1
|
Rumpf C, Lange J, Schwartbeck B, Kahl BC. Staphylococcus aureus and Cystic Fibrosis-A Close Relationship. What Can We Learn from Sequencing Studies? Pathogens 2021; 10:pathogens10091177. [PMID: 34578208 PMCID: PMC8466686 DOI: 10.3390/pathogens10091177] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 01/13/2023] Open
Abstract
Staphylococcus aureus is next to Pseudomonas aeruginosa the most isolated pathogen from the airways of cystic fibrosis (CF) patients, who are often infected by a dominant S. aureus clone for extended periods. To be able to persist, the pathogen has to adapt to the hostile niche of the airways to counteract host defence, antibiotic therapy and the competition with coinfecting pathogens. S. aureus is equipped with many virulence factors including adhesins, toxins that are localized on the chromosome, on plasmids or are phage-related. S. aureus is especially versatile and adaptation and evolution of the pathogen occurs by the acquisition of new genes by horizontal gene transfer (HGT), changes in nucleotides (single nucleotide variations, SNVs) that can cause a selective advantage for the bacteria and become fixed in subpopulations. Methicillin-resistant S. aureus are a special threat to CF patients due to the more severe lung disease occurring in infected patients. Today, with decreasing costs for sequencing, more and more studies using S. aureus isolates cultured from CF patients are being published, which use whole genome sequencing (WGS), multilocus sequence typing (MLST) or spa-sequence typing (spa-typing) to follow the population dynamics of S. aureus, elucidate the underlying mechanisms of phenotypic variants, newly acquired resistance or adaptation to the host response in this particular niche. In the first part of this review, an introduction to the genetic make-up and the pathogenesis of S. aureus with respect to CF is provided. The second part presents an overview of recent studies and their findings using genotypic methods such as single or multilocus sequencing and whole genome sequencing, which identify factors contributing to the adaptation of S. aureus and its evolution in the airways of individuals with CF.
Collapse
|
2
|
Menetrey Q, Sorlin P, Jumas-Bilak E, Chiron R, Dupont C, Marchandin H. Achromobacter xylosoxidans and Stenotrophomonas maltophilia: Emerging Pathogens Well-Armed for Life in the Cystic Fibrosis Patients' Lung. Genes (Basel) 2021; 12:genes12050610. [PMID: 33919046 PMCID: PMC8142972 DOI: 10.3390/genes12050610] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/06/2021] [Accepted: 04/19/2021] [Indexed: 02/07/2023] Open
Abstract
In patients with cystic fibrosis (CF), the lung is a remarkable ecological niche in which the microbiome is subjected to important selective pressures. An inexorable colonization by bacteria of both endogenous and environmental origin is observed in most patients, leading to a vicious cycle of infection–inflammation. In this context, long-term colonization together with competitive interactions among bacteria can lead to over-inflammation. While Pseudomonas aeruginosa and Staphylococcus aureus, the two pathogens most frequently identified in CF, have been largely studied for adaptation to the CF lung, in the last few years, there has been a growing interest in emerging pathogens of environmental origin, namely Achromobacter xylosoxidans and Stenotrophomonas maltophilia. The aim of this review is to gather all the current knowledge on the major pathophysiological traits, their supporting mechanisms, regulation and evolutionary modifications involved in colonization, virulence, and competitive interactions with other members of the lung microbiota for these emerging pathogens, with all these mechanisms being major drivers of persistence in the CF lung. Currently available research on A. xylosoxidans complex and S. maltophilia shows that these emerging pathogens share important pathophysiological features with well-known CF pathogens, making them important members of the complex bacterial community living in the CF lung.
