G Model
YPRRV-974; No. of Pages 3 Paediatric Respiratory Reviews xxx (2014) xxx–xxx
Contents lists available at ScienceDirect
Paediatric Respiratory Reviews
Emerging cystic fibrosis pathogens and the microbiome Eshwar Mahenthiralingam * Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff, UK
A R T I C L E I N F O
S U M M A R Y
Keywords: Cystic fibrosis Emerging pathogen Burkholderia Stenotrophomonas Achromobacter Pandorea Ralstonia Prevotella Streptococcus milleri group CF microbiome
Cystic fibrosis (CF) respiratory infection is characterised by the presence of typical human bacterial pathogens such as Pseudomonas aeruginosa, Haemophilus influenzae and Staphylococcus aureus. Less typical pathogens such as Burkholderia, Stenotrophomonas, Achromobacter, Pandorea and Ralstonia have emerged as problematic infections which are largely unique to people with CF. Using molecular methods, two groups of anaerobic bacteria Prevotella species and the Streptococcus milleri group have also recently been shown to be highly prevalent in CF sputum. Collectively, the diversity of microorganisms present in respiratory specimens has been designated the CF microbiome. The challenges posed by emerging CF pathogens and a microbiome-based view of CF infection are discussed in terms of their impact on clinical outcome, diagnosis and therapy. ß 2014 Elsevier Ltd. All rights reserved.
Microbial lung infection is the major cause of morbidity and mortality in cystic fibrosis [1], and routine therapy relies on the early detection, eradication or continuous treatment of respiratory infections [2]. Pseudomonas aeruginosa is the dominant pathogen infecting more than 70% of people with CF [1,2], however, our understanding of other bacterial infections associated with chronic lung disease has changed considerably in the last 20 years [2]. In addition to P. aeruginosa, well known human pathogens such as Haemophilus influenzae and Staphylococcus aureus also cause CF infection [2], and one could argue that because of the extensive study of these three bacterial species in relation to multiple human infections, we have a good understanding of their pathogenesis and multiple therapeutic options for their treatment. In contrast, emerging antibiotic resistant CF pathogens pose major clinical challenges that are largely unique to people with CF and have typically been less studied than P. aeruginosa. In the context of this review an emerging pathogen will be defined as any microbial infection that poses a challenge in terms of clinical diagnosis, therapy or outcome in CF. Non-tuberculous mycobacteria such as Mycobacterium abscessus, fungal and viral infections, all pose multiple problems for people with CF [2] and hence fit this definition, however, because of the unique complexity of issues each of the latter pose, they will not be explored in detail here. Two groups of bacteria, both multidrug resistant, will be discussed as emerging CF pathogens because they share a number of traits:
* Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Room 0.23 Main Building, Park Place, Cardiff, UK, CF10 3AT. Tel.: +44 (0)29 208 75875; fax: +44 (0)29 208 74305. E-mail address: [email protected].
(i) Multidrug resistant non-fermenting Gram negative (MDRNFGN) bacteria. Pathogens such as Burkholderia cepacia complex (Bcc), Burkholderia gladioli, Achromobacter species, Ralstonia mannitolilytica, Stenotrophomonas maltophilia, and Pandorea species are problematic emerging pathogens, cumulatively infecting approximately 25% of people with CF and being especially resistant to therapy in older CF people with severe lung disease [3–5]. (ii) Novel CF microbiome players. Analyses of CF sputa, using enhanced culture and molecular cultivation-independent techniques, have uncovered an unprecedented diversity of microorganisms, collectively known as the CF airway microbiome [6]. Two dominant CF microbiome players that are missed by routine culture are the Streptococcus milleri group (SMG; Gram positive, facultatively anaerobic bacteria) [7] and Prevotella species (Gram negative, obligate anaerobes) [8]. These bacteria persist in most CF people receiving antibiotic therapy for chronic infection [9], but we know very little about their association with lung disease and whether or how they should be treated. These problematic NFGN bacteria and novel CF microbiome players, Prevotella species and SMG bacteria, are emerging pathogens which constitute a health threat to people with CF because of the following issues. ANTIBIOTIC RESISTANCE NFGN bacteria comprise a pool of highly multidrug resistant CF pathogens [2]. With few effective antibiotics available, there is an
http://dx.doi.org/10.1016/j.prrv.2014.04.006 1526-0542/ß 2014 Elsevier Ltd. All rights reserved.
