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Yin J, Yuan D, Xu Z, Wu Y, Chen Z, Xiang X. Significant Differences in Intestinal Bacterial Communities of Sympatric Bean Goose, Hooded Crane, and Domestic Goose. Animals (Basel) 2024; 14:1688. [PMID: 38891737 PMCID: PMC11170997 DOI: 10.3390/ani14111688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 05/25/2024] [Accepted: 06/01/2024] [Indexed: 06/21/2024] Open
Abstract
The host's physiological well-being is intricately associated with the gut microbiota. However, previous studies regarding the intestinal microbiota have focused on domesticated or captive birds. This study used high-throughput sequencing technology to identify the gut bacterial communities of sympatric bean geese, hooded cranes, and domestic geese. The results indicated that the gut bacterial diversity in domestic geese and hooded cranes showed considerably higher diversity than bean geese. The gut bacterial community compositions varied significantly among the three hosts (p < 0.05). Compared to the hooded crane, the bean goose and domestic goose were more similar in their genotype and evolutionary history, with less difference in the bacterial community composition and assembly processes between the two species. Thus, the results might support the crucial role of host genotypes on their gut microbiota. The gut bacteria of wild hooded cranes and bean geese had a greater capacity for energy metabolism compared to domestic geese, suggesting that wild birds may rely more on their gut microbiota to survive in cold conditions. Moreover, the intestines of the three hosts were identified as harboring potential pathogens. The relative abundance of pathogens was higher in the hooded crane compared to the other two species. The hooded crane gut bacterial community assemblage revealed the least deterministic process with the lowest filtering/selection on the gut microbiota, which might have been a reason for the highest number of pathogens result. Compared to the hooded crane, the sympatric bean goose showed the least diversity and relative abundance of pathogens. The intestinal bacterial co-occurrence network showed the highest stability in the bean goose, potentially enhancing host resistance to adverse environments and reducing the susceptibility to pathogen invasion. In this study, the pathogens were also discovered to overlap among the three hosts, reminding us to monitor the potential for pathogen transmission between poultry and wild birds. Overall, the current findings have the potential to enhance the understanding of gut bacterial and pathogenic community structures in poultry and wild birds.
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Affiliation(s)
- Jing Yin
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (J.Y.); (D.Y.); (Z.X.); (Y.W.)
- Anhui Shengjin Lake Wetland Ecology National Long-Term Scientific Research Base, Chizhou 247230, China
| | - Dandan Yuan
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (J.Y.); (D.Y.); (Z.X.); (Y.W.)
- Anhui Shengjin Lake Wetland Ecology National Long-Term Scientific Research Base, Chizhou 247230, China
| | - Ziqiu Xu
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (J.Y.); (D.Y.); (Z.X.); (Y.W.)
| | - Yuannuo Wu
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (J.Y.); (D.Y.); (Z.X.); (Y.W.)
- Anhui Shengjin Lake Wetland Ecology National Long-Term Scientific Research Base, Chizhou 247230, China
| | - Zhong Chen
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (J.Y.); (D.Y.); (Z.X.); (Y.W.)
- Anhui Shengjin Lake Wetland Ecology National Long-Term Scientific Research Base, Chizhou 247230, China
- International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral Ecology, Hefei 230601, China
| | - Xingjia Xiang
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (J.Y.); (D.Y.); (Z.X.); (Y.W.)
- Anhui Shengjin Lake Wetland Ecology National Long-Term Scientific Research Base, Chizhou 247230, China
- International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral Ecology, Hefei 230601, China
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Kim B, Han SR, Lee H, Oh TJ. Insights into group-specific pattern of secondary metabolite gene cluster in Burkholderia genus. Front Microbiol 2024; 14:1302236. [PMID: 38293557 PMCID: PMC10826400 DOI: 10.3389/fmicb.2023.1302236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/21/2023] [Indexed: 02/01/2024] Open
Abstract
Burkholderia is a versatile strain that has expanded into several genera. It has been steadily reported that the genome features of Burkholderia exhibit activities ranging from plant growth promotion to pathogenicity across various isolation areas. The objective of this study was to investigate the secondary metabolite patterns of 366 Burkholderia species through comparative genomics. Samples were selected based on assembly quality assessment and similarity below 80% in average nucleotide identity. Duplicate samples were excluded. Samples were divided into two groups using FastANI analysis. Group A included B. pseudomallei complex. Group B included B. cepacia complex. The limitations of MLST were proposed. The detection of genes was performed, including environmental and virulence-related genes. In the pan-genome analysis, each complex possessed a similar pattern of cluster for orthologous groups. Group A (n = 185) had 14,066 cloud genes, 2,465 shell genes, 682 soft-core genes, and 2,553 strict-core genes. Group B (n = 181) had 39,867 cloud genes, 4,986 shell genes, 324 soft-core genes, 222 core genes, and 2,949 strict-core genes. AntiSMASH was employed to analyze the biosynthetic gene cluster (BGC). The results were then utilized for network analysis using BiG-SCAPE and CORASON. Principal component analysis was conducted and a table was constructed using the results obtained from antiSMASH. The results were divided into Group A and Group B. We expected the various species to show similar patterns of secondary metabolite gene clusters. For in-depth analysis, a network analysis of secondary metabolite gene clusters was conducted, exemplified by BiG-SCAPE analysis. Depending on the species and complex, Burkholderia possessed several kinds of siderophore. Among them, ornibactin was possessed in most Burkholderia and was clustered into 4,062 clans. There was a similar pattern of gene clusters depending on the species. NRPS_04014 belonged to siderophore BGCs including ornibactin and indigoidine. However, it was observed that each family included a similar species. This suggests that, besides siderophores being species-specific, the ornibactin gene cluster itself might also be species-specific. The results suggest that siderophores are associated with environmental adaptation, possessing a similar pattern of siderophore gene clusters among species, which could provide another perspective on species-specific environmental adaptation mechanisms.
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Affiliation(s)
- Byeollee Kim
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, Republic of Korea
| | - So-Ra Han
- Genome-Based BioIT Convergence Institute, Asan, Republic of Korea
| | - Hyun Lee
- Genome-Based BioIT Convergence Institute, Asan, Republic of Korea
- Division of Computer Science and Engineering, SunMoon University, Asan, Republic of Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, Republic of Korea
- Genome-Based BioIT Convergence Institute, Asan, Republic of Korea
- Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan, Republic of Korea
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Hassan SS, Shams R, Camps I, Basharat Z, Sohail S, Khan Y, Ullah A, Irfan M, Ali J, Bilal M, Morel CM. Subtractive sequence analysis aided druggable targets mining in Burkholderia cepacia complex and finding inhibitors through bioinformatics approach. Mol Divers 2023; 27:2823-2847. [PMID: 36567421 PMCID: PMC9790820 DOI: 10.1007/s11030-022-10584-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 12/05/2022] [Indexed: 12/27/2022]
Abstract
Burkholderia cepacia complex (BCC) is a group of gram-negative bacteria composed of at least 20 different species that cause diseases in plants, animals as well as humans (cystic fibrosis and airway infection). Here, we analyzed the proteomic data of 47 BCC strains by classifying them in three groups. Phylogenetic analyses were performed followed by individual core region identification for each group. Comparative analysis of the three individual core protein fractions resulted in 1766 ortholog/proteins. Non-human homologous proteins from the core region gave 1680 proteins. Essential protein analyses reduced the target list to 37 proteins, which were further compared to a closely related out-group, Burkholderia gladioli ATCC 10,248 strain, resulting in 21 proteins. 3D structure modeling, validation, and druggability step gave six targets that were subjected to further target prioritization parameters which ultimately resulted in two BCC targets. A library of 12,000 ZINC drug-like compounds was screened, where only the top hits were selected for docking orientations. These included ZINC01405842 (against Chorismate synthase aroC) and ZINC06055530 (against Bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/Glucosamine-1-phosphate acetyltransferase glmU). Finally, dynamics simulation (200 ns) was performed for each ligand-receptor complex, followed by ADMET profiling. Of these targets, details of their applicability as drug targets have not yet been elucidated experimentally, hence making our predictions novel and it is suggested that further wet-lab experimentations should be conducted to test the identified BCC targets and ZINC scaffolds to inhibit them.
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Affiliation(s)
- Syed Shah Hassan
- Jamil–ur–Rehman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270 Pakistan
- Centre for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Building “Expansão”, 8th Floor Room 814, Av. Brasil 4036, Manguinhos, Rio de Janeiro, RJ 21040-361 Brazil
- Department of Chemistry, Islamia College Peshawar, Peshawar, 25000 KP Pakistan
| | - Rida Shams
- Department of Chemistry, Islamia College Peshawar, Peshawar, 25000 KP Pakistan
| | - Ihosvany Camps
- Laboratório de Modelagem Computacional—LaModel, Instituto de Ciências Exatas—ICEx. Universidade Federal de Alfenas—UNIFAL-MG, Alfenas, Minas Gerais Brazil
- High Performance & Quantum Computing Labs, Waterloo, Canada
| | - Zarrin Basharat
- Jamil–ur–Rehman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270 Pakistan
| | - Saman Sohail
- Department of Chemistry, Islamia College Peshawar, Peshawar, 25000 KP Pakistan
| | - Yasmin Khan
- Jamil–ur–Rehman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270 Pakistan
| | - Asad Ullah
- Department of Chemistry, Islamia College Peshawar, Peshawar, 25000 KP Pakistan
| | - Muhammad Irfan
- Jamil–ur–Rehman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270 Pakistan
| | - Javed Ali
- Department of Chemistry, Kohat University of Science & Technology–KUST, Kohat, KP Pakistan
| | - Muhammad Bilal
- Department of Chemistry, Kohat University of Science & Technology–KUST, Kohat, KP Pakistan
| | - Carlos M. Morel
- Centre for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Building “Expansão”, 8th Floor Room 814, Av. Brasil 4036, Manguinhos, Rio de Janeiro, RJ 21040-361 Brazil
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Beca FA, Sengillo JD, Robles-Holmes HK, Iyer PG, Miller D, Yannuzzi NA, Flynn HW. Endophthalmitis caused by Burkholderia cepacia complex (BCC): clinical characteristics, antibiotic susceptibilities, and treatment outcomes. J Ophthalmic Inflamm Infect 2023; 13:48. [PMID: 37922028 PMCID: PMC10624773 DOI: 10.1186/s12348-023-00370-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/15/2023] [Indexed: 11/05/2023] Open
Abstract
PURPOSE To report the clinical characteristics, antibiotic susceptibilities, and review the literature of Burkholderia cepacia complex (BCC) associated endophthalmitis. STUDY DESIGN Retrospective, observational case series. METHODS Clinical and microbiology records were reviewed for patients evaluated at the Bascom Palmer Eye Institute and diagnosed wisth culture-confirmed endophthalmitis due to BCC. Antibiotic susceptibility profiles were generated using standard microbiologic protocols via an automated VITEK system. RESULTS Endophthalmitis associated with BCC was diagnosed in three patients. Infection occurred in the setting of post-penetrating keratoplasty (PKP), glaucoma filtering surgery, and suspected trauma. All isolates demonstrated in vitro susceptibility to ceftazidime and meropenem. Presenting visual acuity (VA) ranged from hand motion to light perception. Initial treatment strategies included intravitreal ceftazidime (2.25 mg/0.1 mL) and vancomycin (1.0 mg/0.1 mL) injections with fortified topical antibiotics in 2 patients, and surgical debridement of a corneoscleral melt with patch graft along with both topical fortified antibiotics oral antibiotics in the third patient. In all 3 patients, there was no VA improvement at last follow-up, as 2 eyes ultimately underwent enucleation and 1 eye exhibited phthisis bulbi at last follow-up. BCC related endophthalmitis was reviewed among 13 reports. Treatment outcomes were generally poor and antibiotic resistance was common. These BCC isolates cases demonstrated broad resistance patterns, with susceptibilities to ceftazidime (58%), ciprofloxacin (53%), and gentamicin (33%). CONCLUSIONS Endophthalmitis caused by B. cepacia is a rare clinical entity with generally poor visual outcomes despite prompt treatment with appropriate antibiotics.
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Affiliation(s)
- Flavius A Beca
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jesse D Sengillo
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Hailey K Robles-Holmes
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Prashanth G Iyer
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Darlene Miller
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Nicolas A Yannuzzi
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Harry W Flynn
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA.
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Rivolo M, Ruka E, Piazza S. Burkholderia cepacia skin-related ulceration: a case report. BRITISH JOURNAL OF NURSING (MARK ALLEN PUBLISHING) 2023; 32:S6-S10. [PMID: 37949489 DOI: 10.12968/bjon.2023.32.sup20.s6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Treatment of infected wounds remains a major challenge for clinicians. Antimicrobial stewardship is an important pillar in wound treatment and, as the role of bacteria in wound repair is not well understood, new treatment options and products are constantly being developed to tackle local infection and biofilm. This case report describes a case of antibiotic-resistant Burkholderia cepacia skin infection and subsequent leg ulceration in an 86-year-old man during the COVID pandemic in Italy, which was successfully treated in a conservative way using 1% acetic acid and silver oxysalts in conjunction with compression bandage.
