Prevalence and molecular analysis of antibiotic resistance of Pseudomonas aeruginosa isolated from clinical and environmental specimens in Basra, Iraq
Abstract
Background and Objectives: The steady increase in the spread of multidrug-resistant Pseudomonas aeruginosa (MDR) has become a major threat to the global health systems, including Iraq. This study aimed to investigate the prevalence and the molecular basis of antibiotic resistance in Pseudomonas aeruginosa isolated from clinical and environmental samples.
Materials and Methods: Pseudomonas aeruginosa strains were identified by standard microbiological procedures followed by PCR confirmation. Antibiotic susceptibility testing, for 16 antimicrobials, was conducted according to the Clinical and Laboratory Standard Institute (CLSI) standardized by disk diffusion and VITEK 2 methods. Detection of beta-lactamases (ESBLs, AmpC and carbapenemase) activities and related encoding genes was performed by using phenotypic methods and PCR technique respectively.
Results: A total of 81 clinical specimens and 14 environmental samples were positive for P. aeruginosa. Antimicrobial susceptibility test showed high rates of resistance to antipseudomonal cephalosporines (74.74 to 98.95%), aztreonam (82.11%), antipseudomonal carbapenems (68.4%), piperacillin/tazobactam (69.5%) ciprofloxacin (71.6%), and aminoglycosides (69%), with emergence of resistance to colistin (7.4%) among tested P. aeruginosa. Among the tested isolates, 69 (72.63%) strains were MDR, of which 63 (91.3%) strains were extremely drug resistance (XDR). Most of the isolated strains harbored one or more of ESBL genes (blaSHV-2a, blaCTX-M-28, blaVEB-2, blaOXA-677, blaPER) with predominant blaOXA-677, but none of the MBLs (GIM, SIM, SPM, IMP) and AmpC (FOX) genes were detected.
Conclusion: The results highlighted a high prevalence rate of MDR and XDR and emergence of colistin resistance P. aeruginosa at Basra hospitals, Iraq.
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7. Liu Q, Li X, Li W, Du X, He J-Q, Tao C, et al. Influence of carbapenem resistance on mortality of patients with Pseudomonas aeruginosa infection: a meta-analysis. Sci Rep 2015; 5: 11715.
8. Öztürk H, Ozkirimli E, Özgür A. Classification of beta-lactamases and penicillin binding proteins using Ligand-centric network models. PLoS One 2015; 10(2): e0117874.
9. Bush K, Jacoby GA. Updated functional classification of beta-lactamases. Antimicrob Agents Chemother 2010; 54: 969-976.
10. Berrazeg M, Jeannot K, Ntsogo Enguéné VY, Broutin I, Loeffert S, Fournier D, et al. Mutations in β-lactamase AmpC increase resistance of Pseudomonas aeruginosa isolates to antipseudomonal cephalosporins.
Antimicrob Agents Chemother 2015; 59: 6248-6255.
11. Rawat D, Nair D. Extended-spectrum β-lactamases in Gram negative bacteria. J Glob Infect Dis 2010; 2: 263-274.
12. Weldhagen GF, Poirel L, Nordmann P. Ambler class A extended-spectrum beta-lactamases in Pseudomonas aeruginosa: novel developments and clinical impact. Antimicrob Agents Chemother 2003; 47: 2385-2392.
13. Kang C-I, Pai H, Kim S-H, Kim H-B, Kim E-C, Oh M-D, et al. Cefepime and the inoculum effect in tests with Klebsiella pneumoniae producing plasmid-mediated AmpC-type beta-lactamase. J Antimicrob Chemother 2004; 54: 1130-1133.
14. Helfand MS, Bonomo RA. Current challenges in antimicrobial chemotherapy: the impact of extended-spectrum beta-lactamases and metallo-beta-lactamases on the treatment of resistant Gram-negative pathogens. Curr Opin Pharmacol 2005; 5: 452-458.
