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Research Article

Genomic characterization of carbapenem-non-susceptible Pseudomonas aeruginosa in Singapore

ORCID Icon, , , , , , , , ORCID Icon & ORCID Icon show all
Pages 1706-1716 | Received 05 May 2021, Accepted 09 Aug 2021, Published online: 31 Aug 2021

References

  • Weiner-Lastinger LM, Abner S, Edwards JR, et al. Antimicrobial-resistant pathogens associated with adult healthcare-associated infections: summary of data reported to the national Healthcare safety network, 2015-2017. Infect Control Hosp Epidemiol. 2020 Jan;41(1):1–18.
  • Cai Y, Venkatachalam I, Tee NW, et al. Prevalence of healthcare-associated infections and antimicrobial use among adult inpatients in Singapore acute-care hospitals: results from the first national point prevalence survey. Clin Infect Dis: an official publication of the infectious diseases society of America. 2017 May 15;64(suppl_2):S61–S67.
  • Kadri SS, Adjemian J, Lai YL, et al. Difficult-to-treat resistance in gram-negative bacteremia at 173 US hospitals: retrospective cohort analysis of prevalence. Predictors, and Outcome of Resistance to All First-Line Agents. Clin Infect Dis: an official publication of the infectious diseases society of America. 2018 Nov 28;67(12):1803–1814.
  • Balkhair A, Al-Muharrmi Z, Al'Adawi B, et al. Prevalence and 30-day all-cause mortality of carbapenem-and colistin-resistant bacteraemia caused by Acinetobacter baumannii. Pseudomonas Aeruginosa, and Klebsiella Pneumoniae: description of a decade-long trend. Int J Infect Dis: official publication of the international society for infectious diseases. 2019 Aug;85:10–15.
  • Chen Z, Xu Z, Wu H, et al. The impact of carbapenem-resistant Pseudomonas aeruginosa on clinical and economic outcomes in a Chinese tertiary care hospital: a propensity score-matched analysis. Am J Infect Control. 2019 Jun;47(6):677–682.
  • Tacconelli E, Carrara E, Savoldi A, et al. Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis. Lancet Infect Dis. 2018 Mar;18(3):318–327.
  • Poole K. Pseudomonas aeruginosa: resistance to the max. Front Microbiol. 2011;2:65.
  • Quale J, Bratu S, Gupta J, et al. Interplay of efflux system, ampC, and oprD expression in carbapenem resistance of Pseudomonas aeruginosa clinical isolates. Antimicrob Agents Chemother. 2006 May;50(5):1633–1641.
  • Christaki E, Marcou M, Tofarides A. Antimicrobial resistance in bacteria: mechanisms, evolution, and persistence. J Mol Evol. 2020 Jan;88(1):26–40.
  • Tacconelli E, Sifakis F, Harbarth S, et al. Surveillance for control of antimicrobial resistance. Lancet Infect Dis. 2018 Mar;18(3):e99–e106.
  • Koh TH, Wang GCY, Sng LH. Clonal spread of IMP-1-producing Pseudomonas aeruginosa in two hospitals in Singapore. J Clin Microbiol. 2004 Nov;42(11):5378–5380.
  • Koh TH, Khoo CT, Tan TT, et al. Multilocus sequence types of carbapenem-resistant Pseudomonas aeruginosa in Singapore carrying metallo-beta-lactamase genes, including the novel bla(IMP-26) gene. J Clin Microbiol. 2010 Jul;48(7):2563–2564.
  • Chew KL, Octavia S, Ng OT, et al. Challenge of drug resistance in Pseudomonas aeruginosa: clonal spread of NDM-1-positive ST-308 within a tertiary hospital. J Antimicrob Chemother. 2019 Aug 1;74(8):2220–2224.
  • Center for Disease Control and Prevention. Antimicrobial-resistant phenotype definitions [updated 2021;19 April 2021]. Available from: https://www.cdc.gov/nhsn/pdfs/ps-analysis-resources/phenotype_definitions.pdf.
  • Teo JQ, Lim JC, Tang CY, et al. Ceftolozane/tazobactam resistance and mechanisms in carbapenem-nonsusceptible Pseudomonas aeruginosa. mSphere. 2021 Jan 27;6(1):e01026–20.
  • Clinical and Laboratory Standards Institute. Performance standards for antimicrobial susceptibility testing. 30th ed. CLSI supplement M100S. Wayne (PA); 2020.
  • Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–2120.
  • Andrews S. FastQC: a quality control tool for high throughput sequence data. Cambridge: Babraham Bioinformatics, Babraham Institute; 2010.
  • Bankevich A, Nurk S, Antipov D, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19(5):455–477.
  • Feldgarden M, Brover V, Haft DH, et al. Validating the AMRFinder tool and resistance gene database by using antimicrobial resistance genotype-phenotype correlations in a collection of isolates. Antimicrob Agents Chemother. 2019 Oct 22;63(11):e00483–19.
