1
|
Itoh N, Akazawa N, Ishibana Y, Masuishi T, Nakata A, Murakami H. Clinical and microbiological features of obstructive cholangitis with bloodstream infection caused by Pandoraea apista identified by MALDI-TOF mass spectrometry and ribosomal RNA sequencing in a cancer patient. BMC Infect Dis 2022; 22:529. [PMID: 35672730 PMCID: PMC9171735 DOI: 10.1186/s12879-022-07514-z] [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: 01/16/2022] [Accepted: 06/01/2022] [Indexed: 11/12/2022] Open
Abstract
Background Pandoraea species are multidrug-resistant glucose-nonfermenting gram-negative bacilli that are usually isolated from patients with cystic fibrosis (CF) and from water and soil. Reports of diseases, including bloodstream infections, caused by Pandoraea spp. in non-CF patients are rare, and the clinical and microbiological characteristics are unclear. The identification of Pandorea spp. is limited by conventional microbiological methods and may be misidentified as other species owing to overlapping biochemical profiles. Here, we report the first case of obstructive cholangitis with bacteremia caused by Pandoraea apista in a patient with advanced colorectal cancer. A 61-year-old man with advanced colorectal cancer who underwent right nephrectomy for renal cell carcinoma 4 years earlier with well-controlled diabetes mellitus was admitted to our hospital with fever for 2 days. The last chemotherapy (regorafenib) was administered approximately 3 weeks ago, and an endoscopic ultrasound-guided hepaticogastrostomy was performed 2 weeks ago under hospitalization for obstructive jaundice. Two days prior, he presented with fever with chills. He was treated with piperacillin-tazobactam for obstructive cholangitis and showed improvement but subsequently presented with exacerbation. Bacterial isolates from the blood and bile samples were identified as P. apista using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16S ribosomal RNA sequencing. Based on the susceptibility results of the isolates, he was successfully treated with oral trimethoprim-sulfamethoxazole 160 mg/800 mg/day for 14 days for P. apista infection. Conclusions Pandoraea species are often misidentified. Therefore, multiple approaches should be used to identify them, and decisions regarding antimicrobial treatment should be based on actual in vitro susceptibility. Only seven cases of Pandoraea spp. bloodstream infections have been reported, and we report the first case of cholangitis with bacteremia.
Collapse
Affiliation(s)
- Naoya Itoh
- Division of Infectious Diseases, Aichi Cancer Center Hospital, 1-1 Kanokoden, Chikusa-ku, Nagoya, Aichi, 464-8681, Japan. .,Collaborative Chairs Emerging and Reemerging Infectious Diseases, National Center for Global Health and Medicine, Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan.
| | - Nana Akazawa
- Division of Infectious Diseases, Aichi Cancer Center Hospital, 1-1 Kanokoden, Chikusa-ku, Nagoya, Aichi, 464-8681, Japan
| | - Yuichi Ishibana
- Division of Infectious Diseases, Aichi Cancer Center Hospital, 1-1 Kanokoden, Chikusa-ku, Nagoya, Aichi, 464-8681, Japan
| | - Toshiki Masuishi
- Department of Clinical Oncology, Aichi Cancer Center Hospital, 1-1 Kanokoden, Chikusa-ku, Nagoya, Aichi, 464-8681, Japan
| | - Akinobu Nakata
- Department of Clinical Oncology, Aichi Cancer Center Hospital, 1-1 Kanokoden, Chikusa-ku, Nagoya, Aichi, 464-8681, Japan
| | - Hiromi Murakami
- Division of Infectious Diseases, Aichi Cancer Center Hospital, 1-1 Kanokoden, Chikusa-ku, Nagoya, Aichi, 464-8681, Japan
| |
Collapse
|
2
|
Enespa, Chandra P, Singh DP. Sources, purification, immobilization and industrial applications of microbial lipases: An overview. Crit Rev Food Sci Nutr 2022; 63:6653-6686. [PMID: 35179093 DOI: 10.1080/10408398.2022.2038076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Microbial lipase is looking for better attention with the fast growth of enzyme proficiency and other benefits like easy, cost-effective, and reliable manufacturing. Immobilized enzymes can be used repetitively and are incapable to catalyze the reactions in the system continuously. Hydrophobic supports are utilized to immobilize enzymes when the ionic strength is low. This approach allows for the immobilization, purification, stability, and hyperactivation of lipases in a single step. The diffusion of the substrate is more advantageous on hydrophobic supports than on hydrophilic supports in the carrier. These approaches are critical to the immobilization performance of the enzyme. For enzyme immobilization, synthesis provides a higher pH value as well as greater heat stability. Using a mixture of immobilization methods, the binding force between enzymes and the support rises, reducing enzyme leakage. Lipase adsorption produces interfacial activation when it is immobilized on hydrophobic support. As a result, in the immobilization process, this procedure is primarily used for a variety of industrial applications. Microbial sources, immobilization techniques, and industrial applications in the fields of food, flavor, detergent, paper and pulp, pharmaceuticals, biodiesel, derivatives of esters and amino groups, agrochemicals, biosensor applications, cosmetics, perfumery, and bioremediation are all discussed in this review.
Collapse
Affiliation(s)
- Enespa
- School for Agriculture, Sri Mahesh Prasad Post Graduate College, University of Lucknow, Lucknow, Uttar Pradesh, India
| | - Prem Chandra
- Food Microbiology & Toxicology Laboratory, Department of Microbiology, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar University (A Central) University, Lucknow, Uttar Pradesh, India
| | - Devendra Pratap Singh
- Department of Environmental Science, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar University (A Central) University, Lucknow, Uttar Pradesh, India
| |
Collapse
|
3
|
Burkholderia cepacia Complex, an Emerging Nosocomial Pathogen at Health Care Facilities in Sebha, Libya. JOURNAL OF MEDICAL MICROBIOLOGY AND INFECTIOUS DISEASES 2021. [DOI: 10.52547/jommid.9.4.178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
4
|
Kaze M, Brooks L, Sistrom M. Genomic Sequence Analysis of Methicillin- and Carbapenem-Resistant Bacteria Isolated from Raw Sewage. Microbiol Spectr 2021; 9:e0012821. [PMID: 34132566 PMCID: PMC8552737 DOI: 10.1128/spectrum.00128-21] [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] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 01/07/2023] Open
Abstract
Antibiotic resistance is one of the largest threats facing global health. Wastewater treatment plants are well-known hot spots for interaction between diverse bacteria, genetic exchange, and antibiotic resistance. Nonpathogenic bacteria theoretically act as reservoirs of antibiotic resistance subsequently transferring antibiotic resistance genes to pathogens, indicating that evolutionary processes occur outside clinical settings and may drive patterns of drug-resistant infections. We isolated and sequenced 100 bacterial strains from five wastewater treatment plants to analyze regional dynamics of antibiotic resistance in the California Central Valley. The results demonstrate the presence of a wide diversity of pathogenic and nonpathogenic bacteria, with an arithmetic mean of 5.1 resistance genes per isolate. Forty-three percent of resistance genes were located on plasmids, suggesting that large levels of gene transfer between bacteria that otherwise may not co-occur are facilitated by wastewater treatment. One of the strains detected was a Bacillus carrying pX01 and pX02 anthrax-like plasmids and multiple drug resistance genes. A correlation between resistance genes and taxonomy indicates that taxon-specific evolutionary studies may be useful in determining and predicting patterns of antibiotic resistance. Conversely, a lack of geographic correlation may indicate that landscape genetic studies to understand the spread of antibiotic resistance genes should be carried out at broader scales. This large data set provides insights into how pathogenic and nonpathogenic bacteria interact in wastewater environments and the resistance genes which may be horizontally transferred between them. This can help in determining the mechanisms leading to the increasing prevalence of drug-resistant infections observed in clinical settings. IMPORTANCE The reasons for the increasing prevalence of antibiotic-resistant infections are complex and associated with myriad clinical and environmental processes. Wastewater treatment plants operate as nexuses of bacterial interaction and are known hot spots for genetic exchange between bacteria, including antibiotic resistance genes. We isolated and sequenced 100 drug-resistant bacteria from five wastewater treatment plants in California's Central Valley, characterizing widespread gene sharing between pathogens and nonpathogens. We identified a novel, multiresistant Bacillus carrying anthrax-like plasmids. This empirical study supports the likelihood of evolutionary and population processes in the broader environment affecting the prevalence of clinical drug-resistant infections and identifies several taxa that may operate as reservoirs and vectors of antibiotic resistance genes.
Collapse
Affiliation(s)
- Mo Kaze
- Department of Life and Environmental Sciences, University of California, Merced, California, USA
| | | | - Mark Sistrom
- Department of Life and Environmental Sciences, University of California, Merced, California, USA
| |
Collapse
|
5
|
Abstract
The use of next-generation sequencing and multiomic analysis reveals new insights on the identity of microbes in the lower airways blurring the lines between commensals and pathogens. Microbes are not found in isolation; rather they form complex metacommunities where microbe-host and microbe-microbe interactions play important roles on the host susceptibility to pathogens. In addition, the lower airway microbiota exert significant effects on host immune tone. Thus, this review highlights the roles that microbes in the respiratory tract play in the development of pneumonia.
