Whoel cell MALDI-TOF mass spectra of Escherichia coli isolates

Whoel cell MALDI-TOF mass spectra of Escherichia coli isolate

Additional file 1 of Implementation of the FilmArray ME panel in laboratory routine using a simple sample selection strategy for diagnosis of meningitis and encephalitis

Additional file 1: Table S1. Overview of analytical methods performed and detection rates in n = 4623 CSF samples received

Additional file 2 of Implementation of the FilmArray ME panel in laboratory routine using a simple sample selection strategy for diagnosis of meningitis and encephalitis

Additional file 2: Table S2. Overview of pathogens detected by different methods. Numbers of pathogens detected by routine diagnostic procedures, numbers detected by Film Array ME Panel as well as confirmatory results are given

Marker peak characteristics in spectra from study isolates.

<p>Mean signal to noise ratio of outbreak strain marker peaks (A, B) and mean signal intensitiy (C, D) at marker peak position in formic acid extraction (A, C) and direct sample deposition (B, D) triplicate spectra from 293 study isolates. Black triangles and white circles represent measurements from 104 outbreak and 189 non outbreak <i>E. coli</i> isolates, respectively. Red colour indicates misidentified isolates.</p

Peak detection rates (%) among study isolates.

a<p>Confirmed by visual spectrum inspection and sequencing of the corresponding marker protein gene.</p><p>Abbreviations: OREC outbreak related <i>E. coli</i> isolates, NOREC non outbreak related <i>E. coli</i> isolates, FAE formic acid extraction, DSD direct sample deposition.</p

MOESM1 of Initial therapy affects duration of diarrhoea in critically ill patients with Clostridioides difficile infection (CDI)

Additional file 1: Figure S1. CDI specific therapy in all ICU patients with CDI 2010–2015. Legend: Abbreviations: IV: intravenously, VPR: Vancomycin per rectum. Table S1. Treatment strategy according to CDI severity during first 48 h after diagnosis of CDI. Legend: A: before 2014, B: 2014-October 2015. Table S2. Characteristics of all treated patients with CDI. Legend: Univariate regression analysis of risk factors of 28-day survivors vs. 28-day-nonsurvivors. Abbreviations: BUN: blood urea nitrogen, CRP: C-reactive protein, vol.: volume, MAP: mean arterial pressure. Table S3. Patients’ characteristics of the study population with CDI stratified according to diarrhoea 5 days. Table S4. Patients’ characteristics of the study population with CDI stratified according to initial CDI therapy (first 48 h)

MALDI-TOF mass spectrum of <i>E. coli</i> outbreak isolate TY-2482.

<p>Representative whole cell MALDI-TOF mass spectrum of the Shiga-Toxigenic <i>E. coli</i> outbreak isolate TY-2482 acquired after formic acid extraction. Inlays show enlarged views of outbreak strain specific marker peaks and the amino acid sequence of the corresponding proteins. Peptides identified by LC-MS/MS are indicated by a gray background. The tick mark interval in the enlarged peak views is set to 100.</p

Variants of marker peak protein genes found among non outbreak study isolates by PCR and sequencing.

a<p>See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101924#pone-0101924-t001" target="_blank">table 1</a>.</p>b<p>Outbreak strain variant.</p>c<p>No full length gene sequences for molecular weight prediction could be obtained from the respective isolates. Available partial sequences differ from the outbreak strain variant.</p><p>Abbreviations: MW Molecular weight.</p

Rapid MALDI-TOF Mass Spectrometry Strain Typing during a Large Outbreak of Shiga-Toxigenic <i>Escherichia coli</i>

<div><p>Background</p><p>In 2011 northern Germany experienced a large outbreak of Shiga-Toxigenic <i>Escherichia coli</i> O104:H4. The large amount of samples sent to microbiology laboratories for epidemiological assessment highlighted the importance of fast and inexpensive typing procedures. We have therefore evaluated the applicability of a MALDI-TOF mass spectrometry based strategy for outbreak strain identification.</p><p>Methods</p><p>Specific peaks in the outbreak strain’s spectrum were identified by comparative analysis of archived pre-outbreak spectra that had been acquired for routine species-level identification. Proteins underlying these discriminatory peaks were identified by liquid chromatography tandem mass spectrometry and validated against publicly available databases. The resulting typing scheme was evaluated against PCR genotyping with 294 <i>E. coli</i> isolates from clinical samples collected during the outbreak.</p><p>Results</p><p>Comparative spectrum analysis revealed two characteristic peaks at m/z 6711 and m/z 10883. The underlying proteins were found to be of low prevalence among genome sequenced <i>E. coli</i> strains. Marker peak detection correctly classified 292 of 293 study isolates, including all 104 outbreak isolates.</p><p>Conclusions</p><p>MALDI-TOF mass spectrometry allowed for reliable outbreak strain identification during a large outbreak of Shiga-Toxigenic <i>E. coli</i>. The applied typing strategy could probably be adapted to other typing tasks and might facilitate epidemiological surveys as part of the routine pathogen identification workflow.</p></div

Whole spectrum similarity among non outbreak study isolates.

<p>Distribution of Jaccard distance values from pairwise spectrum comparisons among non outbreak study isolates (dark grey, n = 17955) and single isolate replicate spectra (light grey, n = 189). The dashed line represents a threshold for spectral identity derived from the replicate spectrum distribution (mean+2×SD). The dotted line represents a less conservative threshold that would correctly classify 95% of all isolate pairs that were found spectrally identical upon manual spectrum comparison.</p