Antimicrobial Resistance Outbreak Report

REPORT DATE PROJECT NAME PREPARED BY
2021-11-10 AR Report Example Abigail Shockey

SUMMARY

This report outlines the relationship between a set of samples collected at a facility described by the outbreak ID: 1337. A set of external OXA-24 samples were also included to provide context to the outbreak.

SAMPLES

Lab ID Isolate Collection Date Local ID Species ID Specimen Source MLST Resistance Genes Comments
S01 06/02/2049 WGS3213 Acinetobacter baumannii Skin PubMLST ST406 (Pasteur) blaOXA-24
S02 06/18/2049 WGS3214 Acinetobacter baumannii Skin PubMLST ST2 (Pasteur) blaOXA-72 Outbreak ID: 1337
S03 05/38/2049 WGS3215 Acinetobacter baumannii Skin PubMLST ST2 (Pasteur) blaOXA-72 Outbreak ID: 1337
S04 05/36/2049 WGS3216 Acinetobacter baumannii Blood PubMLST ST406 (Pasteur) blaOXA-24
S05 06/13/2049 WGS3217 Acinetobacter baumannii Skin PubMLST ST406 (Pasteur) blaOXA-24
S06 06/15/2049 WGS3218 Acinetobacter baumannii Skin PubMLST ST2 (Pasteur) blaOXA-72 Outbreak ID: 1337
S07 05/25/2049 WGS3219 Acinetobacter baumannii Floor Drain PubMLST ST2 (Pasteur) blaOXA-72 Environmental Sample obtained from outbreak site.

RELATEDNESS

HEATMAP

The number of Single Nucleotide Polymorphisms (SNPs) between each sample is shown on the heatmap below. There is no established rule for determining how many SNPs are needed to classify an outbreak. Generally it is best to look for patterns in the data between the SNP data and the core-genome tree. The samples are ordered based on the euclidean distance between each sample.

PHYLOGENETIC TREE

The core-genome phylogenetic tree examines the genetic diversity across the core set of genes shared across all samples in the in the analysis. Related samples will generally share a recent common ancestor and a small amount of horizontal distance on the tree. The number of core-genes provides an indication of how diverse the sample is. A low number of core genes suggests the dataset is genetically diverse, or an outlier is present in the dataset.

Core Genes Identified: 2994

Total Genes Identified: 4574

AR GENE SUMMARY

This table shows a summary of all genes detected using the NCBI AMR Finder Plus detection tool.

