Antimicrobial resistance in Africa: a systematic review

1Internationally, there is a growing concern over antimicrobial resistance (AMR) which is currently estimated to account for more than 700,000 deaths per year worldwide. If no appropriate measures are taken to halt its progress, AMR will cost approximately 10 million lives and about US$100 trillion per year by 2050. In contrast to some other health issues, AMR is a problem that concerns every country irrespective of its level of income and development as resistant pathogens do not respect borders.

2Despite the threat presented by AMR, the 2014 World Health Organization (WHO) and the recent O’Neill report describe significant gaps in surveillance, standard methodologies and data sharing. The 2014 WHO report identified Africa and South East Asia as the regions without established AMR surveillance systems. This lack of quality data is problematic often leading to treatment guidelines that are not adequate for the local situation. The gap in public health capacity is also an issue given the changing resistance mechanisms and the emergence of multidrug-resistant bacteria that can only be detected through systematic screening in quality assured microbiology laboratories.

3One factor contributing to AMR is misuse of antibiotics. Improved malaria diagnostics and the recognition that malaria transmission is decreasing globally has highlighted the lack of tests for other infections and many patients who test negative for malaria are treated with antibiotics indiscriminately. Clinical treatment algorithms like the Integrated Management of Neonatal and Childhood Illnesses (IMNCI) and Integrated Management of Adolescent and Adulthood Illnesses (IMAI) guidelines implemented by the WHO have tried to optimize antibiotic prescription in resource-limited settings, however overuse of antibiotics is still happening. Following these guidelines amoxicillin or sulfamethoxazole/trimethoprim are the first line drugs for urinary tract infections (UTI) or acute respiratory tract infections. A combination of ampicillin and gentamicin or ceftriaxone are the drugs of choice for treating blood stream infections (BSI) and sulfamethoxazole/trimethoprim or ciprofloxacin are recommended for the treatment of dysentery.

4A number of recent reviews summarized AMR data in Africa, most recently Leopold et al. (2014) which focused on Sub-Saharan Africa. The authors found a high level of resistance to the commonly used antibiotics in the sub-Saharan African region. For example, 90% of Gram negatives were resistant to chloramphenicol, a commonly used antibiotic. In contrast, resistance to third-generation cephalosporins (like ceftriaxone) was less common, recommending this group for use.

5To design suitable local and global interventions, it is important to understand the current status of AMR and identify knowledge gaps. The purpose of this review is to summarize the available information about the occurrence of AMR on the entire African continent and describe laboratory methods currently in use, to identify knowledge gaps and highlight diagnostic needs.

6PubMed, EMBASE, Science Daily, the Cochrane Database for Systematic Reviews, African Journals Online Library and Free-text Web Searches using Google Scholar were searched for articles published in English from January 1, 2013 through January 31, 2016. Literature before January 2013 was covered in previous reviews. Reference lists of relevant articles were checked for additional titles for inclusion in the review. Key words used for the search were “Antimicrobial Resistance”, “Antimicrobial Susceptibility”, “Surveillance”, “Diagnostic”, “Africa” and specific names of all African countries. The detailed search strategy, as well as details of the article quality assessment can be found in Additional file 1.

7Articles reporting AMR prevalence, availability of AMR surveillance systems or diagnostic needs of antibiotic resistance in the whole African region were included. Based on the abstract, articles of all types with any data on etiology and antibiotic susceptibility pattern were included for further screening. Studies were included or excluded following predefined criteria.

8Inclusion:Reports on AMR in humans from the African regionAbstracts and full text available in EnglishDrug sensitivity testing done in a laboratory setting with defined cutoffs for drug susceptibility testingThe denominator as total isolates clearly described for population based studiesCase reports and case series

9Reports on AMR in humans from the African region

10Abstracts and full text available in English

11Drug sensitivity testing done in a laboratory setting with defined cutoffs for drug susceptibility testing

12The denominator as total isolates clearly described for population based studies

13Case reports and case series

14Exclusion:Reports published before 2013Studies only focused on malaria, HIV or tuberculosis without AMR informationStudies without information on total studied isolates

15Reports published before 2013

16Studies only focused on malaria, HIV or tuberculosis without AMR information

17Studies without information on total studied isolates

18Titles and abstracts of all the articles retrieved through the search were screened. In the event of uncertainty as to whether articles met the criteria for study inclusion they were discussed with two co- authors. Articles selected for full text review were obtained using PubMed, WHO GIFT access, HINARI, institutional websites or by contacting the authors directly. Names of authors from articles in the search results were not blinded for abstract or full-text review.

