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Campoccia D, Montanaro L, Arciola CR. Current Methods for Molecular Epidemiology Studies of Implant Infections. Int J Artif Organs 2018; 32:642-54. [DOI: 10.1177/039139880903200914] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Over the last few decades, the number of surgical procedures involving prosthetic materials has greatly multiplied, along with the rising medical and economic impact of implant-associated infections. The need to appropriately counteract and deal with this phenomenon has led to growing efforts to elucidate the etiology, pathogenesis and epidemiology of these types of infections, characterized by opportunistic pathogens. Molecular epidemiology studies have progressively emerged as a leading multitask tool to identify and fingerprint bacterial strains, unveil the complex clonal nature of important pathogens, detect outbreak events, track the origin of the infections, assess the clinical significance of individual strain types, survey their distribution, recognize associations of strain types with specific virulence determinants and/or pathological conditions, assess the role played by the specific components of the virulon, and reveal the phylogeny and the mechanisms through which new strain types have emerged. Despite the many advances that have been made thanks to these flourishing new approaches to molecular epidemiology, a number of critical aspects remain challenging. In this paper, we briefly discuss the current limitations and possible developments of molecular epidemiology methods in the investigation and surveillance of implant infections.
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Affiliation(s)
- Davide Campoccia
- Research Unit on Implant Infections, Rizzoli Orthopedic Institute, Bologna - Italy
| | - Lucio Montanaro
- Research Unit on Implant Infections, Rizzoli Orthopedic Institute, Bologna - Italy
- Department of Experimental Pathology, University of Bologna, Bologna - Italy
| | - Carla Renata Arciola
- Research Unit on Implant Infections, Rizzoli Orthopedic Institute, Bologna - Italy
- Department of Experimental Pathology, University of Bologna, Bologna - Italy
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Hu Y, Liu J, Xia D, Chen S. Simultaneous analysis of foodborne pathogenic bacteria by an oligonucleotide microarray assay. J Basic Microbiol 2011; 52:27-34. [PMID: 21656816 DOI: 10.1002/jobm.201000458] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Accepted: 03/07/2011] [Indexed: 11/06/2022]
Abstract
A rapid and accurate method for simultaneous identification of foodborne infectious pathogens was developed based on oligonucleotide microarray technology. The proposed identification method is based on PCR amplification of the target region of the groEL genes with degenerate primers, followed by the PCR products hybridization with oligonucleotide probes specific for species. The groEL gene amplification products of seventeen species of pathogenic bacteria were hybridized to the oligonucleotide array. Hybridization results were analyzed with digoxigenin-linked enzyme reaction. Results indicated that fifteen species of pathogenic bacteria showed high sensitivity and specificity for the oligonucleotide array, while two other species gave cross-reaction with the E. coli. Our results suggested that microarray analysis of foodborne infectious pathogens might be very useful for simultaneous identification of bacterial pathogens. The oligonucleotide array can also be applied to samples collected in clinical settings of foodborne infections. The superiority of oligonucleotide array over other tests lies on its rapidity, accuracy and efficiency in the diagnosis, treatment and control of foodborne infections.
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Affiliation(s)
- Yushan Hu
- The Center for Disease Control and Prevention of Guangzhou, Guangzhou, China.
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Newton R, Hinds J, Wernisch L. Empirical Bayesian models for analysing molecular serotyping microarrays. BMC Bioinformatics 2011; 12:88. [PMID: 21453458 PMCID: PMC3076268 DOI: 10.1186/1471-2105-12-88] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Accepted: 03/31/2011] [Indexed: 12/02/2022] Open
Abstract
Background Microarrays offer great potential as a platform for molecular diagnostics, testing clinical samples for the presence of numerous biomarkers in highly multiplexed assays. In this study applied to infectious diseases, data from a microarray designed for molecular serotyping of Streptococcus pneumoniae was used, identifying the presence of any one of 91 known pneumococcal serotypes from DNA extracts. This microarray incorporated oligonucleotide probes for all known capsular polysaccharide synthesis genes and required a statistical analysis of the microarray intensity data to determine which serotype, or combination of serotypes, were present within a sample based on the combination of genes detected. Results We propose an empirical Bayesian model for calculating the probabilities of combinations of serotypes from the microarray data. The model takes into consideration the dependencies between serotypes, induced by genes they have in common, and by homologous genes which, although not identical, are similar to each other in sequence. For serotypes which are very similar in capsular gene composition, extra probes are included on the microarray, providing additional information which is integrated into the Bayesian model. For each serotype combination with high probability, a second model, a Bayesian random effects model is applied to determine the relative abundance of each serotype. Conclusions To assess the accuracy of the proposed analysis we applied our methods to experimental data from samples containing individual serotypes and samples containing combinations of serotypes with known levels of abundance. All but two of the known serotypes of S. pneumoniae that were tested as individual samples could be uniquely determined by the Bayesian model. The model also enabled the presence of combinations of serotypes within samples to be determined. Serotypes with very low abundance within a combination of serotypes can be detected (down to 2% abundance in this study). As well as detecting the presence of serotype combinations, an approximate measure of the percentage abundance of the serotypes within the combination can be obtained.