15. Walsh TR, Toleman MA, Poirel L, Nordmann P. Metallo-beta-lactamases: the quiet before the storm? Clin Microbiol Rev 2005; 18: 306-325.
16. Al-Khudhairy MK, Al-Shammari MMM. Prevalence of metallo-β-lactamase–producing Pseudomonas aeruginosa isolated from diabetic foot infections in Iraq. New Microbes New Infect 2020; 35: 100661.
17. Majeed HT, Aljanaby AAJ. Antibiotic susceptibility patterns and prevalence of some extended spectrum beta-lactamases Genes in Gram-negative bacteria isolated from patients infected with urinary tract infections in Al-Najaf city, Iraq. Avicenna J Med Biotechnol 2019; 11: 192-201.
18. Pitt TL, Simpson AJ. Pseudomonas aeruginosa and Burkholderia spp. In: Hawkey PM, Gillespie SH, editors. Principles and Practice of Clinical Bacteriology. Chichester: John Wiley and Sons; 2006.
19. CLSI. Performance standards for antimicrobial susceptibility testing. 29th ed. CLSI supplement M100. Wayne, PA: Clinical and Laboratory Standards Institute: 2019.
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21. Black JA, Moland ES, Thomson KS. AmpC disk test for detection of plasmid-mediated AmpC beta-lactamases in Enerobacteriaceae lacking chromosomal AmpC beta-lactamases. J Clin Microbiol 2005; 43: 3110-3113.
22. Lee K, Lim YS, Yong D, Yum JH, Chong Y. Evaluation of the Hodge test and the imipenem-EDTA double-disk synergy test for differentiating metallo-beta-lactamase-producing isolates of Pseudomonas spp. and Acinetobacter spp. J Clin Microbiol 2003; 41: 4623-4629.
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24. Ejikeugwu C, Hasson SO, Al-Mosawi RM, Alkhudhairy MK, Saki M, Ezeador C, et al. Occurrence of FOX AmpC gene among Pseudomonas aeruginosa isolates in abattoir samples from south-eastern Nigeria. Rev Med Microbiol 2020; 31: 99-103.
25. Ellington MJ, Kistler J, Livermore DM, Woodford N. Multiplex PCR for rapid detection of genes encoding acquired metallo-beta-lactamases. J Antimicrob Chemother 2007; 59: 321-322.
26. Sanchez-Villeda H, Schroeder S, Flint-Garcia S, Guill KE, Yamasaki M, McMullen MD. DNAAlignEditor: DNA alignment editor tool. BMC Bioinformatics 2008; 9: 154.
27. Jami Al-Ahmadi G, Zahmatkesh Roodsari R. Fast and specific detection of Pseudomonas Aeruginosa from other pseudomonas species by PCR. Ann Burns Fire Disasters 2016; 29: 264-267.
28. Lee S, Park Y-J, Kim M, Lee HK, Han K, Kang CS, et al. Prevalence of Ambler class A and D beta-lactamases among clinical isolates of Pseudomonas aeruginosa in Korea. J Antimicrob Chemother 2005; 56: 122-127.
29. Magiorakos A-P, Srinivasan A, Carey RB, Carmeli Y, Falagas ME, Giske CG, et al. Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Clin Microbiol Infect 2012; 18: 268-281.
30. Zarei O, Shokoohizadeh L, Hossainpour H, Alikhani MY. Molecular analysis of Pseudomonas aeruginosa isolated from clinical, environmental and cockroach sources by ERIC-PCR. BMC Res Notes 2018; 11: 668.
31. Horcajada JP, Montero M, Oliver A, Sorlí L, Luque S, Gómez-Zorrilla S, et al. Epidemiology and treatment of multidrug-resistant and extensively drug-resistant Pseudomonas aeruginosa infections. Clin Microbiol Rev 2019; 32(4): e00031-19.
32. Mirzaei B, Norouzi Bazgir Z, Goli HR, Iranpour F, Mohammadi F, Babaei R. Prevalence of multi-drug resistant (MDR) and extensively drug-resistant (XDR) phenotypes of Pseudomonas aeruginosa and Acinetobacter baumannii isolated in clinical samples from Northeast of Iran. BMC Res Notes 2020; 13: 380.