Collapse
Affiliation(s)
- Benjamin G Wu
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, NYU Human Microbiome Program, New York University School of Medicine, New York, NY 10028, USA
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, NYU Human Microbiome Program, New York University School of Medicine, New York, NY 10028, USA.
| |
Collapse
|
6
|
Lyu J, Zhang J, Ren X. Detection and identification of bacterial pathogens directly from sputum samples by pyrosequencing. J Med Microbiol 2019; 68:368-373. [PMID: 30632958 DOI: 10.1099/jmm.0.000917] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE The standard culture findings for detecting and identifying bacterial pathogens in patients with lower respiratory tract infections (LRTIs) are usually not available for two to three days, which delays the initiation of appropriate antibiotic therapies. We aimed to develop a faster method of identification of bacterial pathogens in LRTIs which would offer a timelier guide to initial antibiotic choices. METHODOLOGY The developed PCR-pyrosequencing-based method was defined as mask PCR-pyrosequencing (MPP). This method uses primer pairs deliberately designed to mask the interference of colonised bacteria in sputum to detect and identify bacterial pathogens directly from LRTI patient sputum samples within 5 h. Accordingly, the standard PCR-pyrosequencing method was defined as normal PCR-pyrosequencing (NPP) here. The clinical performance of the novel system was evaluated by comparing with traditional semi-quantitative culture and identification results. RESULTS The coincidence for culture and MPP was 91.3 %. Compared with the semi-quantitative culture results, NPP identified 89.9 % strains of grade 3+ (corresponding to 1.0×106 c.f.u ml-1) and 100 % of grade 4+ (corresponding to 1.0×107 c.f.u ml-1), both of which were considered to be the presumptive pathogens in the clinics. MPP identified 98.9 % strains of grade 3+ and 100 % of grade 4+. Additionally, PCR-pyrosequencing could detect a minimum concentration of 1.0×106 c.f.u ml-1 of bacteria in sputum, with no significant difference between NPP and MPP. CONCLUSION The PCR-pyrosequencing technique developed in this study is an accurate, fast, and high throughput method for the direct detection and identification of bacterial pathogens from sputum.
Collapse
Affiliation(s)
- Jiangfeng Lyu
- Research and Development Centre, Hangzhou D.A. Medical Laboratory, Hangzhou, Zhejiang, PR China
| | - Jing Zhang
- Research and Development Centre, Hangzhou D.A. Medical Laboratory, Hangzhou, Zhejiang, PR China
| | - Xuyi Ren
- Research and Development Centre, Hangzhou D.A. Medical Laboratory, Hangzhou, Zhejiang, PR China
| |
Collapse
|
7
|
Adegoke AA, Stenström TA, Okoh AI. Stenotrophomonas maltophilia as an Emerging Ubiquitous Pathogen: Looking Beyond Contemporary Antibiotic Therapy. Front Microbiol 2017; 8:2276. [PMID: 29250041 PMCID: PMC5714879 DOI: 10.3389/fmicb.2017.02276] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/06/2017] [Indexed: 12/21/2022] Open
Abstract
Stenotrophomonas maltophilia is a commensal and an emerging pathogen earlier noted in broad-spectrum life threatening infections among the vulnerable, but more recently as a pathogen in immunocompetent individuals. The bacteria are consistently being implicated in necrotizing otitis, cutaneous infections including soft tissue infection and keratitis, endocarditis, meningitis, acute respiratory tract infection (RTI), bacteraemia (with/without hematological malignancies), tropical pyomyositis, cystic fibrosis, septic arthritis, among others. S. maltophilia is also an environmental bacteria occurring in water, rhizospheres, as part of the animals' microflora, in foods, and several other microbiota. This review highlights clinical reports on S. maltophilia both as an opportunistic and as true pathogen. Also, biofilm formation as well as quorum sensing, extracellular enzymes, flagella, pili/fimbriae, small colony variant, other virulence or virulence-associated factors, the antibiotic resistance factors, and their implications are considered. Low outer membrane permeability, natural MDR efflux systems, and/or resistance genes, resistance mechanisms like the production of two inducible chromosomally encoded β-lactamases, and lack of carefully compiled patient history are factors that pose great challenges to the S. maltophilia control arsenals. The fluoroquinolone, some tetracycline derivatives and trimethoprim-sulphamethaxole (TMP-SMX) were reported as effective antibiotics with good therapeutic outcome. However, TMP-SMX resistance and allergies to sulfa together with high toxicity of fluoroquinolone are notable setbacks. S. maltophilia's production and sustenance of biofilm by quorum sensing enhance their virulence, resistance to antibiotics and gene transfer, making quorum quenching an imperative step in Stenotrophomonas control. Incorporating several other proven approaches like bioengineered bacteriophage therapy, Epigallocatechin-3-gallate (EGCG), essential oil, nanoemulsions, and use of cationic compounds are promising alternatives which can be incorporated in Stenotrophomonas control arsenal.
Collapse
Affiliation(s)
- Anthony A Adegoke
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, South Africa.,Applied and Environmental Microbiology Research Group, University of Fort Hare, Alice, South Africa.,SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa
| | - Thor A Stenström
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, South Africa
| | - Anthony I Okoh
- Applied and Environmental Microbiology Research Group, University of Fort Hare, Alice, South Africa.,SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa
| |
Collapse
|
8
|
Turvey ME, Weiland F, Keller EJ, Hoffmann P. The changing face of microbial quality control practices in the brewing industry: Introducing mass spectrometry proteomic fingerprinting for microbial identification. JOURNAL OF THE INSTITUTE OF BREWING 2017. [DOI: 10.1002/jib.428] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- M. E. Turvey
- Adelaide Proteomics Centre; The University of Adelaide; Australia
- Institute of Photonics and Advanced Sensing; Australia
- Singapore-MIT Alliance for Research and Technology Centre; Singapore
| | - F. Weiland
- Adelaide Proteomics Centre; The University of Adelaide; Australia
- Institute of Photonics and Advanced Sensing; Australia
| | - E. J. Keller
- Adelaide Proteomics Centre; The University of Adelaide; Australia
- Institute of Photonics and Advanced Sensing; Australia
| | - P. Hoffmann
- Adelaide Proteomics Centre; The University of Adelaide; Australia
- Institute of Photonics and Advanced Sensing; Australia
| |
Collapse
|
9
|
Fila L, Dřevínek P. Burkholderia cepacia complex in cystic fibrosis in the post-epidemic period: multilocus sequence typing-based approach. Folia Microbiol (Praha) 2017; 62:509-514. [PMID: 28364392 DOI: 10.1007/s12223-017-0523-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 03/22/2017] [Indexed: 12/15/2022]
Abstract
Cystic fibrosis (CF) patients in the Czech Republic suffered in the late 1990s from an epidemic with ST32 strain of Burkholderia cepacia complex (Bcc). Cohort segregation of Bcc and of ST32 positive patients was introduced in 1999 and 2002, respectively. We performed a study to evaluate the molecular epidemiology of Bcc infection after implementation of these infection control measures. Patients attending the Prague CF adult Centre from 2000 to 2015 were included in the present study. Demographic data and microbial statuses were collected from patient records. All Bcc isolates were analyzed using multilocus sequence typing (MLST). The prevalences of epidemic strain ST32 and of other Bcc strains were calculated. Ninety out of 227 CF patients were infected with Bcc during the study period. The prevalence of ST32 cases significantly decreased from 46.5% in 2000-2001 to 10.4% in 2014-2015 (P < 0.001) due to occurrence of only one new case in 2003, as well as to the death of 72% of ST32-infected patients. Conversely, there was a significant increase in prevalence of other Bcc strains, which rose from 0 to 14.9% (P = 0.015) and of transient infections. A micro-epidemic of infection with ST630 strain was observed in 2014 in lung transplant patients hospitalized in intensive care unit. The prevalence of epidemic strain ST32 decreased, whereas that of non-clonal strains of Bcc increased. Routine use of MLST allowed early detection of new and potentially epidemic strains.
Collapse
Affiliation(s)
- Libor Fila
- Department of Pneumology, 2nd Faculty of Medicine, Charles University in Prague, and Motol University Hospital, V Úvalu 84, 150 06, Prague, Czech Republic.
| | - Pavel Dřevínek
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague, and Motol University Hospital, V Úvalu 84, 150 06, Prague, Czech Republic
| |
Collapse
|
10
|
Martina PF, Martínez M, Frada G, Alvarez F, Leguizamón L, Prieto C, Barrias C, Bettiol M, Lagares A, Bosch A, Ferreras J, Von Specht M. First time identification of Pandoraea sputorum from a patient with cystic fibrosis in Argentina: a case report. BMC Pulm Med 2017; 17:33. [PMID: 28173787 PMCID: PMC5297019 DOI: 10.1186/s12890-017-0373-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 01/21/2017] [Indexed: 12/17/2022] Open
Abstract
Background Pandoraea species are considered emerging pathogens in the context of cystic fibrosis (CF) and are difficult to identify by conventional biochemical methods. These multidrug resistant bacteria remain poorly understood particularly in terms of natural resistance, mechanisms of acquired resistance and impact on the prognosis of the disease and the lung function. Among them, Pandoraea sputorum has been previously described in few cases of CF patients from Spain, Australia, France and United States, underlining the need of more clinical data for a better knowledge of its pathogenicity. This is the first report relating to P. sputorum in a CF patient in Argentina. Case presentation Pandoraea sputorum was identified in a nine-year-old cystic fibrosis patient from Argentina, after treatment failure during an exacerbation. The isolates were successfully identified by combining molecular techniques based on 16S rRNA sequencing and mass spectrometry (MS) methods, after reassessing previous misidentified isolates by conventional methods. After first isolation of P. sputorum, patient’s clinical condition worsened but later improved after a change in the treatment. Although isolates showed susceptibility to trimethoprim–sulfamethoxazole and imipenem, in our case, the antibiotic treatment failed in the eradication of P. sputorum. Conclusions All combined data showed a chronic colonization with P. sputorum associated to a deterioration of lung function. We noted that the presence of P. sputorum can be underestimated in CF patients and MALDI-TOF MS appears to be a promising means of accurate identification of Pandoraea species.