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Affiliation(s)
- Massimo Rivolo
- Independent Tissue Viability Nurse Consultant, Clinical Director International Centre Wound Care Nursing, Turin, Italy
| | - Erind Ruka
- Plastic Surgeon, Plastic Surgery Unit, Umberto I Mauriziano Hospital Turin, Italy
| | - Salvatore Piazza
- Vascular Consultant, Vascular and Endovascular Surgery Unit, Umberto I Mauriziano Hospital Turin, Italy
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Liu A, Phillips K, Jia J, Deng P, Zhang D, Chang S, Lu SE. Development of a qPCR detection approach for pathogenic Burkholderia cenocepacia associated with fresh vegetables. Food Microbiol 2023; 115:104333. [PMID: 37567623 DOI: 10.1016/j.fm.2023.104333] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 08/13/2023]
Abstract
Natural environment serves as a reservoir for Burkholderia cepacia complex organisms, including the highly transmissible opportunistic human pathogen B. cenocepacia. Currently, there is a lack of an effective and quantitative method for B. cenocepacia detection in fresh food and other environmental niches. A quantitative real-time PCR (qPCR) detection method for B. cenocepacia bacteria was established in this study and validated using artificially inoculated fresh vegetable samples. Genome-wide comparative methods were applied to identify target regions for the design of species-specific primers. Assay specificity was measured with 12 strains of closely related Burkholderia bacteria and demonstrated the primer pair BCF6/R6 were 100% specific for detection of B. cenocepacia. The described qPCR assay evaluated B. cenocepacia with a 2 pg μl-1 limit of detection and appropriate linearity (R2 = 0.999). In 50 samples of experimentally infected produce (lettuce, onion, and celery), the assay could detect B. cenocepacia as low as 2.6 × 102 cells in each sample equal to 1 g. The established qPCR method quantitatively detects B. cenocepacia with high sensitivity and specificity, making it a promising technique for B. cenocepacia detection and epidemiological research on B. cepacia complex organisms from fresh vegetables.
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Affiliation(s)
- Aixin Liu
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, 39762, USA; College of Plant Protection, Shandong Agricultural University, Shandong, 271018, China
| | - Kate Phillips
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Jiayuan Jia
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Peng Deng
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Dunhua Zhang
- Aquatic Animal Health Research Unit, USDA-ARS, 990 Wire Road, Auburn, AL, 36832, USA
| | - Sam Chang
- Coastal Research and Extension Center, Seafood Processing Laboratory, Department of Food Science, Nutrition and Health Promotion, Mississippi State University, Pascagoula, MS, 39567, USA
| | - Shi-En Lu
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, 39762, USA.
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Beca FA, Sengillo JD, Robles-Holmes HK, Iyer PG, Miller D, Yannuzzi NA, Flynn HW. Endophthalmitis caused by Burkholderia cepacia complex (BCC): Clinical characteristics, antibiotic susceptibilities, and treatment outcomes. RESEARCH SQUARE 2023:rs.3.rs-3181158. [PMID: 37503162 PMCID: PMC10371171 DOI: 10.21203/rs.3.rs-3181158/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Purpose To report the clinical characteristics, antibiotic susceptibilities, and review the literature of Burkholderia cepacia complex (BCC) associated endophthalmitis. Study design Retrospective, observational case series. Methods Clinical and microbiology records were reviewed for patients evaluated at the Bascom Palmer Eye Institute and diagnosed with culture-confirmed endophthalmitis due to BCC. Antibiotic susceptibility profiles were generated using standard microbiologic protocols via an automated VITEK system. Results Endophthalmitis associated with BCC was diagnosed in three patients. Infection occurred in the setting of post-penetrating keratoplasty (PKP), glaucoma filtering surgery, and suspected trauma. All isolates demonstrated in vitro susceptibility to ceftazidime and meropenem. Presenting visual acuity (VA) ranged from hand motion to light perception. Initial treatment strategies included intravitreal ceftazidime (2.25 mg/0.1 mL) and vancomycin (1.0 mg/0.1mL) injections with fortified topical antibiotics in 2 patients, and surgical debridement of a corneoscleral melt with patch graft along with both topical fortified antibiotics oral antibiotics in the third patient. In all 3 patients, there was no VA improvement at last follow-up, as 2 eyes ultimately underwent enucleation and 1 eye exhibited phthisis bulbi at last follow-up. BCC related endophthalmitis was reviewed among 13 reports. Treatment outcomes were generally poor and antibiotic resistance was common. These BCC isolates cases demonstrated broad resistance patterns, with susceptibilities to ceftazidime (58%), ciprofloxacin (53%), and gentamicin (33%). Conclusions Endophthalmitis caused by B. cepacia is a rare clinical entity with generally poor visual outcomes despite prompt treatment with appropriate antibiotics.
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Thornton CS, Parkins MD. Microbial Epidemiology of the Cystic Fibrosis Airways: Past, Present, and Future. Semin Respir Crit Care Med 2023; 44:269-286. [PMID: 36623820 DOI: 10.1055/s-0042-1758732] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Progressive obstructive lung disease secondary to chronic airway infection, coupled with impaired host immunity, is the leading cause of morbidity and mortality in cystic fibrosis (CF). Classical pathogens found in the airways of persons with CF (pwCF) include Pseudomonas aeruginosa, Staphylococcus aureus, the Burkholderia cepacia complex, Achromobacter species, and Haemophilus influenzae. While traditional respiratory-tract surveillance culturing has focused on this limited range of pathogens, the use of both comprehensive culture and culture-independent molecular approaches have demonstrated complex highly personalized microbial communities. Loss of bacterial community diversity and richness, counteracted with relative increases in dominant taxa by traditional CF pathogens such as Burkholderia or Pseudomonas, have long been considered the hallmark of disease progression. Acquisition of these classic pathogens is viewed as a harbinger of advanced disease and postulated to be driven in part by recurrent and frequent antibiotic exposure driven by frequent acute pulmonary exacerbations. Recently, CF transmembrane conductance regulator (CFTR) modulators, small molecules designed to potentiate or restore diminished protein levels/function, have been successfully developed and have profoundly influenced disease course. Despite the multitude of clinical benefits, structural lung damage and consequent chronic airway infection persist in pwCF. In this article, we review the microbial epidemiology of pwCF, focus on our evolving understanding of these infections in the era of modulators, and identify future challenges in infection surveillance and clinical management.
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Affiliation(s)
- Christina S Thornton
- Department of Medicine, Cumming School of Medicine, University of Calgary, Alberta, Canada
| | - Michael D Parkins
- Department of Medicine, Cumming School of Medicine, University of Calgary, Alberta, Canada.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Alberta, Canada
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Behroozian S, Zlosnik JEA, Xu W, Li LY, Davies JE. Antibacterial Activity of a Natural Clay Mineral against Burkholderia cepacia Complex and Other Bacterial Pathogens Isolated from People with Cystic Fibrosis. Microorganisms 2023; 11:microorganisms11010150. [PMID: 36677442 PMCID: PMC9862493 DOI: 10.3390/microorganisms11010150] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/15/2022] [Accepted: 12/28/2022] [Indexed: 01/11/2023] Open
Abstract
There is an impending crisis in healthcare brought about by a new era of untreatable infections caused by bacteria resistant to all available antibiotics. Thus, there is an urgent need to identify novel antimicrobial agents to counter the continuing threat posed by formerly treatable infections. We previously reported that a natural mineral clay known as Kisameet clay (KC) is a potent inhibitor of the organisms responsible for acute infections. Chronic bacterial infections present another major challenge to treatment by antimicrobials, due to their prolonged nature, which results in repeated exposure to antibiotics and a constant selection for antimicrobial resistance. A prime example is bacteria belonging to the Burkholderia cepacia complex (Bcc), which particularly causes some of the most serious chronic lung infections in patients with cystic fibrosis (CF) associated with unpredictable clinical outcomes, poor prognosis, and high mortality rates. Eradication of these organisms from CF patients with limited effective antimicrobial options is a major challenge. Novel therapeutic approaches are urgently required. Here, we report the in vitro antibacterial activity of KC aqueous suspensions (1-10% w/v) and its aqueous extract (L100) against a collection of extensively and multi-drug resistant clinical isolates of Bcc, Pseudomonas aeruginosa, and Stenotrophomonas maltophilia isolated from patients with CF. These findings present a potential novel therapy for further investigation in the clinic.
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Affiliation(s)
- Shekooh Behroozian
- Department of Chemical and Biological Engineering, University of British Columbia, 2360 E Mall, Vancouver, BC V6T 1Z3, Canada
- Correspondence: (S.B.); (J.E.D.)
| | - James E. A. Zlosnik
- Centre for Understanding and Preventing Infection in Children, Division of Infectious Diseases, Department of Pediatrics, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Wanjing Xu
- Department of Civil Engineering, University of British Columbia, 6250 Applied Science Ln, Vancouver, BC V6T 1Z3, Canada
| | - Loretta Y. Li
- Department of Civil Engineering, University of British Columbia, 6250 Applied Science Ln, Vancouver, BC V6T 1Z3, Canada
| | - Julian E. Davies
- Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
- Correspondence: (S.B.); (J.E.D.)
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Jantharadej K, Kongprajug A, Mhuantong W, Limpiyakorn T, Suwannasilp BB, Mongkolsuk S, Sirikanchana K. Comparative genomic analyses of pathogenic bacteria and viruses and antimicrobial resistance genes in an urban transportation canal. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 848:157652. [PMID: 35905960 DOI: 10.1016/j.scitotenv.2022.157652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Water commuting is a major urban transportation method in Thailand. However, urban boat commuters risk exposure to microbially contaminated bioaerosols or splash. We aimed to investigate the microbial community structures, identify bacterial and viral pathogens, and assess the abundance of antimicrobial resistance genes (ARGs) using next-generation sequencing (NGS) at 10 sampling sites along an 18 km transportation boat route in the Saen Saep Canal, which traverses cultural, commercial, and suburban land-based zones. The shotgun metagenomic (Illumina HiSeq) and 16S rRNA gene amplicon (V4 region) (Illumina MiSeq) sequencing platforms revealed diverse microbial clusters aligned with the zones, with explicit segregation between the cultural and suburban sites. The shotgun metagenomic sequencing further identified bacterial and viral pathogens, and ARGs. The predominant bacterial pathogens (>0.5 % relative abundance) were the Burkholderia cepacia complex, Arcobacter butzleri, Burkholderia vietnamiensis, Klebsiella pneumoniae, and the Enterobacter cloacae complex. The viruses (0.28 %-0.67 % abundance in all microbial sequences) comprised mainly vertebrate viruses and bacteriophages, with encephalomyocarditis virus (33.3 %-58.2 % abundance in viral sequences), hepatitis C virus genotype 1, human alphaherpesvirus 1, and human betaherpesvirus 6A among the human viral pathogens. The 15 ARG types contained 611 ARG subtypes, including those resistant to beta-lactam, which was the most diverse and abundant group (206 subtypes; 17.0 %-27.5 %), aminoglycoside (94 subtypes; 9.6 %-15.3 %), tetracycline (80 subtypes; 15.6 %-20.2 %), and macrolide (79 subtypes; 14.5 %-32.1 %). Interestingly, the abundance of ARGs associated with resistance to beta-lactam, trimethoprim, and sulphonamide, as well as A. butzleri and crAssphage, at the cultural sites was significantly different from the other sites (p < 0.05). We demonstrated the benefits of using NGS to deliver insights into microbial communities, and antimicrobial resistance, both of which pose a risk to human health. Using NGS may facilitate microbial risk mitigation and management for urban water commuters and proximal residents.
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Affiliation(s)
- Krittayapong Jantharadej
- Department of Environmental Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok, Thailand
| | - Akechai Kongprajug
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
| | - Wuttichai Mhuantong
- National Center for Genetic Engineering and Biotechnology, Enzyme Technology Research Team, Pathum Thani, Thailand
| | - Tawan Limpiyakorn
- Department of Environmental Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok, Thailand; Center of Excellence on Hazardous Substance Management, Chulalongkorn University, Bangkok, Thailand; Biotechnology for Wastewater Engineering Research Group, Chulalongkorn University, Bangkok, Thailand
| | - Benjaporn Boonchayaanant Suwannasilp
- Department of Environmental Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok, Thailand; Center of Excellence on Hazardous Substance Management, Chulalongkorn University, Bangkok, Thailand; Biotechnology for Wastewater Engineering Research Group, Chulalongkorn University, Bangkok, Thailand
| | - Skorn Mongkolsuk
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok, Thailand
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok, Thailand.
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11
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Abstract
The soil saprophyte, Burkholderia pseudomallei, is the causative agent of melioidosis, a disease endemic in South East Asia and northern Australia. Exposure to B. pseudomallei by either inhalation or inoculation can lead to severe disease. B. pseudomallei rapidly shifts from an environmental organism to an aggressive intracellular pathogen capable of rapidly spreading around the body. The expression of multiple virulence factors at every stage of intracellular infection allows for rapid progression of infection. Following invasion or phagocytosis, B. pseudomallei resists host-cell killing mechanisms in the phagosome, followed by escape using the type III secretion system. Several secreted virulence factors manipulate the host cell, while bacterial cells undergo a shift in energy metabolism allowing for overwhelming intracellular replication. Polymerisation of host cell actin into “actin tails” propels B. pseudomallei to the membranes of host cells where the type VI secretion system fuses host cells into multinucleated giant cells (MNGCs) to facilitate cell-to-cell dissemination. This review describes the various mechanisms used by B. pseudomallei to survive within cells.
