Prediction of Phenotypic Antimicrobial Resistance Profiles From Whole Genome Sequences of Non-typhoidal Salmonella enterica

Surveillance of antimicrobial resistance (AMR) in non-typhoidal Salmonella enterica (NTS), is essential for monitoring transmission of resistance from the food chain to humans, and for establishing effective treatment protocols. We evaluated the prediction of phenotypic resistance in NTS from genotypic profiles derived from whole genome sequencing (WGS). Genes and chromosomal mutations responsible for phenotypic resistance were sought in WGS data from 3,491 NTS isolates received by Public Health England’s Gastrointestinal Bacteria Reference Unit between April 2014 and March 2015. Inferred genotypic AMR profiles were compared with phenotypic susceptibilities determined for fifteen antimicrobials using EUCAST guidelines. Discrepancies between phenotypic and genotypic profiles for one or more antimicrobials were detected for 76 isolates (2.18%) although only 88/52,365 (0.17%) isolate/antimicrobial combinations were discordant. Of the discrepant results, the largest number were associated with streptomycin (67.05%, n = 59). Pan-susceptibility was observed in 2,190 isolates (62.73%). Overall, resistance to tetracyclines was most common (26.27% of isolates, n = 917) followed by sulphonamides (23.72%, n = 828) and ampicillin (21.43%, n = 748). Multidrug resistance (MDR), i.e., resistance to three or more antimicrobial classes, was detected in 848 isolates (24.29%) with resistance to ampicillin, streptomycin, sulphonamides and tetracyclines being the most common MDR profile (n = 231; 27.24%). For isolates with this profile, all but one were S. Typhimurium and 94.81% (n = 219) had the resistance determinants blaTEM-1, strA-strB, sul2 and tet(A). Extended-spectrum β-lactamase genes were identified in 41 isolates (1.17%) and multiple mutations in chromosomal genes associated with ciprofloxacin resistance in 82 isolates (2.35%). This study showed that WGS is suitable as a rapid means of determining AMR patterns of NTS for public health surveillance

Three separate acquisitions of bla NDM-1 in three different bacterial species from a single patient

DATA AVAILABILITY : Sequence data was uploaded to NCBI (BioProject PRJNA948358).To investigate the acquisition and relatedness of New Delhi Metallo-beta-lactamase among multiple separate species from one patient. Five isolates from three species (Pseudomonas aeruginosa; Pa, Acinetobacter baumannii; Ab and Proteus mirabilis; Pm) suspected of harbouring a carbapenemase were investigated by phenotype (antimicrobial susceptibilities) and whole genome sequencing. Epidemiological data was collected on this patient. Three different carbapenemase genes were detected; blaVIM-1 (Pa; ST773), blaOXA-23 (Ab, ST499) and blaNDM-1 identified in all isolates. NDM regions were found chromosomally integrated in all isolates. Data showed no evidence of NDM-1 transfer within this patient suggesting the enzyme was acquired in three separate events.The Public Health Agency of Canada.http://link.springer.com/journal/10096am2024Medical MicrobiologySDG-03:Good heatlh and well-bein

Colistin non-susceptible Pseudomonas aeruginosa ST654 with blaNDM-1 arrives in North America

This study describes 3 different blaNDM-1 genetic platforms in 3 different species obtained from the same patient who was directly transferred to an institution in Calgary, Canada, following a prolonged hospital stay in India. The blaNDM-1 in the Escherichia coli was located on a 176kb IncA/C plasmid contained within an ISCR1 region. The blaNDM-1 in the Providencia rettgeri was located on a 117kb IncT plasmid contained within Tn3000, while the blaNDM-1 in Pseudomonas aeruginosa was located on the chromosome within an ISCR3 region. This report highlights the plasticity of the genetic regions and environments associated with blaNDM-1. To the best of our knowledge, this is the first report of P. aeruginosa with blaNDM-1 identified in North America and the first report of blaOXA-181in P. rettgeri. The P. aeruginosa belonged to the international high risk clone ST654 and was non-susceptible to colistin. This case emphasizes the need for appropriate infection prevention and control measures and vigilant screening for carbapenem resistant Gram negative bacteria in patients with a history of travel to endemic areas, such as the Indian subcontinent.In part by a research grant from the Calgary Laboratory Services (#10009392).http://aac.asm.org2016-09-30hb201

Do we still need Illumina sequencing data?: Evaluating Oxford Nanopore Technologies R10.4.1 flow cells and the Rapid v14 library prep kit for Gram negative bacteria whole genome assemblies

The best whole genome assemblies are currently built from a combination of highly accurate short-read sequencing data and long-read sequencing data that can bridge repetitive and problematic regions. Oxford Nanopore Technologies (ONT) produce long-read sequencing platforms and they are continually improving their technology to obtain higher-quality read data that is approaching the quality obtained from short-read platforms such as Illumina. As these innovations continue, we evaluated how much ONT read coverage produced by the Rapid Barcoding Kit v14 (SQK-RBK114) is necessary to generate high-quality hybrid and long-read-only genome assemblies for a panel of carbapenemase-producing Enterobacterales bacterial isolates. We found that 30X long-read coverage is sufficient if Illumina data is available, and that more (at least 100X) long-read coverage is recommended for long-read-only assemblies. Illumina polishing is still improving SNVs and INDELs in long-read-only assemblies. We also examined if antimicrobial resistance genes could be accurately identified in long-read-only data, and found that Flye assemblies regardless of ONT coverage detected > 96 % of resistance genes at 100% identity and length. Overall, the Rapid Barcoding Kit v14 and long-read-only assemblies can be an optimal sequencing strategy (i.e. plasmid characterization and AMR detection) but finer-scale analyses (i.e. SNV) still benefit from short-read data.The presentation of the authors' names and (or) special characters in the title of the pdf file of the accepted manuscript may differ slightly from what is displayed on the item page. The information in the pdf file of the accepted manuscript reflects the original submission by the author