Andersson DI, Balaban NQ, Baquero F, Courvalin P, Glaser P, Gophna U, Kishony R, Molin S, Tønjum T (2020) Antibiotic resistance: turning evolutionary principles into clinical reality. FEMS Microbiol Rev 44(2):171–188. https://doi.org/10.1093/femsre/fuaa001
Article
CAS
PubMed
Google Scholar
Anjum MF (2015) Screening methods for the detection of antimicrobial resistance genes present in bacterial isolates and the microbiota. Future Microbiol 10(3):317–320. https://doi.org/10.2217/fmb.15.2
Article
CAS
PubMed
Google Scholar
Balouiri M, Sadiki M, Ibnsouda SK (2016) Methods for in vitro evaluating antimicrobial activity: a review. J Pharm Anal 6(2):71–79. https://doi.org/10.1016/j.jpha.2015.11.005
Article
PubMed
Google Scholar
Bayode MT, Alabi MA, Babatunde OJ, Sadibo ME, Lawani BT, Okiti AF, Elabiyi MO, Lawrence DI (2022) Isothermal microcalorimetry (IMC) calscreener: automated peculiarities of antimicrobial therapy and metabolism depth of multidrug resistant bacteria. Bull Natl Res Centre 46:149. https://doi.org/10.1186/s42269-022-00841-w
Article
Google Scholar
Berra L, Sampson J, Wiener-Kronish J (2010) Pseudomonas aeruginosa: acute lung injury or ventilator associated pneumonia? Minerva Anestesiol 76(10):824–832
CAS
PubMed
Google Scholar
Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S, Cattoir V, Philippon A, Allesoe RL, Rebelo AR, Florensa AF, Fagelhauer L, Chakraborty T, Neumann B, Werner G, Bender JK, Stingl K, Nguyen M, Coppens J, Xavier BB, Malhotra-Kumar S, Westh H, Pinholt M, Anjum MF, Duggett NA, Kempf I, Nykäsenoja S, Olkkola S, Wieczorek K, Amaro A, Clemente L, Mossong J, Losch S, Ragimbeau C, Lund O, Aarestrup FM (2020) ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother 75(12):3491–3500. https://doi.org/10.1093/jac/dkaa345
Article
CAS
PubMed
PubMed Central
Google Scholar
Center for Disease Control and Prevention (2009) Guidance for control of infections with carbapenem-resistant of carbapenemase-producing Enterobacteriaceae in acute care facilities. MMWR Morb Mortal Wkly Rep 58:256–260
Google Scholar
de Toro M, Rojo-Bezares B, Vinue L, Undebeitia E, Torres C, Saenz Y (2010) In vivo selection of aac(6’)-Ib-cr and mutations in the gyrA gene in clinical qnrS1-positive Salmonella enterica serovar Typhimurium DT104B strain recovered after fluoroquinolone treatment. J Antimicrob Chemother 65(9):1945–1949. https://doi.org/10.1093/jac/dkq262
Article
CAS
PubMed
Google Scholar
Gundogdu O, Bentley SD, Holden MT, Parkhill J, Dorrell N, Wren BW (2007) Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence. BMC Genom 8:162. https://doi.org/10.1186/1471-2164-8-162
Article
CAS
Google Scholar
Hancock RE (1998) Resistance mechanisms in Pseudomonas aeruginosa and other non-fermentative gram-negative bacteria. Clin Infect Dis 1:S93–S99. https://doi.org/10.1086/514909
Article
Google Scholar
Hayashi K, Morooka N, Yamamoto Y, Fujita K, Isono K, Choi S, Ohtsubo E, Baba T, Wanner BL, Mori H, Horiuchi T (2006) Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Mol Syst Biol 2(2006):0007. https://doi.org/10.1038/msb4100049
Article
PubMed
Google Scholar
