Antimicrobial resistance of Vibrio cholerae isolated from selected counties in Kenya between 2015 and 2023

¹School of Public Health, Mount Kenya University, Thika, Kenya ² Intergovernmental Authority on Development (IGAD), Nairobi, Kenya

^&Corresponding author
Waqo Gufu Boru, School of Public Health, Mount Kenya University, Thika, Kenya

Introduction    

Antimicrobial resistance represents a critical global public health crisis. Data indicate that in 2019 AMR was linked to 4.95 million fatalities, with 1.27 million deaths directly caused by these resistant infections. The widespread mismanagement of antimicrobial agents across human, veterinary, and agricultural sectors is a fundamental factor fueling the proliferation of resistant bacterial strains [1]. Within the African continent, roughly 1.05 million deaths in 2019 were correlated with AMR, predominantly stemming from bloodstream, abdominal, and lower respiratory or thoracic infections[2]. Projections from a UK government assessment estimate that AMR-related mortality could reach 10 million annually by 2050 [3,4]. Bacteria utilize various biochemical strategies to induce resistance, including the enzymatic degradation or modification of antibiotics, alterations to target sites, reduced drug permeability, and the active extrusion of antibiotics via efflux pumps [5]. Consequently, there is a consensus among international authorities, public health organizations, and the scientific community that AMR demands immediate, harmonized global interventions [6,7]. Antimicrobial susceptibility is increasingly compromised, threatening efforts to control endemic bacterial diseases, such as cholera, on both regional and global scales [8]. Resistant pathogens, including Escherichia coli, Klebsiella pneumoniae, Neisseria spp., Salmonella serovars, and Vibrio cholerae, are well-documented [9]. The V. cholerae O1 and O139 serogroups, notably those possessing AMR are linked to the majority of cholera epidemics worldwide [10,11]. There is heightened concern in low- and middle-income nations, including Kenya, regarding the rising prevalence of resistant V. cholerae [12].

Data indicate that resistant V. cholerae often exhibits insensitivity to primary therapeutic antibiotics, leading to frequent treatment failures [13]. Since the emergence of multidrug-resistant enteric bacteria in the 1960s, V. cholerae has experienced rapid mutation and international dissemination, largely driven by the pervasive mismanagement of antibiotics [14,15]. The prevalence of extensive drug resistance is often amplified by mobile genetic elements, which enable the horizontal transmission of resistance determinants to other pathogens[12]. The World Health Organization has noted a scarcity of literature concerning the AMR landscape in Africa, specifically within Kenya, underscoring the necessity for robust data collection regarding V. cholerae [9,16]. AMR remains a critical health concern in Kenya, accounting for 8,500 direct deaths and 37,300 associated fatalities in 2019 alone [17]. Despite the endemic nature of cholera and its history of three major epidemics in recent decades, national-level data on V. cholerae resistance profiles remain inadequate [18]. This study seeks to bridge this knowledge gap by evaluating the AMR characteristics of Kenyan V. cholerae isolates. Through the analysis of biotypes, serotypes, and genetic resistance factors in both clinical and environmental samples, this research aims to elucidate the role of mobile genetic elements, such as SXT, in maintaining multidrug-resistant populations [2]. Furthermore, identifying these resistance determinants is essential for informing targeted surveillance strategies and updating clinical guidelines for the management of enteric infections in the region [19].

Methods     

Study design: the study adopted a retrospective descriptive study design. The study assessed the susceptibility and resistance of V. cholerae clinical isolates.

Study area: the study sampled 277 isolates from 14 counties in Kenya covering the period between 2015 and 2023. The counties were Nairobi, Lamu, Machakos, Mandera, Tana River, Kajiado, Murang´a, Kiambu, Kitui, Garissa, Turkana, Isiolo and Narok.

Study period: the considered study period was between 2015 and 2023

Cholera data source: data on V. cholerae isolates' susceptibility and resistance to various antibiotics were extracted from the National Public Health Laboratories (NPHL) at the Ministry of Health, Kenya. The MDR data were consolidated for the period from 2015 through 2023.

Data analysis: descriptive analysis was done using SPSS version 26, while bar graphs were drawn using RStudio 4.3.3. Data were presented using tables and graphs.

Ethical consideration: ethical approval and authorization to conduct the study were sought from Mount Kenya University Ethical Review Committee (Ref: MKU/ISERC/4306) and National Commission for Science, Technology, and Innovation (NACOSTI) (License no: NACOSTI/P/24/39710), respectively. Approval to access cholera line list data was obtained from the Kenya Ministry of Health Division of Disease Surveillance and Response.

