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Zbinden A, Seth-Smith HMB, Beltrami V, Mancini S, Droz S, Bürgi U, Melillo D, Schuurmans MM, Schwizer B, Schmid I, Casaulta C, Barben J, Mueller NJ, Imkamp F. Burkholderia cenocepacia ST-250 in cystic fibrosis patients in Switzerland: Genomic investigation of transmission routes. Diagn Microbiol Infect Dis 2024; 110:116429. [PMID: 39116652 DOI: 10.1016/j.diagmicrobio.2024.116429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 06/22/2024] [Accepted: 07/05/2024] [Indexed: 08/10/2024]
Abstract
This report describes the characterization of Burkholderia cenocepacia isolates belonging to sequence type (ST)-250, detected in eight patients with cystic fibrosis (CF) in Switzerland. We retrospectively analyzed 18 isolates of B. cenocepacia ST-250 isolated between 2003 and 2015 by whole-genome sequencing and evaluated clinical and epidemiological data. Single nucleotide polymorphism analysis of the B.°cenocepacia ST-250 lineage showed that the isolates from all patients cluster tightly, suggesting that this cluster has a recent common ancestor. Epidemiological investigations showed that six out of eight patients acquired B.°cenocepacia ST-250 in the years 2001-2006, where participation in CF summer camps was common. Two patients were siblings. Genomic relatedness of the B. cenocepacia ST-250 isolates supported transmission by close contact, however, a common source or nosocomial routes cannot be excluded. With respect to the fatal outcome in six patients, our study shows the importance of infection control measurements in CF patients with B.°cenocepacia.
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Affiliation(s)
- Andrea Zbinden
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
| | | | - Vanessa Beltrami
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Stefano Mancini
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Sara Droz
- Institute of Infectious Diseases, University of Bern, Bern, Switzerland
| | - Urs Bürgi
- Division of internal Medicine, Service Pulmonology, Cantonal Hospital Lucerne, Lucerne, Switzerland
| | - David Melillo
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Mace M Schuurmans
- Division of Pulmonology, University Hospital Zurich, Zurich, Switzerland
| | | | - Iris Schmid
- CF-Center, Quartier Bleu, Lindenhofspital, Bern, Switzerland
| | | | - Jürg Barben
- Paediatric Pulmonology & CF Centre, Children's Hospital of Eastern Switzerland, St. Gallen, Switzerland
| | - Nicolas J Mueller
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University Zurich, Zurich, Switzerland
| | - Frank Imkamp
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
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2
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Arsenault C, Harel J, Doualla-Bell F, Cavayas YA, Marchand-Sénécal X, Frenette C, Longtin Y, Lalande L, Diby LMP, Desmarais N. A Burkholderia stabilis outbreak associated with the use of ultrasound gel in multiple healthcare centres in Montréal, Canada, May-October 2021. CANADA COMMUNICABLE DISEASE REPORT = RELEVE DES MALADIES TRANSMISSIBLES AU CANADA 2023; 49:314-319. [PMID: 38455880 PMCID: PMC10917130 DOI: 10.14745/ccdr.v49i78a03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
Background Burkholderia stabilis is a non-fermenting, gram-negative bacteria that has previously been implicated in multiple nosocomial outbreaks through the use of contaminated medical devices and substances. This article reports on an outbreak of B. stabilis infections and colonizations, involving 11 patients from five acute care hospitals in Montréal, Canada. Methods One sample was not available for testing, but the remaining 10 isolates (91%) were sent for phylogenetic testing. Medical materials and the patients' environments were also sampled and cultured. Samples were tested using pulsed field gel electrophoresis and multilocus sequence typing. Results The outbreak was found to be associated with the use of intrinsically contaminated non-sterile ultrasound gel. Relatedness of the gel's and the patients' B. stabilis strains was demonstrated using gel electrophoresis and multilocus sequence typing analyses. The investigation was concluded with a prompt recall of the product, and the outbreak was declared over by the end of October 2021. Conclusion Contaminated non-sterile gel caused infections and pseudo-infections in several patients.