Collapse
Affiliation(s)
- Pablo F Martina
- Instituto de Biología Subtropical (IBS), CONICET-UNaM, Misiones, Argentina.,Centro de Investigación y Desarrollo en Fermentaciones Industriales (CINDEFI) - CONICET/UNLP, La Plata, Argentina.,Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Posadas, Argentina
| | - Mónica Martínez
- Hospital Pediátrico Dr F. Barreyro, Posadas, Misiones, Argentina
| | - Guillermo Frada
- Hospital Pediátrico Dr F. Barreyro, Posadas, Misiones, Argentina
| | - Florencia Alvarez
- Instituto de Biotecnología y Biología Molecular (IBBM) - CONICET/UNLP, La Plata, Argentina
| | | | - Claudia Prieto
- Centro de Investigación y Desarrollo en Fermentaciones Industriales (CINDEFI) - CONICET/UNLP, La Plata, Argentina
| | - Carolina Barrias
- Hospital Pediátrico Dr F. Barreyro, Posadas, Misiones, Argentina
| | - Marisa Bettiol
- Hospital de Niños Sor María Ludovica, La Plata, Argentina
| | - Antonio Lagares
- Instituto de Biotecnología y Biología Molecular (IBBM) - CONICET/UNLP, La Plata, Argentina
| | - Alejandra Bosch
- Centro de Investigación y Desarrollo en Fermentaciones Industriales (CINDEFI) - CONICET/UNLP, La Plata, Argentina
| | - Julián Ferreras
- Instituto de Biología Subtropical (IBS), CONICET-UNaM, Misiones, Argentina. .,Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Posadas, Argentina.
| | - Martha Von Specht
- Hospital Pediátrico Dr F. Barreyro, Posadas, Misiones, Argentina. .,Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Posadas, Argentina.
| |
Collapse
|
11
|
McHugh KE, Rhoads DD, Wilson DA, Highland KB, Richter SS, Procop GW. Inquilinus limosus in pulmonary disease: case report and review of the literature. Diagn Microbiol Infect Dis 2016; 86:446-449. [DOI: 10.1016/j.diagmicrobio.2016.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 09/06/2016] [Accepted: 09/11/2016] [Indexed: 11/25/2022]
|
12
|
Abbott FK, Milne KEN, Stead DA, Gould IM. Combination antimicrobial susceptibility testing of Burkholderia cepacia complex: significance of species. Int J Antimicrob Agents 2016; 48:521-527. [PMID: 27665523 DOI: 10.1016/j.ijantimicag.2016.07.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 07/06/2016] [Accepted: 07/30/2016] [Indexed: 01/08/2023]
Abstract
The Burkholderia cepacia complex (Bcc) is notorious for the life-threatening pulmonary infections it causes in patients with cystic fibrosis. The multidrug-resistant nature of Bcc and differing infective Bcc species make the design of appropriate treatment regimens challenging. Previous synergy studies have failed to take account of the species of Bcc isolates. Etest methodology was used to facilitate minimum inhibitory concentration (MIC) and antimicrobial combination testing on 258 isolates of Bcc, identified to species level by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS). The most active antimicrobials were trimethoprim/sulphamethoxazole, doxycycline and minocycline (52.5%, 46.4% and 45.9% of isolates susceptible, respectively). Synergy was observed in 9.2% of the 1799 combinations tested; the most common synergistic combinations were tobramycin + ceftazidime, meropenem + tobramycin and levofloxacin + piperacillin/tazobactam (35.4%, 32.3% and 22.2% synergy, respectively). Antimicrobial susceptibility analysis revealed differences between Burkholderia cenocepacia and Burkholderia multivorans. Disparity in clinical outcome during infection with these two micro-organisms necessitates further investigation into the clinical outcomes of treatment regimens in light of species identification and in vitro antimicrobial susceptibility studies.
Collapse
Affiliation(s)
- Felicity K Abbott
- Department of Medical Microbiology, Aberdeen Royal Infirmary, Aberdeen, UK.
| | - Kathleen E N Milne
- Department of Medical Microbiology, Aberdeen Royal Infirmary, Aberdeen, UK
| | - David A Stead
- Aberdeen Proteomics, Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen, UK
| | - Ian M Gould
- Department of Medical Microbiology, Aberdeen Royal Infirmary, Aberdeen, UK
| |
Collapse
|
13
|
Della Zuana A, Garcia DDO, Juliani RCTP, Silva Filho LVRFD. Effect that an educational program for cystic fibrosis patients and caregivers has on the contamination of home nebulizers. J Bras Pneumol 2014; 40:119-27. [PMID: 24831395 PMCID: PMC4083641 DOI: 10.1590/s1806-37132014000200004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 02/06/2014] [Indexed: 11/28/2022] Open
Abstract
OBJECTIVE: To describe the pathogens found in home nebulizers and in respiratory samples of
cystic fibrosis (CF) patients, and to evaluate the effect that a standardized
instruction regarding cleaning and disinfection of nebulizers has on the frequency
of nebulizer contamination. METHODS: We included 40 CF patients (22 males), all of whom used the same model of
nebulizer. The median patient age was 11.2 ± 3.74 years. We collected samples from
the nebulizer mouthpiece and cup, using a sterile swab moistened with sterile
saline. Respiratory samples were collected by asking patients to expectorate into
a sterile container or with oropharyngeal swabs after cough stimulation. Cultures
were performed on selective media, and bacteria were identified by classical
biochemical tests. Patients received oral and written instructions regarding the
cleaning and disinfection of nebulizers. All determinations were repeated an
average of two months later. RESULTS: Contamination of the nebulizer (any part) was detected in 23 cases (57.5%). The
nebulizer mouthpiece and cup were found to be contaminated in 16 (40.0%) and 19
(47.5%), respectively. After the standardized instruction had been given, there
was a significant decrease in the proportion of contaminated nebulizers (43.5%).
CONCLUSIONS: In our sample of CF patients, nebulizer contamination was common, indicating the
need for improvement in patient practices regarding the cleaning and disinfection
of their nebulizers. A one-time educational intervention could have a significant
positive impact.
Collapse
Affiliation(s)
- Adriana Della Zuana
- Graduate Program in Health Sciences, School of Medicine, University of São Paulo, São Paulo, Brazil
| | | | | | | |
Collapse
|
14
|
Dorgan DJ, Hadjiliadis D. Lung transplantation in patients with cystic fibrosis: special focus to infection and comorbidities. Expert Rev Respir Med 2014; 8:315-26. [PMID: 24655065 DOI: 10.1586/17476348.2014.899906] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Despite advances in medical care, patients with cystic fibrosis still face limited life expectancy. The most common cause of death remains respiratory failure. End-stage cystic fibrosis can be treated with lung transplantation and is the third most common reason for which the procedure is performed. Outcomes for cystic fibrosis are better than most other lung diseases, but remain limited (5-year survival 60%). For patients with advanced disease lung transplantation appears to improve survival. Outcomes for patients with Burkholderia cepacia remain poor, although they are better for patients with certain genomovars. Controversy exists about Mycobacterium abscessus infection and appropriateness for transplant. More information is also becoming available for comorbidities, including diabetes and pulmonary hypertension among others. Extra-corporeal membrane oxygenation is used more frequently for end-stage disease as a bridge to lung transplantation and will likely be used more in the future.
