SISPA-Seq for rapid whole genome surveys of bacterial isolates

Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases
Meredith S WrightMark D Adams

Abstract

Whole genome sequencing (WGS) of large isolate collections has many applications, yet sequencing costs are still significant. We sought to develop a rapid and cost efficient WGS method to address fundamental questions in clinical microbiology. We evaluated the performance of SISPA (Sequence-Independent, Single-Primer Amplification) combined with next-generation sequencing (SISPA-Seq) of 75 clinical isolates of Acinetobacter baumannii to establish whether SISPA-Seq resulted in sufficient coverage and quality to (1) determine strain phylogenetic placement and (2) and carriage of known antibiotic resistance (AbR) genes. Strains for which whole genome sequences were available were included for validation. Two libraries for each strain were constructed from separate SISPA reactions with different barcoded primers, using genomic DNA prepared from either high quality or rapid heat-lysis preparations. SISPA-Seq resulted in a median of 65× genome coverage when reads from both primer sets were combined. Coverage and quality were sufficient for detection of AbR genes by comparison of reads to the ARG-ANNOT database and were often sufficient to distinguish between different allelic variants of the same gene. kSNP and RAxML were used to con...Continue Reading

References

Nov 25, 1995·Nucleic Acids Research·M M DeAngelisT L Hawkins
Jan 9, 2008·BMC Genomics·Appolinaire DjikengDavid J Spiro
Jun 19, 2008·Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases·H WisplinghoffH Seifert
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Nov 4, 2009·Future Virology·Appolinaire Djikeng, David Spiro
Aug 24, 2012·Science Translational Medicine·Evan S SnitkinJulia A Segre
Jun 8, 2013·Virology Journal·Jessica DepewDerrick E Fouts
Sep 27, 2013·The New England Journal of Medicine·David W EyreA Sarah Walker
Oct 23, 2013·Antimicrobial Agents and Chemotherapy·Sushim Kumar GuptaJean-Marc Rolain
Feb 11, 2014·Nature Genetics·Claire ChewapreechaStephen D Bentley
Mar 5, 2014·Journal of Virological Methods·John D NeillJulia F Ridpath
Apr 16, 2014·Proceedings of the National Academy of Sciences of the United States of America·Waleed NasserJames M Musser
Aug 7, 2014·Trends in Genetics : TIG·Claudio U KöserSharon J Peacock
Aug 27, 2014·Antimicrobial Agents and Chemotherapy·Joshua M Mitchell, David A Leonard
Nov 25, 2014·Genome Biology·Yonatan H Grad, Marc Lipsitch
Nov 25, 2014·Genome Biology·Lucy M LiChristophe Fraser

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Citations

May 22, 2016·Infectious Disease Clinics of North America·Andrea Endimiani, Michael R Jacobs
May 27, 2016·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Scott EvansRobert A Bonomo
Nov 29, 2016·Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases·M J EllingtonN Woodford
Jun 24, 2017·European Journal of Clinical Microbiology & Infectious Diseases : Official Publication of the European Society of Clinical Microbiology·F Tagini, G Greub
Feb 8, 2018·Annual Review of Medicine·Ephraim L TsalikVance G Fowler
Aug 31, 2019·Future Microbiology·Rayane RafeiMonzer Hamze

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