33. Ahmadian L, Haghshenas MR, Mirzaei B, Norouzi Bazgir Z, Goli HR. Distribution and molecular characterization of resistance gene cassettes containing class 1 integrons in multi-drug resistant (MDR) clinical isolates of Pseudomonas aeruginosa. Infect Drug Resist 2020; 13: 2773-2781.
34. De Almeida Silva KCF, Calomino MA, Deutsch G, De Castilho SR, De Paula GR, Esper LMR, et al. Molecular characterization of multidrug-resistant (MDR) Pseudomonas aeruginosa isolated in a burn center. Burns 2017; 43: 137-143.
35. Kishk RM, Abdalla MO, Hashish AA, Nemr NA, El Nahhas N, Alkahtani S, et al. Efflux MexAB-mediated resistance in P. aeruginosa isolated from patients with healthcare associated infections. Pathogens 2020; 9: 471.
36. Al-Orphaly M, Hadi HA, Eltayeb FK, Al-Hail H, Samuel BG, Sultan AA, et al. Epidemiology of multidrug-resistant Pseudomonas aeruginosa in the Middle East and North Africa Region. mSphere 2021; 6(3): e00202-21.
37. Kotsakis SD, Flach C-F, Razavi M, Larsson DGJ. Characterization of the first OXA-10 natural variant with increased carbapenemase activity. Antimicrob Agents Chemother 2018; 63(1): e01817-18.
38. Saderi H, Owlia P. Detection of multidrug resistant (MDR) and extremely drug resistant (XDR) P. aeruginosa isolated from patients in Tehran, Iran. Iran J Pathol 2015; 10: 265-271.
2. Lister PD, Wolter DJ, Hanson ND. Antibacterial-resistant Pseudomonas aeruginosa: clinical impact and complex regulation of chromosomally encoded resistance mechanisms. Clin Microbiol Rev 2009; 22: 582-610.
3. Bassetti M, Vena A, Croxatto A, Righi E, Guery B. How to manage Pseudomonas aeruginosa infections. Drugs Context 2018; 7: 212527.
4. Gales AC, Jones RN, Turnidge J, Rennie R, Ramphal R. Characterization of Pseudomonas aeruginosa isolates: occurrence rates, antimicrobial susceptibility patterns, and molecular typing in the global SENTRY Antimicrobial Surveillance Program, 1997-1999. Clin Infect Dis 2001; 32 Suppl 2: S146-55.
5. Barrasa-Villar JI, Aibar-Remon C, Prieto-Andres P, Mareca-Donate R, Moliner-Lahoz J. Impact on morbidity, mortality, and length of stay of hospital-acquired infections by resistant microorganisms. Clin Infect Dis 2017; 65: 644-652.
6. Righi E, Peri AM, Harris PNA, Wailan AM, Liborio M, Lane SW, 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.
7. Liu Q, Li X, Li W, Du X, He J-Q, Tao C, et al. Influence of carbapenem resistance on mortality of patients with Pseudomonas aeruginosa infection: a meta-analysis. Sci Rep 2015; 5: 11715.
8. Öztürk H, Ozkirimli E, Özgür A. Classification of beta-lactamases and penicillin binding proteins using Ligand-centric network models. PLoS One 2015; 10(2): e0117874.
9. Bush K, Jacoby GA. Updated functional classification of beta-lactamases. Antimicrob Agents Chemother 2010; 54: 969-976.
10. Berrazeg M, Jeannot K, Ntsogo Enguéné VY, Broutin I, Loeffert S, Fournier D, et al. Mutations in β-lactamase AmpC increase resistance of Pseudomonas aeruginosa isolates to antipseudomonal cephalosporins.
Antimicrob Agents Chemother 2015; 59: 6248-6255.
