The role of Gene Mutations (gyrA, parC) in Resistance to Ciprofloxacin in Clinical Isolates of Pseudomonas Aeruginosa

Background & Objective: Pseudomonas aeruginosa is an opportunistic pathogen and one of the most common causes of nosocomial infections. This bacterium's antibiotic resistance to the common fluoroquinolone antibiotics, especially ciprofloxacin, is due to mutations in the gyrA and parC genes. This study aimed to investigate the effect of the mutation in (gyrA, parC) on ciprofloxacin resistance in clinical isolates of Pseudomonas aeruginosa. Methods: A total of 140 clinical samples were collected from hospitals. The samples were identified by standard biochemical tests, and the antibiotic resistance was investigated by the disk diffusion method. DNA was extracted from 30 isolates, and PCR was performed. PCR-sequencing was carried out to assess gyrA and parC mutations in drug-resistant isolates. NCBI-Blast and MEGA7 software was used to analyze the nucleotide sequences. Results: 30 clinical isolates were 80% resistant to ciprofloxacin; meanwhile, in 21 samples, mutations were observed. 87/5% of mutations were related to gyrA (Thr83 → Ile), 79/16 % parC (Ser87 → Leu), and 4/18% (Glu91 → Lys). The antibiotic resistance to ciprofloxacin and mutations in gyrA and parC genes in resistant isolates are significantly related to each other (P<0.05). Conclusion: The mutations in the gyrA and parC genes play an essential role in resistance to ciprofloxacin in clinical isolates of Pseudomonas aeruginosa.


Introduction
Pseudomonas aeruginosa, a genus Gammaproteobacteria, belongs to the large family of Pseudomonas (1,2). In the form of biofilm, this bacterium has higher pathogenicity than planktonic (3). P. aeruginosa is the cause of 10% of common nosocomial infections (4).
Quinolones are broad-spectrum oral antibacterial agents that are widely used in therapy. They are lightweight hydrophilic molecules that inhibit DNA replication without affecting RNA or protein synthesis in susceptible bacteria. Quinolones include four generations, of which ciprofloxacin is the second one (5,6). The bactericidal effect of ciprofloxacin on resistant strains of P. aeruginosa is much more significant than other types of antibiotics that seem to treat pseudomonas-related infections (7,8). Fluoroquinolones can easily enter cells through purines, often used to treat intracellular pathogens such as Legionella pneumophila and Mycoplasma pneumoniae.
In gram-negative bacteria, DNA gyrase, and grampositive bacteria, topoisomerase IV is targeted (9,10). The resistance of P. aeruginosa to fluoroquinolones, including ciprofloxacin, can be mediated by mutations in DNA gyrase and topoisomerase IV, reducing wall permeability and increasing efflux pump expression (11)(12)(13)(14). DNA gyrase and topoisomerase IV are tetrameric enzymes with different subunits, gyrA, and parC from DNA gyrase homologous and, parC and parE from topoisomerase IV (15,16). Genetic, biochemical, and epidemiological studies show that DNA gyrase is the first target, and topoisomerase IV is the second target of fluoroquinolones (17,18). Mutations in the fluoroquinolone resistance determinant region (QR-DR) in the gyrA and parC genes are the major causes of fluoroquinolone resistance in P. aeruginosa (19,20). This study's purpose is to investigate the role of mutations in gyrA and parC genes in the development of ciprofloxacin resistance in clinical isolates.

Sample Preparation and Identification
In 2019, 140 P. aeruginosa strains were collected as cross-section individuals from patients with cystic fibrosis, urinary infections, and diabetic wounds from Imam Khomeini Hospital, Resalat Hospital, and Bouali Hospital in Tehran, Iran. Bacteria were identified from various samples, including urine, blood, wounds, pleura, CSF, and characterized using various biochemical tests, including TSI reaction, OF test, Oxidase test, Catalase test, and Sim-on citrate test following the reference protocols (19,21). The approved isolates were stored in a -70°C freezer for further testing. All tests were done in a microbiology laboratory in Islamic Azad University, Tonekabon, Mazandaran, Iran.