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Affiliation(s)
- Nicole M Bzdyl
- The Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, 6009, Australia
| | - Clare L Moran
- The Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, 6009, Australia
| | - Justine Bendo
- The Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, 6009, Australia
| | - Mitali Sarkar-Tyson
- The Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, 6009, Australia
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12
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McAvoy AC, Threatt PH, Kapcia J, Garg N. Discovery of Homogentisic Acid as a Precursor in Trimethoprim Metabolism and Natural Product Biosynthesis. ACS Chem Biol 2022; 18:711-723. [PMID: 36215670 DOI: 10.1021/acschembio.2c00529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Opportunistic infections by Burkholderia cenocepacia are life threatening for patients suffering from cystic fibrosis and chronic granulomatous disease. These infections are often associated with variable clinical outcomes, prompting an interest in molecular investigations of phenotypes associated with disease severity. The production of the pyomelanin pigment is one such phenotype, which was recently linked to the ability of clinical strains to carry out biotransformation of the antibiotic trimethoprim. However, this biotransformation product was not identified, and differences in metabolite production associated with pyomelanin pigmentation are poorly understood. Here, we identify several key metabolites produced exclusively by the pyomelanin-producing strains. To provide insight into the structures and biosynthetic origin of these metabolites, we developed a mass spectrometry-based strategy coupling unsupervised in silico substructure prediction with stable isotope labeling referred to as MAS-SILAC (Metabolite Annotation assisted by Substructure discovery and Stable Isotope Labeling by Amino acids in Cell culture). This approach led to discovery of homogentisic acid as a precursor for biosynthesis of several natural products and for biotransformation of trimethoprim, representing a previously unknown mechanism of antibiotic tolerance. This work presents application of computational methods for analysis of untargeted metabolomic data to link the chemotype of pathogenic microorganisms with a specific phenotype. The observations made in this study provide insights into the clinical significance of the melanated phenotype.
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Affiliation(s)
- Andrew C McAvoy
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, Georgia 30332-2000, United States
| | - Paxton H Threatt
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, Georgia 30332-2000, United States
| | - Joseph Kapcia
- Department of Molecular Biology and Biochemistry, University of California, Irvine, 3205 McGaugh Hall, Irvine, California 92697-2525, United States
| | - Neha Garg
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, Georgia 30332-2000, United States.,Center for Microbial Dynamics and Infection, Georgia Institute of Technology, 311 Ferst Drive, ES&T, Atlanta, Georgia 30332, United States
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13
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Zhang L, Tolan J, Lavigne N, Montei C, Donofrio R, Biswas P. Soleris® Automated System for the Rapid Detection of Burkholderia cepacia Complex in Cosmetic Products. J AOAC Int 2022; 106:171-178. [PMID: 36130279 PMCID: PMC9779911 DOI: 10.1093/jaoacint/qsac109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/26/2022] [Accepted: 09/07/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND Burkholderia cepacia complex (Bcc) has emerged as an important opportunistic pathogen with rising concern in pharmaceuticals and cosmetic products. The Bcc supplement (S2-BCC-S) was purposely developed and used with the Pseudomonas vial (PD-109) for the detection of Bcc through the Soleris® Next Generation automated instrument system. OBJECTIVE This study aimed to evaluate the performance of the Soleris Bcc testing method for cosmetic products. METHOD Inclusivity and exclusivity were assessed with the Soleris Bcc method and the United States Pharmacopeia (USP) method in three enrichment broths. Matrix testing was conducted using 28 cosmetic products to compare the equivalency of the Soleris Bcc method to that of the USP reference method. Repeatability of the Soleris Bcc assay, method robustness, product stability, and lot-to-lot consistency of the Soleris reagents were also assessed. RESULTS Both the Soleris Bcc and the USP methods supported the growth of all 26 inclusivity strains, except the USP method missed one inclusivity strain in one broth. For exclusivity, 0-6% was presumptive positive with the Soleris Bcc method, and 42-48% was presumptive positive with the reference method. Kappa index was 0.96 for the matrix testing, indicating a good agreement between the Soleris Bcc assay and the reference method for testing Bcc in cosmetics. Repeatability results showed the coefficient of variation was less than 4%. The robustness and ruggedness study yielded detection times within 1 h differences when small variations were introduced. The lot-to-lot study showed consistent results among four lots of the Bcc reagents. CONCLUSIONS The automated Soleris method was successfully demonstrated to be robust, sensitive, and specific for Bcc detection in cosmetic products. HIGHLIGHTS The Soleris Bcc method is user-friendly. It shows the results in real time and generates the report automatically. Implementation of this method for detection of Bcc in cosmetics would save significant time and resources.
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Affiliation(s)
| | - Jerry Tolan
- Microbiology R&D, Neogen Corporation, 620 Lesher Place, Lansing, MI 48912, USA
| | - Nicholas Lavigne
- Microbiology R&D, Neogen Corporation, 620 Lesher Place, Lansing, MI 48912, USA
| | - Carolyn Montei
- Microbiology R&D, Neogen Corporation, 620 Lesher Place, Lansing, MI 48912, USA
| | - Robert Donofrio
- Microbiology R&D, Neogen Corporation, 620 Lesher Place, Lansing, MI 48912, USA
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14
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Alsowayeh N, Albutti A, Al-Shouli ST. Reverse Vaccinology and Immunoinformatic Assisted Designing of a Multi-Epitopes Based Vaccine Against Nosocomial Burkholderia cepacia. Front Microbiol 2022; 13:929400. [PMID: 35875518 PMCID: PMC9297367 DOI: 10.3389/fmicb.2022.929400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/20/2022] [Indexed: 11/29/2022] Open
Abstract
Burkholderia cepacia is a Gram-negative nosocomial pathogen and is considered as a troublesome bacterium due to its resistance to many common antibiotics. There is no licensed vaccine available to prevent the pathogen infections, thus making the condition more alarming and warrant the search for novel therapeutic and prophylactic approaches. In order to identify protective antigens from pathogen proteome, substantial efforts are put forth to prioritized potential vaccine targets and antigens that can be easily evaluated experimentally. In this vaccine design investigation, it was found that B. cepacia completely sequenced proteomes available in NCBI genome database has a total of 28,966 core proteins. Out of total, 25,282 proteins were found redundant while 3,684 were non-redundant. Subcellular localization revealed that 18 proteins were extracellular, 31 were part of the outer membrane, 75 proteins were localized in the periplasm, and 23 were virulent proteins. Five proteins namely flagellar hook protein (FlgE), fimbria biogenesis outer membrane usher protein, Type IV pilus secretin (PilQ), cytochrome c4, flagellar hook basal body complex protein (FliE) were tested for positive for antigenic, non-toxic, and soluble epitopes during predication of B-cell derived T-cell epitopes. A vaccine peptide of 14 epitopes (joined together via GPGPG linkers) and cholera toxin B subunit (CTBS) adjuvant (joined to epitopes peptide via EAAAK linker) was constructed. Binding interaction of the modeled vaccine with MHC-I, MHC-II, and Toll-like receptor 4 (TLR-4) immune receptors was studied using molecular docking studies and further analyzed in molecular dynamics simulations that affirms strong intermolecular binding and stable dynamics. The maximum root mean square deviation (RMSD) score of complexes in the simulation time touches to 2 Å. Additionally, complexes binding free energies were determined that concluded robust interaction energies dominated by van der Waals. The total energy of each complex is < -190 kcal/mol. In summary, the designed vaccine showed promising protective immunity against B. cepacia and needs to be examined in experiments.
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Affiliation(s)
- Noorah Alsowayeh
- Department of Biology, College of Education (Majmaah), Majmaah University, Al-Majmaah, Saudi Arabia
| | - Aqel Albutti
- Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Samia T. Al-Shouli
- Immunology Unit, Pathology Department, College of Medicine, King Saud University, Riyadh, Saudi Arabia
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15
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Antibiotic Therapy for Difficult-to-Treat Infections in Lung Transplant Recipients: A Practical Approach. Antibiotics (Basel) 2022; 11:antibiotics11050612. [PMID: 35625256 PMCID: PMC9137688 DOI: 10.3390/antibiotics11050612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 01/27/2023] Open
Abstract
Lung transplant recipients are at higher risk to develop infectious diseases due to multi-drug resistant pathogens, which often chronically colonize the respiratory tract before transplantation. The emergence of these difficult-to-treat infections is a therapeutic challenge, and it may represent a contraindication to lung transplantation. New antibiotic options are currently available, but data on their efficacy and safety in the transplant population are limited, and clinical evidence for choosing the most appropriate antibiotic therapy is often lacking. In this review, we provide a summary of the best evidence available in terms of choice of antibiotic and duration of therapy for MDR/XDR P. aeruginosa, Burkholderia cepacia complex, Mycobacterium abscessus complex and Nocardia spp. infections in lung transplant candidates and recipients.
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16
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Zhao Q, Yin J, Ma J, Liu X, Wu J, Li C. De novo mutation of CYBB gene in a boy presenting as intra-abdominal infection of Burkholderia contaminans: a case report. Ital J Pediatr 2022; 48:55. [PMID: 35365205 PMCID: PMC8974071 DOI: 10.1186/s13052-022-01246-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/17/2022] [Indexed: 11/23/2022] Open
Abstract
Background Chronic granulomatous disease (CGD) is an inborn error of immunity. It is characterized by recurrent bacterial or fungal infections, including infections by Burkholderia species. This is due to respiratory burst dysfunction of phagocytes. Currently, there is no report on Burkholderia contaminans (B. Contaminans) infection in children with CGD. Case presentation We present a previously healthy, 17-month-old Chinese boy infected with B. Contaminans in the intra-abdominal regions. Immunological screening, including assessment of cellular immunity and humoral immunity did not yield conclusive results. The level of nicotinamide adenine dinucleotide phosphatase (NADPH) activity was decreased and whole-exome sequencing identified a de novo mutation in the CYBB gene. Conclusions For specific pathogens such as B. Contaminans, immune assessment should be carried out even if there is no positive medical history or specificity in basic immunity screening.
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Affiliation(s)
- Qianqian Zhao
- Department of Pediatric Immunology, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China
| | - Jing Yin
- Department of Pediatric Immunology, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China
| | - Jijun Ma
- Department of Pediatric Immunology, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China
| | - Xiaoxue Liu
- Department of Pediatric Immunology, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China
| | - Jiawen Wu
- Department of Pediatric Immunology, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China
| | - Chongwei Li
- Department of Pediatric Immunology, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.
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17
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Wang X, Xie Z, Zhao J, Zhu Z, Yang C, Liu Y. Prospects of Inhaled Phage Therapy for Combatting Pulmonary Infections. Front Cell Infect Microbiol 2021; 11:758392. [PMID: 34938668 PMCID: PMC8685529 DOI: 10.3389/fcimb.2021.758392] [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: 08/13/2021] [Accepted: 10/04/2021] [Indexed: 12/30/2022] Open
Abstract
With respiratory infections accounting for significant morbidity and mortality, the issue of antibiotic resistance has added to the gravity of the situation. Treatment of pulmonary infections (bacterial pneumonia, cystic fibrosis-associated bacterial infections, tuberculosis) is more challenging with the involvement of multi-drug resistant bacterial strains, which act as etiological agents. Furthermore, with the dearth of new antibiotics available and old antibiotics losing efficacy, it is prudent to switch to non-antibiotic approaches to fight this battle. Phage therapy represents one such approach that has proven effective against a range of bacterial pathogens including drug resistant strains. Inhaled phage therapy encompasses the use of stable phage preparations given via aerosol delivery. This therapy can be used as an adjunct treatment option in both prophylactic and therapeutic modes. In the present review, we first highlight the role and action of phages against pulmonary pathogens, followed by delineating the different methods of delivery of inhaled phage therapy with evidence of success. The review aims to focus on recent advances and developments in improving the final success and outcome of pulmonary phage therapy. It details the use of electrospray for targeted delivery, advances in nebulization techniques, individualized controlled inhalation with software control, and liposome-encapsulated nebulized phages to take pulmonary phage delivery to the next level. The review expands knowledge on the pulmonary delivery of phages and the advances that have been made for improved outcomes in the treatment of respiratory infections.
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Affiliation(s)
- Xiang Wang
- Department of Pulmonary and Critical Care Medicine, The Second People's Hospital of Kunming, Kunming, China
| | - Zuozhou Xie
- Department of Pulmonary and Critical Care Medicine, The Second People's Hospital of Kunming, Kunming, China
| | - Jinhong Zhao
- Department of Pulmonary and Critical Care Medicine, The Second People's Hospital of Kunming, Kunming, China
| | - Zhenghua Zhu
- Department of Pulmonary and Critical Care Medicine, The Second People's Hospital of Kunming, Kunming, China
| | - Chen Yang
- Department of Pulmonary and Critical Care Medicine, The Second People's Hospital of Kunming, Kunming, China
| | - Yi Liu
- Department of Pulmonary and Critical Care Medicine, The Second People's Hospital of Kunming, Kunming, China
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18
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Luk KS, Tsang YM, Ho AYM, To WK, Wong BKH, Wong MML, Wong YC. Invasive Burkholderia cepacia Complex Infections among Persons Who Inject Drugs, Hong Kong, China, 2016-2019. Emerg Infect Dis 2021; 28:323-330. [PMID: 34906288 PMCID: PMC8798689 DOI: 10.3201/eid2802.210945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
During March 2016–January 2019, Burkholderia cepacia complex (BCC) infection developed in 13 persons who inject drugs (PWID) in Kowloon West Region, Hong Kong, China. Seven cases were infective spondylitis, 2 endocarditis, 2 septic arthritis, 1 intramuscular abscess and bacteremia, and 1 necrotizing fasciitis. Pulsed-field gel electrophoresis revealed that the isolates from 9 patients were clonally related. This clone caused major illness, and 11 of the 13 patients required surgical treatment. Clinicians should be aware of this pathogen and the appropriate broad-spectrum antimicrobial drugs to empirically prescribe for PWID with this life-threatening infection. Close collaboration among public health authorities, outreach social workers, and methadone clinics is essential for timely prevention and control of outbreaks in the PWID population.
