Abstract
Burkholderia contaminans is a member of the Burkholderia cepacia complex (Bcc), a pathogen with increasing prevalence among cystic fibrosis (CF) patients and the cause of numerous outbreaks due to the use of contaminated commercial products. The antibiotic resistance determinants, particularly β-lactamases, have been poorly studied in this species. In this work, we explored the whole genome sequence (WGS) of a B. contaminans isolate (FFH 2055) and detected four putative β-lactamase-encoding genes. In general, these genes have more than 93% identity with β-lactamase genes found in other Bcc species. Two β-lactamases, a class A (Pen-like, suggested name PenO) and a class D (OXA-like), were further analyzed and characterized. Amino acid sequence comparison showed that Pen-like has 82% and 67% identity with B. multivorans PenA and B. pseudomallei PenI, respectively, while OXA-like displayed strong homology with class D enzymes within the Bcc, but only 22–44% identity with available structures from the OXA family. PCR reactions designed to study the presence of these two genes revealed a heterogeneous distribution among clinical and industrial B. contaminans isolates. Lastly, blaPenO gene was cloned and expressed into E. coli to investigate the antibiotic resistance profile and confers an extended-spectrum β-lactamase (ESBL) phenotype. These results provide insight into the presence of β-lactamases in B. contaminans, suggesting they play a role in antibiotic resistance of these bacteria.
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References
Kelly J (2017) Environmental scan of cystic fibrosis research worldwide. J Cyst Fibros 16(3):367–370. https://doi.org/10.1016/j.jcf.2016.11.002
Gilligan PH (2014) Infections in patients with cystic fibrosis: diagnostic microbiology update. Clin Lab Med 34(2):197–217. https://doi.org/10.1016/j.cll.2014.02.001
Sherrard LJ, Tunney MM, Elborn JS (2014) Antimicrobial resistance in the respiratory microbiota of people with cystic fibrosis. Lancet 384(9944):703–713. https://doi.org/10.1016/S0140-6736(14)61137-5
Mahenthiralingam E, Baldwin A, Dowson CG (2008) Burkholderia cepacia complex bacteria: opportunistic pathogens with important natural biology. J Appl Microbiol 104(6):1539–1551. https://doi.org/10.1111/j.1365-2672.2007.03706.x
De Smet B, Mayo M, Peeters C, Zlosnik JE, Spilker T, Hird TJ, LiPuma JJ, Kidd TJ, Kaestli M, Ginther JL, Wagner DM, Keim P, Bell SC, Jacobs JA, Currie BJ, Vandamme P (2015) Burkholderia stagnalis sp. nov. and Burkholderia territorii sp. nov., two novel Burkholderia cepacia complex species from environmental and human sources. Int J Syst Evol Microbiol 65(7):2265–2271. https://doi.org/10.1099/ijs.0.000251
Isles A, Maclusky I, Corey M, Gold R, Prober C, Fleming P, Levison H (1984) Pseudomonas cepacia infection in cystic fibrosis: an emerging problem. J Pediatr 104(2):206–210
Zhou J, Chen Y, Tabibi S, Alba L, Garber E, Saiman L (2007) Antimicrobial susceptibility and synergy studies of Burkholderia cepacia complex isolated from patients with cystic fibrosis. Antimicrob Agents Chemother 51(3):1085–1088. https://doi.org/10.1128/AAC.00954-06
Song JE, Kwak YG, Um TH, Cho CR, Kim S, Park IS, Hwang JH, Kim N, Oh GB (2017) Outbreak of Burkholderia cepacia pseudobacteraemia caused by intrinsically contaminated commercial 0.5% chlorhexidine solution in neonatal intensive care units. J Hosp Infect. https://doi.org/10.1016/j.jhin.2017.09.012
