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Albuja-Quintana M, Armijos CE, Montero-Oleas A, Torres MDL. Development of novel species-specific and genus-specific primers for the detection of Babaco Mosaic Virus (BabMV). Lett Appl Microbiol 2024; 77:ovae070. [PMID: 39020264 DOI: 10.1093/lambio/ovae070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 06/21/2024] [Accepted: 07/16/2024] [Indexed: 07/19/2024]
Abstract
Babaco is a hybrid cultivar native to the Andean region of Ecuador and Colombia, commercially attractive for its fruit. Babaco production in Ecuador faces losses from plant pathogens like babaco mosaic virus (BabMV), an RNA virus that causes chlorosis, leaf mottling, and deformation. Phylogenetic studies link BabMV to papaya mosaic virus (PapMV), alternanthera mosaic virus, and senna mosaic virus. To address this threat, we developed novel species-specific primers to detect BabMV targeting a 165 bp region of the coat protein (CP). Genus-specific primers were designed to validate the species-specific primers and attest their ability to discriminate between BabMV and its closest relatives. These primers targeted a 175 bp fragment of the CP region. The most effective sets of primers were chosen for reverse transcription polymerase chain reaction (RT-PCR) and SYBR® Green-based quantitative reverse transcription polymerase chain reaction (RT-qPCR) in symptomatic and asymptomatic babaco plants. Among 28 plants tested, 25 were positive and 3 were negative for BabMV using species-specific and genus-specific primers in RT-PCR and RT-qPCR, while the PapMV positive control was detected with the genus-specific primers and was negative for the species-specific primers. These primers represent a valuable molecular tool for detecting BabMV, potentially enhancing crop management.
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Affiliation(s)
- Martina Albuja-Quintana
- Colegio de Ciencias Biológicas y Ambientales, Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito (USFQ), Campus Cumbayá, Quito 170901, Ecuador
| | - Carolina E Armijos
- Colegio de Ciencias Biológicas y Ambientales, Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito (USFQ), Campus Cumbayá, Quito 170901, Ecuador
| | - Andrea Montero-Oleas
- Colegio de Ciencias Biológicas y Ambientales, Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito (USFQ), Campus Cumbayá, Quito 170901, Ecuador
| | - Maria de Lourdes Torres
- Colegio de Ciencias Biológicas y Ambientales, Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito (USFQ), Campus Cumbayá, Quito 170901, Ecuador
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Rathnayake RAC, Zhao Z, McLaughlin N, Li W, Yan Y, Chen LL, Xie Q, Wu CD, Mathew MT, Wang RR. Machine learning enabled multiplex detection of periodontal pathogens by surface-enhanced Raman spectroscopy. Int J Biol Macromol 2024; 257:128773. [PMID: 38096932 PMCID: PMC11282452 DOI: 10.1016/j.ijbiomac.2023.128773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/02/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023]
Abstract
Periodontitis is a chronic inflammation of the periodontium caused by a persistent bacterial infection, resulting in destruction of the supporting structures of teeth. Analysis of microbial composition in saliva can inform periodontal status. Actinobacillus actinomycetemcomitans (Aa), Porphyromonas gingivalis (Pg), and Streptococcus mutans (Sm) are among reported periodontal pathogens, and were used as model systems in this study. Our atomic force microscopic (AFM) study revealed that these pathogens are biological nanorods with dimensions of 0.6-1.1 μm in length and 500-700 nm in width. Current bacterial detection methods often involve complex preparation steps and require labeled reporting motifs. Employing surface-enhanced Raman spectroscopy (SERS), we revealed cell-type specific Raman signatures of these pathogens for label-free detection. It overcame the complexity associated with spectral overlaps among different bacterial species, relying on high signal-to-noise ratio (SNR) spectra carefully collected from pure species samples. To enable simple, rapid, and multiplexed detection, we harnessed advanced machine learning techniques to establish predictive models based on a large set of raw spectra of each bacterial species and their mixtures. Using these models, given a raw spectrum collected from a bacterial suspension, simultaneous identification of all three species in the test sample was achieved at 95.6 % accuracy. This sensing modality can be applied to multiplex detection of a broader range and a larger set of periodontal pathogens, paving the way for hassle-free detection of oral bacteria in saliva with little to no sample preparation.
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Affiliation(s)
- Rathnayake A C Rathnayake
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL 60616, United States of America
| | - Zhenghao Zhao
- Department of Computer Science, Illinois Institute of Technology, Chicago, IL 60616, United States of America
| | - Nathan McLaughlin
- Department of Surgery, University of Illinois Chicago, Chicago, IL 60612, United States of America
| | - Wei Li
- Department of Pediatric Dentistry, University of Illinois Chicago, Chicago, IL 60612, United States of America
| | - Yan Yan
- Department of Computer Science, Illinois Institute of Technology, Chicago, IL 60616, United States of America.
| | - Liaohai L Chen
- Department of Surgery, University of Illinois Chicago, Chicago, IL 60612, United States of America
| | - Qian Xie
- Department of Endodontics, University of Illinois Chicago, Chicago, IL, United States of America
| | - Christine D Wu
- Department of Pediatric Dentistry, University of Illinois Chicago, Chicago, IL 60612, United States of America
| | - Mathew T Mathew
- Department of Restorative Dentistry, University of Illinois Chicago, Chicago, IL 60612, United States of America; Department of Biomedical Sciences, University of Illinois Rockford, Rockford, IL 61107, United States of America
| | - Rong R Wang
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL 60616, United States of America.
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Vakili B, Shoaei P, Shahzamani K, Siadat SD, Shojaei H, Esfandiari Z, Nasri E, Shabani S, Zamani Moghadam A, Ataei B. Gut-Lung Microbiota Characterization in Patients with Non-Small Cell Lung Carcinoma and COVID-19 Coinfection. ARCHIVES OF IRANIAN MEDICINE 2024; 27:62-71. [PMID: 38619029 PMCID: PMC11017262 DOI: 10.34172/aim.2024.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 12/30/2023] [Indexed: 04/16/2024]
Abstract
BACKGROUND Non-small cell lung cancer (NSCLC) patients with COVID-19 have an excessive chance of morbidity and mortality. The fecal-nasopharyngeal microbiota compositions of NSCLC patients were assessed in this study. METHODS In total, 234 samples were collected from 17 NSCLC patients infected with COVID-19, 20 NSCLC patients without confirmed COVID-19, 40 non NSCLC patients with COVID-19, and 40 healthy individuals. RESULTS In lung microbiota, the abundance of Streptococcus spp. in NSCLC patients with confirmed COVID-19 was significantly higher than the two control groups. Pseudomonas aeruginosa and Staphylococcus aureus were listed as the most frequent pulmonary bacterial groups that colonized COVID-19 patients. In fecal specimens, the numbers of Bacteroidetes, Firmicutes, and Actinobacteria phyla were significantly higher amongst NSCLC patients with COVID-19. NSCLC patients infected with COVID-19 showed lower levels of Lactobacillus spp., Akkermansia muciniphila, and Bifidobacterium spp. The counts of Streptococcus spp., in NSCLC patients with COVID-19 were significantly higher than those of healthy individuals (8.49±0.70 log CFU/g wet feces vs 8.49±0.70 log CFU/g wet feces). Prevotella spp. were enriched in the gut and respiratory tracts of COVID-19 patient groups. The unbiased analysis showed an increment in Enterococcus spp., Streptococcus spp., and Prevotella spp. CONCLUSION Eventually, it was found that compared to control groups, COVID-19 patients with NSCLC showed diminished gut bacteria diversity and increase in Lactobacillus spp., A. muciniphila, and Bifidobacterium spp. The overgrowth of Enterococcus spp., Streptococcus spp., and Prevotella spp. could be potential predictive biomarkers in the gut-lung axis of NSCLC patients with COVID-19.
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Affiliation(s)
- Bahareh Vakili
- Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Parisa Shoaei
- Nosocomial Infection Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Kiana Shahzamani
- Hepatitis Research Center, School of Medicine, Lorestan University of Medical Sciences, Khoramabad, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Hasan Shojaei
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Zahra Esfandiari
- Department of Food Science and Technology, Nutrition and Food Security Research Center, School of Nutrition and Food Science, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Elahe Nasri
- Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Shiva Shabani
- Department of Infectious Diseases, School of Medicine, Arak University of Medical Sciences, Arak, Iran
| | - Ali Zamani Moghadam
- Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Behrooz Ataei
- Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
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Gieroń M, Żarnowiec P, Zegadło K, Gmiter D, Czerwonka G, Kaca W, Kręcisz B. Loop-Mediated Isothermal Amplification of DNA (LAMP) as an Alternative Method for Determining Bacteria in Wound Infections. Int J Mol Sci 2023; 25:411. [PMID: 38203582 PMCID: PMC10778741 DOI: 10.3390/ijms25010411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 12/23/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
The increasing number of patients with chronic wounds requires the development of quick and accurate diagnostics methods. One of the key and challenging aspects of treating ulcers is to control wound infection. Early detection of infection is essential for the application of suitable treatment methods, such as systemic antibiotics or other antimicrobial agents. Clinically, the most frequently used method for detecting microorganisms in wounds is through a swab and culture on appropriate media. This test has major limitations, such as the long bacterial growth time and the selectivity of bacterial growth. This article presents an overview of molecular methods for detecting bacteria in wounds, including real-time polymerase chain reaction (rtPCR), quantitative polymerase chain reaction (qPCR), genotyping, next-generation sequencing (NGS), and loop-mediated isothermal amplification (LAMP). We focus on the LAMP method, which has not yet been widely used to detect bacteria in wounds, but it is an interesting alternative to conventional detection methods. LAMP does not require additional complicated equipment and provides the fastest detection time for microorganisms (approx. 30 min reaction). It also allows the use of many pairs of primers in one reaction and determination of up to 15 organisms in one sample. Isothermal amplification of DNA is currently the easiest and most economical method for microbial detection in wound infection. Direct visualization of the reaction with dyes, along with omitting DNA isolation, has increased the potential use of this method.
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Affiliation(s)
- Monika Gieroń
- Faculty of Medicine, Jan Kochanowski University in Kielce, 25-369 Kielce, Poland; (M.G.); (B.K.)
- Dermatology Department, Provincial General Hospital, 25-317 Kielce, Poland
| | - Paulina Żarnowiec
- Department of Microbiology, Institute of Biology, Jan Kochanowski University in Kielce, 25-406 Kielce, Poland; (P.Ż.); (K.Z.); (D.G.); (W.K.)
| | - Katarzyna Zegadło
- Department of Microbiology, Institute of Biology, Jan Kochanowski University in Kielce, 25-406 Kielce, Poland; (P.Ż.); (K.Z.); (D.G.); (W.K.)
| | - Dawid Gmiter
- Department of Microbiology, Institute of Biology, Jan Kochanowski University in Kielce, 25-406 Kielce, Poland; (P.Ż.); (K.Z.); (D.G.); (W.K.)
| | - Grzegorz Czerwonka
- Department of Microbiology, Institute of Biology, Jan Kochanowski University in Kielce, 25-406 Kielce, Poland; (P.Ż.); (K.Z.); (D.G.); (W.K.)
| | - Wiesław Kaca
- Department of Microbiology, Institute of Biology, Jan Kochanowski University in Kielce, 25-406 Kielce, Poland; (P.Ż.); (K.Z.); (D.G.); (W.K.)
| | - Beata Kręcisz
- Faculty of Medicine, Jan Kochanowski University in Kielce, 25-369 Kielce, Poland; (M.G.); (B.K.)
- Dermatology Department, Provincial General Hospital, 25-317 Kielce, Poland
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Wagner BD, Zemanick ET, Sagel SD, Robertson CE, Stevens MJ, Mayer-Hamblett N, Retsch-Bogart G, Ramsey BW, Harris JK. Limited effects of azithromycin on the oropharyngeal microbiome in children with CF and early pseudomonas infection. BMC Microbiol 2023; 23:312. [PMID: 37891457 PMCID: PMC10612347 DOI: 10.1186/s12866-023-03073-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Tobramycin inhalation solution (TIS) and chronic azithromycin (AZ) have known clinical benefits for children with CF, likely due to antimicrobial and anti-inflammatory activity. The effects of chronic AZ in combination with TIS on the airway microbiome have not been extensively investigated. Oropharyngeal swab samples were collected in the OPTIMIZE multicenter, randomized, placebo-controlled trial examining the addition of AZ to TIS in 198 children with CF and early P. aeruginosa infection. Bacterial small subunit rRNA gene community profiles were determined. The effects of TIS and AZ were assessed on oropharyngeal microbial diversity and composition to uncover whether effects on the bacterial community may be a mechanism of action related to the observed changes in clinical outcomes. RESULTS Substantial changes in bacterial communities (total bacterial load, diversity and relative abundance of specific taxa) were observed by week 3 of TIS treatment for both the AZ and placebo groups. On average, these shifts were due to changes in non-traditional CF taxa that were not sustained at the later study visits (weeks 13 and 26). Bacterial community measures did not differ between the AZ and placebo groups. CONCLUSIONS This study provides further evidence that the mechanism for AZ's effect on clinical outcomes is not due solely to action on airway microbial composition.
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Affiliation(s)
- Brandie D Wagner
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, CO, USA.