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Affiliation(s)
- Christine Arsenault
- Hôpital du Sacré-Cœur-de-Montréal, Montréal, QC
- Département de microbiologie, infectiologie et immunologie, Faculté de médecine, Université de Montréal, Montréal, QC
| | - Josée Harel
- Laboratoire de santé publique du Québec/Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, QC
| | - Florence Doualla-Bell
- Laboratoire de santé publique du Québec/Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, QC
| | - Yiorgos Alexandros Cavayas
- Hôpital du Sacré-Cœur-de-Montréal, Montréal, QC
- Département de médecine, Faculté de médecine, Université de Montréal, Montréal, QC
| | - Xavier Marchand-Sénécal
- Département de microbiologie, infectiologie et immunologie, Faculté de médecine, Université de Montréal, Montréal, QC
- Hôpital Maisonneuve-Rosemont, Montréal, QC
| | - Charles Frenette
- McGill University Health Center, Montréal, QC
- Infectious Diseases Division, Faculty of Medicine and Health Sciences, McGill University, Montréal, QC
| | - Yves Longtin
- Infectious Diseases Division, Faculty of Medicine and Health Sciences, McGill University, Montréal, QC
- Jewish General Hospital, Montréal, QC
| | - Linda Lalande
- Hôpital du Sacré-Cœur-de-Montréal, Montréal, QC
- Service de prévention et contrôle des infections du CIUSSS du Nord de l’Ile de Montréal, Montréal, QC
| | - L Marie-Paule Diby
- Hôpital du Sacré-Cœur-de-Montréal, Montréal, QC
- Service de prévention et contrôle des infections du CIUSSS du Nord de l’Ile de Montréal, Montréal, QC
| | - Nadia Desmarais
- Hôpital du Sacré-Cœur-de-Montréal, Montréal, QC
- Service de prévention et contrôle des infections du CIUSSS du Nord de l’Ile de Montréal, Montréal, QC
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Liebhoff AM, Menden K, Laschtowitz A, Franke A, Schramm C, Bonn S. Pathogen detection in RNA-seq data with Pathonoia. BMC Bioinformatics 2023; 24:53. [PMID: 36803415 PMCID: PMC9938591 DOI: 10.1186/s12859-023-05144-z] [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: 08/29/2022] [Accepted: 01/10/2023] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND Bacterial and viral infections may cause or exacerbate various human diseases and to detect microbes in tissue, one method of choice is RNA sequencing. The detection of specific microbes using RNA sequencing offers good sensitivity and specificity, but untargeted approaches suffer from high false positive rates and a lack of sensitivity for lowly abundant organisms. RESULTS We introduce Pathonoia, an algorithm that detects viruses and bacteria in RNA sequencing data with high precision and recall. Pathonoia first applies an established k-mer based method for species identification and then aggregates this evidence over all reads in a sample. In addition, we provide an easy-to-use analysis framework that highlights potential microbe-host interactions by correlating the microbial to the host gene expression. Pathonoia outperforms state-of-the-art methods in microbial detection specificity, both on in silico and real datasets. CONCLUSION Two case studies in human liver and brain show how Pathonoia can support novel hypotheses on microbial infection exacerbating disease. The Python package for Pathonoia sample analysis and a guided analysis Jupyter notebook for bulk RNAseq datasets are available on GitHub.
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Affiliation(s)
- Anna-Maria Liebhoff
- Institute for Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany. .,Department of Computer Science, Whiting School of Engineering, Johns Hopkins University, Baltimore, USA.