Torbeck L, Raccasi D, Guilfoyle DE, Friedman RL, Hussong D (2011) Burkholderia cepacia: this decision is overdue. PDA J Pharm Sci Technol 65(5):535–543. https://doi.org/10.5731/pdajpst.2011.00793
Vonberg RP, Gastmeier P (2007) Hospital-acquired infections related to contaminated substances. J Hosp Infect 65(1):15–23. https://doi.org/10.1016/j.jhin.2006.09.018
Baldwin A, Mahenthiralingam E, Drevinek P, Pope C, Waine DJ, Henry DA, Speert DP, Carter P, Vandamme P, LiPuma JJ, Dowson CG (2008) Elucidating global epidemiology of Burkholderia multivorans in cases of cystic fibrosis by multilocus sequence typing. J Clin Microbiol 46(1):290–295. https://doi.org/10.1128/JCM.01818-07
Lipuma JJ (2010) The changing microbial epidemiology in cystic fibrosis. Clin Microbiol Rev 23(2):299–323. https://doi.org/10.1128/CMR.00068-09
Zlosnik JE, Zhou G, Brant R, Henry DA, Hird TJ, Mahenthiralingam E, Chilvers MA, Wilcox P, Speert DP (2015) Burkholderia species infections in patients with cystic fibrosis in British Columbia, Canada. 30 years’ experience. Ann Am Thorac Soc 12(1):70–78. https://doi.org/10.1513/AnnalsATS.201408-395OC
Vanlaere E, Baldwin A, Gevers D, Henry D, De Brandt E, LiPuma JJ, Mahenthiralingam E, Speert DP, Dowson C, Vandamme P (2009) Taxon K, a complex within the Burkholderia cepacia complex, comprises at least two novel species, Burkholderia contaminans sp. nov. and Burkholderia lata sp. nov. Int J Syst Evol Microbiol 59(Pt 1):102–111. https://doi.org/10.1099/ijs.0.001123-0
Coutinho CP, Barreto C, Pereira L, Lito L, Melo Cristino J, Sa-Correia I (2015) Incidence of Burkholderia contaminans at a cystic fibrosis centre with an unusually high representation of Burkholderia cepacia during 15 years of epidemiological surveillance. J Med Microbiol 64(8):927–935. https://doi.org/10.1099/jmm.0.000094
Martin M, Christiansen B, Caspari G, Hogardt M, von Thomsen AJ, Ott E, Mattner F (2011) Hospital-wide outbreak of Burkholderia contaminans caused by prefabricated moist washcloths. J Hosp Infect 77(3):267–270. https://doi.org/10.1016/j.jhin.2010.10.004
Martina P, Bettiol M, Vescina C, Montanaro P, Mannino MC, Prieto CI, Vay C, Naumann D, Schmitt J, Yantorno O, Lagares A, Bosch A (2013) Genetic diversity of Burkholderia contaminans isolates from cystic fibrosis patients in Argentina. J Clin Microbiol 51(1):339–344. https://doi.org/10.1128/JCM.02500-12
Medina-Pascual MJ, Valdezate S, Carrasco G, Villalon P, Garrido N, Saez-Nieto JA (2015) Increase in isolation of Burkholderia contaminans from Spanish patients with cystic fibrosis. Clin Microbiol Infect 21(2):150–156. https://doi.org/10.1016/j.cmi.2014.07.014
Moehring RW, Lewis SS, Isaacs PJ, Schell WA, Thomann WR, Althaus MM, Hazen KC, Dicks KV, Lipuma JJ, Chen LF, Sexton DJ (2014) Outbreak of bacteremia due to Burkholderia contaminans linked to intravenous fentanyl from an institutional compounding pharmacy. JAMA Intern Med 174(4):606–612. https://doi.org/10.1001/jamainternmed.2013.13768
Peterson AE, Chitnis AS, Xiang N, Scaletta JM, Geist R, Schwartz J, Dement J, Lawlor E, Lipuma JJ, O’Connell H, Noble-Wang J, Kallen AJ, Hunt DC (2013) Clonally related Burkholderia contaminans among ventilated patients without cystic fibrosis. Am J Infect Control 41(12):1298–1300. https://doi.org/10.1016/j.ajic.2013.05.015
Nunvar J, Kalferstova L, Bloodworth RA, Kolar M, Degrossi J, Lubovich S, Cardona ST, Drevinek P (2016) Understanding the pathogenicity of Burkholderia contaminans, an emerging pathogen in cystic fibrosis. PLoS ONE 11(8):e0160975. https://doi.org/10.1371/journal.pone.0160975