- Children's Hospital Colorado, Aurora, CO, USA.
| | - Edith T Zemanick
- Children's Hospital Colorado, Aurora, CO, USA
- Department of Pediatrics, University of Colorado, Aurora, CO, USA
| | - Scott D Sagel
- Children's Hospital Colorado, Aurora, CO, USA
- Department of Pediatrics, University of Colorado, Aurora, CO, USA
| | | | - Mark J Stevens
- Children's Hospital Colorado, Aurora, CO, USA
- Department of Pediatrics, University of Colorado, Aurora, CO, USA
| | - Nicole Mayer-Hamblett
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
- Seattle Children's Hospital, Seattle, WA, USA
| | | | - Bonnie W Ramsey
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Seattle Children's Hospital, Seattle, WA, USA
| | - J Kirk Harris
- Children's Hospital Colorado, Aurora, CO, USA
- Department of Pediatrics, University of Colorado, Aurora, CO, USA
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Harris JK, Wagner BD, Robertson CE, Stevens MJ, Lingard C, Borowitz D, Leung DH, Heltshe SL, Ramsey BW, Zemanick ET. Upper airway microbiota development in infants with cystic fibrosis diagnosed by newborn screen. J Cyst Fibros 2023; 22:644-651. [PMID: 37137746 PMCID: PMC10524365 DOI: 10.1016/j.jcf.2023.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/03/2023] [Accepted: 04/21/2023] [Indexed: 05/05/2023]
Abstract
BACKGROUND Changes in upper airway microbiota may impact early disease manifestations in infants with cystic fibrosis (CF). To investigate early airway microbiota, the microbiota present in the oropharynx of CF infants over the first year of life was assessed along with the relationships between microbiota and growth, antibiotic use and other clinical variables. METHODS Oropharyngeal (OP) swabs were collected longitudinally between 1 and 12 months of age from infants diagnosed with CF by newborn screen and enrolled in the Baby Observational and Nutrition Study (BONUS). DNA extraction was performed after enzymatic digestion of OP swabs. Total bacterial load was determined by qPCR and community composition assessed using 16S rRNA gene analysis (V1/V2 region). Changes in diversity with age were evaluated using mixed models with cubic B-splines. Associations between clinical variables and bacterial taxa were determined using a canonical correlation analysis. RESULTS 1,052 OP swabs collected from 205 infants with CF were analyzed. Most infants (77%) received at least one course of antibiotics during the study and 131 OP swabs were collected while the infant was prescribed an antibiotic. Alpha diversity increased with age and was only marginally impacted by antibiotic use. Community composition was most highly correlated with age and was only moderately correlated with antibiotic exposure, feeding method and weight z-scores. Relative abundance of Streptococcus decreased while Neisseria and other taxa increased over the first year. CONCLUSIONS Age was more influential on the oropharyngeal microbiota of infants with CF than clinical variables including antibiotics in the first year of life.
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Affiliation(s)
- J Kirk Harris
- Department of Pediatrics, University of Colorado Anschutz Medical Campus and Children's Hospital Colorado, 13123 E. 16th Ave, B-395, Aurora, CO 80045, USA.
| | - Brandie D Wagner
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Charles E Robertson
- Department of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Mark J Stevens
- Department of Pediatrics, University of Colorado Anschutz Medical Campus and Children's Hospital Colorado, 13123 E. 16th Ave, B-395, Aurora, CO 80045, USA
| | - Conor Lingard
- Spartanburg Regional Healthcare Systems, Spartanburg, SC, USA
| | - Drucy Borowitz
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, USA
| | - Daniel H Leung
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Sonya L Heltshe
- Cystic Fibrosis Foundation Therapeutic Development Network Coordinating Center, Seattle Children's Research Institute, Seattle, WA, USA; Division of Pulmonary and Sleep Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Bonnie W Ramsey
- Cystic Fibrosis Foundation Therapeutic Development Network Coordinating Center, Seattle Children's Research Institute, Seattle, WA, USA; Division of Pulmonary and Sleep Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Edith T Zemanick
- Department of Pediatrics, University of Colorado Anschutz Medical Campus and Children's Hospital Colorado, 13123 E. 16th Ave, B-395, Aurora, CO 80045, USA
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Barbosa A, Miranda S, Azevedo NF, Cerqueira L, Azevedo AS. Imaging biofilms using fluorescence in situ hybridization: seeing is believing. Front Cell Infect Microbiol 2023; 13:1195803. [PMID: 37284501 PMCID: PMC10239779 DOI: 10.3389/fcimb.2023.1195803] [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: 03/28/2023] [Accepted: 05/08/2023] [Indexed: 06/08/2023] Open
Abstract
Biofilms are complex structures with an intricate relationship between the resident microorganisms, the extracellular matrix, and the surrounding environment. Interest in biofilms is growing exponentially given its ubiquity in so diverse fields such as healthcare, environmental and industry. Molecular techniques (e.g., next-generation sequencing, RNA-seq) have been used to study biofilm properties. However, these techniques disrupt the spatial structure of biofilms; therefore, they do not allow to observe the location/position of biofilm components (e.g., cells, genes, metabolites), which is particularly relevant to explore and study the interactions and functions of microorganisms. Fluorescence in situ hybridization (FISH) has been arguably the most widely used method for an in situ analysis of spatial distribution of biofilms. In this review, an overview on different FISH variants already applied on biofilm studies (e.g., CLASI-FISH, BONCAT-FISH, HiPR-FISH, seq-FISH) will be explored. In combination with confocal laser scanning microscopy, these variants emerged as a powerful approach to visualize, quantify and locate microorganisms, genes, and metabolites inside biofilms. Finally, we discuss new possible research directions for the development of robust and accurate FISH-based approaches that will allow to dig deeper into the biofilm structure and function.
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Affiliation(s)
- Ana Barbosa
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Sónia Miranda
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal
| | - Nuno F. Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Laura Cerqueira
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Andreia S. Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal
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Williamson BD, Hughes JP, Willis AD. A multiview model for relative and absolute microbial abundances. Biometrics 2022; 78:1181-1194. [PMID: 34048057 PMCID: PMC8982138 DOI: 10.1111/biom.13503] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 05/07/2021] [Accepted: 05/19/2021] [Indexed: 12/30/2022]
Abstract
The absolute abundance of bacterial taxa in human host-associated environments plays a critical role in reproductive and gastrointestinal health. However, obtaining the absolute abundance of many bacterial species is typically prohibitively expensive. In contrast, relative abundance data for many species are comparatively cheap and easy to collect (e.g., with universal primers for the 16S rRNA gene). In this paper, we propose a method to jointly model relative abundance data for many taxa and absolute abundance data for a subset of taxa. Our method provides point and interval estimates for the absolute abundance of all taxa. Crucially, our proposal accounts for differences in the efficiency of taxon detection in the relative and absolute abundance data. We show that modeling taxon-specific efficiencies substantially reduces the estimation error for absolute abundance, and controls the coverage of interval estimators. We demonstrate the performance of our proposed method via a simulation study, a study of the effect of HIV acquisition on microbial abundances, and a sensitivity study where we jackknife the taxa with observed absolute abundances.
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Affiliation(s)
| | - James P. Hughes
- Department of BiostatisticsUniversity of WashingtonSeattleWashingtonUSA
| | - Amy D. Willis
- Department of BiostatisticsUniversity of WashingtonSeattleWashingtonUSA
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O’Connor JB, Mottlowitz M, Kruk ME, Mickelson A, Wagner BD, Harris JK, Wendt CH, Laguna TA. Network Analysis to Identify Multi-Omic Correlations in the Lower Airways of Children With Cystic Fibrosis. Front Cell Infect Microbiol 2022; 12:805170. [PMID: 35360097 PMCID: PMC8960254 DOI: 10.3389/fcimb.2022.805170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 02/16/2022] [Indexed: 11/13/2022] Open
Abstract
The leading cause of morbidity and mortality in cystic fibrosis (CF) is progressive lung disease secondary to chronic airway infection and inflammation; however, what drives CF airway infection and inflammation is not well understood. By providing a physiological snapshot of the airway, metabolomics can provide insight into these processes. Linking metabolomic data with microbiome data and phenotypic measures can reveal complex relationships between metabolites, lower airway bacterial communities, and disease outcomes. In this study, we characterize the airway metabolome in bronchoalveolar lavage fluid (BALF) samples from persons with CF (PWCF) and disease control (DC) subjects and use multi-omic network analysis to identify correlations with the airway microbiome. The Biocrates targeted liquid chromatography mass spectrometry (LC-MS) platform was used to measure 409 metabolomic features in BALF obtained during clinically indicated bronchoscopy. Total bacterial load (TBL) was measured using quantitative polymerase chain reaction (qPCR). The Qiagen EZ1 Advanced automated extraction platform was used to extract DNA, and bacterial profiling was performed using 16S sequencing. Differences in metabolomic features across disease groups were assessed univariately using Wilcoxon rank sum tests, and Random forest (RF) was used to identify features that discriminated across the groups. Features were compared to TBL and markers of inflammation, including white blood cell count (WBC) and percent neutrophils. Sparse supervised canonical correlation network analysis (SsCCNet) was used to assess multi-omic correlations. The CF metabolome was characterized by increased amino acids and decreased acylcarnitines. Amino acids and acylcarnitines were also among the features most strongly correlated with inflammation and bacterial burden. RF identified strong metabolomic predictors of CF status, including L-methionine-S-oxide. SsCCNet identified correlations between the metabolome and the microbiome, including correlations between a traditional CF pathogen, Staphylococcus, a group of nontraditional taxa, including Prevotella, and a subnetwork of specific metabolomic markers. In conclusion, our work identified metabolomic characteristics unique to the CF airway and uncovered multi-omic correlations that merit additional study.
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Affiliation(s)
- John B. O’Connor
- Department of Pediatrics, Division of Pulmonary and Sleep Medicine, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, United States
- *Correspondence: John B. O’Connor,
| | - Madison Mottlowitz
- Department of Pediatrics, Division of Pulmonary and Sleep Medicine, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, United States
| | - Monica E. Kruk
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States
| | - Alan Mickelson
- Department of Medicine, University of Minnesota, Minneapolis VA Medical Center, Minneapolis, MN, United States
| | - Brandie D. Wagner
- School of Medicine, University of Colorado, Aurora, CO, United States
- Colorado School of Public Health, University of Colorado Denver, Aurora, CO, United States
| | | | - Christine H. Wendt
- Department of Medicine, University of Minnesota, Minneapolis VA Medical Center, Minneapolis, MN, United States
| | - Theresa A. Laguna
- Department of Pediatrics, Division of Pulmonary and Sleep Medicine, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, United States
- Northwestern University Feinberg School of Medicine, Chicago, IL, United States
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Webb KA, Olagoke O, Baird T, Neill J, Pham A, Wells TJ, Ramsay KA, Bell SC, Sarovich DS, Price EP. Genomic diversity and antimicrobial resistance of Prevotella species isolated from chronic lung disease airways. Microb Genom 2022; 8. [PMID: 35113778 PMCID: PMC8942031 DOI: 10.1099/mgen.0.000754] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD) are characterized by increasingly frequent acute pulmonary exacerbations that reduce life quality and length. Human airways are home to a rich polymicrobial environment, which includes members of the obligately anaerobic genus Prevotella. Despite their commonness, surprisingly little is known about the prevalence, role, genomic diversity and antimicrobial resistance (AMR) potential of Prevotella species and strains in healthy and diseased airways. Here, we used comparative genomics to develop a real-time PCR assay to permit rapid Prevotella species identification and quantification from cultures and clinical specimens. Assay specificity was validated across a panel of Prevotella and non-Prevotella species, followed by PCR screening of CF and COPD respiratory-derived cultures. Next, 35 PCR-positive isolates were subjected to whole-genome sequencing. Of eight identified Prevotella species, P. histicola, P. melaninogenica, P. nanceiensis, P. salivae and P. denticola overlapped between participant cohorts. Phylogenomic analysis revealed considerable interhost but limited intrahost diversity, suggesting patient-specific lineages in the lower airways, probably from oral cavity aspirations. Correlation of phenotypic AMR profiles with AMR genes identified excellent correlation between tetQ presence and decreased doxycycline susceptibility, and ermF presence and decreased azithromycin susceptibility and clindamycin resistance. AMR rates were higher in the CF isolates, reflecting greater antibiotic use in this cohort. All tested Prevotella isolates were tobramycin-resistant, providing a potential selection method to improve Prevotella culture retrieval rates. Our addition of 35 airway-derived Prevotella genomes to public databases will enhance ongoing efforts to unravel the role of this diverse and enigmatic genus in both diseased and healthy lungs.
