1887

Abstract

Carbapenems are potent broad-spectrum β-lactam antibiotics reserved for the treatment of serious infections caused by multidrug-resistant bacteria such as . The surge in resistant to carbapenems is an urgent threat, as very few treatment options remain. Resistance to carbapenems is predominantly due to the presence of carbapenemase enzymes. The assessment of 147 . isolates revealed that 32 isolates were carbapenem non-wild-type. These isolates were screened for carbapenem resistance genes using PCR. One isolate from wastewater contained the Adelaide imipenemase gene ( ) and was compared phenotypically with a highly carbapenem-resistant clinical isolate containing the gene. A further investigation of wastewater samples from various local healthcare and non-healthcare sources as well as river water, using probe-based qPCR, revealed the presence of the gene in all the samples analysed. The widespread occurrence of throughout Adelaide hinted at the possibility of more generally extensive spread of this gene than originally thought. A search revealed the presence of the gene in Asia, North America and Europe. To elucidate the identity of the organism(s) carrying the gene, shotgun metagenomic sequencing was conducted on three wastewater samples from different locations. Comparison of these nucleotide sequences with a whole-genome sequence of a isolate revealed that, unlike the genetic environment and arrangement in , the gene was not carried as part of any mobile genetic elements. A phylogenetic tree constructed with the deduced amino acid sequences of AIM-1 suggested that the potential origin of the gene in might be the non-pathogenic environmental organism, .

Funding
This study was supported by the:
  • National Health and Medical Research Council (Award GN1147538)
    • Principle Award Recipient: HenriettaVenter
  • MRFF (Award GN1152556)
    • Principle Award Recipient: HenriettaVenter
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.000715
2021-12-17
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/mgen/7/12/mgen000715.html?itemId=/content/journal/mgen/10.1099/mgen.0.000715&mimeType=html&fmt=ahah

References

  1. Walters MS, Grass JE, Bulens SN, Hancock EB, Phipps EC et al. Carbapenem-resistant Pseudomonas aeruginosa at US emerging infections program sites, 2015. Emerg Infect Dis 2019; 25:1281–1288 [View Article] [PubMed]
    [Google Scholar]
  2. Hawkey PM, Livermore DM. Carbapenem antibiotics for serious infections. Bmj 2012 [View Article] [PubMed]
    [Google Scholar]
  3. Behzadi P, Baráth Z, Gajdács M. It’s not easy being green: a narrative review on the microbiology, virulence and therapeutic prospects of multidrug-resistant Pseudomonas aeruginosa. Antibiotics (Basel) 2021; 10:42. [View Article] [PubMed]
    [Google Scholar]
  4. Nordmann P, Naas T, Poirel L. Global spread of carbapenemase-producing Enterobacteriaceae. Emerg Infect Dis 2011; 17:1791–1798 [View Article]
    [Google Scholar]
  5. Organization WH. Antimicrobial Resistance: Global Report on Surveillance World Health Organization; 2014
    [Google Scholar]
  6. Elshamy AA, Aboshanab KM. A review on bacterial resistance to carbapenems: epidemiology, detection and treatment options. Future Sci OA 2020; 6:FSO438 [View Article] [PubMed]
    [Google Scholar]
  7. Codjoe FS, Donkor ES. Carbapenem resistance: a review. Medical Sciences 2017; 6:1 [View Article]
    [Google Scholar]
  8. Tacconelli E, Carrara E, Savoldi A, Harbarth S, Mendelson M et al. Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis. Lancet Infect Dis 2018; 18:318–327 [View Article] [PubMed]
    [Google Scholar]