Please cite this article in press as: Mahenthiralingam E. Emerging cystic fibrosis pathogens and the microbiome. Paediatr. Respir. Rev. (2014), http://dx.doi.org/10.1016/j.prrv.2014.04.006
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urgent need to develop novel therapies to improve current treatments for these emerging CF pathogens and Gram-negative bacteria in general [10]. Despite extensive efforts to improve therapy by performing multiple combination bactericidal antibiotic susceptibility testing (MCBT) to aid antibiotic selection for B. cepacia complex, P. aeruginosa, S. maltophilia, or Achromobacter species, Aaron and colleagues [11] were not able to improve on clinical outcome in comparison to patients managed using standard culture and testing approaches. Little progression on how to treat CF patients with NGFN infection has been made since these studies. Both Prevotella and SMG bacteria are not eradicated by routine therapy and also demonstrate resistance to antibiotics commonly used to treat CF pulmonary infection. They are present in the airways at levels equivalent to that of established pathogens like P. aeruginosa [8,9] and can be considered as chronic infections in many patients, but are not specifically targeted for therapy. CHALLENGING CONVENTIONAL MICROBIOLOGY, IDENTIFICATION AND TAXONOMY All the NFGN species are often mis-identified by routine culture [2] or non-specifically reported as a ‘‘Gram Negative Rod?’’ prior to full species identification which may take additional time to resolve. Even more concerning, Prevotella and SMG group bacteria are not captured by routine diagnostic microbiology and to better understand their role in lung disease, accurate, quantitative diagnostics are urgently required [9,12]. While the taxonomy of Bcc has become much better understood [2], all the remaining emerging CF species show genetic diversity and the presence of novel species groups; the pathogenic significance of this diversity has not been fully established. For example, multiple novel species groups have been recently defined within the genus Achromobacter using a genomics-based multilocus sequence typing (MLST) scheme and polyphasic taxonomy [13,14]. The vast majority of CF isolates were historically reported as just one species ‘‘A. xylosoxidans’’ [15]. However, recent systematic analysis of Achromobacter species demonstrated a very different epidemiological picture with prevalence rates of A. xylosoxidans 42%, A. ruhlandii 23% and A. dolens 17% occurring in CF [15]. The taxonomy of the anaerobic species found in CF respiratory infection is also not fully defined. The SMG group comprise three species, S. constellatus, S. intermedius and S. aginosus, and all have been found in patients with CF [7]. The taxonomy of these SMG species was last reviewed in 1997 and it is highly likely further taxonomic diversity may be present in this historically defined group of streptococci [16]. Multiple Prevotella species have been cultivated from CF respiratory infections with P. melaninogenica, P. histicola and an unnamed species, Prevotella oral taxon 313, being most commonly cultivated in a study of 12 patients [17]. Overall, both Streptococcus and Prevotella have high species diversity as bacteria genera and further systematic analysis will be required to characterise the species most commonly associated with CF respiratory infection. PATHOGENIC POTENTIAL Bcc bacteria are established CF pathogens, with B. cenocepacia and B. multivorans, being the dominant CF species associated with transmission, clinical decline, loss of lung function and multiple cases of ‘‘cepacia syndrome’’ [2,18,19]. Cases of poor prognosis associated with B. gladioli CF infection have also been reported [20,21]. Furthermore, variation in outcome post-lung transplantation ranging from poor [21,22] to acceptable [23], has been reported in B. gladioli infected CF patients. Severe lung disease [24] and bacteraemia [25] have also been observed for Pandorea species infection in CF. The pathogenic potential of the remaining
emerging species, Achromobacter, Stenotrophomonas, Ralstonia, Prevotella and SMG, remains uncertain. A rise in the number of SMG group bacteria in CF sputum has been linked with the onset of acute pulmonary exacerbation [7]; however, there has been little further follow-up of the Streptococcus species even though it is very clear that they are frequently dominant and chronic microbiome players in CF [8,9,12]. What is also clear from the literature outside of CF is that instances of highly inflammatory and fatal infection have been reported for all these emerging CF pathogens.
TRANSMISSIBILITY AND EPIDEMIOLOGY The devastating infection control risk associated with Bcc bacteria is well known [2,26]. Elucidation of Bcc epidemiology [2,27] and improved molecular species identification methods [28,29] played a major role in designing international infection control measures for this species [30]. These interventions have successfully halted the large scale epidemic spread of Bcc bacteria in CF, particularly for B. cenocepacia [2,31]. However, the prevalence of certain species such as B. multivorans and the non-Bcc species, B. gladioli, appear to be rising, with the overall incidence of Bcc infection (3 to 4%) remaining stable in CF [2]. Although specific markers of transmission [32] and virulence [33,34] have been defined for the B. cenocepacia ET12 strain, no such markers have been identified for B. multivorans, other Bcc species, B. gladioli, Pandorea apista and A. xylosoxidans, despite reports of patient to patient spread [24,35–37]. Finally, antibiotic resistance, a known transmission risk factor for multiple pathogens, is a trait which links all emerging CF pathogens, flagging them as potential infection control risks in nosocomial settings.
CONTRA-INDICATION FOR LUNG TRANSPLANT AND EXCLUSION FROM CLINICAL TRIALS Lung transplantation remains the only therapeutic option for CF individuals with end-stage respiratory disease. B. cepacia complex bacteria, B. gladioli and Pandorea species bacteria are associated with poor outcome post-transplantation [21,22]. Access to this therapy is specifically restricted for B. cenocepacia infected individuals. Additional issues associated with CF patients culture positive for emerging CF pathogens includes the antibiotic resistance of these infections which hinders clinical management pre- and post-transplant and the frequent exclusion of infected patients from clinical trials.
ASSOCIATION WITH LOSS OF MICROBIAL DIVERSITY AND SEVERE LUNG DISEASE Recent sputum microbiome analysis of individuals with severe lung disease [3,5], and sampling of explanted lungs from adults with end-stage disease [4], has demonstrated that the microbial diversity of these CF infections is considerably reduced. The airways of these severely ill people with CF were dominated by a single pathogen such as P. aeruginosa or frequently one of the MDRNGFN emerging CF species, Burkholderia, Achromobacter or Stenotrophomonas [3–5]. Furthermore, various studies have reported a positive correlation between microbial diversity and lung function [5,38,39]. Overall, these data suggest that considerable interactions occur between members of the CF microbiome, administered anti-bacterial therapies, and the host immune system, which lead to either the reduced diversity during severe lung disease or stable, more diverse respiratory infections in healthy CF individuals.
