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

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

Klebsiella pneumoniae ST147 : and then there were three carbapenemases

DATA AVAILABITY: Sequence data was uploaded to NCBI (BioProject PRJNA861987).Please read abstract in the article.The Alberta Precision Laboratories.https://link.springer.com/journal/100962023-10-22hj2023Medical Microbiolog

Investigation of a Carbapenemase-producing Acinetobacter baumannii outbreak using whole genome sequencing versus a standard epidemiologic investigation

Abstract Background The standard epidemiologic investigation of outbreaks typically relies on spatiotemporal data and pulsed-field gel electrophoresis (PFGE), but whole genome sequencing (WGS) is becoming increasingly used. This investigation aimed to characterize a carbapenemase-producing Acinetobacter baumannii (CPAb) nosocomial outbreak using WGS compared to a standard outbreak investigation. Methods The CPAb outbreak occurred in a single center between 2012 and 2014. The standard investigation used spatiotemporal data and PFGE to generate a chain of transmission. A separate WGS investigation generated a chain of transmission based solely on WGS and date of sampling and was blinded to all other spatiotemporal data and PFGE. Core single nucleotide variant (SNV) phylogenetic analysis was performed on WGS data generated using the Illumina MiSeq platform. The chains of transmission were compared quantitatively and qualitatively to assess the concordance between both methods. Results 28 colonized and infected cases were included. Of the 27 transmission events identified using the standard investigation, 12 (44%) were identical to the transmission events using WGS. WGS identified several transmission events that had not been detected by traditional method, and numerous transmission events that had occurred on different hospital wards than suspected by standard methods. The average number (standard deviation [SD]) of SNVs per transmission events was 1.63 (SD, 1.31) by traditional method and 0.63 (SD, 0.79) by WGS (p = 0.001) All isolates harbored the rare carbapenemase bla OXA-237. Conclusions The traditional and WGS investigations had moderate concordance. When used alongside epidemiologic data and clinical information, WGS could help improve the mapping of transmission events

Characterization of Cefoxitin-Resistant Escherichia coli Isolates from Recreational Beaches and Private Drinking Water in Canada between 2004 and 2006 ▿ †

A total of 142 cefoxitin-resistant Escherichia coli isolates from water sources were collected across Canada. Multidrug resistance was observed in 65/142 (45.8%) isolates. The blaCMY-2 gene was identified in 110/142 (77.5%) isolates. Sequencing of the chromosomal ampC promoter region showed mutations from the wild type, previously shown to hyperproduce AmpC. CMY-2-producing plasmids predominantly belonged to replicon groups I1-Iγ, A/C, and K/B. The majority of the E. coli isolates belonged to the nonvirulent phylogenetic groups A and B1