Unrestricted access to antimicrobials over the counter coupled with the unguided use of antibiotics in developing countries especially Nigeria, has contributed in no small portion to the rapid rise in antibiotic resistance. This has negatively affected the efficacy of most antibiotics in the treatment of infections, such as UTIs. Owing to the increased patronage of fluoroquinolone antibiotics since the 2000s, there has been an uncontrollable rise in the level of resistance shown to these agents in Nigeria. This has also fueled the need for bacteria to evolve several coping mechanisms to deal with the increased exposure to these antibiotics (Lamikanra et al. 2011; Chattaway et al. 2016; Ogbolu et al. 2016).
In this study, the most frequently isolated uropathogenic bacteria were from the genus Escherichia, which accounted for 42.5% (31/73) of the ciprofloxacin-resistant uropathogens. This was followed by the genus Klebsiella with 27/73 (36.9%). Pasom et al. (2013) reported the recovery of Escherichia coli and Klebsiella spp. in samples of urinary origin obtained from a Teaching Hospital in Thailand. In their study, 49/75 (65.3%) of Klebsiella spp. obtained were resistant to quinolone antibiotic, with 22.3% (27/121) of the Escherichia coli isolates showing resistance to the quinolone antibiotic used in the study. The only difference between their study and this current study is that Klebsiella spp. occurred more frequently in their study as against Escherichia coli in this present study. Numerous studies have reported the predominance of Escherichia coli in samples of clinical origin, and they even went ahead to conclude that the organism accounts for a very high percentage of Urinary Tract Infections (UTIs).
A study carried out by Marei et al. (2019) on ESBL- and non-ESBL- producing Enterobacteriaceae from UTI reported a percentage occurrence of 61.2% of Escherichia coli, followed by Klebsiella spp., accounting for 21.8% of the total isolates obtained. This same trend of Escherichia coli and Klebsiella spp. dominating in isolates from urinary sources was observed in this study. Other bacteria notably the members of the Enterobacterales have also been recovered from samples of UTI infected patients. In a study carried out by Ezeh et al. (2017), bacteria of the genera Salmonella, Enterobacter, Serratia, Klebsiella, Escherichia and Acinetobacter were encountered from urinary sources, with Acinetobacter being prevalent. This is in concordance with this study, where all the aforementioned genera with the exception of Serratia spp., and inclusive of Citrobacter spp. were also obtained in the urine samples of patients diagnosed with UTI infections.
The occurrence of PMQR determinants in isolates obtained from urine samples of patients diagnosed with UTI has been well documented in several countries of the world. In a study carried out in Italy by Musumeci et al. (2012), the carriage of PMQR genes by uropathogenic Escherichia coli was reported, while Deepak et al. (2009), Nazik et al. (2011), Sheikh et al. (2019), Badamchi et al. (2019), Hashemizadeh et al. (2019), Kammili et al. (2020), in their respective studies have all reported the prevalence and distribution of PMQR determinants in bacteria from urinary sources in different parts of the globe. This current study reports the occurrence of PMQR genes in bacteria obtained from urine samples of patients diagnosed with UTI and attending the University College Hospital (UCH), Ibadan, South-west Nigeria, over a period of 4 months.
The qnr genes are pentapeptide proteins whose major function is the protection of the quinolone targets, topoisomerase IV and DNA gyrase. They have been reported in bacteria from different compartments including human, animal and environment (Briales et al. 2012; Chen et al. 2012). The genes which are housed on mobile genetic elements (MGE) have five major phylogenetic groups. In this present study, three qnr genes (qnrA, qnrB and qnrS) were targeted in the ciprofloxacin-resistant uropathogens. Of these three genes, qnrB was predominant, as it was detected in 32.9% of the isolates, followed by qnrS (20.5%) and qnrA (10.9%). The predominance of the qnrB among the qnr genes is consistent with the study of Badamchi et al. (2019) who reported a percentage occurrence of 41.8% of the gene, making it the most predominant PMQR gene in their study. This is in addition to the work of Nourozi et al. (2020), who reported the detection of qnr genes among Klebsiella spp. isolated from different clinical samples, including urine. The predominant quinolone resistance gene in their study was qnrB (43%), followed by qnrS (34%) and qnrA (23%). Several other studies have reported the detection of qnr- encoding genes in isolates of urinary origins. Notable among them were Nazik et al. (2011), Pasom et al. (2013), Hashemizadeh et al. (2019) and Salah et al. (2019).
The qnr genes have also been widely reported in other isolates apart from the usual suspects, Escherichia coli and Klebsiella spp., which are the major organisms extensively worked upon by most researchers. In a study by Yang et al. (2015), the detection of plasmid-mediated qnr genes was reported in Acinetobacter baumannii, with qnrB frequently occurring having been detected in 92/95 (96.8%) of the isolates obtained, while the other variants, qnrA and qnrS, were not detected. In this present study, only one of the two ciprofloxacin-resistant Acinetobacter baumannii showed the carriage of qnrB. Bacteria of the following genera: Enterobacter, Pseudomonas, Proteus, Salmonella and Citrobacter were also found to carry the targeted PMQR genes in this study. The isolation of Acinetobacter baumannii and Salmonella spp., showing the carriage of PMQR genes is in concordance with the work of Ezeh et al. (2017) who reported the isolation of Acinetobacter baumannii and Salmonella species showing the carriage of PMQR determinants from uropathogens isolated from the urine samples of asymptomatic female students in a University in Northern Nigeria.
Apart from the qnr genes which were detected in the ciprofloxacin-resistant isolates from this study, the quinolone efflux pump (qepA) was also detected in the isolates. Until 2007, when the qepA gene was detected in a clinical Escherichia coli isolate from Japan, as a novel plasmid-mediated efflux pump, no PMQR efflux pump was in existence. The gene, which is responsible for the reduction of quinolone accumulation in bacteria cell has been widely detected in many Gram-negative genera in many Asian countries and Africa, most notably Nigeria. There is a relative low occurrence of the gene in quinolone-resistant strains, and this has been largely attributed to its limited host spectrum, as a result of its newness in comparison with other PMQR genes (Chen et al. 2007, 2012; Yamane et al. 2007; Ogbolu et al. 2011). In this study, nine of the seventy-three ciprofloxacin-resistant isolates (12.3%) carried qepA gene, with eight of them identified as Escherichia coli and the ninth being Enterobacter cloacae. The frequency of occurrence of the gene in this study is higher than what was reported in some other studies on uropathogenic bacteria. Nazik et al. (2011) reported a frequency of 5.7% in their study carried out at two Turkish hospitals, while Badamchi et al. (2019) detected qepA in 7.3% of the isolates in their study. Pasom et al. (2013) on the other hand reported the absence of the gene in uropathogenic isolates obtained from a Teaching hospital in Thailand, same as Ehwarieme et al. (2021). In contrast however, Ezeh et al. (2017) reported the occurrence of the gene in 70% of the isolates obtained in their study, while Ogbolu et al. (2016) in their study on gram-negative bacteria from a Nigerian hospital reported 18.7% occurrence of qepA. There was co-occurrence of PMQR genes in thirteen of the seventy-three ciprofloxacin-resistant bacteria in this study, and this presents a rather worrisome situation, as these genes could be transmitted to bacteria in other compartments notably the environment, which could further facilitate the proliferation of quinolone resistance.