Collapse
Affiliation(s)
- Daniel J Dorgan
- Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | |
Collapse
|
15
|
Li D, March J, Bills T, Holt B, Wilson C, Lowe W, Tolley H, Lee M, Robison R. Gas chromatography-mass spectrometry method for rapid identification and differentiation of Burkholderia pseudomallei
and Burkholderia mallei
from each other, Burkholderia thailandensis
and several members of the Burkholderia cepacia
complex. J Appl Microbiol 2013; 115:1159-71. [DOI: 10.1111/jam.12310] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 07/07/2013] [Accepted: 07/18/2013] [Indexed: 10/26/2022]
Affiliation(s)
- D. Li
- Department of Chemistry and Biochemistry; Brigham Young University; Provo UT USA
| | - J.K. March
- Department of Microbiology and Molecular Biology; Brigham Young University; Provo UT USA
| | - T.M. Bills
- Department of Microbiology and Molecular Biology; Brigham Young University; Provo UT USA
| | - B.C. Holt
- Department of Statistics; Brigham Young University; Provo UT USA
| | - C.E. Wilson
- Department of Chemistry and Biochemistry; Brigham Young University; Provo UT USA
| | - W. Lowe
- Department of Microbiology and Molecular Biology; Brigham Young University; Provo UT USA
| | - H.D. Tolley
- Department of Statistics; Brigham Young University; Provo UT USA
| | - M.L. Lee
- Department of Chemistry and Biochemistry; Brigham Young University; Provo UT USA
| | - R.A. Robison
- Department of Microbiology and Molecular Biology; Brigham Young University; Provo UT USA
| |
Collapse
|
16
|
Braga PAC, Tata A, Gonçalves dos Santos V, Barreiro JR, Schwab NV, Veiga dos Santos M, Eberlin MN, Ferreira CR. Bacterial identification: from the agar plate to the mass spectrometer. RSC Adv 2013. [DOI: 10.1039/c2ra22063f] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
17
|
Brizendine K, Baddley J, Pappas P, Leon K, Rodriguez J. Fatal Burkholderia gladioli infection misidentified as Empedobacter brevis in a lung transplant recipient with cystic fibrosis. Transpl Infect Dis 2012; 14:E13-8. [DOI: 10.1111/j.1399-3062.2012.00726.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 12/06/2011] [Accepted: 12/08/2011] [Indexed: 12/31/2022]
Affiliation(s)
- K.D. Brizendine
- Division of Infectious Diseases; Department of Medicine; University of Alabama at Birmingham; Birmingham; Alabama; USA
| | | | - P.G. Pappas
- Division of Infectious Diseases; Department of Medicine; University of Alabama at Birmingham; Birmingham; Alabama; USA
| | - K.J. Leon
- Division of Pulmonary; Allergy and Critical Care Medicine; Department of Medicine; University of Alabama at Birmingham; Birmingham; Alabama; USA
| | - J.M. Rodriguez
- Division of Infectious Diseases; Department of Medicine; University of Alabama at Birmingham; Birmingham; Alabama; USA
| |
Collapse
|
18
|
Gautam V, Singhal L, Ray P. Burkholderia cepacia complex: beyond pseudomonas and acinetobacter. Indian J Med Microbiol 2011; 29:4-12. [PMID: 21304187 DOI: 10.4103/0255-0857.76516] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Burkholderia cepacia complex (BCC) is an important nosocomial pathogen in hospitalised patients, particularly those with prior broad-spectrum antibacterial therapy. BCC causes infections that include bacteraemia, urinary tract infection, septic arthritis, peritonitis and respiratory tract infection. Due to high intrinsic resistance and being one of the most antimicrobial-resistant organisms encountered in the clinical laboratory, these infections can prove very difficult to treat and, in some cases, result in death. Patients with cystic fibrosis (CF) and those with chronic granulomatous disease are predisposed to infection by BCC bacteria. BCC survives and multiplies in aqueous hospital environments, including disinfectant agents and intravenous fluids, where it may persist for long periods. Outbreaks and pseudo-outbreaks of BCC septicaemia have been documented in intensive care units, oncology units and renal failure patients. BCC is phenotypically unremarkable, and the complex exhibits an extensive diversity of genotypes. BCC is of increasing importance for agriculture and bioremediation because of their antinematodal and antifungal properties as well as their capability to degrade a wide range of toxic compounds. It has always been a tedious task for a routine microbiological laboratory to identify the nonfermenting gram-negative bacilli, and poor laboratory proficiency in identification of this nonfermenter worldwide still prevails. In India, there are no precise reports of the prevalence of BCC infection, and in most cases, these bacteria have been ambiguously reported as nonfermenting gram-negative bacilli or simply Pseudomonas spp. The International Burkholderia cepacia Working Group is open to clinicians and scientists interested in advancing knowledge of BCC infection/colonisation in persons with CF through the collegial exchange of information and promotion of coordinated approaches to research.
Collapse
Affiliation(s)
- V Gautam
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
| | | | | |
Collapse
|
19
|
Jacquier H, Carbonnelle E, Corvec S, Illiaquer M, Monnier A, Bille E, Zahar JR, Beretti JL, Jauréguy F, Fihman V, Tankovic J, Cattoir V. Revisited distribution of nonfermenting Gram-negative bacilli clinical isolates. Eur J Clin Microbiol Infect Dis 2011; 30:1579-86. [DOI: 10.1007/s10096-011-1263-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Accepted: 03/28/2011] [Indexed: 12/01/2022]
|
20
|
Bittar F, Rolain JM. Detection and accurate identification of new or emerging bacteria in cystic fibrosis patients. Clin Microbiol Infect 2011; 16:809-20. [PMID: 20880410 DOI: 10.1111/j.1469-0691.2010.03236.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Respiratory infections remain a major threat to cystic fibrosis (CF) patients. The detection and correct identification of the bacteria implicated in these infections is critical for the therapeutic management of patients. The traditional methods of culture and phenotypic identification of bacteria lack both sensitivity and specificity because many bacteria can be missed and/or misidentified. Molecular analyses have recently emerged as useful means to resolve these problems, including molecular methods for accurate identification or detection of bacteria and molecular methods for evaluation of microbial diversity. These recent molecular technologies have increased the list of new and/or emerging pathogens and epidemic strains associated with CF patients. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of intact cells has also emerged recently as a powerful and rapid method for the routine identification of bacteria in clinical microbiology laboratories and will certainly represent the method of choice also for the routine identification of bacteria in the context of CF. Finally, recent data derived from molecular culture-independent analyses indicate the presence of a previously underestimated, complex microbial community in sputa from CF patients. Interestingly, full genome sequencing of some bacteria frequently recovered from CF patients has highlighted the fact that the lungs of CF patients are hotspots for lateral gene transfer and the adaptation of these ecosystems to a specific chronic condition.
Collapse
Affiliation(s)
- F Bittar
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS-IRD, UMR 6236, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille Cedex 05, France
| | | |
Collapse
|
21
|
Identification of potential diagnostic markers among Burkholderia cenocepacia and B. multivorans supernatants. J Clin Microbiol 2010; 48:4186-92. [PMID: 20810766 DOI: 10.1128/jcm.00577-10] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Patients with cystic fibrosis (CF) are susceptible to chronic respiratory infections with a number of bacterial pathogens. Among them, the Burkholderia cepacia complex (Bcc) bacteria, consisting of nine related species, have emerged as problematic CF pathogens due to their antibiotic resistance, incidence of nosocomial infection, and person-to-person transmission. Bcc organisms present the clinical microbiologist with a diagnostic dilemma due to the lack of phenotypic biochemical or growth-related characterization tests that reliably distinguish among these organisms. The complex taxonomy of the Bcc species colonizing the CF respiratory tract makes accurate identification problematic. Despite the clinical implications of Bcc identification, a clinical laboratory differentiation of species within the Bcc is lacking. Additionally, no commercial assays are available to further identify the Bcc species. In the current study, secretory proteins present in the cultured supernatants of Burkholderia cenocepacia and Burkholderia multivorans were analyzed by two-dimensional gel electrophoresis (2-DE), followed by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). To assess differential expression, protein spots of B. cenocepacia and B. multivorans that were unique or displayed different intensities were chosen for MALDI-TOF MS analysis. In total, 341 protein spots were detected, of which 23 were unique to each species, demonstrating that potential diagnostic candidates between these two members of the Bcc exist.
Collapse
|
22
|
Abstract
Infection of the airways remains the primary cause of morbidity and mortality in persons with cystic fibrosis (CF). This review describes salient features of the epidemiologies of microbial species that are involved in respiratory tract infection in CF. The apparently expanding spectrum of species causing infection in CF and recent changes in the incidences and prevalences of infection due to specific bacterial, fungal, and viral species are described. The challenges inherent in tracking and interpreting rates of infection in this patient population are discussed.
Collapse
|
23
|
Abstract
Bacteria infect the respiratory tract early in the course of cystic fibrosis disease, often fail to be eradicated, and together with an aggressive host inflammatory response, are thought to be key players in the irreversible airway damage from which most patients ultimately die. Although incompletely understood, certain aspects of the cystic fibrosis airway itself appear to favor the development of chronic modes of survival, in particular biofilm formation; this and the development of antibiotic resistance following exposure to multiple antibiotic courses lead to chronic, persistent infection. In addition to the common cystic fibrosis pathogens, such as Staphylococcus aureus, Haemophilus influenzae, and Pseudomonas aeruginosa, several newer species are becoming more common. Furthermore, new molecular techniques have led to the identification of multiple different organisms within respiratory secretions, many of which are not cultured with conventional tools. Future work should aim to develop clinically applicable methods to identify these and to determine which have the potential to impact pulmonary health. We outline the basic tenets of infection control and treatment.