Please cite this article in press as: Mahenthiralingam E. Emerging cystic fibrosis pathogens and the microbiome. Paediatr. Respir. Rev. (2014), http://dx.doi.org/10.1016/j.prrv.2014.04.006
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CONCLUSIONS AND PERSPECTIVE Burkholderia, Stenotrophomonas, Achromobacter, Pandorea, Ralstonia, Streptococcus and Prevotella species can all be considered as emerging bacterial pathogens in the context of CF respiratory infection. Their multi-antibiotic resistance and recalcitrance to clearance by routine therapy are shared traits which make them a clinical challenge. The linkage of MDR-NGFN species to the loss of microbial diversity seen in the respiratory microbiota of individuals with severe lung disease is a recent finding that raises many questions about how to optimally treat chronic lung infection. Given the cumulatively high prevalence of NFGN species and the almost uniform presence of Prevotella and SMG bacteria in individuals with chronic lung infection, all these emerging CF pathogens are worthy of further systematic study in the context of CF respiratory infection and the wider role of the lung microbiome. CONFLICT OF INTEREST The author has no conflict of interest to report.
[15] [16]
[17] [18]
[19]
[20] [21]
[22]
[23]
Acknowledgements [24]
EM thanks Alan Brown, Thomas Connor, Aras Kadioglu, Dervla Kenna, Julian Parkhill, Michael Tunney, Miguel Valvano and Craig Winstanley for their helpful comments on this text. EM acknowledges the European Cooperation in Science and Technology (COST) action BM1003 for promoting networking on microbial CF pathogens.
[25]
[26] [27]
References [1] O’Sullivan BP, Freedman SD. Cystic fibrosis. Lancet 2009;373:1891–904. [2] Lipuma JJ. The changing microbial epidemiology in cystic fibrosis. Clin Microbiol Rev 2010;23:299–323. [3] Blainey PC, Milla CE, Cornfield DN, Quake SR. Quantitative analysis of the human airway microbial ecology reveals a pervasive signature for cystic fibrosis. Sci Transl Med 2012;4. 153ra30. [4] Goddard AF, Staudinger BJ, Dowd SE, Joshi-Datar A, Wolcott RD, Aitken ML, et al. Direct sampling of cystic fibrosis lungs indicates that DNA-based analyses of upper-airway specimens can misrepresent lung microbiota. Proc Natl Acad Sci USA 2012;109:13769–74. [5] Zhao J, Schloss PD, Kalikin LM, Carmody LA, Foster BK, Petrosino JF, et al. Decade-long bacterial community dynamics in cystic fibrosis airways. Proc Natl Acad Sci USA 2012;109:5809–14. [6] Rogers GB, Daniels TW, Tuck A, Carroll MP, Connett GJ, David GJ, et al. Studying bacteria in respiratory specimens by using conventional and molecular microbiological approaches. BMC Pulm Med 2009;9:14. PubMed PMID: 19368727. [7] Sibley CD, Parkins MD, Rabin HR, Duan K, Norgaard JC, Surette MG. A polymicrobial perspective of pulmonary infections exposes an enigmatic pathogen in cystic fibrosis patients. Proc Natl Acad Sci USA 2008;105:15070–5. [8] Tunney MM, Field TR, Moriarty TF, Patrick S, Doering G, Muhlebach MS, et al. Detection of anaerobic bacteria in high numbers in sputum from patients with cystic fibrosis. Am J Respir Crit Care Med 2008;177:995–1001. [9] Tunney MM, Klem ER, Fodor AA, Gilpin DF, Moriarty TF, McGrath SJ, et al. Use of culture and molecular analysis to determine the effect of antibiotic treatment on microbial community diversity and abundance during exacerbation in patients with cystic fibrosis. Thorax 2011;66:579–84. [10] Talbot GH. The Antibiotic Development Pipeline for Multidrug-Resistant Gram-Negative Bacilli: Current and Future Landscapes. Infect Cont Hosp Ep 2010;31. S55–S8. [11] Aaron SD, Vandemheen KL, Ferris W, Fergusson D, Tullis E, Haase D, et al. Combination antibiotic susceptibility testing to treat exacerbations of cystic fibrosis associated with multiresistant bacteria: a randomised, double-blind, controlled clinical trial. Lancet 2005;366:463–71. [12] Sibley CD, Grinwis ME, Field TR, Eshaghurshan CS, Faria MM, Dowd SE, et al. Culture enriched molecular profiling of the cystic fibrosis airway microbiome. PloS one 2011;6:e22702. [13] Spilker T, Vandamme P, Lipuma JJ. A multilocus sequence typing scheme implies population structure and reveals several putative novel Achromobacter species. J Clin Microbiol 2012;50:3010–5. [14] Vandamme P, Moore ER, Cnockaert M, De Brandt E, Svensson-Stadler L, Houf K, et al. Achromobacter animicus sp. nov., Achromobacter mucicolens sp. nov.,
[28]
[29]
[30]
[31]
[32]
[33]
[34]
[35]
[36]
[37]
[38]
[39]
3