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Affiliation(s)
- Kasey A Webb
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia.,Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Olusola Olagoke
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia.,Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Timothy Baird
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia.,Sunshine Coast Hospital and Health Service, Sunshine Coast University Hospital, Birtinya, Queensland, Australia
| | - Jane Neill
- Sunshine Coast Hospital and Health Service, Sunshine Coast University Hospital, Birtinya, Queensland, Australia
| | - Amy Pham
- University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, Queensland, Australia
| | - Timothy J Wells
- University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, Queensland, Australia
| | - Kay A Ramsay
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.,Present address: Child Health Research Centre, The University of Queensland, Centre for Children's Health Research, South Brisbane, Queensland, Australia
| | - Scott C Bell
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.,Adult Cystic Fibrosis Centre, The Prince Charles Hospital, Chermside, Queensland, Australia.,Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Derek S Sarovich
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia.,Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Erin P Price
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia.,Sunshine Coast Health Institute, Birtinya, Queensland, Australia
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11
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O’Connor JB, Mottlowitz MM, Wagner BD, Boyne KL, Stevens MJ, Robertson CE, Harris JK, Laguna TA. Divergence of bacterial communities in the lower airways of CF patients in early childhood. PLoS One 2021; 16:e0257838. [PMID: 34613995 PMCID: PMC8494354 DOI: 10.1371/journal.pone.0257838] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/10/2021] [Indexed: 11/18/2022] Open
Abstract
Rationale Chronic airway infection and inflammation resulting in progressive, obstructive lung disease is the leading cause of morbidity and mortality in cystic fibrosis. Understanding the lower airway microbiota across the ages can provide valuable insight and potential therapeutic targets. Objectives To characterize and compare the lower airway microbiota in cystic fibrosis and disease control subjects across the pediatric age spectrum. Methods Bronchoalveolar lavage fluid samples from 191 subjects (63 with cystic fibrosis) aged 0 to 21 years were collected along with relevant clinical data. We measured total bacterial load using quantitative polymerase chain reaction and performed 16S rRNA gene sequencing to characterize bacterial communities with species-level sensitivity for select genera. Clinical comparisons were investigated. Measurements and main results Cystic fibrosis samples had higher total bacterial load and lower microbial diversity, with a divergence from disease controls around 2–5 years of age, as well as higher neutrophilic inflammation relative to bacterial burden. Cystic fibrosis samples had increased abundance of traditional cystic fibrosis pathogens and decreased abundance of the Streptococcus mitis species group in older subjects. Interestingly, increased diversity in the heterogeneous disease controls was independent of diagnosis and indication. Sequencing was more sensitive than culture, and antibiotic exposure was more common in disease controls, which showed a negative relationship with load and neutrophilic inflammation. Conclusions Analysis of lower airway samples from people with cystic fibrosis and disease controls across the ages revealed key differences in airway microbiota and inflammation. The divergence in subjects during early childhood may represent a window of opportunity for intervention and additional study.
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Affiliation(s)
- John B. O’Connor
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, United States of America
- * E-mail:
| | - Madison M. Mottlowitz
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, United States of America
| | - Brandie D. Wagner
- Department of Pediatrics, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Kathleen L. Boyne
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, United States of America
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Mark J. Stevens
- Department of Pediatrics, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Charles E. Robertson
- Department of Pediatrics, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Jonathan K. Harris
- Department of Pediatrics, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Theresa A. Laguna
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, United States of America
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
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12
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Williamson KM, Wagner BD, Robertson CE, Stevens MJ, Sontag MK, Mourani PM, Harris JK. Modified PCR protocol to increase sensitivity for determination of bacterial community composition. MICROBIOME 2021; 9:90. [PMID: 33849648 PMCID: PMC8045227 DOI: 10.1186/s40168-020-00958-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 12/06/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND The objective of this project was to increase the sensitivity of sequence-based bacterial community determination without impacting community composition or interfering with cluster formation during sequencing. Two PCR protocols (standard and modified) were examined in airway samples where we observed a large range in bacterial load (3.1-6.2 log10 16S rRNA gene copies/reaction). Tracheal aspirate (TA) samples (n = 99) were collected from sixteen children requiring mechanical ventilation at a single center. DNA was extracted, and total bacterial load (TBL) was assessed using qPCR. Amplification of 16S rRNA was attempted with both protocols in all samples. RESULTS PCR product was observed using both protocols in 52 samples and in 24 additional samples only with the modified protocol. TBL, diversity metrics, and prominent taxa were compared for samples in three groups based on success of the two protocols (successful with both, success with modified only, unsuccessful for both). TBL differed significantly across the three groups (p<0.001). Specifically, the modified protocol allowed amplification from samples with intermediate TBL. Shannon diversity was similar between the two protocols, and Morisita-Horn beta diversity index showed high agreement between the two protocols within samples (median value 0.9997, range 0.9947 to 1). We show that both protocols identify similar communities, and the technical variability of both protocols was very low. The use of limited PCR cycles was a key feature to limit impact of background by exclusion of 24% of samples with no evidence of bacterial DNA present in the sample. CONCLUSION The modified amplification protocol represents a viable approach that increased sensitivity of bacterial community analysis, which is important for study of the human airway microbiome where bacterial load is highly variable. Video abstract.
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Affiliation(s)
- Kayla M. Williamson
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado School of Medicine, 13001 17th Place, Mail Stop B119, Aurora, CO 80045 USA
| | - Brandie D. Wagner
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado School of Medicine, 13001 17th Place, Mail Stop B119, Aurora, CO 80045 USA
- Section of Critical Care, Department of Pediatrics, University of Colorado School of Medicine and Children’s Hospital Colorado, 13123 E. 16th Ave. Box B395, Aurora, CO 80045 USA
| | - Charles E. Robertson
- Division of Infectious Diseases, School of Medicine, University of Colorado, 12700 East 19th Avenue, Mail Stop B168, Aurora, CO 80045 USA
| | - Mark J. Stevens
- Section of Critical Care, Department of Pediatrics, University of Colorado School of Medicine and Children’s Hospital Colorado, 13123 E. 16th Ave. Box B395, Aurora, CO 80045 USA
| | - Marci K. Sontag
- Department of Epidemiology, Colorado School of Public Health, University of Colorado School of Medicine, 13001 17th Place, Mail Stop B119, Aurora, CO 80045 USA
| | - Peter M. Mourani
- Section of Critical Care, Department of Pediatrics, University of Colorado School of Medicine and Children’s Hospital Colorado, 13123 E. 16th Ave. Box B395, Aurora, CO 80045 USA
| | - J. Kirk Harris
- Section of Critical Care, Department of Pediatrics, University of Colorado School of Medicine and Children’s Hospital Colorado, 13123 E. 16th Ave. Box B395, Aurora, CO 80045 USA
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13
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Khalaf RT, Furuta GT, Wagner BD, Robertson CE, Andrews R, Stevens MJ, Fillon SA, Zemanick ET, Harris JK. Influence of Acid Blockade on the Aerodigestive Tract Microbiome in Children With Cystic Fibrosis. J Pediatr Gastroenterol Nutr 2021; 72:520-527. [PMID: 33394582 PMCID: PMC8315410 DOI: 10.1097/mpg.0000000000003010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Acid blockade is commonly prescribed in patients with cystic fibrosis (CF). Growing concerns, however, exist about its possible role in the pathophysiology of pulmonary infections. We aimed to investigate if acid blockade alters esophageal and respiratory microbiota leading to dysbiosis and inflammation. METHODS We performed a cross sectional study of children with CF who were either prescribed acid blockade or not. Samples from the gastrointestinal and respiratory tracts were obtained and microbiome analyzed. Mixed effect models were used to compare outcomes between cohorts and across sampling sites. A random subject intercept was included to account for the multiple sampling sites per individual. RESULTS A cohort of 25 individuals, 44% girls with median age of 13.8 years [IQR 11.2--14.8] were enrolled. Alpha diversity, total bacterial load, and beta diversity were similar across anatomic compartments, across the upper gastrointestinal tract, and in respiratory samples. Similar alpha diversity, total bacterial load, and beta diversity results were also observed when comparing individuals on versus those off acid blockade. IL-8 was elevated in the distal versus proximal esophagus in the whole cohort (P < 0.01). IL-8 concentrations were similar in the distal esophagus in patients on and off acid blockade, but significantly greater in the proximal esophagus of subjects on treatment (P < 0.01). CONCLUSIONS On the basis of these data, acid blockade use does not appear to influence the microbiome of the aerodigestive tract in children with cystic fibrosis suggesting a complex interplay between these medications and the bacterial composition of the esophagus and lung.
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Affiliation(s)
- Racha T. Khalaf
- Department of Pediatrics, Gastrointestinal Eosinophilic Diseases Program, Section of Pediatric Gastroenterology, Hepatology and Nutrition, University of Colorado School of Medicine, Digestive Health Institute, Children’s Hospital Colorado, Aurora, CO
- Department of Pediatrics, University of South Florida Morsani College of Medicine, Tampa, FL
| | - Glenn T. Furuta
- Department of Pediatrics, Gastrointestinal Eosinophilic Diseases Program, Section of Pediatric Gastroenterology, Hepatology and Nutrition, University of Colorado School of Medicine, Digestive Health Institute, Children’s Hospital Colorado, Aurora, CO
- Department of Pediatrics, University of South Florida Morsani College of Medicine, Tampa, FL
| | - Brandie D. Wagner
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora
| | - Charles E. Robertson
- Department of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Rachel Andrews
- Department of Pediatrics, Gastrointestinal Eosinophilic Diseases Program, Section of Pediatric Gastroenterology, Hepatology and Nutrition, University of Colorado School of Medicine, Digestive Health Institute, Children’s Hospital Colorado, Aurora, CO
| | - Mark J. Stevens
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Sophie A. Fillon
- Department of Pediatrics, Gastrointestinal Eosinophilic Diseases Program, Section of Pediatric Gastroenterology, Hepatology and Nutrition, University of Colorado School of Medicine, Digestive Health Institute, Children’s Hospital Colorado, Aurora, CO
- Mucosal Inflammation Program, University of Colorado School of Medicine, University of Colorado Anschutz Medical Campus, Aurora
- Department of Cancer Immunology and Immune Modulation, Boehringer Ingelheim Pharma GmbH & Co.KG, Biberach, Germany
| | - Edith T. Zemanick
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - J. Kirk Harris
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO
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14
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Abstract
Cystic fibrosis (CF) is the most common, lethal genetic disease among the Caucasian population. The leading cause of mortality is recurrent acute exacerbations resulting in chronic airway inflammation and subsequent downward progression of pulmonary function. Traditionally, these periods of clinical deterioration have been associated with several principal pathogens. However, a growing body of literature has demonstrated a polymicrobial lower respiratory community compromised of facultative and obligate anaerobes. Despite the understanding of a complex bacterial milieu in CF patient airways, specific roles of anaerobes in disease progression have not been established. In this paper, we first present a brief review of the anaerobic microorganisms that have been identified within CF lower respiratory airways. Next, we discuss the potential contribution of these organisms to CF disease progression, in part by pathogenic potential and also through synergistic interaction with principal pathogens. Finally, we propose a variety of clinical scenarios in which these anaerobic organisms indirectly facilitate principal CF pathogens by modulating host defense and contribute to treatment failure by antibiotic inactivation. These mechanisms may affect patient clinical outcomes and contribute to further disease progression.
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15
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Changes in Airway Microbiome and Inflammation with Ivacaftor Treatment in Patients with Cystic Fibrosis and the G551D Mutation. Ann Am Thorac Soc 2021; 17:212-220. [PMID: 31604026 DOI: 10.1513/annalsats.201907-493oc] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rationale: Modulation of the cystic fibrosis (CF) transmembrane conductance regulator (CFTR) protein improves clinical outcomes in patients with CF and specific CFTR genetic mutations. It remains unclear how improving CFTR function modifies existing airway infection and inflammation.Objectives: To compare sputum microbiome and markers of inflammation before and after 6 months of ivacaftor treatment.Methods: The study included 31 people with CF, ages 10 years and older, with at least one G551D CFTR allele and an forced expiratory volume in 1 second (FEV1) of 40% predicted or greater who were enrolled in the GOAL (G551D Observational) study. Sputum samples were collected either by induction (n = 14) or by spontaneous expectoration (n = 17) before and 6 months after initiation of ivacaftor. Changes in bacterial community indices by sequencing of 16S rRNA amplicons, total and specific bacterial load, and a panel of proteases, antiproteases, and inflammatory cytokines were determined.Results: The cohort that spontaneously expectorated sputum had a lower FEV1, a higher proportion with Pseudomonas aeruginosa infection, and higher concentrations of sputum inflammatory markers compared with the cohort that provided sputum by induction. Although the overall cohort experienced significant improvements in FEV1 and reductions in sweat chloride, no significant changes in bacterial diversity, specific bacterial pathogens, or markers of inflammation were observed in these subjects. Neither total bacterial load nor presence of Pseudomonas changed significantly between paired samples with ivacaftor treatment. Younger patients experienced more shifts in their microbial communities than older patients.Conclusions: In this multicenter cohort, 6 months of ivacaftor treatment were not associated with significant changes in airway microbial communities or measures of inflammation. These data suggest that concomitant antimicrobial and antiinflammatory treatments will still be needed to manage airway disease in patients with CF treated with highly effective CFTR modulator therapy, especially in older patients with more advanced disease.