19Data extraction was done using a predesigned and pretested database, developed for the purposes of this review using Microsoft Excel 2013. Information extracted included article information (PMID, first author, year of publication, duration of data collection and country), study design (sample size, age group, hospital acquired or community acquired, number of specimens collected, and clinical syndrome), pathogen identification and antimicrobial susceptibility testing methodology, laboratory accreditation information and antibacterial resistance data.

20The quality of each article was assessed using a tool modified for the purposes of this study from criteria published by Omulo et al. and the Cochrane guidelines for assessing bias in observational studies. Since a limited number of articles was available, results of the quality assessment were not used for inclusion/exclusion. The quality criteria included 26 items to assess the design, details of sample collection, processing and storage, reporting on AMR methodologies and quality assurance strategies.

21We calculated prevalence, median resistance (MR) and inter quartile range (IQR) of resistance for each bacterium-antibiotic combination to calculate a standardized measure from the collected data. Pediatric age was considered less than 18 years and neonatal age less than 28 days. Meta-analysis was not conducted because of the large variability in AMR methodology, geography and the small number of articles available per country. Since the number of studies from hospital/in-patient settings was small, they were combined and median percentages with interquartile ranges were generated. Statistical analyses and visualization were performed using Microsoft Excel 2013, STATA v14 (STATA, College Station, TX, USA) and R-software 3.3.1.

22In total, 1704 articles were identified. Of those, 144 studies met the inclusion criteria and were included in the final analysis (Fig. 1). Samples from a total of 149,733 patients were analyzed in the selected studies. The majority of the studies were from East Africa (59/144, 40.9%) while the smallest number of studies were from the South African region (6/144, 4.2%) (Fig. 2). No suitable report was identified from 23/54, 42.6% countries. While the articles were published between 2013 and 2016, the reported data were collected from 1995 to 2015 with the majority from before 2013 (98/144, 68.1%). Most of the studies (92/144, 63.9%) were cross sectional studies or case series (Table 1). Similar numbers of studies were published with susceptibility data for isolates from blood culture (25/144, 17.4%), urine culture (25/144, 17.4%), wound discharge/pus isolates (22/144, 15.3%); and multiple sample types (21/144, 14.6%). More than 80% of the studies fulfilled more than half of the quality parameters (121/144, 84.0%) used to score the articles (Additional file 1). Among the different studies, four different methods for susceptibility testing and five different interpretation guidelines were used (Table 1).

23The most commonly reported bacterium was Escherichia coli (87/144, 60.4%) with the most frequent susceptibility data for gentamicin (77/144, 53.5%), ciprofloxacin (71/144, 49.3%) and sulfamethoxazole/trimethoprim (68/144, 47.2%) (Table 2). In total, 13 Gram negative opportunistic pathogens were tested against 37 antibiotics (Table 3, Additional file 2). Overall resistance to commonly used drugs, like amoxicillin (MR 72.9%, IQR9.1%–87.3%) and trimethoprim/sulfamethoxazole (MR 75.0%, IQR 49.5%–92.3%) was high. Low to moderate resistance was found to gentamicin (MR 22.1%, IQR 2.0%–45.0%), ciprofloxacin (MR 16.7%, IQR 0%–38.5%) and ceftriaxone (MR 17.2%, IQR 0%-45.0%). Gentamicin resistance in Klebsiella spp., which is naturally resistant to ampicillin, was reported in 1031/2715, 38.0% of tested isolates. Resistance to either ceftriaxone or cefotaxime, which is suggestive of extended–spectrum beta lactamase (ESBL) production was reported in 593/2963, 20.0% and 1051/5395, 19.5% of E. coli as well as 545/1594, 34.2% and 560/1199, 46.7% of the K. pneumoniae isolates, respectively. Imipenem, a drug rarely available in rural Africa, was investigated in 21/144 (14.6%) of the studies and showed the lowest overall MR (MR 3.0%, IQR 0%- 26.6%) (Table 3). Of the Acinetobacter isolates reported in three studies, 32.3% (10/31) were resistant to meropenem. Ciprofloxacin resistance in S. Typhi was reported rarely (MR 0%, IQR 0%–11.7%) while ampicillin resistance in Haemophilus influenza was high (MR 100%, IQR76.6%–100%). There was no documented ceftriaxone resistance in N. gonorrhoeae but ciprofloxacin resistance was reported in 37.5% (IQR 30.7%–83.9%) of the isolates.