| | - Kevin Menden
- grid.424247.30000 0004 0438 0426Department of Genome Biology of Neurodegenerative Diseases, DZNE, Tübingen, Germany
| | - Alena Laschtowitz
- grid.13648.380000 0001 2180 3484I. Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Andre Franke
- grid.9764.c0000 0001 2153 9986Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Christoph Schramm
- grid.13648.380000 0001 2180 3484I. Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany ,grid.13648.380000 0001 2180 3484Martin Zeitz Center for Rare Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany ,grid.13648.380000 0001 2180 3484Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Bonn
- grid.13648.380000 0001 2180 3484Institute for Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Brangsch H, Singha H, Laroucau K, Elschner M. Sequence-based detection and typing procedures for Burkholderia mallei: Assessment and prospects. Front Vet Sci 2022; 9:1056996. [PMID: 36452150 PMCID: PMC9703372 DOI: 10.3389/fvets.2022.1056996] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 10/26/2022] [Indexed: 10/28/2023] Open
Abstract
Although glanders has been eradicated in most of the developed world, the disease still persists in various countries such as Brazil, India, Pakistan, Bangladesh, Nepal, Iran, Bahrain, UAE and Turkey. It is one of the notifiable diseases listed by the World Organization for Animal Health. Occurrence of glanders imposes restriction on equestrian events and restricts equine movement, thus causing economic losses to equine industry. The genetic diversity and global distribution of the causing agent, Burkholderia (B.) mallei, have not been assessed in detail and are complicated by the high clonality of this organism. Among the identification and typing methods, PCR-based methods for distinguishing B. mallei from its close relative B. pseudomallei as well as genotyping using tandem repeat regions (MLVA) are established. The advent and continuous advancement of the sequencing techniques and the reconstruction of closed genomes enable the development of genome guided epidemiological tools. For achieving a higher genomic resolution, genotyping methods based on whole genome sequencing data can be employed, like genome-wide single nucleotide polymorphisms. One of the limitations in obtaining complete genomic sequences for further molecular characterization of B. mallei is its high GC content. In this review, we aim to provide an overview of the widely used detection and typing methods for B. mallei and illustrate gaps that still require development. The genomic features of Burkholderia, their high homology and clonality will be first described from a comparative genomics perspective. Then, the commonly used molecular detection (PCR systems) and typing systems (e.g., multilocus sequence typing, variable number of tandem repeat analysis) will be presented and put in perspective with recently developed genomic methods. Also, the increasing availability of B. mallei genomic sequences and evolution of the sequencing methods offers exciting prospects for further refinement of B. mallei typing, that could overcome the difficulties presently encountered with this particular bacterium.
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Affiliation(s)
- Hanka Brangsch
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut – Federal Research Institute for Animal Health, Jena, Germany
| | | | - Karine Laroucau
- Bacterial Zoonosis Unit, Animal Health Laboratory, French Food Agency (Anses), Maisons-Alfort, France
| | - Mandy Elschner
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut – Federal Research Institute for Animal Health, Jena, Germany
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5
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Contamination analysis of Arctic ice samples as planetary field analogs and implications for future life-detection missions to Europa and Enceladus. Sci Rep 2022; 12:12379. [PMID: 35896693 PMCID: PMC9329357 DOI: 10.1038/s41598-022-16370-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/08/2022] [Indexed: 11/09/2022] Open
Abstract
Missions to detect extraterrestrial life are being designed to visit Europa and Enceladus in the next decades. The contact between the mission payload and the habitable subsurface of these satellites involves significant risk of forward contamination. The standardization of protocols to decontaminate ice cores from planetary field analogs of icy moons, and monitor the contamination in downstream analysis, has a direct application for developing clean approaches crucial to life detection missions in these satellites. Here we developed a comprehensive protocol that can be used to monitor and minimize the contamination of Arctic ice cores in processing and downstream analysis. We physically removed the exterior layers of ice cores to minimize bioburden from sampling. To monitor contamination, we constructed artificial controls and applied culture-dependent and culture-independent techniques such as 16S rRNA amplicon sequencing. We identified 13 bacterial contaminants, including a radioresistant species. This protocol decreases the contamination risk, provides quantitative and qualitative information about contamination agents, and allows validation of the results obtained. This study highlights the importance of decreasing and evaluating prokaryotic contamination in the processing of polar ice cores, including in their use as analogs of Europa and Enceladus.
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Bender JK, Haller S, Pfeifer Y, Hogardt M, Hunfeld KP, Thürmer A, Zanuzdana A, Werner M, Kunz B, Eisenberger D, Pfennigwerth N, Kempf VAJ, Werner G, Eckmanns T. Combined clinical, epidemiological and genome-based analysis identified a nationwide outbreak of Burkholderia cepacia complex infections caused by contaminated mouthwash solutions. Open Forum Infect Dis 2022; 9:ofac114. [PMID: 35434175 PMCID: PMC9007922 DOI: 10.1093/ofid/ofac114] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/07/2022] [Indexed: 11/21/2022] Open
Abstract
Background In September 2018, Burkholderia cepacia complex (BCC) infections in 3 patients associated with exposure to a mouthwash solution (MWS) were reported to the Robert Koch Institute (RKI). As the product was still on the market and the scale of the outbreak was unclear, a nation-wide investigation was initiated. Methods We aimed to investigate BCC infections/colonizations associated with MWS. Hospitals, laboratories, and public health services were informed that BCC isolates should be sent to the RKI. These isolates were typed by pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing (WGS) including development of an ad hoc core genome MLST (cgMLST) scheme. Results In total, 36 patients from 6 hospitals met the case definition, the last patient in November 2018. Twenty-nine isolates from 26 of these patients were available for typing. WGS analysis revealed 2 distinct cgMLST clusters. Cluster 1 (Burkholderia arboris) contained isolates from patients and MWS obtained from 4 hospitals and isolates provided by the manufacturer. Patient and MWS isolates from another hospital were assigned to cluster 2 (B. cepacia). Conclusions The combined clinical, epidemiological, and microbiological investigation, including whole-genome analysis, allowed for uncovering a supraregional BCC outbreak in health care settings. Strains of B. arboris and B. cepacia were identified as contaminating species of MWS bottles and subsequent colonization and putative infection of patients in several hospitals. Despite a recall of the product by the manufacturer in August 2018, the outbreak lasted until December 2018. Reporting of contaminated medical products and recalls should be optimized to protect patients.