Henwood CJ, Livermore DM, James D, Warner M (2001) Antimicrobial susceptibility of Pseudomonas aeruginosa: results of a UK survey and evaluation of the British Society for Antimicrobial Chemotherapy disc susceptibility test. J Antimicrob Chemother 47:789–799. https://doi.org/10.1093/jac/47.6.789
Article
CAS
PubMed
Google Scholar
Hong JS, Kim D, Kang DY, Park BY, Yang S, Yoon E, Lee H, Jeong SH (2019) Evaluation of the BD phoenix M50 automated microbiology system for antimicrobial susceptibility testing with clinical isolates in Korea. Microb Drug Resist 25(8):1142–1148. https://doi.org/10.1089/mdr.2018.0370
Article
CAS
PubMed
Google Scholar
Jayol A, Nordmann P, Lehours P, Poirel L, Dubois V (2018) Comparison of methods for detection of plasmid-mediated and chromosomally encoded colistin resistance in Enterobacteriaceae. Clin Microbiol Infect 24(2):175–179. https://doi.org/10.1089/mdr.2018.0370
Article
CAS
PubMed
Google Scholar
Mahfouz N, Ferreira I, Beisken S, von Haeseler A, Posch AE (2020) Large-scale assessment of antimicrobial resistance marker databases for genetic phenotype prediction: a systematic review. J Antimicrob Chemother 75(11):3099–3108. https://doi.org/10.1093/jac/dkaa257
Article
CAS
PubMed
PubMed Central
Google Scholar
McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA, Baylay AJ, Bhullar K, Canova MJ, De Pascale G, Ejim L, Kalan L, King AM, Koteva K, Morar M, Mulvey MR, O’Brien JS, Pawlowski AC, Piddock LJ, Spanogiannopoulos P, Sutherland AD, Tang I, Taylor PL, Thaker M, Wang W, Yan M, Yu T, Wright GD (2013) The comprehensive antibiotic resistance database. Antimicrob Agents Chemother 57(7):3348–3357. https://doi.org/10.1128/AAC.00419-13
Article
CAS
PubMed
PubMed Central
Google Scholar
Moradigaravand D, Palm M, Farewell A, Mustonen V, Warringer J, Parts L (2018) Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data. PLoS Comput Biol 14(12):e1006258. https://doi.org/10.1371/journal.pcbi.1006258
Article
ADS
CAS
PubMed
PubMed Central
Google Scholar
Ochman H, Gerber AS, Harti DL (1998) Genetic applications of an inverse polymerase chain reaction. Genetics 120(3):621–623. https://doi.org/10.1093/genetics/120.3.621
Article
Google Scholar
Ong SY, Pratap CB, Wan X, Hou S, Abdul Rahman AY, Saito JA, Nath G, Alam M (2012) Complete genome sequence of Salmonella enterica subsp. enterica serovar Typhi P-stx-12. J Bacteriol 194(8):2115–2116. https://doi.org/10.1128/JB.00121-12
Article
CAS
PubMed
PubMed Central
Google Scholar
Pedersen SK, Wagenaar JA, Vigre H, Roer L, Mikoleit M, Aidara-Kane A, Cawthorne AL, Aarestrup FM, Hendriksen RS (2018) Proficiency of WHO global foodborne infections network external quality assurance system participants in identification and susceptibility testing of thermotolerant Campylobacter spp. from 2003 to 2012. J Clin Microbiol 56(11):e01066-18. https://doi.org/10.1128/JCM.01066-18
Article
PubMed
PubMed Central
Google Scholar
Pesesky MW, Hussain T, Wallace M, Patel S, Andleeb S, Burnham CD, Dantas G (2016) Evaluation of machine learning and rules-based approaches for predicting antimicrobial resistance profiles in gram-negative bacilli from whole genome sequence data. Front Microbiol 7:1887. https://doi.org/10.3389/fmicb.2016.01887
Article
PubMed
PubMed Central
Google Scholar