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19
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Metabolomic profiling of Burkholderia cenocepacia in synthetic cystic fibrosis sputum medium reveals nutrient environment-specific production of virulence factors. Sci Rep 2021; 11:21419. [PMID: 34725378 PMCID: PMC8560942 DOI: 10.1038/s41598-021-00421-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/12/2021] [Indexed: 12/13/2022] Open
Abstract
Infections by Burkholderia cenocepacia lead to life-threatening disease in immunocompromised individuals, including those living with cystic fibrosis (CF). While genetic variation in various B. cenocepacia strains has been reported, it remains unclear how the chemical environment of CF lung influences the production of small molecule virulence factors by these strains. Here we compare metabolomes of three clinical B. cenocepacia strains in synthetic CF sputum medium (SCFM2) and in a routine laboratory medium (LB), in the presence and absence of the antibiotic trimethoprim. Using a mass spectrometry-based untargeted metabolomics approach, we identify several compound classes which are differentially produced in SCFM2 compared to LB media, including siderophores, antimicrobials, quorum sensing signals, and various lipids. Furthermore, we describe that specific metabolites are induced in the presence of the antibiotic trimethoprim only in SCFM2 when compared to LB. Herein, C13-acyl-homoserine lactone, a quorum sensing signal previously not known to be produced by B. cenocepacia as well as pyochelin-type siderophores were exclusively detected during growth in SCFM2 in the presence of trimethoprim. The comparative metabolomics approach described in this study provides insight into environment-dependent production of secondary metabolites by B. cenocepacia strains and suggests future work which could identify personalized strain-specific regulatory mechanisms involved in production of secondary metabolites. Investigations into whether antibiotics with different mechanisms of action induce similar metabolic alterations will inform development of combination treatments aimed at effective clearance of Burkholderia spp. pathogens.
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20
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Hamahata A, Mitsusada S, Iwata T, Nakajima K, Ogawa Y, Miyazaki A, Kobayashi M, Fujiwara Y, Asano Y, Mabuchi K, Yoshida M, Misawa A. Liver Cirrhosis Complicated by Spontaneous Bacterial Peritonitis Caused by the Burkholderia cepacia Complex. Intern Med 2021; 60:3435-3440. [PMID: 33994438 PMCID: PMC8627796 DOI: 10.2169/internalmedicine.7170-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
A 79-year-old man with underlying alcoholic liver cirrhosis presented with complaints of a fever, abdominal pain, and difficulty walking. A diagnostic work-up revealed liver atrophy and chylous ascites, and spontaneous bacterial peritonitis (SBP) was diagnosed based on the cell and neutrophil counts. The Burkholderia cepacia complex (Bcc) was detected on blood and ascitic fluid cultures. Although broad-spectrum antibiotic therapy was initiated, the infection was difficult to control, and the patient died of multiple organ failure. Bcc is often multidrug-resistant and difficult to treat. SBP caused by Bcc has been rarely reported and may have a serious course, thus necessitating caution.
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Affiliation(s)
- Arisa Hamahata
- Department of Gastroenterology, Tokyo-Kita Medical Center, Japan
| | - Seiya Mitsusada
- Department of Gastroenterology, Tokyo-Kita Medical Center, Japan
| | - Tomoyuki Iwata
- Department of Gastroenterology, Tokyo-Kita Medical Center, Japan
| | - Ken Nakajima
- Department of Gastroenterology, Tokyo-Kita Medical Center, Japan
| | - Yuki Ogawa
- Department of Gastroenterology, Tokyo-Kita Medical Center, Japan
| | - Akira Miyazaki
- Department of Gastroenterology, Tokyo-Kita Medical Center, Japan
| | - Marina Kobayashi
- Department of Gastroenterology, Tokyo-Kita Medical Center, Japan
| | - Yushi Fujiwara
- Department of Gastroenterology, Tokyo-Kita Medical Center, Japan
| | - Yu Asano
- Department of Gastroenterology, Tokyo-Kita Medical Center, Japan
| | - Kazuhisa Mabuchi
- Department of Gastroenterology, Tokyo-Kita Medical Center, Japan
| | - Miki Yoshida
- Department of Gastroenterology, Tokyo-Kita Medical Center, Japan
| | - Ayako Misawa
- Department of Gastroenterology, Tokyo-Kita Medical Center, Japan
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21
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Rana A, Patton D, Turner NT, Dillon MM, Cooper VS, Sung W. Precise measurement of the fitness effects of spontaneous mutations by droplet digital PCR in Burkholderia cenocepacia. Genetics 2021; 219:6325026. [PMID: 34849876 DOI: 10.1093/genetics/iyab117] [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: 04/04/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 11/12/2022] Open
Abstract
Understanding how mutations affect survivability is a key component to knowing how organisms and complex traits evolve. However, most mutations have a minor effect on fitness and these effects are difficult to resolve using traditional molecular techniques. Therefore, there is a dire need for more accurate and precise fitness measurements methods. Here, we measured the fitness effects in Burkholderia cenocepacia HI2424 mutation accumulation (MA) lines using droplet-digital polymerase chain reaction (ddPCR). Overall, the fitness measurements from ddPCR-MA are correlated positively with fitness measurements derived from traditional phenotypic marker assays (r = 0.297, P = 0.05), but showed some differences. First, ddPCR had significantly lower measurement variance in fitness (F = 3.78, P < 2.6 × 10-13) in control experiments. Second, the mean fitness from ddPCR-MA measurements were significantly lower than phenotypic marker assays (-0.0041 vs -0.0071, P = 0.006). Consistent with phenotypic marker assays, ddPCR-MA measurements observed multiple (27/43) lineages that significantly deviated from mean fitness, suggesting that a majority of the mutations are neutral or slightly deleterious and intermixed with a few mutations that have extremely large effects. Of these mutations, we found a significant excess of mutations within DNA excinuclease and Lys R transcriptional regulators that have extreme deleterious and beneficial effects, indicating that modifications to transcription and replication may have a strong effect on organismal fitness. This study demonstrates the power of ddPCR as a ubiquitous method for high-throughput fitness measurements in both DNA- and RNA-based organisms regardless of cell type or physiology.
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Affiliation(s)
- Anita Rana
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - David Patton
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Nathan T Turner
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Marcus M Dillon
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S3B2, Canada
| | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Way Sung
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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22
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Conservation of Resistance-Nodulation-Cell Division Efflux Pump-Mediated Antibiotic Resistance in Burkholderia cepacia Complex and Burkholderia pseudomallei Complex Species. Antimicrob Agents Chemother 2021; 65:e0092021. [PMID: 34181473 DOI: 10.1128/aac.00920-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Burkholderia cepacia complex (Bcc) and Burkholderia pseudomallei complex (Bpc) species include pathogens that are typically multidrug resistant. Dominant intrinsic and acquired multidrug resistance mechanisms are efflux mediated by pumps of the resistance-nodulation-cell division (RND) family. From comparative bioinformatic and, in many instances, functional studies, we infer that RND pump-based resistance mechanisms are conserved in Burkholderia. We propose to use these findings as a foundation for adoption of a uniform RND efflux pump nomenclature.
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23
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Batura D, Boakes E, Hashemzehi T, Khanna P. Burkholderia cenocepacia urosepsis with a perinephric haematoma in an immunocompetent patient with ureteral calculus obstruction. Br J Hosp Med (Lond) 2021; 82:1. [PMID: 34431337 DOI: 10.12968/hmed.2020.0648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Deepak Batura
- Department of Urology, London North West University Healthcare NHS Trust, London, UK
| | - Eve Boakes
- Department of Urology, London North West University Healthcare NHS Trust, London, UK
| | - Tumaj Hashemzehi
- Department of Urology, London North West University Healthcare NHS Trust, London, UK
| | - Priya Khanna
- Department of Microbiology, London North West University Healthcare NHS Trust, London, UK
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24
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Ibrahim S, Madigubba H, N HY, Chawla K. Burkholderia cepacia infection in a non-cystic fibrosis patient: an arcane presentation. Access Microbiol 2021; 3:000222. [PMID: 34151173 PMCID: PMC8208758 DOI: 10.1099/acmi.0.000222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/21/2021] [Indexed: 11/29/2022] Open
Abstract
Introduction Burkholderia cepacia is an aerobic, Gram-negative bacillus, which exhibits innate resistance to multiple antibiotics and disinfectants. Although it is a chronic colonizer of the respiratory tract, it may rarely present with fatal necrotizing pneumonia-like features in immunosuppressed individuals, as those with chronic granulomatous disease, or patients with significant pulmonary compromise, like cystic fibrosis. Case Presentation A 76-year-old male presented with complaints of breathlessness, cough with mucoid expectoration and fever for 3 days. He had a history of coronary artery disease, chronic obstructive pulmonary disease (COPD), diabetes mellitus and hypertension, under treatment. Pulmonary function tests were suggestive of very severe obstruction (FEV1/FVC was 55 %). So, clinical diagnosis of acute exacerbation of COPD was established. Sputum culture grew B. cepacia. The patient was treated with ceftazidime and meropenem along with inhalational bronchodilators and steroids, and showed symptomatic response to therapy. Conclusion There is paucity of the literature describing B. cepacia as a potential cause for acute exacerbations in relatively common clinical conditions, such as COPD. This case report highlights the speculation of this rare possibility, thereby alerting a clinician dealing with such cases.
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Affiliation(s)
- Sufyan Ibrahim
- Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Haritha Madigubba
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Himanshu Y N
- Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Kiran Chawla
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
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An Overview of Metabolic Activity, Beneficial and Pathogenic Aspects of Burkholderia Spp. Metabolites 2021; 11:metabo11050321. [PMID: 34067834 PMCID: PMC8156019 DOI: 10.3390/metabo11050321] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 12/24/2022] Open
Abstract
Burkholderia is an important bacterial species which has different beneficial effects, such as promoting the plant growth, including rhizosphere competence for the secretion of allelochemicals, production of antibiotics, and siderophores. In addition, most of Burkholderia species have demonstrated promising biocontrol action against different phytopathogens for diverse crops. In particular, Burkholderia demonstrates significant biotechnological potential as a source of novel antibiotics and bioactive secondary metabolites. The current review is concerned with Burkholderia spp. covering the following aspects: discovering, classification, distribution, plant growth promoting effect, and antimicrobial activity of different species of Burkholderia, shedding light on the most important secondary metabolites, their pathogenic effects, and biochemical characterization of some important species of Burkholderia, such as B. cepacia, B. andropogonis, B. plantarii, B. rhizoxinica, B. glumae, B. caryophylli and B. gladioli.
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26
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Miryala R, Marathe N, Mallepally AR, Das K, Mohapatra B. Iatrogenic postoperative spondylodiscitis attributed to Burkholderia cepacia infection in an immunocompetent patient. Surg Neurol Int 2021; 12:138. [PMID: 33948309 PMCID: PMC8088530 DOI: 10.25259/sni_518_2020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 08/29/2020] [Indexed: 11/04/2022] Open
Abstract
Background Pyogenic spondylodiscitis (PS) is a rare infection involving the intervertebral disk space, adjacent vertebral endplates, and vertebral bodies. PS occurs in the elderly and immunocompromised patients, and is an uncommon cause of initial and/or postoperative PS. There are only seven cases involving this organism reported in literature. Case Description Here, we present a 35-year-old male who following a lumbar discectomy developed a postoperative iatrogenic PS uniquely attributed to Burkholderia cepacia. The patient was successfully managed with postoperative surgical debridement and antibiotic therapy. Conclusion Rarely, B. cepacia may be the offending organism resulting in a postoperative lumbar PS.