11. Rawat D, Nair D. Extended-spectrum β-lactamases in Gram negative bacteria. J Glob Infect Dis 2010; 2: 263-274.
12. Weldhagen GF, Poirel L, Nordmann P. Ambler class A extended-spectrum beta-lactamases in Pseudomonas aeruginosa: novel developments and clinical impact. Antimicrob Agents Chemother 2003; 47: 2385-2392.
13. Kang C-I, Pai H, Kim S-H, Kim H-B, Kim E-C, Oh M-D, et al. Cefepime and the inoculum effect in tests with Klebsiella pneumoniae producing plasmid-mediated AmpC-type beta-lactamase. J Antimicrob Chemother 2004; 54: 1130-1133.
14. Helfand MS, Bonomo RA. Current challenges in antimicrobial chemotherapy: the impact of extended-spectrum beta-lactamases and metallo-beta-lactamases on the treatment of resistant Gram-negative pathogens. Curr Opin Pharmacol 2005; 5: 452-458.
15. Walsh TR, Toleman MA, Poirel L, Nordmann P. Metallo-beta-lactamases: the quiet before the storm? Clin Microbiol Rev 2005; 18: 306-325.
16. Al-Khudhairy MK, Al-Shammari MMM. Prevalence of metallo-β-lactamase–producing Pseudomonas aeruginosa isolated from diabetic foot infections in Iraq. New Microbes New Infect 2020; 35: 100661.
17. Majeed HT, Aljanaby AAJ. Antibiotic susceptibility patterns and prevalence of some extended spectrum beta-lactamases Genes in Gram-negative bacteria isolated from patients infected with urinary tract infections in Al-Najaf city, Iraq. Avicenna J Med Biotechnol 2019; 11: 192-201.
18. Pitt TL, Simpson AJ. Pseudomonas aeruginosa and Burkholderia spp. In: Hawkey PM, Gillespie SH, editors. Principles and Practice of Clinical Bacteriology. Chichester: John Wiley and Sons; 2006.
19. CLSI. Performance standards for antimicrobial susceptibility testing. 29th ed. CLSI supplement M100. Wayne, PA: Clinical and Laboratory Standards Institute: 2019.
20. Tzelepi E, Giakkoupi P, Sofianou D, Loukova V, Kemeroglou A, Tsakris A. Detection of extended-spectrum beta-lactamases in clinical isolates of enterobacter cloacae and enterobacter aerogenes. J Clin Microbiol 2000; 38: 542-546.
21. Black JA, Moland ES, Thomson KS. AmpC disk test for detection of plasmid-mediated AmpC beta-lactamases in Enerobacteriaceae lacking chromosomal AmpC beta-lactamases. J Clin Microbiol 2005; 43: 3110-3113.
22. Lee K, Lim YS, Yong D, Yum JH, Chong Y. Evaluation of the Hodge test and the imipenem-EDTA double-disk synergy test for differentiating metallo-beta-lactamase-producing isolates of Pseudomonas spp. and Acinetobacter spp. J Clin Microbiol 2003; 41: 4623-4629.
23. Jiang X, Ni Y, Jiang Y, Yuan F, Han L, Li M, et al. Outbreak of infection caused by Enterobacter cloacae producing the novel VEB-3 beta-lactamase in China. J Clin Microbiol 2005; 43: 826-831.
24. Ejikeugwu C, Hasson SO, Al-Mosawi RM, Alkhudhairy MK, Saki M, Ezeador C, et al. Occurrence of FOX AmpC gene among Pseudomonas aeruginosa isolates in abattoir samples from south-eastern Nigeria. Rev Med Microbiol 2020; 31: 99-103.
25. Ellington MJ, Kistler J, Livermore DM, Woodford N. Multiplex PCR for rapid detection of genes encoding acquired metallo-beta-lactamases. J Antimicrob Chemother 2007; 59: 321-322.
26. Sanchez-Villeda H, Schroeder S, Flint-Garcia S, Guill KE, Yamasaki M, McMullen MD. DNAAlignEditor: DNA alignment editor tool. BMC Bioinformatics 2008; 9: 154.