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16
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Weiser R, Rye PD, Mahenthiralingam E. Implementation of microbiota analysis in clinical trials for cystic fibrosis lung infection: Experience from the OligoG phase 2b clinical trials. J Microbiol Methods 2021; 181:106133. [PMID: 33421446 DOI: 10.1016/j.mimet.2021.106133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/02/2021] [Accepted: 01/04/2021] [Indexed: 11/28/2022]
Abstract
Culture-independent microbiota analysis is widely used in research and being increasingly used in translational studies. However, methods for standardisation and application of these analyses in clinical trials are limited. Here we report the microbiota analysis that accompanied two phase 2b clinical trials of the novel, non-antibiotic therapy OligoG CF-5/20 for cystic fibrosis (CF) lung infection. Standardised protocols (DNA extraction, PCR, qPCR and 16S rRNA gene sequencing analysis) were developed for application to the Pseudomonas aeruginosa (NCT02157922) and Burkholderia cepacia complex (NCT02453789) clinical trials involving 45 and 13 adult trial participants, respectively. Microbiota analysis identified that paired sputum samples from an individual participant, taken within 2 h of each other, had reproducible bacterial diversity profiles. Although culture microbiology had identified patients as either colonised by P. aeruginosa or B. cepacia complex species at recruitment, microbiota analysis revealed patient lung infection communities were not always dominated by these key CF pathogens. Microbiota profiles were patient-specific and remained stable over the course of both clinical trials (6 sampling points over the course of 140 days). Within the Burkholderia trial, participants were infected with B. cenocepacia (n = 4), B. multivorans (n = 6), or an undetermined species (n = 3). Colonisation with either B. cenocepacia or B. multivorans influenced the overall bacterial community structure in sputum. Overall, we have shown that sputum microbiota in adults with CF is stable over a 2 h time-frame, suggesting collection of a single sample on a collection day is sufficient to capture the microbiota diversity. Despite the uniform pathogen culture-positivity status at recruitment, trial participants were highly heterogeneous in their lung microbiota. Understanding the microbiota profiles of individuals with CF ahead of future clinical trials would be beneficial in the context of patient stratification and trial design.
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Affiliation(s)
- Rebecca Weiser
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff, Wales, CF10 3AX, UK.
| | - Philip D Rye
- AlgiPharma AS, Industriveien 33, N-1337, Sandvika, Norway.
| | - Eshwar Mahenthiralingam
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff, Wales, CF10 3AX, UK.
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17
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Grainha T, Magalhães AP, Melo LDR, Pereira MO. Pitfalls Associated with Discriminating Mixed-Species Biofilms by Flow Cytometry. Antibiotics (Basel) 2020; 9:antibiotics9110741. [PMID: 33121057 PMCID: PMC7694060 DOI: 10.3390/antibiotics9110741] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 11/21/2022] Open
Abstract
Since biofilms are ubiquitous in different settings and act as sources of disease for humans, reliable methods to characterize and quantify these microbial communities are required. Numerous techniques have been employed, but most of them are unidirectional, labor intensive and time consuming. Although flow cytometry (FCM) can be a reliable choice to quickly provide a multiparametric analysis, there are still few applications on biofilms, and even less on the study of inter-kingdom communities. This work aimed to give insights into the application of FCM in order to more comprehensively analyze mixed-species biofilms, formed by different Pseudomonas aeruginosa and Candida albicans strains, before and after exposure to antimicrobials. For comparison purposes, biofilm culturability was also assessed determining colony-forming units. The results showed that some aspects, namely the microbial strain used, the morphological state of the cells and the biofilm matrix, make the accurate analysis of FCM data difficult. These aspects were even more challenging when double-species biofilms were being inspected, as they could engender data misinterpretations. The outcomes draw our attention towards the need to always take into consideration the characteristics of the biofilm samples to be analyzed through FCM, and undoubtedly link to the need for optimization of the processes tailored for each particular case study.
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Affiliation(s)
| | | | - Luís D. R. Melo
- Correspondence: (L.D.R.M.); (M.O.P.); Tel.: +351-253-601-989 (L.D.R.M.); +351-253-604-402 (M.O.P.)
| | - Maria O. Pereira
- Correspondence: (L.D.R.M.); (M.O.P.); Tel.: +351-253-601-989 (L.D.R.M.); +351-253-604-402 (M.O.P.)
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18
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Clinical and Molecular Microbiological Evaluation of Regenerative Endodontic Procedures in Immature Permanent Teeth. J Endod 2020; 46:1448-1454. [DOI: 10.1016/j.joen.2020.07.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/17/2020] [Accepted: 07/04/2020] [Indexed: 11/17/2022]
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19
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RNA-based qPCR as a tool to quantify and to characterize dual-species biofilms. Sci Rep 2019; 9:13639. [PMID: 31541147 PMCID: PMC6754382 DOI: 10.1038/s41598-019-50094-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 09/06/2019] [Indexed: 12/22/2022] Open
Abstract
While considerable research has focused on studying individual-species, we now face the challenge of determining how interspecies interactions alter bacterial behaviours and pathogenesis. Pseudomonas aeruginosa and Staphylococcus aureus are often found to co-infect cystic-fibrosis patients. Curiously, their interaction is reported as competitive under laboratory conditions. Selecting appropriate methodologies is therefore critical to analyse multi-species communities. Herein, we demonstrated the major biases associated with qPCR quantification of bacterial populations and optimized a RNA-based qPCR able not only to quantify but also to characterize microbial interactions within dual-species biofilms composed by P. aeruginosa and S. aureus, as assessed by gene expression quantification. qPCR quantification was compared with flow-cytometry and culture-based quantification. Discrepancies between culture independent and culture dependent methods could be the result of the presence of viable but not-cultivable bacteria within the biofilm. Fluorescence microscopy confirmed this. A higher sensitivity to detect viable cells further highlights the potentialities of qPCR approach to quantify biofilm communities. By using bacterial RNA and an exogenous mRNA control, it was also possible to characterize bacterial transcriptomic profile, being this a major advantage of this method.
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20
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Rajapaksha P, Elbourne A, Gangadoo S, Brown R, Cozzolino D, Chapman J. A review of methods for the detection of pathogenic microorganisms. Analyst 2019; 144:396-411. [PMID: 30468217 DOI: 10.1039/c8an01488d] [Citation(s) in RCA: 244] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The testing and rapid detection of pathogenic organisms is a crucial protocol in the prevention and identification of crises related to health, safety and wellbeing. Pathogen detection has become one of the most challenging aspects in the food and water industries, because of the rapid spread of waterborne and foodborne diseases in the community and at significant costs. With the prospect of inevitable population growth, and an influx of tourism to certain water bodies testing will become a requirement to control and prevent possible outbreaks of potentially fatal illnesses. The legislation is already particularly rigorous in the food industry, where failure to detect pathogenic materials represents a catastrophic event, particularly for the elderly, very young or immune-compromised population types. In spite of the need and requirement for rapid analytical testing, conventional and standard bacterial detection assays may take up to seven days to yield a result. Given the advent of new technologies, biosensors, chemical knowledge and miniaturisation of instrumentation this timescale is not acceptable. This review presents an opportunity to fill a knowledge gap for an extremely important research area; discussing the main techniques, biology, chemistry, miniaturisation, sensing and the emerging state-of-the-art research and developments for detection of pathogens in food, water, blood and faecal samples.
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Affiliation(s)
- P Rajapaksha
- School of Science, RMIT University, La Trobe Street, Melbourne, 3000, Victoria, Australia.
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21
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Kawada T, Kuroyanagi J, Okazaki F, Taniguchi M, Nakayama H, Suda N, Abiko S, Kaneco S, Nishimura N, Shimada Y. An Integrative Evaluation Method for the Biological Safety of Down and Feather Materials. Int J Mol Sci 2019; 20:ijms20061434. [PMID: 30901881 PMCID: PMC6471580 DOI: 10.3390/ijms20061434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/15/2019] [Accepted: 03/18/2019] [Indexed: 11/21/2022] Open
Abstract
Background: Down and feather materials have been commonly used and promoted as natural stuffing for warm clothing and bedding. These materials tend to become more allergenic as they become contaminated with microorganisms, in addition to being subjected to several kinds of chemical treatments. The biological or chemical contaminants in these materials pose a major risk to human health, to consumers and manufacturers alike. Here, we report the development of an integrative evaluation method for down and feather materials to assess bacterial contamination and in vivo toxicity. Methods: To assess bacterial contamination, we quantified 16S ribosomal RNA, performed culture tests, and established a conversion formula. To determine in vivo toxicity, we performed a zebrafish embryo toxicity testing (ZFET). Results: Washing the material appropriately decreases the actual number of bacteria in the down and feather samples; in addition, after washing, 16S rRNA sequencing revealed that the bacterial compositions were similar to those in rinse water. The ZFET results showed that even materials with low bacterial contamination showed high toxicity or high teratogenicity, probably because of the presence of unknown chemical additives. Conclusions: We established an integrative evaluation method for down and feather safety, based on bacterial contamination with in vivo toxicity testing.
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Affiliation(s)
| | | | - Fumiyoshi Okazaki
- Department of Life Sciences, Graduate School of Bioresources, Mie University, Tsu, Mie 514-8507, Japan.
- Department of Bioinformatics, Mie University Advanced Science Research Promotion Center, Tsu, Mie 514-8507, Japan.
- Mie University Zebrafish Drug Screening Center, Tsu, Mie 514-8507, Japan.
| | - Mizuki Taniguchi
- Department of Life Sciences, Graduate School of Bioresources, Mie University, Tsu, Mie 514-8507, Japan.
| | - Hiroko Nakayama
- Mie University Zebrafish Drug Screening Center, Tsu, Mie 514-8507, Japan.
- Graduate School of Regional Innovation Studies, Mie University, Tsu, Mie 514-8507, Japan.
| | - Narumi Suda
- UMOU Science Lab, Mastusaka, Mie 515-0074, Japan.
| | - Souta Abiko
- Boken Quality Evaluation Institute, Minato-Ku, Osaka 552-0021, Japan.
| | - Satoshi Kaneco
- Department of Chemistry for Materials, Graduate School of Engineering, Mie University, Tsu, Mie 514-8507, Japan.
| | - Norihiro Nishimura
- Mie University Zebrafish Drug Screening Center, Tsu, Mie 514-8507, Japan.
- Graduate School of Regional Innovation Studies, Mie University, Tsu, Mie 514-8507, Japan.
| | - Yasuhito Shimada
- Department of Bioinformatics, Mie University Advanced Science Research Promotion Center, Tsu, Mie 514-8507, Japan.
- Mie University Zebrafish Drug Screening Center, Tsu, Mie 514-8507, Japan.
- Department of Integrative Pharmacology, Mie University Graduate School of Medicine, Tsu, Mie 514-8507, Japan.
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Hahn A, Burrell A, Fanous H, Chaney H, Sami I, Perez GF, Koumbourlis AC, Freishtat RJ, Crandall KA. Antibiotic multidrug resistance in the cystic fibrosis airway microbiome is associated with decreased diversity. Heliyon 2018; 4:e00795. [PMID: 30238064 PMCID: PMC6143701 DOI: 10.1016/j.heliyon.2018.e00795] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 08/30/2018] [Accepted: 09/12/2018] [Indexed: 12/22/2022] Open
Abstract
Background Cystic fibrosis (CF) is associated with significant morbidity and early mortality due to recurrent acute and chronic lung infections. The chronic use of multiple antibiotics increases the possibility of multidrug resistance (MDR). Antibiotic susceptibility determined by culture-based techniques may not fully represent the resistance profile. The study objective was to detect additional antibiotic resistance using molecular methods and relate the presence of MDR to airway microbiome diversity and pulmonary function. Methods Bacterial DNA was extracted from sputum samples and amplified for the V4 region of the 16S rRNA gene. An qPCR array was used to detect antibiotic resistance genes. Clinical culture results and pulmonary function were also noted for each encounter. Results Six study participants contributed samples from 19 encounters. Those samples with MDR (n = 7) had significantly lower diversity measured by inverse Simpson's index than those without (n = 12) (2.193 ± 0.427 vs 6.023 ± 1.564, p = 0.035). Differential abundance showed that samples with MDR had more Streptococcus (p = 0.002) and Alcaligenaceae_unclassified (p = 0.002). Pulmonary function was also decreased when MDR was present (FEV1, 51 ± 22.9 vs 77 ± 26.7, p = 0.054; FVC, 64.5 ± 22.7 vs 91.6 ± 27.7, p = 0.047). Conclusions The presence of MDR within the CF airway microbiome was associated with decreased microbial diversity, the presence of Alcaligenes, and decreased pulmonary function.
