Epidemiological characterization of a nosocomial outbreak of extended spectrum β‐lactamase <i>Escherichia coli</i> ST‐131 confirms the clinical value of core genome multilocus sequence typing

Woksepp, Hanna; Ryberg, Anna; Berglind, Linda; Schӧn, Thomas; Söderman, Jan

doi:10.1111/apm.12753

Cited by 9 publications

(8 citation statements)

References 38 publications

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“…The genomic analyses showed that clonal dissemination of mcr-carrying Enterobacterales in Emilia-Romagna was limited compared to horizontal gene transfer through plasmids or transposable element dissemination. In addition, the minimal pairwise distance observed between isolates belonging to the same genomic cluster (i.e., 138 SNPs) was much higher than usually observed in nosocomial clonal infections [33]. This suggests that E. coli lineages carrying mcr did not clonally spread within the regional hospital system.…”

Section: Discussionmentioning

confidence: 80%

Reduction trend of mcr-1 circulation in Emilia-Romagna Region, Italy

Gagliotti

Bolzoni

Carretto

et al. 2021

Eur J Clin Microbiol Infect Dis

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This study aims to describe trends of mcr-positive Enterobacterales in humans based on laboratory surveillance with a defined catchment population. The data source is the Micro-RER surveillance system, established in Emilia-Romagna region (Italy), to monitor the trend of mcr resistance. Enterobacterales isolates from human clinical samples with minimum inhibitory concentration (MIC) ≥ 2 mg/L for colistin were sent to the study reference laboratory for the detection of mcr genes. Isolates prospectively collected in the period 2018-2020 were considered for the assessment of population rates and trends; further analyses were carried out for the evaluation of clonality and horizontal mcr gene transfer. Previous isolates from local laboratory collection were also described. In the period 2018-2020, 1164 isolates were sent to the reference laboratory, and 51 (4.4%) were confirmed as mcr-positive: 50 mcr-1 (42 Escherichia coli, 6 Klebsiella pneumoniae, 2 Salmonella enterica) and 1 mcr-4 (Enterobacter cloacae). The number of mcr-positive isolates dropped from 24 in the first half of 2018 to 3 in the whole of 2020 (trend p value < 0.001). Genomic analyses showed the predominant role of the horizontal transfer of mcr genes through plasmids or dissemination of transposable elements compared to clonal dissemination of mcr-positive microorganisms. The study results demonstrate a substantial decrease in the circulation of mcr-1 plasmid genes in Emilia-Romagna Region.

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Section: Discussionmentioning

confidence: 80%

Reduction trend of mcr-1 circulation in Emilia-Romagna Region, Italy

Gagliotti

Bolzoni

Carretto

et al. 2021

Eur J Clin Microbiol Infect Dis

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“…Unfortunately, due to poor metadata pertaining to such strains, little insight can be gained into the origins of these samples, highlighting the importance of researcher diligence in uploading metadata sufficient to facilitate epidemiological investigations; such situations are commonplace when utilizing online sequence repositories. It does, however, indicate a potential shared origin of these strains which, by metrics used in other research, may constitute clonal outbreaks (Woksepp et al, 2017). This data highlights the value of EnteroBase, and other similar tools such as BacWGSTdb (Ruan and Feng, 2016), in the undertaking of investigations involving en-masse genotypic and phylogenomic characterization; an increasingly important area of research as AMR prospects continue to worsen at a global level.…”

Section: Discussionmentioning

confidence: 99%

Genetic Features of mcr-1 Mediated Colistin Resistance in CMY-2-Producing Escherichia coli From Romanian Poultry

et al. 2019

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Colistin is a last resort antibiotic used for the treatment of human infections associated with carbapenemase-producing Enterobacteriales. Here, we evaluated the occurrence of mcr-1 and -2 plasmid-mediated colistin resistance in colistin and/or carbapenem resistant human clinical Enterobacteriales and other gram-negative bacteria (n = 543) as well as third generation cephalosporin-resistant (3GCR) Escherichia coli isolates from poultry abattoir workers (n = 15) and poultry fecal samples (n = 92) collected from two geographically separate abattoirs in Romania. which revealed that mcr-1 was present within four sequence types (STs): ST744 (n = 7), ST57 (n = 7), ST156 (n = 2), and ST10 (n = 1). Within STs, serotypes were conserved and, notably, all except one of the mcr-1-positive isolates were found to exhibit fluoroquinolone-resistance (FQR) associated SNPs in both gyrA and parC. While there were variations in genotypes, all isolates belonging to ST744, ST57, and ST156 were rich in resistance determinants, carrying aminoglycoside-modifying enzymes genes, sulfonamide resistance gene blaTEM–1 as well as blaCMY–2 AmpC β-lactamase resistance genes. They also exhibited high similarity in carriage of virulence genes; ST10, however, only carried the mcr-1 gene. Whole genome sequencing (WGS) analysis also revealed that although the mcr-1 gene was identified in a diverse population of E. coli, two STs (ST57 and ST744) predominated and interestingly, were found in isolates across both abattoirs providing evidence for clonal transmission. Also, two main genomic contexts of mcr-1 isolates were revealed with all ST57 isolates harboring the mcr-1 gene between two copies of ISApl1 (or the Tn6330 transposon) whilst a common mcr-1 containing scaffold, highly similar to IncX type mcr-1-bearing plasmids (pWI2-mcr, Accession number: LT838201), was present among mcr-1 isolates of varying phylogenetic backgrounds (ST10, ST744 and ST156). The high prevalence of the mcr-1 gene in poultry E. coli isolates with co-resistance to cephalosporins and quinolones, in a country where antimicrobial use in food production species is poorly regulated, is concerning and the findings from this study should lead to better surveillance of antimicrobial resistance (AMR) in food-production animals in Romania.

