Bacterial Whole-Genome Sequencing Revisited: Portable, Scalable, and Standardized Analysis for Typing and Detection of Virulence and Antibiotic Resistance Genes

Leopold, Shana R.; Goering, Richard V.; Witten, Anika; Harmsen, Dag; Mellmann, Alexander

doi:10.1128/jcm.00262-14

Cited by 251 publications

(248 citation statements)

References 21 publications

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“…Fast detection of resistance and virulence genes and rapid typing of MRSA are crucial for effective infection control [22]. As a result of the implementation of infection-preventing strategies in healthcare settings and the community in the USA, the incidence of invasive MRSA infections in hospitals dropped by 54% between 2005 and 2011 [23].…”

Section: Discussionmentioning

confidence: 99%

High Prevalence and Resistance Patterns of Community-Associated Methicillin-Resistant Staphylococcus Aureus in the Pomoravlje Region, Serbia

Lepsanovic

Jeremić

Lazic

et al. 2016

Acta Microbiologica et Immunologica Hungarica

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With a view to estimating the prevalence and resistance patterns of CA-MR-SA in one region of Serbia, we performed an analysis of MRSA isolates from healthy people and hospitalised patients. The detection of CA-MRSA was carried out by SCCmec typing. In MRSA isolates from hospitalised patients SCCmec types IV and V were found in 76% of the strains. Similar percentage (80%) of CA-MRSA genotypes was present in healthy people. SCCmec type V harbouring MRSA was the most successful clone. Higher prevalence of type V in hospitalised patients to that in healthy people (70% vs 54%) may indicate nosocomial transmissions in at least some hospital units. All MRSA strains from hospitalised patients were resistant to one or more non-β-lactam antibiotics while 52% were multi-resistant. In isolates from healthy people, 16% were sensitive to all non-β-lactam antibiotics and 40% were multi-resistant. Similar percentage of multi-resistant CA-and HA-genotypes occurred in a particular environment (53% vs 50% in hospitalised patients, and 37.5% vs 37.5% in healthy people) indicating selective pressure of antibiotics as a leading force conferring antibiotic resistance. High prevalence of CA-MRSA and high resistance rate both in hospitals and the community suggest that this pathogen has been present in the Pomoravlje Region, central Serbia for years.

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Section: Discussionmentioning

confidence: 99%

High Prevalence and Resistance Patterns of Community-Associated Methicillin-Resistant Staphylococcus Aureus in the Pomoravlje Region, Serbia

Lepsanovic

Jeremić

Lazic

et al. 2016

Acta Microbiologica et Immunologica Hungarica

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“…Whole-genome multilocus sequence typing (wgMLST) is a WGS-based typing method that extends MLST to the genome level (20). Today, such gene-bygene comparison of WGS data has been applied successfully for several species in outbreak settings, but data for Enterobacteriaceae and nonoutbreak settings are still limited (22)(23)(24)(25)(26)(27). The aim of this study was to develop representative wgMLST schemes for the Citation Kluytmans-van den Bergh MFQ, Rossen JWA, Bruijning-Verhagen PCJ, Bonten MJM, Friedrich AW, Vandenbroucke-Grauls CMJE, Willems RJL, Kluytmans JAJW, on behalf of the SoM Study Group.…”

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confidence: 99%

Whole-Genome Multilocus Sequence Typing of Extended-Spectrum-Beta-Lactamase-Producing Enterobacteriaceae