Collapse
Affiliation(s)
- Quentin Menetrey
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, 34093 Montpellier, France; (Q.M.); (P.S.)
| | - Pauline Sorlin
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, 34093 Montpellier, France; (Q.M.); (P.S.)
| | - Estelle Jumas-Bilak
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, Department d’Hygiène Hospitalière, CHU Montpellier, 34093 Montpellier, France; (E.J.-B.); (C.D.)
| | - Raphaël Chiron
- HydroSciences Montpellier, Université de Montpellier, CNRS, IRD, Centre de Ressources et de Compétences de la Mucoviscidose, CHU de Montpellier, 34093 Montpellier, France;
| | - Chloé Dupont
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, Department d’Hygiène Hospitalière, CHU Montpellier, 34093 Montpellier, France; (E.J.-B.); (C.D.)
| | - Hélène Marchandin
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 34093 Nîmes, France
- UMR 5151 HydroSciences Montpellier, Equipe Pathogènes Hydriques Santé Environnements, U.F.R. des Sciences Pharmaceutiques et Biologiques, Université de Montpellier, 15, Avenue Charles Flahault, BP 14491, CEDEX 5, 34093 Montpellier, France
- Correspondence:
| |
Collapse
|
3
|
Harris TM, Price EP, Sarovich DS, Nørskov-Lauritsen N, Beissbarth J, Chang AB, Smith-Vaughan HC. Comparative genomic analysis identifies X-factor (haemin)-independent Haemophilus haemolyticus: a formal re-classification of ' Haemophilus intermedius'. Microb Genom 2020; 6. [PMID: 31860436 PMCID: PMC7067038 DOI: 10.1099/mgen.0.000303] [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] [Indexed: 01/19/2023] Open
Abstract
The heterogeneous and highly recombinogenic genus Haemophilus comprises several species, some of which are pathogenic to humans. All share an absolute requirement for blood-derived factors during growth. Certain species, such as the pathogen Haemophilus influenzae and the commensal Haemophilus haemolyticus, are thought to require both haemin (X-factor) and nicotinamide adenine dinucleotide (NAD, V-factor), whereas others, such as the informally classified 'Haemophilus intermedius subsp. intermedius', and Haemophilus parainfluenzae, only require V-factor. These differing growth requirements are commonly used for species differentiation, although a number of studies are now revealing issues with this approach. Here, we perform large-scale phylogenomics of 240 Haemophilus spp. genomes, including five 'H. intermedius' genomes generated in the current study, to reveal that strains of the 'H. intermedius' group are in fact haemin-independent H. haemolyticus (hiHh). Closer examination of these hiHh strains revealed that they encode an intact haemin biosynthesis pathway, unlike haemin-dependent H. haemolyticus and H. influenzae, which lack most haemin biosynthesis genes. Our results suggest that the common ancestor of modern-day H. haemolyticus and H. influenzae lost key haemin biosynthesis loci, likely as a consequence of specialized adaptation to otorhinolaryngeal and respiratory niches during their divergence from H. parainfluenzae. Genetic similarity analysis demonstrated that the haemin biosynthesis loci acquired in the hiHh lineage were likely laterally transferred from a H. parainfluenzae ancestor, and that this event probably occurred only once in hiHh. This study further challenges the validity of phenotypic methods for differentiating among Haemophilus species, and highlights the need for whole-genome sequencing for accurate characterization of species within this taxonomically challenging genus.
Collapse
Affiliation(s)
- Tegan M Harris
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia
| | - Erin P Price
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia.,Child Health Division, Menzies School of Health Research, Darwin, NT, Australia
| | - Derek S Sarovich
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia.,Child Health Division, Menzies School of Health Research, Darwin, NT, Australia
| | | | - Jemima Beissbarth
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia
| | - Anne B Chang
- Department of Respiratory and Sleep Medicine, Queensland Children's Hospital, Brisbane, QLD, Australia.,Child Health Division, Menzies School of Health Research, Darwin, NT, Australia
| | - Heidi C Smith-Vaughan
- School of Medicine, Griffith University, Gold Coast, QLD, Australia.,Child Health Division, Menzies School of Health Research, Darwin, NT, Australia
| |
Collapse
|
4
|
Isler B, Kidd TJ, Stewart AG, Harris P, Paterson DL. Achromobacter Infections and Treatment Options. Antimicrob Agents Chemother 2020; 64:e01025-20. [PMID: 32816734 PMCID: PMC7577122 DOI: 10.1128/aac.01025-20] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Achromobacter is a genus of nonfermenting Gram-negative bacteria under order Burkholderiales Although primarily isolated from respiratory tract of people with cystic fibrosis, Achromobacter spp. can cause a broad range of infections in hosts with other underlying conditions. Their rare occurrence and ever-changing taxonomy hinder defining their clinical features, risk factors for acquisition and adverse outcomes, and optimal treatment. Achromobacter spp. are intrinsically resistant to several antibiotics (e.g., most cephalosporins, aztreonam, and aminoglycosides), and are increasingly acquiring resistance to carbapenems. Carbapenem resistance is mainly caused by multidrug efflux pumps and metallo-β-lactamases, which are not expected to be overcome by new β-lactamase inhibitors. Among the other new antibiotics, cefiderocol, and eravacycline were used as salvage therapy for a limited number of patients with Achromobacter infections. In this article, we aim to give an overview of the antimicrobial resistance in Achromobacter species, highlighting the possible place of new antibiotics in their treatment.