  9. Righi E, Peri AM, Harris PNA, Wailan AM, Liborio M et al. Global prevalence of carbapenem resistance in neutropenic patients and association with mortality and carbapenem use: systematic review and meta-analysis. J Antimicrob Chemother 2017; 72:668–677 [View Article] [PubMed]
    [Google Scholar]
  10. Bassetti M, Vena A, Croxatto A, Righi E, Guery B. How to manage Pseudomonas aeruginosa infections. Drugs Context 2018; 7:212527 [View Article] [PubMed]
    [Google Scholar]
  11. Neyestanaki DK, Mirsalehian A, Rezagholizadeh F, Jabalameli F, Taherikalani M et al. Determination of extended spectrum beta-lactamases, metallo-beta-lactamases and AmpC-beta-lactamases among carbapenem resistant Pseudomonas aeruginosa isolated from burn patients. Burns 2014; 40:1556–1561 [View Article] [PubMed]
    [Google Scholar]
  12. Poole K. Pseudomonas aeruginosa: resistance to the max. Front Microbiol 2011; 2:65 [View Article] [PubMed]
    [Google Scholar]
  13. Bonomo RA, Burd EM, Conly J, Limbago BM, Poirel L et al. Carbapenemase-producing organisms: a global scourge. Clin Infect Dis 2018; 66:1290–1297 [View Article]
    [Google Scholar]
  14. Yoon E-J, Jeong SH. Mobile carbapenemase genes in Pseudomonas aeruginosa. Front Microbiol 2021; 12:614058 [View Article] [PubMed]
    [Google Scholar]
  15. Schäfer E, Malecki M, Tellez-Castillo CJ, Pfennigwerth N, Marlinghaus L et al. Molecular surveillance of carbapenemase-producing Pseudomonas aeruginosa at three medical centres in Cologne, Germany. Antimicrob Resist Infect Control 2019; 8:1–7 [View Article]
    [Google Scholar]
  16. Sahuquillo-Arce JM, Hernández-Cabezas A, Yarad-Auad F, Ibáñez-Martínez E, Falomir-Salcedo P et al. Carbapenemases: a worldwide threat to antimicrobial therapy. WJP 2015; 4:75 [View Article]
    [Google Scholar]
  17. Bush K, Jacoby GA. Updated functional classification of beta-lactamases. Antimicrob Agents Chemother 2010; 54:969–976 [View Article] [PubMed]
    [Google Scholar]
  18. Sawa T, Kooguchi K, Moriyama K. Molecular diversity of extended-spectrum β-lactamases and carbapenemases, and antimicrobial resistance. J Intensive Care 2020; 8:13 [View Article] [PubMed]
    [Google Scholar]
  19. Pedroso MM, Waite D, Melse O, Wilson L, Mitic N et al. Broad spectrum antibiotic-degrading metallo-β-lactamases are phylogenetically diverse and widespread in the environment. bioRxiv 2019737403
    [Google Scholar]
  20. Zhao W-H, Hu Z-Q. Acquired metallo-β-lactamases and their genetic association with class 1 integrons and ISCR elements in Gram-negative bacteria. Future Microbiol 2015; 10:873–887 [View Article] [PubMed]
    [Google Scholar]
  21. Yong D, Toleman MA, Bell J, Ritchie B, Pratt R et al. Genetic and biochemical characterization of an acquired subgroup B3 metallo-β-lactamase gene, bla AIM-1, and its unique genetic context in Pseudomonas aeruginosa from Australia. Antimicrob Agents Chemother 2012; 56:6154–6159 [View Article]
    [Google Scholar]
  22. Leiros H-KS, Borra PS, Brandsdal BO, Edvardsen KSW, Spencer J et al. Crystal structure of the mobile metallo-β-lactamase AIM-1 from Pseudomonas aeruginosa: insights into antibiotic binding and the role of Gln157. Antimicrob Agents Chemother 2012; 56:4341–4353 [View Article]
    [Google Scholar]
  23. Amsalu A, Sapula SA, De Barros Lopes M, Hart BJ, Nguyen AH et al. Efflux pump-driven antibiotic and biocide cross-resistance in Pseudomonas aeruginosa isolated from different ecological niches: a case study in the development of multidrug resistance in environmental hotspots. Microorganisms 2020; 8:11 [View Article] [PubMed]
    [Google Scholar]
  24. Poirel L, Walsh TR, Cuvillier V, Nordmann P. Multiplex PCR for detection of acquired carbapenemase genes. Diagn Microbiol Infect Dis 2011; 70:119–123 [View Article] [PubMed]