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Affiliation(s)
- Andrea Hahn
- Division of Infectious Diseases, Children's National Health System, Washington, DC, USA.,Center for Genetic Medicine Research, The Children's Research Institute, Washington, DC, USA.,Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Aszia Burrell
- Center for Genetic Medicine Research, The Children's Research Institute, Washington, DC, USA
| | - Hani Fanous
- Division of Pulmonary and Sleep Medicine, Children's National Health System, Washington, DC, USA
| | - Hollis Chaney
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.,Division of Pulmonary and Sleep Medicine, Children's National Health System, Washington, DC, USA
| | - Iman Sami
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.,Division of Pulmonary and Sleep Medicine, Children's National Health System, Washington, DC, USA
| | - Geovanny F Perez
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.,Division of Pulmonary and Sleep Medicine, Children's National Health System, Washington, DC, USA
| | - Anastassios C Koumbourlis
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.,Division of Pulmonary and Sleep Medicine, Children's National Health System, Washington, DC, USA
| | - Robert J Freishtat
- Center for Genetic Medicine Research, The Children's Research Institute, Washington, DC, USA.,Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.,Division of Emergency Medicine, Children's National Health System, Washington, DC, USA
| | - Keith A Crandall
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
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23
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Caverly LJ, LiPuma JJ. Good cop, bad cop: anaerobes in cystic fibrosis airways. Eur Respir J 2018; 52:52/1/1801146. [PMID: 29997183 DOI: 10.1183/13993003.01146-2018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 06/19/2018] [Indexed: 11/05/2022]
Affiliation(s)
- Lindsay J Caverly
- Dept of Pediatrics and Communicable Diseases, C.S. Mott Children's Hospital, University of Michigan, Ann Arbor, MI, USA
| | - John J LiPuma
- Dept of Pediatrics and Communicable Diseases, C.S. Mott Children's Hospital, University of Michigan, Ann Arbor, MI, USA
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24
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Quantitative assessment of individual populations within polymicrobial biofilms. Sci Rep 2018; 8:9494. [PMID: 29934504 PMCID: PMC6015014 DOI: 10.1038/s41598-018-27497-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/24/2018] [Indexed: 02/06/2023] Open
Abstract
Selecting appropriate tools providing reliable quantitative measures of individual populations in biofilms is critical as we now recognize their true polymicrobial and heterogeneous nature. Here, plate count, quantitative real-time polymerase chain reaction (q-PCR) and peptide nucleic acid probe-fluorescence in situ hybridization (PNA-FISH) were employed to quantitate cystic fibrosis multispecies biofilms. Growth of Pseudomonas aeruginosa, Inquilinus limosus and Dolosigranulum pigrum was assessed in dual- and triple-species consortia under oxygen and antibiotic stress. Quantification methods, that were previously optimized and validated in planktonic consortia, were not always in agreement when applied in multispecies biofilms. Discrepancies in culture and molecular outcomes were observed, particularly for triple-species consortia and antibiotic-stressed biofilms. Some differences were observed, such as the higher bacterial counts obtained by q-PCR and/or PNA-FISH (≤4 log10 cells/cm2) compared to culture. But the discrepancies between PNA-FISH and q-PCR data (eg D. pigrum limited assessment by q-PCR) demonstrate the effect of biofilm heterogeneity in method’s reliability. As the heterogeneity in biofilms is a reflection of a myriad of variables, tailoring an accurate picture of communities´ changes is crucial. This work demonstrates that at least two, but preferentially three, quantification techniques are required to obtain reliable measures and take comprehensive analysis of polymicrobial biofilm-associated infections.
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25
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Rocchetti TT, Silbert S, Gostnell A, Kubasek C, Jerris R, Vong J, Widen R. Rapid detection of four non-fermenting Gram-negative bacteria directly from cystic fibrosis patient's respiratory samples on the BD MAX™ system. Pract Lab Med 2018; 12:e00102. [PMID: 30009245 PMCID: PMC6041425 DOI: 10.1016/j.plabm.2018.e00102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/13/2018] [Accepted: 05/23/2018] [Indexed: 12/30/2022] Open
Abstract
The aim of this study was to develop a multiplex PCR test to detect Achromobacter xylosoxidans (AX), Burkholderia cepacia (BC), Pseudomonas aeruginosa (PSA) and Stenotrophomonas maltophilia (SM) directly from CF patient's respiratory samples using the open mode of the BD MAX™ System. A total of 402 CF respiratory samples were evaluated by culture and PCR. Specific sets of primers and probes for each target were designed in-house. Out of 402 samples tested, 196 were identified as negative and 206 as positive by culture for AX, PSA, BC and SM. Among culture positive samples, PCR detected 21/27 AX, 4/5 BC, 138/140 PSA and 29/34 SM. In addition, PCR assay identified 35 samples as positive that were initially negative by culture for those 4 targets. The CF BDM test proved to be an excellent tool to detect AX, BC, PSA and SM by real-time PCR on an automated platform.
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Affiliation(s)
- Talita T. Rocchetti
- Esoteric Testing Laboratory, Pathology Department, Tampa General Hospital, Tampa, FL, USA
- Laboratório Especial de Microbiologia Clínica (LEMC), Federal University of São Paulo/UNIFESP, São Paulo, SP, Brazil
| | - Suzane Silbert
- Esoteric Testing Laboratory, Pathology Department, Tampa General Hospital, Tampa, FL, USA
- Correspondence to: Esoteric Testing Laboratory, Tampa General Hospital, 1 Tampa General Circle, Tampa, FL 33606-3571, USA.
| | - Alicia Gostnell
- Esoteric Testing Laboratory, Pathology Department, Tampa General Hospital, Tampa, FL, USA
| | - Carly Kubasek
- Esoteric Testing Laboratory, Pathology Department, Tampa General Hospital, Tampa, FL, USA
| | | | | | - Raymond Widen
- Esoteric Testing Laboratory, Pathology Department, Tampa General Hospital, Tampa, FL, USA
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26
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Mourani PM, Sontag MK. Ventilator-Associated Pneumonia in Critically Ill Children: A New Paradigm. Pediatr Clin North Am 2017; 64:1039-1056. [PMID: 28941534 DOI: 10.1016/j.pcl.2017.06.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Ventilator-associated pneumonia (VAP) is a serious complication of critical illness. Surveillance definitions have undergone revisions for more objective and consistent reporting. The 1 organism-1 disease paradigm for microbial involvement may not adequately apply to many cases of VAP, in which pathogens are introduced to a pre-existing and often complex microbial community that facilitates or hinders the potential pathogen, consequently determining whether progression to VAP occurs. As omics technology is applied to VAP, a paradigm is emerging incorporating simultaneous assessments of microbial populations and their activity, as well as the host response, to personalize prevention and treatment.
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Affiliation(s)
- Peter M Mourani
- Section of Critical Care, Department of Pediatrics, University of Colorado Denver, School of Medicine, Children's Hospital Colorado, 13121 East 17th Avenue, MS8414, Aurora, CO 80045, USA.
| | - Marci K Sontag
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver Anschutz Medical Campus, 13001 East 17th, B119, Aurora, CO 80045, USA
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27
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Pyo H, Lee CY, Kim D, Kim G, Lee S, Yun WS. Electrical Detection of Pneumococcus through the Nanoparticle Decoration Method. SENSORS 2017; 17:s17092012. [PMID: 28869504 PMCID: PMC5621115 DOI: 10.3390/s17092012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/19/2017] [Accepted: 08/31/2017] [Indexed: 11/21/2022]
Abstract
A simple method of nanoparticle decoration can be used in the detection of pneumococcus. After the pneumococcal bacteria were captured by an antibody (pneumococcal C-polysaccharide (PnC) antibody) between the interdigitated electrodes, the gold nanoparticles conjugated with the PnC antibodies were let to bind onto an outer membrane of the bacteria. Upon successfully dense decoration, the bacteria surface will become conductive owing to the metal nanoparticles, and a distinctive conductance change between the electrodes can be observed. Since this success ratio, or the probability of the conductance change, reflects the concentration of the analyte, a number of repeated measurements can be used in the quantification of the bacteria. In this way, we have successfully detected S. pneumoniae in the range of 10–108 CFU/mL. The limit of detection in this work is lower than that in the commercial detection kit. We hope that the nanoparticle decoration method will play a role in the facile detection of various bacteria.
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Affiliation(s)
- Hannah Pyo
- Department of Chemistry, Sungkyunkwan University (SKKU), Suwon 440-746, Korea.
| | - Cho Yeon Lee
- Department of Chemistry, Sungkyunkwan University (SKKU), Suwon 440-746, Korea.
| | - Daehee Kim
- Department of Chemistry, Sungkyunkwan University (SKKU), Suwon 440-746, Korea.
| | - Gyuhee Kim
- Department of Biological Sciences, Sungkyunkwan University (SKKU), Suwon 440-746, Korea.
| | - Sangho Lee
- Department of Biological Sciences, Sungkyunkwan University (SKKU), Suwon 440-746, Korea.
| | - Wan Soo Yun
- Department of Chemistry, Sungkyunkwan University (SKKU), Suwon 440-746, Korea.
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Wagner BD, Sontag MK, Harris JK, Miller JI, Morrow L, Robertson CE, Stephens M, Poindexter BB, Abman SH, Mourani PM. Airway Microbial Community Turnover Differs by BPD Severity in Ventilated Preterm Infants. PLoS One 2017; 12:e0170120. [PMID: 28129336 PMCID: PMC5271346 DOI: 10.1371/journal.pone.0170120] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 12/29/2016] [Indexed: 12/19/2022] Open
Abstract
Preterm birth exposes the developing lung to an environment with direct exposure to bacteria, often facilitated by endotracheal intubation. Despite evidence linking bacterial infections to the pathogenesis of bronchopulmonary dysplasia (BPD), systematic studies of airway microbiota are limited. The objective was to identify specific patterns of the early respiratory tract microbiome from tracheal aspirates of mechanically ventilated preterm infants that are associated with the development and severity of BPD. Infants with gestational age ≤34 weeks, and birth weight 500-1250g were prospectively enrolled. Mechanically ventilated infants had tracheal aspirate samples collected at enrollment, 7, 14, and 21 days of age. BPD was determined by modified NIH criteria with oxygen reduction tests; infants without BPD were excluded due to low numbers. Aspirates were processed for bacterial identification by 16S rRNA sequencing, and bacterial load by qPCR. Cross-sectional analysis was performed using 7 day samples and longitudinal analysis was performed from subjects with at least 2 aspirates. Microbiome analysis was performed on tracheal aspirates from 152 infants (51, 49, and 52 with mild, moderate, and severe BPD, respectively). Seventy-nine of the infants were included in the cross-sectional analysis and 94 in the longitudinal. Shannon Diversity, bacterial load, and relative abundance of individual taxa were not strongly associated with BPD status. Longitudinal analysis revealed that preterm infants who eventually developed severe BPD exhibited greater bacterial community turnover with age, acquired less Staphylococcus in the first days after birth, and had higher initial relative abundance of Ureaplasma. In conclusion, longitudinal changes in the airway microbial communities of mechanically ventilated preterm infants may be associated with BPD severity, whereas cross-sectional analysis of airway ecology at 7 days of age did not reveal an association with BPD severity. Further evaluation is necessary to determine whether the observed longitudinal changes are causal or in response to clinical management or other factors that lead to BPD.
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Affiliation(s)
- Brandie D. Wagner
- Department of Biostatistics, Colorado School of Public Health, University of Colorado, Aurora, Colorado, United States of America
- Section of Pulmonary, Department of Pediatrics, School of Medicine, University of Colorado, Aurora, Colorado, United States of America
| | - Marci K. Sontag
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, Colorado, United States of America
| | - J. Kirk Harris
- Section of Pulmonary, Department of Pediatrics, School of Medicine, University of Colorado, Aurora, Colorado, United States of America
| | - Joshua I. Miller
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Lindsey Morrow
- Department of Biostatistics, Colorado School of Public Health, University of Colorado, Aurora, Colorado, United States of America
| | - Charles E. Robertson
- Section of Infectious Disease, Department of Medicine, School of Medicine, University of Colorado, Aurora, Colorado, United States of America
| | - Mark Stephens
- Section of Pulmonary, Department of Pediatrics, School of Medicine, University of Colorado, Aurora, Colorado, United States of America
| | - Brenda B. Poindexter
- Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Steven H. Abman
- Section of Pulmonary, Department of Pediatrics, School of Medicine, University of Colorado, Aurora, Colorado, United States of America
- The Pediatric Heart-Lung Center, Department of Pediatrics, School of Medicine, University of Colorado, Aurora, Colorado, United States of America
| | - Peter M. Mourani
- The Pediatric Heart-Lung Center, Department of Pediatrics, School of Medicine, University of Colorado, Aurora, Colorado, United States of America
- Section of Critical Care Medicine, Department of Pediatrics, School of Medicine, University of Colorado, Aurora, Colorado, United States of America
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Microbiome in the pathogenesis of cystic fibrosis and lung transplant-related disease. Transl Res 2017; 179:84-96. [PMID: 27559681 DOI: 10.1016/j.trsl.2016.07.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 07/26/2016] [Accepted: 07/27/2016] [Indexed: 01/01/2023]
Abstract
Significant advances in culture-independent methods have expanded our knowledge about the diversity of the lung microbial environment. Complex microorganisms and microbial communities can now be identified in the distal airways in a variety of respiratory diseases, including cystic fibrosis (CF) and the posttransplantation lung. Although there are significant methodologic concerns about sampling the lung microbiome, several studies have now shown that the microbiome of the lower respiratory tract is distinct from the upper airway. CF is a disease characterized by chronic airway infections that lead to significant morbidity and mortality. Traditional culture-dependent methods have identified a select group of pathogens that cause exacerbations in CF, but studies using bacterial 16S rRNA gene-based microarrays have shown that the CF microbiome is an intricate and dynamic bacterial ecosystem, which influences both host immune health and disease pathogenesis. These microbial communities can shift with external influences, including antibiotic exposure. In addition, there have been a number of studies suggesting a link between the gut microbiome and respiratory health in CF. Compared with CF, there is significantly less knowledge about the microbiome of the transplanted lung. Risk factors for bronchiolitis obliterans syndrome, one of the leading causes of death, include microbial infections. Lung transplant patients have a unique lung microbiome that is different than the pretransplanted microbiome and changes with time. Understanding the host-pathogen interactions in these diseases may suggest targeted therapies and improve long-term survival in these patients.
