Genetic relatedness in carbapenem-resistant isolates from clinical specimens in Ghana using ERIC-PCR technique

English version

Autoři: Francis S. Codjoe ^aff001; Charles A. Brown ^aff001; Thomas J. Smith ^aff002; Keith Miller ^aff002; Eric S. Donkor ^aff003
Působiště autorů: Department of Medical Laboratory Sciences, School of Biomedical & Allied Health Sciences, College of Health Sciences, University of Ghana, Ghana ^aff001; Biomolecular Science Research Centre, Sheffield Hallam University, Sheffield, England, United Kingdom ^aff002; Department of Medical Microbiology, School of Biomedical & Allied Health Sciences, College of Health Sciences, University of Ghana, Ghana ^aff003
Vyšlo v časopise: PLoS ONE 14(9)
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pone.0222168

Souhrn

Aim

Enterobacterial repetitive intergenic consensus (ERIC) sequence analysis is a powerful tool for epidemiological analysis of bacterial species. This study aimed to determine the genetic relatedness or variability in carbapenem-resistant isolates by species using this technique.

Methods

A total of 111 non-duplicated carbapenem-resistant (CR) Gram-negative bacilli isolates from a three-year collection period (2012–2014) were investigated by enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC–PCR) in four selected hospital laboratories in Ghana. The isolates were also screened for carbapenemase and extended spectrum β-lactamase genes by PCR.

Results

A proportion of 23.4% (26/111) of the genomic DNA extracts were carriers of PCR-positive carbapenemase genes, including 14.4% blaNDM-1, 7.2% blaVIM-1 and 1.8% blaOXA-48. The highest prevalence of carbapenemase genes was from non-fermenters, Acinetobacter baumannii and Pseudomonas aeruginosa. For the ESBL genes tested, 96.4% (107/111) of the CR isolates co-harboured both TEM-1 and SHV-1 genes. The ERIC-PCR gel analysis exhibited 1 to 8 bands ranging from 50 to 800 bp. Band patterns of 93 complex dissimilarities were visually distinguished from the 111 CR isolates studied, while the remaining 18 showed band similarities in pairs.

Conclusion

Overall, ERIC-PCR fingerprints have shown a high level of diversity among the species of Gram-negative bacterial pathogens and specimen collection sites in this study. ERIC-PCR optimisation assays may serve as a suitable genotyping tool for the assessment of genetic diversity or close relatedness of isolates that are found in clinical settings.

Klíčová slova:

Biology and life sciences – Organisms – Research and analysis methods – Molecular biology – Molecular biology techniques – Medicine and health sciences – Microbiology – Medical microbiology – Microbial pathogens – Bacterial pathogens – Pseudomonas aeruginosa – Bacteria – Pseudomonas – Pathology and laboratory medicine – Pathogens – Pharmacology – Infectious diseases – Bacterial diseases – Microbial control – Artificial gene amplification and extension – Polymerase chain reaction – Antimicrobial resistance – Acinetobacter – Acinetobacter baumannii – Genetic fingerprinting and footprinting – Genetic fingerprinting – Acinetobacter infections – Pseudomonas infections

Zdroje

1. Moosavian M, Emam N. The first report of emerging mobilized colistin-resistance (mcr) genes and ERIC-PCR typing in Escherichia coli and Klebsiella pneumoniae clinical isolates in southwest Iran. Infect Drug Resist. 2019; 12:1001–1010. doi: 10.2147/IDR.S192597 31118706

2. Londero A, Costa M, Sucari A, Leotta G. Comparison of three molecular subtyping techniques for Listeria monocytogenes. Rev Argent Microbiol. 2019 pii: S0325-7541(19)30004-5.

3. Guimarães Ade S, Dorneles EMS, Andrade GI, Lage AP, Miyoshi A, Azevedo V, et al. Molecular characterization of Corynebacterium pseudotuberculosis isolates using ERIC-PCR. Vet Microbiol. 2011; 153(3–4):99–306.