Deng P, Wang X, Baird SM, Showmaker KC, Smith L, Peterson DG, Lu S (2016) Comparative genome-wide analysis reveals that Burkholderia contaminans MS14 possesses multiple antimicrobial biosynthesis genes but not major genetic loci required for pathogenesis. MicrobiologyOpen 5(3):353–369. https://doi.org/10.1002/mbo3.333
Haim MS, Mollerach M, Van Domselaar G, Teves SA, Degrossi J, Cardona ST (2016) Draft genome sequences of Burkholderia contaminans FFI-28, a strain isolated from a contaminated pharmaceutical solution. Genome Announcements. https://doi.org/10.1128/genomeA.01177-16
Jung JY, Ahn Y, Kweon O, LiPuma JJ, Hussong D, Marasa BS, Cerniglia CE (2017) Improved high-quality draft genome sequence and annotation of Burkholderia contaminans LMG 23361(T). Genome Announcements. https://doi.org/10.1128/genomeA.00245-17
Burns J (2006) Antibiotic resistance of Burkholderia spp. In: Coenye PVT (ed) Burkholderia: molecular microbiology and genomics. Horizon Bioscience, Norfolk, pp 81–91
Drevinek P, Mahenthiralingam E (2010) Burkholderia cenocepacia in cystic fibrosis: epidemiology and molecular mechanisms of virulence. Clin Microbiol Infect 16(7):821–830. https://doi.org/10.1111/j.1469-0691.2010.03237.x
Ramirez MS, Vargas LJ, Cagnoni V, Tokumoto M, Centron D (2005) Class 2 integron with a novel cassette array in a Burkholderia cenocepacia isolate. Antimicrob Agents Chemother 49(10):4418–4420. https://doi.org/10.1128/AAC.49.10.4418-4420.2005
Trepanier S, Prince A, Huletsky A (1997) Characterization of the penA and penR genes of Burkholderia cepacia 249 which encode the chromosomal class A penicillinase and its LysR-type transcriptional regulator. Antimicrob Agents Chemother 41(11):2399–2405
Poirel L, Rodriguez-Martinez JM, Plesiat P, Nordmann P (2009) Naturally occurring Class A ss-lactamases from the Burkholderia cepacia complex. Antimicrob Agents Chemother 53(3):876–882. https://doi.org/10.1128/AAC.00946-08
Papp-Wallace KM, Taracila MA, Gatta JA, Ohuchi N, Bonomo RA, Nukaga M (2013) Insights into beta-lactamases from Burkholderia species, two phylogenetically related yet distinct resistance determinants. J Biol Chem 288(26):19090–19102. https://doi.org/10.1074/jbc.M113.458315
Papp-Wallace KM, Becka SA, Taracila MA, Zeiser ET, Gatta JA, LiPuma JJ, Bonomo RA (2017) Exploring the role of the Omega-loop in the evolution of Ceftazidime resistance in the PenA beta-lactamase from Burkholderia multivorans, an important cystic fibrosis pathogen. Antimicrob Agents Chemother. https://doi.org/10.1128/AAC.01941-16
Everaert A, Coenye T (2016) Effect of beta-Lactamase inhibitors on in vitro activity of beta-Lactam antibiotics against Burkholderia cepacia complex species. Antimicrob Resist Infect Control 5:44. https://doi.org/10.1186/s13756-016-0142-3
Holden MT, Seth-Smith HM, Crossman LC, Sebaihia M, Bentley SD, Cerdeno-Tarraga AM, Thomson NR, Bason N, Quail MA, Sharp S, Cherevach I, Churcher C, Goodhead I, Hauser H, Holroyd N, Mungall K, Scott P, Walker D, White B, Rose H, Iversen P, Mil-Homens D, Rocha EP, Fialho AM, Baldwin A, Dowson C, Barrell BG, Govan JR, Vandamme P, Hart CA, Mahenthiralingam E, Parkhill J (2009) The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients. J Bacteriol 191(1):261–277. https://doi.org/10.1128/JB.01230-08