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Laguna TA, Wagner BD, Williams CB, Stevens MJ, Robertson CE, Welchlin CW, Moen CE, Zemanick ET, Harris JK. Airway Microbiota in Bronchoalveolar Lavage Fluid from Clinically Well Infants with Cystic Fibrosis. PLoS One 2016; 11:e0167649. [PMID: 27930727 PMCID: PMC5145204 DOI: 10.1371/journal.pone.0167649] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 11/17/2016] [Indexed: 12/15/2022] Open
Abstract
Background Upper airway cultures guide the identification and treatment of lung pathogens in infants with cystic fibrosis (CF); however, this may not fully reflect the spectrum of bacteria present in the lower airway. Our objectives were to characterize the airway microbiota using bronchoalveolar lavage fluid (BALF) from asymptomatic CF infants during the first year of life and to investigate the relationship between BALF microbiota, standard culture and clinical characteristics. Methods BALF, nasopharyngeal (NP) culture and infant pulmonary function testing data were collected at 6 months and one year of age during periods of clinical stability from infants diagnosed with CF by newborn screening. BALF was analyzed for total bacterial load by qPCR and for bacterial community composition by 16S ribosomal RNA sequencing. Clinical characteristics and standard BALF and NP culture results were recorded over five years of longitudinal follow-up. Results 12 BALF samples were collected from 8 infants with CF. Streptococcus, Burkholderia, Prevotella, Haemophilus, Porphyromonas, and Veillonella had the highest median relative abundance in infant CF BALF. Two of the 3 infants with repeat BALF had changes in their microbial communities over six months (Morisita-Horn diversity index 0.36, 0.38). Although there was excellent percent agreement between standard NP and BALF cultures, these techniques did not routinely detect all bacteria identified by sequencing. Conclusions BALF in asymptomatic CF infants contains complex microbiota, often missed by traditional culture of airway secretions. Anaerobic bacteria are commonly found in the lower airways of CF infants.
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Affiliation(s)
- Theresa A. Laguna
- Department of Pediatrics, University of Minnesota School of Medicine and the Masonic Children’s Hospital, Minneapolis, Minnesota, United States of America
- * E-mail:
| | - Brandie D. Wagner
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Cynthia B. Williams
- Department of Pediatrics, University of Minnesota School of Medicine and the Masonic Children’s Hospital, Minneapolis, Minnesota, United States of America
| | - Mark J. Stevens
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Charles E. Robertson
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Cole W. Welchlin
- Department of Pediatrics, University of Minnesota School of Medicine and the Masonic Children’s Hospital, Minneapolis, Minnesota, United States of America
| | - Catherine E. Moen
- Department of Pediatrics, University of Minnesota School of Medicine and the Masonic Children’s Hospital, Minneapolis, Minnesota, United States of America
| | - Edith T. Zemanick
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Jonathan K. Harris
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
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Biomarkers for cystic fibrosis drug development. J Cyst Fibros 2016; 15:714-723. [PMID: 28215711 DOI: 10.1016/j.jcf.2016.10.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 10/12/2016] [Indexed: 12/14/2022]
Abstract
PURPOSE To provide a review of the status of biomarkers in cystic fibrosis drug development, including regulatory definitions and considerations, a summary of biomarkers in current use with supportive data, current gaps, and future needs. METHODS Biomarkers are considered across several areas of CF drug development, including cystic fibrosis transmembrane conductance regulator modulation, infection, and inflammation. RESULTS Sweat chloride, nasal potential difference, and intestinal current measurements have been standardized and examined in the context of multicenter trials to quantify CFTR function. Detection and quantification of pathogenic bacteria in CF respiratory cultures (e.g.: Pseudomonas aeruginosa) are commonly used in early phase antimicrobial clinical trials, and to monitor safety of therapeutic interventions. Sputum (e.g.: neutrophil elastase, myeloperoxidase, calprotectin) and blood biomarkers (e.g.: C reactive protein, calprotectin, serum amyloid A) have had variable success in detecting response to inflammatory treatments. CONCLUSIONS Biomarkers are used throughout the drug development process in CF, and many have been used in early phase clinical trials to provide proof of concept, detect drug bioactivity, and inform dosing for later-phase studies. Advances in the precision of current biomarkers, and the identification of new biomarkers with 'omics-based technologies, are needed to accelerate CF drug development.
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Clinical Insights into Pulmonary Exacerbations in Cystic Fibrosis from the Microbiome. What Are We Missing? Ann Am Thorac Soc 2016; 12 Suppl 2:S207-11. [PMID: 26595741 DOI: 10.1513/annalsats.201506-353aw] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pulmonary exacerbations account for much of the decrease in lung function and consequently most of the morbidity and mortality in patients with cystic fibrosis. These events are driven by an acute inflammatory response to infection. Recent technological advancements in molecular profiling techniques have allowed for a proliferation of microbiome studies of the lower airways of patients with cystic fibrosis. But these methods may not provide a comprehensive and unbiased measure of the lung microbiota in these patients and molecular profiles do not always translate to quantitative microbiology. Furthermore, these studies have not yet been able to provide much in the way of mechanistic insights into exacerbations or to guide patient therapy. We propose a model in which pulmonary exacerbations may be driven by an active subpopulation of the lung microbiota, which may represent only a small portion of the microbiota measured in a clinical sample. Methodology should be focused on the ultimate goal, which is to use the best available approaches to provide accurate quantitative measures of the microbiome to inform clinical decisions and provide rapid assessment of treatment efficacy. These strategies would be relevant to other chronic lung diseases such as chronic obstructive pulmonary disease and neutrophilic asthma.
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Molecular Identification of Staphylococcus aureus in Airway Samples from Children with Cystic Fibrosis. PLoS One 2016; 11:e0147643. [PMID: 26808658 PMCID: PMC4726467 DOI: 10.1371/journal.pone.0147643] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 01/06/2016] [Indexed: 02/05/2023] Open
Abstract
Background Staphylococcus aureus is a common and significant pathogen in cystic fibrosis. We sought to determine if quantitative PCR (qPCR) and 16S rRNA gene sequencing could provide a rapid, culture-independent approach to the identification of S. aureus airway infections. Methods We examined the sensitivity and specificity of two qPCR assays, targeting the femA and 16S rRNA gene, using culture as the gold standard. In addition, 16S rRNA gene sequencing to identify S. aureus directly from airway samples was evaluated. DNA extraction was performed with and without prior enzymatic digestion. Results 87 samples [42 oropharyngeal (OP) and 45 expectorated sputum (ES)] were analyzed. 59 samples (68%) cultured positive for S. aureus. Using standard extraction techniques, sequencing had the highest sensitivity for S. aureus detection (85%), followed by FemA qPCR (52%) and 16SrRNA qPCR (34%). For all assays, sensitivity was higher from ES samples compared to OP swabs. Specificity of the qPCR assays was 100%, but 21.4% for sequencing due to detection of S. aureus in low relative abundance from culture negative samples. Enzymatic digestion increased the sensitivity of qPCR assays, particularly for OP swabs. Conclusion Sequencing had a high sensitivity for S. aureus, but low specificity. While femA qPCR had higher sensitivity than 16S qPCR for detection of S. aureus, neither assay was as sensitive as sequencing. The significance of S. aureus detection with low relative abundance by sequencing in culture-negative specimens is not clear.
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Wu SJ, Cheng YS, Liu HL, Wang HH, Huang HL. Global transcriptional expression in ovarian follicles from Tsaiya ducks (Anas platyrhynchos) with a high-fertilization rate. Theriogenology 2016; 85:1439-1445.e1. [PMID: 26861074 DOI: 10.1016/j.theriogenology.2016.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 11/06/2015] [Accepted: 01/04/2016] [Indexed: 02/07/2023]
Abstract
Novel candidates for biomarkers of a high-fertilization rate were identified here through global transcriptional profiling of ovarian follicles. Some other differentially expressed candidate genes were first noted to influence animal reproduction in our previous cDNA microarray analysis and are now recognized as markers for marker-assisted selection. In the present study, we compared gene expression in ovarian follicles from animals with high- and low-fertilization rates using an oligonucleotide array. On the basis of a fold change of greater than 1.2 and less than -1.2, a difference of >100 Affymetrix arbitrary units between the two groups, and a P value of less than 0.05, 47 genes were found to be associated with fertilization rate. GOEAST and MetaCore software were further used to identify the functional categories of genes that were differentially expressed. Then, we focused on three interesting genes associated with a high-fertilization rate: one of these genes was discovered to participate in signaling pathways of fertilization, and two genes take roles in lipid metabolism. An oligonucleotide array showed that the levels of orthodenticle homeobox 2 (OTX2) and lecithin:cholesterol acyltransferase (LCAT) gene expression were 1.62-fold and 1.95-fold higher in the high-fertilization rate group than in the low-fertilization rate group, respectively (P < 0.05). The level of apolipoprotein A-I (APOA1) gene expression was also higher in the high-fertilization rate group, with a difference of 2.31-fold (P < 0.05). The data were validated through quantitative polymerase chain reaction analysis. These results confirm the usefulness of the array technique and data mining methods in the discovery of new biomarkers and add knowledge to our understanding of the factors affecting fertilization rates in ovarian follicles.
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Affiliation(s)
- Shyh-Jong Wu
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yu-Shin Cheng
- Livestock Research Institute, Council of Agriculture, Tainan, Taiwan
| | - Hsiao-Lung Liu
- Livestock Research Institute, Council of Agriculture, Tainan, Taiwan
| | - Hsing-He Wang
- Department of Post-Modern Agriculture, MingDao University, Changhua, Taiwan
| | - Hsiu-Lin Huang
- Department of Post-Modern Agriculture, MingDao University, Changhua, Taiwan.
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35
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Culture-Based and Culture-Independent Bacteriologic Analysis of Cystic Fibrosis Respiratory Specimens. J Clin Microbiol 2015; 54:613-9. [PMID: 26699705 DOI: 10.1128/jcm.02299-15] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 12/17/2015] [Indexed: 01/10/2023] Open
Abstract
Cystic fibrosis (CF) is characterized by chronic infection and inflammation of the airways. In vitro culture of select bacterial species from respiratory specimens has been used to guide antimicrobial therapy in CF for the past few decades. More recently, DNA sequence-based, culture-independent approaches have been used to assess CF airway microbiology, although the role that these methods will (or should) have in routine microbiologic analysis of CF respiratory specimens is unclear. We performed DNA sequence analyses to detect bacterial species in 945 CF sputum samples that had been previously analyzed by selective CF culture. We determined the concordance of results based on culture and sequence analysis, highlighting the comparison of the results for the most prevalent genera. Although overall prevalence rates were comparable between the two methods, results varied by genus. While sequence analysis was more likely to detect Achromobacter, Stenotrophomonas, and Burkholderia, it was less likely to detect Staphylococcus. Streptococcus spp. were rarely reported in culture results but were the most frequently detected species by sequence analysis. A variety of obligate and facultative anaerobic species, not reported by culture, was also detected with high prevalence by sequence analysis. Sequence analysis indicated that in a considerable proportion of samples, taxa not reported by selective culture constituted a relatively high proportion of the total bacterial load, suggesting that routine CF culture may underrepresent significant segments of the bacterial communities inhabiting CF airways.
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Assessment of airway microbiota and inflammation in cystic fibrosis using multiple sampling methods. Ann Am Thorac Soc 2015; 12:221-9. [PMID: 25474078 DOI: 10.1513/annalsats.201407-310oc] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
RATIONALE Oropharyngeal (OP) swabs and induced sputum (IS) are used for airway bacteria surveillance in nonexpectorating children with cystic fibrosis (CF). Molecular analyses of these airway samples detect complex microbial communities. However, the optimal noninvasive sampling approach for microbiota analyses and the clinical relevance of microbiota, particularly its relationship to airway inflammation, is not well characterized. OBJECTIVES The goals of this study were to compare molecular analyses of concurrently collected saliva, OP swabs, IS, and expectorated sputum (ES) from children with CF and to determine the association between microbiota, lung function, and airway inflammation. METHODS Saliva, OP swabs, IS, and ES were collected from 16 children with CF. Spirometry was performed. MEASUREMENTS AND MAIN RESULTS Respiratory and saliva samples (n = 61) were sequenced for bacterial microbial communities, and total and CF-specific bacterial quantitative PCR assays were performed. Airway samples underwent conventional culture for CF-specific pathogens. Neutrophil elastase, IL-1β, IL-1ra, IL-6, Il-8, TNF-α, and vascular endothelial growth factor were measured in ES and IS. Sequencing results from individual subjects were similar across samples, with greater between-subject than within-subject variation. However, Pseudomonas and Staphylococcus were detected in higher relative abundance from lower airways (ES and IS) compared with paired upper airway samples (OP and saliva). Pseudomonas, Staphylococcus, and Enterobacteriaceae correlated with increased airway inflammation. Divergence between microbiota in upper airway compared with lower airway samples, indicating greater differences between communities, was associated with increased sputum neutrophil elastase. CONCLUSIONS Bacteria detected in IS samples resemble ES samples, whereas OP samples may underrepresent bacteria associated with airway inflammation. Divergence of lower airway communities from upper airway was associated with airway inflammation and may portend disease progression.
