Clinical and genomic epidemiology of carbapenem-non-susceptibleCitrobacterspp. at a tertiary healthcare center over two decades

Abstract

22Carbapenem-non-susceptible Citrobacter spp. (CNSC) are increasingly recognized as healthcare-23 associated pathogens. Information regarding their clinical epidemiology, genetic diversity, and 24 mechanisms of carbapenem resistance is lacking. We examined microbiology records of adult 25 patients at the University of Pittsburgh Medical Center (UMPC) Presbyterian Hospital (PUH) from 26 2000-2018 for CNSC, as defined by ertapenem non-susceptibility. Over this timeframe, the 27 proportion of CNSC increased from 4% to 10% (P=0.03), as did carbapenem daily defined 28 doses/1000 patient days (6.52 to 34.5, R 2 =0.831, P<0.001), which correlated with the observed 29 increase in CNSC (lag=0 years, R 2 =0.660). Twenty CNSC isolates from 19 patients at PUH and 30 other UPMC hospitals were available for further analysis, including whole-genome short-read 31 sequencing and additional antimicrobial susceptibility testing. Of the 19 patients, nearly all 32 acquired CNSC in the healthcare setting and over half had polymicrobial cultures containing at 33 least one other organism. Among the 20 CNSC isolates, C. freundii was the predominant species 34 identified (60%). CNSC genomes were compared with genomes of carbapenem-susceptible 35Citrobacter spp. from UPMC, and with other publicly available CNSC genomes. Isolates encoding 36 carbapenemases (blaKPC-2, blaKPC-3, and blaNDM-1) were also long-read sequenced, and their 37 carbapenemase-encoding plasmid sequences were compared with one another and with publicly 38 available sequences. Phylogenetic analysis of 102 UPMC Citrobacter spp. genomes showed that 39 CNSC from our setting did not cluster together. Similarly, a global phylogeny of 64 CNSC 40 genomes showed a diverse population structure. Our findings suggest that both local and global 41 CNSC populations are genetically diverse, and that CNSC harbor carbapenemase-encoding 42 plasmids found in other Enterobacterales. 43 isolated from a specimen collected within 72 hours following hospital admission; isolates collected 91 after 72 hours were considered healthcare-associated (22). Clinical characteristics and outcomes 92 of patients with CNSC isolates that underwent further characterization were collected through 93 retrospective chart review. The primary clinical outcome was in-hospital mortality and/or transfer 94 to hospice. 95 96 CNSC isolate characterization 97 Initial species assignment was performed using standard clinical microbiology laboratory 98 methods, and was confirmed or modified after whole-genome sequencing. Carbapenem non-99 susceptibility was initially determined by standard clinical microbiology laboratory methods, and 100 was confirmed by the Kirby-Bauer disk diffusion method as per the 2017 Clinical Laboratory 101 Standards Institute (CLSI) interpretative criteria (20). Susceptibility to additional agents was 102 determined by the broth microdilution method (20). Presence of carbapenemase enzyme activity 103 was assessed by modified carbapenem inactivation (mCIM) test (23). 104 105 Genome sequencing and a...