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Affiliation(s)
- Rakesh Miryala
- Department of Orthopedics, Division of Spine Services, Indian Spinal Injuries Centre, New Delhi, India
| | - Nandan Marathe
- Department of Orthopedics, Division of Spine Services, Indian Spinal Injuries Centre, New Delhi, India
| | | | - Kalidutta Das
- Department of Orthopedics, Division of Spine Services, Indian Spinal Injuries Centre, New Delhi, India
| | - Bibhudendu Mohapatra
- Department of Orthopedics, Division of Spine Services, Indian Spinal Injuries Centre, New Delhi, India
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27
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Lind C, Olsen K, Angelsen NK, Krefting EA, Fossen K, Gravningen K, Depoorter E, Vandamme P, Bertelsen G. Clinical course, treatment and visual outcome of an outbreak of Burkholderia contaminans endophthalmitis following cataract surgery. J Ophthalmic Inflamm Infect 2021; 11:12. [PMID: 33870459 PMCID: PMC8053629 DOI: 10.1186/s12348-021-00242-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/09/2021] [Indexed: 02/06/2023] Open
Abstract
Background Postoperative endophthalmitis is a rare but dreaded complication of intraocular surgery and often results in severe visual impairment or blindness. The present study describes the clinical course, treatment and visual outcome of an outbreak of Burkholderia contaminans endophthalmitis following cataract surgery. Methods Among 290 patients who underwent uneventful phacoemulsification cataract surgery at one outpatient clinic between January 4th and 28th 2019, 6 cases developed Burkholderia contaminans endophthalmitis. Clinical data were collected by retrospective review of patient records. Microbiological samples from vitreous aspirates, intraocular lenses (IOL) and lens capsules were cultured, and recA and draft whole genome sequences analysed. Results The recA sequences of all Burkholderia contaminans isolates and the allelic profile of the isolates were identical. All cases had a similar clinical presentation with rapid development of endophthalmitis symptoms with variable time to onset. The mean time to admission was 34 days (12–112 days). All cases had a seemingly favourable response to intravitreal antibiotics. However, acute recurrences occurred after long time periods (12–71 days). The cases experienced between 0 and 3 recurrences. Due to persistent infection, the cases received between 5 and 15 treatments (mean 7.8) including IOL and lens capsule explantation in 5 of 6 cases. Burkholderia contaminans was detected in all explanted lens capsules. The final corrected distance visual acuity (CDVA, Snellen chart) was between 0.8 and 1.2 and all cases had final CDVA ≥0.8. Conclusions A persistent and intensive treatment approach including total lens capsule and IOL explantation is recommended for Burkholderia contaminans endophthalmitis following cataract surgery and may lead to a favourable visual result.
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Affiliation(s)
- Caroline Lind
- Department of Ophthalmology, University Hospital of North Norway, Tromsø, Norway
| | - Karina Olsen
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Nina K Angelsen
- Department of Ophthalmology, University Hospital of North Norway, Tromsø, Norway
| | - Einar A Krefting
- Department of Ophthalmology, University Hospital of North Norway, Tromsø, Norway
| | - Kristian Fossen
- Department of Ophthalmology, University Hospital of North Norway, Tromsø, Norway
| | - Kirsten Gravningen
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway.,Department of Infection Prevention and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Eliza Depoorter
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Geir Bertelsen
- Department of Ophthalmology, University Hospital of North Norway, Tromsø, Norway. .,Department of Community Medicine, UiT - The Arctic University of Norway, Tromsø, Norway.
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28
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Ho MC, Kang EYC, Yeh LK, Ma DHK, Lin HC, Tan HY, Chen HC, Hsiao CH. Clinico-microbiological profile of Burkholderia cepacia keratitis: a case series. Ann Clin Microbiol Antimicrob 2021; 20:6. [PMID: 33413453 PMCID: PMC7792197 DOI: 10.1186/s12941-020-00407-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 12/03/2020] [Indexed: 11/10/2022] Open
Abstract
Background Burkholderia cepacia, an opportunistic pathogen mainly affecting patients with cystic fibrosis or immunocompromised, has rarely been documented as a cause of corneal infection. The clinical and microbiological profiles of B. cepacia keratitis are reported herein. Methods We retrospectively reviewed the medical record of 17 patients with culture-proven B. cepacia keratitis, treated between 2000 and 2019 at Chang Gung Memorial Hospital, Taiwan. Our data included predisposing factors, clinical presentations, treatments, and visual outcomes of B. cepacia keratitis as well as the drug susceptibility of the causative agent. Results The most common predisposing factor for B. cepacia keratitis was preexisting ocular disease (seven, 41.2%), particularly herpetic keratitis (five). Polymicrobial infection was detected in seven (41.2%) eyes. All B. cepacia isolates were susceptible to ceftazidime. Main medical treatments included levofloxacin or ceftazidime. Surgical treatment was required in five (29.4%) patients. Only four (23.5%) patients exhibited final visual acuity better than 20/200. Conclusions B. cepacia keratitis primarily affects patients with preexisting ocular disease, particularly herpetic keratitis, and responds well to ceftazidime or fluoroquinolones. However, the visual outcomes are generally poor.
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Affiliation(s)
- Ming-Chih Ho
- Department of Ophthalmology, Chang Gung Memorial Hospital, No. 199, Tung-Hwa North Road, Linkou, Taipei, Taiwan
| | - Eugene Yu-Chuan Kang
- Department of Ophthalmology, Chang Gung Memorial Hospital, No. 199, Tung-Hwa North Road, Linkou, Taipei, Taiwan
| | - Lung-Kun Yeh
- Department of Ophthalmology, Chang Gung Memorial Hospital, No. 199, Tung-Hwa North Road, Linkou, Taipei, Taiwan.,College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - David H K Ma
- Department of Ophthalmology, Chang Gung Memorial Hospital, No. 199, Tung-Hwa North Road, Linkou, Taipei, Taiwan.,College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Hsin-Chiung Lin
- Department of Ophthalmology, Chang Gung Memorial Hospital, No. 199, Tung-Hwa North Road, Linkou, Taipei, Taiwan.,College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Hsin-Yuan Tan
- Department of Ophthalmology, Chang Gung Memorial Hospital, No. 199, Tung-Hwa North Road, Linkou, Taipei, Taiwan.,College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Hung-Chi Chen
- Department of Ophthalmology, Chang Gung Memorial Hospital, No. 199, Tung-Hwa North Road, Linkou, Taipei, Taiwan.,College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Ching-Hsi Hsiao
- Department of Ophthalmology, Chang Gung Memorial Hospital, No. 199, Tung-Hwa North Road, Linkou, Taipei, Taiwan. .,College of Medicine, Chang Gung University, Taoyuan, Taiwan.
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29
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Wong MY, Tseng YH, Huang TY, Lin BS, Tung CW, Chu C, Huang YK. Comparison of Microbiological Characteristics and Genetic Diversity between Burkholderia cepacia Complex Isolates from Vascular Access and Other Clinical Infections. Microorganisms 2020; 9:microorganisms9010051. [PMID: 33375496 PMCID: PMC7824166 DOI: 10.3390/microorganisms9010051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/19/2020] [Accepted: 12/23/2020] [Indexed: 11/24/2022] Open
Abstract
Burkholderia cepacia complex (BCC) is a group of closely related bacteria with widespread environmental distribution. BCC bacteria are opportunistic pathogens that cause nosocomial infections in patients, especially cystic fibrosis (CF). Multilocus sequence typing (MLST) is used nowadays to differentiate species within the BCC complex. This study collected 41 BCC isolates from vascular access infections (VAIs) and other clinical infections between 2014 and 2020. We preliminarily identified bacterial isolates using standard biochemical procedures and further conducted recA gene sequencing and MLST for species identification. We determined genetic diversity indices using bioinformatics software. We studied 14 isolates retrieved from patients with VAIs and observed that Burkholderia cepacia was the predominant bacterial species, and B. contaminans followed by B. cenocepacia were mainly retrieved from patients with other infections. According to MLST data, we identified that all B. contaminans isolates belonged to ST102, while a wide variety of sequence types (STs) were found in B. cenocepacia isolates. In summary, the high diversity and easy transmission of BCC increase BCC infections, which provides insights into their potential clinical effects in non-CF infections.
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Affiliation(s)
- Min Yi Wong
- Division of Thoracic and Cardiovascular Surgery, Chiayi Chang Gung Memorial Hospital, Chiayi County 61363, Taiwan; (M.Y.W.); (Y.-H.T.)
- Microbiology Research and Treatment Center, Chiayi Chang Gung Memorial Hospital, Chiayi County 61363, Taiwan;
- Institute of Imaging and Biomedical Photonics, National Chiao Tung University, Tainan 71150, Taiwan;
| | - Yuan-Hsi Tseng
- Division of Thoracic and Cardiovascular Surgery, Chiayi Chang Gung Memorial Hospital, Chiayi County 61363, Taiwan; (M.Y.W.); (Y.-H.T.)
- College of Medicine, Chang Gung University, Taoyuan City 33302, Taiwan;
| | - Tsung-Yu Huang
- Microbiology Research and Treatment Center, Chiayi Chang Gung Memorial Hospital, Chiayi County 61363, Taiwan;
- College of Medicine, Chang Gung University, Taoyuan City 33302, Taiwan;
- Division of Infectious Diseases, Department of Internal Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi County 61363, Taiwan
| | - Bor-Shyh Lin
- Institute of Imaging and Biomedical Photonics, National Chiao Tung University, Tainan 71150, Taiwan;
| | - Chun-Wu Tung
- College of Medicine, Chang Gung University, Taoyuan City 33302, Taiwan;
- Department of Nephrology, Chiayi Chang Gung Memorial Hospital, Chiayi County 61363, Taiwan
| | - Chishih Chu
- Department of Microbiology, Immunology and Biopharmaceuticals, National Chiayi University, Chiayi City 60004, Taiwan;
| | - Yao-Kuang Huang
- Division of Thoracic and Cardiovascular Surgery, Chiayi Chang Gung Memorial Hospital, Chiayi County 61363, Taiwan; (M.Y.W.); (Y.-H.T.)
- College of Medicine, Chang Gung University, Taoyuan City 33302, Taiwan;
- Division of Infectious Diseases, Department of Internal Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi County 61363, Taiwan
- Correspondence: ; Tel.: +886-975368209
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30
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Lee YM, Park KH, Moon C, Kim DY, Lee MS, Kim T, Choo EJ, Chong YP, Kim SH, Kim YS, Woo JH, Chang MS. Management and outcomes of Burkholderia cepacia complex bacteremia in patients without cystic fibrosis: a retrospective observational study. Eur J Clin Microbiol Infect Dis 2020; 39:2057-2064. [PMID: 32583228 DOI: 10.1007/s10096-020-03960-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 06/18/2020] [Indexed: 11/24/2022]
Abstract
Burkholderia cepacia complex (BCC) is an emerging pathogen of nosocomial infection in chronic or critically ill patients without cystic fibrosis (CF). The objective was to evaluate the management and outcomes of BCC bacteremia in patients without CF. We conducted a retrospective study of non-CF adult patients with BCC bacteremia between January 1997 and December 2016 at 4 tertiary hospitals in South Korea. A total of 216 non-CF patients with BCC bacteremia were identified. Most cases were hospital-acquired (79.2%), and the most common source was a central venous catheter (CVC) (42.1%). The rates of susceptibility to trimethoprim-sulfamethoxazole and piperacillin-tazobactam of BCC isolates were high as 92.8% and 90.3%, respectively. The rates of susceptibility to ceftazidime, meropenem, and levofloxacin were 75.5%, 72.3%, and 64.1%, respectively. The 14-day, 30-day, and in-hospital mortality rate was 19.4%, 23.1%, and 31.0%, respectively. Female (OR = 3.1; 95% CI, 1.4-6.8), liver cirrhosis (OR = 6.2; 95% CI, 1.6-16.6), septic shock (OR = 11.2; 95% CI, 5.1-24.8), and catheter-related infection (OR = 2.6, 95% CI, 1.2-5.8) were the independent risk factors for 30-day mortality. The outcome did not differ according to type of antibiotics used. Among 91 patients with CVC-related BCC bacteremia, delayed CVC removal (> 3 days) had a higher rate of persistent bacteremia (54.5 vs. 26.1%; P = 0.03) and lower rate of clinical response (49.0 vs. 71.9%; P = 0.04), compared with early CVC removal (within 3 days). BCC bacteremia occurring in non-CF patients was mostly hospital-acquired and CVC-related. Early removal of the catheter is crucial in treatment of CVC-related BCC bacteremia.
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Affiliation(s)
- Yu-Mi Lee
- Division of Infectious Diseases, Department of Internal Medicine, Kyung Hee University Hospital, Kyung Hee University School of Medicine, Seoul, Republic of Korea
| | - Ki-Ho Park
- Division of Infectious Diseases, Department of Internal Medicine, Kyung Hee University Hospital, Kyung Hee University School of Medicine, Seoul, Republic of Korea
| | - Chisook Moon
- Department of Infectious Diseases, Busan Paik Hospital, Inje University College of Medicine, Busan, Republic of Korea
| | - Dong Youn Kim
- Division of Infectious Diseases, Department of Internal Medicine, Kyung Hee University Hospital, Kyung Hee University School of Medicine, Seoul, Republic of Korea
| | - Mi Suk Lee
- Division of Infectious Diseases, Department of Internal Medicine, Kyung Hee University Hospital, Kyung Hee University School of Medicine, Seoul, Republic of Korea
| | - Tark Kim
- Department of Internal Medicine, SoonChunHyang University Bucheon Hospital, Bucheon, Republic of Korea
| | - Eun Ju Choo
- Department of Internal Medicine, SoonChunHyang University Bucheon Hospital, Bucheon, Republic of Korea
| | - Yong Pil Chong
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea
| | - Sung-Han Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea
| | - Yang Soo Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea
| | - Jun Hee Woo
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea.
| | - Mee Soo Chang
- Department of Pathology, Seoul National University Boramae Hospital, Seoul National University College of Medicine, 20 Boramae-ro 5-gil, Dongjak-gu, Seoul, 07061, Republic of Korea.
