1
|
Lin JN, Lai CH, Lin SY, Lee CC, Lee NY, Liu PY, Yang CH, Huang YH. Effect of Intragenomic Sequence Heterogeneity among Multiple 16S rRNA Genes on Species Identification of Elizabethkingia. Microbiol Spectr 2022; 10:e0133822. [PMID: 36036645 PMCID: PMC9604143 DOI: 10.1128/spectrum.01338-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/15/2022] [Indexed: 12/30/2022] Open
Abstract
Accurate identification of Elizabethkingia species mostly requires the use of molecular techniques, and 16S rRNA gene sequencing is generally considered the method of choice. In this study, we evaluated the effect of intraspecific diversity among the multiple copies of the 16S rRNA gene on the accuracy of species identification in the genus Elizabethkingia. Sequences of 16S rRNA genes obtained from the 32 complete whole-genome sequences of Elizabethkingia deposited in GenBank and from 218 clinical isolates collected from 5 hospitals in Taiwan were analyzed. Four or five copies of 16S rRNA were identified in the Elizabethkingia species with complete genome sequences. The dissimilarity among the copies of the16S rRNA gene was <1% in all Elizabethkingia strains. E. meningoseptica demonstrated a significantly higher rate of nucleotide variations in the 16S rRNA than did E. anophelis (P = 0.011). Nucleotide alterations occurred more frequently in regions V2 and V6 than in other hypervariable regions (P < 0.001). E. meningoseptica, E. anophelis, and E. argenteiflava strains were clustered distinctly in the phylogenetic tree inferred from 16S rRNA genes, and the intragenomic variation of gene sequences had no profound effect on the classification of taxa. However, E. miricola, E. bruuniana, E. ursingii, and E. occulta were grouped closely in the phylogenetic analysis, and the variation among the multiple copies of the 16S rRNA in one E. ursingii strain affected species classification. Other marker genes may be required to supplement the species classification of closely related taxa in the genus Elizabethkingia. IMPORTANCE Incorrect identification of bacterial species would influence the epidemiology and clinical analysis of patients infected with Elizabethkingia. The results of the present study suggest that 16S rRNA gene sequencing should not be considered the gold standard for the accurate identification of Elizabethkingia species.
Collapse
Affiliation(s)
- Jiun-Nong Lin
- College of Medical Science and Technology, I-Shou University, Kaohsiung, Taiwan
- Department of Critical Care Medicine, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
- Division of Infectious Diseases, Department of Internal Medicine, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung, Taiwan
| | - Chung-Hsu Lai
- Division of Infectious Diseases, Department of Internal Medicine, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung, Taiwan
| | - Shang-Yi Lin
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ching-Chi Lee
- Clinical Medicine Research Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Nan-Yao Lee
- Division of Infectious Diseases, Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
- School of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Po-Yu Liu
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chih-Hui Yang
- Department of Biological Science and Technology, Meiho University, Pingtung, Taiwan
| | - Yi-Han Huang
- College of Medical Science and Technology, I-Shou University, Kaohsiung, Taiwan
| |
Collapse
|
2
|
Watts GS, Youens-Clark K, Slepian MJ, Wolk DM, Oshiro MM, Metzger GS, Dhingra D, Cranmer LD, Hurwitz BL. 16S rRNA gene sequencing on a benchtop sequencer: accuracy for identification of clinically important bacteria. J Appl Microbiol 2017; 123:1584-1596. [PMID: 28940494 PMCID: PMC5765505 DOI: 10.1111/jam.13590] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 06/02/2017] [Accepted: 08/18/2017] [Indexed: 12/20/2022]
Abstract