  • Choi Y, Chan AP. PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels. Bioinformatics. 2015 Aug 15;31(16):2745–2747.
  • Carattoli A, Zankari E, Garcia-Fernandez A, et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother. 2014 Jul;58(7):3895–3903.
  • Roosaare M, Puustusmaa M, Mols M, et al. Plasmidseeker: identification of known plasmids from bacterial whole genome sequencing reads. PeerJ. 2018;6:e4588.
  • Thrane SW, Taylor VL, Lund O, et al. Application of whole-genome sequencing data for O-specific antigen analysis and in silico serotyping of Pseudomonas aeruginosa isolates. J Clin Microbiol. 2016 Jul;54(7):1782–1788.
  • Croucher NJ, Page AJ, Connor TR, et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using gubbins. Nucleic Acids Res. 2015 Feb 18;43(3):e15.
  • Nguyen LT, Schmidt HA, von Haeseler A, et al. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015 Jan;32(1):268–274.
  • Kalyaanamoorthy S, Minh BQ, Wong TKF, et al. Modelfinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 2017 Jun;14(6):587–589.
  • Chavez-Jacobo VM, Hernandez-Ramirez KC, Romo-Rodriguez P, et al. Crpp is a novel ciprofloxacin-modifying enzyme encoded by the Pseudomonas aeruginosa pUM505 plasmid. Antimicrob Agents Chemother. 2018 May 25;62(6):e02629–17.
  • Sekizuka T, Inamine Y, Segawa T, et al. Potential KPC-2 carbapenemase reservoir of environmental Aeromonas hydrophila and Aeromonas caviae isolates from the effluent of an urban wastewater treatment plant in Japan. Environ Microbiol Rep. 2019 Aug;11(4):589–597.
  • Haines AS, Jones K, Cheung M, et al. The IncP-6 plasmid Rms149 consists of a small mobilizable backbone with multiple large insertions. J Bacteriol. 2005 Jul;187(14):4728–4738.
  • Dai X, Zhou D, Xiong W, et al. The IncP-6 plasmid p10265-KPC from Pseudomonas aeruginosa carries a novel DeltaISEc33-associated bla KPC-2 gene cluster. Front Microbiol. 2016;7:310.
  • Naas T, Bonnin RA, Cuzon G, et al. Complete sequence of two KPC-harbouring plasmids from Pseudomonas aeruginosa. J Antimicrob Chemother. 2013 Aug;68(8):1757–1762.
  • Hammer-Dedet F, Jumas-Bilak E, Licznar-Fajardo P. The hydric environment: a hub for clinically relevant carbapenemase encoding genes. Antibiotics (Basel). 2020 Oct 15;9(10):699.
  • Teo JQ, Cai Y, Lim TP, et al. Carbapenem resistance in gram-negative bacteria: the not-so-little problem in the Little Red Dot. Microorganisms. 2016 Feb 16;4(1):13.
  • Berrazeg M, Jeannot K, Ntsogo Enguene VY, et al. Mutations in beta-lactamase AmpC increase resistance of Pseudomonas aeruginosa isolates to antipseudomonal cephalosporins. Antimicrob Agents Chemother. 2015 Oct;59(10):6248–6255.
  • LoVullo ED, Schweizer HP. Pseudomonas aeruginosa mexT is an indicator of PAO1 strain integrity. J Med Microbiol. 2020 Jan;69(1):139–145.
  • Horcajada JP, Montero M, Oliver A, et al. Epidemiology and treatment of multidrug-resistant and extensively drug-resistant Pseudomonas aeruginosa infections. Clin Microbiol Rev. 2019 Aug 28;32(4):e00031–19.
  • Ranjitkar S, Reck F, Ke X, et al. Identification of mutations in the mrdA gene encoding PBP2 that reduce carbapenem and diazabicyclooctane susceptibility of Escherichia coli clinical isolates with mutations in ftsI (PBP3) and which carry bla NDM-1. mSphere. 2019 Jul 3;4(4)
  • Shu JC, Kuo AJ, Su LH, et al. Development of carbapenem resistance in Pseudomonas aeruginosa is associated with OprD polymorphisms, particularly the amino acid substitution at codon 170. J Antimicrob Chemother. 2017 Sep 1;72(9):2489–2495.
  • Del Barrio-Tofino E, Causape CL, Oliver A. Pseudomonas aeruginosa epidemic high-risk clones and their association with horizontally-acquired beta-lactamases: 2020 update. Int J Antimicrob Agents. 2020 Oct 9;106196.
  • Pirnay JP, Bilocq F, Pot B, et al. Pseudomonas aeruginosa population structure revisited. PLoS One. 2009 Nov 13;4(11):e7740.