Collapse
Affiliation(s)
- Burcu Isler
- University of Queensland, Faculty of Medicine, UQ Center for Clinical Research, Brisbane, Australia
| | - Timothy J Kidd
- Central Microbiology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
- University of Queensland, Faculty of Science, School of Chemistry and Molecular Biosciences, Brisbane, Australia
| | - Adam G Stewart
- University of Queensland, Faculty of Medicine, UQ Center for Clinical Research, Brisbane, Australia
- Infectious Diseases Unit, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Patrick Harris
- University of Queensland, Faculty of Medicine, UQ Center for Clinical Research, Brisbane, Australia
- Central Microbiology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - David L Paterson
- University of Queensland, Faculty of Medicine, UQ Center for Clinical Research, Brisbane, Australia
- Infectious Diseases Unit, Royal Brisbane and Women's Hospital, Brisbane, Australia
| |
Collapse
|
5
|
Genomic information on Stenotrophomonas maltophilia ST264 isolated from a cystic fibrosis pediatric patient in Brazil. Braz J Microbiol 2019; 51:1125-1127. [PMID: 31858443 DOI: 10.1007/s42770-019-00214-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/11/2019] [Indexed: 10/25/2022] Open
Abstract
Stenotrophomonas maltophilia is one of the Gram-negative bacilli most frequently found in the airways of cystic fibrosis patients. This opportunistic pathogen is intrinsically multidrug-resistant, and therefore, its treatment presents a challenge. The genetic characterization of S. maltophilia is largely unknown, especially from those strains that colonize/infect the airways of cystic fibrosis patients. This work reports the draft genome sequences of three S. maltophilia isolates recovered from the sputum of a cystic fibrosis pediatric patient in Southeast Brazil. Several resistance- and virulence-related genes were detected. Furthermore, one intact phage and one incomplete prophage region were also identified in all strains. Multilocus sequence typing showed that all strains belonged to a new sequence type (ST264). Interestingly, all S. maltophilia strains were genetically identical, showing persistence for at least 16 months. To our knowledge, this is the first report of S. maltophilia draft genome sequences obtained from a cystic fibrosis pediatric patient in Brazil.
Collapse
|
6
|
Proteomic identification of Axc, a novel beta-lactamase with carbapenemase activity in a meropenem-resistant clinical isolate of Achromobacter xylosoxidans. Sci Rep 2018; 8:8181. [PMID: 29802257 PMCID: PMC5970244 DOI: 10.1038/s41598-018-26079-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 05/04/2018] [Indexed: 01/24/2023] Open
Abstract
The development of antibiotic resistance during treatment is a threat to patients and their environment. Insight in the mechanisms of resistance development is important for appropriate therapy and infection control. Here, we describe how through the application of mass spectrometry-based proteomics, a novel beta-lactamase Axc was identified as an indicator of acquired carbapenem resistance in a clinical isolate of Achromobacter xylosoxidans. Comparative proteomic analysis of consecutively collected susceptible and resistant isolates from the same patient revealed that high Axc protein levels were only observed in the resistant isolate. Heterologous expression of Axc in Escherichia coli significantly increased the resistance towards carbapenems. Importantly, direct Axc mediated hydrolysis of imipenem was demonstrated using pH shift assays and 1H-NMR, confirming Axc as a legitimate carbapenemase. Whole genome sequencing revealed that the susceptible and resistant isolates were remarkably similar. Together these findings provide a molecular context for the fast development of meropenem resistance in A. xylosoxidans during treatment and demonstrate the use of mass spectrometric techniques in identifying novel resistance determinants.
