Intraclonal Genome Stability of the Metallo-β-lactamase SPM-1-producing ST277, an Endemic Clone Disseminated in Brazilian Hospitals

Overview

Journal Front Microbiol

Specialty Microbiology

Date 2016 Dec 21

PMID 27994579

Citations 19

Authors

Ana P B Nascimento

Mauro F Ortiz

Willames M B S Martins

Guilherme L Morais

Lorena C C Fehlberg

Luiz G P Almeida

Luciane P Ciapina

Ana C Gales

Ana T R Vasconcelos

Affiliations

Soon will be listed here.

Abstract

Carbapenems represent the mainstay therapy for the treatment of serious infections. However, the emergence of carbapenem resistance has jeopardized the clinical use of this important class of compounds. The production of SPM-1 metallo-β-lactamase has been the most common mechanism of carbapenem resistance identified in isolated from Brazilian medical centers. Interestingly, a single SPM-1-producing clone belonging to the ST277 has been widely spread within the Brazilian territory. In the current study, we performed a next-generation sequencing of six SPM-1-producing ST277 isolates. The core genome contains 5899 coding genes relative to the reference strain a PAO1. A total of 26 genomic islands were detected in these isolates. We identified remarkable elements inside these genomic islands, such as copies of the gene conferring resistance to carbapenems and a type I-C CRISPR-Cas system, which is involved in protection of the chromosome against foreign DNA. In addition, we identified single nucleotide polymorphisms causing amino acid changes in antimicrobial resistance and virulence-related genes. Together, these factors could contribute to the marked resistance and persistence of the SPM-1-producing ST277 clone. A comparison of the SPM-1-producing ST277 genomes showed that their core genome has a high level nucleotide similarity and synteny conservation. The variability observed was mainly due to acquisition of genomic islands carrying several antibiotic resistance genes.

Citing Articles

Boolean model of the gene regulatory network of CCBH4851.

Chagas M, Trindade Dos Santos M, Argollo de Menezes M, Silva F Front Microbiol. 2023; 14:1274740.

PMID: 38152377 PMC: 10752298. DOI: 10.3389/fmicb.2023.1274740.

Phenotyping and Genotyping Evaluation of Produces Carbapenemase Isolated from Cancer Patients in Al-Basrah, Iraq.

Ali Albadery A, Shakir Mahdi Al-Amara S, Abd-Al-Ridha Al-Abdullah A Arch Razi Inst. 2023; 78(3):823-829.

PMID: 38028834 PMC: 10657934. DOI: 10.22092/ARI.2022.359869.2493.

Abundant diversity of accessory genetic elements and associated antimicrobial resistance genes in pseudomonas aeruginosa isolates from a single Chinese hospital.

Mu X, Li X, Yin Z, Jing Y, Chen F, Gao H Ann Clin Microbiol Antimicrob. 2023; 22(1):51.

PMID: 37386463 PMC: 10311859. DOI: 10.1186/s12941-023-00600-3.

PorinPredict: Identification of OprD Loss from WGS Data for Improved Genotype-Phenotype Predictions of P. aeruginosa Carbapenem Resistance.

Biggel M, Johler S, Roloff T, Tschudin-Sutter S, Bassetti S, Siegemund M Microbiol Spectr. 2023; :e0358822.

PMID: 36715510 PMC: 10100854. DOI: 10.1128/spectrum.03588-22.

An updated gene regulatory network reconstruction of multidrug-resistant Pseudomonas aeruginosa CCBH4851.

Chagas M, Filho F, Trindade Dos Santos M, Argollo de Menezes M, DAlincourt Carvalho-Assef A, Silva F Mem Inst Oswaldo Cruz. 2022; 117:e220111.

PMID: 36259790 PMC: 9565603. DOI: 10.1590/0074-02760220111.

References

Hachani A, Allsopp L, Oduko Y, Filloux A . The VgrG proteins are "à la carte" delivery systems for bacterial type VI effectors. J Biol Chem. 2014; 289(25):17872-84. PMC: 4067218. DOI: 10.1074/jbc.M114.563429. View

Fonseca E, Marin M, Encinas F, Vicente A . Full characterization of the integrative and conjugative element carrying the metallo-β-lactamase bla SPM-1 and bicyclomycin bcr1 resistance genes found in the pandemic Pseudomonas aeruginosa clone SP/ST277. J Antimicrob Chemother. 2015; 70(9):2547-50. DOI: 10.1093/jac/dkv152. View

Gellatly S, Hancock R . Pseudomonas aeruginosa: new insights into pathogenesis and host defenses. Pathog Dis. 2013; 67(3):159-73. DOI: 10.1111/2049-632X.12033. View

