Dag Harmsen
Other
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LanguagesGerman, English, Dutch
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Other InterestsJournal of Clinical Microbiology
Publications
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6.79Impact points
Identification of Intermediate in Evolutionary Model of Enterohemorrhagic Escherichia coli O157.
Emerging infectious diseases. 04/2012; 18(4):582-8.
Highly pathogenic enterohemorrhagic Escherichia coli (EHEC) O157 cause a spectrum of clinical signs that include diarrhea, bloody diarrhea, and hemolytic uremic syndrome. The current evolutionary model of EHEC O157:H7/H(-) consists of a stepwise evolution scenario proceeding from O55:H7 to a node (h... [more] Highly pathogenic enterohemorrhagic Escherichia coli (EHEC) O157 cause a spectrum of clinical signs that include diarrhea, bloody diarrhea, and hemolytic uremic syndrome. The current evolutionary model of EHEC O157:H7/H(-) consists of a stepwise evolution scenario proceeding from O55:H7 to a node (hypothetical intermediate) that then branches into sorbitol-fermenting (SF) O157:H(-) and non-SF (NSF) O157:H7. To identify this hypothetical intermediate, we performed single nucleotide polymorphism analysis by sequencing of 92 randomly distributed backbone genomic regions of 40 O157:H7/H(-) isolates. Overall, 111 single nucleotide polymorphisms were identified in 75/92 partial open reading frames after sequencing 51,041 nt/strain. The EHEC O157:H7 strain LSU-61 from deer occupied an intermediate position between O55:H7 and both O157 branches (SF and NSF O157), complementing the stepwise evolutionary model of EHEC O157:H7/H(-). The animal origin of this intermediate emphasizes the value of nonhuman reservoirs in the clarification of the evolution of human pathogens.
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4.16Impact points
Ion Torrent PGM sequencing for genomic typing of Neisseria meningitidis for rapid determination of multiple layers of typing information.
Journal of clinical microbiology. 03/2012;
Neisseria meningitidis causes invasive meningococcal disease in infants, toddlers and adolescents worldwide. DNA sequence based typing has become the standard for molecular epidemiology of the organism including multilocus sequence typing, analysis of genetic determinants of antibiotic resistance, a... [more] Neisseria meningitidis causes invasive meningococcal disease in infants, toddlers and adolescents worldwide. DNA sequence based typing has become the standard for molecular epidemiology of the organism including multilocus sequence typing, analysis of genetic determinants of antibiotic resistance, and sequence typing of vaccine antigens. However, PCR of multiple targets and consecutive Sanger sequencing provides logistic constraints to reference laboratories. Taking advantage of the recent development of benchtop next generation sequencers (NGS) and of BIGSdb, a database accommodating and analyzing genome sequence data, we therefore explored the feasibility and accuracy of Ion Torrent Personal Genome Machine™ (PGM™) sequencing for genomic typing of meningococci. Three strains from a previous meningococcus B community outbreak were selected to compare conventional typing results with data generated by semiconductor chip based sequencing. In addition, sequencing of the meningococcal type strain MC58 provided information about the general performance of the technology. The PGM™ technology generated sequence information for almost all target genes addressed. The results were 100% concordant with conventional typing results with no further editing necessary. In addition, the amount of typing information, i.e. nucleotides and target genes analyzed, could be substantially increased by the combined use of genome sequencing and BIGSdb compared to conventional methods. In a near future, affordable and fast benchtop-NGS machines like the PGM™ might enable reference laboratories to switch to genomic typing on a routine basis. This will reduce workload and rapidly provide information for laboratory surveillance, outbreak investigation, assessment of vaccine preventability and antibiotic resistance gene monitoring.
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3.22Impact points
Online tools for polyphasic analysis of Mycobacterium tuberculosis complex genotyping data: Now and next.