Collapse
|
7
|
Vinuesa P, Ochoa-Sánchez LE, Contreras-Moreira B. GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the Genus Stenotrophomonas. Front Microbiol 2018; 9:771. [PMID: 29765358 PMCID: PMC5938378 DOI: 10.3389/fmicb.2018.00771] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/05/2018] [Indexed: 12/17/2022] Open
Abstract
The massive accumulation of genome-sequences in public databases promoted the proliferation of genome-level phylogenetic analyses in many areas of biological research. However, due to diverse evolutionary and genetic processes, many loci have undesirable properties for phylogenetic reconstruction. These, if undetected, can result in erroneous or biased estimates, particularly when estimating species trees from concatenated datasets. To deal with these problems, we developed GET_PHYLOMARKERS, a pipeline designed to identify high-quality markers to estimate robust genome phylogenies from the orthologous clusters, or the pan-genome matrix (PGM), computed by GET_HOMOLOGUES. In the first context, a set of sequential filters are applied to exclude recombinant alignments and those producing anomalous or poorly resolved trees. Multiple sequence alignments and maximum likelihood (ML) phylogenies are computed in parallel on multi-core computers. A ML species tree is estimated from the concatenated set of top-ranking alignments at the DNA or protein levels, using either FastTree or IQ-TREE (IQT). The latter is used by default due to its superior performance revealed in an extensive benchmark analysis. In addition, parsimony and ML phylogenies can be estimated from the PGM. We demonstrate the practical utility of the software by analyzing 170 Stenotrophomonas genome sequences available in RefSeq and 10 new complete genomes of Mexican environmental S. maltophilia complex (Smc) isolates reported herein. A combination of core-genome and PGM analyses was used to revise the molecular systematics of the genus. An unsupervised learning approach that uses a goodness of clustering statistic identified 20 groups within the Smc at a core-genome average nucleotide identity (cgANIb) of 95.9% that are perfectly consistent with strongly supported clades on the core- and pan-genome trees. In addition, we identified 16 misclassified RefSeq genome sequences, 14 of them labeled as S. maltophilia, demonstrating the broad utility of the software for phylogenomics and geno-taxonomic studies. The code, a detailed manual and tutorials are freely available for Linux/UNIX servers under the GNU GPLv3 license at https://github.com/vinuesa/get_phylomarkers. A docker image bundling GET_PHYLOMARKERS with GET_HOMOLOGUES is available at https://hub.docker.com/r/csicunam/get_homologues/, which can be easily run on any platform.
Collapse
Affiliation(s)
- Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Luz E Ochoa-Sánchez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Bruno Contreras-Moreira
- Estación Experimental de Aula Dei - Consejo Superior de Investigaciones Científicas, Zaragoza, Spain.,Fundación Agencia Aragonesa para la Investigacion y el Desarrollo (ARAID), Zaragoza, Spain
| |
Collapse
|
8
|
Garbacz K, Piechowicz L, Podkowik M, Mroczkowska A, Empel J, Bania J. Emergence and spread of worldwide Staphylococcus aureus clones among cystic fibrosis patients. Infect Drug Resist 2018; 11:247-255. [PMID: 29503574 PMCID: PMC5826090 DOI: 10.2147/idr.s153427] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background The aim of this study was to assess the relatedness of molecular types of Staphylococcus aureus isolates colonizing cystic fibrosis (CF) patients with their antimicrobial resistance and prevalence of toxin genes. Methods A total of 215 isolates from the airways of 107 patients with CF were tested for spa and SCCmec type, antimicrobial resistance and carriage of toxin genes. Results t015, t084, t091, t700 and t002 were the largest group (approximately 25%) among all 69 identified spa types. Five new spa types, t14286, t14287, t14288, t14289 and t14290, were identified and registered. Isolates from CF patients were clustered into 11 multi-locus sequence typing clonal complexes, with CC30, CC22, CC97, CC45, CC15 and CC5 being the most frequent ones. Twelve (5.6%) methicillin-resistant S. aureus (MRSA) isolates and 102 (47.7%) multidrug-resistant isolates were identified, along with three SCCmec types (I, III and V). All isolates (both MRSA and methicillin-sensitive S. aureus) were Panton–Valentine leucocidin-negative, and 56.7% harbored egc genes. This was the first study documenting the presence of ST398-V-t571 livestock-associated MRSA in a European patient with CF. Conclusion These findings imply that individuals with CF can also be colonized with animal-related ST398 MRSA, and justify constant monitoring of staphylococcal colonization and identification of epidemic S. aureus clones in this group.
