Co-occurrence of 3 different resistance plasmids in a multi-drug resistant Cronobacter sakazakii isolate causing neonatal infections

Abstract

Cronobacter sakazakii 505108 was isolated from a sputum specimen of a neonate with severe pneumonia. C. sakazakii 505108 co-harbors 3 resistance plasmids of the IncHI2, IncX3, and IncFIB incomparability groups, respectively. These 3 plasmids have acquired several accessory modules, which carry an extremely large number of resistance genes, especially including those involved in resistance to carbapenems, aminoglycoside, tetracyclines, and phenicols and sulphonamide/trimethoprim. These plasmid-borne antibiotic resistance genes were associated with insertion sequences, integrons, and transposons, indicating that the assembly and mobilization of the corresponding accessory modules with complex chimera structures are facilitated by transposition and/or homologous recombination. This is the first report of fully sequence plasmids in clinical Cronobacter, which provides a deeper insight into plasmid-mediated multi-drug resistance in Cronobacter from hospital settings.

Analysis of the Molecular Diversity Among Cronobacter Species Isolated From Filth Flies Using Targeted PCR, Pan Genomic DNA Microarray, and Whole Genome Sequencing Analyses

“…In contrast, CFSAN’s Galaxy’s AMRFinderPlus tool correctly identified all antimicrobial resistence/tolerance genes present on p505108-MDR (KY978628) which included the following antimicrobial resistance/tolerance genes: bla TEM– 1 , dfrA19, aph(3′′)-Ib, aph(6)-Id, mcr-9.1, aph(3′)-Ia, catA2, tet(D), aac(6′)-Ib3, bla SHV– 12 , sul1, bla DHA– 1 , qnrB4, qacEdelta1, arr, aac(3)-II, and aac(6′)-IIc with predicted resistances/tolerances to β-Lactam based compounds, Trimethoprim, Aminoglycoside, Colistin, Phenicol, Tetracycline, Sulfonamide, Quinolone, Quaternary Ammonium, and Rifamycin antibiotics, respectively. The antimicrobial resistance genes found on plasmid p505108-NDM (KY978629) were identified as ble, bla NDM– 1 , and bla SHV– 12 with predicted resistances to bleomycin and NDM-1 β-Lactam antibiotics, consistent with previously results reported by Shi et al (2018) .…”

“…, arr, aac(3)-II, and aac(6 )-IIc with predicted resistances/tolerances to β-Lactam based compounds, Trimethoprim, Aminoglycoside, Colistin, Phenicol, Tetracycline, Sulfonamide, Quinolone, Quaternary Ammonium, and Rifamycin antibiotics, respectively. The antimicrobial resistance genes found on plasmid p505108-NDM (KY978629) were identified as ble, bla NDM−1 , and bla SHV−12 with predicted resistances to bleomycin and NDM-1 β-Lactam antibiotics, consistent with previously results reported by Shi et al (2018).…”

“…More details can be found at https://github.com/ncbi/amr/wiki (last accessed 5/7/2020) ( Zankari et al, 2012 , 2017 ; Feldgarden et al, 2019 ). C. sakazakii strain 505108 co-harbors three plasmids of different incompatibility classes: IncHI2, IncX3, and IncFIB, respectively ( Shi et al, 2018 ). p505108-MDR [National Center for Biotechnology Information (NCBI) accession #: KY978628 ] and p505108-NDM (New Delhi metallo-beta-lactamase 1, NCBI accession #: KY978629 ) FASTA files were downloaded from NCBI and used as the positive control for determining antimicrobial resistance genes in the fly strains.…”

“…Taken together, MLST analysis of these Cronobacter strains (shown in Table 1) demonstrated that there were nine different STs found among the filth fly strains. FASTA formatted files of plasmids p505108-multidrug resistant (MDR, NCBI accession #: KY978628.1) and p505108-NDM (New Delhi metallo-β-lactamase 1, NCBI accession #: KY978629.1) reported by Shi et al (2018) were downloaded from NCBI. The corresponding C. sakazakii 505108 (ST1) sequences were used as positive control sequences, for comparison with the filth fly strains using the CFSAN AMRFinderPlus tool.…”

Novel Multidrug-ResistantCronobacter sakazakiiCausing Meningitis in Neonate, China, 2015

“…By performing plasmid multilocus sequence typing ( https://pubmlst.org/bigsdb?db=pubmlst_plasmid_seqdef&page=sequenceQuery ), we determined that pGW1 is IncHI2-ST1 and is mainly found in other countries ( 9 ). Full-plasmid comparison revealed that pGW1 is closely related to p505108-MDR ( 5 ).…”