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases. 02/2012;
Molecular diagnostics and genotyping of pathogens have become indispensable tools in clinical microbiology and disease surveillance. For isolates of the Mycobacterium tuberculosis complex (MTBC, causative agents of tuberculosis), multilocus variable number tandem repeat analysis (MLVA) targeting myc... [more] Molecular diagnostics and genotyping of pathogens have become indispensable tools in clinical microbiology and disease surveillance. For isolates of the Mycobacterium tuberculosis complex (MTBC, causative agents of tuberculosis), multilocus variable number tandem repeat analysis (MLVA) targeting mycobacterial interspersed repetitive units (MIRU) has been internationally adopted as the new standard, portable, reproducible, and discriminatory typing method. Here, we review new sets of specialized web based bioinformatics tools that have become available for analyzing MLVA data especially in combination with other, complementary genotyping markers (polyphasic analysis). Currently, there are only two databases available that are not restricted to store one kind of genotyping data only, namely SITVIT/SpolDB4 and MIRU-VNTRplus. SITVIT/SpolDB4 (http://www.pasteur-guadeloupe.fr:8081/SITVITDemo) contains spoligotyping data from a large number of strains of diverse origin. However, besides options to query the data, the actual version of SITVIT/SpolDB4 offers no functionality for more complex analysis e.g. tree-based analysis. In comparison, the MIRU-VNTRplus web application (http://www.miru-vntrplus.org), represents a freely accessible service that enables users to analyze genotyping data of their strains alone or in comparison with a currently limited but well characterized reference database of strains representing the major MTBC lineages. Data (MLVA-, spoligotype-, large sequence polymorphism, and single nucleotide polymorphism) can be visualized and analyzed using just one genotyping method or a weighted combination of several markers. A variety of analysis tools are available such as creation of phylogenetic and minimum spanning trees, semi-automated phylogenetic lineage identification based on comparison with the reference database and mapping of geographic information. To facilitate scientific communication, a universal, expanding genotype nomenclature (MLVA MtbC15-9 type) service that can be queried via a web- or a SOAP-interface has been implemented. An extensive documentation guides users through all application functions. Perspectives for future development, including generalization to other bacterial species, are presented.
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4.16Impact points
Comparison of multilocus variable-number tandem-repeat analysis and multilocus sequence typing for differentiation of hemolytic-uremic syndrome-associated Escherichia coli (HUSEC) collection strains.
Journal of clinical microbiology. 08/2011; 49(10):3644-6.
Multilocus variable-number tandem-repeat analysis (MLVA) was compared to multilocus sequence typing (MLST) to differentiate hemolytic uremic syndrome-associated enterohemorrhagic Escherichia coli strains. Although MLVA--like MLST--was highly discriminatory (index of diversity, 0.988 versus 0.984), a... [more] Multilocus variable-number tandem-repeat analysis (MLVA) was compared to multilocus sequence typing (MLST) to differentiate hemolytic uremic syndrome-associated enterohemorrhagic Escherichia coli strains. Although MLVA--like MLST--was highly discriminatory (index of diversity, 0.988 versus 0.984), a low level of concordance demonstrated the limited ability of MLVA to reflect long-term evolutionary events.
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4.41Impact points
Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology.
PloS one. 01/2011; 6(7):e22751.
An ongoing outbreak of exceptionally virulent Shiga toxin (Stx)-producing Escherichia coli O104:H4 centered in Germany, has caused over 830 cases of hemolytic uremic syndrome (HUS) and 46 deaths since May 2011. Serotype O104:H4, which has not been detected in animals, has rarely been associated with... [more] An ongoing outbreak of exceptionally virulent Shiga toxin (Stx)-producing Escherichia coli O104:H4 centered in Germany, has caused over 830 cases of hemolytic uremic syndrome (HUS) and 46 deaths since May 2011. Serotype O104:H4, which has not been detected in animals, has rarely been associated with HUS in the past. To prospectively elucidate the unique characteristics of this strain in the early stages of this outbreak, we applied whole genome sequencing on the Life Technologies Ion Torrent PGM™ sequencer and Optical Mapping to characterize one outbreak isolate (LB226692) and a historic O104:H4 HUS isolate from 2001 (01-09591). Reference guided draft assemblies of both strains were completed with the newly introduced PGM™ within 62 hours. The HUS-associated strains both carried genes typically found in two types of pathogenic E. coli, enteroaggregative E. coli (EAEC) and enterohemorrhagic E. coli (EHEC). Phylogenetic analyses of 1,144 core E. coli genes indicate that the HUS-causing O104:H4 strains and the previously published sequence of the EAEC strain 55989 show a close relationship but are only distantly related to common EHEC serotypes. Though closely related, the outbreak strain differs from the 2001 strain in plasmid content and fimbrial genes. We propose a model in which EAEC 55989 and EHEC O104:H4 strains evolved from a common EHEC O104:H4 progenitor, and suggest that by stepwise gain and loss of chromosomal and plasmid-encoded virulence factors, a highly pathogenic hybrid of EAEC and EHEC emerged as the current outbreak clone. In conclusion, rapid next-generation technologies facilitated prospective whole genome characterization in the early stages of an outbreak.