Collapse
Affiliation(s)
- Jane C Davies
- Department of Gene Therapy, Imperial College, Emmanuel Kaye Building, Manresa Road, London SW3 6NP, United Kingdom.
| | | |
Collapse
|
24
|
Miñán A, Bosch A, Lasch P, Stämmler M, Serra DO, Degrossi J, Gatti B, Vay C, D'aquino M, Yantorno O, Naumann D. Rapid identification of Burkholderia cepacia complex species including strains of the novel Taxon K, recovered from cystic fibrosis patients by intact cell MALDI-ToF mass spectrometry. Analyst 2009; 134:1138-48. [PMID: 19475140 DOI: 10.1039/b822669e] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two approaches based on intact cell matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (IC-MALDI-ToF MS) have been evaluated in order to discriminate and identify nine former Burkholderia cepacia complex (Bcc) species, Burkholderia contaminans belonging to the novel Taxon K, Burkholderia gladioli, and the most relevant non-fermentative (NF) Gram-negative rods recovered from cystic fibrosis (CF) sputum cultures. In total, 146 clinical isolates and 26 reference strains were analysed. IC mass spectra were obtained with high reproducibility applying a recently developed inactivation protocol which is based on the extraction of microbial proteins by trifluoroacetic acid (TFA). In a first approach, spectral analysis was carried out by means of a gel-view representation of mass spectra, which turned out to be useful to recognize specific identifying biomarker proteins (SIBPs). A series of prominent mass peaks, mainly assigned to constitutively expressed proteins, were selected as SIBPs for identifications at the genus and species level. Two distinctive mass peaks present in B. contaminans spectra (7501 and 7900 Da) were proposed as SIBPs for the identification of this novel species. A second approach of spectral analysis based on data reduction, feature selection and subsequent hierarchical cluster analysis was used to obtain an objective discrimination of all species analysed. Both complementary modalities of analyzing complex IC-MALDI-ToF MS data open the path towards a rapid, accurate and objective means of routine clinical microbiology diagnosis of pathogens from sputum samples of CF patients.
Collapse
Affiliation(s)
- Alejandro Miñán
- CINDEFI (CONICET-La Plata), Facultad de Ciencias Exactas, UNLP, Calle 50 y 115, (1900) La Plata, Argentina
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Low rates of Pseudomonas aeruginosa misidentification in isolates from cystic fibrosis patients. J Clin Microbiol 2009; 47:1503-9. [PMID: 19261796 DOI: 10.1128/jcm.00014-09] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas aeruginosa is an important cause of pulmonary infection in cystic fibrosis (CF). Its correct identification ensures effective patient management and infection control strategies. However, little is known about how often CF sputum isolates are falsely identified as P. aeruginosa. We used P. aeruginosa-specific duplex real-time PCR assays to determine if 2,267 P. aeruginosa sputum isolates from 561 CF patients were correctly identified by 17 Australian clinical microbiology laboratories. Misidentified isolates underwent further phenotypic tests, amplified rRNA gene restriction analysis, and partial 16S rRNA gene sequence analysis. Participating laboratories were surveyed on how they identified P. aeruginosa from CF sputum. Overall, 2,214 (97.7%) isolates from 531 (94.7%) CF patients were correctly identified as P. aeruginosa. Further testing with the API 20NE kit correctly identified only 34 (59%) of the misidentified isolates. Twelve (40%) patients had previously grown the misidentified species in their sputum. Achromobacter xylosoxidans (n = 21), Stenotrophomonas maltophilia (n = 15), and Inquilinus limosus (n = 4) were the species most commonly misidentified as P. aeruginosa. Overall, there were very low rates of P. aeruginosa misidentification among isolates from a broad cross section of Australian CF patients. Additional improvements are possible by undertaking a culture history review, noting colonial morphology, and performing stringent oxidase, DNase, and colistin susceptibility testing for all presumptive P. aeruginosa isolates. Isolates exhibiting atypical phenotypic features should be evaluated further by additional phenotypic or genotypic identification techniques.
Collapse
|
26
|
Elborn JS. Identification and management of unusual pathogens in cystic fibrosis. J R Soc Med 2008; 101 Suppl 1:S2-5. [PMID: 18607011 DOI: 10.1258/jrsm.2008.s18002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
|
27
|
Murray S, Charbeneau J, Marshall BC, LiPuma JJ. Impact ofBurkholderiaInfection on Lung Transplantation in Cystic Fibrosis. Am J Respir Crit Care Med 2008; 178:363-71. [DOI: 10.1164/rccm.200712-1834oc] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
|
28
|
Matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of nonfermenting gram-negative bacilli isolated from cystic fibrosis patients. J Clin Microbiol 2008; 46:3361-7. [PMID: 18685005 DOI: 10.1128/jcm.00569-08] [Citation(s) in RCA: 169] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The identification of nonfermenting gram-negative bacilli isolated from cystic fibrosis (CF) patients is usually achieved by using phenotype-based techniques and eventually molecular tools. These techniques remain time-consuming, expensive, and technically demanding. We used a method based on matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) for the identification of these bacteria. A set of reference strains belonging to 58 species of clinically relevant nonfermenting gram-negative bacilli was used. To identify peaks discriminating between these various species, the profile of 10 isolated colonies obtained from 10 different passages was analyzed for each referenced strain. Conserved peaks with a relative intensity greater than 0.1 were retained. The spectra of 559 clinical isolates were then compared to that of each of the 58 reference strains as follows: 400 Pseudomonas aeruginosa, 54 Achromobacter xylosoxidans, 32 Stenotrophomonas maltophilia, 52 Burkholderia cepacia complex (BCC), 1 Burkholderia gladioli, 14 Ralstonia mannitolilytica, 2 Ralstonia pickettii, 1 Bordetella hinzii, 1 Inquilinus limosus, 1 Cupriavidus respiraculi, and 1 Burkholderia thailandensis. Using this database, 549 strains were correctly identified. Nine BCC strains and one R. mannnitolilytica strain were identified as belonging to the appropriate genus but not the correct species. We subsequently engineered BCC- and Ralstonia-specific databases using additional reference strains. Using these databases, correct identification for these species increased from 83 to 98% and from 94 to 100% of cases, respectively. Altogether, these data demonstrate that, in CF patients, MALDI-TOF-MS is a powerful tool for rapid identification of nonfermenting gram-negative bacilli.
Collapse
|
29
|
Bittar F, Richet H, Dubus JC, Reynaud-Gaubert M, Stremler N, Sarles J, Raoult D, Rolain JM. Molecular detection of multiple emerging pathogens in sputa from cystic fibrosis patients. PLoS One 2008; 3:e2908. [PMID: 18682840 PMCID: PMC2483419 DOI: 10.1371/journal.pone.0002908] [Citation(s) in RCA: 165] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Accepted: 07/17/2008] [Indexed: 12/25/2022] Open
Abstract
Background There is strong evidence that culture-based methods detect only a small proportion of bacteria present in the respiratory tracts of cystic fibrosis (CF) patients. Methodology/Principal Findings Standard microbiological culture and phenotypic identification of bacteria in sputa from CF patients have been compared to molecular methods by the use of 16S rDNA amplification, cloning and sequencing. Twenty-five sputa from CF patients were cultured that yield 33 isolates (13 species) known to be pathogens during CF. For molecular cloning, 760 clones were sequenced (7.2±3.9 species/sputum), and 53 different bacterial species were identified including 16 species of anaerobes (30%). Discrepancies between culture and molecular data were numerous and demonstrate that accurate identification remains challenging. New or emerging bacteria not or rarely reported in CF patients were detected including Dolosigranulum pigrum, Dialister pneumosintes, and Inquilinus limosus. Conclusions/Significance Our results demonstrate the complex microbial community in sputa from CF patients, especially anaerobic bacteria that are probably an underestimated cause of CF lung pathology. Metagenomic analysis is urgently needed to better understand those complex communities in CF pulmonary infections.
Collapse
Affiliation(s)
- Fadi Bittar
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), CNRS-IRD, UMR 6236, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Hervé Richet
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), CNRS-IRD, UMR 6236, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Jean-Christophe Dubus
- Département des Maladies Respiratoires, Centre de Ressources et de Compétences pour la Mucoviscidose Enfants (CRCM), Hôpital Timone, Marseille, France
| | - Martine Reynaud-Gaubert
- Département des Maladies Respiratoires, Centre de Ressources et de Compétences pour la Mucoviscidose Adultes (CRCM), Hôpital Sainte Marguerite, Marseille, France
| | - Nathalie Stremler
- Département des Maladies Respiratoires, Centre de Ressources et de Compétences pour la Mucoviscidose Enfants (CRCM), Hôpital Timone, Marseille, France
| | - Jacques Sarles
- Département des Maladies Respiratoires, Centre de Ressources et de Compétences pour la Mucoviscidose Enfants (CRCM), Hôpital Timone, Marseille, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), CNRS-IRD, UMR 6236, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Jean-Marc Rolain
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), CNRS-IRD, UMR 6236, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
- * E-mail:
| |
Collapse
|
30
|
Genomovar status, virulence markers and genotyping of Burkholderia cepacia complex strains isolated from Brazilian cystic fibrosis patients. J Cyst Fibros 2008; 7:336-339. [DOI: 10.1016/j.jcf.2007.12.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2007] [Revised: 11/06/2007] [Accepted: 12/10/2007] [Indexed: 11/17/2022]
|
31
|
Comparason of extraction methods for PCR detection of Burkholderia cepacia complex (BCC) from cystic fibrosis patients. Open Med (Wars) 2008. [DOI: 10.2478/s11536-007-0069-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AbstractDirect detection of Burkholderia cepacia complex (BCC) and its genomovars from sputum by molecular tests emerges as a method for rapid identification. In this study, four DNA extraction methods were evaluated for the identification for BCC from sputum of CF patients. Sputa from 28 CF patients were aliquoted and spiked with BCC reference strain. Boiling, phenol-chloroform, CTAB methods and a commercial spin column kit was used for DNA extraction. Total DNA yields were determined by spectrophotometry and single-round recA PCR was used for detection of BCC. No significant difference was observed in DNA yields from different extraction methods. Lower limit of detection for recA PCR was determined as 106 cfu/ml. Amplification was observed in 7/16 (43.7%) of sputa for boiling, 8/16 (50%) of sputa for CTAB and 13/16 (81.2%) of sputa for phenol-chloroform method and spin column kit in the assay sensitivity range determined in the study. Phenol-chloroform and commercial spin column kit were found to be better suited for DNA purification from sputum of CF patients for BCC identification. Diagnostic impact of single-round recA PCR directly from sputum was limited to chronically-infected patients.