Results     

Socio demographic characteristics: the study sampled 277 cases from 14 counties in Kenya covering the period between 2015 and 2023 as shown in Table 1. A majority (56.6%) of the samples were from Nairobi County, followed by Lamu County and the least were from Isiolo and Narok Counties. A majority (65.9%) of the samples were from male patients while the least (34.1%) were from female patients. The mean age of the cholera patients was 33.73 ±15.94 years.

Antimicrobial susceptibility of V. cholerae: over three quarters of the isolates were sensitive to chloramphenicol (94.0%), gentamicin (86.8%), cefuroxime (85.5%), tetracycline (90.2%) and Levofloxacin (94.1%) as shown in Table 2. Further slightly over a half of the isolates were sensitive to ciprofloxacin (57.9%), amikacin (53.5%) and cefotaxime (56.0%). A high number of the isolates were resistance to ampicillin (94.0%), nalidixic acid (100%), erythromycin (77.3%) and ceftazidime (66.7%). Additionally, over a half (61.8%, 57.7%, 57.7% and 51.1%) of the isolates were resistant to Trimethoprim-sulfamethoxazole, meropenem, cefoxitin and cefepime respectively.

Dual resistance and multidrug resistance: slightly above two thirds of the isolates (67.74%) exhibited dual resistance and MDR to antibiotics out of which 40.32% exhibited dual resistance and 27.42% exhibited MDR (Figure 1). The predominant pattern of dual resistance of the isolates was Ciprofloxacin+Cefepime followed by Ampicillin Ciprofloxacin and then Ampicillin+Ceftazidime. For isolates that exhibited MDR the predominant pattern was Ampicillin+Ciprofloxacin+Nalidixic acid followed by Piperacilin+Amikacin+Cefoxitin+Meropenem, Ceftazidime+Piperacilin+Amikacin Imipenem, Piperacilin+Cefepime+Imipenem and Ceftazidime+Piperacilin+Amikacin.

Discussion     

The study findings indicate that the cholera cases were discriminatory among males. This was similar to a Kenyan study which investigated the cholera epidemic of 2007 to 2010 and 2015 and 2016 which documented that the incidence of cholera was higher in males as compared to females [18]. This observation could be attributed to men having poor health seeking behavior, high tendency of eating and drinking out and working in unhygienic environments which increases risk of exposure [20,21]. The majority of the isolates demonstrated high sensitivity to Chloramphenicol, Gentamicin, Cefuroxime, Tetracycline and Levofloxacin which indicates that these antibiotics would be effective treatment options. Equally isolates from the 2007 to 2010 cholera epidemic in Kenya, cholera outbreaks in Kisumu County in 2014 and cholera outbreak in Uganda in 2017 showed high sensitivity to Chloramphenicol, Tetracycline and Gentamicin respectively [18,22,23]. Further a Cuban study reported high sensitivity of V. cholerae isolates to Chloramphenicol (92.0%) and Tetracycline (91.2%) [24]. Studies from East Delhi and Mozambique have documented sensitivity of V. cholerae to Chloramphenicol [25,26]. A meta-analysis of the global status of antimicrobial status of V. cholera identified Gentamicin and Cefotaxime among other drugs as highly effective against V. cholerae [16]. Additionally, more than half of the isolates were sensitive to Ciprofloxacin, Amikacin and Cefotaxime suggesting potential emerging resistance to these antibiotics which could limit their clinical efficacy. Similarly, other studies done in Haiti, United States and France have reported low resistance of V. cholera to Ciprofloxacin and Cefotaxime [27-29]. Antimicrobial resistance of V. cholera isolates has been increasing over the recent years and has become a major risk to cholera treatment strategies [30]. The study findings revealed high resistance rates to Ampicillin (94.0%), Nalidixic acid (100%), Erythromycin (77.3%) and Ceftazidime (66.7%). This high resistance to first line antibiotics indicates that these drugs would largely be ineffective for treatment. Similarly, Kenyan studies have reported high resistance of V. cholera to Ampicillin (64%),Trimethoprim-sulfamethoxazole (54%) and Nalidixic acid (100%) [31].