Lehoux D, Sanschagrin F, Levesque R . Genomics of the 35-kb pvd locus and analysis of novel pvdIJK genes implicated in pyoverdine biosynthesis in Pseudomonas aeruginosa. FEMS Microbiol Lett. 2000; 190(1):141-6. DOI: 10.1111/j.1574-6968.2000.tb09276.x. View

Xavier D, Picao R, Girardello R, Fehlberg L, Gales A . Efflux pumps expression and its association with porin down-regulation and beta-lactamase production among Pseudomonas aeruginosa causing bloodstream infections in Brazil. BMC Microbiol. 2010; 10:217. PMC: 2927533. DOI: 10.1186/1471-2180-10-217. View

Almeida L, Paixao R, Souza R, Costa G, Barrientos F, dos Santos M . A System for Automated Bacterial (genome) Integrated Annotation--SABIA. Bioinformatics. 2004; 20(16):2832-3. DOI: 10.1093/bioinformatics/bth273. View

Matsui H, Sano Y, Ishihara H, Shinomiya T . Regulation of pyocin genes in Pseudomonas aeruginosa by positive (prtN) and negative (prtR) regulatory genes. J Bacteriol. 1993; 175(5):1257-63. PMC: 193209. DOI: 10.1128/jb.175.5.1257-1263.1993. View

Langmead B, Salzberg S . Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012; 9(4):357-9. PMC: 3322381. DOI: 10.1038/nmeth.1923. View

Lister P, Wolter D, Hanson N . Antibacterial-resistant Pseudomonas aeruginosa: clinical impact and complex regulation of chromosomally encoded resistance mechanisms. Clin Microbiol Rev. 2009; 22(4):582-610. PMC: 2772362. DOI: 10.1128/CMR.00040-09. View

10.

Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M . ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res. 2005; 34(Database issue):D32-6. PMC: 1347377. DOI: 10.1093/nar/gkj014. View

11.

Bezuidt O, Klockgether J, Elsen S, Attree I, Davenport C, Tummler B . Intraclonal genome diversity of Pseudomonas aeruginosa clones CHA and TB. BMC Genomics. 2013; 14:416. PMC: 3697988. DOI: 10.1186/1471-2164-14-416. View

12.

Overbeek R, Fonstein M, DSouza M, Pusch G, Maltsev N . The use of gene clusters to infer functional coupling. Proc Natl Acad Sci U S A. 1999; 96(6):2896-901. PMC: 15866. DOI: 10.1073/pnas.96.6.2896. View

13.

Robicsek A, Strahilevitz J, Jacoby G, Macielag M, Abbanat D, Park C . Fluoroquinolone-modifying enzyme: a new adaptation of a common aminoglycoside acetyltransferase. Nat Med. 2005; 12(1):83-8. DOI: 10.1038/nm1347. View

14.

Oliver A, Mulet X, Lopez-Causape C, Juan C . The increasing threat of Pseudomonas aeruginosa high-risk clones. Drug Resist Updat. 2015; 21-22:41-59. DOI: 10.1016/j.drup.2015.08.002. View

15.

Tenover F, Arbeit R, Goering R, Mickelsen P, Murray B, Persing D . Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. J Clin Microbiol. 1995; 33(9):2233-9. PMC: 228385. DOI: 10.1128/jcm.33.9.2233-2239.1995. View

16.

Mendes R, Kiyota K, Monteiro J, Castanheira M, Andrade S, Gales A . Rapid detection and identification of metallo-beta-lactamase-encoding genes by multiplex real-time PCR assay and melt curve analysis. J Clin Microbiol. 2006; 45(2):544-7. PMC: 1829038. DOI: 10.1128/JCM.01728-06. View

17.

Stover C, Pham X, Erwin A, Mizoguchi S, Warrener P, Hickey M . Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature. 2000; 406(6799):959-64. DOI: 10.1038/35023079. View

18.

Rossi F . The challenges of antimicrobial resistance in Brazil. Clin Infect Dis. 2011; 52(9):1138-43. DOI: 10.1093/cid/cir120. View

19.

Balasubramanian D, Schneper L, Merighi M, Smith R, Narasimhan G, Lory S . The regulatory repertoire of Pseudomonas aeruginosa AmpC ß-lactamase regulator AmpR includes virulence genes. PLoS One. 2012; 7(3):e34067. PMC: 3315558. DOI: 10.1371/journal.pone.0034067. View

20.

Verhoeven E, Wyman C, Moolenaar G, Goosen N . The presence of two UvrB subunits in the UvrAB complex ensures damage detection in both DNA strands. EMBO J. 2002; 21(15):4196-205. PMC: 126143. DOI: 10.1093/emboj/cdf396. View