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Affiliation(s)
- Jennifer K Bender
- Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | - Sebastian Haller
- Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Yvonne Pfeifer
- Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | - Michael Hogardt
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Frankfurt am Main, Germany
- German National Consiliary Laboratory on Cystic Fibrosis Bacteriology, Frankfurt am Main, Germany
| | - Klaus-Peter Hunfeld
- Institute for Laboratory Medicine, Microbiology & Infection Control, Northwest Medical Centre, Medical Faculty, Goethe University, Frankfurt am Main, Germany
| | | | - Arina Zanuzdana
- Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Markus Werner
- Institute for Clinical Microbiology, Immunology and Hygiene, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Bernd Kunz
- Institute for Clinical Microbiology, Immunology and Hygiene, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | | | - Niels Pfennigwerth
- National Reference Center for Multidrug-resistant Gram-negative Bacteria, Ruhr-University Bochum, Bochum, Germany
| | - Volkhard A J Kempf
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Frankfurt am Main, Germany
- German National Consiliary Laboratory on Cystic Fibrosis Bacteriology, Frankfurt am Main, Germany
| | - Guido Werner
- Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | - Tim Eckmanns
- Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
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Burkholderiaceae and Multidrug Resistance Genes Are Key Players in Resistome Development in a Germfree Soil Model. mSystems 2021; 6:e0098821. [PMID: 34726494 PMCID: PMC8562478 DOI: 10.1128/msystems.00988-21] [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] [Indexed: 01/04/2023] Open
Abstract
Assembly of a resistome in parallel with the establishment of a microbial community is not well understood. Germfree models can reveal microbiota interactions and shed light on bacterial colonization and resistance development under antibiotic pressure. In this study, we exposed germfree soil (GS), GS with diluted nontreated soil (DS), and nontreated soil (NS) to various concentrations of tetracycline (TET) in a nongermfree environment for 10 weeks, followed by 2 weeks of exposure to water. High-throughput sequencing was used to profile bacterial communities and antibiotic resistance genes (ARGs) in the soils. The initial bacterial loads were found to shape the profiles of bacterial communities and the resistomes. GS and DS treated with TET and the same soils left untreated had similar profiles, whereas NS showed different profiles. Soils with the same initial bacterial loads had their profiles shifted by TET treatment. Multidrug resistance (MDR) genes were the most abundant ARG types in all soils, with multidrug efflux pump genes being the discriminatory ARGs in GS regardless of different TET treatments and in GS, DS, and NS after TET. Furthermore, MDR genes were significantly enriched by TET treatment. In contrast, tetracycline resistance genes were either absent or low in relative abundance. The family Burkholderiaceae was predominant in all soils (except in NS treated with water) and was positively selected for by TET treatment. Most importantly, Burkholderiaceae were the primary carrier of ARGs, including MDR genes. IMPORTANCE This is the first study to examine how resistomes develop and evolve using GS. GS can be used to study the colonization and establishment of bacterial communities under antibiotic selection. Surprisingly, MDR genes were the main ARGs detected in GS, and TET treatments did not positively select for specific tetracycline resistance genes. Additionally, Burkholderiaceae were the key bacterial hosts for MDR genes in the current GS model under the conditions investigated. These results show that the family Burkholderiaceae underpins the development of resistome and serves as a source of ARGs. The ease of establishment of Burkholderiaceae and MDR genes in soils has serious implications for human health, since these bacteria are versatile and ubiquitous in the environment.