Achromobacter pulmonis sp. nov. and Achromobacter spiritinus sp. nov., from human clinical samples. Syst Appl Microbiol 2013;36:1–10. Spilker T, Vandamme P, LiPuma JJ. Identification and distribution of Achromobacter species in cystic fibrosis. J Cyst Fibros 2013;12:298–301. Jacobs JA. The ‘Streptococcus milleri’ group: Streptococcus anginosus, Streptococcus constellatus and Streptococcus intermedius. Rev Med Microbiol 1997;8: 73–80. Field TR, Sibley CD, Parkins MD, Rabin HR, Surette MG. The genus Prevotella in cystic fibrosis airways. Anaerobe 2010;16:337–44. Jones AM, Dodd ME, Govan JR, Barcus V, Doherty CJ, Morris J, et al. Burkholderia cenocepacia and Burkholderia multivorans: influence on survival in cystic fibrosis. Thorax 2004;59:948–51. Mahenthiralingam E, Vandamme P, Campbell ME, Henry DA, Gravelle AM, Wong LT, et al. Infection with Burkholderia cepacia complex genomovars in patients with cystic fibrosis: virulent transmissible strains of genomovar III can replace Burkholderia multivorans. Clin Infect Dis 2001;33:1469–75. Jones AM, Stanbridge TN, Isalska BJ, Dodd ME, Webb AK. Burkholderia gladioli: recurrent abscesses in a patient with cystic fibrosis. J Infect 2001;42:69–71. Quon BS, Reid JD, Wong P, Wilcox PG, Javer A, Wilson JM, et al. Burkholderia gladioli - a predictor of poor outcome in cystic fibrosis patients who receive lung transplants?. A case of locally invasive rhinosinusitis and persistent bacteremia in a 36-year-old lung transplant recipient with cystic fibrosis. Can Resp J 2011;18:e64–5. Murray S, Charbeneau J, Marshall BC, LiPuma JJ. Impact of Burkholderia infection on lung transplantation in cystic fibrosis. Am J Respir Crit Care Med 2008;178:363–71. Kennedy MP, Coakley RD, Donaldson SH, Aris RM, Hohneker K, Wedd JP, et al. Burkholderia gladioli: five year experience in a cystic fibrosis and lung transplantation center. J Cyst Fibros 2007;6:267–73. Jorgensen IM, Johansen HK, Frederiksen B, Pressler T, Hansen A, Vandamme P, et al. Epidemic spread of Pandorea apista, a new pathogen causing severe lung disease in cystic fibrosis patients. Pediatr Pulmonol 2003;36:439–46. Johnson LN, Han JY, Moskowitz SM, Burns JL, Qin X, Englund JA. Pandorea bacteremia in a cystic fibrosis patient with associated systemic illness. Pediatr Infect Dis J 2004;23:881–2. Saiman L, Siegel J. Infection control in cystic fibrosis. Clin Microbiol Rev 2004;17:57–71. Mahenthiralingam E, Baldwin A, Dowson CG. Burkholderia cepacia complex bacteria: opportunistic pathogens with important natural biology. J Appl Microbiol 2008;104:1539–51. Mahenthiralingam E, Bischof J, Byrne SK, Radomski C, Davies JE, Av-Gay Y, et al. DNA-Based diagnostic approaches for identification of Burkholderia cepacia complex, Burkholderia vietnamiensis, Burkholderia multivorans, Burkholderia stabilis, and Burkholderia cepacia genomovars I and III. J Clinical Microbiol 2000;38:3165–73. Turton JF, Arif N, Hennessy D, Kaufmann ME, Pitt TL. Revised approach for identification of isolates within the Burkholderia cepacia complex and description of clinical isolates not assigned to any of the known genomovars. J Clin Microbiol 2007;45:3105–8. Saiman L, MacDonald N, Burns JL, Hoiby N, Speert DP, Weber D. Infection control in cystic fibrosis: Practical recommendations for the hospital, clinic, and social settings. Am J Infect Control 2000;28:381–5. Drevinek P, Mahenthiralingam E. Burkholderia cenocepacia in cystic fibrosis: epidemiology and molecular mechanisms of virulence. Clin Microbiol Infect 2010;16:821–30. Mahenthiralingam E, Simpson DA, Speert DP. Identification and characterization of a novel DNA marker associated with epidemic Burkholderia cepacia strains recovered from patients with cystic fibrosis. J Clin Microbiol 1997;35:808–16. Baldwin A, Sokol PA, Parkhill J, Mahenthiralingam E. The Burkholderia cepacia epidemic strain marker is part of a novel genomic island encoding both virulence and metabolism-associated genes in Burkholderia cenocepacia. Infection and immunity 2004;72:1537–47. Sajjan U, Wu YJ, Kent G, Forstner J. Preferential adherence of cable-piliated Burkholderia cepacia to respiratory epithelia of CF knockout mice and human cystic fibrosis lung explants. J Med Microbiol 2000;49:875–85. Biddick R, Spilker T, Martin A, LiPuma JJ. Evidence of transmission of Burkholderia cepacia, Burkholderia multivorans and Burkholderia dolosa among persons with cystic fibrosis. FEMS Microbiol Lett 2003;228:57–62. Van Daele S, Verhelst R, Claeys G, Verschraegen G, Franckx H, Van Simaey L, et al. Shared genotypes of Achromobacter xylosoxidans strains isolated from patients at a cystic fibrosis rehabilitation center. J Clin Microbiol 2005;43: 2998–3002. Wilsher ML, Kolbe J, Morris AJ, Welch DF, Vandamme PAR. Nosocomial acquisition of Burkholderia gladioli in patients with cystic fibrosis. Am J Resp Crit Care 1999;160:374–5. Cox MJ, Allgaier M, Taylor B, Baek MS, Huang YJ, Daly RA, et al. Airway Microbiota and Pathogen Abundance in Age-Stratified Cystic Fibrosis Patients. Plos One 2010;5:e0011044. Klepac-Ceraj V, Lemon KP, Martin TR, Allgaier M, Kembel SW, Knapp AA, et al. Relationship between cystic fibrosis respiratory tract bacterial communities and age, genotype, antibiotics and Pseudomonas aeruginosa. Environ Microbiol 2010;12:1293–303.
