Antibiogram of clinical isolates from primary and secondary healthcare facilities: A step towards antimicrobial stewardship

The discovery and development of antimicrobial agents has significantly changed the negative narrative of how infectious diseases has plagued the human race over history. However, due to slow pace at which these agents are developed and the emergence of resistance to antimicrobials, treating common pathogens has become a challenge. Different types of resistance have developed over time resulting in their classification as multidrug resistance MDR, extended resistance (XDR) and Pandrug resistance (PDR) [1].

There is an increasing prevalence of pathogenic multidrug-resistant bacteria globally. Infections with multidrug-resistant bacteria are hard to treat since fewer or no treatment options remain. In some cases, health care providers have to use antibiotics that are more toxic for the patient resulting in increased duration of illness and prolonged hospital stay, excess costs, number of complications, and deaths. Data from U.S intensive care unit studies and surveillance studies estimate that by 2050, 10 million deaths are projected to occur due to antimicrobial resistance (AMR), while another study projected AMR to cost the global economy US$100 trillion, in the same period [2, 3]. Against this backdrop, the World Health Organization (WHO) On 27 February 2017, published the list of global priority pathogens (GPP)–a catalog developed through a consultative process [4, 5]. The most critical organisms in this catalog includes multidrug resistant bacteria that pose a particular threat in hospitals, nursing homes, and among patients whose care requires devices such as ventilators and blood catheters. They include Acinetobacter, Pseudomonas and various Enterobacteriaceae (including Klebsiella, E. coli, Serratia, and Proteus) [4].

The World Health Organization (WHO) emphasizes the key role of the microbiology laboratory in antimicrobial stewardship (AMS) by informing the appropriate use of antibiotics through development of antibiograms [6]. Comprehensive data on the antibiogram of bacterial pathogens isolated from different body sites of infections is needed for surveillance systems which aid in monitoring antimicrobial use and resistance thus improving decision making and assessing the effect of interventions at the local, national and international level. There is scarcity of such data in developing countries including Nigeria [7]. Networking between laboratories may increase infection surveillance within a huge geographical region. The WHO supports the establishment of national networks for the regular exchange of information and proper support for the laboratory. However, only a few countries have local, national and international laboratory networks. The establishment of an integrated laboratory system is very important to combat many infectious diseases. In Low- Middle- Income- Countries (LMICs), there are few or no documented data on the bacterial isolates and antibiogram profiles in healthcare facilities even at local level and integrated systems are financially neglected in developing countries [8]. Therefore, this study aims to determine the epidemiology of microbial isolates, to appraise and compare the antibiogram and resistogram in secondary and primary healthcare facilities in Benin City, Nigeria.

Urine (50.7%) sample represented half of all samples followed by semen (16.1%) and vagina swab (13.2). Urine (51.8%), semen (16.5%), wound swab (13.3%) and vagina swab (6.9%) represented majority of the specimen in SHC, while urine (46.9%), vaginal swab (32.8%) and semen (14.6%) were most encountered in PHC. S.aureus (60.6%) was the microorganism most isolated while coliform organism (31.9%) represented about one-third of the microorganisms. Ps aeruginosa and proteus were isolated from SHC only. The only Gonorrhea isolate was seen from PHC while the PHC differentiated E.coli from other coliforms unlike in SHC where all are grouped together (See Table 1). About half (51.8%) of the isolates were collected from females with urine (54.7%), wound swab (12.3%) and vagina swab (25.5%) constituting most of the samples. In males, most samples were from urine (46.3%), semen (33.4%) and wound swab (8.8%). Coliform organisms and S.aureus constituted majority of the organisms isolated from all cultures with highest isolates of S.aureus from urine (45.7%), semen (21.7%), vagina swab (16.3%); for coliform, urine (44.4%) and wound swab (16.8%). Ps Aeruginosa was more isolated from wound swab (22.7%) and semen (27.2%). Most E. coli isolated was from urine (56.2%) and vagina swab (31.2%), all streptococci pneumonia was isolated from urine, proteus specie was isolated from urine (50%) and ear swab (50%) respectively, while the only N. Gonorrhea was found in vagina swab.

Table 2 describes the number of antimicrobials isolates are sensitive to in accord with the individual healthcare institution. Only one isolate is sensitive to all antimicrobials. From the PHC, majority of the isolates are sensitive to between 3 to 5 antimicrobials, while in the SHC, majority of the organisms are sensitive to between 1 to 3 antimicrobials. More resistance was seen in the SHC as 15.4% of isolates were resistant to all antimicrobials. Of the 819 microorganisms, at least 61.4% are multidrug resistant (MDR). Multidrug resistance of specific microorganisms was noted, for ps. Aeruginosa (95.5%), coliform (67.3%), E.coli (25.6%), and S.aureus (82.6%).

Seven antimicrobials (amox-clav, ampicilin, ceftazidime, cefixime, cloxacillin, streptomycin and amoxycillin) showed more than 90% resistance to majority of the isolates. Ciprofloxacin, cefuroxime and erythromycin showed more than 75% resistance. N. Gonorrhae was only sensitive to Cefixime, amox-clav and azithromycin. Proteus was resistant to all antimicrobial agent, while Ps. Aureginosa showed more sensitivity to ciprofloxacin and ofloxacin but high resistance to other antimicrobials. Coliform was highly sensitive to ciprofloxacin (96%) but showed less than 40% sensitivity to other antimicrobials. S aureus showed the highest sensitivity to levofloxacin (62.6%) (See Table 3).

