Advertisement

Epidemiological investigation of Pseudomonas aeruginosa isolates including multidrug-resistant serogroup O12 isolates, by use of a rapid and simplified multiple-locus variable-number of tandem repeats analysis and whole genome sequencing

Published:September 28, 2022DOI:https://doi.org/10.1016/j.jhin.2022.09.012

      Summary

      Background

      Clustered cases of Pseudomonas aeruginosa infection in immunocompromised patients' wards require rapid characterization of a potential epidemic to guide investigations and identify the potential source of contamination.

      Aim

      To design and evaluate a rapid and simple typing method for P. aeruginosa in comparison to whole genome sequencing (WGS).

      Methods

      A simplified polymerase chain reaction based on multiple-locus variable-number of tandem repeats analysis (MLVA) was designed and used to investigate cases of P. aeruginosa infection and colonization in a paediatric haematology department. The method was compared to WGS by using the Illumina method.

      Findings

      On the 17 isolates recovered from 15 children (eight from blood cultures, three from urinary tract infections, one from sputum and five stool isolates), MLVA distinguished 10 different profiles, and seven isolates from six children shared the same profile. Analysis by WGS revealed that these seven isolates belonged to sequence type ST111 and serotype O12, allowing at least three different genotypes to be distinguished among them. Five environmental strains had three MLVA profiles; one was shared with a clinical isolate but WGS excluded any relationship.

      Conclusion

      The simplified and inexpensive MLVA method enabled the exclusion, in less than 5 h, of most of the unrelated isolates and thus to focus investigations on a small number of cases, whereas WGS, taking several days of work, drew definitive conclusions concerning the outbreak and the genetic relationships of the ST111 isolates circulating in the department. We conclude that sequential use of both methods is the optimal strategy to investigate clustered cases of P. aeruginosa infections.

      Keywords

      To read this article in full you will need to make a payment

      Purchase one-time access:

      Academic & Personal: 24 hour online accessCorporate R&D Professionals: 24 hour online access
      One-time access price info
      • For academic or personal research use, select 'Academic and Personal'
      • For corporate R&D use, select 'Corporate R&D Professionals'

      Subscribe:

      Subscribe to Journal of Hospital Infection
      Already a print subscriber? Claim online access
      Already an online subscriber? Sign in
      Institutional Access: Sign in to ScienceDirect