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31
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McAvoy AC, Jaiyesimi O, Threatt PH, Seladi T, Goldberg JB, da Silva RR, Garg N. Differences in Cystic Fibrosis-Associated Burkholderia spp. Bacteria Metabolomes after Exposure to the Antibiotic Trimethoprim. ACS Infect Dis 2020; 6:1154-1168. [PMID: 32212725 DOI: 10.1021/acsinfecdis.9b00513] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The Burkholderia cepacia complex is a group of closely related bacterial species with large genomes that infect immunocompromised individuals and those living with cystic fibrosis. Some of these species are found more frequently and cause more severe disease than others, yet metabolomic differences between these have not been described. Furthermore, our understanding of how these species respond to antibiotics is limited. We investigated the metabolomics differences between three most prevalent Burkholderia spp. associated with cystic fibrosis: B. cenocepacia, B. multivorans, and B. dolosa in the presence and absence of the antibiotic trimethoprim. Using a combination of supervised and unsupervised metabolomics data visualization and analysis tools, we describe the overall differences between strains of the same species and between species. Specifically, we report, for the first time, the role of the pyomelanin pathway in the metabolism of trimethoprim. We also report differences in the detection of known secondary metabolites such as fragin, ornibactin, and N-acylhomoserine lactones and their analogs in closely related strains. Furthermore, we highlight the potential for the discovery of new secondary metabolites in clinical strains of Burkholderia spp. The metabolomics differences described in this study highlight the personalized nature of closely related Burkholderia strains.
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Affiliation(s)
- Andrew C. McAvoy
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, Georgia 30332-2000, United States
| | - Olakunle Jaiyesimi
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, Georgia 30332-2000, United States
| | - Paxton H. Threatt
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, Georgia 30332-2000, United States
| | - Tyler Seladi
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, Georgia 30332-2000, United States
| | - Joanna B. Goldberg
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, Emory University School of Medicine, 1510 Clifton Road NE, Suite 3009, Atlanta, Georgia 30322, United States
- Emory-Children’s Cystic Fibrosis Center, Atlanta, Georgia 30322, United States
| | - Ricardo R. da Silva
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Av. do Café - Vila Monte Alegre, Ribeirão Preto, São Paulo 14040-903, Brazil
| | - Neha Garg
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, Georgia 30332-2000, United States
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, Emory University School of Medicine, 1510 Clifton Road NE, Suite 3009, Atlanta, Georgia 30322, United States
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, 311 Ferst Drive, ES&T, Atlanta, Georgia 30332, United States
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 311 Ferst Drive, ES&T, Atlanta, Georgia 30322, United States
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Kim JS, Yoon SJ, Park YJ, Kim SY, Ryu CM. Crossing the kingdom border: Human diseases caused by plant pathogens. Environ Microbiol 2020; 22:2485-2495. [PMID: 32307848 DOI: 10.1111/1462-2920.15028] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 12/16/2022]
Abstract
Interactions between pathogenic microorganisms and their hosts are varied and complex, encompassing open-field scale interactions to interactions at the molecular level. The capacity of plant pathogenic bacteria and fungi to cause diseases in human and animal systems was, until recently, considered of minor importance. However, recent evidence suggests that animal and human infections caused by plant pathogenic fungi, bacteria and viruses may have critical impacts on human and animal health and safety. This review analyses previous research on plant pathogens as causal factors of animal illness. In addition, a case study involving disruption of type III effector-mediated phagocytosis in a human cell line upon infection with an opportunistic phytopathogen, Pseudomonas syringae pv. tomato, is discussed. Further knowledge regarding the molecular interactions between plant pathogens and human and animal hosts is needed to understand the extent of disease incidence and determine mechanisms for disease prevention.
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Affiliation(s)
- Jun-Seob Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseng-gu, Daejeon, South Korea
| | - Sung-Jin Yoon
- Environmental Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseng-gu, Daejeon, South Korea
| | - Young-Jun Park
- Environmental Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseng-gu, Daejeon, South Korea
| | - Seon-Yeong Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseng-gu, Daejeon, South Korea.,Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, South Korea
| | - Choong-Min Ryu
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseng-gu, Daejeon, South Korea
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33
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Li SS, Saleh M, Xiang RF, Ogbomo H, Stack D, Huston SH, Mody CH. Natural killer cells kill Burkholderia cepacia complex via a contact-dependent and cytolytic mechanism. Int Immunol 2020; 31:385-396. [PMID: 31051036 DOI: 10.1093/intimm/dxz016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 04/19/2019] [Indexed: 12/15/2022] Open
Abstract
Burkholderia cepacia complex (Bcc), which includes B. cenocepacia and B. multivorans, pose a life-threatening risk to patients with cystic fibrosis. Eradication of Bcc is difficult due to the high level of intrinsic resistance to antibiotics, and failure of many innate immune cells to control the infection. Because of the pathogenesis of Bcc infections, we wondered if a novel mechanism of microbial host defense involving direct antibacterial activity by natural killer (NK) cells might play a role in the control of Bcc. We demonstrate that NK cells bound Burkholderia, resulting in Src family kinase activation as measured by protein tyrosine phosphorylation, granule release of effector proteins such as perforin and contact-dependent killing of the bacteria. These studies provide a means by which NK cells could play a role in host defense against Bcc infection.
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Affiliation(s)
- Shu Shun Li
- Department of Microbiology, Immunology and Infectious Diseases, Alberta, Canada.,The Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Alberta, Canada
| | - Marwah Saleh
- Department of Microbiology, Immunology and Infectious Diseases, Alberta, Canada
| | - Richard F Xiang
- Department of Microbiology, Immunology and Infectious Diseases, Alberta, Canada.,The Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Alberta, Canada
| | - Henry Ogbomo
- Department of Microbiology, Immunology and Infectious Diseases, Alberta, Canada.,The Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Alberta, Canada
| | - Danuta Stack
- Department of Microbiology, Immunology and Infectious Diseases, Alberta, Canada.,The Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Alberta, Canada
| | - Shaunna H Huston
- The Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Alberta, Canada
| | - Christopher H Mody
- Department of Microbiology, Immunology and Infectious Diseases, Alberta, Canada.,The Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Alberta, Canada.,Department of Medicine, University of Calgary, Calgary, Alberta, Canada
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34
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Jin Y, Zhou J, Zhou J, Hu M, Zhang Q, Kong N, Ren H, Liang L, Yue J. Genome-based classification of Burkholderia cepacia complex provides new insight into its taxonomic status. Biol Direct 2020; 15:6. [PMID: 32131884 PMCID: PMC7057466 DOI: 10.1186/s13062-020-0258-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 01/21/2020] [Indexed: 02/06/2023] Open
Abstract
Background Accurate classification of different Burkholderia cepacia complex (BCC) species is essential for therapy, prognosis assessment and research. The taxonomic status of BCC remains problematic and an improved knowledge about the classification of BCC is in particular needed. Methods We compared phylogenetic trees of BCC based on 16S rRNA, recA, hisA and MLSA (multilocus sequence analysis). Using the available whole genome sequences of BCC, we inferred a species tree based on estimated single-copy orthologous genes and demarcated species of BCC using dDDH/ANI clustering. Results We showed that 16S rRNA, recA, hisA and MLSA have limited resolutions in the taxonomic study of closely related bacteria such as BCC. Our estimated species tree and dDDH/ANI clustering clearly separated 116 BCC strains into 36 clusters. With the appropriate reclassification of misidentified strains, these clusters corresponded to 22 known species as well as 14 putative novel species. Conclusions This is the first large-scale and systematic study of the taxonomic status of the BCC and could contribute to further insights into BCC taxonomy. Our study suggested that conjunctive use of core phylogeny based on single-copy orthologous genes, as well as pangenome-based dDDH/ANI clustering would provide a preferable framework for demarcating closely related species. Reviewer This article was reviewed by Dr. Xianwen Ren.
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Affiliation(s)
- Yuan Jin
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China.,State Key Laboratory of Pathogen and Biosecurity, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Jianglin Zhou
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Jing Zhou
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Mingda Hu
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Qi Zhang
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Na Kong
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China.,Anhui University, Hefei, 230039, Anhui, China
| | - Hongguang Ren
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China. .,State Key Laboratory of Pathogen and Biosecurity, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China.
| | - Long Liang
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China. .,State Key Laboratory of Pathogen and Biosecurity, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China. .,Anhui University, Hefei, 230039, Anhui, China.
| | - Junjie Yue
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China. .,State Key Laboratory of Pathogen and Biosecurity, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China.
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Abstract
Cystic fibrosis (CF) is a genetic, multisystem disease due to defects in the cystic fibrosis transmembrane conductance regulator (CFTR) protein, an anion channel responsible for chloride and bicarbonate trafficking. Although this channel is expressed in many tissues, its impaired function in airway epithelial cells leads to hyperviscous mucous secretions impeding effective mucociliary clearance. Impaired clearance of inhaled microorganisms results in the establishment of chronic infection, triggering an overexaggerated inflammatory response. The resulting release of inflammatory cytokines and enzymes causes pulmonary damage in the form of bronchiectasis, further impairing mucociliary action, forming a vicious cycle. Subsequent respiratory failure remains the leading cause of death in individuals with CF.
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Affiliation(s)
- Stephanie Duggins Davis
- The University of North Carolina at Chapel Hill, Department of Pediatrics, UNC Children’s Hospital, Chapel Hill, NC USA
| | - Margaret Rosenfeld
- Department of Pediatrics, University of Washington School of Medicine, Division of Pulmonary and Sleep Medicine Seattle Children’s Hospital, Seattle, WA USA
| | - James Chmiel
- Department of Pediatrics, Indiana University School of Medicine, Division of Pediatric Pulmonology, Allergy and Sleep Medicine, Riley Hospital for Children at IU Health, Indianapolis, IN USA
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36
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Wallner A, King E, Ngonkeu ELM, Moulin L, Béna G. Genomic analyses of Burkholderia cenocepacia reveal multiple species with differential host-adaptation to plants and humans. BMC Genomics 2019; 20:803. [PMID: 31684866 PMCID: PMC6829993 DOI: 10.1186/s12864-019-6186-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 10/15/2019] [Indexed: 12/17/2022] Open
Abstract
Background Burkholderia cenocepacia is a human opportunistic pathogen causing devastating symptoms in patients suffering from immunodeficiency and cystic fibrosis. Out of the 303 B. cenocepacia strains with available genomes, the large majority were isolated from a clinical context. However, several isolates originate from other environmental sources ranging from aerosols to plant endosphere. Plants can represent reservoirs for human infections as some pathogens can survive and sometimes proliferate in the rhizosphere. We therefore investigated if B. cenocepacia had the same potential. Results We selected genome sequences from 31 different strains, representative of the diversity of ecological niches of B. cenocepacia, and conducted comparative genomic analyses in the aim of finding specific niche or host-related genetic determinants. Phylogenetic analyses and whole genome average nucleotide identity suggest that strains, registered as B. cenocepacia, belong to at least two different species. Core-genome analyses show that the clade enriched in environmental isolates lacks multiple key virulence factors, which are conserved in the sister clade where most clinical isolates fall, including the highly virulent ET12 lineage. Similarly, several plant associated genes display an opposite distribution between the two clades. Finally, we suggest that B. cenocepacia underwent a host jump from plants/environment to animals, as supported by the phylogenetic analysis. We eventually propose a name for the new species that lacks several genetic traits involved in human virulence. Conclusion Regardless of the method used, our studies resulted in a disunited perspective of the B. cenocepacia species. Strains currently affiliated to this taxon belong to at least two distinct species, one having lost several determining animal virulence factors.
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Affiliation(s)
- Adrian Wallner
- IRD, CIRAD, University of Montpellier, IPME; 911 avenue Agropolis, BP 64501, 34394, Montpellier, France
| | - Eoghan King
- IRD, CIRAD, University of Montpellier, IPME; 911 avenue Agropolis, BP 64501, 34394, Montpellier, France
| | - Eddy L M Ngonkeu
- Institute of Agronomic Research for Development (IRAD), PO Box 2123, Yaoundé, Cameroon
| | - Lionel Moulin
- IRD, CIRAD, University of Montpellier, IPME; 911 avenue Agropolis, BP 64501, 34394, Montpellier, France
| | - Gilles Béna
- IRD, CIRAD, University of Montpellier, IPME; 911 avenue Agropolis, BP 64501, 34394, Montpellier, France.
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37
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Sass AM, De Waele S, Daled S, Devreese B, Deforce D, Van Nieuwerburgh F, Coenye T. Small RNA NcS27 co-regulates utilization of carbon sources in Burkholderia cenocepacia J2315. MICROBIOLOGY-SGM 2019; 165:1135-1150. [PMID: 31464662 DOI: 10.1099/mic.0.000848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Small non-coding sRNAs have versatile roles in regulating bacterial metabolism. Four short homologous Burkholderia cenocepacia sRNAs strongly expressed under conditions of growth arrest were recently identified. Here we report the detailed investigation of one of these, NcS27. sRNA NcS27 contains a short putative target recognition sequence, which is conserved throughout the order Burkholderiales. This sequence is the reverse complement of the Shine-Dalgarno sequence of a large number of genes involved in transport and metabolism of amino acids and carbohydrates. Overexpression of NcS27 sRNA had a distinct impact on growth, attenuating growth on a variety of substrates such as phenylalanine, tyrosine, glycerol and galactose, while having no effect on growth on other substrates. Transcriptomics and proteomics of NcS27 overexpression and silencing mutants revealed numerous predicted targets changing expression, notably of genes involved in degradation of aromatic amino acids phenylalanine and tyrosine, and in transport of carbohydrates. The conserved target recognition sequence was essential for growth phenotypes and gene expression changes. Cumulatively, our data point to a role of NcS27 in regulating the shutdown of metabolism upon nutrient deprivation in B. cenocepacia. We propose Burkholderiadouble-hairpin sRNA regulator bdhR1 as designation for ncS27.