Collapse
Affiliation(s)
- Katarzyna Garbacz
- Department of Oral Microbiology, Medical University of Gdansk, Gdansk, Poland
| | - Lidia Piechowicz
- Department of Medical Microbiology, Medical University of Gdansk, Gdansk, Poland
| | - Magdalena Podkowik
- Department of Food Hygiene and Consumer Health Protection, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
| | - Aneta Mroczkowska
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | - Joanna Empel
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | - Jacek Bania
- Department of Food Hygiene and Consumer Health Protection, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
| |
Collapse
|
9
|
Garg N, Wang M, Hyde E, da Silva RR, Melnik AV, Protsyuk I, Bouslimani A, Lim YW, Wong R, Humphrey G, Ackermann G, Spivey T, Brouha SS, Bandeira N, Lin GY, Rohwer F, Conrad DJ, Alexandrov T, Knight R, Dorrestein PC. Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung. Cell Host Microbe 2017; 22:705-716.e4. [PMID: 29056429 DOI: 10.1016/j.chom.2017.10.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 07/12/2017] [Accepted: 09/14/2017] [Indexed: 12/12/2022]
Abstract
Our understanding of the spatial variation in the chemical and microbial makeup of an entire human organ remains limited, in part due to the size and heterogeneity of human organs and the complexity of the associated metabolome and microbiome. To address this challenge, we developed a workflow to enable the cartography of metabolomic and microbiome data onto a three-dimensional (3D) organ reconstruction built off radiological images. This enabled the direct visualization of the microbial and chemical makeup of a human lung from a cystic fibrosis patient. We detected host-derived molecules, microbial metabolites, medications, and region-specific metabolism of medications and placed it in the context of microbial distributions in the lung. Our tool further created browsable maps of a 3D microbiome/metabolome reconstruction map on a radiological image of a human lung and forms an interactive resource for the scientific community.
Collapse
Affiliation(s)
- Neha Garg
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mingxun Wang
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Embriette Hyde
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ricardo R da Silva
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ivan Protsyuk
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yan Wei Lim
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Richard Wong
- Department of Pathology, University of California, San Diego Health, San Diego, CA 92103, USA
| | - Greg Humphrey
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Timothy Spivey
- Department of Radiology, University of California, San Diego Health, San Diego, CA 92103, USA
| | - Sharon S Brouha
- Department of Radiology, University of California, San Diego Health, San Diego, CA 92103, USA
| | - Nuno Bandeira
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Grace Y Lin
- Department of Pathology, University of California, San Diego Health, San Diego, CA 92103, USA
| | - Forest Rohwer
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Douglas J Conrad
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Theodore Alexandrov
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany.
| | - Rob Knight
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
10
|
Esposito A, Pompilio A, Bettua C, Crocetta V, Giacobazzi E, Fiscarelli E, Jousson O, Di Bonaventura G. Evolution of Stenotrophomonas maltophilia in Cystic Fibrosis Lung over Chronic Infection: A Genomic and Phenotypic Population Study. Front Microbiol 2017; 8:1590. [PMID: 28894437 PMCID: PMC5581383 DOI: 10.3389/fmicb.2017.01590] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/04/2017] [Indexed: 12/18/2022] Open
Abstract
Stenotrophomonas maltophilia has been recognized as an emerging multi-drug resistant opportunistic pathogen in cystic fibrosis (CF) patients. We report a comparative genomic and phenotypic analysis of 91 S. maltophilia strains from 10 CF patients over a 12-year period. Draft genome analyses included in silico Multi-Locus Sequence Typing (MLST), Single-Nucleotide Polymorphisms (SNPs), and pangenome characterization. Growth rate, biofilm formation, motility, mutation frequency, in vivo virulence, and in vitro antibiotic susceptibility were determined and compared with population structure over time. The population consisted of 20 different sequence types (STs), 11 of which are new ones. Pangenome and SNPs data showed that this population is composed of three major phylogenetic lineages. All patients were colonized by multiple STs, although most of them were found in a single patient and showed persistence over years. Only few phenotypes showed some correlation with population phylogenetic structure. Our results show that S. maltophilia adaptation to CF lung is associated with consistent genotypic and phenotypic heterogeneity. Stenotrophomonas maltophilia infecting multiple hosts likely experiences different selection pressures depending on the host environment. The poor genotype-phenotype correlation suggests the existence of complex regulatory mechanisms that need to be explored in order to better design therapeutic strategies.