Ugandan and Cuban studies also reported 100% and 60% resistance of V. cholerae isolates to Ampicillin respectively [23,24]. Additionally, isolates from the 2012 to 2015 Mozambique cholera outbreak exhibited 100% resistance to Ampicillin and Nalidixic acid [32]. Further over a half of the isolates were resistant to Trimethoprim-sulfamethoxazole, Meropenem, Cefoxitin and Cefepime. Similarly studies in Zambia, DRC and North India also documented considerable medium resistance of V.cholerae to Trimethoprim-sulfamethoxazole (SXT) [33-35]. The study findings indicate concerning levels of resistance particularly to important classes of antibiotics such as fluoroquinolones (ciprofloxacin, Nalidixic acid), extended spectrum cephalosporins (Cefepime and Ceftazidime), carbapenems (meropenem and Imipenem) and penicillins (ampicillin and piperacillin). The high rates of resistance to multiple drug classes especially carbapenems which are often considered as last resort antibiotics is particularly worrying from a clinical perspective. In the present study slightly over a quarter (27.42%) of the isolates demonstrated MDR with the most predominant pattern being Ampicillin+Ciprofloxacin+Nalidixic acid. Similarly Bangladesh study conducted among children and older adults documented an MDR rate of 28.1% with the most predominant pattern being TMP-SMX+ erythromycin + ampicillin[36]. Evidence suggests that MDR V. cholerae isolates with resistance to Ampicillin, Nalidixic acid, chloramphenicol and tetracycline begun appearing in the 1990s [37]. Interestingly a high number (64.5%) of V. cholera isolates from the 2007 to 2010 and 2015 to 2016 cholera epidemics in Kenya exhibited MDR[18]. Further a Kenyan study in 2021 detected and characterized MDR V. cholera with genes encoding for ESBL enzymes. The ESBL isolates were resistant to chloramphenicol, streptomycin, sulfamethoxazole, trimethoprim, tetracycline, rifampicin and erythromycin[8]. Evidence further suggests an increase of MDR V.cholerae in Kenya and in the region [23,38]. Interestingly a Ghanaian and South African study reported that over 97% and 36-50% of clinical isolates exhibited MDR respectively[39,40]. A South African study reported that the MDR among V. cholera isolates could be attributed to spontaneous mutation or horizontal transfer of resistance genes through the co-existence of gut coliforms and Vibrio species[41]. Further evidence indicates that wide usage of antibiotics has increased antibiotic resistance leading to the emergence of MDR strains which are a significant public health problem globally[18]. Evidence suggests that recent trends indicates that most clinical V. cholera isolates are resistant to almost all routinely used antibiotics [12].

Conclusion     

In conclusion, V. cholerae isolates from Kenya reveal a concerning antimicrobial resistance profile with profound clinical implications. While demonstrating high susceptibility rates to chloramphenicol, gentamicin, cefuroxime, tetracycline, and levofloxacin, there was alarming resistance to critical therapeutics, including absolute resistance to nalidixic acid and elevated resistance to ampicillin, erythromycin, and ceftazidime. The V. cholerae isolates concurrently exhibited high dual resistance and multidrug-resistant phenotypes. A key concern is the emergence of resistance to carbapenems, considered last-resort antibiotics, alongside a predominant multidrug-resistant (MDR) pattern involving ampicillin, ciprofloxacin, and nalidixic acid. This trajectory severely limits clinical treatment options, underscoring an urgent imperative for enhanced surveillance and the development of targeted containment strategies within Kenyan cholera management frameworks.

Competing interests     

The authors declare no competing interests.

Authors' contributions     

Conceptualization: Waqo Gufu Boru, Alfred Owino Odongo Methodology:Waqo Gufu Boru, Alfred Owino Odongo, John Kariuki. Validation: Waqo Gufu Boru, Alfred Owino Odongo, John Kariuki; Data collection: Waqo Gufu Boru. Data curation: Waqo Gufu Boru, Alfred Owino Odongo. Formal analysis and drafting paper: Waqo Gufu Boru. Review and Editing of the manuscript: Waqo Gufu Boru, Alfred Owino Odongo, John Kariuki. All the authors have read and agreeed to the final manuscript.

Tables and figures     

Table 1: socio demographic characteristics of the cholera cases among patients aged 1 to 92 years between 2015 to 2023 (n= 277 cases)

Table 2: antimicrobial susceptibility of V. cholerae among patients aged 1 to 92 years between 2015 to 2023 (n= 277 cases)

Figure 1: multi drug resistance (MDR) of V. cholerae among patients aged 1 to 92 years between 2015 to 2023 (n= 277 cases)

References