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“…In addition to SNV-based methods, IRIDA provides functionality for performing MLST. Current MLST approaches that extend classical MLST schemes to include an organism's core genome (cgMLST) or whole genome (wgMLST) have been validated for surveillance of foodborne disease, and are quickly being adopted by surveillance programs such as PulseNet International, and used for a variety of nosocomial, zoonotic, and tuberculosis outbreaks (45)(46)(47)(48)(49). IRIDA has adopted the fast, accurate, and computationally efficient MentaLiST system as its main pipeline for cgMLST-based analysis.…”

Section: Irida Performs Analyses Of Sequence Data and Metadata With Vmentioning

confidence: 99%

The Integrated Rapid Infectious Disease Analysis (IRIDA) Platform

Fr²,

Ej³

et al. 2018

Preprint

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Whole genome sequencing (WGS) is a powerful tool for public health infectious disease investigations owing to its higher resolution, greater efficiency, and cost-effectiveness over traditional genotyping methods. Implementation of WGS in routine public health microbiology laboratories is impeded by a lack of user-friendly automated and semi-automated pipelines, restrictive jurisdictional data sharing policies, and the proliferation of non-interoperable analytical and reporting systems. To address these issues, we developed the Integrated Rapid Infectious Disease Analysis (IRIDA) platform (irida.ca), a user-friendly, decentralized, open-source bioinformatics and analytical web platform to support real-time infectious disease outbreak investigations using WGS data. Instances can be independently installed on local highperformance computing infrastructure, enabling private and secure data management and analyses according to organizational policies and governance. IRIDA's data management capabilities enable secure upload, storage and sharing of all WGS data and metadata. The core platform currently includes pipelines for quality control, assembly, annotation, variant detection, phylogenetic analysis, in silico serotyping, multi-locus sequence typing, and genome distance calculation. Analysis pipeline results can be visualized within the platform through dynamic line lists and integrated phylogenomic clustering for research and discovery, and for enhancing decision-making support and hypothesis generation in epidemiological investigations. Communication and data exchange between instances are provided through customizable access controls. IRIDA complements centralized systems, empowering local analytics and visualizations for genomics-based microbial pathogen investigations. IRIDA is currently transforming the Canadian public health ecosystem and is freely available at https://github.com/phac-nml/irida and www.irida.ca. Impact StatementWhole genome sequencing (WGS) is revolutionizing infectious disease analysis and surveillance due to its cost effectiveness, utility, and improved analytical power. To date, no . CC-BY-NC-ND 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/381830 doi: bioRxiv preprint first posted online Jul. 31, 2018; 3 "one-size-fits-all" genomics platform has been universally adopted, owing to differences in national (and regional) health information systems, data sharing policies, computational infrastructures, lack of interoperability and prohibitive costs. The Integrated Rapid Infectious Disease Analysis (IRIDA) platform is a user-friendly, decentralized, open-source bioinformatics and analytical web platform developed to support real-time infectious disease outbreak investigations using WGS data. IRIDA empowers public health, regulatory and clinical microbiology laboratory personnel to bett...

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Epidemiological characterization of a nosocomial outbreak of extended spectrum β‐lactamase Escherichia coli ST‐131 confirms the clinical value of core genome multilocus sequence typing

Cited by 9 publications

References 38 publications

Reduction trend of mcr-1 circulation in Emilia-Romagna Region, Italy

Reduction trend of mcr-1 circulation in Emilia-Romagna Region, Italy

Genetic Features of mcr-1 Mediated Colistin Resistance in CMY-2-Producing Escherichia coli From Romanian Poultry

The Integrated Rapid Infectious Disease Analysis (IRIDA) Platform

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