Please cite this article in press as: Mahenthiralingam E. Emerging cystic fibrosis pathogens and the microbiome. Paediatr. Respir. Rev. (2014), http://dx.doi.org/10.1016/j.prrv.2014.04.006
YPRRV-974; No. of Pages 3 Paediatric Respiratory Reviews xxx (2014) xxx–xxx
Contents lists available at ScienceDirect
Paediatric Respiratory Reviews
Emerging cystic fibrosis pathogens and the microbiome Eshwar Mahenthiralingam * Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff, UK
A R T I C L E I N F O
S U M M A R Y
Keywords: Cystic fibrosis Emerging pathogen Burkholderia Stenotrophomonas Achromobacter Pandorea Ralstonia Prevotella Streptococcus milleri group CF microbiome
Cystic fibrosis (CF) respiratory infection is characterised by the presence of typical human bacterial pathogens such as Pseudomonas aeruginosa, Haemophilus influenzae and Staphylococcus aureus. Less typical pathogens such as Burkholderia, Stenotrophomonas, Achromobacter, Pandorea and Ralstonia have emerged as problematic infections which are largely unique to people with CF. Using molecular methods, two groups of anaerobic bacteria Prevotella species and the Streptococcus milleri group have also recently been shown to be highly prevalent in CF sputum. Collectively, the diversity of microorganisms present in respiratory specimens has been designated the CF microbiome. The challenges posed by emerging CF pathogens and a microbiome-based view of CF infection are discussed in terms of their impact on clinical outcome, diagnosis and therapy. ß 2014 Elsevier Ltd. All rights reserved.
Microbial lung infection is the major cause of morbidity and mortality in cystic fibrosis [1], and routine therapy relies on the early detection, eradication or continuous treatment of respiratory infections [2]. Pseudomonas aeruginosa is the dominant pathogen infecting more than 70% of people with CF [1,2], however, our understanding of other bacterial infections associated with chronic lung disease has changed considerably in the last 20 years [2]. In addition to P. aeruginosa, well known human pathogens such as Haemophilus influenzae and Staphylococcus aureus also cause CF infection [2], and one could argue that because of the extensive study of these three bacterial species in relation to multiple human infections, we have a good understanding of their pathogenesis and multiple therapeutic options for their treatment. In contrast, emerging antibiotic resistant CF pathogens pose major clinical challenges that are largely unique to people with CF and have typically been less studied than P. aeruginosa. In the context of this review an emerging pathogen will be defined as any microbial infection that poses a challenge in terms of clinical diagnosis, therapy or outcome in CF. Non-tuberculous mycobacteria such as Mycobacterium abscessus, fungal and viral infections, all pose multiple problems for people with CF [2] and hence fit this definition, however, because of the unique complexity of issues each of the latter pose, they will not be explored in detail here. Two groups of bacteria, both multidrug resistant, will be discussed as emerging CF pathogens because they share a number of traits:
* Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Room 0.23 Main Building, Park Place, Cardiff, UK, CF10 3AT. Tel.: +44 (0)29 208 75875; fax: +44 (0)29 208 74305. E-mail address: [email protected].
(i) Multidrug resistant non-fermenting Gram negative (MDRNFGN) bacteria. Pathogens such as Burkholderia cepacia complex (Bcc), Burkholderia gladioli, Achromobacter species, Ralstonia mannitolilytica, Stenotrophomonas maltophilia, and Pandorea species are problematic emerging pathogens, cumulatively infecting approximately 25% of people with CF and being especially resistant to therapy in older CF people with severe lung disease [3–5]. (ii) Novel CF microbiome players. Analyses of CF sputa, using enhanced culture and molecular cultivation-independent techniques, have uncovered an unprecedented diversity of microorganisms, collectively known as the CF airway microbiome [6]. Two dominant CF microbiome players that are missed by routine culture are the Streptococcus milleri group (SMG; Gram positive, facultatively anaerobic bacteria) [7] and Prevotella species (Gram negative, obligate anaerobes) [8]. These bacteria persist in most CF people receiving antibiotic therapy for chronic infection [9], but we know very little about their association with lung disease and whether or how they should be treated. These problematic NFGN bacteria and novel CF microbiome players, Prevotella species and SMG bacteria, are emerging pathogens which constitute a health threat to people with CF because of the following issues. ANTIBIOTIC RESISTANCE NFGN bacteria comprise a pool of highly multidrug resistant CF pathogens [2]. With few effective antibiotics available, there is an
http://dx.doi.org/10.1016/j.prrv.2014.04.006 1526-0542/ß 2014 Elsevier Ltd. All rights reserved.
