. acnes is detected in clinical samples. We advocate that detection of P. acnes always be accompanied by experiments validating the association between this bacterium and any clinical condition.
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Dekio I, Culak R, Misra R, Gaulton T, Fang M, Sakamoto M, Ohkuma M, Oshima K, Hattori M, Klenk HP, Rajendram D, Gharbia SE, Shah HN. Dissecting the taxonomic heterogeneity within Propionibacterium acnes: proposal for Propionibacterium acnes subsp. acnes subsp. nov. and Propionibacterium acnes subsp. elongatum subsp. nov. Int J Syst Evol Microbiol 2015; 65:4776-4787. [PMID: 26432704 DOI: 10.1099/ijsem.0.000648] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Propionibacterium acnes subsp. acnes subsp. nov. and Propionibacterium acnes subsp. elongatum subsp. nov. are described. These emanate from the three known phylotypes of P. acnes, designated types I, II and III. Electron microscopy confirmed the filamentous cell shape of type III, showing a striking difference from types I/II, which were short rods. Biochemical tests indicated that, in types I/II, either the pyruvate, l-pyrrolidonyl arylamidase or d-ribose 2 test was positive, whereas all of these were negative among type III strains. Matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) spectra, which profile mainly their ribosomal proteins, were different between these two groups. Surface-enhanced laser-desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) spectra of all phylotypes revealed a specific protein biomarker that was overexpressed in type III strains compared with types I/II only when grown aerobically. Reference strains had high whole-genome similarity between types I (>91 %) and II (>75 %), but a considerably lower level of 72 % similarity with type III. recA and gyrB sequence dendrograms confirmed the distant relatedness of type III, indicating the presence of two distinct centres of variation within the species P. acnes. On the other hand, cellular fatty acid profiles and 16S rRNA gene sequence relatedness (>99.3 %) circumscribed the species. Thus, we propose two subspecies, Propionibacterium acnes subsp. acnes subsp. nov. for types I/II and Propionibacterium acnes subsp. elongatum subsp. nov. for type III. The type strain of Propionibacterium acnes subsp. acnes is NCTC 737T ( = ATCC 6919T = JCM 6425T = DSM 1897T = CCUG 1794T), while the type strain of Propionibacterium acnes subsp. elongatum is K124T ( = NCTC 13655T = JCM 18919T).
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Affiliation(s)
- Itaru Dekio
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Japan.,Proteomics Research Unit, Culture Collections, Public Health England, Colindale, London, UK.,Department of Dermatology, Medical Centre East, Tokyo Women's Medical University, Tokyo, Japan
| | - Renata Culak
- Proteomics Research Unit, Culture Collections, Public Health England, Colindale, London, UK
| | - Raju Misra
- Genomic Research Unit, Public Health England, Colindale, London, UK
| | - Tom Gaulton
- Proteomics Research Unit, Culture Collections, Public Health England, Colindale, London, UK
| | - Min Fang
- Proteomics Research Unit, Culture Collections, Public Health England, Colindale, London, UK
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Japan
| | - Kenshiro Oshima
- Hattori Lab, The University of Tokyo Kashiwa Campus, Kashiwa, Japan
| | - Masahira Hattori
- Hattori Lab, The University of Tokyo Kashiwa Campus, Kashiwa, Japan
| | - Hans-Peter Klenk
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | | | - Saheer E Gharbia
- Genomic Research Unit, Public Health England, Colindale, London, UK
| | - Haroun N Shah
- Proteomics Research Unit, Culture Collections, Public Health England, Colindale, London, UK
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