Bloodworth RA, Selin C, Lopez De Volder MA, Drevinek P, Galanternik L, Degrossi J, Cardona ST (2015) Draft genome sequences of Burkholderia contaminans, a Burkholderia cepacia complex species that is increasingly recovered from cystic fibrosis patients. Genome Announcements. https://doi.org/10.1128/genomeA.00766-15
Becka SA, Zeiser ET, Marshall SH, Gatta JA, Nguyen K, Singh I, Greco C, Sutton GG, Fouts DE, LiPuma JJ, Papp-Wallace KM (2018) Sequence heterogeneity of the PenA carbapenemase in clinical isolates of Burkholderia multivorans. Diagn Microbiol Infect Dis 92(3):253–258. https://doi.org/10.1016/j.diagmicrobio.2018.06.005
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O (2008) The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. https://doi.org/10.1186/1471-2164-9-75
Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R (2014) The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 42(Database issue):D206–D214. https://doi.org/10.1093/nar/gkt1226
Winsor GL, Khaira B, Van Rossum T, Lo R, Whiteside MD, Brinkman FS (2008) The Burkholderia genome database: facilitating flexible queries and comparative analyses. Bioinformatics 24(23):2803–2804. https://doi.org/10.1093/bioinformatics/btn524
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
Gouet P, Robert X, Courcelle E (2003) ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic Acids Res 31(13):3320–3323
Notredame C, Higgins DG, Heringa J (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 302(1):205–217. https://doi.org/10.1006/jmbi.2000.4042
Muñoz V, Serrano L (1997) Development of the multiple sequence approximation within the AGADIR model of alpha-helix formation: comparison with Zimm-Bragg and Lifson-Roig formalisms. Biopolymers 41(5):495–509
Krieger E, Darden T, Nabuurs SB, Finkelstein A, Vriend G (2004) Making optimal use of empirical energy functions: force-field parameterization in crystal space. Proteins 57(4):678–683. https://doi.org/10.1002/prot.20251
Schrödinger L The PyMOL molecular Graphics System., 1.5.0.4 edn.
Koressaar T, Remm M (2007) Enhancements and modifications of primer design program Primer3. Bioinformatics 23(10):1289–1291. https://doi.org/10.1093/bioinformatics/btm091
Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG (2012) Primer3–new capabilities and interfaces. Nucleic Acids Res 40(15):e115. https://doi.org/10.1093/nar/gks596
Clinical and Laboratory Standards Institute (2017) Performance standards for antimicrobial susceptibility testing; twenty-sixth informational supplement M100-S27, vol 37. vol 1. Clinical and Laboratory Standards Institute, Wayne
Bret L, Chaibi EB, Chanal-Claris C, Sirot D, Labia R, Sirot J (1997) Inhibitor-resistant TEM (IRT) b-lactamases with different substitutions at position 244. Antimicrob Agents Chemother 41(11):2547–2549
Perez-Llarena FJ, Cartelle M, Mallo S, Beceiro A, Perez A, Villanueva R, Romero A, Bonnet R, Bou G (2008) Structure-function studies of arginine at position 276 in CTX-M b-lactamases. J Antimicrob Chemother 61(4):792–797. https://doi.org/10.1093/jac/dkn031
Ruggiero M, Kerff F, Herman R, Sapunaric F, Galleni M, Gutkind G, Charlier P, Sauvage E, Power P (2014) Crystal structure of the extended-spectrum beta-lactamase PER-2 and insights into the role of specific residues in the interaction with beta-lactams and beta-lactamase inhibitors. Antimicrob Agents Chemother. https://doi.org/10.1128/AAC.00089-14
Ruggiero M, Curto L, Brunetti F, Sauvage E, Galleni M, Power P, Gutkind G (2017) Impact of mutations at Arg220 and Thr237 in PER-2 beta-lactamase on conformation, activity, and susceptibility to inhibitors. Antimicrob Agents Chemother. https://doi.org/10.1128/AAC.02193-16