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7.48Impact points
MIRU-VNTRplus: a web tool for polyphasic genotyping of Mycobacterium tuberculosis complex bacteria.
Nucleic acids research. 05/2010; 38(Web Server issue):W326-31.
Harmonized typing of bacteria and easy identification of locally or internationally circulating clones are essential for epidemiological surveillance and disease control. For Mycobacterium tuberculosis complex (MTBC) species, multi-locus variable number tandem repeat analysis (MLVA) targeting mycoba... [more] Harmonized typing of bacteria and easy identification of locally or internationally circulating clones are essential for epidemiological surveillance and disease control. For Mycobacterium tuberculosis complex (MTBC) species, multi-locus variable number tandem repeat analysis (MLVA) targeting mycobacterial interspersed repetitive units (MIRU) has been internationally adopted as the new standard, portable, reproducible and discriminatory typing method. However, no specialized bioinformatics web tools are available for analysing MLVA data in combination with other, complementary typing data. Therefore, we have developed the web application MIRU-VNTRplus (http://www.miru-vntrplus.org). This freely accessible service allows users to analyse genotyping data of their strains alone or in comparison with a reference database of strains representing the major MTBC lineages. Analysis and comparisons of genotypes can be based on MLVA-, spoligotype-, large sequence polymorphism and single nucleotide polymorphism data, or on a weighted combination of these markers. Tools for data exploration include search for similar strains, creation of phylogenetic and minimum spanning trees and mapping of geographic information. To facilitate scientific communication, an expanding genotype nomenclature (MLVA MtbC15-9 type) that can be queried via a web- or a SOAP-interface has been implemented. An extensive documentation guides users through all application functions.
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6.79Impact points
Phylogenetic analysis of enterohemorrhagic Escherichia coli O157, Germany, 1987-2008.
Emerging infectious diseases. 04/2010; 16(4):610-6.
Multilocus variable number tandem repeat analysis (MLVA) is a subtyping technique for characterizing human pathogenic bacteria such as enterohemorrhagic Escherichia coli (EHEC) O157. We determined the phylogeny of 202 epidemiologically unrelated EHEC O157:H7/H- clinical isolates through 8 MLVA loci ... [more] Multilocus variable number tandem repeat analysis (MLVA) is a subtyping technique for characterizing human pathogenic bacteria such as enterohemorrhagic Escherichia coli (EHEC) O157. We determined the phylogeny of 202 epidemiologically unrelated EHEC O157:H7/H- clinical isolates through 8 MLVA loci obtained in Germany during 1987-2008. Biodiversity in the loci ranged from 0.66 to 0.90. Four of 8 loci showed null alleles and a frequency < or =44.1%. These loci were distributed among 48.5% of all strains. Overall, 141 MLVA profiles were identified. Phylogenetic analysis assigned 67.3% of the strains to 19 MLVA clusters. Specific MLVA profiles with an evolutionary persistence were identified, particularly within sorbitol-fermenting EHEC O157:H-.These pathogens belonged to the same MLVA cluster. Our findings indicate successful persistence of this clone.