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Affiliation(s)
- Andrea M Sass
- Laboratory of Pharmaceutical Microbiology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Stijn De Waele
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Simon Daled
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Bart Devreese
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
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38
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Mereghetti V, Chouaia B, Limonta L, Locatelli DP, Montagna M. Evidence for a conserved microbiota across the different developmental stages of Plodia interpunctella. INSECT SCIENCE 2019; 26:466-478. [PMID: 29090848 DOI: 10.1111/1744-7917.12551] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 08/24/2017] [Accepted: 09/17/2017] [Indexed: 06/07/2023]
Abstract
Diversity and composition of lepidopteran microbiotas are poorly investigated, especially across the different developmental stages. To improve this knowledge, we characterize the microbiota among different developmental stages of the Indian meal moth, Plodia interpunctella, which is considered one of the major pest of commodities worldwide. Using culture-independent approach based on Illumina 16S rRNA gene sequencing we characterized the microbiota of four developmental stages: eggs, first-, and last-instar larvae, and adult. A total of 1022 bacterial OTUs were obtained, showing a quite diversified microbiota associated to all the analyzed stages. The microbiotas associated with P. interpunctella resulted almost constant throughout the developmental stages, with approximately 77% of bacterial OTUs belonging to the phylum of Proteobacteria. The dominant bacterial genus is represented by Burkholderia (∼64%), followed by Propionibacterium, Delftia, Pseudomonas, and Stenotrophomonas. A core bacterial community, composed of 139 OTUs, was detected in all the developmental stages, among which 112 OTUs were assigned to the genus Burkholderia. A phylogenetic reconstruction, based on the 16S rRNA, revealed that our Burkholderia OTUs clustered with Burkholderia cepacia complex, in the same group of those isolated from the hemipterans Gossyparia spuria and Acanthococcus aceris. The functional profiling, predicted on the base of the bacterial 16S rRNA, indicates differences in the metabolic pathways related to metabolism of amino acids between preimaginal and adult stages. We can hypothesize that bacteria may support the insect host during preimaginal stages.
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Affiliation(s)
- Valeria Mereghetti
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milan, Italy
| | - Bessem Chouaia
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milan, Italy
| | - Lidia Limonta
- Dipartimento di Scienze per gli Alimenti la Nutrizione, l'Ambiente, Università degli Studi di Milano, Milan, Italy
| | - Daria Patrizia Locatelli
- Dipartimento di Scienze per gli Alimenti la Nutrizione, l'Ambiente, Università degli Studi di Milano, Milan, Italy
| | - Matteo Montagna
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milan, Italy
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39
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Adamski M, Pietr SJ. Biodiversity of Bacteria Associated with Eight Pleurotus ostreatus (Fr.) P. Kumm. Strains from Poland, Japan and the USA. Pol J Microbiol 2019; 68:71-81. [PMID: 31050255 PMCID: PMC7256699 DOI: 10.21307/pjm-2019-009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2018] [Indexed: 11/11/2022] Open
Abstract
Few publications report the occurrence of bacteria associated with fungal cells. The presence of bacteria associated with one strain of Pleurotus ostreatus (Fr.) P. Kumm. was described in the literature. We describe the biodiversity of bacteria associated with eight oyster mushroom strains from Japan, Poland, and the USA. The presence of microorganisms associated with all tested P. ostreatus strains was confirmed using fluorescent microscopy. Among 307 sequences, 233 of clones representing 34 genera and 74 sequences were identified as Bacteria. Most of the bacteria associated with the strain PUSAS were related to E. coli and two clones were related to Cupriavidus genus. The biodiversity of clones isolated from fungal strains originating from Japan and Poland ranged from 15 to 32 different bacterial clones. The most often the bacteria related to genus Curvibacter, Pseudomonas, Bacillus, Cupriavidus, Pelomonas, and Propionibacterium were associated with the strains of fungi mentioned above. Laccase-like (LMCO) genes were identified in whole bacterial DNA isolated from the associated bacteria but β-glucosidase and β-xylanase genes were not detected. Few publications report the occurrence of bacteria associated with fungal cells. The presence of bacteria associated with one strain of Pleurotus ostreatus (Fr.) P. Kumm. was described in the literature. We describe the biodiversity of bacteria associated with eight oyster mushroom strains from Japan, Poland, and the USA. The presence of microorganisms associated with all tested P. ostreatus strains was confirmed using fluorescent microscopy. Among 307 sequences, 233 of clones representing 34 genera and 74 sequences were identified as Bacteria. Most of the bacteria associated with the strain PUSAS were related to E. coli and two clones were related to Cupriavidus genus. The biodiversity of clones isolated from fungal strains originating from Japan and Poland ranged from 15 to 32 different bacterial clones. The most often the bacteria related to genus Curvibacter, Pseudomonas, Bacillus, Cupriavidus, Pelomonas, and Propionibacterium were associated with the strains of fungi mentioned above. Laccase-like (LMCO) genes were identified in whole bacterial DNA isolated from the associated bacteria but β-glucosidase and β-xylanase genes were not detected.
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Affiliation(s)
- Mariusz Adamski
- Agricultural Microbiology Lab , Department of Plant Protection , The Faculty of Life Sciences and Technology , Wroclaw University of Environmental and Life Sciences , Wroclaw , Poland
| | - Stanislaw J Pietr
- Agricultural Microbiology Lab , Department of Plant Protection , The Faculty of Life Sciences and Technology , Wroclaw University of Environmental and Life Sciences , Wroclaw , Poland
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40
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A selective genome-guided method for environmental Burkholderia isolation. J Ind Microbiol Biotechnol 2019; 46:345-362. [PMID: 30680473 DOI: 10.1007/s10295-018-02121-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/19/2018] [Indexed: 12/31/2022]
Abstract
The genus Burkholderia is an emerging source of novel natural products chemistry, yet to date few methods exist for the selective isolation of strains of this genus from the environment. More broadly, tools to efficiently design selection media for any given genus would be of significant value to the natural products and microbiology communities. Using a modification of the recently published SMART protocol, we have developed a two-stage isolation protocol for strains from the genus Burkholderia. This method uses a combination of selective agar isolation media and multiplexed PCR profiling to derive Burkholderia strains from environmental samples with 95% efficiency. Creation of this new method paves the way for the systematic exploration of natural products chemistry from this important genus and offers new insight into potential methods for selective isolation method development for other priority genera.
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41
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Diaz Caballero J, Clark ST, Wang PW, Donaldson SL, Coburn B, Tullis DE, Yau YCW, Waters VJ, Hwang DM, Guttman DS. A genome-wide association analysis reveals a potential role for recombination in the evolution of antimicrobial resistance in Burkholderia multivorans. PLoS Pathog 2018; 14:e1007453. [PMID: 30532201 PMCID: PMC6300292 DOI: 10.1371/journal.ppat.1007453] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 12/19/2018] [Accepted: 11/02/2018] [Indexed: 01/05/2023] Open
Abstract
Cystic fibrosis (CF) lung infections caused by members of the Burkholderia cepacia complex, such as Burkholderia multivorans, are associated with high rates of mortality and morbidity. We performed a population genomics study of 111 B. multivorans sputum isolates from one CF patient through three stages of infection including an early incident isolate, deep sampling of a one-year period of chronic infection occurring weeks before a lung transplant, and deep sampling of a post-transplant infection. We reconstructed the evolutionary history of the population and used a lineage-controlled genome-wide association study (GWAS) approach to identify genetic variants associated with antibiotic resistance. We found the incident isolate was basally related to the rest of the strains and more susceptible to antibiotics from three classes (β-lactams, aminoglycosides, quinolones). The chronic infection isolates diversified into multiple, distinct genetic lineages and showed reduced antimicrobial susceptibility to the same antibiotics. The post-transplant reinfection isolates derived from the same source as the incident isolate and were genetically distinct from the chronic isolates. They also had a level of susceptibility in between that of the incident and chronic isolates. We identified numerous examples of potential parallel pathoadaptation, in which multiple mutations were found in the same locus or even codon. The set of parallel pathoadaptive loci was enriched for functions associated with virulence and resistance. Our GWAS analysis identified statistical associations between a polymorphism in the ampD locus with resistance to β-lactams, and polymorphisms in an araC transcriptional regulator and an outer membrane porin with resistance to both aminoglycosides and quinolones. Additionally, these three loci were independently mutated four, three and two times, respectively, providing further support for parallel pathoadaptation. Finally, we identified a minimum of 14 recombination events, and observed that loci carrying putative parallel pathoadaptations and polymorphisms statistically associated with β-lactam resistance were over-represented in these recombinogenic regions. Cystic fibrosis (CF) is the most common lethal genetic disorder affecting individuals of European descent. Most CF patients die at a young age due to chronic lung infections. Among the organisms involved in these infections are bacteria from the Burkholderia cepacia complex (BCC), which are strongly associated with poor clinical prognosis. This study examines how the most prevalent BCC species among CF patients, B. multivorans, evolves within a single CF patient by studying the first B. multivorans isolate recovered from the patient, one hundred isolates recovered over a one year period during the chronic infection phase, and an additional ten isolates recovered after the reinfection of the transplanted lungs. We found that B. multivorans diversify phenotypically and genetically within the CF lung over the course of the infection, and evolves into a complex population during the chronic infection phase. We found that isolates collected from the post-transplant reinfection were more closely related to descendants of the original isolate rather than those recovered in the chronic infection. We identify genetic variants statistically associated with resistance to the antibiotics, and showed that some of these variants were found in regions that show patterns of recombination (genetic exchange) between strains. We also found that genes which were mutated multiple times during overall infection were more likely to be found in regions showing signals consistent with recombination. The presence of multiple independent mutations in a gene is a very strong signal that the gene helps bacteria adapt to their environment. Overall, this study provides insight into how pathogens adapt to the host during long-term infections, specific genes associated with antibiotic resistance, and the origin of new and recurrent infections.
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Affiliation(s)
- Julio Diaz Caballero
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Shawn T. Clark
- Latner Thoracic Surgery Laboratories, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Pauline W. Wang
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Sylva L. Donaldson
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Bryan Coburn
- Division of Infectious Diseases, Department of Medicine, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - D. Elizabeth Tullis
- Adult Cystic Fibrosis Clinic, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Yvonne C. W. Yau
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Pediatric Laboratory Medicine, Division of Microbiology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Valerie J. Waters
- Department of Pediatrics, Division of Infectious Diseases, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - David M. Hwang
- Latner Thoracic Surgery Laboratories, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Pathology, University Health Network, Toronto, Ontario, Canada
| | - David S. Guttman
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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42
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Ravnholt C, Kolpen M, Skov M, Moser C, Katzenstein TL, Pressler T, Høiby N, Qvist T. The importance of early diagnosis of Mycobacterium abscessus complex in patients with cystic fibrosis. APMIS 2018; 126:885-891. [PMID: 30456869 DOI: 10.1111/apm.12903] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 10/09/2018] [Indexed: 12/18/2022]
Abstract
Mycobacterium abscessus complex can cause severe lung infections and has proven to be a serious threat to patients with cystic fibrosis and a challenge for clinicians due to difficulties in timely diagnosis and complex multidrug treatment regimes. Mycobacterial culture is the gold standard for diagnosis, but in most cystic fibrosis centers it is performed less frequently than culture for other pathogens. Consensus today recommends just one annual mycobacterial culture for asymptomatic patients with cystic fibrosis, a strategy likely to lead to diagnostic delays. Postponement of diagnosis might be the deciding factor in whether an early colonization turns into chronic infection. This review highlights the latest developments in knowledge about the pathogenicity and clinical consequences of M. abscessus complex pulmonary disease, addressing the central theme of why pulmonary infection requires early identification and aggressive antibiotic treatment. The window of opportunity, before M. abscessus complex transforms from a mucosal colonizer to a chronic biofilm infection, is where microbial eradication is most likely to be successful, making early diagnosis essential for improved outcomes.