Collapse
Affiliation(s)
- Alfonso Esposito
- Centre for Integrative Biology, University of TrentoTrento, Italy
| | - Arianna Pompilio
- Department of Medical, Oral, and Biotechnological Sciences, Center of Excellence on Aging and Translational Medicine (CeSI-MeT), Università degli Studi "G. d'Annunzio" Chieti-PescaraChieti, Italy
| | - Clotilde Bettua
- Centre for Integrative Biology, University of TrentoTrento, Italy
| | - Valentina Crocetta
- Department of Medical, Oral, and Biotechnological Sciences, Center of Excellence on Aging and Translational Medicine (CeSI-MeT), Università degli Studi "G. d'Annunzio" Chieti-PescaraChieti, Italy
| | | | - Ersilia Fiscarelli
- Laboratory of Cystic Fibrosis Microbiology, "Bambino Gesù" HospitalRome, Italy
| | - Olivier Jousson
- Centre for Integrative Biology, University of TrentoTrento, Italy
| | - Giovanni Di Bonaventura
- Department of Medical, Oral, and Biotechnological Sciences, Center of Excellence on Aging and Translational Medicine (CeSI-MeT), Università degli Studi "G. d'Annunzio" Chieti-PescaraChieti, Italy
| |
Collapse
|
11
|
Price EP, Harris TM, Spargo J, Nosworthy E, Beissbarth J, Chang AB, Smith-Vaughan HC, Sarovich DS. Simultaneous identification of Haemophilus influenzae and Haemophilus haemolyticus using real-time PCR. Future Microbiol 2017; 12:585-593. [PMID: 28604066 DOI: 10.2217/fmb-2016-0215] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
AIM To design a highly specific and sensitive multiplex real-time PCR assay for the differentiation of the pathogen Haemophilus influenzae from its nonpathogenic near-neighbor Haemophilus haemolyticus. MATERIALS & METHODS A comparison of 380 Haemophilus spp. genomes was used to identify loci specific for each species. Novel PCR assays targeting H. haemolyticus (hypD) and H. influenzae (siaT) were designed. RESULTS & DISCUSSION PCR screening across 143 isolates demonstrated 100% specificity for hypD and siaT. These two assays were multiplexed with the recently described fucP assay for further differentiation among H. influenzae. CONCLUSION The triplex assay provides rapid, unambiguous, sensitive and highly specific genotyping results for the simultaneous detection of hypD and siaT, including fucose-positive H. influenzae (fucP), in a single PCR.