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4.16Impact points
Comparison of traditional phenotypic identification methods with partial 5' 16S rRNA gene sequencing for species-level identification of nonfermenting Gram-negative bacilli.
Journal of clinical microbiology. 02/2010; 48(4):1442-4.
Correct identification of nonfermenting Gram-negative bacilli (NFB) is crucial for patient management. We compared phenotypic identifications of 96 clinical NFB isolates with identifications obtained by 5' 16S rRNA gene sequencing. Sequencing identified 88 isolates (91.7%) with >99% similarit... [more] Correct identification of nonfermenting Gram-negative bacilli (NFB) is crucial for patient management. We compared phenotypic identifications of 96 clinical NFB isolates with identifications obtained by 5' 16S rRNA gene sequencing. Sequencing identified 88 isolates (91.7%) with >99% similarity to a sequence from the assigned species; 61.5% of sequencing results were concordant with phenotypic results, indicating the usability of sequencing to identify NFB.
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13.05Impact points
Geographic distribution of Staphylococcus aureus causing invasive infections in Europe: a molecular-epidemiological analysis.
PLoS medicine. 01/2010; 7(1):e1000215.
Staphylococcus aureus is one of the most important human pathogens and methicillin-resistant variants (MRSAs) are a major cause of hospital and community-acquired infection. We aimed to map the geographic distribution of the dominant clones that cause invasive infections in Europe. In each country, ... [more] Staphylococcus aureus is one of the most important human pathogens and methicillin-resistant variants (MRSAs) are a major cause of hospital and community-acquired infection. We aimed to map the geographic distribution of the dominant clones that cause invasive infections in Europe. In each country, staphylococcal reference laboratories secured the participation of a sufficient number of hospital laboratories to achieve national geo-demographic representation. Participating laboratories collected successive methicillin-susceptible (MSSA) and MRSA isolates from patients with invasive S. aureus infection using an agreed protocol. All isolates were sent to the respective national reference laboratories and characterised by quality-controlled sequence typing of the variable region of the staphylococcal spa gene (spa typing), and data were uploaded to a central database. Relevant genetic and phenotypic information was assembled for interactive interrogation by a purpose-built Web-based mapping application. Between September 2006 and February 2007, 357 laboratories serving 450 hospitals in 26 countries collected 2,890 MSSA and MRSA isolates from patients with invasive S. aureus infection. A wide geographical distribution of spa types was found with some prevalent in all European countries. MSSA were more diverse than MRSA. Genetic diversity of MRSA differed considerably between countries with dominant MRSA spa types forming distinctive geographical clusters. We provide evidence that a network approach consisting of decentralised typing and visualisation of aggregated data using an interactive mapping tool can provide important information on the dynamics of MRSA populations such as early signalling of emerging strains, cross border spread, and importation by travel. In contrast to MSSA, MRSA spa types have a predominantly regional distribution in Europe. This finding is indicative of the selection and spread of a limited number of clones within health care networks, suggesting that control efforts aimed at interrupting the spread within and between health care institutions may not only be feasible but ultimately successful and should therefore be strongly encouraged.
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4.16Impact points
High Inter-Laboratory Reproducibility of MALDI-TOF Mass Spectrometry-Based Species Identification of Nonfermenting Bacteria.
Journal of clinical microbiology. 09/2009;
MALDI-TOF MS has emerged as rapid, cost-effective alternative for bacterial species identification. Identifying 60 blind-coded nonfermenting bacteria samples, this international study (eight laboratories) achieved 98.75% inter-laboratory reproducibility. Only six of 480 samples were misidentified du... [more] MALDI-TOF MS has emerged as rapid, cost-effective alternative for bacterial species identification. Identifying 60 blind-coded nonfermenting bacteria samples, this international study (eight laboratories) achieved 98.75% inter-laboratory reproducibility. Only six of 480 samples were misidentified due to interchanges (4 samples) or contamination (1), or not identified because of insufficient signal intensity (1).
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6.79Impact points
Phylogeny and disease association of Shiga toxin-producing Escherichia coli O91.
Emerging infectious diseases. 09/2009; 15(9):1474-7.