AIMS Test the choice of 16S rRNA gene amplicon and data analysis method on the accuracy of identification of clinically important bacteria utilizing a benchtop sequencer. METHODS AND RESULTS Nine 16S rRNA amplicons were tested on an Ion Torrent PGM to identify 41 strains of clinical importance. The V1-V2 region identified 40 of 41 isolates to the species level. Three data analysis methods were tested, finding that the Ribosomal Database Project's SequenceMatch outperformed BLAST and the Ion Reporter Metagenomics analysis pipeline. Lastly, 16S rRNA gene sequencing mixtures of four species through a six log range of dilution showed species were identifiable even when present as 0·1% of the mixture. CONCLUSIONS Sequencing the V1-V2 16S rRNA gene region, made possible by the increased read length Ion Torrent PGM sequencer's 400 base pair chemistry, may be a better choice over other commonly used regions for identifying clinically important bacteria. In addition, the SequenceMatch algorithm, freely available from the Ribosomal Database Project, is a good choice for matching filtered reads to organisms. Lastly, 16S rRNA gene sequencing's sensitivity to the presence of a bacterial species at 0·1% of a mixture suggests it has sufficient sensitivity for samples in which important bacteria may be rare. SIGNIFICANCE AND IMPACT OF THE STUDY We have validated 16S rRNA gene sequencing on a benchtop sequencer including simple mixtures of organisms; however, our results highlight deficits for clinical application in place of current identification methods.
Collapse
Affiliation(s)
- G S Watts
- The University of Arizona Cancer Center, University of Arizona, Tucson, AZ, USA.,Department of Pharmacology, University of Arizona, Tucson, AZ, USA
| | - K Youens-Clark
- Department of Agricultural and Biosystems Engineering, University of Arizona, Tucson, AZ, USA
| | - M J Slepian
- Department of Medicine, University of Arizona, Tucson, AZ, USA.,Department of Biomedical Engineering, University of Arizona, Tucson, AZ, USA.,Arizona Center for Accelerated Biomedical Innovation, University of Arizona, Tucson, AZ, USA
| | - D M Wolk
- Pharmaceutical Sciences, Geisinger Health System, Danville, PA, USA.,Center for Infectious Disease Diagnostics and Research, Wilkes University, Geisinger Health System, Danville, PA, USA
| | - M M Oshiro
- The University of Arizona Cancer Center, University of Arizona, Tucson, AZ, USA
| | - G S Metzger
- The University of Arizona Cancer Center, University of Arizona, Tucson, AZ, USA
| | - D Dhingra
- Life Technologies, Thermo Fisher Scientific, Carlsbad, CA, USA
| | - L D Cranmer
- School of Medicine, Seattle, WA, USA.,University of Washington, Fred Hutchinson Cancer Research Center and Seattle Cancer Care Alliance, Seattle, WA, USA
| | - B L Hurwitz
- Department of Agricultural and Biosystems Engineering, University of Arizona, Tucson, AZ, USA
| |
Collapse
|
3
|
Dupont C, Aujoulat F, Chiron R, Condom P, Jumas-Bilak E, Marchandin H. Highly Diversified Pandoraea pulmonicola Population during Chronic Colonization in Cystic Fibrosis. Front Microbiol 2017; 8:1892. [PMID: 29056926 PMCID: PMC5635052 DOI: 10.3389/fmicb.2017.01892] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 09/15/2017] [Indexed: 01/03/2023] Open
Abstract
Several environmental bacteria are considered as opportunistic pathogens in cystic fibrosis (CF) and are able to persistently colonize the CF respiratory tract (CFRT). Beside Pseudomonas aeruginosa and Burkholderia cepacia complex, Pandoraea spp. are defined as pathogenic. During chronic colonization, adaptive evolution and diversified population have been demonstrated, notably for P. aeruginosa. However, the persistence of Pandoraea in the CFRT remains largely unexplored. We studied genomic and phenotypic traits of Pandoraea pulmonicola isolates successively recovered from the airways of a single CF patient and relate the results to qualitative and quantitative evolution of other cultivable pathogens and to patient clinical status. A total of 31 isolates recovered from 18 sputum samples over a 7-year period in a single CF patient were studied. Genome dynamics was assessed by pulsed-field gel electrophoresis, ERIC-PCR fingerprinting and 16S rRNA gene PCR-temporal temperature gel electrophoresis. Phenotypic features included antimicrobial susceptibility, motility, biofilm production, and virulence in Caenorhabditis elegans model. Variability was observed for all the characteristics studied leading to highly diversified patterns (24 patterns) for the 31 clonally related isolates. Some of these modifications, mainly genomic events were concomitantly observed with CFRT microbiota composition shifts and with severe exacerbations. The diversity of P. pulmonicola population studied, observed for isolates recovered from successive samples but also within a sample suggested that existence of a diversified population may represent a patho-adaptive strategy for host persistence in the heterogeneous and fluctuating CFRT environment.
Collapse
Affiliation(s)
- Chloé Dupont
- Equipe Pathogènes Hydriques, Santé, Environnements, UMR 5569 Hydrosciences Montpellier, U.F.R des Sciences Pharmaceutiques et Biologiques and Université Montpellier, Montpellier, France
| | - Fabien Aujoulat
- Equipe Pathogènes Hydriques, Santé, Environnements, UMR 5569 Hydrosciences Montpellier, U.F.R des Sciences Pharmaceutiques et Biologiques and Université Montpellier, Montpellier, France
| | - Raphaël Chiron
- Centre de Ressources et de Compétences pour la Mucoviscidose, Hôpital Arnaud de Villeneuve, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Pauline Condom
- Equipe Pathogènes Hydriques, Santé, Environnements, UMR 5569 Hydrosciences Montpellier, U.F.R des Sciences Pharmaceutiques et Biologiques and Université Montpellier, Montpellier, France
| | - Estelle Jumas-Bilak
- Equipe Pathogènes Hydriques, Santé, Environnements, UMR 5569 Hydrosciences Montpellier, U.F.R des Sciences Pharmaceutiques et Biologiques and Université Montpellier, Montpellier, France.,Laboratoire d'Hygiène Hospitalière, Hôpital Saint-Eloi, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Hélène Marchandin
- Equipe Pathogènes Hydriques, Santé, Environnements, UMR 5569 Hydrosciences Montpellier, U.F.R des Sciences Pharmaceutiques et Biologiques and Université Montpellier, Montpellier, France.,Service de Microbiologie, Hôpital Carémeau, Centre Hospitalier Universitaire de Nîmes, Nîmes, France.,Laboratoire de Bactériologie, Hôpital Arnaud de Villeneuve, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| |
Collapse
|
4
|
Wijers CD, Chmiel JF, Gaston BM. Bacterial infections in patients with primary ciliary dyskinesia: Comparison with cystic fibrosis. Chron Respir Dis 2017; 14:392-406. [PMID: 29081265 PMCID: PMC5729729 DOI: 10.1177/1479972317694621] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Primary ciliary dyskinesia (PCD) is an autosomal recessive disorder associated with severely impaired mucociliary clearance caused by defects in ciliary structure and function. Although recurrent bacterial infection of the respiratory tract is one of the major clinical features of this disease, PCD airway microbiology is understudied. Despite the differences in pathophysiology, assumptions about respiratory tract infections in patients with PCD are often extrapolated from cystic fibrosis (CF) airway microbiology. This review aims to summarize the current understanding of bacterial infections in patients with PCD, including infections with Pseudomonas aeruginosa, Staphylococcus aureus, and Moraxella catarrhalis, as it relates to bacterial infections in patients with CF. Further, we will discuss current and potential future treatment strategies aimed at improving the care of patients with PCD suffering from recurring bacterial infections.