et al. 2016

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e Molecular typing has become indispensable in the detection of nosocomial transmission of bacterial pathogens and the identification of sources and routes of transmission in outbreak settings, but current methods are labor-intensive, are difficult to standardize, or have limited resolution. Whole-genome multilocus sequence typing (wgMLST) has emerged as a whole-genome sequencing (WGS)-based gene-by-gene typing method that may overcome these limitations and has been applied successfully for several species in outbreak settings. In this study, genus-, genetic-complex-, and species-specific wgMLST schemes were developed for Citrobacter spp., the Enterobacter cloacae complex, Escherichia coli, Klebsiella oxytoca, and Klebsiella pneumoniae and used to type a national collection of 1,798 extended-spectrum-beta-lactamase-producing Enterobacteriaceae (ESBL-E) isolates obtained from patients in Dutch hospitals. Genus-, genetic-complex-, and species-specific thresholds for genetic distance that accurately distinguish between epidemiologically related and unrelated isolates were defined for Citrobacter spp., the E. cloacae complex, E. coli, and K. pneumoniae. wgMLST was shown to have higher discriminatory power and typeability than in silico MLST. In conclusion, the wgMLST schemes developed in this study facilitate high-resolution WGS-based typing of the most prevalent ESBL-producing species in clinical practice and may contribute to further elucidation of the complex epidemiology of antimicrobial-resistant Enterobacteriaceae. wgMLST opens up possibilities for the creation of a Web-accessible database for the global surveillance of ESBL-producing bacterial clones. The continuing global spread of extended-spectrum-beta-lactamase-producing Enterobacteriaceae (ESBL-E) constitutes a major public health threat in both health care and community settings (1-4). Extended-spectrum beta-lactamases (ESBL) confer resistance to the majority of beta-lactam antibiotics, including third-generation cephalosporins, which limits the options for antimicrobial therapy and results in increased morbidity and mortality and health care costs (5, 6). Infection control guidelines recommend prevention of the spread of ESBL-E in health care settings (7,8). Molecular typing has become an important tool in infection control, as it enables the detection of nosocomial transmission of bacterial pathogens and the identification of sources and routes of transmission in outbreak settings. Different molecular typing methods have been used, ranging from fingerprintbased methods, like pulsed-field gel electrophoresis (PFGE) and amplified fragment length polymorphism (AFLP), to sequencebased methods, like multilocus sequence typing (MLST) (9-11). Although widely adopted, PFGE is labor-intensive and difficult to standardize and has limited interlaboratory reproducibility (12)(13)(14). AFLP is less time-consuming than PFGE but may have lower discriminatory power for typing of Enterobacteriaceae (13, 15). MLST targets 7 or 8 housekeeping genes, depending on the Ent...

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“…Phylogenetic trees based on single nucleotide polymorphisms (SNPs) were built using the SNP comparison tool in Ridom SeqSphere v4.1.9 (Münster, Germany) with default settings [46]. Properties of the enterobacteriaceal genomes used for phylogenetic analyses are summarized in Supplemental Table S2.…”

Section: Methodsmentioning

confidence: 99%

An ancient family of mobile genomic islands introducing cephalosporinase and carbapenemase genes in Enterobacteriaceae

et al. 2018

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The exchange of mobile genomic islands (MGIs) between microorganisms is often mediated by phages, which may provide benefits to the phage’s host. The present study started with the identification of Enterobacter cloacae, Klebsiella pneumoniae and Escherichia coli isolates with exceptional cephalosporin and carbapenem resistance phenotypes from patients in a neonatal ward. To identify possible molecular connections between these isolates and their β-lactam resistance phenotypes, the respective bacterial genome sequences were compared. This unveiled the existence of a family of ancient MGIs that were probably exchanged before the species E. cloacae, K. pneumoniae and E. coli emerged from their common ancestry. A representative MGI from E. cloacae was named MIR17-GI, because it harbors the novel β-lactamase gene variant blaMIR17. Importantly, our observations show that the MIR17-GI-like MGIs harbor genes associated with high-level resistance to cephalosporins. Among them, MIR17-GI stands out because MIR17 also displays carbapenemase activity. As shown by mass spectrometry, the MIR17 carbapenemase is among the most abundantly expressed proteins of the respective E. cloacae isolate. Further, we show that MIR17-GI-like islands are associated with integrated P4-like prophages. This implicates phages in the spread of cephalosporin and carbapenem resistance amongst Enterobacteriaceae. The discovery of an ancient family of MGIs, mediating the spread of cephalosporinase and carbapenemase genes, is of high clinical relevance, because high-level cephalosporin and carbapenem resistance have serious implications for the treatment of patients with enterobacteriaceal infections.

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Bacterial Whole-Genome Sequencing Revisited: Portable, Scalable, and Standardized Analysis for Typing and Detection of Virulence and Antibiotic Resistance Genes

Cited by 251 publications

References 21 publications

High Prevalence and Resistance Patterns of Community-Associated Methicillin-Resistant Staphylococcus Aureus in the Pomoravlje Region, Serbia

High Prevalence and Resistance Patterns of Community-Associated Methicillin-Resistant Staphylococcus Aureus in the Pomoravlje Region, Serbia

Whole-Genome Multilocus Sequence Typing of Extended-Spectrum-Beta-Lactamase-Producing Enterobacteriaceae

An ancient family of mobile genomic islands introducing cephalosporinase and carbapenemase genes in Enterobacteriaceae

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