4. Munoz V, Ibanez F, Tonelli ML, Valetti L, Anzuay MS, Fabra A. Phenotypic and phylogenetic characterization of native peanut Bradyrhizobium isolates obtained from Cordoba, Argentina. Syst Appl Microbiol. 2011; 34(6):446–452. doi: 10.1016/j.syapm.2011.04.007 21742454

5. Rai S, Das D, Niranjan DK, Singh NP, Kaur IR. Carriage prevalence of carbapenem-resistant Enterobacteriaceae in stool samples: a surveillance study. Australas Med J. 2014; 7(2):64–67. doi: 10.4066/AMJ.2014.1926 24611074

6. Durmaz S, Bal EBB, Gunaydin M, Erkan Yula E, Percin D. Detection of β-lactamase genes, ERIC-PCR typing and phylogenetic groups of ESBL producing quinolone resistant clinical Escherichia coli isolates. Biomed Res-India. 2015; 26(1):43–50.

7. Bakhshi B, Afshari N, Fallah F. Enterobacterial Repetitive intergenic consensus (ERIC)-PCR Analysis as a reliable evidence for suspected Shigella spp. outbreaks. Braz J Microbiol. 2018; 49(3):529–533. doi: 10.1016/j.bjm.2017.01.014 29482996

8. Khor WC, Puah SM, Koh TH, Tan JAMA, Puthucheary SD, Chua KH. Comparison of Clinical Isolates of Aeromonas from Singapore and Malaysia with Regard to Molecular Identification, Virulence, and Antimicrobial Profiles. Microb Drug Resist. 2018; 24(4):469–478. doi: 10.1089/mdr.2017.0083 29461928

9. Sivakumar M, Dubal ZB, Kumar A, Bhilegaonkar K, Vinodh Kumar OR, Kumar S, Kadwalia A, Shagufta B, Grace MR, Ramees TP, Dwivedi A. Virulent methicillin resistant Staphylococcus aureus (MRSA) in street vended foods. J Food Sci Technol. 2019;56(3):1116–1126. doi: 10.1007/s13197-019-03572-5 30956291

10. Wei X, Jian-Zhong W, Xiao-Hui H, Zong-Jun Y, Pei S, Yu L. The research of KRG serotyping and ERIC-PCR and PCR-RFLP genotyping of Haemophilus parasuis isolates from Anhui Province of China. J Anim Vet Adv. 2011; 10(20):2669–2674.

11. Aljindan R, Alsamman K, Elhadi N. ERIC-PCR genotyping of Acinetobacter baumannii isolated from different clinical specimens. Saudi J Med Med Sci. 2018; 6:13–17. doi: 10.4103/sjmms.sjmms_138_16 30787810

12. Urban C, Segal-Maurer S, Rahal JJ. Considerations in the control and treatment of hospital infections due to Acinetobacter baumannii. Clin Infect Dis. 2003; 36(10):1268–1274. 12746772

13. Nigro SJ, Post V, Hall RM. Aminoglycoside resistance in multiply antibiotic-resistant Acinetobacter baumannii belonging to global clone 2 from Australian hospitals. J Antimicrob Chemother. 2011; 66(7):1504–1509. doi: 10.1093/jac/dkr163 21586593

14. Siqueira VLD, Cardoso RF, Pádua RAF, Caleffi-Ferracioli KR, Helbel C, Santos ACB, et al. High genetic diversity among Pseudomonas aeruginosa and Acinetobacter spp. isolated in a public hospital in Brazil. Braz. J. Pharm. Sci. 2013; 49(1):49–56.

15. Freeman R, Moore LSP, Charlett A, Donaldson H, Holmes AH. Exploring the epidemiology of carbapenem-resistant Gram-negative bacteria in west London and the utility of routinely collected hospital microbiology data. J Antimicrob Chemother. 2015; 70(4):1212–1218). doi: 10.1093/jac/dku500 25525198

16. Kateete DP, Nakanjako R, Okee M, Joloba ML, Najjuka CF. Genotypic diversity among multidrug resistant Pseudomonas aeruginosa and Acinetobacter species at Mulago Hospital in Kampala, Uganda. BMC Res Notes. 2017; 10:284. doi: 10.1186/s13104-017-2612-y 28705201

17. Armand-Lefèvre L, Angebault C, Barbier F, Hamelet E, Defrance G, Ruppé E, et al. Emergence of imipenem-resistant Gram-negative bacilli in intestinal flora of intensive care patients. Antimicrob Agents Chemother. 2013; 57(3):1488–1495. doi: 10.1128/AAC.01823-12 23318796