Collapse
Affiliation(s)
- Christiaan Dm Wijers
- 1 Department of Pediatrics, Rainbow Babies and Children's Hospital, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - James F Chmiel
- 1 Department of Pediatrics, Rainbow Babies and Children's Hospital, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Benjamin M Gaston
- 1 Department of Pediatrics, Rainbow Babies and Children's Hospital, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| |
Collapse
|
5
|
Dupont C, Michon AL, Jumas-Bilak E, Nørskov-Lauritsen N, Chiron R, Marchandin H. Intrapatient diversity of Achromobacter spp. involved in chronic colonization of Cystic Fibrosis airways. INFECTION GENETICS AND EVOLUTION 2015; 32:214-23. [PMID: 25791931 DOI: 10.1016/j.meegid.2015.03.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 02/27/2015] [Accepted: 03/09/2015] [Indexed: 11/28/2022]
Abstract
Achromobacter spp. are increasingly identified in Cystic Fibrosis (CF) patients and their ability to persistently colonize the CF respiratory tract (CFRT) suggests that Achromobacter species possess adaptive characteristics. We studied genome dynamics in 118 isolates recovered from 13 patients with Achromobacter chronic colonization (5-26 isolates per patient recovered over 13-61 months). Isolates were identified to species level by nrdA gene sequencing, subjected to Pulsed-Field Gel Electrophoresis (PFGE) and multiplex rep-PCR (MR-PCR), and rrs intragenomic diversity was studied by PCR-Temporal Temperature Gel Electrophoresis (TTGE). Intrapatient diversity was assessed: (i) from dynamics of XbaI and/or SpeI-based pulsotypes, (ii) from comparison of MR-PCR profiles, and (iii) by longitudinal analysis of rrs intragenomic diversity. Patients were chronically colonized by Achromobacter xylosoxidans (n=10), Achromobacter dolens (n=1) or Achromobacter insuavis (n=2). All strains displayed genomic diversification over time but A. insuavis showed higher pulsotype diversity compared to other species. Intragenomic rrs heterogeneity was found in strains from 6 of 13 patients and may be persistently observed. Achromobacter genome evolution observed during chronic colonization of the CFRT warrants further investigation of the adaptation features of the different species, as well as of the selective forces driving this adaptation in the CFRT.
Collapse
Affiliation(s)
- Chloé Dupont
- Université Montpellier 1, UMR5119 ECOSYM, Equipe Pathogènes et Environnements, U.F.R des Sciences Pharmaceutiques et Biologiques, 15 avenue Charles Flahault, 34093 Montpellier Cedex 5, France
| | - Anne-Laure Michon
- Université Montpellier 1, UMR5119 ECOSYM, Equipe Pathogènes et Environnements, U.F.R des Sciences Pharmaceutiques et Biologiques, 15 avenue Charles Flahault, 34093 Montpellier Cedex 5, France; Centre Hospitalier Régional Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France
| | - Estelle Jumas-Bilak
- Université Montpellier 1, UMR5119 ECOSYM, Equipe Pathogènes et Environnements, U.F.R des Sciences Pharmaceutiques et Biologiques, 15 avenue Charles Flahault, 34093 Montpellier Cedex 5, France; Centre Hospitalier Régional Universitaire de Montpellier, Hôpital Saint-Eloi, Laboratoire d'Hygiène hospitalière, 80 avenue Augustin Fliche, 34295 Montpellier Cedex 5, France
| | - Niels Nørskov-Lauritsen
- Department of Clinical Microbiology, Aarhus University Hospital, Skejby, 8200 Aarhus, Denmark
| | - Raphaël Chiron
- Centre Hospitalier Régional Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Centre de Ressources et de Compétences de la Mucoviscidose, 371 avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France
| | - Hélène Marchandin
- Université Montpellier 1, UMR5119 ECOSYM, Equipe Pathogènes et Environnements, U.F.R des Sciences Pharmaceutiques et Biologiques, 15 avenue Charles Flahault, 34093 Montpellier Cedex 5, France; Centre Hospitalier Régional Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France.
| |
Collapse
|