Proietti PC, Guelfi G, Belluci S, De Luca S, Di Gregorio S, Pieramati C, Franciosini MP (2020) Beta-lactam resistance in Campylobacter coli and Campylobacter jejuni chicken isolates and the association between blaOXA-61 gene expression and the action of β-lactamase inhibitors. Vet Microbiol 241:108553. https://doi.org/10.1016/j.vetmic.2019.108553
Article
CAS
Google Scholar
Rozwandowicz M, Brouwer MSM, Fischer J, Wagenaar JA, Gonzalez-Zorn B, Guerra B, Mevius DJ, Hordijk J (2018) Plasmids carrying antimicrobial resistance genes in Enterobacteriaceae. J Antimicrob Chemother 73(5):1121–1137. https://doi.org/10.1093/jac/dkx488
Article
CAS
PubMed
Google Scholar
Sivaraman GK, Rajan V, Vijayan A, Elangovan R, Prendiville A, Bachmann TT (2021) Antibiotic resistance profiles and molecular characteristics of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli and Klebsiella pneumoniae isolated from shrimp aquaculture farms in Kerala, India. Front Microbiol. https://doi.org/10.3389/fmicb.2021.622891
Article
PubMed
PubMed Central
Google Scholar
Souvorov A, Agarwala R, Lipman DJ (2018) SKESA: strategic k-mer extension for scrupulous assemblies. Genome Biol 19(1):153. https://doi.org/10.1186/s13059-018-1540-z
Article
CAS
PubMed
PubMed Central
Google Scholar
Stoesser N, Batty EM, Eyre DW, Morgan M, Wyllie DH, Del Ojo EC, Johnson JR, Walker AS, Peto TE, Crook DW (2013) Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data. J Antimicrob Chemother 68(10):2234–2244. https://doi.org/10.1093/jac/dkt180
Article
CAS
PubMed
PubMed Central
Google Scholar
Stubberfield E, AbuOun M, Sayers E, O’Connor HM, Card RM, Anjum MF (2019) Use of whole genome sequencing of commensal Escherichia coli in pigs for antimicrobial resistance surveillance, United Kingdom, 2018. Euro Surveillance: Bulletin Europeen Sur Les Maladies Transmissibles = Eur Commun Dis Bull 24(50):1900136. https://doi.org/10.2807/1560-7917.ES.2019.24.50.1900136
Article
Google Scholar
Su M, Satola SW, Read TD (2019) Genome-based prediction of bacterial antibiotic resistance. J Clin Microbiol 57(3):e01405-e1418. https://doi.org/10.1128/JCM.01405-18
Article
CAS
PubMed
PubMed Central
Google Scholar
Tamma PD, Fan Y, Bergman Y, Pertea G, Kazmi AQ, Lewis S, Carroll KC, Schatz MC, Timp W, Simner PJ (2018) Applying rapid whole-genome sequencing to predict phenotypic antimicrobial susceptibility testing results among carbapenem-resistant Klebsiella pneumoniae clinical isolates. Antimicrob Agents Chemother 63(1):e01923-e2018. https://doi.org/10.1128/AAC.01923-18
Article
PubMed
PubMed Central
Google Scholar
Winsor GL, Lo R, Ho Sui SJ, Ung KS, Huang S, Cheng D, Ching WK, Hancock RE, Brinkman FS (2005) Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation. Nucleic Acids Res 33(Database issue):D338–D343. https://doi.org/10.1093/nar/gki047
Article
CAS
PubMed
Google Scholar
Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, Aarestrup FM, Larsen MV (2012) Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 67(11):2640–2644. https://doi.org/10.1093/jac/dks261
Article
CAS
PubMed
PubMed Central
Google Scholar
Zankari E, Allesøe R, Joensen KG, Cavaco LM, Lund O, Aarestrup FM (2017) PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens. J Antimicrob Chemother 72(10):2764–2768. https://doi.org/10.1093/jac/dkx217
Article
CAS
PubMed
PubMed Central
Google Scholar