MSCSA and Sanger sequencing of 70 pH1N1 virus specimens.

$<p>Sanger sequencing was succesful in 63 of 65 specimens determined by MSCSA.</p>#<p>Sequence match using MSCSA and Sanger sequencing.</p>1<p>SNPs in MSCSA and not in Sanger sequencing;</p>2<p>SNPs in Sanger and not MSCSA.</p

A graphic representation of the first wave of the 2009 H1N1 pandemic in the region of Leiden (The Netherlands).

<p>A graphic representation of the first wave of the 2009 H1N1 pandemic in the region of Leiden (The Netherlands).</p

Overview of pH1N1 Sanger sequencing and MSCSA primers and amplicon sizes.

<p>Bp, base pairs.</p>$<p>5′ position of the first nucleotide of the forward primer in the corresponding gene;</p>#<p>5′ position of the last nucleotide of the reverse primer in the corresponding gene.</p

Surveillance of pH1N1 genetic markers associated with virulence or antiviral resistance.

<p>Relevant amino acid genetic positions are depicted for each corresponding gene.</p

Circular presentation of the <i>mcr-1</i> containing <i>IncX4</i> plasmid in the colistin susceptible <i>E</i>.<i>coli</i>.

<p>In green the <i>mcr-1</i> sequence. In red the IS10R insertion sequence, interrupting the <i>mcr-1</i> gene at position 572. Arrows indicate open reading frames (ORFs), dark blue ORFs with annotation, light blue ORFs without annotation (hypothetical protein). Numbers indicate nucleotide positions.</p

Antibiotic phenotype with the corresponding molecular resistance of cultured <i>mcr-1</i> containing <i>E</i>.<i>coli</i>.

<p>Antibiotic phenotype with the corresponding molecular resistance of cultured <i>mcr-1</i> containing <i>E</i>.<i>coli</i>.</p

Primers and probe used to screen for the presence of <i>mcr</i>-genes.

<p>Primers and probe used to screen for the presence of <i>mcr</i>-genes.</p

Data_Sheet_1_Livestock-associated methicillin-resistant Staphylococcus aureus epidemiology, genetic diversity, and clinical characteristics in an urban region.PDF

ObjectivesWhile Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA), defined as CC398, is a well-known pathogen among those working with livestock, there are indications that LA-MRSA prevalence among the general population is increasing. However, the clinical impact in urban areas remains unknown. The aim of this study was to assess the genetic epidemiology and clinical characteristics of LA-MRSA in an urban area with a limited livestock population.MethodsIn this retrospective study, we evaluated LA-MRSA strains that were collected between 2014 and 2018 from patients who received clinical care in a single urban area in Netherlands. Patient files were assessed for livestock exposure data, clinical findings, and contact tracing information. Next-generation sequencing (NGS) analysis in combination with wgMLST was conducted to assess genetic diversity and relatedness and to detect virulence and resistance genes.ResultsLA-MRSA strains were cultured from 81 patients, comprising 12% of all the MRSA strains found in seven study laboratories between 2014 and 2018. No livestock link was found in 76% of patients (n = 61), and 28% of patients (n = 23) had an infection, mostly of the skin or soft tissue. Contact tracing had been initiated in 14 cases, leading to the identification of two hospital transmissions: a cluster of 9 cases and one of 2 cases. NGS data were available for 91% (n = 75) of the patients. wgMLST confirmed the clusters detected via contact tracing (n = 2) and identified 5 additional clusters without a known epidemiological link. Relevant resistance and virulence findings included the PVL virulence gene (3 isolates) and tetracycline resistance (79 isolates).ConclusionLA-MRSA may cause a relevant burden of disease in urban areas. Surprisingly, most infections in the present study occurred in the absence of a livestock link, suggesting inter-human transmission. These findings and the presence of PVL and other immune evasive complex virulence genes warrant future surveillance and preventative measures.</p