18. Meletis G. Carbapenem resistance: overview of the problem and future perspectives. Ther Adv Infect Dis. 2016; 3(1):15–21. doi: 10.1177/2049936115621709 26862399

19. Poirel L, Walsh TR, Cuvillier V, Nordmann P. Multiplex PCR for detection of acquired carbapenemase genes. Diagn Microbiol Infect Dis. 2011; 70:119–123. doi: 10.1016/j.diagmicrobio.2010.12.002 21398074

20. Schlesinger J, Navon-Venezia S, Chmelnitsky I, Hammer-Münz O, Leavitt A, Gold HS, et al. Extended-Spectrum Beta-Lactamases among Enterobacter Isolates Obtained in Tel Aviv, Israel. Antimicrob Agents Chemother. 2005; 49:1150–1156. doi: 10.1128/AAC.49.3.1150-1156.2005 15728917

21. Ye Y, Wu Q, Yao L, Dong X, Wu K, Zhang J. Analysis of a consensus fragment in ERIC-PCR fingerprinting of Enterobacter sakazakii. Int J Food Microbiol. 2009; 132(2–3):172–175. doi: 10.1016/j.ijfoodmicro.2009.03.018 19427046

22. Abdalhamid B, Elhadi N, Alabdulqader N, Alsamman K, Aljindan R. Rates of gastrointestinal tract colonization of carbapenem-resistant Enterobacteriaceae and Pseudomonas aeruginosa in hospitals in Saudi Arabia. New Microbes New Infect. 2016; 10(C):77–83.

23. Bassetti M, Ginocchio F, Mikulska M. New treatment options against Gram-negative organisms. Crit Care. 2011; 15(2):215. doi: 10.1186/cc9997 21457501

24. Nordmann P, Poirel L. The difficult-to-control spread of carbapenemase producers in Enterobacteriaceae worldwide. Clin Microbiol Infect. 2014; 20(9):821–830. doi: 10.1111/1469-0691.12719 24930781

25. Stehling EG, Leite DS, Silveira WD. Molecular typing and biological characteristics of Pseudomonas aeruginosa isolated from cystic fibrosis patients in Brazil. Braz J Infect Dis. 2010; 14(5):462–467. 21221474

26. Kaase M, Nordmann P, Wichelhaus TA, Gatermann SG, Bonnin RA, Poirel L. NDM-2 carbapenemase in Acinetobacter baumannii from Egypt. J Antimicrob Chemother. 2011;66(6):1260–1262. doi: 10.1093/jac/dkr135 21427107

27. Diene SM, Rolain JM. Carbapenemase genes and genetic platforms in Gram-negative bacilli: Enterobacteriaceae, Pseudomonas, and Acinetobacter species. Clin Microbiol Infect. 2014; 20(9):831–838. doi: 10.1111/1469-0691.12655 24766097

28. Mathlouthi N, Areig Z, Al Bayssari C, Bakour S, El Salabi AA, Gwierif SB, et al. Emergence of carbapenem-resistant Pseudomonas aeruginosa and Acinetobacter baumannii clinical isolates collected from some Libyan hospitals. Microb Drug Resist. 2015; 21(3): 335–341. doi: 10.1089/mdr.2014.0235 25587875

29. Hewitt KM, Mannino FL, Gonzalez A, Chase JH, Caporaso JG, Knight R, et al. Bacterial diversity in two neonatal intensive care units (NICUs). PLoS One. 2013; 8(1):e54703. doi: 10.1371/journal.pone.0054703 23372757

30. Berezin EN, Solórzano F, Latin America Working Group on Bacterial Resistance. Gram-negative infections in pediatric and neonatal intensive care units of Latin America. J Infect Dev Ctries. 2014; 8(8):942–953. doi: 10.3855/jidc.4590 25116658

31. Bush K, Jacoby GA. Updated functional classification of β-lactamases. Antimicrob Agents Chemother. 2010; 5 4(3):969–976.

32. Roca I, Espinal P, Vila-Farrés X, Vila J. The Acinetobacter baumannii oxymoron: commensal hospital dweller turned pan-drug-resistant menace. Front Microbiol. 2012; 3:148. doi: 10.3389/fmicb.2012.00148 eCollection 2012. 22536199