Collapse
Affiliation(s)
- Erin P Price
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia.,Centre for Animal Health Innovation, Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Tegan M Harris
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia
| | - Jessie Spargo
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia
| | - Elizabeth Nosworthy
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia
| | - Jemima Beissbarth
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia
| | - Anne B Chang
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia
| | | | - Derek S Sarovich
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia.,Centre for Animal Health Innovation, Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| |
Collapse
|
12
|
Prevalence and Outcomes of Achromobacter Species Infections in Adults with Cystic Fibrosis: a North American Cohort Study. J Clin Microbiol 2017; 55:2074-2085. [PMID: 28446570 DOI: 10.1128/jcm.02556-16] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 03/20/2017] [Indexed: 02/07/2023] Open
Abstract
Achromobacter species are increasingly being detected in cystic fibrosis (CF) patients, with an unclear epidemiology and impact. We studied a cohort of patients attending a Canadian adult CF clinic who had positive sputum cultures for Achromobacter species in the period from 1984 to 2013. Infection was categorized as transient or persistent (≥50% positive cultures for 1 year). Those with persistent infection were matched 2:1 with age-, sex-, and time-matched controls without a history of Achromobacter infection, and mixed-effects models were used to assess pulmonary exacerbation (PEx) frequency and lung function decline. Isolates from a biobank were retrospectively assessed, identified to the species level by nrdA sequencing, and genotyped using pulsed-field gel electrophoresis (PFGE). Thirty-four patients (11% of those in our clinic), with a median age of 24 years (interquartile range [IQR], 20.3 to 29.8 years), developed Achromobacter infection. Ten patients (29%) developed persistent infection. Persistence did not denote permanence, as most patients ultimately cleared infection, often after years. Patients were more likely to experience PEx at incident isolation than at prior or subsequent visits (odds ratio [OR], 2.7 [95% confidence interval {CI}, 1.2 to 6.7]; P = 0.03). Following persistent infection, there was no difference in annual lung function decline (-1.08% [95% CI, -2.73 to 0.57%] versus -2.74% [95% CI, -4.02 to 1.46%]; P = 0.12) or the odds of PEx (OR, 1.21 [95% CI, 0.45 to 3.28]; P = 0.70). Differential virulence among Achromobacter species was not observed, and no cases of transmission occurred. We demonstrated that incident Achromobacter infection was associated with a greater risk of PEx; however, neither transient nor chronic infection was associated with a worsened long-term prognosis. Large, multicenter studies are needed to clarify the clinical impact, natural history, and transmissibility of Achromobacter.
Collapse
|
13
|
Feigelman R, Kahlert CR, Baty F, Rassouli F, Kleiner RL, Kohler P, Brutsche MH, von Mering C. Sputum DNA sequencing in cystic fibrosis: non-invasive access to the lung microbiome and to pathogen details. MICROBIOME 2017; 5:20. [PMID: 28187782 PMCID: PMC5303297 DOI: 10.1186/s40168-017-0234-1] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 01/24/2017] [Indexed: 05/17/2023]
Abstract
BACKGROUND Cystic fibrosis (CF) is a life-threatening genetic disorder, characterized by chronic microbial lung infections due to abnormally viscous mucus secretions within airways. The clinical management of CF typically involves regular respiratory-tract cultures in order to identify pathogens and to guide treatment. However, culture-based methods can miss atypical or slow-growing microbes. Furthermore, the isolated microbes are often not classified at the strain level due to limited taxonomic resolution. RESULTS Here, we show that untargeted metagenomic sequencing of sputum DNA can provide valuable information beyond the possibilities of culture-based diagnosis. We sequenced the sputum of six CF patients and eleven control samples (including healthy subjects and chronic obstructive pulmonary disease patients) without prior depletion of human DNA or cell size selection, thus obtaining the most unbiased and comprehensive characterization of CF respiratory tract microbes to date. We present detailed descriptions of the CF and healthy lung microbiome, reconstruct near complete pathogen genomes, and confirm that the CF lungs consistently exhibit reduced microbial diversity. Crucially, the obtained genomic sequences enabled a detailed identification of the exact pathogen strain types, when analyzed in conjunction with existing multi-locus sequence typing databases. We also detected putative pathogenicity islands and indicators of antibiotic resistance, in good agreement with independent clinical tests. CONCLUSIONS Unbiased sputum metagenomics provides an in-depth profile of the lung pathogen microbiome, which is complementary to and more detailed than standard culture-based reporting. Furthermore, functional and taxonomic features of the dominant pathogens, including antibiotics resistances, can be deduced-supporting accurate and non-invasive clinical diagnosis.