Antimicrobial Susceptibility
For further molecular studies, we initially selected all ciprofloxacin-resistant strains to ensure that the strains contain the potential resistance genes. Strains were incubated in LB broth overnight at 37°C. Using antibiotic disks (CONDA, Spain), include Rifampin, Trimethoprim-sulfamethoxazole, Ampicillin-sulbactam, Ciprofloxacin, Ceftriaxone, Amikacin, Imipenem, Gentamicin, Piperacillintazobactam, and Ceftazidime. Antibiotic resistance was determined based on the resistance patterns of the isolates by the disk diffusion method. A concentration of 1.5x10^8 CFU/mL of each overnight fresh culture was made individually, and an amount of 100μL were spread on Mueller-Hinton agar plates using sterile cotton swabs. Disks were placed on each plate with distinct space between to observe the inhibitory zones and incubated for another 24 h in 37°C.

Molecular Assay
The GeneMarkbio product kit extracted the DNA of 30 ciprofloxacin-resistant isolates from Taiwan. The primer sequence was examined at the NCBI website using Blast software and subsequently produced by the Danish company (Tag-Copenhagen, Denmark). The sequence and size of the primer are mentioned in Table  1 (22). Following this, PCR was performed on 30 isolates and a negative control for possible contaminations. Following that, the PCR samples were sent to BIONEER, South Korea for sequencing, and then the results were analyzed using MEGA software and NCBI. The gyrA and parC genes sequence were compared with associated locus in Pseudo-monas aeruginosa PAO1 AE004091 wild strain from NCBI GenBank as reference. Finally, the gene mutations that cause changes in the nucleotide sequence, including deletion or insertion of nucleotides, resulting in a shift in the amino acid sequence, were analyzed by MEGA7 software.

Gene name
Nucleotide sequences Band size Reference

Antibiotic Susceptibility
The antibiotic susceptibility pattern in 30 samples out of 140, which are confirmed to be ciprofloxacinresistant to P. aeruginosa using biochemical identifiers and disk diffusion assay, in random infected patients gathered from several hospitals in Tehran, as we mentioned before, showed different antibiotic resistance percentages and patterns, as shown in Figure 1. Strains were collected mostly from cystic fibrosis lungs, blood, urine, and wound samples of patients regardless of their age, medical history, or gender.

Gene Screening Results
According to the results obtained from PCR products of 30 clinical samples, as shown in Figure 2, the product size of gyrA is 460 bp, and parC is 270 bp.
Findings of frequency percentages were analyzed by descriptive statistical methods such as Chi-Square, considering that the P-value from the frequency of antibiotic resistance and susceptibility to ciprofloxacin and mutations in gyrA and parC genes (0.023) is less than 0.05. Therefore, there is a significant relationship between ciprofloxacin antibiotic resistance and mutations in gyrA and parC genes.
The point mutations in 24 ciprofloxacin-resistant isolates are as follow: 87.5% of mutations in codon 83 gyrA gene (Thr83→ Ile), 79.16% in codon 87 parC gene (Ser87 → Leu), and 4.18% in codon 91 parC gene (Glu91→Lys). Association between antibiotic susceptibility and mutations in the gyrA and parC genes in 30 clinical isolates is shown in Table 3 and Figure 3. These mutations are caused by the mismatch of nucleotides in a location of two strands (23), as shown in Figure 4. Besides, no mutations were observed in any of the sensitive isolates. The number and location of mutations in gyrA (Thr83 → Ile) and parC (Ser87 → Leu) genes were the same in 6 blood samples, 11 urine samples, and three tracheal samples. While in 1 isolate from the wound sample, a mutation in the parC gene was confirmed in codon 91 (Glu91→lys) and codon 87 (Ser87 → Leu), as shown in Table 3.

