Molecular characterization of multidrug-resistant ESKAPEE pathogens from clinical samples in Chonburi, Thailand (2017–2018)

Abstract

Background ESKAPEE pathogens Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp. and Escherichia coli are multi-drug resistant (MDR) bacteria that present increasing treatment challenges for healthcare institutions and public health worldwide. Methods 431 MDR ESKAPEE pathogens were collected from Queen Sirikit Naval Hospital, Chonburi, Thailand between 2017 and 2018. Species identification and antimicrobial resistance (AMR) phenotype were determined following CLSI and EUCAST guidelines on the BD Phoenix System. Molecular identification of antibiotic resistant genes was performed by polymerase chain reaction (PCR), real-time PCR assays, and whole genome sequencing (WGS). Results Of the 431 MDR isolates collected, 1.2% were E. faecium, 5.8% were S. aureus, 23.7% were K. pneumoniae, 22.5% were A. baumannii, 4.6% were P. aeruginosa, 0.9% were Enterobacter spp., and 41.3% were E. coli. Of the 401 Gram-negative MDR isolates, 51% were carbapenem resistant, 45% were ESBL producers only, 2% were colistin resistance and ESBLs producers (2%), and 2% were non-ESBLs producers. The most prevalent carbapenemase genes were blaOXA-23 (23%), which was only identified in A. baumannii, followed by blaNDM (17%), and blaOXA-48-like (13%). Beta-lactamase genes detected included blaTEM,blaSHV, blaOXA, blaCTX-M, blaDHA, blaCMY, blaPER and blaVEB. Seven E. coli and K. pneumoniae isolates showed resistance to colistin and carried mcr-1 or mcr-3, with 2 E. coli strains carrying both genes. Among 30 Gram-positive MDR ESKAPEE, all VRE isolates carried the vanA gene (100%) and 84% S. aureus isolates carried the mecA gene. Conclusions This report highlights the prevalence of AMR among clinical ESKAPEE pathogens in eastern Thailand. E. coli was the most common MDR pathogen collected, followed by K. pneumoniae, and A. baumannii. Carbapenem-resistant Enterobacteriaceae (CRE) and extended spectrum beta-lactamases (ESBLs) producers were the most common resistance profiles. The co-occurrence of mcr-1 and mcr-3 in 2 E. coli strains, which did not affect the level of colistin resistance, is also reported. The participation of global stakeholders and surveillance of MDR remain essential for the control and management of MDR ESKAPEE pathogens.

Resistance Gene Association and Inference Network (ReGAIN): A Bioinformatics Pipeline for Assessing Probabilistic Co-Occurrence Between Resistance Genes in Bacterial Pathogens

“…In addition to Gram-negative pathogens, four Gram-positive bacterial pathogens − E. faecalis, E. faecium, S. aureus, and S. pneumoniae − were analyzed (Table 1), though it is worth nothing that S. pneumoniae represents our smallest Bayesian network (10 nodes). To assess the accuracy of our system, the Bayesian networks were initially analyzed for the presence of previously observed co- resistance patterns, including the co-occurrence of phenicol and lincosamide resistance genes (38,52). In S. aureus , the phenicol resistance gene fexA exhibited an overall positive probability of co- occurrence with the lincosamide resistance gene lnuB (cond.…”

Bithionol Restores Sensitivity of Multidrug-Resistant Gram-Negative Bacteria to Colistin with Antimicrobial and Anti-biofilm Effects

“…Cells stained with fluorescent nucleic acid stain SYTO 9 and PI exhibited green and red fluorescence, respectively. , SYTO 9 stains living and dead cells, and PI stains the DNA nucleus, emitting red fluorescence after embedding double-stranded DNA. PI is often used to detect apoptosis. , Compared with the LB broth control group and the monotherapy group, the combination group exhibited an increased red fluorescence, thereby indicating an increase in bacterial cell membrane permeability during early growth (2 h) (Supporting Figure S2). The CLSM result revealed that in the combination group, the red fluorescence was significantly enhanced, which indicated that a large amount of PI entered the cells and bound to the DNA (Figure ).…”

“…PI is often used to detect apoptosis. 24,25 Compared with the LB broth control group and the monotherapy group, the combination group exhibited an increased red fluorescence, thereby indicating an increase in bacterial cell membrane permeability during early growth (2 h) (Supporting Figure S2). The CLSM result revealed that in the combination group, the red fluorescence was significantly enhanced, which indicated that a large amount of PI entered the cells and bound to the DNA (Figure 5).…”

MetaCompare 2.0: Differential ranking of ecological and human health resistome risks

“…The range of pathogens used in HHRR was confined to the ESKAPE pathogens as well as any contig annotated as Enterobacteraciae. This was done to include Escherichia coli (as in the “ESKAPEE”) [26, 27] as well as to ensure that contigs without complete taxonomic annotations but which are likely derived from the ESKAPE organisms would be captured. This is common for contigs originating from ESKAPE-associated plasmids and MGEs [28, 29].…”