31Carbapenem-resistant Enterobacteriaceae (CRE) are emerging as a major health threat in North 32 America. The mechanism of resistance to carbapenems has therapeutic and public health 33 implications. We comprehensively characterized the underlying mechanisms of carbapenem 34 resistance in CRE isolates recovered between 2013 and 2016 at a health system in Northern 35 California. Genotypic methods were used to detect carbapenemases and plasmid-encoded 36 cephalosporinases, and mass spectrometry was used to quantify relative porin levels for OmpC 37 and OmpF and their analogs. MICs for imipenem-relebactam, meropenem-vaborbactam, 38 ceftazidime-avibactam, and ceftolozane-tazobactam were measured. Whole genome sequencing 39 was used for strain typing. A carbapenemase gene encoding blaOXA-48 like, blaNDM, blaKPC, blaSME, 40 blaIMP, and blaVIM was detected in 38.7% (24/62) of CRE isolates. Porin levels was down at least 41 2-fold in 91.9% (57/62) of isolates. Including carbapenemase genes and porin loss, the 42 mechanism of resistance was identified in 95.2% (59/62) of CRE isolates. Of the carbapenemase 43 gene-positive isolates, blaKPC -positive isolates were 100% susceptible to ceftazidime-avibactam, 44 meropenem-vaborbactam, and imipenem-relebactam; blaOXA-48 like-positive isolates were 100% 45 susceptible to ceftazidime-avibactam; and blaSME-positive isolates were 100% susceptible to 46 meropenem-vaborbactam and ceftolozane-tazobactam. 100% (38/38), 92.1% (35/38), 89.5% 47 48 ceftazidime-avibactam, meropenem-vaborbactam, imipenem-relebactam, and ceftolozane-49 tazobactam, respectively. None of the CRE strains were genetically identical. In conclusion, at 50 this health system in Silicon Valley, carbapenemase-producing CRE occurred sporadically and 51 were mediated by diverse mechanisms. Nucleic acid testing for blaOXA-48 like, blaNDM, blaKPC, 52 blaIMP, and blaVIM was sufficient to distinguish between carbapenemase-producing and non-53 4 producing CRE and accurately predicted susceptibility to ceftazidime-avibactam, meropenem-54 vaborbactam and imipenem-relebactam. 55 56 57Carbapenemase-producing carbapenem-resistant Enterobacteriaceae (CP-CRE) have 58 successfully spread worldwide over the recent decades (1, 2). In some regions, CP-CRE have 59 become endemic in hospital settings (2). The proportion of CRE in acute-care hospitals in the 60 U.S. has increased steadily (3, 4). Infection with CRE is associated with increased morbidity and 61 mortality (5-7). Thus, early diagnosis of CRE infection is essential for timely initiation of 62 targeted-antimicrobial therapy and early implementation of infection prevention precautions 63 aimed to prevent nosocomial spread (8, 9).
64The main mechanisms of resistance to carbapenems in CRE include hydrolysis of carbapenems 65 by a plasmid-encoded carbapenemase, impaired outer membrane permeability due to inactivation 66 of particular porins (i.e., OmpC and OmpF in E. coli and their analogs) coupled with high-level 67 expression of cephalosporinases such as AmpC an...