{"doi":"10.1101/2022.05.20.492874","title":"Systematic Analysis of Mobile Genetic Elements Mediating β-lactamase Gene Amplification in Non-Carbapenemase-Producing Carbapenem Resistant <i>Enterobacterales</i> Bloodstream Infections","abstract":"ABSTRACT Non-carbapenemase-producing carbapenem resistant Enterobacterales (non-CP-CRE) are increasingly recognized as important contributors to prevalent carbapenem resistant Enterobacterales (CRE) infections. However, there is limited understanding of mechanisms underlying non-CP-CRE causing invasive disease. Long- and short-read whole genome sequencing (WGS) was used to elucidate carbapenem non-susceptibility determinants in Enterobacterales bloodstream isolates at MD Anderson Cancer Center in Houston, Texas. We investigated carbapenem non-susceptible Enterobacterales (CNSE) mechanisms through a combination of phylogenetic analysis, antimicrobial resistant (AMR) gene detection/copy number quantification, porin assessment, and mobile genetic element (MGE) characterization. Most CNSE isolates sequenced were non-CP-CRE (41/79; 51.9%) whereas 25.3% (20/79) were carbapenem intermediate Enterobacterales (CIE) and 22.8% (18/79) were carbapenemase producing Enterobacterales (CPE). Statistically significant copy number variants (CNVs) of extended-spectrum β-lactamase (ESBL) genes (Wilcoxon Test; p-value &lt; 0.001) were present in both non-CP-CR E. coli (median CNV = 2.6X; n= 17) and K. pneumoniae (median CNV = 3.2X, n = 17). All non-CP-CR E. coli and K. pneumoniae had predicted reduced expression of at least one outer membrane porin gene ( i.e., ompC/ompF or ompK36/ompK35 ). Completely resolved CNSE genomes revealed that IS 26 and IS Ecp1 structures harboring bla CTX-M variants along with other AMR elements were the primary drivers of gene amplification, occurring in mostly IncFIB/IncFII plasmid contexts. MGE mediated β-lactamase gene amplifications resulted in either tandem arrays, primarily mediated by IS 26 ‘translocatable units’, or segmental duplication, typically due to IS Ecp1 ‘transposition units’. Non-CP-CRE strains were the most prevalent cause of CRE bacteremia with carbapenem non-susceptibility driven by concurrent porin loss and MGE-mediated amplification of bla CTX-M genes. IMPORTANCE Carbapenem resistant Enterobacterales (CRE) are considered urgent antimicrobial resistance (AMR) threats. The vast majority of CRE research has focused on carbapenemase producing Enterobacterales (CPE) even though non-carbapenemase-producing CRE (non-CP-CRE) comprise 50% or more of isolates in some surveillance studies. Thus, carbapenem resistance mechanisms in non-CP-CRE remain poorly characterized. To address this problem, we applied a combination of short- and long-read sequencing technologies to a cohort of CRE bacteremia isolates and used these data to unravel complex mobile genetic element structures mediating β- lactamase gene amplification. By generating complete genomes of 65 carbapenem non-susceptible Enterobacterales (CNSE) covering a genetically diverse array of isolates, our findings both generate novel insights into how non-CP-CRE overcome carbapenem treatments and provide researchers scaffolds for characterization of their own non-CP-CRE isolates. Improved recognition of mechanisms driving development of non-CP-CRE could assist with design and implementation of future strategies to mitigate the impact of these increasingly recognized AMR pathogens.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2022,"id":308777,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9515,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":869629,"name":"Anna Konovalova","orcid":"0000-0002-2238-8849","position":1,"is_corresponding":false},{"id":869630,"name":"Patrick M. McDaneld","orcid":"0000-0001-9214-9774","position":2,"is_corresponding":false},{"id":418125,"name":"Manjit Gohel","orcid":"0000-0001-5685-0723","position":3,"is_corresponding":false},{"id":870453,"name":"Benjamin Strope","orcid":null,"position":4,"is_corresponding":false},{"id":484064,"name":"Pranoti Sahasrabhojane","orcid":null,"position":5,"is_corresponding":false},{"id":1003966,"name":"CN Tran","orcid":null,"position":6,"is_corresponding":false},{"id":259008,"name":"David Greenberg","orcid":"0000-0001-8959-8640","position":7,"is_corresponding":false},{"id":254306,"name":"Jinu Kim","orcid":"0000-0002-1313-4791","position":8,"is_corresponding":false},{"id":14650,"name":"Xiaowei Zhan","orcid":"0000-0002-6249-7193","position":9,"is_corresponding":false},{"id":483385,"name":"Samuel L Aitken","orcid":"0000-0002-8659-4238","position":10,"is_corresponding":false},{"id":286578,"name":"M. Tariq Bhatti","orcid":"0000-0001-7190-5630","position":11,"is_corresponding":false},{"id":1003967,"name":"TC Savidge","orcid":null,"position":12,"is_corresponding":false},{"id":1003968,"name":"TJ Treangen","orcid":null,"position":13,"is_corresponding":false},{"id":1003969,"name":"BM Hanson","orcid":null,"position":14,"is_corresponding":false},{"id":1003970,"name":"CA Arias","orcid":null,"position":15,"is_corresponding":false},{"id":1003971,"name":"SA Shelburne","orcid":null,"position":16,"is_corresponding":false},{"id":232751,"name":"William C. Shropshire","orcid":"0000-0001-8556-3248","position":0,"is_corresponding":true}],"reference_count":69,"raw_metadata":null,"created_at":"2026-07-19T00:33:07.132912Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}