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Affiliation(s)
- Cecilie Ravnholt
- Cystic Fibrosis Center Copenhagen, Rigshospitalet, Copenhagen, Denmark.,Department of Infectious Diseases, Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Mette Kolpen
- Cystic Fibrosis Center Copenhagen, Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Marianne Skov
- Cystic Fibrosis Center Copenhagen, Rigshospitalet, Copenhagen, Denmark.,Department of Pediatrics, Rigshospitalet, Copenhagen, Denmark
| | - Claus Moser
- Cystic Fibrosis Center Copenhagen, Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Terese L Katzenstein
- Cystic Fibrosis Center Copenhagen, Rigshospitalet, Copenhagen, Denmark.,Department of Infectious Diseases, Rigshospitalet, Copenhagen, Denmark
| | - Tania Pressler
- Cystic Fibrosis Center Copenhagen, Rigshospitalet, Copenhagen, Denmark.,Department of Infectious Diseases, Rigshospitalet, Copenhagen, Denmark
| | - Niels Høiby
- Cystic Fibrosis Center Copenhagen, Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark.,Institute of Immunology and Medical Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Tavs Qvist
- Cystic Fibrosis Center Copenhagen, Rigshospitalet, Copenhagen, Denmark.,Department of Infectious Diseases, Rigshospitalet, Copenhagen, Denmark
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43
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Rouse SL, Matthews SJ, Dueholm MS. Ecology and Biogenesis of Functional Amyloids in Pseudomonas. J Mol Biol 2018; 430:3685-3695. [PMID: 29753779 PMCID: PMC6173800 DOI: 10.1016/j.jmb.2018.05.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/03/2018] [Accepted: 05/04/2018] [Indexed: 12/02/2022]
Abstract
Functional amyloids can be found in the extracellular matrix produced by many bacteria during biofilm growth. They mediate the initial attachment of bacteria to surfaces and provide stability and functionality to mature biofilms. Efficient amyloid biogenesis requires a highly coordinated system of amyloid subunits, molecular chaperones and transport systems. The functional amyloid of Pseudomonas (Fap) represents such a system. Here, we review the phylogenetic diversification of the Fap system, its potential ecological role and the dedicated machinery required for Fap biogenesis, with a particular focus on the amyloid exporter FapF, the structure of which has been recently resolved. We also present a sequence covariance-based in silico model of the FapC fiber-forming subunit. Finally, we highlight key questions that remain unanswered and we believe deserve further attention by the scientific community.
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Affiliation(s)
- Sarah L Rouse
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Stephen J Matthews
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Morten S Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
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44
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Ernst J, Klinger-Strobel M, Arnold K, Thamm J, Hartung A, Pletz MW, Makarewicz O, Fischer D. Polyester-based particles to overcome the obstacles of mucus and biofilms in the lung for tobramycin application under static and dynamic fluidic conditions. Eur J Pharm Biopharm 2018; 131:120-129. [PMID: 30063969 DOI: 10.1016/j.ejpb.2018.07.025] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/25/2018] [Indexed: 02/07/2023]
Abstract
Pulmonary infections with Pseudomonas aeruginosa and Burkholderia cepacia complex (Bcc) are difficult to treat and related with high mortality in some diseases like cystic fibrosis due to the recurrent formation of biofilms. The biofilm formation hinders efficient treatment with inhaled antibiotics due to a low penetration of the antibiotics through the polyanionic biofilm matrix and increased antimicrobial resistance of the biofilm-embedded bacteria. In this study, tobramycin (Tb) was encapsulated in particles based on poly(d,l,-lactide-co-glycolide) (PLGA) and poly(ethylene glycol)-co-poly(d,l,-lactide-co-glycolide) diblock (PEG-PLGA) to overcome the biofilm barrier with particle sizes of 225-231 nm (nanoparticles) and 896-902 nm (microparticles), spherical shape and negative zeta potentials. The effectiveness against biofilms of P. aeruginosa and B. cepacia was strongly enhanced by the encapsulation under fluidic experimental condition as well as under static conditions in artificial mucus. The biofilm-embedded bacteria were killed by less than 0.77 mg/l encapsulated Tb, whereas 1,000 mg/l of free Tb or the bulk mixtures of Tb and the particles were ineffective against the biofilms. Moreover, encapsulated Tb was even effective against biofilms of the intrinsically aminoglycoside-resistant B. cepacia, indicating a supportive effect of PEG and PLGA on Tb. No cytotoxicity was detected in vitro in human lung epithelial cells with any formulation.
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Affiliation(s)
- Julia Ernst
- Pharmaceutical Technology and Biopharmacy, Institute for Pharmacy, Friedrich Schiller University Jena, Jena, Germany
| | - Mareike Klinger-Strobel
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Kathrin Arnold
- Pharmaceutical Technology and Biopharmacy, Institute for Pharmacy, Friedrich Schiller University Jena, Jena, Germany
| | - Jana Thamm
- Pharmaceutical Technology and Biopharmacy, Institute for Pharmacy, Friedrich Schiller University Jena, Jena, Germany
| | - Anita Hartung
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Mathias W Pletz
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Oliwia Makarewicz
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany.
| | - Dagmar Fischer
- Pharmaceutical Technology and Biopharmacy, Institute for Pharmacy, Friedrich Schiller University Jena, Jena, Germany; Jena Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Jena, Germany
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45
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Bach E, Sant'Anna FH, Magrich Dos Passos JF, Balsanelli E, de Baura VA, Pedrosa FDO, de Souza EM, Passaglia LMP. Detection of misidentifications of species from the Burkholderia cepacia complex and description of a new member, the soil bacterium Burkholderia catarinensis sp. nov. Pathog Dis 2018; 75:3934654. [PMID: 28859310 DOI: 10.1093/femspd/ftx076] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 07/04/2017] [Indexed: 12/31/2022] Open
Abstract
The correct identification of bacteria from the Burkholderia cepacia complex (Bcc) is crucial for epidemiological studies and treatment of cystic fibrosis infections. However, genome-based identification tools are revealing many controversial Bcc species assignments. The aim of this work is to re-examine the taxonomic position of the soil bacterium B. cepacia 89 through polyphasic and genomic approaches. recA and 16S rRNA gene sequence analysis positioned strain 89 inside the Bcc group. However, based on the divergence score of seven concatenated allele sequences, and values of average nucleotide identity, and digital DNA:DNA hybridization, our results suggest that strain 89 is different from other Bcc species formerly described. Thus, we propose to classify Burkholderia sp. 89 as the novel species Burkholderia catarinensis sp. nov. with strain 89T (=DSM 103188T = BR 10601T) as the type strain. Moreover, our results call the attention to some probable misidentifications of Bcc genomes at the National Center for Biotechnology Information database.
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Affiliation(s)
- Evelise Bach
- Laboratório de Microbiologia Agrícola, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Bento Goncalves 9500, Porto Alegre, RS 91501-970, Brazil
| | - Fernando Hayashi Sant'Anna
- Laboratório de Microbiologia Agrícola, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Bento Goncalves 9500, Porto Alegre, RS 91501-970, Brazil
| | | | - Eduardo Balsanelli
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Centro Politécnico, Curitiba, PR 80060-000, Brazil
| | - Valter Antonio de Baura
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Centro Politécnico, Curitiba, PR 80060-000, Brazil
| | - Fábio de Oliveira Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Centro Politécnico, Curitiba, PR 80060-000, Brazil
| | - Emanuel Maltempi de Souza
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Centro Politécnico, Curitiba, PR 80060-000, Brazil
| | - Luciane Maria Pereira Passaglia
- Laboratório de Microbiologia Agrícola, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Bento Goncalves 9500, Porto Alegre, RS 91501-970, Brazil
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Daly SM, Sturge CR, Marshall-Batty KR, Felder-Scott CF, Jain R, Geller BL, Greenberg DE. Antisense Inhibitors Retain Activity in Pulmonary Models of Burkholderia Infection. ACS Infect Dis 2018; 4:806-814. [PMID: 29461800 DOI: 10.1021/acsinfecdis.7b00235] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The Burkholderia cepacia complex is a group of Gram-negative bacteria that are opportunistic pathogens in immunocompromised individuals, such as those with cystic fibrosis (CF) or chronic granulomatous disease (CGD). Burkholderia are intrinsically resistant to many antibiotics and the lack of antibiotic development necessitates novel therapeutics. Peptide-conjugated phosphorodiamidate morpholino oligomers are antisense molecules that inhibit bacterial mRNA translation. Targeting of PPMOs to the gene acpP, which is essential for membrane synthesis, lead to defects in the membrane and ultimately bactericidal activity. Exploration of additional PPMO sequences identified the ATG and Shine-Dalgarno sites as the most efficacious for targeting acpP. The CF lung is a complex microenvironment, but PPMO inhibition was still efficacious in an artificial model of CF sputum. PPMOs had low toxicity in human CF cells at doses that were antibacterial. PPMOs also reduced the bacterial burden in the lungs of immunocompromised CyBB mice, a model of CGD. Finally, the use of multiple PPMOs was efficacious in inhibiting the growth of both Burkholderia and Pseudomonas in an in vitro model of coinfection. Due to the intrinsic resistance of Burkholderia to traditional antibiotics, PPMOs represent a novel and viable approach to the treatment of Burkholderia infections.
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Affiliation(s)
- Seth M. Daly
- Department of Internal Medicine, UT Southwestern, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
| | - Carolyn R. Sturge
- Department of Internal Medicine, UT Southwestern, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
| | - Kimberly R. Marshall-Batty
- Department of Internal Medicine, UT Southwestern, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
| | - Christina F. Felder-Scott
- Department of Internal Medicine, UT Southwestern, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
| | - Raksha Jain
- Department of Internal Medicine, UT Southwestern, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
- Department of Microbiology, UT Southwestern, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
| | - Bruce L. Geller
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, Oregon 97331, United States
| | - David E. Greenberg
- Department of Internal Medicine, UT Southwestern, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
- Department of Microbiology, UT Southwestern, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
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Sass A, Kiekens S, Coenye T. Identification of small RNAs abundant in Burkholderia cenocepacia biofilms reveal putative regulators with a potential role in carbon and iron metabolism. Sci Rep 2017; 7:15665. [PMID: 29142288 PMCID: PMC5688073 DOI: 10.1038/s41598-017-15818-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 11/02/2017] [Indexed: 12/23/2022] Open
Abstract
Small RNAs play a regulatory role in many central metabolic processes of bacteria, as well as in developmental processes such as biofilm formation. Small RNAs of Burkholderia cenocepacia, an opportunistic pathogenic beta-proteobacterium, are to date not well characterised. To address that, we performed genome-wide transcriptome structure analysis of biofilm grown B. cenocepacia J2315. 41 unannotated short transcripts were identified in intergenic regions of the B. cenocepacia genome. 15 of these short transcripts, highly abundant in biofilms, widely conserved in Burkholderia sp. and without known function, were selected for in-depth analysis. Expression profiling showed that most of these sRNAs are more abundant in biofilms than in planktonic cultures. Many are also highly abundant in cells grown in minimal media, suggesting they are involved in adaptation to nutrient limitation and growth arrest. Their computationally predicted targets include a high proportion of genes involved in carbon metabolism. Expression and target genes of one sRNA suggest a potential role in regulating iron homoeostasis. The strategy used for this study to detect sRNAs expressed in B. cenocepacia biofilms has successfully identified sRNAs with a regulatory function.
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Affiliation(s)
- Andrea Sass
- Department of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Sanne Kiekens
- Department of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Tom Coenye
- Department of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium.
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Butt AT, Thomas MS. Iron Acquisition Mechanisms and Their Role in the Virulence of Burkholderia Species. Front Cell Infect Microbiol 2017; 7:460. [PMID: 29164069 PMCID: PMC5681537 DOI: 10.3389/fcimb.2017.00460] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/18/2017] [Indexed: 11/19/2022] Open
Abstract
Burkholderia is a genus within the β-Proteobacteriaceae that contains at least 90 validly named species which can be found in a diverse range of environments. A number of pathogenic species occur within the genus. These include Burkholderia cenocepacia and Burkholderia multivorans, opportunistic pathogens that can infect the lungs of patients with cystic fibrosis, and are members of the Burkholderia cepacia complex (Bcc). Burkholderia pseudomallei is also an opportunistic pathogen, but in contrast to Bcc species it causes the tropical human disease melioidosis, while its close relative Burkholderia mallei is the causative agent of glanders in horses. For these pathogens to survive within a host and cause disease they must be able to acquire iron. This chemical element is essential for nearly all living organisms due to its important role in many enzymes and metabolic processes. In the mammalian host, the amount of accessible free iron is negligible due to the low solubility of the metal ion in its higher oxidation state and the tight binding of this element by host proteins such as ferritin and lactoferrin. As with other pathogenic bacteria, Burkholderia species have evolved an array of iron acquisition mechanisms with which to capture iron from the host environment. These mechanisms include the production and utilization of siderophores and the possession of a haem uptake system. Here, we summarize the known mechanisms of iron acquisition in pathogenic Burkholderia species and discuss the evidence for their importance in the context of virulence and the establishment of infection in the host. We have also carried out an extensive bioinformatic analysis to identify which siderophores are produced by each Burkholderia species that is pathogenic to humans.
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Affiliation(s)
- Aaron T Butt
- Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield, United Kingdom
| | - Mark S Thomas
- Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield, United Kingdom
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Bi N, Xiong C, Jin G, Guo Z, Gu G. Synthesis of a trisaccharide repeating unit of the O-antigen from Burkholderia cenocepacia and its dimer. Carbohydr Res 2017; 451:1-11. [DOI: 10.1016/j.carres.2017.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 09/05/2017] [Accepted: 09/05/2017] [Indexed: 12/13/2022]
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50
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Lumbar Spondylodiscitis Caused by Burkholderia cepacia in a Previously Healthy Patient. Case Rep Orthop 2017; 2017:1396950. [PMID: 29163994 PMCID: PMC5661097 DOI: 10.1155/2017/1396950] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 09/13/2017] [Indexed: 12/17/2022] Open
Abstract
Burkholderia cepacia spondylodiscitis is a rare entity that has been reported in only four cases. We hereby report the case of a 43-year-old, previously healthy, woman who was found to have a B. cepacia spondylodiscitis after a cholecystectomy. She was treated with a three-month regimen of ceftazidime and ciprofloxacin with complete clinical, biological, and radiological remission.
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