    [Google Scholar]
  25. Hoban DJ, Jones RN, Yamane N, Frei R, Trilla A et al. In vitro activity of three carbapenem antibiotics. Comparative studies with biapenem (L-627), imipenem, and meropenem against aerobic pathogens isolated worldwide. Diagn Microbiol Infect Dis 1993; 17:299–305 [View Article] [PubMed]
    [Google Scholar]
  26. Quijada NM, Rodríguez-Lázaro D, Eiros JM, Hernández M. TORMES: an automated pipeline for whole bacterial genome analysis. Bioinformatics 2019; 35:4207–4212 [View Article] [PubMed]
    [Google Scholar]
  27. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article] [PubMed]
    [Google Scholar]
  28. Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol 2014; 15:R46 [View Article]
    [Google Scholar]
  29. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
    [Google Scholar]
  30. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
    [Google Scholar]
  31. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucl Acids Res 2014; 42:D206–D214 [View Article]
    [Google Scholar]
  32. Jolley KA, Maiden MCJ. BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC bioinformatics 2010; 11:1–11 [View Article] [PubMed]
    [Google Scholar]
  33. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 2012; 67:2640–2644 [View Article] [PubMed]
    [Google Scholar]
  34. Jia B, Raphenya AR, Alcock B, Waglechner N, Guo P et al. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res 2017; 45:D566–D573 [View Article] [PubMed]
    [Google Scholar]
  35. Gupta SK, Padmanabhan BR, Diene SM, Lopez-Rojas R, Kempf M et al. ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrob Agents Chemother 2014; 58:212–220 [View Article]
    [Google Scholar]
  36. Venter H, Mowla R, Ohene-Agyei T, Ma S. RND-type drug efflux pumps from Gram-negative bacteria: molecular mechanism and inhibition. Front Microbiol 2015; 6:377 [View Article] [PubMed]
    [Google Scholar]
  37. Yuan JS, Reed A, Chen F, Stewart CN. Statistical analysis of real-time PCR data. BMC bioinformatics 2006; 7:85 [View Article] [PubMed]
    [Google Scholar]
  38. Centers for Disease Control and Prevention Multiplex Real-Time PCR Detection of Klebsiella pneumoniae Carbapenemase (KPC) and New Delhi metallo-β-lactamase (NDM-1) genes; 2011
  39. Tamames J, Puente-Sánchez F. SqueezeMeta, a highly portable, fully automatic metagenomic analysis pipeline. Front Microbiol 2018; 9:3349 [View Article] [PubMed]
    [Google Scholar]
  40. Li D, Liu C-M, Luo R, Sadakane K, Lam T-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 2015; 31:1674–1676 [View Article] [PubMed]
    [Google Scholar]
  41. Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics 2011; 27:863–864 [View Article] [PubMed]
    [Google Scholar]
  42. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC bioinformatics 2010; 11:119 [View Article] [PubMed]
    [Google Scholar]
  43. Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods 2015; 12:59–60 [View Article] [PubMed]
    [Google Scholar]
  44. Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res 2016; 44:D286–D293 [View Article]
    [Google Scholar]
  45. Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000; 28:27–30 [View Article] [PubMed]
    [Google Scholar]
  46. Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY et al. Pfam: the protein families database. Nucl Acids Res 2014; 42:D222–D230 [View Article]
    [Google Scholar]
  47. Sievers F, Higgins DG. Clustal Omega for making accurate alignments of many protein sequences. Protein Sci 2018; 27:135–145 [View Article] [PubMed]
    [Google Scholar]
  48. Robert X, Gouet P. Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res 2014; 42:W320–W324 [View Article]
