Application of Next-Generation Sequencing for Characterization of Surveillance and Clinical Trial Isolates: Analysis of the Distribution of β-lactamase Resistance Genes and Lineage Background in the United States

Abstract

Background Sequencing technologies and techniques have seen remarkable transformation and innovation that have significantly affected sequencing capability. Data analyses have replaced sequencing as the main challenge. This paper provides an overview on applying next-generation sequencing (NGS) and analysis and discusses the benefits and challenges. In addition, this document shows results from using NGS and bioinformatics tools to screen for β-lactamase genes and assess the epidemiological structure of Escherichia coli– and Klebsiella pneumoniae–causing bloodstream (BSIs) and urinary tract (UTIs) infections in patients hospitalized in the United States during the SENTRY Antimicrobial Surveillance Program for 2016. Methods A total of 3525 isolates (2751 E. coli and 774 K. pneumoniae) causing BSIs (n = 892) and UTIs (n = 2633) in hospitalized patients in the United States were included. Isolates were tested for susceptibility by broth microdilution, and those that met a minimum inhibitory concentration (MIC)–based screening criteria had their genomes sequenced and analyzed. Results A total of 11.6% and 16.1% of E. coli–causing UTIs and BSIs, respectively, met the MIC-based criteria, whereas 11.0% and 13.7% of K. pneumoniae isolates causing UTIs and BSIs, respectively, met the criteria. Among E. coli, blaCTX-M variants (87.6% overall) prevailed (60.5% of CTX-M group 1 and 26.9% of group 9). A total of 60.3% of K. pneumoniae isolates carried blaCTX-M variants (52.7% and 7.6% of groups 1 and 9, respectively). Two E. coli (0.6%) and 13 K. pneumoniae (12.9%) isolates harbored blaKPC. Among KPC-producing K. pneumoniae (2 from BSIs and 11 from UTIs), 84.6% (11/13) were ST258 (CC258). Seventeen and 38 unique clonal complexes (CCs) were noted in E. coli that caused BSIs and UTIs, respectively, and CC131 (or ST131) was the most common CC among BSI (53.6%) and UTI (58.2%) isolates. Twenty-three and 26 CCs were noted among K. pneumoniae–causing BSIs and UTIs, respectively. CC258 (28.3%) prevailed in UTI pathogens, whereas CC307 (15.0%) was the most common CC among BSI isolates. Conclusions This study provides a benchmark for the distribution of β-lactamase genes and the population structure information for the most common Enterobacteriaceae species responsible for BSIs and UTIs in US medical centers during the 2016 SENTRY Program.

Evaluation of Empiric β-Lactam Susceptibility Prediction among Enterobacteriaceae by Molecular β-Lactamase Gene Testing

“…Similarly, the data used here were from 2012, 6 years ago. However, the spectrum of beta-lactamases in the United States remains largely the same, as documented by Castanheira and coworkers in 2014 and 2016 (16,18). Data from 2014 demonstrated no major changes in the bla CTX-M -carrying isolates overall and a decrease in isolates carrying bla KPC from 16.5 to 10.9%, mostly due to the decrease in isolates harboring bla KPC in hospitals in the Mid-Atlantic and South Atlantic regions (16).…”

Genomic Surveillance of Ceftriaxone-Resistant Escherichia coli in Western New York Suggests the Extended-Spectrum β-Lactamase blaCTX-M-27 Is Emerging on Distinct Plasmids in ST38

“…Extended-spectrum β-lactamase (ESBL)-producing organisms are responsible for ~26,000 drug-resistant infections and ~1,700 deaths per year in the US, where they are categorized as a serious and increasing threat within the Centers for Disease Control and Prevention's (CDC) 2019 Antibiotic Resistance Threat Report (CDC, 2019). Among hospitalized patients, ESBL-producers may account for up to 11.6 and 16.1% of Escherichia coli causing urinary tract infection (UTI) and bloodstream infections (BSIs), respectively (Mendes et al, 2019). At present, CTX-M β-lactamases are the prevailing family of ESBLs and include more than 150 genes (Zhao and Hu, 2013).…”

“…In the US, the bla CTX-M-15 gene has also been frequently reported in the context of ST131 (often carried on IncF plasmids; Chandramohan and Revell, 2012;Banerjee et al, 2013;Doi et al, 2013;Chen et al, 2014;Kanamori et al, 2017). However, hinting that the epidemiology may be changing, the 2016 SENTRY Antimicrobial Surveillance Study demonstrated that the bla CTX-M-27 gene (17.3%) is also significant in E. coli UTI and BSI isolates, compared to the bla CTX-M-15 gene (55.5%; Mendes et al, 2019). Similarly, ST131 carrying the bla CTX-M-27 gene is also a frequent minority around the globe (Livermore et al, 2007;Cao et al, 2011;Dahbi et al, 2013;Matsumura et al, 2013;Seiffert et al, 2013;Roer et al, 2017;Guiral et al, 2019;Peirano and Pitout, 2019;Birgy et al, 2020).…”

Antimicrobial Activity Evaluation of Tebipenem (SPR859), an Orally Available Carbapenem, against a Global Set of Enterobacteriaceae Isolates, Including a Challenge Set of Organisms

“…A previous study reported an occurrence of 45% of ST131 among E. coli isolates in 2009 in the United States (7). More recently, a rate of 57% of ST131 was described among ESBL-producing E. coli causing UTI or bloodstream infections in the United States in 2016 (13). A similar rate (56.8%) was observed in a recent clinical trial comparing piperacillin-tazobactam and meropenem for treating bloodstream infections (BSIs) caused by E. coli or Klebsiella spp.…”