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Caverly LJ, Zhao J, LiPuma JJ. Cystic fibrosis lung microbiome: opportunities to reconsider management of airway infection. Pediatr Pulmonol 2015; 50 Suppl 40:S31-8. [PMID: 26335953 DOI: 10.1002/ppul.23243] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 06/09/2015] [Accepted: 06/16/2015] [Indexed: 11/06/2022]
Abstract
The importance of infection in the pathogenesis of cystic fibrosis (CF) lung disease has been long recognized, and the use of antibiotics targeting bacteria identified in cultures of respiratory specimens has played a critical role in improving outcomes for individuals with CF. Over the past ∼15 years, the use of culture-independent methods to assess airway microbiology in CF has revealed complex and dynamic CF airway bacterial communities. Recent areas of investigation of the CF lung microbiome have included exploring how bacterial community structures change over time, particularly with respect to disease progression or pulmonary exacerbation, and in response to antibiotic therapies. This review will discuss what has been learned from these studies as well as how these findings offer opportunities to further refine management of CF airway infection.
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Affiliation(s)
- Lindsay J Caverly
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan
| | - Jiangchao Zhao
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan
| | - John J LiPuma
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan
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Three clinically distinct chronic pediatric airway infections share a common core microbiota. Ann Am Thorac Soc 2015; 11:1039-48. [PMID: 24597615 DOI: 10.1513/annalsats.201312-456oc] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
RATIONALE DNA-based microbiological studies are moving beyond studying healthy human microbiota to investigate diverse infectious diseases, including chronic respiratory infections, such as those in the airways of people with cystic fibrosis (CF) and non-CF bronchiectasis. The species identified in the respiratory secretion microbiota from such patients can be classified into those that are common and abundant among similar subjects (core) versus those that are infrequent and rare (satellite). This categorization provides a vital foundation for investigating disease pathogenesis and improving therapy. However, whether the core microbiota of people with different respiratory diseases, which are traditionally associated with specific culturable pathogens, are unique or shared with other chronic infections of the lower airways is not well studied. Little is also known about how these chronic infection microbiota change from childhood to adulthood. OBJECTIVES We sought to compare the core microbiota in respiratory specimens from children and adults with different chronic lung infections. METHODS We used bacterial 16S rRNA gene pyrosequencing, phylogenetic analysis, and ecological statistical tools to compare the core microbiota in respiratory samples from three cohorts of symptomatic children with clinically distinct airway diseases (protracted bacterial bronchitis, bronchiectasis, CF), and from four healthy children. We then compared the core pediatric respiratory microbiota with those in samples from adults with bronchiectasis and CF. MEASUREMENTS AND MAIN RESULTS All three pediatric disease cohorts shared strikingly similar core respiratory microbiota that differed from adult CF and bronchiectasis microbiota. The most common species in pediatric disease cohort samples were also detected in those from healthy children. The adult CF and bronchiectasis microbiota also differed from each other, suggesting common early infection airway microbiota that diverge by adulthood. The shared core pediatric microbiota included both traditional pathogens and many species not routinely identified by standard culture. CONCLUSIONS Our results indicate that these clinically distinct chronic airway infections share common early core microbiota, which are likely shaped by natural aspiration and impaired clearance of the same airway microbes, but that disease-specific characteristics select for divergent microbiota by adulthood. Longitudinal and interventional studies will be required to define the relationships between microbiota, treatments, and disease progression.
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Harris JK, Fang R, Wagner BD, Choe HN, Kelly CJ, Schroeder S, Moore W, Stevens MJ, Yeckes A, Amsden K, Kagalwalla AF, Zalewski A, Hirano I, Gonsalves N, Henry LN, Masterson JC, Robertson CE, Leung DY, Pace NR, Ackerman SJ, Furuta GT, Fillon SA. Esophageal microbiome in eosinophilic esophagitis. PLoS One 2015; 10:e0128346. [PMID: 26020633 PMCID: PMC4447451 DOI: 10.1371/journal.pone.0128346] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 04/26/2015] [Indexed: 01/07/2023] Open
Abstract
Objective The microbiome has been implicated in the pathogenesis of a number of allergic and inflammatory diseases. The mucosa affected by eosinophilic esophagitis (EoE) is composed of a stratified squamous epithelia and contains intraepithelial eosinophils. To date, no studies have identified the esophageal microbiome in patients with EoE or the impact of treatment on these organisms. The aim of this study was to identify the esophageal microbiome in EoE and determine whether treatments change this profile. We hypothesized that clinically relevant alterations in bacterial populations are present in different forms of esophagitis. Design In this prospective study, secretions from the esophageal mucosa were collected from children and adults with EoE, Gastroesophageal Reflux Disease (GERD) and normal mucosa using the Esophageal String Test (EST). Bacterial load was determined using quantitative PCR. Bacterial communities, determined by 16S rRNA gene amplification and 454 pyrosequencing, were compared between health and disease. Results Samples from a total of 70 children and adult subjects were examined. Bacterial load was increased in both EoE and GERD relative to normal subjects. In subjects with EoE, load was increased regardless of treatment status or degree of mucosal eosinophilia compared with normal. Haemophilus was significantly increased in untreated EoE subjects as compared with normal subjects. Streptococcus was decreased in GERD subjects on proton pump inhibition as compared with normal subjects. Conclusions Diseases associated with mucosal eosinophilia are characterized by a different microbiome from that found in the normal mucosa. Microbiota may contribute to esophageal inflammation in EoE and GERD.
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Affiliation(s)
- J. Kirk Harris
- Division of Pulmonology, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Rui Fang
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, CO, United States of America
| | - Brandie D. Wagner
- Division of Pulmonology, University of Colorado School of Medicine, Aurora, CO, United States of America
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, CO, United States of America
| | - Ha Na Choe
- Digestive Health Institute, Section of Pediatric Gastroenterology, Hepatology and Nutrition, Children’s Hospital Colorado, Gastrointestinal Eosinophilic Diseases Program, Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Caleb J. Kelly
- Digestive Health Institute, Section of Pediatric Gastroenterology, Hepatology and Nutrition, Children’s Hospital Colorado, Gastrointestinal Eosinophilic Diseases Program, Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Shauna Schroeder
- Digestive Health Institute, Section of Pediatric Gastroenterology, Hepatology and Nutrition, Children’s Hospital Colorado, Gastrointestinal Eosinophilic Diseases Program, Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Wendy Moore
- Digestive Health Institute, Section of Pediatric Gastroenterology, Hepatology and Nutrition, Children’s Hospital Colorado, Gastrointestinal Eosinophilic Diseases Program, Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Mark J. Stevens
- Division of Pulmonology, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Alyson Yeckes
- Digestive Health Institute, Section of Pediatric Gastroenterology, Hepatology and Nutrition, Children’s Hospital Colorado, Gastrointestinal Eosinophilic Diseases Program, Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Katie Amsden
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Ann & Robert H. Lurie Children’s Hospital of Chicago and Northwestern University, Chicago, IL, United States of America
- Department of Pediatrics, John H. Stroger Hospital of Cook County, Chicago, IL, United States of America
| | - Amir F. Kagalwalla
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Ann & Robert H. Lurie Children’s Hospital of Chicago and Northwestern University, Chicago, IL, United States of America
- Department of Pediatrics, John H. Stroger Hospital of Cook County, Chicago, IL, United States of America
| | - Angelika Zalewski
- Department of Medicine, Division of Gastroenterology & Hepatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, United States of America
| | - Ikuo Hirano
- Department of Medicine, Division of Gastroenterology & Hepatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, United States of America
| | - Nirmala Gonsalves
- Department of Medicine, Division of Gastroenterology & Hepatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, United States of America
| | - Lauren N. Henry
- Digestive Health Institute, Section of Pediatric Gastroenterology, Hepatology and Nutrition, Children’s Hospital Colorado, Gastrointestinal Eosinophilic Diseases Program, Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Joanne C. Masterson
- Digestive Health Institute, Section of Pediatric Gastroenterology, Hepatology and Nutrition, Children’s Hospital Colorado, Gastrointestinal Eosinophilic Diseases Program, Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Charles E. Robertson
- Molecular Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
| | - Donald Y. Leung
- Department of Pediatrics, National Jewish Health, Denver, CO, United States of America
| | - Norman R. Pace
- Molecular Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
| | - Steven J. Ackerman
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Glenn T. Furuta
- Digestive Health Institute, Section of Pediatric Gastroenterology, Hepatology and Nutrition, Children’s Hospital Colorado, Gastrointestinal Eosinophilic Diseases Program, Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Sophie A. Fillon
- Digestive Health Institute, Section of Pediatric Gastroenterology, Hepatology and Nutrition, Children’s Hospital Colorado, Gastrointestinal Eosinophilic Diseases Program, Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, CO, United States of America
- * E-mail:
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Brukner I, Longtin Y, Oughton M, Forgetta V, Dascal A. Assay for estimating total bacterial load: relative qPCR normalisation of bacterial load with associated clinical implications. Diagn Microbiol Infect Dis 2015; 83:1-6. [PMID: 26008123 DOI: 10.1016/j.diagmicrobio.2015.04.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 04/03/2015] [Accepted: 04/20/2015] [Indexed: 12/26/2022]
Abstract
Relative microorganism abundance is a parameter describing biodiversity, referring to how common a bacterial species is within the total bacterial flora. Anal, rectal, skin, mucal, and respiratory swabs are typical clinical samples where knowledge of relative bacterial abundance might make distinction between asymptomatic carriers and symptomatic cases. Assays trying to measure total bacterial load are usually based on the amplification of universal segments of 16S rRNA genes. Previous assays were not adoptable to "direct" PCR protocols, and/or they were not compatible with hydrolysis-based detection. Using the latest summary of universal 16S sequence motifs present in literature and testing our design with 500 liquid and 50 formed stool samples, we illustrate the performance characteristics of a new 16S quantitative PCR (qPCR) assay, which addresses well-known technical problems, including a) positive priming reaction in the absence of intended target due to self-priming and/or mispriming of unintended targets; b) amplification bias due to nonoptimal primer/probe coverage; and c) too large amplicons for clinical qPCR. Stool swabs ranked into bins of different bacterial loads show significant correlation with threshold cycle values of our new assay. To the best of our knowledge, this is the first description of qPCR assay measuring individual differences of total bacterial load present in human stool.
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Affiliation(s)
- Ivan Brukner
- Medical Faculty, McGill University, Montreal, Quebec, Canada; SMBD-Jewish General Hospital, Montreal, Quebec, Canada.
| | - Yves Longtin
- Medical Faculty, McGill University, Montreal, Quebec, Canada; SMBD-Jewish General Hospital, Montreal, Quebec, Canada
| | - Matthew Oughton
- Medical Faculty, McGill University, Montreal, Quebec, Canada; SMBD-Jewish General Hospital, Montreal, Quebec, Canada
| | | | - Andre Dascal
- Medical Faculty, McGill University, Montreal, Quebec, Canada; SMBD-Jewish General Hospital, Montreal, Quebec, Canada
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Genetic Evidence of Vertical Transmission and Cycling of Yersinia ruckeri in Hatchery-Origin Fall Chinook Salmon Oncorhynchus tshawytscha. JOURNAL OF FISH AND WILDLIFE MANAGEMENT 2014. [DOI: 10.3996/012014-jfwm-010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Abstract
Enteric redmouth disease, caused by the bacterium Yersinia ruckeri, can be a severe problem in the culture of salmonid fishes, and can persist as a chronic infection within hatchery facilities for an indefinite amount of time ranging from months to years. Using a nested polymerase chain reaction (nPCR) assay and a real-time quantitative PCR (qPCR) assay, the prevalence of Y. ruckeri deoxyribonucleic acid (DNA) was documented across a single production cycle of fall Chinook salmon Oncorhynchus tshawytscha reared at a hatchery. Ovarian fluid from spawning female adults, unfertilized eggs, eyed eggs, sac fry, and juvenile fish all tested positive for Y. ruckeri DNA using both nPCR and qPCR assays. Presence of Y. ruckeri DNA in ovarian fluids and unfertilized eggs indicates that vertical transmission of the pathogen from females to their progeny is possible. Juvenile fish had the highest level of Y. ruckeri DNA at a log10-transformed level of 4.3 DNA copies per gram of kidney tissue. The limited mortality observed was attributed to handling and hatchery procedures during the study period and indicates that the low levels of the pathogen's DNA can persist without severe detrimental effects over the hatchery rearing cycle.
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Stoeva MK, Aris-Brosou S, Chételat J, Hintelmann H, Pelletier P, Poulain AJ. Microbial community structure in lake and wetland sediments from a high Arctic polar desert revealed by targeted transcriptomics. PLoS One 2014; 9:e89531. [PMID: 24594936 PMCID: PMC3940601 DOI: 10.1371/journal.pone.0089531] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 01/22/2014] [Indexed: 11/18/2022] Open
Abstract
While microbial communities play a key role in the geochemical cycling of nutrients and contaminants in anaerobic freshwater sediments, their structure and activity in polar desert ecosystems are still poorly understood, both across heterogeneous freshwater environments such as lakes and wetlands, and across sediment depths. To address this question, we performed targeted environmental transcriptomics analyses and characterized microbial diversity across three depths from sediment cores collected in a lake and a wetland, located on Cornwallis Island, NU, Canada. Microbial communities were characterized based on 16S rRNA and two functional gene transcripts: mcrA, involved in archaeal methane cycling and glnA, a bacterial housekeeping gene implicated in nitrogen metabolism. We show that methane cycling and overall bacterial metabolic activity are the highest at the surface of lake sediments but deeper within wetland sediments. Bacterial communities are highly diverse and structured as a function of both environment and depth, being more diverse in the wetland and near the surface. Archaea are mostly methanogens, structured by environment and more diverse in the wetland. McrA transcript analyses show that active methane cycling in the lake and wetland corresponds to distinct communities with a higher potential for methane cycling in the wetland. Methanosarcina spp., Methanosaeta spp. and a group of uncultured Archaea are the dominant methanogens in the wetland while Methanoregula spp. predominate in the lake.