Collapse
|
32
|
Evaluation of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry in comparison to 16S rRNA gene sequencing for species identification of nonfermenting bacteria. J Clin Microbiol 2008; 46:1946-54. [PMID: 18400920 DOI: 10.1128/jcm.00157-08] [Citation(s) in RCA: 273] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nonfermenting bacteria are ubiquitous environmental opportunists that cause infections in humans, especially compromised patients. Due to their limited biochemical reactivity and different morphotypes, misidentification by classical phenotypic means occurs frequently. Therefore, we evaluated the use of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) for species identification. By using 248 nonfermenting culture collection strains composed of 37 genera most relevant to human infections, a reference database was established for MALDI-TOF MS-based species identification according to the manufacturer's recommendations for microflex measurement and MALDI BioTyper software (Bruker Daltonik GmbH, Leipzig, Germany), i.e., by using a mass range of 2,000 to 20,000 Da and a new pattern-matching algorithm. To evaluate the database, 80 blind-coded clinical nonfermenting bacterial strains were analyzed. As a reference method for species designation, partial 16S rRNA gene sequencing was applied. By 16S rRNA gene sequencing, 57 of the 80 isolates produced a unique species identification (>or=99% sequence similarity); 11 further isolates gave ambiguous results at this threshold and were rated as identified to the genus level only. Ten isolates were identified to the genus level (>or=97% similarity); and two isolates had similarity values below this threshold, were counted as not identified, and were excluded from further analysis. MALDI-TOF MS identified 67 of the 78 isolates (85.9%) included, in agreement with the results of the reference method; 9 were misidentified and 2 were unidentified. The identities of 10 randomly selected strains were 100% correct when three different mass spectrometers and four different cultivation media were used. Thus, MALDI-TOF MS-based species identification of nonfermenting bacteria provided accurate and reproducible results within 10 min without any substantial costs for consumables.
Collapse
|
33
|
Drevinek P, Baldwin A, Dowson CG, Mahenthiralingam E. Diversity of the parB and repA genes of the Burkholderia cepacia complex and their utility for rapid identification of Burkholderia cenocepacia. BMC Microbiol 2008; 8:44. [PMID: 18328098 PMCID: PMC2324101 DOI: 10.1186/1471-2180-8-44] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2007] [Accepted: 03/07/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Burkholderia cenocepacia is the most prominent species of the B. cepacia complex (Bcc), a group of nine closely related and difficult to identify bacteria that cause serious infections in patients with cystic fibrosis. Despite its clinical relevance, identification of B. cenocepacia as a single species is unavailable, as it splits by a widely used recA gene-based PCR identification method into discrete phylogenetic subgroups IIIA, IIIB, IIIC and IIID. With the aim of identifying gene targets suitable for unified detection of B. cenocepacia strains, we examined sequence polymorphisms in the repA and parB genes. These essential genes are involved in the replication and partitioning of bacterial replicons, hence we also had the opportunity for the first time to investigate the evolution of the multireplicon (three chromosome) structure of Bcc genomes. RESULTS Alignment of the repA and parB genes from publicly available Bcc genome sequences enabled the design of primers for their amplification and sequence analysis. Multilocus sequencing typing, a highly discriminatory method for Bcc species and strain discrimination, was used to select strains of unique sequence types (STs) that spanned the known Bcc genetic diversity. Sequence datasets of repA (83 isolates, 67 STs) and parB (120 isolates, 95 STs) genes from the second chromosome were aligned and examined phylogenetically to identify polymorphisms suitable for identification of B. cenocepacia. In contrast to parB, the Bcc repA sequences demonstrated distinct clustering of B. cenocepacia from other species, which enabled the design a species-specific multiplex PCR. The novel single-reaction B. cenocepacia detection method was tested on a panel of 142 different Bcc strains (142 STs) and distinguished recA groups IIIA, IIIB and IIID, from all other Bcc members with 100% sensitivity and 93% specificity. CONCLUSION The repA-based multiplex PCR is a useful aid to the rapid identification of the most clinically relevant B. cenocepacia recA subgroups IIIA, IIIB and IIID. Phylogenetic analysis of repA and parB genes demonstrated that acquisition of the second and third replicons of Bcc genomes occurred prior to their differentiation into discrete species and that the sharing of replicons across species had not occurred.
Collapse
Affiliation(s)
- Pavel Drevinek
- Cardiff School of Biosciences, Cardiff University, Cardiff, CF10 3TL, UK.
| | | | | | | |
Collapse
|
34
|
Development of a species-specific fur gene-based method for identification of the Burkholderia cepacia complex. J Clin Microbiol 2007; 46:447-55. [PMID: 18057135 DOI: 10.1128/jcm.01460-07] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Burkholderia is an important bacterial genus with a complex taxonomy that contains species of both ecological and pathogenic importance, including nine closely related species collectively termed the Burkholderia cepacia complex (BCC). Unfortunately, 16S rRNA gene analysis has proven to be not sensitive enough to discriminate between species of the BCC. Alternative species identification strategies such as recA-based PCR followed by restriction fragment length polymorphism analysis, although initially useful, have proven to be inaccurate with the increasing species diversity of the BCC. recA gene sequence analysis is more discriminatory and corroborates other biochemical and polyphasic means of taxonomic differentiation. However, it is limited by the fact that certain BCC species are subdivided into discrete recA sequence subgroups that may confuse clinical diagnoses. In this study, an effective approach is described for the rapid differentiation of BCC species from both environmental and clinical sources by means of a single-locus sequencing and PCR assay using fur as a target gene that provides sequence phylogenies that are species specific and, with few exceptions, not divided into subspecies clusters. This assay is specific and can be used to correctly determine the species status of BCC strains tested following sequencing and amplification of the fur gene by both general and species-specific primers. Based on our results, this typing strategy is simpler than and as sensitive as established tests currently in use clinically. This assay is useful for the rapid, definitive identification of all nine current BCC species and potentially novel species groups.
Collapse
|
35
|
Abstract
Cystic fibrosis (CF) is the most common lethal genetic disease in the Caucasian population, and should be considered an infectious disease because of the basic pathophysiology. Chronic lower airway infections cause a progressive pathologic deterioration of lung tissue, a decline in pulmonary function and, ultimately, respiratory failure and death in 90% of CF patients. Historically, very few bacterial species have been implicated as principal CF pathogens. However, molecular evidence suggests the presence of a diverse mosaic of bacteria in CF lungs, and infections can be defined as polymicrobial. Here we review the work that supports this concept and we discuss the potential significance of the polymicrobial community in lung pathology. Understanding the dynamics of polymicrobial infections, the interplay between pathogen(s), normal oropharyngeal flora and the host immune system may lead to future advances in the therapeutic management of chronic lung infections.
Collapse
Affiliation(s)
- Christopher D Sibley
- University of Calgary, Department of Microbiology and Infectious Diseases, Calgary, AB, Canada.
| | | | | |
Collapse
|
36
|
Abstract
In this article, the authors outline some of the major historical events that signaled the need to better understand mechanisms of infection in cystic fibrosis (CF). The authors discuss general principles of infection control, focusing on issues of particular importance to patients who have CF. The authors also describe the major pathogens associated with the CF airway, provide a review of findings from inpatient and outpatient studies of infection control, and provide an outline of future directions for investigation.
Collapse
Affiliation(s)
- Jonathan B Zuckerman
- Department of Medicine, The University of Vermont College of Medicine, E-126 Given Building, 89 Beaumont Avenue, Burlington, VT 05405-0068, USA.
| | | |
Collapse
|
37
|
Brown AR, Govan JRW. Assessment of fluorescent in situ hybridization and PCR-based methods for rapid identification of Burkholderia cepacia complex organisms directly from sputum samples. J Clin Microbiol 2007; 45:1920-6. [PMID: 17460050 PMCID: PMC1933040 DOI: 10.1128/jcm.00147-07] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Several species within the Burkholderia cepacia complex (BCC) have emerged as significant opportunistic pathogens of patients with cystic fibrosis (CF). BCC infection is typically associated with a poor clinical prognosis and decreased survival. These factors, combined with the existence of highly transmissible epidemic strains, have resulted in strict segregation of BCC- and non-BCC-infected patients to minimize cross infection. Accurate and rapid diagnosis of infections is essential to enable appropriate patient management. However, the rapidly evolving taxonomy of BCC poses a considerable challenge to diagnostics. In the present study, we assessed a commercially available fluorescent in situ hybridization (FISH) assay (seaFAST Cystic Fibrosis I kit) and a novel rRNA gene-based PCR assay for the rapid identification of BCC-positive sputa, irrespective of the BCC species. We report that, while the FISH assay fails to identify all BCC species, it does identify the majority of species, including the two most clinically relevant species, B. multivorans and B. cenocepacia. The sensitivity of the assay applied to sputum was limited by nonspecific background fluorescence. While sputum processing was optimized to minimize background, the resulting sensitivity for BCC detection was 8 x 10(5) CFU/ml. In contrast, the novel PCR assay reported herein exhibits 100% sensitivity and specificity for all BCC species and can detect 10(4) CFU/ml when applied to sputum. This novel rRNA gene-based assay is currently the most sensitive BCC-specific PCR assay for the detection of BCC direct from clinical samples and as such is a valuable addition to the field of BCC diagnostics.
Collapse
Affiliation(s)
- A R Brown
- Cystic Fibrosis Group, Centre for Infectious Diseases, University of Edinburgh, The Chancellor's Building, Edinburgh EH16 4SB, United Kingdom.
| | | |
Collapse
|
38
|
Zhou J, Chen Y, Tabibi S, Alba L, Garber E, Saiman L. Antimicrobial susceptibility and synergy studies of Burkholderia cepacia complex isolated from patients with cystic fibrosis. Antimicrob Agents Chemother 2006; 51:1085-8. [PMID: 17158942 PMCID: PMC1803131 DOI: 10.1128/aac.00954-06] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Susceptibility (18 antimicrobial agents including high-dose tobramycin) and checkerboard synergy (23 combinations) studies were performed for 2,621 strains of Burkholderia cepacia complex isolated from 1,257 cystic fibrosis patients. Minocycline, meropenem, and ceftazidime were the most active, inhibiting 38%, 26%, and 23% of strains, respectively. Synergy was rarely noted (range, 1% to 15% of strains per antibiotic combination).
Collapse
Affiliation(s)
- Juyan Zhou
- Division of Infectious Diseases, Department of Pediatrics, Columbia University, College of Physicians & Surgeons, 650 West 168th Street, PH 4 West Room 470, New York, NY 10032, USA
| | | | | | | | | | | |
Collapse
|
39
|
Zhou J, Garber E, Desai M, Saiman L. Compliance of clinical microbiology laboratories in the United States with current recommendations for processing respiratory tract specimens from patients with cystic fibrosis. J Clin Microbiol 2006; 44:1547-9. [PMID: 16597890 PMCID: PMC1448617 DOI: 10.1128/jcm.44.4.1547-1549.2006] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Respiratory tract specimens from patients with cystic fibrosis (CF) require unique processing by clinical microbiology laboratories to ensure detection of all potential pathogens. The present study sought to determine the compliance of microbiology laboratories in the United States with recently published recommendations for CF respiratory specimens. Microbiology laboratory protocols from 150 of 190 (79%) CF care sites were reviewed. Most described the use of selective media for Burkholderia cepacia complex (99%), Staphylococcus aureus (82%), and Haemophilus influenzae (89%) and identified the species of all gram-negative bacilli (87%). Only 52% delineated the use of agar diffusion assays for susceptibility testing of Pseudomonas aeruginosa. Standardizing laboratory practices will improve treatment, infection control, and our understanding of the changing epidemiology of CF microbiology.
Collapse
Affiliation(s)
- Juyan Zhou
- Division of Infectious Diseases, Department of Pediatrics, Columbia University, College of Physicians & Surgeons, 650 West 168th St., PH 4 West Room 470, New York, NY 10032, USA
| | | | | | | |
Collapse
|
40
|
Wellinghausen N, Wirths B, Poppert S. Fluorescence in situ hybridization for rapid identification of Achromobacter xylosoxidans and Alcaligenes faecalis recovered from cystic fibrosis patients. J Clin Microbiol 2006; 44:3415-7. [PMID: 16954289 PMCID: PMC1594702 DOI: 10.1128/jcm.00508-06] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Achromobacter xylosoxidans is frequently isolated from the respiratory secretions of cystic fibrosis (CF) patients, but identification with biochemical tests is unreliable. We describe fluorescence in situ hybridization assays for the rapid identification of Achromobacter xylosoxidans and Alcaligenes faecalis. Both assays showed high sensitivities and high specificities with a collection of 155 nonfermenters from CF patients.
Collapse
Affiliation(s)
- Nele Wellinghausen
- Institute of Medical Microbiology and Hygiene, University Hospital of Ulm, Robert-Koch Str. 8, D-89081 Ulm, Germany.
| | | | | |
Collapse
|
41
|
Affiliation(s)
- J S Elborn
- Respiratory Medicine Group, Queens' University of Belfast, Belfast, N. Ireland.
| |
Collapse
|
42
|
Lo Cascio G, Bonora MG, Zorzi A, Mortani E, Tessitore N, Loschiavo C, Lupo A, Solbiati M, Fontana R. A napkin-associated outbreak of Burkholderia cenocepacia bacteraemia in haemodialysis patients. J Hosp Infect 2006; 64:56-62. [PMID: 16859809 DOI: 10.1016/j.jhin.2006.04.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2005] [Accepted: 04/13/2006] [Indexed: 11/20/2022]
Abstract
This article reports a catheter-related outbreak of bacteraemia involving 38 patients in two haemodialysis units in Verona. Burkholderia cepacia complex strains were isolated from human blood and from an individually wrapped disinfection napkin that was contained in a commercially available, sterile dressing kit used to handle central venous catheters. Micro-organisms isolated from blood cultures and from the napkin were identified by standard procedures and confirmed as B. cenocepacia (genomovar III) by molecular analysis. Using pulsed-field gel electrophoresis analysis, the clinical isolates were indistinguishable or closely related to the B. cenocepacia isolated from the napkin. In conclusion, this study found that a contaminated commercial napkin soaked in quaternary ammonium, even when quality certified, was the source of infection.
Collapse
Affiliation(s)
- G Lo Cascio
- Dipartimento di Patologia, Sezione di Microbiologia, Università di Verona, Verona, Italy.
| | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Orens JB, Estenne M, Arcasoy S, Conte JV, Corris P, Egan JJ, Egan T, Keshavjee S, Knoop C, Kotloff R, Martinez FJ, Nathan S, Palmer S, Patterson A, Singer L, Snell G, Studer S, Vachiery JL, Glanville AR. International guidelines for the selection of lung transplant candidates: 2006 update--a consensus report from the Pulmonary Scientific Council of the International Society for Heart and Lung Transplantation. J Heart Lung Transplant 2006; 25:745-55. [PMID: 16818116 DOI: 10.1016/j.healun.2006.03.011] [Citation(s) in RCA: 699] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2006] [Revised: 01/12/2006] [Accepted: 03/13/2006] [Indexed: 10/24/2022] Open
Affiliation(s)
- Jonathan B Orens
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Campana S, Taccetti G, Ravenni N, Favari F, Cariani L, Sciacca A, Savoia D, Collura A, Fiscarelli E, De Intinis G, Busetti M, Cipolloni A, d'Aprile A, Provenzano E, Collebrusco I, Frontini P, Stassi G, Trancassini M, Tovagliari D, Lavitola A, Doherty CJ, Coenye T, Govan JRW, Vandamme P. Transmission of Burkholderia cepacia complex: evidence for new epidemic clones infecting cystic fibrosis patients in Italy. J Clin Microbiol 2005; 43:5136-42. [PMID: 16207975 PMCID: PMC1248445 DOI: 10.1128/jcm.43.10.5136-5142.2005] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To analyze national prevalence, genomovar distribution, and epidemiology of the Burkholderia cepacia complex in Italy, 225 putative B. cepacia complex isolates were obtained from 225 cystic fibrosis (CF) patients attending 18 CF centers. The genomovar status of these isolates was determined by a polyphasic approach, which included whole-cell protein electrophoresis and recA restriction fragment length polymorphism (RFLP) analysis. Two approaches were used to genotype B. cepacia complex isolates: BOX-PCR fingerprinting and pulsed-field gel electrophoresis (PFGE) of genomic macrorestriction fragments. A total of 208 (92%) of 225 isolates belonged to the B. cepacia complex, with Burkholderia cenocepacia as the most prevalent species (61.1%). Clones delineated by PFGE were predominantly linked to a single center; in contrast, BOX-PCR clones were composed of isolates collected either from the same center or from different CF centers and comprised multiple PFGE clusters. Three BOX-PCR clones appeared of special interest. One clone was composed of 17 B. cenocepacia isolates belonging to recA RFLP type H. These isolates were collected from six centers and represented three PFGE clusters. The presence of insertion sequence IS 1363 in all isolates and the comparison with PHDC reference isolates identified this clone as PHDC, an epidemic clone prominent in North American CF patients. The second clone included 22 isolates from eight centers and belonged to recA RFLP type AT. The genomovar status of strains with the latter RFLP type is not known. Most of these isolates belonged to four different PFGE clusters. Finally, a third clone comprised nine B. pyrrocinia isolates belonging to recA RFLP type Se 13. They represented three PFGE clusters and were collected in three CF centers.