Chen Y, Delmas J, Sirot J, Shoichet B, Bonnet R (2005) Atomic resolution structures of CTX-M beta-lactamases: extended spectrum activities from increased mobility and decreased stability. J Mol Biol 348(2):349–362. https://doi.org/10.1016/j.jmb.2005.02.010
Delmas J, Chen Y, Prati F, Robin F, Shoichet BK, Bonnet R (2008) Structure and dynamics of CTX-M enzymes reveal insights into substrate accommodation by extended-spectrum beta-lactamases. J Mol Biol 375(1):192–201. https://doi.org/10.1016/j.jmb.2007.10.026
Toleman MA, Rolston K, Jones RN, Walsh TR (2003) Molecular and biochemical characterization of OXA-45, an extended-spectrum class 2d’ beta-lactamase in Pseudomonas aeruginosa. Antimicrob Agents Chemother 47(9):2859–2863
Stojanoski V, Chow DC, Fryszczyn B, Hu L, Nordmann P, Poirel L, Sankaran B, Prasad BV, Palzkill T (2015) Structural basis for different substrate profiles of two closely related class d beta-lactamases and their inhibition by halogens. Biochemistry 54(21):3370–3380. https://doi.org/10.1021/acs.biochem.5b00298
Acknowledgements
Research reported in this publication was supported in part by funds and/or facilities provided by the Cleveland Department of Veterans Affairs, the Veterans Affairs Merit Review Program BX002872 (KMP-W) and BX001974 (RAB) from the United States (U.S.) Department of Veterans Affairs Biomedical Laboratory Research and Development Service, and the Geriatric Research Education and Clinical Center VISN 10 to RAB. The contents do not represent the views of the U.S. Department of Veterans Affairs or the United States Government. This study was partially supported by National Institute of Allergy and Infectious Diseases of the National Institutes of Health under Award Numbers R21AI114508, R01AI100560, R01AI063517, and R01AI072219 to RAB. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. We want to thank Dr. Ana P. Meo (Hospital Ramos Mejía) and Dr. Carlos Vay (Hospital de Clínicas General San Martín) for providing the non-CF B. contaminans isolates for this study. Special thanks are offered to Dr. German M. Traglia for his technical help in bioinformatics analysis.
Funding
This work was funded by grants from Agencia Nacional de Promoción Científica y Tecnológica (PICT 2014-0457 to PP). P. Power is a researcher for the Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET, Argentina). JF has a SOAR-ELEVAR Scholar Fellowship from Latina/o Graduate Students from the U.S. Department of Education.
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Figure S1
. Burkholderia cepacia complex (Bcc) whole-genome phylogram of representative genomes showing the distribution of class B, C and D β-lactamases using the composition vector method. (JPEG 4616 KB)
Figure S2
. Genetic context of blaPen genes. Arrows represent the direction of transcription. (TIF 251 KB)
Figure S3
. Genetic environment of blaOXA-like. Arrows represent the direction of transcription. (TIF 213 KB)
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Degrossi, J.J., Merino, C., Isasmendi, A.M. et al. Whole Genome Sequence Analysis of Burkholderia contaminans FFH2055 Strain Reveals the Presence of Putative β-Lactamases. Curr Microbiol 76, 485–494 (2019). https://doi.org/10.1007/s00284-019-01653-4
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DOI: https://doi.org/10.1007/s00284-019-01653-4