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Global burden, point sources, and outbreak management of healthcare-associated Burkholderia cepacia infections: An integrative review. Infect Control Hosp Epidemiol 2021; 41:777-783. [PMID: 32441235 DOI: 10.1017/ice.2020.184] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
OBJECTIVE To examine the global burden, associated point sources, and successful prevention and control measures for documented outbreaks of Burkholderia cepacia healthcare-associated infections (HAIs). DESIGN Integrative review. METHODS A review of all outbreaks of Burkholderia cepacia HAIs published in the peer-reviewed literature between January 1970 and October 2019 was conducted to identify the global burden, associated point sources, and successful prevention and control measures using the Guidelines for Outbreak Reports and Intervention Studies of Nosocomial Infections (ORION). RESULTS In total, we reviewed 125 documented outbreaks of Burkholderia cepacia-related HAIs worldwide. The reported B. cepacia HAIs for this period involved 3,287 patients. The point sources were identified in most outbreaks of B. cepacia HAIs (n = 93; 74.4%); they included medication vials, disinfectants, and antiseptics. Moreover, 95 of the outbreak reports (76%) described effective prevention and control measures, but only 33 reports indicated the use of a combination of environment-, patient- and staff-related measures. None of the outbreak reports used the ORION guidelines. CONCLUSIONS Outbreaks of Burkholderia cepacia HAIs are an ongoing challenge. They are often associated with immunocompromised patients who acquire the infection from exposure to contaminated medications, products, and equipment. These outbreaks are not infrequent, and a range of infection prevention and control measures have been effective in arresting spread. The use of ORION guidelines for outbreak reporting would improve the quality of information and data to generate evidence for translation into practice.
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Häfliger E, Atkinson A, Marschall J. Systematic review of healthcare-associated Burkholderia cepacia complex outbreaks: presentation, causes and outbreak control. Infect Prev Pract 2020; 2:100082. [PMID: 34368718 PMCID: PMC8335909 DOI: 10.1016/j.infpip.2020.100082] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Indexed: 11/29/2022] Open
Abstract
Background Over the past decades, the Burkholderia cepacia complex (BCC) has been linked to multiple healthcare-associated outbreaks. No systematic analysis of these outbreaks has been carried out to date. The aim of this study was to conduct a systematic review of reports on nosocomial BCC outbreaks. Methods Published studies from 1971 until 9/12/2019 presenting nosocomial BCC outbreaks were identified using Embase, Pubmed and abstracts from professional meetings. Results We identified a total of 111 outbreak reports. Thirty-two percent of the affected institutions were academic hospitals and 43.8% community hospitals. The average outbreak duration was 198.6 ± 604.4 days. A total of 240 deaths (10% of the 2390 case patients) were reported but only 28 (1.2% of the 2390 case patients and 11.7% of the 240 deaths) were directly attributable to BCC. The source could be identified in 73.9% of the outbreaks; 53.2% were caused by contaminated medical solutions and medications, 12% were due to a contaminated disinfectant. In 28.2% of the outbreaks intrinsic product contamination was reported. Multidrug resistance was noted in 26.1% of the BCC strains. PFGE was the most frequently used typing method (43.2%) in the context of outbreak work-up. Conclusion Medical products are the most frequent source of BCC outbreaks, representing over half of the identified sources, with 12% of the outbreaks caused by disinfectant products. Intrinsic product contamination was detected frequently, suggesting a need for stricter regulation. While BCC-related mortality was low, our systematic review revealed significant heterogeneity in both investigations and reporting of BCC outbreaks.