The diversity and relatedness of 100 Shiga toxin-producing Escherichia coli O91 isolates from different patients were examined by multilocus sequence typing. We identified 10 specific sequence types (ST) and 4 distinct clonal groups. ST442 was significantly associated with hemolytic uremic syndrome.... [more] The diversity and relatedness of 100 Shiga toxin-producing Escherichia coli O91 isolates from different patients were examined by multilocus sequence typing. We identified 10 specific sequence types (ST) and 4 distinct clonal groups. ST442 was significantly associated with hemolytic uremic syndrome.
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3.01Impact points
Cross-border comparison of the admission prevalence and clonal structure of meticillin-resistant Staphylococcus aureus.
The Journal of hospital infection. 02/2009;
Since patient exchange between hospitals sharing a common catchment area might favour regional spread of meticillin-resistant Staphylococcus aureus (MRSA), the reliable detection of patients colonised at admission is crucial. This, hospitals in the Dutch-German border area EUREGIO MRSA-net aim at sy... [more] Since patient exchange between hospitals sharing a common catchment area might favour regional spread of meticillin-resistant Staphylococcus aureus (MRSA), the reliable detection of patients colonised at admission is crucial. This, hospitals in the Dutch-German border area EUREGIO MRSA-net aim at synchronising their local MRSA standards in order to prevent unidentified inter-hospital as well as cross-border spread. This assumes enhanced knowledge of MRSA prevalence and risk factors associated with MRSA carriage at admission. We conducted nasal MRSA screening of all inpatients admitted to 39 German hospitals (in the period 1 November to 30 November 2006) and to one Dutch hospital (in the period 1 July to 30 September 2007) in the EUREGIO MRSA-net. A total of 390 MRSA cases were detected among 25 540 patients screened. The admission prevalence was 1.6 MRSA/100 patients (6.5% of all S. aureus) in the German and 0.5 MRSA/100 patients (1.4% of all S. aureus) in the Dutch part of the border region. Overall, the predominating S. aureus protein A gene (spa) sequence types were t003, t032 and t011. One isolate (t044) carried Panton-Valentine leukocidin (PVL) encoding genes. Altogether, 79% and 67% of all MRSA patients in the German and Dutch regions respectively, were identifiable by the classical nosocomial risk factors assessed. In patients lacking all risk factors assessed, spa types t011 and t034 were predominant (P<0.001).
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EUREGIO MRSA-net Twente/Münsterland--a Dutch-German cross-border network for the prevention and control of infections caused by methicillin-resistant Staphylococcus aureus.
Euro surveillance : bulletin européen sur les maladies transmissibles = European communicable disease bulletin. 09/2008; 13(35).
Methicillin-resistant Staphylococcus aureus (MRSA) is associated with increased mortality and morbidity and a leading cause of hospital-acquired infections. Community-acquired (CA)-MRSA are a growing concern worldwide. In the last 10 years, an increase in the MRSA rate from 2% to approximately 23% h... [more] Methicillin-resistant Staphylococcus aureus (MRSA) is associated with increased mortality and morbidity and a leading cause of hospital-acquired infections. Community-acquired (CA)-MRSA are a growing concern worldwide. In the last 10 years, an increase in the MRSA rate from 2% to approximately 23% has been observed in Germany, while a rate under 5% has been recorded for many years in the Netherlands and Scandinavia. In the Netherlands in particular, MRSA rates have become very low in stationary care due to a consistent 'search and destroy' policy. The main focus in Germany lies on hospital-acquired MRSA, whereas the Netherlands focus on the control of the importation of MRSA cases from abroad and on CA-MRSA. As MRSA in hospitals and in the community can be a problem in cross-border health care, the European Union-funded EUREGIO MRSA-net project was established in the bordering regions Twente/Achterhoek, the Netherlands and Münsterland, Germany. The main aim of the project is the creation of a network of the major health care providers in the EUREGIO and the surveillance and prevention of MRSA infections. A spa-typing network was established in order to understand the regional and cross-border dissemination of epidemic and potentially highly virulent MRSA genotypes. As the reduction of differences in health care quality is an important prerequisite for cross-border health care, a transborder quality group comprising hospitals, general practitioners, public health authorities, laboratories, and insurerance companies has been established since 2005 equalising the quality criteria for the control of MRSA on both sides of the border.
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6.79Impact points
Analysis of collection of hemolytic uremic syndrome-associated enterohemorrhagic Escherichia coli.
Emerging infectious diseases. 09/2008; 14(8):1287-90.
Multilocus sequence typing of 169 non-O157 enterohemorrhagic Escherichia coli (EHEC) isolated from patients with hemolytic uremic syndrome (HUS) demonstrated 29 different sequence types (STs); 78.1% of these strains clustered in 5 STs. From all STs and serotypes identified, we established a referenc... [more] Multilocus sequence typing of 169 non-O157 enterohemorrhagic Escherichia coli (EHEC) isolated from patients with hemolytic uremic syndrome (HUS) demonstrated 29 different sequence types (STs); 78.1% of these strains clustered in 5 STs. From all STs and serotypes identified, we established a reference panel of EHEC associated with HUS (HUSEC collection).
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2.45Impact points
EpiScanGIS: an online geographic surveillance system for meningococcal disease.
International journal of health geographics. 08/2008; 7(1):33.
ABSTRACT: BACKGROUND: Surveillance of infectious diseases increasingly relies on Geographic Information Systems (GIS). The integration of pathogen fine typing data in dynamic systems and visualization of spatio-temporal clusters are a technical challenge for system development. RESULTS: An online ge... [more] ABSTRACT: BACKGROUND: Surveillance of infectious diseases increasingly relies on Geographic Information Systems (GIS). The integration of pathogen fine typing data in dynamic systems and visualization of spatio-temporal clusters are a technical challenge for system development. RESULTS: An online geographic information system (EpiScanGIS) based on open source components has been launched in Germany in May 2006 for real time provision of meningococcal typing data in conjunction with demographic information (age, incidence, population density). Spatio-temporal clusters of disease detected by computer assisted cluster analysis (SaTScanTM) are visualized on maps. EpiScanGIS enables dynamic generation of animated maps. The system is based on open source components; its architecture is open for other infectious agents and geographic regions. EpiScanGIS is available at www.episcangis.org, and currently has 80 registered users, mostly from the public health service in Germany. At present more than 2,900 cases of invasive meningococcal disease are stored in the database (data as of June 3, 2008). CONCLUSIONS: EpiScanGIS exemplifies GIS applications and early-warning systems in laboratory surveillance of infectious diseases.
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4.16Impact points
Characterization of clonal relatedness among the natural population of Staphylococcus aureus strains by using spa sequence typing and the BURP (based upon repeat patterns) algorithm.
Journal of clinical microbiology. 08/2008; 46(8):2805-8.
We evaluated the BURP (based upon repeat patterns) algorithm, which relies on sequencing of the Staphylococcus aureus protein A gene (spa), for its ability to infer clonal relatedness within a population of 110 wild-type strains. BURP clustering of the resulting 66 spa types was highly concordant wi... [more] We evaluated the BURP (based upon repeat patterns) algorithm, which relies on sequencing of the Staphylococcus aureus protein A gene (spa), for its ability to infer clonal relatedness within a population of 110 wild-type strains. BURP clustering of the resulting 66 spa types was highly concordant with multilocus sequence typing (96.5% concordance) and pulsed-field gel electrophoresis (94.9%).
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4.16Impact points
Evaluation and user-strategy of MIRU-VNTRplus, a multifunctional database for on-line analysis of genotyping data and phylogenetic identification of Mycobacterium tuberculosis complex isolates.