24In the Gram positive group, Coagulase Negative Staphylococcus spp. (CoNS), S. aureus, Streptococcus pneumoniae and Group A streptococcus were the most commonly investigated bacteria (Table 4). Methicillin resistant S. aureus (MRSA) was reported in 7/79 (8.9%) of the studies, however as cefoxitin is typically used to screen for MRSA, the MRSA rate is likely underestimated. Erythromycin resistance in S. aureus was found in 33.9% (IQR 13%–46.4%). Methods used to assess penicillin susceptibility in S. pneumoniae varied: median oxacillin resistance was reported in 40.7% (IQR 0%–55.7%) compared to 26.7% (IQR 8.4%–33.6%) for penicillin and 22.5% (IQR 20%–32.5%) for amoxicillin.Vancomycin showed the lowest resistance pattern for all the tested Gram positive bacteria (Table 4).

25In the reviewed literature, E. coli was commonly isolated from patients with BSI (17/87, 19.5%), UTI (17/87, 19.5%) and wound infection (16/87, 18.4%). Citrobacter spp. were reported most commonly among patients with UTIs (7/19; 36.8%), followed by BSI (5/19, 26.3%). Two (2/19, 10.6%) of the studies which reported on Citrobacter spp. were from HAI; five (5/19, 26.3%) from community acquired infections of which three (3/5) came from pregnant women at antenatal care follow up and two (2/5) had unknown risk factors. S. Typhi was most frequently reported from patients with BSI (13/28, 46.4%) followed by patients with diarrhea (6/28, 21.4%). It was also more commonly reported in children below 18 years (12/28, 48.9%) than in adults (2/28, 7.1%) (Table 2).

26In the current review, the susceptibility results were taken at face value, however there were inconsistencies casting the credibility of several results in doubt. For example a study reporting more than 80% of Proteus isolates (n = 6) as resistant to imipenem also reported that 80% of them were susceptible to ceftriaxone and 50% were susceptible to vancomycin, a combination that is highly unusual. There were other unverified reports of highly unusual resistance patterns from some centers, such as penicillin resistant S. pyogenes and vancomycin-resistant S. aureus.

27Generally, a lower level of resistance of S. aureus, Klebsiella spp., E. coli and S. pneumoniae to carbapenems and fluoroquinolones was observed in all the regions as compared to the other antibiotic-bacterium combinations. However, Klebsiella spp. resistance to ciprofloxacin in West Africa was observed to be higher than in other regions. Resistance to the trimethoprim (MR: 33.9%–100%), ampicillin (MR: 7.9%–100%) and penicillin (MR: 0%–75%) was generally high in all regions (Fig. 3).

28The rise and spread of AMR threatens the effective control and treatment of various bacterial diseases worldwide. The achievements gained in reducing mortality and morbidity through early use of antibiotics based on empiric guidelines are in serious jeopardy if appropriate actions are not taken to control AMR. Availability of routine and research data on pathogen susceptibilities is an important step towards designing targeted strategies to tackle the global AMR crisis. The current review describes recently (2013–2016) published data on antibiotic drug susceptibility from Africa.

29The lack of consistency in the measurement and reporting of susceptibility data makes it difficult to compare findings among different countries and laboratories, sometimes even within one country. To address this issue, high income countries have implemented harmonization efforts. For example, laboratories in Europe are encouraged to use the European Committee on Antimicrobial Susceptibility Testing (EUCAST) standard over the Clinical and Laboratory Standards Institute (CSLI) guidelines. Furthermore, in an effort to enable coherent data synthesis and reporting in January 2016 the British Society for Antimicrobial Chemotherapy (BSAC) actively promoted the EUCAST methods in favour of the current BSAC methodology. Given the findings of our review, similar harmonization efforts are urgently needed in Africa. Standardizing AMR methods and interpretation guidelines could allow for better comparability of results and improved resistance tracking. Furthermore, improved access to reference laboratories and EQA schemes are needed augmenting the current WHO initiative to scale up the global antimicrobial surveillance system (GLASS) based on country specific priority pathogens. Currently, in the absence of a uniform laboratory methodology the GLASS goals will be very difficult to meet.