      References

        • Stover C.K.
        • Pham X.Q.
        • Erwin A.L.
        • Mizoguchi S.D.
        • Warrener P.
        • Hickey M.J.
        • et al.
        Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen.
        Nature. 2000; 406: 959-964https://doi.org/10.1038/35023079
        • Oliver A.
        • Mulet X.
        • López-Causapé C.
        • Juan C.
        The increasing threat of Pseudomonas aeruginosa high-risk clones.
        Drug Resist Updat. 2015; 21–22: 41-59https://doi.org/10.1016/j.drup.2015.08.002
        • Slekovec C.
        • Robert J.
        • van der Mee-Marquet N.
        • Berthelot P.
        • Rogues A.-M.
        • Derouin V.
        • 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; 38: 921-926https://doi.org/10.1007/s10096-019-03519-w
        • Bicking Kinsey C.
        • Koirala S.
        • Solomon B.
        • Rosenberg J.
        • Robinson B.F.
        • Neri A.
        • et al.
        Pseudomonas aeruginosa outbreak in a neonatal intensive care unit attributed to hospital tap water.
        Infect Control Hosp Epidemiol. 2017; 38: 801-808https://doi.org/10.1017/ice.2017.87
        • Buttery J.P.
        • Alabaster S.J.
        • Heine R.G.
        • Scott S.M.
        • Crutchfield R.A.
        • Bigham A.
        • et al.
        Multiresistant Pseudomonas aeruginosa outbreak in a pediatric oncology ward related to bath toys.
        Pediatr Infect Dis J. 1998; 17: 509-513https://doi.org/10.1097/00006454-199806000-00015
        • Decraene V.
        • Ghebrehewet S.
        • Dardamissis E.
        • Huyton R.
        • Mortimer K.
        • Wilkinson D.
        • et al.
        An outbreak of multidrug-resistant Pseudomonas aeruginosa in a burns service in the North of England: challenges of infection prevention and control in a complex setting.
        J Hosp Infect. 2018; 100: e239-e245https://doi.org/10.1016/j.jhin.2018.07.012
        • Gbaguidi-Haore H.
        • Varin A.
        • Cholley P.
        • Thouverez M.
        • Hocquet D.
        • Bertrand X.
        A bundle of measures to control an outbreak of Pseudomonas aeruginosa associated with P-Trap contamination.
        Infect Control Hosp Epidemiol. 2018; 39: 164-169https://doi.org/10.1017/ice.2017.304
        • Lanini S.
        • D’Arezzo S.
        • Puro V.
        • Martini L.
        • Imperi F.
        • Piselli P.
        • et al.
        Molecular epidemiology of a Pseudomonas aeruginosa hospital outbreak driven by a contaminated disinfectant-soap dispenser.
        PloS One. 2011; 6e17064https://doi.org/10.1371/journal.pone.0017064
        • Weng M.K.
        • Brooks R.B.
        • Glowicz J.
        • Keckler M.S.
        • Christensen B.E.
        • Tsai V.
        • et al.
        Outbreak investigation of Pseudomonas aeruginosa infections in a neonatal intensive care unit.
        Am J Infect Control. 2019; 47: 1148-1150https://doi.org/10.1016/j.ajic.2019.03.009
        • Dekker J.P.
        • Frank K.M.
        Next-generation epidemiology: using real-time core genome multilocus sequence typing to support infection control policy.
        J Clin Microbiol. 2016; 54: 2850-2853https://doi.org/10.1128/JCM.01714-16
        • Schürch A.C.
        • Arredondo-Alonso S.
        • Willems R.J.L.
        • Goering R.V.
        Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene-based approaches.
        Clin Microbiol Infect. 2018; 24: 350-354https://doi.org/10.1016/j.cmi.2017.12.016
        • Sobral D.
        • Mariani-Kurkdjian P.
        • Bingen E.
        • Vu-Thien H.
        • Hormigos K.
        • Lebeau B.
        • et al.
        A new highly discriminatory multiplex capillary-based MLVA assay as a tool for the epidemiological survey of Pseudomonas aeruginosa in cystic fibrosis patients.
        Eur J Clin Microbiol Infect Dis. 2012; 31: 2247-2256https://doi.org/10.1007/s10096-012-1562-5
        • Lalancette C.
        • Charron D.
        • Laferrière C.
        • Dolcé P.
        • Déziel E.
        • Prévost M.
        • et al.
        Hospital drains as reservoirs of Pseudomonas aeruginosa: multiple-locus variable-number of tandem repeats analysis genotypes recovered from faucets, sink surfaces and patients.
        Pathog Basel Switz. 2017; 6: 36https://doi.org/10.3390/pathogens6030036
        • Wang H.
        • Qi M.
        • Cutler A.J.
        A simple method of preparing plant samples for PCR.
        Nucleic Acids Res. 1993; 21: 4153-4154https://doi.org/10.1093/nar/21.17.4153
        • Curran B.
        • Jonas D.
        • Grundmann H.
        • Pitt T.
        • Dowson C.G.
        Development of a multilocus sequence typing scheme for the opportunistic pathogen Pseudomonas aeruginosa.
        J Clin Microbiol. 2004; 42: 5644-5649https://doi.org/10.1128/JCM.42.12.5644-5649.2004
        • Jolley K.A.
        • Bray J.E.
        • Maiden M.C.J.
        Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications.
        Wellcome Open Res. 2018; 3: 124https://doi.org/10.12688/wellcomeopenres.14826.1
        • Raymond C.K.
        • Sims E.H.
        • Kas A.
        • Spencer D.H.
        • Kutyavin T.V.
        • Ivey R.G.
        • et al.
        Genetic variation at the O-antigen biosynthetic locus in Pseudomonas aeruginosa.
        J Bacteriol. 2002; 184: 3614-3622https://doi.org/10.1128/jb.184.13.3614-3622.2002
        • Kaas R.S.
        • Leekitcharoenphon P.
        • Aarestrup F.M.
        • Lund O.
        Solving the problem of comparing whole bacterial genomes across different sequencing platforms.
        PloS One. 2014; 9: e104984https://doi.org/10.1371/journal.pone.0104984
        • Snyder L.A.
        • Loman N.J.
        • Faraj L.A.
        • Levi K.
        • Weinstock G.
        • Boswell T.C.
        • et al.
        Epidemiological investigation of Pseudomonas aeruginosa isolates from a six-year-long hospital outbreak using high-throughput whole genome sequencing.
        Euro Surveill. 2013; 18: 20611https://doi.org/10.2807/1560-7917.es2013.18.42.20611
        • Robicsek A.
        • Strahilevitz J.
        • Jacoby G.A.
        • Macielag M.
        • Abbanat D.
        • Park C.H.
        • et al.
        Fluoroquinolone-modifying enzyme: a new adaptation of a common aminoglycoside acetyltransferase.
        Nat Med. 2006; 12: 83-88https://doi.org/10.1038/nm1347
        • Ocampo-Sosa A.A.
        • Cabot G.
        • Rodríguez C.
        • Roman E.
        • Tubau F.
        • Macia M.D.
        • et al.
        Alterations of OprD in carbapenem-intermediate and -susceptible strains of Pseudomonas aeruginosa isolated from patients with bacteremia in a Spanish multicenter study.
        Antimicrob Agents Chemother. 2012; 56: 1703-1713https://doi.org/10.1128/AAC.05451-11
        • Sawa T.
        • Momiyama K.
        • Mihara T.
        • Kainuma A.
        • Kinoshita M.
        • Moriyama K.
        Molecular epidemiology of clinically high-risk Pseudomonas aeruginosa strains: practical overview.
        Microbiol Immunol. 2020; 64: 331-344https://doi.org/10.1111/1348-0421.12776
        • Speert D.P.
        Molecular epidemiology of Pseudomonas aeruginosa.
        Front Biosci J Virtual Libr. 2002; 7: e354-e361
        • Caméléna F.
        • Birgy A.
        • Smail Y.
        • Courroux C.
        • Mariani-Kurkdjian P.
        • Le Hello S.
        • et al.
        Rapid and simple universal Escherichia coli genotyping method based on multiple-locus variable-number tandem-repeat analysis using single-tube multiplex PCR and standard gel electrophoresis.
        Appl Environ Microbiol. 2019; 85https://doi.org/10.1128/AEM.02812-18
        • Feng W.
        • Sun F.
        • Wang Q.
        • Xiong W.
        • Qiu X.
        • Dai X.
        • et al.
        Epidemiology and resistance characteristics of Pseudomonas aeruginosa isolates from the respiratory department of a hospital in China.
        J Glob Antimicrob Resist. 2017; 8: 142-147https://doi.org/10.1016/j.jgar.2016.11.012
        • Roy Chowdhury P.
        • Scott M.J.
        • Djordjevic S.P.
        Genomic islands 1 and 2 carry multiple antibiotic resistance genes in Pseudomonas aeruginosa ST235, ST253, ST111 and ST175 and are globally dispersed.
        J Antimicrob Chemother. 2017; 72: 620-622https://doi.org/10.1093/jac/dkw471