Journal of clinical microbiology. 06/2008;
Because of its portable data, discriminatory power, and recently proposed standardization, mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) typing has become a major method for epidemiological tracking of Mycobacterium tuberculosis complex (MTBC) clones. Howeve... [more] Because of its portable data, discriminatory power, and recently proposed standardization, mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) typing has become a major method for epidemiological tracking of Mycobacterium tuberculosis complex (MTBC) clones. However, no public MIRU-VNTR database based on well-characterized reference strains was available hitherto for easy strain identification. Therefore, a collection of 186 reference strains representing the primary MTBC lineages was used to build up a database freely accessible at http://www.MIRU-VNTRplus.org. For each strain, geographical origin and drug-susceptibility profile was stored together with comprehensive genetic lineage information including 24-locus MIRU-VNTR profile, spoligotyping pattern, single nucleotide and large sequence polymorphism profile, and IS6110 restriction fragment length polymorphism fingerprint. Thanks to flexible import functions, single or multiple user strain(s) can be analyzed e.g. for lineage identification with or without using reference strains, by best-match or tree-based analyses employing single or combined marker datasets. Results can be easily exported. Here, we evaluated the database consistency and various analysis parameters, both by testing the reference collection against itself and by using an external population-based dataset comprising 629 different strains. In the optimal conditions found, lineage predictions based on 24-locus MIRU-VNTR-typing optionally combined with spoligotyping were verified in > 99% of the cases. Based on this evaluation, a user-strategy was defined, including best match analysis followed, if necessary, by tree-based analysis. The MIRU-VNTRplus database is a powerful tool for high-resolution clonal identification, which has little equivalent in terms of functionalities among the bacterial genotyping databases available so far.
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4.16Impact points
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.
Journal of clinical microbiology. 06/2008; 46(6):1946-54.
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... [more] 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.
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4.16Impact points
Acinetobacter septicus sp. nov. association with a nosocomial outbreak of bacteremia in a neonatal intensive care unit.
Journal of clinical microbiology. 04/2008; 46(3):902-8.
Acinetobacter species other than Acinetobacter baumannii have rarely been reported to be associated with nosocomial outbreaks of bloodstream infections. Within a period of 1 week, seven Acinetobacter-like isolates were recovered from peripheral blood and catheter specimens of five patients at a neon... [more] Acinetobacter species other than Acinetobacter baumannii have rarely been reported to be associated with nosocomial outbreaks of bloodstream infections. Within a period of 1 week, seven Acinetobacter-like isolates were recovered from peripheral blood and catheter specimens of five patients at a neonatal intensive care unit (NICU) in a tertiary hospital in Turkey. All five patients had placement of central venous catheters and had received total parenteral nutrition before the onset of bacteremia. Two of the five patients died. Medical devices, tap water, aerators, water samples, various surfaces, intravenous fluids, and the hands of health care workers in the NICU were sampled and were culture negative for the bacterium. All seven of the isolates had identical biochemical reactions, antimicrobial susceptibility results, and pulsed-field gel electrophoresis patterns, indicating a clonal nosocomial outbreak. A panel of standard biochemical reaction profiles and three phenotypic commercial identification systems failed to identify these isolates. Phenotypically, the isolate differed from Acinetobacter ursingii by its hemolysis on sheep blood agar and its negative citrate utilization. Sequences of the full 16S rRNA gene, which contained at least three different gene copies with polymorphic sequences between nucleotide positions 70 and 206, were determined from the first recovered isolate. The complete 1,529- to 1,531-bp 16S rRNA gene sequences and partial 801-bp rpoB gene sequences had similarities of 99.5% and 97.2%, respectively, to an A. ursingii isolate. The DNA-DNA similarities of the strain against the type strain of A. ursingii were 64.7 and 68.7%, which were lower than the recommended threshold value of 70% for the definition of bacterial species. These data indicate that a novel Acinetobacter organism caused the nosocomial outbreak of bacteremia in the NICU unit. We propose the designation of Acinetobacter septicus sp. nov. for these isolates, with isolate AK001 as the type strain.
Following (4)
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Sebastian Suerbaum
Medizinische Hochschule Hannover -
Ijad Madisch
Massachusetts General Hospital -
Suzan Oraibi
King Abdullah International Medical Research Center -
Alexander Mellmann
Westfälische Wilhelms-Universität Münster
