Genomic surveillance of multidrug-resistant organisms based on long-read sequencing

Background Multidrug-resistant organisms (MDRO) pose a significant threat to public-health world-wide. The ability to identify antimicrobial resistance determinants, to assess changes in molecular types, and to detect transmission are essential for effective surveillance and infection prevention of MDRO. Molecular characterization based on long-read sequencing has emerged as a promising alternative to short-read sequencing. The aim of this study was to rapidly and accurately characterize MDRO for surveillance and transmission studies based on long-read sequencing only. Methods Genomic DNA of 356 MDRO was automatically extracted using the Maxwell-RSC48. The MDRO included 106 Klebsiella pneumoniae isolates, 85 Escherichia coli , 15 Enterobacter cloacae complex, 10 Citrobacter freundii , 34 Pseudomonas aeruginosa , 16 Acinetobacter baumannii , and 69 methicillin-resistant Staphylococcus aureus (MRSA), of which 24 were from an outbreak. MDRO were sequenced using both short-read (Illumina NextSeq 550) and long-read (Nanopore Rapid Barcoding Kit-24-V14, R10.4.1) whole-genome sequencing (WGS). Basecalling was performed for two distinct models using Dorado-0.3.2 duplex mode. Long-read data was assembled using Flye, Canu, Miniasm, Unicycler, Necat, Raven and Redbean assemblers. Long-read WGS data with >40x coverage was used for multi-locus sequence typing (MLST), whole-genome MLST (wgMLST), in silico multiple locus variable-number of tandem repeat analysis (iMLVA) for MRSA, and identification of resistance genes (Abricate). Results Comparison of wgMLST profiles based on long-read and short-read WGS data revealed >95% of wgMLST profiles within the species-specific cluster cut-off, except for P. aeruginosa. The wgMLST profiles obtained by long-read and short-read WGS differed only one to nine wgMLST alleles for K. pneumoniae , E. coli , E. cloacae complex, C. freundii , A. baumannii complex and MRSA. For P. aeruginosa differences were up to 27 wgMLST alleles between long-read and short-read wgMLST. MLST sequence types and in silico MLVA types were concordant between long-read and short-read WGS data and conventional MLVA typing. Antimicrobial resistance genes were detected in long-read sequencing data with high sensitivity/specificity (92-100%/99-100%). Long-read sequencing enabled analysis of an MRSA outbreak. Conclusions We demonstrate that molecular characterization of automatically extracted DNA followed by long-read sequencing is as accurate and more cost-effective compared to short-read sequencing. Long-read sequencing is suitable for molecular typing and outbreak analysis as part of genomic surveillance of MDRO. However, the analysis of P. aeruginosa requires further improvement which may be obtained by other basecalling algorithms. The low implementation costs, low price per isolate, and rapid library preparation for long-read sequencing of MDRO extends its applicability to resource-constrained settings and low-income countries world-wide. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This research was funded by the Dutch Ministry of Health, Welfare and Sport (V/150302/22/BR). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes