146
Shabbir MAB, Shabbir MZ, Wu Q, Mahmood S, Sajid A, Maan MK ea (2019) CRISPR-cas system: biological function in microbes and its use to treat antimicrobial resistant pathogens. Ann
Clin Microbiol Antimicrob 18:21. https://doi.org/10.1186/s12941-019-0317-x
Shah SA, Erdmann S, Mojica FJ, Garrett RA (2013) Protospacer recognition motifs: mixed identities and functional diversity. RNA Biol 10(5):891–899. https://doi.org/10.4161/rna.23764
Shah SA, Hansen NR, Garrett RA (2009) Distribution of CRISPR spacer matches in viruses and
plasmids of crenarchaeal acido thermophiles and implications for their inhibitory mechanism.
Biochem Soc Trans 37(Pt 1):23–28. https://doi.org/10.1042/BST0370023
Spencer SJ, Tamminen MV, Preheim SP, Guo MT, Briggs AW, Brito IL (2016) Massively parallel sequencing of single cells by epic PCR links functional genes with phylogenetic markers.
ISME J 10(2):427–436. https://doi.org/10.1038/ismej.2015.124
Strich JR, Chertow DS (2019) CRISPR-Cas biology and its application to infectious diseases. J
Clin Microbiol. 57(4):e01307-18. https://doi.org/10.1128/JCM.01307-18
Strong A, Musunuru K (2016) Genome editing in cardiovascular diseases. Nat Rev Cardiol
14:11–20. https://doi.org/10.1038/nrcardio.2016.139
Swarts DC, Mosterd C, Van Passel MW, Mark WJ, Brouns SJ (2012) CRISPR interference directs
strand specific spacer acquisition. PLoS One 7(4):e35888. https://doi.org/10.1371/journal.
pone.0035888
Terns MP, Terns RM (2011) CRISPR-based adaptive immune systems. Curr Opin Microbiol
14(3):321–327. https://doi.org/10.1016/j.mib.2011.03.005
Thomas CM, Nielsen KM (2005) Mechanisms of, and barriers to, horizontal gene transfer between
bacteria. Nat Rev Microbiol 3(9):711–721. https://doi.org/10.1038/nrmicro1234
Theriot CM, Koenigsknecht MJ, Carlson PE, Hatton GE, Nelson AM, Li B et al (2014) Antibioticinduced shifts in the mouse gut microbiome and metabolome increase susceptibility to
Clostridium difficile infection. Nat Commun 5:3114. https://doi.org/10.1038/ncomms4114
Tsai SQ, Zheng Z, Nguyen NT, Liebers M, Topkar VV, Thapar V, Wyvekens N, Khayter C et al
(2015) GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas
nucleas. Nat Biotechnol 33(2):187–197. https://doi.org/10.1038/nbt.3117
Tyson GW, Banfield JF (2008) Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. Environ Microbiol 10(1):200–207. https://doi.
org/10.1111/j.1462-2920.2007.01444.x
Vercoe RB, Chang JT, Dy RL, Taylor C, Gristwood T, Clulow JS et al (2013) Cytotoxic chromosomal targeting by CRISPR/Cas systems can reshape bacterial genomes and expel or
remodel pathogenicity islands. PLoS Genet 9(4):e1003454. https://doi.org/10.1371/journal.
pgen.1003454
Vikesland P, Garner E, Gupta S, Kang S, Maile-Moskowitz A, Zhu N (2019) Differential drivers of antimicrobial resistance across the world. Acc Chem Res 52(4):916–924. https://doi.
org/10.1021/acs.accounts.8b00643
Waters LS, Storz G (2009) Regulatory RNAs in bacteria. Cell 136(4):615–628. https://doi.
org/10.1016/j.cell.2009.01.043
Wu ZY, Huang YT, Chao WC, Ho SP, Cheng JF, Liu PY (2019) Reversal of carbapenem- resistance
in Shewanella algae by CRISPR/Cas9 genome editing. doi: https://doi.org/10.1016/j.
jare.2019.01.011.
Yosef I, Goren MG, Qimron U (2012) Proteins and DNA elements essential for the CRISPR
adaptation process in Escherichia coli. Nucleic Acids Res 40(12):5569–5576. https://doi.
org/10.1093/nar/gks216
Zhang Y, Ge X, Yang F, Zhang L, Zheng J, Tan X et al (2014a) Comparison of non-canonical
PAMs for CRISPR/Cas9-mediated DNA cleavage in human cells. Sci Rep 4:5405. https://doi.
org/10.1038/srep05405
Zhang F, Wen Y, Guo X (2014b) CRISPR/Cas9 for genome editing: progress, implications and
challenges. Hum Mol Genet 23(R1):R406. https://doi.org/10.1093/hmg/ddu125
A. P. Sarma et al.
Shabbir MAB, Shabbir MZ, Wu Q, Mahmood S, Sajid A, Maan MK ea (2019) CRISPR-cas system: biological function in microbes and its use to treat antimicrobial resistant pathogens. Ann
Clin Microbiol Antimicrob 18:21. https://doi.org/10.1186/s12941-019-0317-x
Shah SA, Erdmann S, Mojica FJ, Garrett RA (2013) Protospacer recognition motifs: mixed identities and functional diversity. RNA Biol 10(5):891–899. https://doi.org/10.4161/rna.23764
Shah SA, Hansen NR, Garrett RA (2009) Distribution of CRISPR spacer matches in viruses and
plasmids of crenarchaeal acido thermophiles and implications for their inhibitory mechanism.
Biochem Soc Trans 37(Pt 1):23–28. https://doi.org/10.1042/BST0370023
Spencer SJ, Tamminen MV, Preheim SP, Guo MT, Briggs AW, Brito IL (2016) Massively parallel sequencing of single cells by epic PCR links functional genes with phylogenetic markers.
ISME J 10(2):427–436. https://doi.org/10.1038/ismej.2015.124
Strich JR, Chertow DS (2019) CRISPR-Cas biology and its application to infectious diseases. J
Clin Microbiol. 57(4):e01307-18. https://doi.org/10.1128/JCM.01307-18
Strong A, Musunuru K (2016) Genome editing in cardiovascular diseases. Nat Rev Cardiol
14:11–20. https://doi.org/10.1038/nrcardio.2016.139
Swarts DC, Mosterd C, Van Passel MW, Mark WJ, Brouns SJ (2012) CRISPR interference directs
strand specific spacer acquisition. PLoS One 7(4):e35888. https://doi.org/10.1371/journal.
pone.0035888
Terns MP, Terns RM (2011) CRISPR-based adaptive immune systems. Curr Opin Microbiol
14(3):321–327. https://doi.org/10.1016/j.mib.2011.03.005
Thomas CM, Nielsen KM (2005) Mechanisms of, and barriers to, horizontal gene transfer between
bacteria. Nat Rev Microbiol 3(9):711–721. https://doi.org/10.1038/nrmicro1234
Theriot CM, Koenigsknecht MJ, Carlson PE, Hatton GE, Nelson AM, Li B et al (2014) Antibioticinduced shifts in the mouse gut microbiome and metabolome increase susceptibility to
Clostridium difficile infection. Nat Commun 5:3114. https://doi.org/10.1038/ncomms4114
Tsai SQ, Zheng Z, Nguyen NT, Liebers M, Topkar VV, Thapar V, Wyvekens N, Khayter C et al
(2015) GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas
nucleas. Nat Biotechnol 33(2):187–197. https://doi.org/10.1038/nbt.3117
Tyson GW, Banfield JF (2008) Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. Environ Microbiol 10(1):200–207. https://doi.
org/10.1111/j.1462-2920.2007.01444.x
Vercoe RB, Chang JT, Dy RL, Taylor C, Gristwood T, Clulow JS et al (2013) Cytotoxic chromosomal targeting by CRISPR/Cas systems can reshape bacterial genomes and expel or
remodel pathogenicity islands. PLoS Genet 9(4):e1003454. https://doi.org/10.1371/journal.
pgen.1003454
Vikesland P, Garner E, Gupta S, Kang S, Maile-Moskowitz A, Zhu N (2019) Differential drivers of antimicrobial resistance across the world. Acc Chem Res 52(4):916–924. https://doi.
org/10.1021/acs.accounts.8b00643
Waters LS, Storz G (2009) Regulatory RNAs in bacteria. Cell 136(4):615–628. https://doi.
org/10.1016/j.cell.2009.01.043
Wu ZY, Huang YT, Chao WC, Ho SP, Cheng JF, Liu PY (2019) Reversal of carbapenem- resistance
in Shewanella algae by CRISPR/Cas9 genome editing. doi: https://doi.org/10.1016/j.
jare.2019.01.011.
Yosef I, Goren MG, Qimron U (2012) Proteins and DNA elements essential for the CRISPR
adaptation process in Escherichia coli. Nucleic Acids Res 40(12):5569–5576. https://doi.
org/10.1093/nar/gks216
Zhang Y, Ge X, Yang F, Zhang L, Zheng J, Tan X et al (2014a) Comparison of non-canonical
PAMs for CRISPR/Cas9-mediated DNA cleavage in human cells. Sci Rep 4:5405. https://doi.
org/10.1038/srep05405
Zhang F, Wen Y, Guo X (2014b) CRISPR/Cas9 for genome editing: progress, implications and
challenges. Hum Mol Genet 23(R1):R406. https://doi.org/10.1093/hmg/ddu125
A. P. Sarma et al.