Collapse
Affiliation(s)
- S Campana
- Department of Pediatrics, Cystic Fibrosis Center, University of Florence, 50132 Florence, Italy.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Baldwin A, Mahenthiralingam E, Thickett KM, Honeybourne D, Maiden MCJ, Govan JR, Speert DP, Lipuma JJ, Vandamme P, Dowson CG. Multilocus sequence typing scheme that provides both species and strain differentiation for the Burkholderia cepacia complex. J Clin Microbiol 2005; 43:4665-73. [PMID: 16145124 PMCID: PMC1234123 DOI: 10.1128/jcm.43.9.4665-4673.2005] [Citation(s) in RCA: 162] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A single multilocus sequence typing (MLST) scheme was developed for precise characterization of the opportunistic pathogens of Burkholderia cepacia complex (BCC), a group composed of at least nine closely related species. Seven conserved housekeeping genes were selected after a comparison of five Burkholderia species, and a collection of strains was subjected to nucleotide sequence analysis using a nested PCR amplification approach for each gene. MLST differentiated all nine current BCC species and identified 114 sequence types within a collection of 119 strains. No differentiation was found between strains recovered from environmental or clinical sources. The improved resolution in strain identification offered by MLST was able to identify previously characterized epidemic strain lineages and also demonstrated the presence of four novel potential species groups within the complex. There was also evidence for recombination having an important role in the recent evolution of individual BCC species. This highly transferable, validated, MLST scheme provides a new means to assist in species identification as well as unambiguous strain discrimination of the BCC by a single approach. It is also the first MLST scheme designed at the outset to incorporate multiple species and should facilitate global epidemiological investigations of the BCC.
Collapse
Affiliation(s)
- Adam Baldwin
- Department of Biological Sciences, University of Warwick, Coventry, UK
| | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Wellinghausen N, Köthe J, Wirths B, Sigge A, Poppert S. Superiority of molecular techniques for identification of gram-negative, oxidase-positive rods, including morphologically nontypical Pseudomonas aeruginosa, from patients with cystic fibrosis. J Clin Microbiol 2005; 43:4070-5. [PMID: 16081953 PMCID: PMC1233906 DOI: 10.1128/jcm.43.8.4070-4075.2005] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phenotypic identification of gram-negative bacteria from Cystic Fibrosis (CF) patients carries a high risk of misidentification. Therefore, we compared the results of biochemical identification by API 20NE with 16S rRNA gene sequencing in 88 gram-negative, oxidase-positive rods, other than morphologically and biochemically typical P. aeruginosa, from respiratory secretions of CF patients. The API 20NE allowed correct identification of the bacterial species in 15 out of 88 (17%) isolates investigated. Agreement between the API and the 16S rRNA gene sequencing results was high only in isolates with an API result classified as "excellent identification". Even API results classified as "very good identification" or "good identification" showed a high rate of misidentification (67% and 84%). Fifty-two isolates of morphological and biochemical nontypical Pseudomonas aeruginosa, representing 59% of all isolates investigated, were not identifiable or misidentified in the API 20NE. Therefore, rapid molecular diagnostic techniques like real-time PCR and fluorescence in situ hybridization (FISH) were evaluated in this particular group of bacteria for identification of the clinically most relevant pathogen, P. aeruginosa. The LightCycler PCR assay with a P. aeruginosa-specific probe showed a sensitivity and specificity of 98.1% and 100%, respectively. For FISH analysis, a newly designed P. aeruginosa-specific probe had a sensitivity and specificity of 100%. In conclusion, molecular methods are superior over biochemical tests for identification of gram-negative, oxidase-positive rods in CF patients. In addition, real-time PCR and FISH allowed identification of morphologically nontypical isolates of P. aeruginosa within a few hours.
Collapse
Affiliation(s)
- Nele Wellinghausen
- Department of Medical Microbiology and Hygiene, University of Ulm, Robert-Koch-Str. 8, D-89081 Ulm, Germany.
| | | | | | | | | |
Collapse
|
47
|
Mahenthiralingam E, Urban TA, Goldberg JB. The multifarious, multireplicon Burkholderia cepacia complex. Nat Rev Microbiol 2005; 3:144-56. [PMID: 15643431 DOI: 10.1038/nrmicro1085] [Citation(s) in RCA: 622] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The Burkholderia cepacia complex (Bcc) is a collection of genetically distinct but phenotypically similar bacteria that are divided into at least nine species. Bcc bacteria are found throughout the environment, where they can have both beneficial and detrimental effects on plants and some members can also degrade natural and man-made pollutants. Bcc bacteria are now recognized as important opportunistic pathogens that can cause variable lung infections in cystic fibrosis patients, which result in asymptomatic carriage, chronic infection or 'cepacia syndrome', which is characterized by a rapid decline in lung function that can include invasive disease. Here we highlight the unique characteristics of the Bcc, focusing on the factors that determine virulence.
Collapse
|
48
|
Brisse S, Cordevant C, Vandamme P, Bidet P, Loukil C, Chabanon G, Lange M, Bingen E. Species distribution and ribotype diversity of Burkholderia cepacia complex isolates from French patients with cystic fibrosis. J Clin Microbiol 2004; 42:4824-7. [PMID: 15472352 PMCID: PMC522310 DOI: 10.1128/jcm.42.10.4824-4827.2004] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A total of 153 Burkholderia cepacia strains obtained from 153 French patients with cystic fibrosis were identified as Burkholderia multivorans (51.6%) or Burkholderia cenocepacia (45.1%). Eighty-two genotypes were identified using PvuII and EcoRI ribotyping. B. multivorans genotype A (found in 32 French patients) and two other genotypes were also identified among isolates from Austrian, German, Italian, and Canadian patients.
Collapse
Affiliation(s)
- Sylvain Brisse
- Unité Biodiversité des Bactéries Pathogènes Emergents (U389 INSERM), Institut Pasteur Paris, France
| | | | | | | | | | | | | | | |
Collapse
|
49
|
Taylor PC, McLaws ML, De Borde M, Pritchard R. Isolation and identification of Burkholderia cepacia by participants in an external Quality Assurance Program (QAP) between 1994 and 1999. Pathology 2004; 36:352-7. [PMID: 15370136 DOI: 10.1080/00313020410001721636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
AIM External quality assurance programs (QAPs) provide an opportunity to benchmark laboratory performance according to the profile of specimens received. Participant confidentiality is maintained within each group of laboratories whose performance is measured using similar, repetitive exercises. Isolation and identification of Burkholderia cepacia from simulated cystic fibrosis (CF) sputa was a clinically relevant exercise that provided a model for this analytical approach. METHODS Between 1994 and 1999, six Royal College of Pathologists of Australasia (RCPA) Microbiology QAPs included four simulated CF sputa and two panels of oxidative Gram-negative bacilli. Laboratories were grouped according to experience with CF sputa disclosed by two questionnaires. Data were analysed by laboratory group for ability to isolate and identify B. cepacia. RESULTS Three laboratory groups annually received >100 CF sputa (CF>100), 100 CF sputa or fewer, or did not regularly receive CF sputa. CF>100 laboratories inoculated more isolation media, were more likely to use selective media and were less likely to misidentify B. cepacia than the other groups. Improved performance by CF>100 laboratories was marked after the first exercise and remained at a high level compared with the other two groups. This trend in performance was also apparent for Pseudomonas aeruginosa although the numbers of errors were less than for B. cepacia. CONCLUSIONS These exercises demonstrated consistently improved performance only among CF>100 laboratories. The future criteria for laboratory accreditation may include performance as well as participation in QAPs, placing additional burdens on organisers and participants.
Collapse
Affiliation(s)
- Peter C Taylor
- Department of Microbiology, South Eastern Area Laboratory Service, The Prince of Wales Hospital, Randwick, NSW 2031, Australia.
| | | | | | | |
Collapse
|
50
|
da Silva Filho LVF, Tateno AF, Velloso LDF, Levi JE, Fernandes S, Bento CNO, Rodrigues JC, Ramos SRTS. Identification of Pseudomonas aeruginosa, Burkholderia cepacia complex, and Stenotrophomonas maltophilia in respiratory samples from cystic fibrosis patients using multiplex PCR. Pediatr Pulmonol 2004; 37:537-47. [PMID: 15114555 DOI: 10.1002/ppul.20016] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A multiplex PCR method was developed to identify P. aeruginosa, B. cepacia complex, and S. maltophilia directly in sputum and oropharyngeal samples from CF patients. One hundred and six patients (53 male, and 53 female) attending our pulmonology clinic were studied from September 2000-April 2001. Two hundred and fifty-seven samples were cultured in selective media and submitted to multiplex PCR reactions, using three primer pairs targeting specific genomic sequences of each species, with an additional primer pair targeting a stretch of ribosomal 16S DNA, universal for bacteria, to act as a control. P. aeruginosa was isolated by culture in 56% of samples, B. cepacia complex in 4.3%, and S. maltophilia in 2.7%, while multiplex PCR identified P. aeruginosa in 78.7%, B. cepacia complex in 3.9%, and S. maltophilia in 3.1% of samples. Multiplex PCR results were verified by PCR reactions using different species-specific primers described in the literature and DNA sequencing of amplicons from a few samples. Comparing to culture results, the sensitivity and specificity values of multiplex PCR for bacterial identification were, respectively, 97.2% and 45.5% for P. aeruginosa, 45.5% and 97.9% for B. cepacia complex, and 40% and 97.6% for S. maltophilia. All 10 multiplex PCR-positive results for B. cepacia complex were confirmed using other species-specific primers described in the literature, while this approach confirmed results for S. maltophilia identification in 7/8 samples (87.5%). Sequencing of amplicons from samples culture-negative but multiplex PCR-positive for P. aeruginosa and B. cepacia complex confirmed their identity, while minor nucleotide differences among amplicons ruled out the hypothesis of PCR contamination.
Collapse
Affiliation(s)
- Luiz V F da Silva Filho
- Instituto da Criança Prof. Pedro de Alcântara, Hospital das Clínicas, University of São Paulo Medical School, São Paulo, Brazil.
| | | | | | | | | | | | | | | |
Collapse
|