Please cite this article in press as: Mahenthiralingam E. Emerging cystic fibrosis pathogens and the microbiome. Paediatr. Respir. Rev. (2014), http://dx.doi.org/10.1016/j.prrv.2014.04.006
G Model
YPRRV-974; No. of Pages 3 2
E. Mahenthiralingam / Paediatric Respiratory Reviews xxx (2014) xxx–xxx
urgent need to develop novel therapies to improve current treatments for these emerging CF pathogens and Gram-negative bacteria in general [10]. Despite extensive efforts to improve therapy by performing multiple combination bactericidal antibiotic susceptibility testing (MCBT) to aid antibiotic selection for B. cepacia complex, P. aeruginosa, S. maltophilia, or Achromobacter species, Aaron and colleagues [11] were not able to improve on clinical outcome in comparison to patients managed using standard culture and testing approaches. Little progression on how to treat CF patients with NGFN infection has been made since these studies. Both Prevotella and SMG bacteria are not eradicated by routine therapy and also demonstrate resistance to antibiotics commonly used to treat CF pulmonary infection. They are present in the airways at levels equivalent to that of established pathogens like P. aeruginosa [8,9] and can be considered as chronic infections in many patients, but are not specifically targeted for therapy. CHALLENGING CONVENTIONAL MICROBIOLOGY, IDENTIFICATION AND TAXONOMY All the NFGN species are often mis-identified by routine culture [2] or non-specifically reported as a ‘‘Gram Negative Rod?’’ prior to full species identification which may take additional time to resolve. Even more concerning, Prevotella and SMG group bacteria are not captured by routine diagnostic microbiology and to better understand their role in lung disease, accurate, quantitative diagnostics are urgently required [9,12]. While the taxonomy of Bcc has become much better understood [2], all the remaining emerging CF species show genetic diversity and the presence of novel species groups; the pathogenic significance of this diversity has not been fully established. For example, multiple novel species groups have been recently defined within the genus Achromobacter using a genomics-based multilocus sequence typing (MLST) scheme and polyphasic taxonomy [13,14]. The vast majority of CF isolates were historically reported as just one species ‘‘A. xylosoxidans’’ [15]. However, recent systematic analysis of Achromobacter species demonstrated a very different epidemiological picture with prevalence rates of A. xylosoxidans 42%, A. ruhlandii 23% and A. dolens 17% occurring in CF [15]. The taxonomy of the anaerobic species found in CF respiratory infection is also not fully defined. The SMG group comprise three species, S. constellatus, S. intermedius and S. aginosus, and all have been found in patients with CF [7]. The taxonomy of these SMG species was last reviewed in 1997 and it is highly likely further taxonomic diversity may be present in this historically defined group of streptococci [16]. Multiple Prevotella species have been cultivated from CF respiratory infections with P. melaninogenica, P. histicola and an unnamed species, Prevotella oral taxon 313, being most commonly cultivated in a study of 12 patients [17]. Overall, both Streptococcus and Prevotella have high species diversity as bacteria genera and further systematic analysis will be required to characterise the species most commonly associated with CF respiratory infection. PATHOGENIC POTENTIAL Bcc bacteria are established CF pathogens, with B. cenocepacia and B. multivorans, being the dominant CF species associated with transmission, clinical decline, loss of lung function and multiple cases of ‘‘cepacia syndrome’’ [2,18,19]. Cases of poor prognosis associated with B. gladioli CF infection have also been reported [20,21]. Furthermore, variation in outcome post-lung transplantation ranging from poor [21,22] to acceptable [23], has been reported in B. gladioli infected CF patients. Severe lung disease [24] and bacteraemia [25] have also been observed for Pandorea species infection in CF. The pathogenic potential of the remaining
emerging species, Achromobacter, Stenotrophomonas, Ralstonia, Prevotella and SMG, remains uncertain. A rise in the number of SMG group bacteria in CF sputum has been linked with the onset of acute pulmonary exacerbation [7]; however, there has been little further follow-up of the Streptococcus species even though it is very clear that they are frequently dominant and chronic microbiome players in CF [8,9,12]. What is also clear from the literature outside of CF is that instances of highly inflammatory and fatal infection have been reported for all these emerging CF pathogens.
TRANSMISSIBILITY AND EPIDEMIOLOGY The devastating infection control risk associated with Bcc bacteria is well known [2,26]. Elucidation of Bcc epidemiology [2,27] and improved molecular species identification methods [28,29] played a major role in designing international infection control measures for this species [30]. These interventions have successfully halted the large scale epidemic spread of Bcc bacteria in CF, particularly for B. cenocepacia [2,31]. However, the prevalence of certain species such as B. multivorans and the non-Bcc species, B. gladioli, appear to be rising, with the overall incidence of Bcc infection (3 to 4%) remaining stable in CF [2]. Although specific markers of transmission [32] and virulence [33,34] have been defined for the B. cenocepacia ET12 strain, no such markers have been identified for B. multivorans, other Bcc species, B. gladioli, Pandorea apista and A. xylosoxidans, despite reports of patient to patient spread [24,35–37]. Finally, antibiotic resistance, a known transmission risk factor for multiple pathogens, is a trait which links all emerging CF pathogens, flagging them as potential infection control risks in nosocomial settings.
CONTRA-INDICATION FOR LUNG TRANSPLANT AND EXCLUSION FROM CLINICAL TRIALS Lung transplantation remains the only therapeutic option for CF individuals with end-stage respiratory disease. B. cepacia complex bacteria, B. gladioli and Pandorea species bacteria are associated with poor outcome post-transplantation [21,22]. Access to this therapy is specifically restricted for B. cenocepacia infected individuals. Additional issues associated with CF patients culture positive for emerging CF pathogens includes the antibiotic resistance of these infections which hinders clinical management pre- and post-transplant and the frequent exclusion of infected patients from clinical trials.
ASSOCIATION WITH LOSS OF MICROBIAL DIVERSITY AND SEVERE LUNG DISEASE Recent sputum microbiome analysis of individuals with severe lung disease [3,5], and sampling of explanted lungs from adults with end-stage disease [4], has demonstrated that the microbial diversity of these CF infections is considerably reduced. The airways of these severely ill people with CF were dominated by a single pathogen such as P. aeruginosa or frequently one of the MDRNGFN emerging CF species, Burkholderia, Achromobacter or Stenotrophomonas [3–5]. Furthermore, various studies have reported a positive correlation between microbial diversity and lung function [5,38,39]. Overall, these data suggest that considerable interactions occur between members of the CF microbiome, administered anti-bacterial therapies, and the host immune system, which lead to either the reduced diversity during severe lung disease or stable, more diverse respiratory infections in healthy CF individuals.