    [Google Scholar]
  49. Letunic I, Bork P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res 2019; 47:W256–W259 [View Article]
    [Google Scholar]
  50. Fernández L, Hancock REW. Adaptive and mutational resistance: role of porins and efflux pumps in drug resistance. Clin Microbiol Rev 2012; 25:661–681 [View Article] [PubMed]
    [Google Scholar]
  51. Shu J-C, Kuo A-J, Su L-H, Liu T-P, Lee M-H 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; 72:2489–2495 [View Article] [PubMed]
    [Google Scholar]
  52. Australian Commission on Safety and Quality in Health Care (ACSQHC) AURA 2019: Third Australian Report on Antimicrobial Use and Resistance in Human Health Sydney: ACSQHC; 2019
    [Google Scholar]
  53. Hussein Al-abedi KJ, Abd Al-Mayahi F. Molecular detection of metallo-β-lactamase genes in carbapenem-resistant isolates of Pseudomonas aeruginosa recovered from patients in Al-Diwaniyah province, Iraq. QJPS 2019; 24: [View Article]
    [Google Scholar]
  54. Chalhoub H, Sáenz Y, Rodriguez-Villalobos H, Denis O, Kahl BC et al. High-level resistance to meropenem in clinical isolates of Pseudomonas aeruginosa in the absence of carbapenemases: role of active efflux and porin alterations. Int J Antimicrob Agents 2016; 48:740–743 [View Article] [PubMed]
    [Google Scholar]
  55. Poirel L, Lebessi E, Castro M, Fèvre C, Foustoukou M et al. Nosocomial outbreak of extended-spectrum β-lactamase SHV-5-producing isolates of Pseudomonas aeruginosa in Athens, Greece. Antimicrob Agents Chemother 2004; 48:2277–2279 [View Article]
    [Google Scholar]
  56. Fischer S, Dethlefsen S, Klockgether J, Tümmler B. Phenotypic and genomic comparison of the two most common ExoU-positive Pseudomonas aeruginosa clones, PA14 and ST235. Msystems 2020; 5: [View Article] [PubMed]
    [Google Scholar]
  57. Hutinel M, Fick J, Larsson DGJ, Flach C-F. Investigating the effects of municipal and hospital wastewaters on horizontal gene transfer. Environ Pollut 2021; 276:116733 [View Article] [PubMed]
    [Google Scholar]
  58. Tacão M, Araújo S, Vendas M, Alves A, Henriques I. Shewanella species as the origin of blaOXA-48 genes: insights into gene diversity, associated phenotypes and possible transfer mechanisms. Int J Antimicrob Agents 2018; 51:340–348 [View Article] [PubMed]
    [Google Scholar]
  59. Thierry S, Macarie H, Iizuka T, Geißdörfer W, Assih EA et al. Pseudoxanthomonas mexicana sp. nov. and Pseudoxanthomonas japonensis sp. nov., isolated from diverse environments, and emended descriptions of the genus Pseudoxanthomonas Finkmann et al. 2000 and of its type species. Int J Syst Evol Microbiol 2004; 54:2245–2255 [View Article] [PubMed]
    [Google Scholar]
  60. Queenan AM, Bush K. Carbapenemases: the versatile beta-lactamases. Clin Microbiol Rev 2007; 20:440–458 [View Article] [PubMed]
    [Google Scholar]
  61. Pehrsson EC, Tsukayama P, Patel S, Mejía-Bautista M, Sosa-Soto G et al. Interconnected microbiomes and resistomes in low-income human habitats. Nature 2016; 533:212–216 [View Article] [PubMed]
    [Google Scholar]
  62. Kahan JS, Kahan FM, Goegelman R, Currie SA, Jackson M et al. Thienamycin, a new.BETA.-lactam antibiotic. I. Discovery, taxonomy, isolation and physical properties. J Antibiot 1979; 32:1–12 [View Article]
    [Google Scholar]
  63. Hussein Al-abedi KJ, Abd Al-Mayahi F. Molecular detection of metallo-β-lactamase genes in carbapenem-resistant isolates of Pseudomonas aeruginosa recovered from patients in Al-Diwaniyah province, Iraq. QJPS 2019; 24:6–11 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000715
Loading
/content/journal/mgen/10.1099/mgen.0.000715
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error