Discussion
Pseudomonas aeruginosa is the most common pathogen in the genus Pseudomonas and is the third most common nosocomial infection after Staphylococcus aureus and Escherichia coli (13,24). This opportunistic pathogen has acquired high resistance to antibiotics, causing various infections, and is responsible for one of the deadliest sepsis among gramnegative bacteria by entering the bloodstream (25)(26)(27).
In recent years, extensive use of antibiotics causes resistance to broad-spectrum antibiotics among pathogenic bacteria. Multidrug-resist-ant strains (MDR) are currently the main problem in treating nosocomial infections in different hospital wards, such as burn centers or intensive care (28)(29)(30). The mechanism of action of ciprofloxacin is inhibition of DNA gyrase and topoisomerase IV. DNA gyrase is the bacterial topoisomerase II that controls the topology of the double helix of DNA during the replication and translation process (31)(32)(33).
However, several cases of resistance of Pseudomonas isolates to this group of antibiotics have been reported. The most important mechanism of bacterial resistance to fluoroquinolones is the mutation in genes encoding DNA gyrase (gyrA) and topoisomerase IV (parC) (34).
P. aeruginosa antibiotic resistance has been the subject of many studies with different results regarding the surveys' time and geographical location. The   (37) on the clinical isolation of ciprofloxacin-resistant P. aeruginosa, mutations in codon 83 of the gyrA gene, which converts the amino acid threonine to isoleucine, and mutations in the codon 87 of the parC gene, which changes the amino acid serine to leucine, played a significant role in resistance to ciprofloxacin. In addition to the above mutations, another mutation in the parC gene changes the amino acid glutamine to lysine in the present study. The findings are almost identical, and this slight difference may be related to sample collection and time variability.
In another study in Japan by Kobayashi et al. (2013), the cause of fluoroquinolone resistance in clinical strains of P. aeruginosa was caused by mutations in the gyrA (Thr83 → Ile), parC (Ser87 → Leu) genes, and overexpression of the efflux pump. This research on mutations in gyrA and parC genes is the same as the present study (38); however, there is a noticeable difference in antibiotic resistance to Ciprofloxacin, which may be due to geographical differences and arbitrary use of antibiotics in our country.
In Denmark (2000), Shah Jalal et al. researched on fluoroquinolone-resistant isolates found that the efflux pump is more effective than studied genes in terms of developing resistance in isolates from cystic fibrosis patients (33). With few studies in other countries, it has been shown that in strains isolated from cystic fibrosis patients, mutations in the gyrA and parC genes play a less important role than efflux pumps in fluoroquinolone resistance (39).
In Lebanon in 2013, Selma et al. reported 19 mutations in the gyrA and parC genes in ciprofloxacinresistant P. aeruginosa strains (40). In Bulgaria in 2014, Estavov et al. identified mutations in gyrA, parC, and MexR, which were in the gyrA gene at codon 83, in the parC gene codons 87 and 136, and the MexR gene at codons 126 and 44. Finally, they realized that mutations in the gyrA gene were present in all ciprofloxacin-resistant strains of P. aeruginosa (41,42). In this mutation, converting the polar amino acid threonine to a non-polar amino acid and hydrophobic isoleucine gyrA (Thr83 → Ile), the structure of DNA gyrase is altered, resulting in a decrease in the enzyme's tendency to react with antibiotics, eventually leading to drug resistance (18). Several studies have been performed on the gyrA gene, resulting in mutations in codons 83 and 87, including (Thr83 → Ile), (Asp87 → Asn) and (Asp87 → Tyr) (10,26). While in the present study, only one mutation was observed in gyrA because of the dissimilarity in the type of clinical samples, time, and geographical area.

Conclusion
Based on the data obtained from other studies and present research, it was established that Pseudomonas aeruginosa, due to its genetic, is potentially receptive to a variety of genes such as transposons and plasmids, and therefore can quickly become resistant to antibiotics. Thereby, due to this organism's capabilities in acquiring resistance to various antibiotics, continuous monitoring of changes in bacterial susceptibility is essential. Improper use of antibiotics, especially fluoroquinolones, is a risk factor for this bacterium's resistance to medicine in Iran. Because P. aeruginosa is an opportunistic pathogen in hospital settings, these isolates should be detected in clinical laboratories to provide appropriate treatment for infections to prevent their spread. Regarding two genes encoding gyrA and parC that were investigated in this study, further studies should be performed on other possible genes that are involved in the development of ciprofloxacin resistance in order to achieve more comprehensive and complete results, and find better outcomes comparing phenotypic and genotypic methods.