Please cite this article in press as: Mahenthiralingam E. Emerging cystic fibrosis pathogens and the microbiome. Paediatr. Respir. Rev. (2014), http://dx.doi.org/10.1016/j.prrv.2014.04.006
G Model
YPRRV-974; No. of Pages 3 E. Mahenthiralingam / Paediatric Respiratory Reviews xxx (2014) xxx–xxx
CONCLUSIONS AND PERSPECTIVE Burkholderia, Stenotrophomonas, Achromobacter, Pandorea, Ralstonia, Streptococcus and Prevotella species can all be considered as emerging bacterial pathogens in the context of CF respiratory infection. Their multi-antibiotic resistance and recalcitrance to clearance by routine therapy are shared traits which make them a clinical challenge. The linkage of MDR-NGFN species to the loss of microbial diversity seen in the respiratory microbiota of individuals with severe lung disease is a recent finding that raises many questions about how to optimally treat chronic lung infection. Given the cumulatively high prevalence of NFGN species and the almost uniform presence of Prevotella and SMG bacteria in individuals with chronic lung infection, all these emerging CF pathogens are worthy of further systematic study in the context of CF respiratory infection and the wider role of the lung microbiome. CONFLICT OF INTEREST The author has no conflict of interest to report.
[15] [16]
[17] [18]
[19]
[20] [21]
[22]
[23]
Acknowledgements [24]
EM thanks Alan Brown, Thomas Connor, Aras Kadioglu, Dervla Kenna, Julian Parkhill, Michael Tunney, Miguel Valvano and Craig Winstanley for their helpful comments on this text. EM acknowledges the European Cooperation in Science and Technology (COST) action BM1003 for promoting networking on microbial CF pathogens.
[25]
[26] [27]
References [1] O’Sullivan BP, Freedman SD. Cystic fibrosis. Lancet 2009;373:1891–904. [2] Lipuma JJ. The changing microbial epidemiology in cystic fibrosis. Clin Microbiol Rev 2010;23:299–323. [3] Blainey PC, Milla CE, Cornfield DN, Quake SR. Quantitative analysis of the human airway microbial ecology reveals a pervasive signature for cystic fibrosis. Sci Transl Med 2012;4. 153ra30. [4] Goddard AF, Staudinger BJ, Dowd SE, Joshi-Datar A, Wolcott RD, Aitken ML, et al. Direct sampling of cystic fibrosis lungs indicates that DNA-based analyses of upper-airway specimens can misrepresent lung microbiota. Proc Natl Acad Sci USA 2012;109:13769–74. [5] Zhao J, Schloss PD, Kalikin LM, Carmody LA, Foster BK, Petrosino JF, et al. Decade-long bacterial community dynamics in cystic fibrosis airways. Proc Natl Acad Sci USA 2012;109:5809–14. [6] Rogers GB, Daniels TW, Tuck A, Carroll MP, Connett GJ, David GJ, et al. Studying bacteria in respiratory specimens by using conventional and molecular microbiological approaches. BMC Pulm Med 2009;9:14. PubMed PMID: 19368727. [7] Sibley CD, Parkins MD, Rabin HR, Duan K, Norgaard JC, Surette MG. A polymicrobial perspective of pulmonary infections exposes an enigmatic pathogen in cystic fibrosis patients. Proc Natl Acad Sci USA 2008;105:15070–5. [8] Tunney MM, Field TR, Moriarty TF, Patrick S, Doering G, Muhlebach MS, et al. Detection of anaerobic bacteria in high numbers in sputum from patients with cystic fibrosis. Am J Respir Crit Care Med 2008;177:995–1001. [9] Tunney MM, Klem ER, Fodor AA, Gilpin DF, Moriarty TF, McGrath SJ, et al. Use of culture and molecular analysis to determine the effect of antibiotic treatment on microbial community diversity and abundance during exacerbation in patients with cystic fibrosis. Thorax 2011;66:579–84. [10] Talbot GH. The Antibiotic Development Pipeline for Multidrug-Resistant Gram-Negative Bacilli: Current and Future Landscapes. Infect Cont Hosp Ep 2010;31. S55–S8. [11] Aaron SD, Vandemheen KL, Ferris W, Fergusson D, Tullis E, Haase D, et al. Combination antibiotic susceptibility testing to treat exacerbations of cystic fibrosis associated with multiresistant bacteria: a randomised, double-blind, controlled clinical trial. Lancet 2005;366:463–71. [12] Sibley CD, Grinwis ME, Field TR, Eshaghurshan CS, Faria MM, Dowd SE, et al. Culture enriched molecular profiling of the cystic fibrosis airway microbiome. PloS one 2011;6:e22702. [13] Spilker T, Vandamme P, Lipuma JJ. A multilocus sequence typing scheme implies population structure and reveals several putative novel Achromobacter species. J Clin Microbiol 2012;50:3010–5. [14] Vandamme P, Moore ER, Cnockaert M, De Brandt E, Svensson-Stadler L, Houf K, et al. Achromobacter animicus sp. nov., Achromobacter mucicolens sp. nov.,
[28]
[29]
[30]
[31]
[32]
[33]
[34]
[35]
[36]
[37]
[38]
[39]
3