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Affiliation(s)
- Richard Newton
- MRC Biostatistics Unit, Robinson Way, Cambridge, CB2 0SR, UK.
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Nhu NTK, Vinh H, Nga TVT, Stabler R, Duy PT, Thi Minh Vien L, van Doorn HR, Cerdeño-Tárraga A, Thomson N, Campbell J, Van Minh Hoang N, Thi Thu Nga T, Minh PV, Thuy CT, Wren B, Farrar J, Baker S. The sudden dominance of blaCTX-M harbouring plasmids in Shigella spp. Circulating in Southern Vietnam. PLoS Negl Trop Dis 2010; 4:e702. [PMID: 20544028 PMCID: PMC2882334 DOI: 10.1371/journal.pntd.0000702] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Accepted: 04/08/2010] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Plasmid mediated antimicrobial resistance in the Enterobacteriaceae is a global problem. The rise of CTX-M class extended spectrum beta lactamases (ESBLs) has been well documented in industrialized countries. Vietnam is representative of a typical transitional middle income country where the spectrum of infectious diseases combined with the spread of drug resistance is shifting and bringing new healthcare challenges. METHODOLOGY We collected hospital admission data from the pediatric population attending the hospital for tropical diseases in Ho Chi Minh City with Shigella infections. Organisms were cultured from all enrolled patients and subjected to antimicrobial susceptibility testing. Those that were ESBL positive were subjected to further investigation. These investigations included PCR amplification for common ESBL genes, plasmid investigation, conjugation, microarray hybridization and DNA sequencing of a bla(CTX-M) encoding plasmid. PRINCIPAL FINDINGS We show that two different bla(CTX-M) genes are circulating in this bacterial population in this location. Sequence of one of the ESBL plasmids shows that rather than the gene being integrated into a preexisting MDR plasmid, the bla(CTX-M) gene is located on relatively simple conjugative plasmid. The sequenced plasmid (pEG356) carried the bla(CTX-M-24) gene on an ISEcp1 element and demonstrated considerable sequence homology with other IncFI plasmids. SIGNIFICANCE The rapid dissemination, spread of antimicrobial resistance and changing population of Shigella spp. concurrent with economic growth are pertinent to many other countries undergoing similar development. Third generation cephalosporins are commonly used empiric antibiotics in Ho Chi Minh City. We recommend that these agents should not be considered for therapy of dysentery in this setting.
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Affiliation(s)
- Nguyen Thi Khanh Nhu
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- The Oxford University Clinical Research Unit, The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Ha Vinh
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- The Oxford University Clinical Research Unit, The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Tran Vu Thieu Nga
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- The Oxford University Clinical Research Unit, The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Richard Stabler
- The Pathogen Molecular Biology Unit, The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Pham Thanh Duy
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- The Oxford University Clinical Research Unit, The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Le Thi Minh Vien
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- The Oxford University Clinical Research Unit, The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - H. Rogier van Doorn
- The Oxford University Clinical Research Unit, The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
| | | | - Nicholas Thomson
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - James Campbell
- The Oxford University Clinical Research Unit, The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
| | - Nguyen Van Minh Hoang
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- The Oxford University Clinical Research Unit, The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Tran Thi Thu Nga
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- The Oxford University Clinical Research Unit, The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Pham Van Minh
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- The Oxford University Clinical Research Unit, The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Cao Thu Thuy
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- The Oxford University Clinical Research Unit, The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Brendan Wren
- The Pathogen Molecular Biology Unit, The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Jeremy Farrar
- The Oxford University Clinical Research Unit, The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
| | - Stephen Baker
- The Oxford University Clinical Research Unit, The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
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