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Affiliation(s)
- Emmanuel Häfliger
- Department of Infectious Diseases, Bern University Hospital, Bern, Switzerland
| | - Andrew Atkinson
- Department of Infectious Diseases, Bern University Hospital, Bern, Switzerland
| | - Jonas Marschall
- Department of Infectious Diseases, Bern University Hospital, Bern, Switzerland
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Burkholderia cepacia Complex Bacteria: a Feared Contamination Risk in Water-Based Pharmaceutical Products. Clin Microbiol Rev 2020; 33:33/3/e00139-19. [PMID: 32295766 DOI: 10.1128/cmr.00139-19] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Burkholderia cepacia (formerly Pseudomonas cepacia) was once thought to be a single bacterial species but has expanded to the Burkholderia cepacia complex (Bcc), comprising 24 closely related opportunistic pathogenic species. These bacteria have a widespread environmental distribution, an extraordinary metabolic versatility, a complex genome with three chromosomes, and a high capacity for rapid mutation and adaptation. Additionally, they present an inherent resistance to antibiotics and antiseptics, as well as the abilities to survive under nutrient-limited conditions and to metabolize the organic matter present in oligotrophic aquatic environments, even using certain antimicrobials as carbon sources. These traits constitute the reason that Bcc bacteria are considered feared contaminants of aqueous pharmaceutical and personal care products and the frequent reason behind nonsterile product recalls. Contamination with Bcc has caused numerous nosocomial outbreaks in health care facilities, presenting a health threat, particularly for patients with cystic fibrosis and chronic granulomatous disease and for immunocompromised individuals. This review addresses the role of Bcc bacteria as a potential public health problem, the mechanisms behind their success as contaminants of pharmaceutical products, particularly in the presence of biocides, the difficulties encountered in their detection, and the preventive measures applied during manufacturing processes to control contamination with these objectionable microorganisms. A summary of Bcc-related outbreaks in different clinical settings, due to contamination of diverse types of pharmaceutical products, is provided.
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11
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Lo Priore E, Bernasconi S, Schlotterbeck H, Seth-Smith HM, Egli A, Martinetti G, Balmelli C. Burkholderia cepacia complex outbreak originating from contaminated wash gloves. Infect Prev Pract 2020; 2:100039. [PMID: 34368691 PMCID: PMC8335913 DOI: 10.1016/j.infpip.2020.100039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/27/2020] [Indexed: 11/15/2022] Open
Abstract
Burkholderia cepacia complex isolates were detected from four patients who were admitted to the heart centre of southern Switzerland, between April and June 2019. An outbreak investigation was conducted. The three available patient samples were whole genome sequenced, showing that they all are Burkholderia cepacia species, and that two are identical. Isolates grown from sealed packages of disinfectant-free wash gloves used for personal hygiene were also genomically identical. The wash gloves appear to be the origin of the outbreak, contamination of which most likely occurred at the manufacturing site.
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Affiliation(s)
- Elia Lo Priore
- Division of Hospital Epidemiology, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | | | - Hervè Schlotterbeck
- Anesthaesia and Intensive Care Department, Cardiocentro Ticino, Lugano, Switzerland
| | - Helena Mb Seth-Smith
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.,Applied Microbiology Research Unit, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Adrian Egli
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.,Applied Microbiology Research Unit, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Gladys Martinetti
- Laboratory of Bacteriology, Department of Laboratory Medicine, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | - Carlo Balmelli
- Division of Hospital Epidemiology, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
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12
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Cunningham-Oakes E, Weiser R, Pointon T, Mahenthiralingam E. Understanding the challenges of non-food industrial product contamination. FEMS Microbiol Lett 2020; 366:5707401. [PMID: 31977006 PMCID: PMC6986549 DOI: 10.1093/femsle/fnaa010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 01/14/2020] [Indexed: 12/14/2022] Open
Abstract
Preventing microbial contamination of non-food products is a major area of industrial microbiology where preservatives are used to stop microbial growth. However, microorganisms occasionally overcome product preservation, causing recalls and the implementation of multiple procedures to prevent further contamination. Correct reporting of microbial contamination in non-food industrial products is vital, especially if spoilage organisms are antimicrobial resistant and pose a health threat. Gram-negative bacteria such as Pseudomonas, Burkholderia and Enterobacteriaceae are frequently reported as non-food product contaminants, including species that overlap current antimicrobial resistance priorities. Historical analysis of recall databases highlighted that for greater than 15% of contamination incidents, the causative microbial agents are reported as unidentified. Here we review the current antimicrobial resistant bacterial species associated with non-food product contamination and evaluate recall reporting in Europe from 2005 to 2018. Our review shows that 49% of microbial contaminants are reported as unidentified despite frequent detection of antimicrobial resistant pathogens; in contrast, 98% of food-related microbial contaminants are classified. Recommendations to fill this microbial identification gap in non-food product recalls are made. Overall, reporting standards for microbial contamination in non-food products must be improved to enable surveillance and for understanding the risks associated with antimicrobial resistant microorganisms.