Achromobacter pulmonis sp. nov. and Achromobacter spiritinus sp. nov., from human clinical samples. Syst Appl Microbiol 2013;36:1–10. Spilker T, Vandamme P, LiPuma JJ. Identification and distribution of Achromobacter species in cystic fibrosis. J Cyst Fibros 2013;12:298–301. Jacobs JA. The ‘Streptococcus milleri’ group: Streptococcus anginosus, Streptococcus constellatus and Streptococcus intermedius. Rev Med Microbiol 1997;8: 73–80. Field TR, Sibley CD, Parkins MD, Rabin HR, Surette MG. The genus Prevotella in cystic fibrosis airways. Anaerobe 2010;16:337–44. Jones AM, Dodd ME, Govan JR, Barcus V, Doherty CJ, Morris J, et al. Burkholderia cenocepacia and Burkholderia multivorans: influence on survival in cystic fibrosis. Thorax 2004;59:948–51. Mahenthiralingam E, Vandamme P, Campbell ME, Henry DA, Gravelle AM, Wong LT, et al. Infection with Burkholderia cepacia complex genomovars in patients with cystic fibrosis: virulent transmissible strains of genomovar III can replace Burkholderia multivorans. Clin Infect Dis 2001;33:1469–75. Jones AM, Stanbridge TN, Isalska BJ, Dodd ME, Webb AK. Burkholderia gladioli: recurrent abscesses in a patient with cystic fibrosis. J Infect 2001;42:69–71. Quon BS, Reid JD, Wong P, Wilcox PG, Javer A, Wilson JM, et al. Burkholderia gladioli - a predictor of poor outcome in cystic fibrosis patients who receive lung transplants?. A case of locally invasive rhinosinusitis and persistent bacteremia in a 36-year-old lung transplant recipient with cystic fibrosis. Can Resp J 2011;18:e64–5. Murray S, Charbeneau J, Marshall BC, LiPuma JJ. Impact of Burkholderia infection on lung transplantation in cystic fibrosis. Am J Respir Crit Care Med 2008;178:363–71. Kennedy MP, Coakley RD, Donaldson SH, Aris RM, Hohneker K, Wedd JP, et al. Burkholderia gladioli: five year experience in a cystic fibrosis and lung transplantation center. J Cyst Fibros 2007;6:267–73. Jorgensen IM, Johansen HK, Frederiksen B, Pressler T, Hansen A, Vandamme P, et al. Epidemic spread of Pandorea apista, a new pathogen causing severe lung disease in cystic fibrosis patients. Pediatr Pulmonol 2003;36:439–46. Johnson LN, Han JY, Moskowitz SM, Burns JL, Qin X, Englund JA. Pandorea bacteremia in a cystic fibrosis patient with associated systemic illness. Pediatr Infect Dis J 2004;23:881–2. Saiman L, Siegel J. Infection control in cystic fibrosis. Clin Microbiol Rev 2004;17:57–71. Mahenthiralingam E, Baldwin A, Dowson CG. Burkholderia cepacia complex bacteria: opportunistic pathogens with important natural biology. J Appl Microbiol 2008;104:1539–51. Mahenthiralingam E, Bischof J, Byrne SK, Radomski C, Davies JE, Av-Gay Y, et al. DNA-Based diagnostic approaches for identification of Burkholderia cepacia complex, Burkholderia vietnamiensis, Burkholderia multivorans, Burkholderia stabilis, and Burkholderia cepacia genomovars I and III. J Clinical Microbiol 2000;38:3165–73. Turton JF, Arif N, Hennessy D, Kaufmann ME, Pitt TL. Revised approach for identification of isolates within the Burkholderia cepacia complex and description of clinical isolates not assigned to any of the known genomovars. J Clin Microbiol 2007;45:3105–8. Saiman L, MacDonald N, Burns JL, Hoiby N, Speert DP, Weber D. Infection control in cystic fibrosis: Practical recommendations for the hospital, clinic, and social settings. Am J Infect Control 2000;28:381–5. Drevinek P, Mahenthiralingam E. Burkholderia cenocepacia in cystic fibrosis: epidemiology and molecular mechanisms of virulence. Clin Microbiol Infect 2010;16:821–30. Mahenthiralingam E, Simpson DA, Speert DP. Identification and characterization of a novel DNA marker associated with epidemic Burkholderia cepacia strains recovered from patients with cystic fibrosis. J Clin Microbiol 1997;35:808–16. Baldwin A, Sokol PA, Parkhill J, Mahenthiralingam E. The Burkholderia cepacia epidemic strain marker is part of a novel genomic island encoding both virulence and metabolism-associated genes in Burkholderia cenocepacia. Infection and immunity 2004;72:1537–47. Sajjan U, Wu YJ, Kent G, Forstner J. Preferential adherence of cable-piliated Burkholderia cepacia to respiratory epithelia of CF knockout mice and human cystic fibrosis lung explants. J Med Microbiol 2000;49:875–85. Biddick R, Spilker T, Martin A, LiPuma JJ. Evidence of transmission of Burkholderia cepacia, Burkholderia multivorans and Burkholderia dolosa among persons with cystic fibrosis. FEMS Microbiol Lett 2003;228:57–62. Van Daele S, Verhelst R, Claeys G, Verschraegen G, Franckx H, Van Simaey L, et al. Shared genotypes of Achromobacter xylosoxidans strains isolated from patients at a cystic fibrosis rehabilitation center. J Clin Microbiol 2005;43: 2998–3002. Wilsher ML, Kolbe J, Morris AJ, Welch DF, Vandamme PAR. Nosocomial acquisition of Burkholderia gladioli in patients with cystic fibrosis. Am J Resp Crit Care 1999;160:374–5. Cox MJ, Allgaier M, Taylor B, Baek MS, Huang YJ, Daly RA, et al. Airway Microbiota and Pathogen Abundance in Age-Stratified Cystic Fibrosis Patients. Plos One 2010;5:e0011044. Klepac-Ceraj V, Lemon KP, Martin TR, Allgaier M, Kembel SW, Knapp AA, et al. Relationship between cystic fibrosis respiratory tract bacterial communities and age, genotype, antibiotics and Pseudomonas aeruginosa. Environ Microbiol 2010;12:1293–303.
Please cite this article in press as: Mahenthiralingam E. Emerging cystic fibrosis pathogens and the microbiome. Paediatr. Respir. Rev. (2014), http://dx.doi.org/10.1016/j.prrv.2014.04.006