30Comparing our findings with previous reviews in the region like Leopold et al. (2014), overall, we identify a similarly high report of resistance to commonly used antibiotics. The same review reported a high level of resistance of Enterobacteriaceae to ampicillin and co-trimoxazole which is in agreement with our findings. Similarly, resistance to co-trimoxazole and tetracycline by S. pneumoniae was reported to be high. However, discrepancies were observed in various antibiotic/bacterium combinations. For instance, our finding of resistance to chloramphenicol in Salmonella Typhi isolates is lower than that previously reported. Resistance to oxacillin by S. aureus was also much higher in the current review than the review by Leopold et al.. The observed differences between data published in 2014 and the current work could indicate a rising pattern in AMR in certain pathogens. However it could also be because of the differences in AMR testing methodologies underlining the need for harmonization of laboratory methods in the region.

31A notable finding of this review was the high resistance rate of common causes of UTI to common first line regimes like amoxicillin and sulfamethoxazole/trimethoprim. In the presence of a failing treatment, patients with UTIs are at increased risk of developing renal damage and future risks of renal insufficiency or hypertension. Similarly, given the resistance profiles in the current review, neonatal sepsis or BSI caused by E. coli, K. pneumoniae and S. aureus are not being effectively treated by first line drugs like ampicillin, aminoglycosides and cephalosporins, which will result in increased mortality in patients with life-threatening infections. The high levels of resistance to amoxicillin and penicillin in S. pneumoniae and H. influenzae are also concerning given that pneumonia is a leading cause of death in children. Reported MRSA rates were variable and doubts remain about reliability of identification at all sites which are confirmed by the findings of one Kenyan study which found that MRSA rates dropped dramatically after switching to an automated identification method.

32Compared to reports from Asia, quinolone resistance in S. Typhi was rare and, reassuringly, there were no reports of ceftriaxone resistance in N. gonorrhoeae. Less commonly prescribed antibiotics like imipenem and vancomycin also showed low level resistance and they should be preserved as alternative drugs in severe infections. Most of the imipenem resistance was described in isolates of P. aeruginosa which has been reported from other centers. Oxacillin resistance should predict penicillin resistance in S. pneumoniae reliably, however in the current review resistance to oxacillin was much higher than to penicillin, possibly because of the differences in the number of isolates tested for both antibiotics and the use of different cut-offs for meningitis and non-meningitis strains.

33The results also yielded data on the susceptibility of less commonly described bacteria like Acinetobacter spp. and Citrobacter spp. Acinetobacter spp. are especially important given their importance in clinical infections and the reported rising trend of resistance, further they have been included in the priority pathogens for global surveillance based on the GLASS initiative. Citrobacter spp. were reported from hospital and community settings, including in pregnant mothers and can cause UTI which puts pregnant women at risk of preterm labor. Our results would suggest that current frontline treatments are ineffective against most common uro-pathogens.

34The limitations of the current review include the exclusion of non-English language reports, as articles from French speaking African countries might have been missed, biasing this review. The representativeness of the data is hard to assess as it is possible that the absence of resistance is not routinely reported and focus is given to reports of resistance. There were very few reports from South Africa, which has a better functioning health system than neighboring countries and better national AMR surveillance. These data were not accessible by our search and therefore larger AMR trends might have been missed. A further limitation is combining AMR results from different patient groups across different countries to compare the data. This approach might have leveled out peaks of resistance in different settings. However, given the observed trends, we believe that the resolution of the obtained data was sufficient to show general developments. Moreover, since case reports were not excluded with intention of capturing as much data as possible in the current review, the findings from the three case (3/144, 2.1% of the studies) might bias the resistance testing results as case reports tend to report on specific multi-drug resistant pathogens. Finally, resistance data obtained with different laboratory methodologies were combined for the purposes of this review. However, as the majority of studies used the disk diffusion method and CLSI guidelines, the impact of the variation in AMR methodology on the validity of the final results is thought to be minimal.

35In summary, our review highlights three important findings: first, more than a third of the countries on the continent did not have recent AMR data published in the public domain and only a few of those were surveillance data. Second, a high level of drug resistance exists to commonly prescribed antibiotics in the African continent. Third, the standardization and quality of the microbiological identification and susceptibility testing methods needs to be improved to allow national and international organizations to monitor the extent of the AMR problem. All of the identified areas of concern need urgent attention by the global health community in order to halt the public health threat associated with spreading AMR.