Background As cefiderocol is increasingly being prescribed in clinical practice, it is critical that we understand key mechanisms contributing to acquired resistance to this agent. Methods We report the case of a patient with acute lymphoblastic leukemia with an NDM-5 producing Escherichia coli intra-abdominal infection where resistance to cefiderocol evolved approximately 2 weeks after initiating cefiderocol therapy. Through WGS investigations, mRNA expression studies, and EDTA inhibition analysis, we investigate the role of increased NDM-5 production and genetic mutations contributing to the development of cefiderocol resistance using 5 sequential clinical E. coli isolates obtained from the patient. Results blaNDM-5 genes were identified in all 5 isolates. Cefiderocol MICs were 2, 4, and >32 mcg/mL for isolates 1-2, 3, 4-5, respectively. WGS showed that isolates 1-3 contained a single copy of the blaNDM-5 gene, whereas isolates 4 and 5 had 5 copies and 10 copies of the blaNDM-5 gene on an IncFIA/FIB/IncFII plasmid, respectively. These findings correlated with NDM-5 mRNA expression analysis in which isolates 4 and 5 expressed NDM 1.7x and 2.8x greater than isolate 1. Synergy testing with the combination of ceftazidime-avibactam and aztreonam demonstrated expansion of the zone of inhibition between the disks for all isolates. The patient was eventually successfully treated with this combination and remained infection free 10 months later. Conclusions Our patient’s case suggests that increased copy numbers of bla NDM genes through translocation events is used by Enterobacterales to evade cefiderocol-mediated cell death. The frequency of increased NDM expression in contributing to cefiderocol resistance needs investigation.

Objective: Understanding bacterial species at highest risk for harboring blaCTX-M genes is necessary to guide antibiotic treatment. We identified the species-specific prevalence of blaCTX-M genes in clinical isolates from the United States. Methods: 24 microbiology laboratories representing 66 hospitals using the GenMark Dx ePlex® Blood Culture Identification Gram-Negative (BCID-GN) Panel extracted blood culture results from April 2019 to July 2020. The BCID-GN Panel includes 21 Gram-negative targets. Along with identifying blaCTX-M genes, it detects major carbapenemase gene families. Results: 4,209 Gram-negative blood cultures were included. blaCTX-M genes were identified in 462 (11%) specimens. The species-specific prevalence of blaCTX-M genes were as follows: Escherichia coli (16%), Klebsiella pneumoniae (14%), Klebsiella oxytoca (6%), Salmonella spp. (6%), Acinetobacter baumannii (5%), Enterobacter species (3%), Proteus mirabilis (2%), Serratia marcenscens (0.6%), and Pseudomonas aeruginosa (0.5%). blaCTX-M prevalence was 26%, 24%, and 22% among participating hospitals in the District of Columbia, New York, and Florida, respectively. Carbapenemase genes were identified in 61 (2%) organisms with the following distribution: blaKPC (59%), blaVIM (16%), blaOXA (10%), blaNDM (8%), and blaIMP (7%). The species-specific prevalence of carbapenemase genes were as follows: A. baumannii (5%), K. pneumoniae (3%), P. mirabilis (3%), Enterobacter species (3%), Citrobacter spp. (3%), P. aeruginosa (2%), E. coli (<1%), K. oxytoca (<1%), and S. marcescens (<1%). Conclusion: Approximately 11% of Gram-negative organisms in our US cohort contain blaCTX-M genes. blaCTX-M genes remain uncommon in organisms beyond E. coli, K. pneumoniae, and K. oxytoca. Future molecular diagnostic panels would benefit from the inclusion of plasmid-mediated ampC and SHV and TEM ESBL targets.

The late genes of the temperate phage of Pseudomonas aeruginosa are organized in an analogous fashion to the corresponding transcription units of the Escherichia coli P2 and P2-like phages. Sequence analysis of four putative late promoter regions, PP(phiCTX), PO(phiCTX), PV(phiCTX) and PF(phiCTX), reveals no similarity to sigma(70)-type promoters or promoter consensus sequences found in Pseudomonas, indicating the apparent need for a phage-encoded protein to control the expression of phiCTX late genes. To elucidate the mode of expression of the late genes, we fused the putative late promoter regions to the promoterless lacZalpha gene, which encodes the N-terminal part of beta-galactosidase as a reporter enzyme, in the promoter-probe vector pME4510. The candidate transactivator gene orf34 was cloned into expression vector pHA10, to generate the plasmid pHA34. The two recombinant plasmids were introduced together into E. coli XL1-Blue and P. aeruginosa PAO1S-Lac. Our results demonstrate that in phiCTX three late promoters (PP(phiCTX), PO(phiCTX), and PF(phiCTX)) are activated upon induction by IPTG in PAO1S-Lac carrying the cloned promoters and pHA34. Deletions and base-pair substitutions obtained by PCR-mediated mutagenesis demonstrated that two conserved sequences, TTGTAG-N(9)-cTACAa and GcCGCGCGCGCGgC, are essential for effective late gene expression. Whereas the late promoters were active in P. aeruginosa, only weak beta-galactosidase activity was obtained in E. coli.