Collapse
Affiliation(s)
- Rounak Feigelman
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Christian R. Kahlert
- Infectious Diseases and Hospital Epidemiology, Children’s Hospital of Eastern Switzerland, St. Gallen, Switzerland
- Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Florent Baty
- Pneumology and Sleep Medicine, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Frank Rassouli
- Pneumology and Sleep Medicine, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Rebekka L. Kleiner
- Pneumology and Sleep Medicine, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Philipp Kohler
- Pneumology and Sleep Medicine, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
- Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Martin H. Brutsche
- Pneumology and Sleep Medicine, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Christian von Mering
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Zurich, Switzerland
| |
Collapse
|
14
|
Liu Y, Zhang J, Zhong D, Ji L, Yang J, Phillips J, Ji Y. Characterization of Staphylococcus aureus isolates from pediatric patients with cystic fibrosis. World J Microbiol Biotechnol 2016; 32:162. [DOI: 10.1007/s11274-016-2122-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/08/2016] [Indexed: 01/15/2023]
|
15
|
Mika M, Korten I, Qi W, Regamey N, Frey U, Casaulta C, Latzin P, Hilty M. The nasal microbiota in infants with cystic fibrosis in the first year of life: a prospective cohort study. THE LANCET RESPIRATORY MEDICINE 2016; 4:627-635. [PMID: 27180018 DOI: 10.1016/s2213-2600(16)30081-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 04/04/2016] [Accepted: 04/14/2016] [Indexed: 12/20/2022]
Abstract
BACKGROUND Respiratory tract infections and subsequent airway inflammation occur early in the life of infants with cystic fibrosis. However, detailed information about the microbial composition of the respiratory tract in infants with this disorder is scarce. We aimed to undertake longitudinal in-depth characterisation of the upper respiratory tract microbiota in infants with cystic fibrosis during the first year of life. METHODS We did this prospective cohort study at seven cystic fibrosis centres in Switzerland. Between Feb 1, 2011, and May 31, 2014, we enrolled 30 infants with a diagnosis of cystic fibrosis. Microbiota characterisation was done with 16S rRNA gene pyrosequencing and oligotyping of nasal swabs collected every 2 weeks from the infants with cystic fibrosis. We compared these data with data for an age-matched cohort of 47 healthy infants. We additionally investigated the effect of antibiotic treatment on the microbiota of infants with cystic fibrosis. Statistical methods included regression analyses with a multivariable multilevel linear model with random effects to correct for clustering on the individual level. FINDINGS We analysed 461 nasal swabs taken from the infants with cystic fibrosis; the cohort of healthy infants comprised 872 samples. The microbiota of infants with cystic fibrosis differed compositionally from that of healthy infants (p=0·001). This difference was also found in exclusively antibiotic-naive samples (p=0·001). The disordering was mainly, but not solely, due to an overall increase in the mean relative abundance of Staphylococcaceae in infants with cystic fibrosis compared with healthy infants (multivariable linear regression model stratified by age and adjusted for season; second month: coefficient 16·2 [95% CI 0·6-31·9]; p=0·04; third month: 17·9 [3·3-32·5]; p=0·02; fourth month: 21·1 [7·8-34·3]; p=0·002). Oligotyping analysis enabled differentiation between Staphylococcus aureus and coagulase-negative Staphylococci. Whereas the analysis showed a decrease in S aureus at and after antibiotic treatment, coagulase-negative Staphylococci increased. INTERPRETATION Our study describes compositional differences in the microbiota of infants with cystic fibrosis compared with healthy controls, and disordering of the microbiota on antibiotic administration. Besides S aureus, coagulase-negative Staphylococci also contributed to the disordering identified in these infants. These findings are clinically important in view of the crucial role that bacterial pathogens have in the disease progression of cystic fibrosis in early life. Our findings could be used to inform future studies of the effect of antibiotic treatment on the microbiota in infants with cystic fibrosis, and could assist in the prevention of early disease progression in infants with this disorder. FUNDING Swiss National Science Foundation, Fondation Botnar, the Swiss Society for Cystic Fibrosis, and the Swiss Lung Association Bern.
Collapse
Affiliation(s)
- Moana Mika
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Insa Korten
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland; Division of Respiratory Medicine, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland; University Children's Hospital (UKBB), Basel, Switzerland
| | - Weihong Qi
- Functional Genomics Center, Swiss Federal Institute of Technology Zurich, University of Zurich, Zurich, Switzerland
| | - Nicolas Regamey
- Division of Respiratory Medicine, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland; Children's Hospital, Lucerne, Switzerland
| | - Urs Frey
- University Children's Hospital (UKBB), Basel, Switzerland
| | - Carmen Casaulta
- Division of Respiratory Medicine, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Philipp Latzin
- Division of Respiratory Medicine, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland; University Children's Hospital (UKBB), Basel, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland; Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland.
| | | |
Collapse
|