27. Jami Al-Ahmadi G, Zahmatkesh Roodsari R. Fast and specific detection of Pseudomonas Aeruginosa from other pseudomonas species by PCR. Ann Burns Fire Disasters 2016; 29: 264-267.
28. Lee S, Park Y-J, Kim M, Lee HK, Han K, Kang CS, et al. Prevalence of Ambler class A and D beta-lactamases among clinical isolates of Pseudomonas aeruginosa in Korea. J Antimicrob Chemother 2005; 56: 122-127.
29. Magiorakos A-P, Srinivasan A, Carey RB, Carmeli Y, Falagas ME, Giske CG, et al. Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Clin Microbiol Infect 2012; 18: 268-281.
30. Zarei O, Shokoohizadeh L, Hossainpour H, Alikhani MY. Molecular analysis of Pseudomonas aeruginosa isolated from clinical, environmental and cockroach sources by ERIC-PCR. BMC Res Notes 2018; 11: 668.
31. Horcajada JP, Montero M, Oliver A, Sorlí L, Luque S, Gómez-Zorrilla S, et al. Epidemiology and treatment of multidrug-resistant and extensively drug-resistant Pseudomonas aeruginosa infections. Clin Microbiol Rev 2019; 32(4): e00031-19.
32. Mirzaei B, Norouzi Bazgir Z, Goli HR, Iranpour F, Mohammadi F, Babaei R. Prevalence of multi-drug resistant (MDR) and extensively drug-resistant (XDR) phenotypes of Pseudomonas aeruginosa and Acinetobacter baumannii isolated in clinical samples from Northeast of Iran. BMC Res Notes 2020; 13: 380.
33. Ahmadian L, Haghshenas MR, Mirzaei B, Norouzi Bazgir Z, Goli HR. Distribution and molecular characterization of resistance gene cassettes containing class 1 integrons in multi-drug resistant (MDR) clinical isolates of Pseudomonas aeruginosa. Infect Drug Resist 2020; 13: 2773-2781.
34. De Almeida Silva KCF, Calomino MA, Deutsch G, De Castilho SR, De Paula GR, Esper LMR, et al. Molecular characterization of multidrug-resistant (MDR) Pseudomonas aeruginosa isolated in a burn center. Burns 2017; 43: 137-143.
35. Kishk RM, Abdalla MO, Hashish AA, Nemr NA, El Nahhas N, Alkahtani S, et al. Efflux MexAB-mediated resistance in P. aeruginosa isolated from patients with healthcare associated infections. Pathogens 2020; 9: 471.
36. Al-Orphaly M, Hadi HA, Eltayeb FK, Al-Hail H, Samuel BG, Sultan AA, et al. Epidemiology of multidrug-resistant Pseudomonas aeruginosa in the Middle East and North Africa Region. mSphere 2021; 6(3): e00202-21.
37. Kotsakis SD, Flach C-F, Razavi M, Larsson DGJ. Characterization of the first OXA-10 natural variant with increased carbapenemase activity. Antimicrob Agents Chemother 2018; 63(1): e01817-18.
38. Saderi H, Owlia P. Detection of multidrug resistant (MDR) and extremely drug resistant (XDR) P. aeruginosa isolated from patients in Tehran, Iran. Iran J Pathol 2015; 10: 265-271.
| Files | ||
| Issue | Vol 15 No 1 (2023) | |
| Section | Original Article(s) | |
| DOI | https://doi.org/10.18502/ijm.v15i1.11917 | |
| Keywords | ||
| Pseudomonas aeruginosa; Multidrug resistant; Extremely drug resistant; Colistin | ||
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How to Cite
1.
Alkhulaifi Z, Mohammed K. Prevalence and molecular analysis of antibiotic resistance of Pseudomonas aeruginosa isolated from clinical and environmental specimens in Basra, Iraq. Iran J Microbiol. 2023;15(1):45-54.