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Affiliation(s)
- Edward Cunningham-Oakes
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Park Place, Cardiff, UK, Wales CF10 3AX, UK
| | - Rebecca Weiser
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Park Place, Cardiff, UK, Wales CF10 3AX, UK
| | - Tom Pointon
- Unilever Research and Development, Port Sunlight, Wirral, CH62 4ZD, UK
| | - Eshwar Mahenthiralingam
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Park Place, Cardiff, UK, Wales CF10 3AX, UK
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13
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Seth-Smith HMB, Casanova C, Sommerstein R, Meinel DM, Abdelbary MMH, Blanc DS, Droz S, Führer U, Lienhard R, Lang C, Dubuis O, Schlegel M, Widmer A, Keller PM, Marschall J, Egli A. Phenotypic and Genomic Analyses of Burkholderia stabilis Clinical Contamination, Switzerland. Emerg Infect Dis 2020; 25:1084-1092. [PMID: 31107229 PMCID: PMC6537712 DOI: 10.3201/eid2506.172119] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A recent hospital outbreak related to premoistened gloves used to wash patients exposed the difficulties of defining Burkholderia species in clinical settings. The outbreak strain displayed key B. stabilis phenotypes, including the inability to grow at 42°C; we used whole-genome sequencing to confirm the pathogen was B. stabilis. The outbreak strain genome comprises 3 chromosomes and a plasmid, sharing an average nucleotide identity of 98.4% with B. stabilis ATCC27515 BAA-67, but with 13% novel coding sequences. The genome lacks identifiable virulence factors and has no apparent increase in encoded antimicrobial drug resistance, few insertion sequences, and few pseudogenes, suggesting this outbreak was an opportunistic infection by an environmental strain not adapted to human pathogenicity. The diversity among outbreak isolates (22 from patients and 16 from washing gloves) is only 6 single-nucleotide polymorphisms, although the genome remains plastic, with large elements stochastically lost from outbreak isolates.
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14
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Becker SL, Berger FK, Feldner SK, Karliova I, Haber M, Mellmann A, Schäfers HJ, Gärtner B. Outbreak of Burkholderia cepacia complex infections associated with contaminated octenidine mouthwash solution, Germany, August to September 2018. ACTA ACUST UNITED AC 2019; 23. [PMID: 30352639 PMCID: PMC6199865 DOI: 10.2807/1560-7917.es.2018.23.42.1800540] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Three German patients developed nosocomial pneumonia after cardiac surgery and had Burkholderia cepacia complex detected in respiratory specimens. Two patients died of septic multi-organ failure. Whole-genome sequencing detected genetically identical B. cepacia complex strains in patient samples, from a batch of octenidine mouthwash solution, which had been used for nursing care, as well as in samples obtained from the manufacturer during production. Contamination of medical products during manufacturing may lead to international outbreaks.
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Affiliation(s)
- Sören L Becker
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg/Saar, Germany
| | - Fabian K Berger
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg/Saar, Germany
| | - Susanne K Feldner
- Department of Thoracic and Cardiovascular Surgery, Saarland University, Homburg/Saar, Germany
| | - Irem Karliova
- Department of Thoracic and Cardiovascular Surgery, Saarland University, Homburg/Saar, Germany
| | - Manfred Haber
- Hospital Pharmacy, Saarland University, Homburg/Saar, Germany
| | | | - Hans-Joachim Schäfers
- Department of Thoracic and Cardiovascular Surgery, Saarland University, Homburg/Saar, Germany
| | - Barbara Gärtner
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg/Saar, Germany
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15
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Seth-Smith HM, Casanova C, Sommerstein R, Meinel DM, Abdelbary MM, Blanc DS, Droz S, Führer U, Lienhard R, Lang C, Dubuis O, Schlegel M, Widmer A, Keller PM, Marschall J, Egli A. Phenotypic and Genomic Analyses of Burkholderia stabilisClinical Contamination, Switzerland. Emerg Infect Dis 2019. [DOI: 10.3201/eid2406.172119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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16
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Adaptive microbial response to low-level benzalkonium chloride exposure. J Hosp Infect 2018; 100:e1-e22. [DOI: 10.1016/j.jhin.2018.05.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 05/24/2018] [Indexed: 12/12/2022]
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17
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Sfeir MM. Burkholderia cepacia complex infections: More complex than the bacterium name suggest. J Infect 2018; 77:166-170. [DOI: 10.1016/j.jinf.2018.07.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 07/07/2018] [Accepted: 07/09/2018] [Indexed: 01/23/2023]
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