  • Ozer EA, Nnah E, Didelot X, et al. The population structure of Pseudomonas aeruginosa is characterized by genetic isolation of exoU+ and exoS+ lineages. Genome Biol Evol. 2019 Jul 1;11(1):1780–1796.
  • Treepong P, Kos VN, Guyeux C, et al. Global emergence of the widespread Pseudomonas aeruginosa ST235 clone. Clin Microbiol Infect: the Official publication of the European society of clinical microbiology and infectious diseases. 2018 Mar;24(3):258–266.
  • Oliver A, Mulet X, Lopez-Causape C, et al. The increasing threat of Pseudomonas aeruginosa high-risk clones. Drug Resistance Updates: Reviews and Commentaries in Antimicrob Anticancer Chemother. 2015 Jul-Aug;21-22:41–59.
  • Juan C, Zamorano L, Mena A, et al. Metallo-beta-lactamase-producing Pseudomonas putida as a reservoir of multidrug resistance elements that can be transferred to successful Pseudomonas aeruginosa clones. J Antimicrob Chemother. 2010 Mar;65(3):474–478.
  • Pelegrin AC, Saharman YR, Griffon A, et al. High-risk international clones of carbapenem-nonsusceptible Pseudomonas aeruginosa endemic to Indonesian intensive care units: impact of a multifaceted infection control intervention analyzed at the genomic level. mBio. 2019 Nov 12;10(6):e02384–19.
  • Hishinuma T, Tada T, Kuwahara-Arai K, et al. Spread of GES-5 carbapenemase-producing Pseudomonas aeruginosa clinical isolates in Japan due to clonal expansion of ST235. PLoS One. 2018;13(11):e0207134.
  • Hong DJ, Bae IK, Jang IH, et al. Epidemiology and characteristics of metallo-beta-lactamase-producing Pseudomonas aeruginosa. Infect Chemother. 2015 Jun;47(2):81–97.
  • Potron A, Poirel L, Nordmann P. Emerging broad-spectrum resistance in Pseudomonas aeruginosa and Acinetobacter baumannii: mechanisms and epidemiology. Int J Antimicrob Agents. 2015 Jun;45(6):568–585.
  • Liew SM, Rajasekaram G, Puthucheary SD, et al. Detection of VIM-2-, IMP-1- and NDM-1-producing multidrug-resistant Pseudomonas aeruginosa in Malaysia. J Glob Antimicrob Resist. 2018 Jun;13:271–273.
  • Abdouchakour F, Aujoulat F, Licznar-Fajardo P, et al. Intraclonal variations of resistance and phenotype in Pseudomonas aeruginosa epidemic high-risk clone ST308: a key to success within a hospital? Internat J Med Microbiol. 2018 Mar;308(2):279–289.
  • Willmann M, Bezdan D, Zapata L, et al. Analysis of a long-term outbreak of XDR Pseudomonas aeruginosa: a molecular epidemiological study. J Antimicrob Chemother. 2015 May;70(5):1322–1330.
  • Slekovec C, Robert J, van der Mee-Marquet N, et al. Molecular epidemiology of Pseudomonas aeruginosa isolated from infected ICU patients: a French multicenter 2012-2013 study. Eur J Clin Microbiol Infect Dis. 2019 May;38(5):921–926.
  • Fournier D, Jeannot K, Robert-Nicoud M, et al. Spread of the bla(IMP-13) gene in French Pseudomonas aeruginosa through sequence types ST621, ST308 and ST111. Int J Antimicrob Agents. 2012 Dec;40(6):571–573.
  • Ling ML, How KB. Pseudomonas aeruginosa outbreak linked to sink drainage design. Healthc Infect. 2013;18(4):143–146.
  • Tan TT, Ling ML, Tan BH, et al. Multidrug resistant, blaVEB positive Pseudomonas aeruginosa causing high mortality among haematology patients. Pathologys. 2014 Dec;46(7):650–652.
  • Liakopoulos A, Mavroidi A, Katsifas EA, et al. Carbapenemase-producing Pseudomonas aeruginosa from central Greece: molecular epidemiology and genetic analysis of class I integrons. BMC Infect Dis. 2013 Oct 29;13:505.
  • Walters MS, Grass JE, Bulens SN, et al. Carbapenem-resistant Pseudomonas aeruginosa at US emerging infections program sites, 2015. Emerging Infect Dis. 2019 Jul;25(7):1281–1288.
  • De Rosa A, Mutters NT, Mastroianni CM, et al. Distribution of carbapenem resistance mechanisms in clinical isolates of XDR Pseudomonas aeruginosa. Eur J Clin Microbiol Infect Dis. 2019 Aug;38(8):1547–1552.
  • Wang W, Wang X. Prevalence of metallo-β-lactamase genes among Pseudomonas aeruginosa isolated from various clinical samples in China. J Laborat Med. 2020;0(0).