Clonal Lineages and Virulence Factors of Carbapenem Resistant in Alameda County, California, 2017-2019.

The prevalence of carbapenem-resistant (CRE) has been increasing since the year 2000 and is considered a serious public health threat according to the Centers for Disease Control and Prevention. Limited studies have genotyped Carbapenem-resistant using whole genome sequencing to characterize the most common lineages and resistance and virulence genes. The aim of this study was to characterize sequence data from carbapenem-resistant isolates ( = 82) collected longitudinally by the Alameda County Public Health Laboratory (ACPHL) between 2017 and 2019. genomes were screened for antibiotic resistance genes (ARGs) and extraintestinal pathogenic virulence factor genes (VFGs). The carbapenem-resistant lineages were diverse, with 24 distinct sequence types (STs) represented, including clinically important STs: ST131, ST69, ST95, and ST73. All Ambler classes of Carbapenemases were present, with NDM-5 being most the frequently detected. Nearly all isolates (90%) contained genes encoding resistance to third-generation cephalosporins; genes were most common. The number of virulence genes present within pandemic STs was significantly higher than the number in non-pandemic lineages ( = 0.035). Virulence genes A (92%), t (71%), M (54%), and A (46%) were the most prevalent within the isolates. Considering the public health risk associated with CRE, these data enhance our understanding of the diversity of clinically important that are circulating in Alameda County, California.