Sample Gene Coverage Identity
S01
S01 blaADC 100.0 98.17
S01 ant(3’’)-IIa 100.0 100.0
S01 ant(2’’)-Ia 100.0 100.0
S01 aadA2 100.0 100.0
S01 qacEdelta1 100.0 100.0
S01 sul1 100.0 100.0
S01 blaOXA 100.0 99.27
S01 blaOXA-24 100.0 100.0
S02
S02 blaOXA-66 100.0 100.0
S02 tet(B) 99.75 100.0
S02 aph(6)-Id 100.0 100.0
S02 aph(3’’)-Ib 100.0 100.0
S02 blaADC-30 100.0 100.0
S02 ant(3’’)-IIa 100.0 98.85
S02 qacEdelta1 100.0 100.0
S02 aadA5 100.0 100.0
S02 dfrA17 100.0 100.0
S02 msr(E) 100.0 100.0
S02 armA 100.0 100.0
S02 mph(E) 100.0 100.0
S02 sul1 100.0 100.0
S02 aac(3)-I 100.0 100.0
S02 aacA16 100.0 100.0
S02 blaOXA-72 100.0 100.0
S03
S03 blaOXA-66 100.0 100.0
S03 blaADC-30 100.0 100.0
S03 ant(3’’)-IIa 100.0 98.85
S03 tet(B) 99.75 100.0
S03 aph(6)-Id 100.0 100.0
S03 aph(3’’)-Ib 100.0 100.0
S03 mph(E) 100.0 100.0
S03 dfrA17 100.0 100.0
S03 qacEdelta1 100.0 100.0
S03 sul1 100.0 100.0
S03 armA 100.0 100.0
S03 aadA5 100.0 100.0
S03 msr(E) 100.0 100.0
S03 aac(3)-I 100.0 100.0
S03 sul2 100.0 100.0
S03 aacA16 100.0 100.0
S03 blaOXA-72 100.0 100.0
S04
S04 blaADC 100.0 98.17
S04 ant(3’’)-IIa 100.0 100.0
S04 blaOXA-829 100.0 100.0
S04 ant(2’’)-Ia 100.0 100.0
S04 aadA2 100.0 100.0
S04 qacEdelta1 100.0 100.0
S04 sul1 100.0 100.0
S04 msr(E) 100.0 100.0
S04 mph(E) 100.0 100.0
S04 armA 75.1 100.0
S04 aph(3’)-Ia 100.0 99.26
S04 aph(3’)-VIa 100.0 96.14
S04 blaOXA-24 100.0 100.0
S05
S05 blaADC 100.0 98.17
S05 ant(3’’)-IIa 100.0 100.0
S05 ant(2’’)-Ia 100.0 100.0
S05 aadA2 100.0 100.0
S05 qacEdelta1 100.0 100.0
S05 sul1 100.0 100.0
S05 blaOXA 100.0 99.27
S05 blaOXA-24 100.0 100.0
S06
S06 blaOXA-66 100.0 100.0
S06 blaADC-30 100.0 100.0
S06 tet(B) 99.75 100.0
S06 aph(6)-Id 100.0 100.0
S06 aph(3’’)-Ib 100.0 100.0
S06 ant(3’’)-IIa 100.0 98.85
S06 mph(E) 100.0 100.0
S06 dfrA17 100.0 100.0
S06 qacEdelta1 100.0 100.0
S06 sul1 100.0 100.0
S06 armA 100.0 100.0
S06 aadA5 100.0 100.0
S06 msr(E) 100.0 100.0
S06 aac(3)-I 100.0 100.0
S06 sul2 100.0 100.0
S06 aacA16 100.0 100.0
S06 blaOXA-72 100.0 100.0
S07
S07 blaOXA-66 100.0 100.0
S07 ant(3’’)-IIa 100.0 98.85
S07 blaADC-30 100.0 100.0
S07 aph(3’’)-Ib 100.0 100.0
S07 aph(6)-Id 100.0 100.0
S07 tet(B) 99.75 100.0
S07 qacEdelta1 100.0 100.0
S07 aadA5 100.0 100.0
S07 dfrA17 100.0 100.0
S07 msr(E) 100.0 100.0
S07 armA 100.0 100.0
S07 mph(E) 100.0 100.0
S07 sul1 100.0 100.0
S07 aacA16 100.0 100.0
S07 aac(3)-I 100.0 100.0
S07 sul2 100.0 100.0
S07 blaOXA-72 100.0 100.0

ADDITIONAL ANALYSES

This table shows the MLST scheme(s) identified for each sample using mlst:

Sample MLST.Scheme
S01 PubMLST ST406 (Pasteur)
S02 PubMLST ST2 (Pasteur)
S03 PubMLST ST2 (Pasteur)
S04 PubMLST ST406 (Pasteur)
S05 PubMLST ST406 (Pasteur)
S06 PubMLST ST2 (Pasteur)
S07 PubMLST ST2 (Pasteur)

METHODS

The figures shown here were generated using sequence data processed with the Dryad v3.0 and Spriggan v1.1.0 analysis pipelines. If you have questions about this report please contact .

DISCLAIMER

The information included in this report should only be used to support infection prevention measures. This report should not be used to guide treatment decisions, nor should it be included in the patient record. Whole-genome sequencing analysis is a rapidly evolving technology. Whole-genome sequencing and SNP analysis will continue to be adjusted and refined over time due to the varied nature of bacterial genomes, limitations on available reference genomes and continual assessment of the inclusion of mobile genetic elements in this analysis. These results represent the most advanced method currently available for genome comparisons.