Isolates from males and females were more sensitive to gentamicin (30% versus 39%), ofloxacin (34% versus 38%) and ceftriaxone (35% versus 39%) compared to other antimicrobial agents. In addition, isolates from females showed sensitivity to nitrofurantoin (30%). Table 4 describes the relationship between gender and sensitivity pattern to antimicrobials. Isolates from males were more sensitive to amox-clav (p-0.021), erythromycin (p-0.012) and azithromycin (p-0.018) compared to females, while females showed more sensitivity compared to males to ciprofloxacin (p-0.002), nitrofuratoin (p-0.000), ceftazidime (p-0.047), gentamicin (p-0.006) and clindamycin (p-0.043). All isolates from males were resistant to streptomycin compared to those from females, similar resistance can be observed for cefixime, ofloxacin and ceftriaxone which is about 50% for either gender. Of the isolates sensitive to levofloxacin, 60% were from females, although there was no statistical significance compared to isolates from males.

Isolates from SHC had the highest sensitivity to gentamincin (30%) and nitrofurantoin (31%), while those from PHC showed highest sensitivity to ceftriaxone (86.4%), gentamicin (47.5%) and cefuroxime (30%). It is observed that few isolates were used to test for sensitivity with some antibiotics such as streptomycin, ciprofloxacin, ampicillin and ceftazidime in both facilities due to differences in antibiotic discs used from both centers, and at some point, the facility also changed the discs used for sensitivity testing. Table 5 shows that isolates from PHC were more resistant to augmentin (p<0.05) compared to those from SHC, while isolates from SHC were more resistant to ceftriaxone, ofloxacin, cefuroxime, cefixime, erythromycin and gentamicin (p<0.05) than isolates from PHC.

The sensitivity patterns were analyzed in both PHC and SHC over the study period, and the resistance profiles were observed. Resistogram shows that microorganisms have been consistently resistant (>60%) to Ciprofloxacin, Amox-Clav, Nitrofurantoin, Ampicillin, Ceftazidime, Erythromycin, Cloxacillin and Gentamicin in SHC over the past three years. There was a rise in the resistance profiles of cefuroxime and ceftriaxone between 2019 and 2020, followed by a drop in resistance between the year 2020 and 2021 (Fig 1). Similarly, in the PHC over the past 4 years, resistance to Amox-Clav, Cefixime, Streptomycin and Amoxicillin was noted (Fig 2), resistance to Azithromycin rose from 30% in 2018 to 74% in 2021. Resistance to Ceftriaxone seems to be increasing after a 2 years drop in resistance. Resistance to gentamicin was observed to be fluctuating with alternate year of increase resistance. There has been a steady decrease in resistance to levofloxacin over the study period. Clindamycin saw a drop in resistance from 49% to 40% in between 2020 and 2021. Similar pattern of resistance were observed for Cefixime, Amox-Clav, Ofloxacin and Gentamicin in both PHC and SHC over the years.

This study sought to determine and compare the antimicrobial sensitivity pattern over time in PHC and SHC facilities. Urine, semen and vagina swab were the most common samples isolates were collected for microbiology investigation over the study periods from both facilities. This suggests that urinary tract infections (UTIs) and infections of the reproductive organs were common reasons for ordering microbial culture and sensitivity tests in these facilities. One reason for this observation is that respiratory samples and cerebrospinal fluid are more associated with paediatric patients and physicians in these facilities may tend to adopt presumptive diagnosis in treatment of these patients, and considering the fact that viruses cause respiratory infections more than bacteria. Moreso, investigation with CSF requires more expertise which may be lacking in primary care settings Another possibility is that some patients might have treated infections associated with urinary tract and the vagina on their own from patent medicine dealers and pharmacy outlets most of which do not ask patients to conduct microbial test before treatment as is common in LMICS, hence recurrent infections warrant them to visit these facilities [6]. Urine sample made up half of all culture, majority of which was from females. This could be because UTIs occur more frequently in females than in males at a ratio of 8:1, approximately 50–60% of women will report at least one UTI in their lifetime [10]. S.aureus was most isolated from semen, urine and vagina swab followed by E.coli from vaginal swab. More evidence is currently emerging to show that Staphylococcus, particularly Staphylococcus aureus, can colonize the reproductive systems and affect their structure and function. In a study of a total of 140 sperm samples collected from the University of Benin Teaching Hospital, S. aureus (28.3%) was the most common pathogens [11], in a related study a prevalence rate of 38.7% for S. aureus from high vaginal swab and endocervical swabs and a prevalence of 75% from semen cultures of infertile couples was reported [12]. Another investigation identified S. aureus as the most prevalent vaginal pathogen (57.33%) among local infertile women, followed by Escherichia coli (25.33%) [13].

The relationship between S. aureus and E. coli causing urinary tract and reproductive infections is linked with the fact that approximately 30% of the human population is colonized with these microbe, and E.coli is a common contaminate of drinking water and the environment [14]. Transmission of urinary tract infections into the reproductive system is unavoidable. Moreover, a range of 50–80% of UTI patients are infected repeatedly by the same bacterial strain, indicating the presence of reservoirs within the host [15]. Few studies from other parts of the world show that Staph aureus is a cause of UTI or vaginal/prostatic infections, our study however reveals increased infections associated with this organism. More studies should give attention to this finding for possible inclusion in guidelines for treatment.

Results from this study show that most of the coliforms isolated were from the secondary health care facility, whereas in the PHC, E.coli was clearly differentiated. It is possible that the method of identification and reporting is adopted either out of convenience or limitations in laboratory differential of this group of organisms. Ideally identification and reporting as E. coli and non- E coli coliforms or further characterization of the non-E coli coliform as Klebsiella or Citrobacter can help the clinician to make appropriate decision when interpreting the microbial sensitivity results, this is important as some coliform like Klebsiella and E coli are classified among the WHO GPP [4, 16].