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Affiliation(s)
| | - Stéphane Aris-Brosou
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada
| | - John Chételat
- Environment Canada, National Wildlife Research Centre, Ottawa, Ontario, Canada
| | - Holger Hintelmann
- Department of Chemistry, Trent University, Peterborough, Ontario, Canada
| | - Philip Pelletier
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
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Abstract
RATIONALE In persons with cystic fibrosis (CF), repeated exacerbations of pulmonary symptoms are associated with a progressive decline in lung function. Changes in the airway microbiota around the time of exacerbations are not well understood. OBJECTIVES To characterize changes in airway bacterial communities around the time of exacerbations and to identify predictors for these changes. METHODS DNA prepared from 68 paired baseline and exacerbation sputum samples collected from 28 patients with CF were subjected to barcoded 16S rRNA gene pyrosequencing. Bacterial density was calculated by quantitative PCR. MEASUREMENTS AND MAIN RESULTS Overall, significant differences in bacterial community diversity and bacterial density between baseline and exacerbation samples were not observed. However, considerable changes in community structures were observed in a subset of patients. In these patients, the dominant taxa and initial level of community diversity were significant predictors of the magnitude of community structure changes at exacerbation. Pseudomonas-dominant communities became more diverse at exacerbation compared with communities with other or no dominant species. The relative abundance of Gemella increased in 24 (83%) of 29 samples at exacerbation and was found to be the most discriminative genus between baseline and exacerbation samples. CONCLUSIONS The magnitude of changes in the CF lung microbiota around the time of exacerbation was found to be largely dependent on community diversity and composition at baseline. Certain genera appear to play important roles in driving change in airway bacterial community composition at exacerbation. Gemella might play a direct role in and/or be a biomarker for pulmonary exacerbation.
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Price KE, Hampton TH, Gifford AH, Dolben EL, Hogan DA, Morrison HG, Sogin ML, O’Toole GA. Unique microbial communities persist in individual cystic fibrosis patients throughout a clinical exacerbation. MICROBIOME 2013; 1:27. [PMID: 24451123 PMCID: PMC3971630 DOI: 10.1186/2049-2618-1-27] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 10/04/2013] [Indexed: 05/21/2023]
Abstract
BACKGROUND Cystic fibrosis (CF) is caused by inherited mutations in the cystic fibrosis transmembrane conductance regulator gene and results in a lung environment that is highly conducive to polymicrobial infection. Over a lifetime, decreasing bacterial diversity and the presence of Pseudomonas aeruginosa in the lung are correlated with worsening lung disease. However, to date, no change in community diversity, overall microbial load or individual microbes has been shown to correlate with the onset of an acute exacerbation in CF patients. We followed 17 adult CF patients throughout the course of clinical exacerbation, treatment and recovery, using deep sequencing and quantitative PCR to characterize spontaneously expectorated sputum samples RESULTS We identified approximately 170 bacterial genera, 12 of which accounted for over 90% of the total bacterial load across all patient samples. Genera abundant in any single patient sample tended to be detectable in most samples. We found that clinical stages could not be distinguished by absolute Pseudomonas aeruginosa load, absolute total bacterial load or the relative abundance of any individual genus detected, or community diversity. Instead, we found that the microbial structure of each patient's sputum microbiome was distinct and resilient to exacerbation and antibiotic treatment. CONCLUSION Consistent with previously reported sputum microbiome studies we found that total and relative abundance of genera at the population level were remarkably stable for individual patients regardless of clinical status. Patient-by-patient analysis of diversity and relative abundance of each individual genus revealed a complex microbial landscape and highlighted the difficulty of identifying a universal microbial signature of exacerbation. Overall, at the genus level, we find no evidence of a microbial signature of clinical stage.
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Affiliation(s)
- Katherine E Price
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Thomas H Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Alex H Gifford
- Dartmouth-Hitchcock Medical Center, Section of Pulmonary and Critical Care Medicine, Lebanon 03756, New Hampshire, USA
| | - Emily L Dolben
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Deborah A Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Hilary G Morrison
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Mitchell L Sogin
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - George A O’Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
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Burns JL, Rolain JM. Culture-based diagnostic microbiology in cystic fibrosis: can we simplify the complexity? J Cyst Fibros 2013; 13:1-9. [PMID: 24094376 DOI: 10.1016/j.jcf.2013.09.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 09/16/2013] [Accepted: 09/17/2013] [Indexed: 10/26/2022]
Abstract
Cystic fibrosis (CF) diagnostic microbiology has evolved from a focus on Staphylococcus aureus as primary pathogen to identification of the contribution of Pseudomonas aeruginosa and other non-fermenting gram negatives; studies of the lung microbiome have added new complexity. This review summarizes state-of-the art culture methods and makes recommendations for addition of non-culture based methods in the diagnostic laboratory. Plating on selective media is recommended, with organism identification by matrix assisted laser desorption-time of flight mass spectroscopy and real-time polymerase chain reaction (PCR) supplanting both biochemical identification and other less accurate and more time-consuming molecular methods. Conventional antibiotic susceptibility testing, possibly at less frequent intervals, remains the standard but more CF-relevant methods may arise in the future. There is a role for direct identification of organisms in clinical samples using quantitative real-time PCR, next generation sequencing, and metagenomic studies for the re-examination of samples that do not yield traditional CF pathogens.
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Affiliation(s)
- Jane L Burns
- Seattle Children's Hospital, University of Washington School of Medicine, Department of Pediatrics, Division of Infectious Diseases, Seattle, WA, USA.
| | - Jean-Marc Rolain
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), CNRS-IRD UMR 6236, Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
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Assessment of persistence of Bartonella henselae in Ctenocephalides felis. Appl Environ Microbiol 2013; 79:7439-44. [PMID: 24056468 DOI: 10.1128/aem.02598-13] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bartonella henselae (Rhizobiales: Bartonellaceae) is a Gram-negative fastidious bacterium of veterinary and zoonotic importance. The cat flea Ctenocephalides felis (Siphonaptera: Pulicidae) is the main recognized vector of B. henselae, and transmission among cats and humans occurs mainly through infected flea feces. The present study documents the use of a quantitative molecular approach to follow the daily kinetics of B. henselae within the cat flea and its excreted feces after exposure to infected blood for 48 h in an artificial membrane system. B. henselae DNA was detected in both fleas and feces for the entire life span of the fleas (i.e., 12 days) starting from 24 h after initiation of the blood meal.
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Tunney MM, Einarsson GG, Wei L, Drain M, Klem ER, Cardwell C, Ennis M, Boucher RC, Wolfgang MC, Elborn JS. Lung microbiota and bacterial abundance in patients with bronchiectasis when clinically stable and during exacerbation. Am J Respir Crit Care Med 2013; 187:1118-26. [PMID: 23348972 PMCID: PMC3734618 DOI: 10.1164/rccm.201210-1937oc] [Citation(s) in RCA: 220] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 01/17/2013] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Characterization of bacterial populations in infectious respiratory diseases will provide improved understanding of the relationship between the lung microbiota, disease pathogenesis, and treatment outcomes. OBJECTIVES To comprehensively define lung microbiota composition during stable disease and exacerbation in patients with bronchiectasis. METHODS Sputum was collected from patients when clinically stable and before and after completion of antibiotic treatment of exacerbations. Bacterial abundance and community composition were analyzed using anaerobic culture and 16S rDNA pyrosequencing. MEASUREMENTS AND MAIN RESULTS In clinically stable patients, aerobic and anaerobic bacteria were detected in 40 of 40 (100%) and 33 of 40 (83%) sputum samples, respectively. The dominant organisms cultured were Pseudomonas aeruginosa (n = 10 patients), Haemophilus influenzae (n = 12), Prevotella (n = 18), and Veillonella (n = 13). Pyrosequencing generated more than 150,000 sequences, representing 113 distinct microbial taxa; the majority of observed community richness resulted from taxa present in low abundance with similar patterns of phyla distribution in clinically stable patients and patients at the onset of exacerbation. After treatment of exacerbation, there was no change in total (P = 0.925), aerobic (P = 0.917), or anaerobic (P = 0.683) load and only a limited shift in community composition. Agreement for detection of bacteria by culture and pyrosequencing was good for aerobic bacteria such as P. aeruginosa (κ = 0.84) but poorer for other genera including anaerobes. Lack of agreement was largely due to bacteria being detected by pyrosequencing but not by culture. CONCLUSIONS A complex microbiota is present in the lungs of patients with bronchiectasis and remains stable through treatment of exacerbations, suggesting that changes in microbiota composition do not account for exacerbations.
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Affiliation(s)
- Michael M Tunney
- Cystic Fibrosis and Airways Microbiology Research Group, School of Medicine, Dentistry, and Biomedical Sciences, Queen's University Belfast, Belfast, United Kingdom.
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Phenotypic and genotypic properties of Microbacterium yannicii, a recently described multidrug resistant bacterium isolated from a lung transplanted patient with cystic fibrosis in France. BMC Microbiol 2013; 13:97. [PMID: 23642186 PMCID: PMC3655929 DOI: 10.1186/1471-2180-13-97] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 04/30/2013] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Cystic fibrosis (CF) lung microbiota consists of diverse species which are pathogens or opportunists or have unknown pathogenicity. Here we report the full characterization of a recently described multidrug resistant bacterium, Microbacterium yannicii, isolated from a CF patient who previously underwent lung transplantation. RESULTS Our strain PS01 (CSUR-P191) is an aerobic, rod shaped, non-motile, yellow pigmented, gram positive, oxidase negative and catalase positive bacterial isolate. Full length 16S rRNA gene sequence showed 98.8% similarity with Microbacterium yannicii G72T type strain, which was previously isolated from Arabidopsis thaliana. The genome size is 3.95Mb, with an average G+C content of 69.5%. In silico DNA-DNA hybridization analysis between our Microbacterium yannicii PS01isolate in comparison with Microbacterium testaceum StLB037 and Microbacterium laevaniformans OR221 genomes revealed very weak relationship with only 28% and 25% genome coverage, respectively. Our strain, as compared to the type strain, was resistant to erythromycin because of the presence of a new erm 43 gene encoding a 23S rRNA N-6-methyltransferase in its genome which was not detected in the reference strain. Interestingly, our patient received azithromycin 250 mg daily for bronchiolitis obliterans syndrome for more than one year before the isolation of this bacterium. CONCLUSIONS Although significance of isolating this bacterium remains uncertain in terms of clinical evolution, this bacterium could be considered as an opportunistic human pathogen as previously reported for other species in this genus, especially in immunocompromised patients.
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Zemanick ET, Harris JK, Wagner BD, Robertson CE, Sagel SD, Stevens MJ, Accurso FJ, Laguna TA. Inflammation and airway microbiota during cystic fibrosis pulmonary exacerbations. PLoS One 2013; 8:e62917. [PMID: 23646159 PMCID: PMC3639911 DOI: 10.1371/journal.pone.0062917] [Citation(s) in RCA: 138] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 03/27/2013] [Indexed: 12/22/2022] Open
Abstract
Background Pulmonary exacerbations (PEx), frequently associated with airway infection and inflammation, are the leading cause of morbidity in cystic fibrosis (CF). Molecular microbiologic approaches detect complex microbiota from CF airway samples taken during PEx. The relationship between airway microbiota, inflammation, and lung function during CF PEx is not well understood. Objective To determine the relationships between airway microbiota, inflammation, and lung function in CF subjects treated for PEx. Methods Expectorated sputum and blood were collected and lung function testing performed in CF subjects during early (0–3d.) and late treatment (>7d.) for PEx. Sputum was analyzed by culture, pyrosequencing of 16S rRNA amplicons, and quantitative PCR for total and specific bacteria. Sputum IL-8 and neutrophil elastase (NE); and circulating C-reactive protein (CRP) were measured. Results Thirty-seven sputum samples were collected from 21 CF subjects. At early treatment, lower diversity was associated with high relative abundance (RA) of Pseudomonas (r = −0.67, p<0.001), decreased FEV1% predicted (r = 0.49, p = 0.03) and increased CRP (r = −0.58, p = 0.01). In contrast to Pseudomonas, obligate and facultative anaerobic genera were associated with less inflammation and higher FEV1. With treatment, Pseudomonas RA and P. aeruginosa by qPCR decreased while anaerobic genera showed marked variability in response. Change in RA of Prevotella was associated with more variability in FEV1 response to treatment than Pseudomonas or Staphylococcus. Conclusions Anaerobes identified from sputum by sequencing are associated with less inflammation and higher lung function compared to Pseudomonas at early exacerbation. CF PEx treatment results in variable changes of anaerobic genera suggesting the need for larger studies particularly of patients without traditional CF pathogens.
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Affiliation(s)
- Edith T Zemanick
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America.
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